Vastus lateralis muscle biopsy from 69 year old healthy male. Analysis done with Affymetrix Microarray Suite 5.0 sotware. Keywords = muscle, aging Source GEO sample is GSM2397 Last updated (according to GEO): May 27 2005 1025 1008 peripheral retina Nose 1000 Study of in vitro granulocyte differentiation Source GEO sample is GSM137457 Last updated (according to GEO): Jun 06 2007 861 Intestines Acetaminophen 6hr Rat 1550 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool Normal Source GEO sample is GSM176388 Last updated (according to GEO): Apr 09 2007 331 307 in central nervous system Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225676 Last updated (according to GEO): Nov 02 2007 to the nose 599 609 29 0 Aged hematopoietic stem cells days nasal epithelium 1127 1148 (No additional Information) Source GEO sample is GSM114425 Last updated (according to GEO): Jun 19 2006 Coronary artery 901 of somatomotor cortex 21 41 in the brain 150 162 Mammary Neoplasms 901 CNS-SC_CtrA14d-2C-s2 spinal cord, spinal cord: G5B_le1 SVGR2 subclone 1-C4 GeneChip U133B testis 52 58 Cockayne syndrome B cell Source GEO sample is GSM226613 Last updated (according to GEO): Sep 04 2007 lung cancer. 305 317 1000 Structure of entorhinal cortex Gene expression data from postmorten brain regions Source GEO sample is GSM145672 Last updated (according to GEO): Nov 20 2006 861 Cerebral cortex of the stria terminalis 51 73 Patient2D M_U133Plus_55_nAcc 1000 Brain myocardial infarction 383 403 Nose 1000 Recurrent Adenocarcinoma 10 brain, unknown: Sample49_e1_le1 na Source GEO sample is GSM181276 Last updated (according to GEO): Apr 10 2007 Liver 4 Normal SN:Human Glioblastoma Biopsy 10459 Normal Source GEO sample is GSM176327 Last updated (according to GEO): Apr 09 2007 brain, Left frontal Lobe: Extract8_le1 brain 0 5 445 435 cerebellum UACC-257CL10021_MELANOMA Lymphoblastoid Cell Line for Individual 8004.3 log phase MuscleRegen-con8wk-1RLA-s2 TUMOR 10 0 7 NA Source GEO sample is GSM84331 Last updated (according to GEO): Dec 01 2005 Osteoblasts 1000 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188776 Last updated (according to GEO): Jun 06 2007 Ova C3H 2 vs control C3H pool 334 320 Keywords = HIV serotonin receptor 4 1263 1282 Fluid-percussion head injury 83 110 of the colon 28 39 Ganglia 861 13 7 cochlea B6 day 1, biological rep 2, tech rep 1 A HID B D091 Wild type P18 mouse visual cortex ipsilateral to monocular enucleation Source GEO sample is GSM97201 Last updated (according to GEO): Feb 17 2006 ExpressionLevel:GXN-00539 on Affymetrix GeneChip Mouse Expression Array 430A and Mouse Genome 430A 2.0 Array from ventral prostate 21 41 Occipital lobe 983 952 929 of the pituitary gland Pool of 9 (1 utricle and 3 ampullae) at E13.5 Source GEO sample is GSM182602 Last updated (according to GEO): Aug 14 2007 from the olfactory epithelium tissue 140 176 H9LMS00061601 1000 Structure of atrioventricular node 861 Cerebral cortex Cerebellar astrocyte 1 Comprehensive description of the transcriptome of PVN in euhydrated and dehydrated rat Sample is skeletal muscle from a morbidly obese patient undergoing elective abdominal surgery Source GEO sample is GSM3983 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145459 Last updated (according to GEO): Nov 20 2006 865 Disorder of artery Saccule structure 1000 NA11830 an inherited neurodegenerative disease 29 66 ALLB-cell59 on Affymetrix GeneChip Human Full Length Array HuGeneFL ileum 1000 ZR75_1_Untreated_10% Category: Cell-line Subcategory: Breast HMEC+IFNalpha 24hours done by chuck perou Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc500 Source GEO sample is GSM1884 Last updated (according to GEO): Nov 21 2005 BPH-23 on NHGRI-6.5k_c 928 Endometrium Cord blood, primary Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed for 48 h to hydrostatic pressure (HP48), pressure experiment # 2 (PE2). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11425 Last updated (according to GEO): Dec 15 2006 861 Blood M_U133A_32_DLPFC_R PGA-Band_Sham_1h_7-m5 Spleen vs Lipopolysaccharide (LPS) Treated B cell 240min (set1) HTI-286 in docetaxel-refractory prostate cancer_docet (Dye flip1) 1000 Brain Wild type inbred mice Source GEO sample is GSM82968 Last updated (according to GEO): Nov 10 2005 of Parkinson's disease 450 471 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155047 Last updated (according to GEO): Jun 04 2007 861 Hippocampus Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 30 minutes following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10954 Last updated (according to GEO): May 27 2005 Kidney (NL078) 424 415 infection Plasma 861 1672 1658 the hippocampus Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68045.gif Source GEO sample is GSM137411 Last updated (according to GEO): Sep 26 2006 Subcutaneous Tissue 913 Expression profiling of spinal cord section (T8) extracted from rats 4h following laminectomy (sham) Source GEO sample is GSM31412 Last updated (according to GEO): May 27 2005 gene expression data from ODC mouse skin samples Source GEO sample is GSM216668 Last updated (according to GEO): Aug 09 2007 trigeminal Source GEO sample is GSM18608 Last updated (according to GEO): May 27 2005 861 Blood Infection 861 amygdala rattus_norvegicus_strain iP animal_number 6 20 0 human caudate nucleus metastasis 20 29 I_U133A_92_AnCg in the brain 150 162 Plasma 861 Large-scale analysis of the mouse transcriptome. Skeletal muscle C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 312.31 Stdv: 13.51 Min: 291.96 Max: 338.98 Source GEO sample is GSM2952 Last updated (according to GEO): May 27 2005 1000 Hippocampus Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118555 Last updated (according to GEO): Jul 11 2006 1000 Breast Carcinoma 1000 jejunum Wild type inbred mice Source GEO sample is GSM82996 Last updated (according to GEO): Nov 10 2005 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3276 Last updated (according to GEO): Mar 10 2006 Expression profiling of somatomotor cortex extracted from rats at 14d following moderate injury Source GEO sample is GSM41691 Last updated (according to GEO): May 27 2005 352 340 encephalitis 861 Brain P7_1 Cell Culture: Hippocampal cells from E18 rat embryos were plated at a density of 500,000 cells per 60 mm poly-L-lysine (1mg/ml; Sigma) coated dish. Cultures were maintained at 37 C in 5% CO2 humidified incubator and used for experiments at 21 day in vitro (DIV). Control and experimental group cultures were incubated with 10 micro M TTX for 15 min followed by addition of 100 micro M baclofen or vehicle. Total RNA preparation: Each experimental group was compared as replicates of three. For each replicate cultured hippocampal neurones were harvested after 2 hours incubation +/- baclofen and total RNA was isolated using RNeasy Mini kit (Qiagen, UK) according to the manufacturer's protocol. Microarray Target Labelling and Hybridisation: Targets for cDNA microarrays were generated using 5 micro g of total RNA in a standard reverse transcription (RT) reaction. RNA was annealed, in 16 micro l water, with 1 micro g of 24-mer poly(dT) primer (Invitrogen, UK), by heating at 65oC for 10 min and cooling on ice for 2 min. The RT reaction was performed by adding 8 micro l of 5X first strand RT buffer (Life technologies, MD), 4 micro l of 20mM dNTPs minus dCTP (Pharmacia, UK), 4 micro l of 0.1M DTT, 40U of RNAse OUT (Life Technologies, MD), 6 micro l of 3000 Ci/mmol 33P-dCTP (ICN Biomedicals, UK) to the RNA/primer mixture to a final volume of 40 micro l. Two micro l (400 U) of Superscript II reverse transcriptase (Life Technologies, MD) was then added and the sample incubated for 30 min at 42oC followed by additional 2 micro l of Superscript II reverse transcriptase and another 30 min incubation. The reaction was stopped by addition of 5 micro l 0.5 M EDTA. Samples were incubated at 65oC for 30 min after addition of 10 micro l of 0.1M NaOH to hydrolyse and remove RNA. Samples were pH neutralized with 45 micro l 0.5M Tris, pH 8.0 and purified using Bio-Rad 6 purification columns (BioRad, UK). The NIA NeuroArray consists of 1152 cDNAs printed on nylon membrane in duplicate. The arrays were hybridised with alpha-33P-dCTP labelled cDNA probes overnight at 50oC in 4ml of hybridisation solution. Hybridised arrays were rinsed in 50ml of 2XSSC and 1%SDS twice at 55oC followed by two washes in 2X SSC and 1% SDS at 55oC for 15 min each. The microarrays were exposed to phosphorimager screens for 1-3 days. The screens were then scanned with Molecular Dynamics STORM PhosphorImager (Sunnyvale, CA) at 25 micro m resolution. Source GEO sample is GSM28535 Last updated (according to GEO): May 27 2005 Epithelium 861 Cerebral cortex 861 17 7 hippocampus 861 Amyotrophic Lateral Sclerosis mild cognitive impairment - entorhinal cortex 3 O377 homozygotes brains 11 plasma cells 50 61 Gene expression data from postmorten brain regions Source GEO sample is GSM145533 Last updated (according to GEO): Nov 20 2006 Two groups of 3 days old mice were treated with oil or retinoic acid. At day 4 one half of each group was treated with saline solution or dexametasone. Lungs were removed snap frozed for RNA extraction Source GEO sample is GSM4146 Last updated (according to GEO): May 27 2005 1000 Communicable Diseases Cerebral cortex 1000 1000 Retina BPH-36 on UMich-10k Macrophage 14smi121 none Source GEO sample is GSM149599 Last updated (according to GEO): Jan 03 2007 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13420.gif Source GEO sample is GSM79657 Last updated (according to GEO): Sep 22 2006 Measles 1000 1000 Pulmonary Fibrosis 21 0 Heart failure sample 3 861 Brain 3 0 Lung Gene expression data from a hippocampus from mouse injected 10 mg/kg nicotine Source GEO sample is GSM147425 Last updated (according to GEO): Jan 03 2007 1000 Parietal Lobe 7 0 prostate Ciliary muscle structure 901 901 Bone structure of thoracic vertebra Normal Source GEO sample is GSM176048 Last updated (according to GEO): Apr 09 2007 Huntington Disease 1000 ovary 45 50 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181074 Last updated (according to GEO): Jul 12 2007 Spleen 1000 amygdala 24 32 HA99-96B n/a Source GEO sample is GSM178003 Last updated (according to GEO): Jun 11 2007 CNS-SpinalCmod-Adult-7d-4C-s2 Cerebellum 1000 23 13 spinal cord Nervous system structure 901 Colonic mucous membrane 913 The genomic influcence of the combination of three reagents on cultured cortical neurons (9-11 DIV). Bursts of action potential firing were induced by the treatment of cultured cortical neurons with 50 ?M bicuculline (Bic) and 5 ?M 4-aminopyridine (4AP), which were significantly affected by the addition of the L-type VGCC antagonist 5 ?M nifedipine (Nif). Source GEO sample is GSM144061 Last updated (according to GEO): Nov 24 2006 eTat - Noco0hr - 1 epidermis 0 8 39 21 from mammary glands M_95A_2835_AnCg_1_GS stria terminalis 1000 Human lung tissue 54 70 Mesenchymal Stem Cells 1000 WT_IL-6_100_rep1 Expression profiling of moderately injured raphe at 24h in rats Source GEO sample is GSM41583 Last updated (according to GEO): May 27 2005 PE_D_587 Cortex from rats with cerebral cortical contusion 1 day post injury, injured cortex (ipsilateral side) -uninjured cortex (contralateral side) were hybridised onto a 6240 cDNA probe microarray. Expression ratios were calculated using injured/ un-injured cortex Source GEO sample is GSM76157 Last updated (according to GEO): Sep 29 2005 901 Heart Diseases Large-scale analysis of the human transcriptome. Spinal cord Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 180.89 Stdv: 10.26 Min: 160.74 Max: 200.46 Source GEO sample is GSM2852 Last updated (according to GEO): Mar 20 2006 G1E_0_B Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213484 Last updated (according to GEO): Jul 31 2007 1000 Cardiomyopathies Cultured_cortical_astrocyte_wild_type_rep3 901 Bone structure of thoracic vertebra Sample15, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53266 Last updated (according to GEO): Jul 06 2005 Primary small cell lung carcinoma 5395 0 37 for liver 26 35 very advanced HCC Source GEO sample is GSM155936 Last updated (according to GEO): Jun 21 2007 1000 Coronary Arteriosclerosis Normal Source GEO sample is GSM176166 Last updated (according to GEO): Apr 09 2007 T1 gr3 tumour Source GEO sample is GSM2539 Last updated (according to GEO): Mar 21 2006 1-4 Dentate Gyrus 8 24 Wild type inbred mice Source GEO sample is GSM82931 Last updated (according to GEO): Nov 10 2005 Duodenum [JunctionChip 4 of 5] Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213471 Last updated (according to GEO): Jul 31 2007 CNS-SC_InjA7d-4B-s2 Normal human tissue:Normal Thymus Keywords = Human, Normal Tissue, Normal Thymus Source GEO sample is GSM44672 Last updated (according to GEO): May 27 2005 cerebellum 7 16 Nasal Epithelium 901 no doxycycline, mutant Source GEO sample is GSM213368 Last updated (according to GEO): Jul 26 2007 VDXRHU_1917 CNS-RM_Mod4h-2C-s2 5 0 brain mouse cerebral cortex 0 20 9 0 Blood Test Plasma 861 Gene expression data from dorsal pancreas at e12.5, MG-U74B version2 Source GEO sample is GSM199453 Last updated (according to GEO): Jun 08 2007 DMSO treated MCF7 breast cancer cells [HG-U133A] Exp 3 M-20-90-UN on UMich-10k PGA-MAH-OuJO3-1aAv2-s1 Neoplasm 861 27 0 cerebral cortex sprague 3916 Liver 0 4 AR-R-270pM Hippocampus 1982 15 month Old 129:3-3-5 perirhinal cortex The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160221 Last updated (according to GEO): Feb 08 2007 Brain 861 none Source GEO sample is GSM244578 Last updated (according to GEO): Nov 23 2007 PF382 DMSO control 24h rep1 olfactory epithelium 194 213 Acetaminophen 24hr Rat 0184 blood vs. Acetaminophen 24hr Rat Pooled Control blood Brain 861 brain 0 5 Brain 1000 of primary breast tumours 416 441 1000 Synovial Membrane small intestine PPARa knockout mice, fasted for 24 hours Source GEO sample is GSM154795 Last updated (according to GEO): Jul 04 2007 liver 134 139 Plasma 861 GM12239 861 Occipital lobe Acetaminophen 6hr Rat 9203 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool Heart 861 GSE412 Expression profiling of spinal cord section (T9) extracted from rats 14d following severe injury Source GEO sample is GSM31615 Last updated (according to GEO): May 27 2005 neurological disease control sample x009 1000 Nervous system structure 19 0 human frontal cortex Cerebral cortex 861 17 7 hippocampus infection 255 264 Brain trauma 0 11 Gene expression data from mouse primary visual cortex Source GEO sample is GSM101720 Last updated (according to GEO): Jun 15 2006 mouse brains 187 198 heart 1169 1173 12 frontal Lobe 23 A combination drug therapy improves cognition and reverses gene expression changes in a mouse model of Huntington's disease. 861 Heart Brain 861 865 Disorder of artery Primary large cell carcinoma 4222 0 32 GBM Treatment, type=remove Source GEO sample is GSM99495 Last updated (according to GEO): Apr 21 2006 (cortex 19 25 9 0 Blood Test 1000 Bladder Myeloid Leukemia 901 CCRF-CEM hgu95e Gene expression data from dorsal pancreas at e13.5, MG-U74B version2 Source GEO sample is GSM199456 Last updated (according to GEO): Jun 08 2007 HapMap YRI_parent Female Source GEO sample is GSM159709 Last updated (according to GEO): Feb 01 2007 that the adult brain 392 411 Thyroid Gland BD Normal PBMCs-Type 1 Diabetes-IDDM54_T1D_1MO Down Syndrome 1000 The most common congenital cardiac abnormalities 50 97 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92358 Last updated (according to GEO): Jan 13 2006 861 Infection 1000 Creutzfeldt-Jakob Syndrome Malignant Neoplasms 861 14 7 amygdala AML_5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A DBA/2J periaqueductal gray rep2 858 Mesodermal cell 129/SvImJ Cerebellum C 1000 Hypothalamic structure 861 Cerebellum Brain_MD_3_Medulloblastoma_Classic_D on Affymetrix GeneChip Human Full Length Array HuGeneFL Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15729 Last updated (according to GEO): May 28 2005 Gut 861 Neoplasm 861 Dendrites 1000 V5-P144 861 Blood Gene expression data from skeletal muscle following 240 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230452 Last updated (according to GEO): Sep 19 2007 1000 Hippocampus 136 131 Aortae Date : 5/30/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 10 mg/kg Time : 3 hrs post-injection Intervention : none Risk: 40% increased risk for encephalopathy Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AO091 Source GEO sample is GSM12242 Last updated (according to GEO): May 28 2005 3AJZ02051711_Testi_LeydigCell Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2708 Source GEO sample is GSM2124 Last updated (according to GEO): Nov 21 2005 Disease Source GEO sample is GSM175912 Last updated (according to GEO): Apr 09 2007 Brain 861 Acetaminophen 24hr Rat 7375 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool dorsal root ganglia 121 139 80 68 Control blood brain, frontal cortex: Sample50_e1_le1 PCA17_localized prostate cancer bronchial epithelia 224 243 Organ 966 Kidney (fetal) [JunctionChip 1 of 5] Expression profile of genes in mouse brain Source GEO sample is GSM21062 Last updated (according to GEO): May 27 2005 468 459 the rectum 597 576 In corneal epithelium Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=720610 LaserPower=2.061.29 Lot batch = LC17N097 Source GEO sample is GSM4820 Last updated (according to GEO): Nov 21 2005 ileum (pool of 4 animals)_72h monoassociation with L.innocua_B_5548 Source GEO sample is GSM161569 Last updated (according to GEO): Apr 23 2007 D_U133A_97_DLPFC By using high-density oligonucleotide arrays, we profiled gene expression in reward-related brain regions of rats that developed escalated cocaine intake after extended access to cocaine (6 h per day). Rats allowed restricted daily access to cocaine (only 1 h) that displayed a stable level of cocaine intake and cocaine naive rats were used for controls. Four analysis methods were compared: Affymetrix microarray suite 4 and microarray suite 5, which use perfect-match-minus-mismatch models, and dchip and rma, which use perfect-match-only models to generate expression values. Results were validated by RT-PCR in individual animals from an independent replication of the experiment. A small number of genes was associated with escalated cocaine intake (ESC genes). Unexpectedly, of the brain regions examined [prefrontal cortex, nucleus accumbens, septum, lateral hypothalamus (LH), amygdala, and ventral tegmental area], the LH was the most transcriptionally responsive in escalation of cocaine intake. Most of the ESC genes identified are also expressed during synaptogenesis and synaptic plasticity and include genes that code for several presynaptic and postsynaptic proteins involved in neurotransmission. These results suggest that LH intrinsic circuitry undergoes a structural reorganization during escalation of cocaine use. This remodeling of LH circuitry could contribute to the chronic deficit in reward function that has been hypothesized to drive the transition to drug addiction. Results also support the value of using multiple analysis strategies to identify the most robust changes in gene expression and to compensate for the biases that affect each strategy. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Jan 26 2006 Contributers: Robert Lutjens Lena D van der Stap Serge H Ahmed George F Koob Vez Repunte-Canonigo Marisela Morales Dusan Lekic Pietro P Sanna Vincenzo Romano-Spica Includes GDS1608. Update date: Aug 17 2006. Dataset description GDS1608: Analysis of reward-related brain regions from Wistar males with restricted (1 h) or extended (6 h) daily access to cocaine. Escalated cocaine intake (ESC) developed in subjects with extended access. Results provide insight into molecular mechanisms underlying the transition to compulsive drug use.. Plasma 861 0029_1245_H95A2_KF0140_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Brain Plasma 861 1000 Lupus Erythematosus, Systemic Brain 861 Lungs 153 157 DU-145 hgu95a brain, cerebellum: Lh-/-_Crb1_e1_le1 Expression profiling of spinal cord section (T9) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM4466 Last updated (according to GEO): May 28 2005 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225353 Last updated (according to GEO): Aug 31 2007 Brain 861 jzo012-rp1-v5-u74av2-met MCF7 pre-treated for 1h with cycloheximide, treated with E2 for 24h Source GEO sample is GSM213320 Last updated (according to GEO): Jul 26 2007 Several recent reports show that the cerebral cortex in humans and animals with altered expressions of Wnt/cadherin network-associate molecules display cytoarchitectural abnormalities reminiscent of cortical dysplasias seen in some (mouse-, rat-, and monkey-based) animal models of prenatal cocaine exposure. Therefore, we employed oligo microarrays followed by real-time RT-PCR to compare expressions of genes involved in Wnt and cadherin systems in the cerebral wall of 18-day-old (E18) fetuses from cocaine-treated (20 mg/kg cocaine, s.c., b.i.d., E8-18) and drug-naive (saline, s.c.) mice. The pregnant mice chronically treated with cocaine in the above-described manner represent one of the animal models producing offspring with widespread cortical dysplasias. Out of more than 150 relevant genes in the arrays, 32 were upregulated and 9 were downregulated in cocaine-exposed fetuses. The majority of these genes (30 out of 41) were similarly affected in the frontal and occipital regions of the cerebral wall. We also used Western immunoblotting to examine the ability of cocaine to regulate the protein levels of beta-catenin, the key functional component of both Wnt and cadherin systems. While the total cell levels of beta-catenin were increased throughout the cerebral wall of cocaine-exposed fetuses, its nuclear (gene-transcription driving) levels remained unaltered. This suggests a transcription-unrelated role for cocaine-induced upregulation of this protein. Overall, our findings point to an intriguing possibility that that cerebral cortical dysplasias observed in several animal models of prenatal cocaine exposure may be at least in part related to alterations in the Wnt/cadherin molecular network. Normal Source GEO sample is GSM176217 Last updated (according to GEO): Apr 09 2007 Prosencephalon 861 from brain 21 30 Epithelium of bronchus 983 brain, hippocampus: CH2_e1_le1 with some respiratory epithelium. 1039 1072 brain, hippocampus: LH4_e1_le1 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202677 Last updated (according to GEO): Jun 20 2007 I_U133A_14_CB 25 0 Superior_Cervical_Ganglion plasma cells 50 61 PBMCs-Healthy-H125_Healthy Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10172.gif Source GEO sample is GSM79714 Last updated (according to GEO): Sep 22 2006 861 Cerebral cortex midbrain_10 Source GEO sample is GSM80706 Last updated (according to GEO): Mar 31 2006 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181160 Last updated (according to GEO): Jul 12 2007 Parkinson Disease 861 410_2 Category: Lymphoma Classification Subcategory: Chronic Lymphocytic Leukemia Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b069 Source GEO sample is GSM2017 Last updated (according to GEO): Nov 21 2005 FVB/NJ periaqueductal gray rep2 (430 2.0 Array) mouse hippocampus 0 17 HC65 CN B none Source GEO sample is GSM239951 Last updated (according to GEO): Dec 07 2007 119 96 in embryonic stem cells 861 Blood of adenocarcinoma 395 411 861 Ovary 53 30 (interventricular septum no additional Source GEO sample is GSM199302 Last updated (according to GEO): Jun 08 2007 861 Brain Acute leukemia 896 1000 Cerebral cortex MuscleRegen-ctx14d-1LLAv2-s2 Colonic mucous membrane 913 1000 Liver Whole Brain 62 72 Expression profiling of somatomotor cortex extracted from rats at 7d following moderate injury Lot batch = Source GEO sample is GSM44720 Last updated (according to GEO): May 27 2005 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14953 Last updated (according to GEO): Oct 28 2005 865 Cerebral cortex Interatrial septum 865 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188712 Last updated (according to GEO): Jun 06 2007 KT3_AR3 Knockout cocaine, technical replicate 1 Simple annotation: RNA coimmunoprecipitation, development Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8815.gif Source GEO sample is GSM78460 Last updated (according to GEO): Sep 22 2006 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19238 Last updated (according to GEO): May 27 2005 Left hemidiaphragm 884 NHE1 null mutation brain stem-diencephalon-DS1 Arteries 861 78 66 Control blood Spleen 1000 placenta; females with E18 embryos Source GEO sample is GSM18682 Last updated (according to GEO): May 27 2005 Myocardium 861 M_U133A_83_nAcc 1000 Spinal Cord Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10161.gif Source GEO sample is GSM79672 Last updated (according to GEO): Sep 22 2006 Bone marrow, Mesenchymal stem cells: T1-181203_e1_le1 Macrophage smi108 D_95Av2_2978_CB_0_GS Spleen 1000 1000 ovarian neoplasm no additional Source GEO sample is GSM199283 Last updated (according to GEO): Jun 08 2007 861 Cerebellum Heart 1000 Spleen 1000 Whole blood 0 10 NCI60.41_LABEL45EXTRACT44SUB3 Source GEO sample is GSM134198 Last updated (according to GEO): Aug 06 2007 861 Malignant neoplasm of prostate 123 FC BA9 B 3AJZ02022758_thymus 901 Caudate nucleus structure L_AK_Control_ZT 6_3 f2#244 versus pool Mouse Brain tissue Cerebellum_naive_ISS56_B Mental Retardation 1000 Oxidative stress is a major source of injury from cerebral ischemia and reperfusion. We hypothesized that a catalytic antioxidant AEOL 10150 [manganese (III) meso-tetrakis (di-N-ethylimidazole) porphyrin] would attenuate changes in brain gene expression in a mouse model of transient middle cerebral artery occlusion (MCAO). C57BL/6J mice were subjected to either sham surgery or 60 min of right MCAO. AEOL 10150 or phosphate-buffered saline was given intravenously 5 min after onset of reperfusion (n = 6 per group). Six hours later, parenchyma within the MCA distribution was harvested. RNA from the six brains in each group was pooled and mRNA expression determined using an Affymetrix murine MG_U74A v. 2.0 expression microarray. Each experiment was performed three times. The largest changes in expression occurred in stress response and inflammatory genes such as heat shock protein, interleukin-6, and macrophage inflammatory protein-2. Treatment with AEOL 10150 attenuated only the increase in expression of inflammatory genes. This suggests that AEOL 10150 protects brain by attenuating the immune response to ischemia and reperfusion. NCI60.16_LABEL20EXTRACT19SUB3 Source GEO sample is GSM134072 Last updated (according to GEO): Aug 06 2007 c10 Spleen vs NGF (Nerve Growth Factor)Treated B cell 240min (set2) Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15746 Last updated (according to GEO): May 28 2005 Arteries 861 Treated Source GEO sample is GSM175971 Last updated (according to GEO): Apr 09 2007 Primary large cell neuroendocrine carcinoma 6042 Source GEO sample is GSM17331 Last updated (according to GEO): May 28 2005 GC (HKG37T) Temporal Cortex Control (AD) 6 Skeletal bone 861 4535 4527 hepatoma 901 Temporal Lobe Cytoskeleton 861 Cultured in DMEM with 10% FBS and penicillin (100U/ml)/streptomycin (100ug/ml). Media changed every other day. 37ºC, 5% CO2. Source GEO sample is GSM15792 Last updated (according to GEO): Oct 28 2005 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48017.gif Developmental Stage: E7.5 Source GEO sample is GSM229823 Last updated (according to GEO): Nov 06 2007 M_U133A_14_AnCg GM10859 C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P18 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25146 Last updated (according to GEO): May 27 2005 73 54 of hyperinsulinaemic Macrophage smi107 NA18948 Heart 861 Lung; Day 1 postnatal Keywords = mouse gene expression database Source GEO sample is GSM29379 Last updated (according to GEO): May 27 2005 861 Prostate carcinoma Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour.This animal was sacrificed at 4 hours after lights on.Original sample code = CM22A Source GEO sample is GSM227316 Last updated (according to GEO): Sep 10 2007 from the forebrain 20 37 NHE1 null mutation cortex-3 human muscle 627 638 861 Neostriatum MDA Mb231 6h 3 Control 865 Disorder of artery 19 0 human frontal cortex via insulin resistance. 291 314 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226082 Last updated (according to GEO): Nov 02 2007 Human lung tissue 53 69 pfc_1047_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Communicable Diseases 1000 Whole blood 0 10 Standard Affymetrix Protocol Source GEO sample is GSM15852 Last updated (according to GEO): May 28 2005 67 40 with coronary artery disease Tissue Source GEO sample is GSM67242 Last updated (according to GEO): Jan 19 2006 Cerebral cortex 861 5 0 Spleen 4M_122002 Liver Test (Blinded) Sample Source GEO sample is GSM130088 Last updated (according to GEO): Sep 18 2007 861 Cerebral cortex Alzheimer's Disease 1000 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13148.gif Source GEO sample is GSM79690 Last updated (according to GEO): Sep 22 2006 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195267 Last updated (according to GEO): Sep 13 2007 HCC (HBV+, HK64, T3) Subject code A21 high gestational age Source GEO sample is GSM213084 Last updated (according to GEO): Jul 25 2007 3AMH02030601_Colorectal Adenocarcinoma 2 Retina 13 20 Sample is skeletal muscle from morbidly obese patient undergoing elective abdominal surgery Source GEO sample is GSM3979 Last updated (according to GEO): May 28 2005 HDF-Skin 715 702 After the eyes 861 Brain ZR-75-1 4089 4084 liver Blood Test (Blinded) Sample Source GEO sample is GSM129912 Last updated (according to GEO): Sep 18 2007 1000 Brain AML_24 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Cerebellum Lymphoblastoid Cell Line for Individual 8134.4 log phase normal testis 54 66 613 595 with these cancers Spleen 1000 5 0 brain Status Epilepticus 901 Large-scale analysis of the mouse transcriptome. Uterus C57BL/6L, female, 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 362.43 Stdv: 21.44 Min: 335.17 Max: 412.41 Source GEO sample is GSM2963 Last updated (according to GEO): Mar 20 2006 Macrophage smi111 Liver 1000 Pituitary Gland 861 H115 FC BA4 A Normal Source GEO sample is GSM176097 Last updated (according to GEO): Apr 09 2007 Expression profiling of spinal cord section (T8) extracted from rats 24h following severe injury Source GEO sample is GSM31468 Last updated (according to GEO): May 27 2005 Pituitary Gland 861 913 Coronary heart disease Osteoblasts 1000 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210401 Last updated (according to GEO): Jul 16 2007 D_U133Plus_122_Amy 1000 Odontoblasts 5 0 brain Plasma 861 1000 Brain in fibroblasts 1222 1236 Oat cell carcinoma 888 Small cell carcinoma of lung 901 on the muscle host cells 2154 2178 Brain 861 of familial non-BRCA1/BRCA2 breast cancer 25 66 861 Heart 1BJZ02050813_Ovary Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226146 Last updated (according to GEO): Nov 02 2007 30 19 Solid tumor 1000 Spleen 1BRS02080876b_skin 861 Lung Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120685 Last updated (according to GEO): May 14 2007 D_U133A_34_HC 278 255 ischemic cardiomyopathy of hypertension 51 65 Bone structure of tibia 1000 1BJZ02022648_cerebellum Macrophage 14smi073 Ligament, primary 1000 Brain Primary typical carcinoid 6618 healthy subject Source GEO sample is GSM211065 Last updated (according to GEO): Sep 10 2007 brain, frontal cortex: pADX PM FC_e1_le1 Skeletal muscle structure 1000 Adipose tissue 884 A complex profile of gene expression elicited by autocrine platelet-derived growth factor (PDGF) signaling was identified in U87 MG glioblastoma cells by microarray analysis. The most striking pattern observed was a PDGF-dependent activation of at least 25 genes involved with biosynthesis and/or uptake of cholesterol and isoprenoids, including mevalonate pyrophosphate decarboxylase, 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase, HMG-CoA reductase, and low-density lipoprotein receptor. Activity of the HMG-CoA synthase promoter was induced by autocrine PDGF activity as indicated by significant reductions following forced expression of dominant-negative PDGF-A (88%) or treatment with the PDGF receptor antagonist CT52923 (50%). Induction of the HMG-CoA synthase promoter required a binding site for sterol regulatory element binding proteins (SRE-BP), consistent with a key role for these transcription factors in the induction of this gene network. Neither proteolytic activation nor nuclear localization of SRE-BP was affected by disruption of the PDGF autocrine loop, indicating that PDGF signaling is required for other signaling events involved in activation of SRE-BP target genes. Analysis of an expression databank derived from human glial tumors (n = 77) identified a subgroup exhibiting a profile consistent with PDGF dependence, including increased expression of SRE-BP target genes. This subgroup displayed an absence of epidermal growth factor receptor gene amplification, decreased incidence of allelic loss of 10q, increased frequency of TP53 mutations and allelic losses of 1p and 19q, and longer patient survival. This study identifies genes associated with oncogenic activity of PDGF and provides important insights into biomarkers and therapeutic targets in malignant gliomas. 861 Cerebral cortex of coronary artery disease 258 284 Donor E, prior to G-CSF Source GEO sample is GSM178553 Last updated (according to GEO): Aug 09 2007 brain 0 5 Transitional epithelium 1000 Nanog-iPS cells Source GEO sample is GSM190231 Last updated (according to GEO): May 18 2007 FL-11 Prostate carcinoma 1000 in retinas 230 239 403 394 in cancers Epithelium of bronchus 983 1000 Cerebellum Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198622 Last updated (according to GEO): Jun 06 2007 Brain 861 1000 Neoplasm Semeralul_PFC_Development_Week4_Batch1_Animal_6 gene expression of 3 day LIF differentiated ESCs Source GEO sample is GSM181952 Last updated (according to GEO): Apr 12 2007 R6/1 wildtype, brain hemisphere Source GEO sample is GSM83876 Last updated (according to GEO): Apr 20 2007 861 Malignant neoplasm of prostate Brain 1000 Laser capture lung cancer cells Source GEO sample is GSM191018 Last updated (according to GEO): May 25 2007 PGA_PA-D_319 A2780_cis_IC90_16h_2 Intestines, Small 1000 Fasted Mouse 3 901 frontal lobe Amygdala Source GEO sample is GSM107916 Last updated (according to GEO): Jun 06 2006 Wild type inbred mice Source GEO sample is GSM82919 Last updated (according to GEO): Nov 10 2005 M_U133A_91_DLPFC 1000 Encephalitis f2#158 versus pool Mouse Brain tissue /3T3 fibroblasts 295 310 Fibroblasts 1000 Brain 861 84 69 by heart failure 052401_HF_321CB Skeletal bone 861 Coronary Arteriosclerosis 1000 1000 Brain 1_cerebral_cortex_12hrs_sleep_deprivation_#9 allander-gist 0 12 B6 4:1and2 CA1 861 Cerebral cortex forebrain 7 15 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113967 Last updated (according to GEO): Jun 16 2006 NCI60.12_LABEL15EXTRACT14SUB3 Source GEO sample is GSM134050 Last updated (according to GEO): Aug 06 2007 913 frontal lobe E8.75_rep2 CNS-SC_Inj24h-5A-s2b Expression profiling of spinal cord section (T9) extracted from rats 4h following laminectomy (sham) Lot batch = Source GEO sample is GSM1334 Last updated (according to GEO): May 28 2005 1000 Hippocampus brain, Left Parietal Lobe: Extract41_le2 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9933.gif Source GEO sample is GSM79911 Last updated (according to GEO): Sep 22 2006 GC (HKG90T) AML 65 0 5 SK-MEL-28_CL10008_Melanoma on Affymetrix GeneChip Human Full Length Array HuGeneFL brain, cerebellum: 3 hrs A GW_e1_le1 smooth muscle 595 607 Endometrium 0 10 861 Anterior Myocardium 861 comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247388 Last updated (according to GEO): Dec 11 2007 Cerebral cortex 861 40 21 from skeletal muscle Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2729 Source GEO sample is GSM2113 Last updated (according to GEO): Nov 21 2005 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181180 Last updated (according to GEO): Jul 12 2007 YFPH-SomatosensoryCortex-replicate3 D3_TP-48_I Lymphoblastoid Cell Line for Individual 8006.4 log phase Cell line dependent RNA expression profiles of prion-infected mouse neuronal cells. Parkinson's disease sample x102 0 30 striatum 35 43 7 0 Pancreas of the normal mucosa 7 26 spleen 265 270 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51114.gif Developmental Stage: E6.75 Source GEO sample is GSM229830 Last updated (according to GEO): Nov 06 2007 19 0 human frontal cortex Brain [JunctionChip 3 of 5] Adenocarcinoma 4 0 15 901 frontal lobe Expression profiling of spinal cord section (T9) extracted from rats 4h following laminectomy (sham) Lot batch = Source GEO sample is GSM6674 Last updated (according to GEO): May 28 2005 Liver Test (Blinded) Sample Source GEO sample is GSM130096 Last updated (according to GEO): Sep 18 2007 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181109 Last updated (according to GEO): Jul 12 2007 A2780_oxa_IC75_16h_2 721_BLymphoblasts Source GEO sample is GSM18889 Last updated (according to GEO): Sep 25 2006 1000 Structure of entorhinal cortex liver_wildtype_control_5d_rep1 5 0 Uterus Expression profiling of spinal cord section (T9) extracted from rats 14d following severe injury Source GEO sample is GSM31598 Last updated (according to GEO): May 27 2005 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225751 Last updated (according to GEO): Nov 02 2007 1237 CP0_12 50 41 mouse lung Colorectal Adenocarcinoma (SW480) [JunctionChip 3 of 5] with autism spectrum disorder 37 65 Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Dye-swap. Source GEO sample is GSM15945 Last updated (according to GEO): May 28 2005 861 Cerebral cortex Category: Lymphoma Classification Subcategory: Hematopoetic cell lines Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b041 Source GEO sample is GSM1963 Last updated (according to GEO): Nov 21 2005 none Source GEO sample is GSM239914 Last updated (according to GEO): Dec 07 2007 Heart 1000 no_pre_no_restimulation_rep_A human frontal cortex Source GEO sample is GSM87019 Last updated (according to GEO): Feb 08 2006 brain, cerebral cortex: Rat_02-47_VHL_Lipska_e1_le1 Neoplasm 1000 329 306 valvular cardiomyopathy Cell source of DN2_1, DN3_1, and DN4_1 are identical. Cell source of DN2_2, DN3_2, and DN4_2 are identical. Cell source of DN2_3, DN3_3, and DN4_3 are identical. Cell source of DN2_4, DN3_4, and DN4_4 are identical. Each cell sorce was derived from four mice. Source GEO sample is GSM188621 Last updated (according to GEO): May 16 2007 MGJZ030211001Aadiposetissue The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160326 Last updated (according to GEO): Feb 08 2007 Large-scale analysis of the human transcriptome. Lymphoma Burkitt's Raji Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 124.96 Stdv: 7.76 Min: 113.67 Max: 138.77 Source GEO sample is GSM2893 Last updated (according to GEO): Mar 20 2006 Small Pre-BII cells 8b Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181215 Last updated (according to GEO): Jul 12 2007 Cerebral cortex 1000 Keywords = Infectious diseases 1070 1100 "5 hr Hela Double Thymidine, exp3" 57 39 with endometriosis none Source GEO sample is GSM239840 Last updated (according to GEO): Dec 07 2007 ventral_tegmental_area_9 Source GEO sample is GSM80894 Last updated (according to GEO): Mar 31 2006 20 0 human caudate nucleus 1000 Amygdaloid structure Liver 0 4 861 Cardiomyopathies CNS-SCsev_InjB7d-1C-s2 total spinal cord from a wild type mouse. Source GEO sample is GSM113715 Last updated (according to GEO): Jun 09 2006 GSE4269 Myocardial Infarction 1000 Lung 861 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153360 Last updated (according to GEO): Dec 27 2006 HC105 CN B 1000 Substantia nigra structure MP-1 1000 Ventricular septum 21 0 acute myeloid leukemia Gene expression data from aneurismal tissues obtained from patients with bicuspid valves. Source GEO sample is GSM116785 Last updated (according to GEO): Jun 28 2006 GBM Treatment, type=remove Source GEO sample is GSM99451 Last updated (according to GEO): Apr 21 2006 Spinocerebellar Ataxias 901 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225663 Last updated (according to GEO): Aug 31 2007 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc131 Source GEO sample is GSM1927 Last updated (according to GEO): Nov 21 2005 normal 1345 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225964 Last updated (according to GEO): Nov 02 2007 1000 Infection 1000 Prostate Brain 1000 plasma cells 332 344 Colon 1000 in the mammalian nervous system 110 141 861 Anterior 1000 Liver Coronary Arteriosclerosis 1000 in bronchial epithelia 311 332 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201279 Last updated (according to GEO): Jun 14 2007 PNS BMI-1 KO Chip B 473 459 from the brains To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18446 Last updated (according to GEO): May 27 2005 Primary Neoplasm 1000 7 0 Lymphoma Gene expression data from postmorten brain regions Source GEO sample is GSM145293 Last updated (according to GEO): Nov 20 2006 Brain 861 H111 CN B 901 Caudate nucleus structure no additional Source GEO sample is GSM199407 Last updated (according to GEO): Jun 08 2007 Locus Coeruleus Source GEO sample is GSM107976 Last updated (according to GEO): Jun 06 2006 days nasal epithelium 1126 1147 1000 Spleen 1000 Heart ER negative human primary breast tumor EA02014_41269_H133A_JA-1497 Cochlea at E11, replicate2 ND004 CD3 + CD28 beads 01.00 hr. T-Cell; trunc. Gene expression data from postmorten brain regions Source GEO sample is GSM145016 Last updated (according to GEO): Nov 20 2006 114 101 brains quickly Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b058 Source GEO sample is GSM2001 Last updated (according to GEO): Nov 21 2005 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120678 Last updated (according to GEO): May 14 2007 Lymphoblastoid Cell Line for Individual 8116.3 log phase brain, left frontal temporal lobe: Extract1_le2 CNS-RM_Ctr7d-1B-s2 Osteoblasts 1000 334 320 Keywords = HIV Ovarian_Tumor_Serous_KU-OS-018 CNS-RM_Mod28d-1C-s2 CNS-SC_InjA30m-2B-s2 MCF7_Treated dorsal_root_ganglia_3 "Sample 24,>5 yr survival(106 months) age 49 erp no" on vantveer-oligo Small Intestine; proximal jejunum Keywords = mouse gene expression database Source GEO sample is GSM29307 Last updated (according to GEO): May 27 2005 1000 Brain whole blood_100652 660 mesenchymal stem cell 639 Normal__Pancreas_Pan_42N on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 3AJZ02052305_TestiIntersitial Gene expression data from human prostate tissue with 90 percent tumor content Source GEO sample is GSM119316 Last updated (according to GEO): Feb 23 2007 CAD_replicate94 12 0 ovarian tumor 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201301 Last updated (according to GEO): Jun 14 2007 from the femurs 95 109 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181163 Last updated (according to GEO): Jul 12 2007 Coronary Arteriosclerosis 1000 861 Neoplasm none Source GEO sample is GSM239956 Last updated (according to GEO): Dec 07 2007 outer medulla 31 43 no additional Source GEO sample is GSM199075 Last updated (according to GEO): Jun 08 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withSLC (Secondary lymphoid-organ chemokine) for 120min Source GEO sample is GSM5775 Last updated (according to GEO): May 27 2005 DR6h(2) Gene expression data from whole tumor Source GEO sample is GSM182285 Last updated (according to GEO): Apr 16 2007 D_U133A_44_nAcc 1000 Brain 727 721 spleens HC61 CB A 1000 Structure of parenchyma of lung from ventral prostate 21 41 Leukemia, Lymphocytic, Chronic 1000 1000 Kidney Mammalian target of rapamycin (mTOR) is implicated in synaptic plasticity and local translation in dendrites. Here we found that the mTOR inhibitor, rapamycin, increased the Kv1.1 voltage-gated potassium channel protein in hippocampal neurons and promoted Kv1.1 surface expression on dendrites without altering its axonal expression. Moreover, endogenous Kv1.1 mRNA was detected in dendrites. Using Kv1.1 fused to the photo-convertible fluorescence protein Kaede as a reporter for local synthesis, we observed Kv1.1 synthesis in dendrites upon inhibition of mTOR or the N-methyl-D-aspartate (NMDA) glutamate receptor. Thus, synaptic excitation may cause local suppression of dendritic Kv1 channels by reducing their local synthesis. Last Updated (by provider): Nov 21 2006 Contributers: Patrick C Haddick Lily Y Jan Kimberly F Raab-Graham YuhNung Jan n/a Source GEO sample is GSM178072 Last updated (according to GEO): Jun 11 2007 913 Coronary heart disease Timed pregnant C57Bl6 mice were exposed to ethanol during gestational day 15 to day 18 and ethanol exposed fetuses were delivered by cessarian section on gestational day 19. Alcohol exposed fetuses were compared to control timed pregnant mice and to pair fed controls (animals fed with maltose dextrose) Source GEO sample is GSM116853 Last updated (according to GEO): Jul 03 2006 Probeset expression data from NA12751 growth 3, replicate 3 Source GEO sample is GSM195215 Last updated (according to GEO): Aug 08 2007 5 0 brain Expression profiling of spinal cord section (T8) extracted from rats 30m following mild injury Source GEO sample is GSM31445 Last updated (according to GEO): May 27 2005 EOM 56 Day Control rep 3 PBMCs-Type 1 Diabetes-IDDM30_T1D_New very early HCC Source GEO sample is GSM155991 Last updated (according to GEO): Jun 21 2007 1694 1684 for obesity Clone 8.1 plus PDGF chip 1 Primary large cell carcinoma 1531 1000 Antibodies 901 Nervous system structure Myocardial Infarction 1000 DLBC28 on Affymetrix GeneChip Human Full Length Array HuGeneFL Spleen vs IL4 Treated B cell 240min (set1) 901 Coronary artery Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs//12403.gif Source GEO sample is GSM79822 Last updated (according to GEO): Sep 22 2006 of a colorectal adenoma 7 29 Cardiac-specific TNF-alpha transgenic mice are an excellent model to study the pathologenesis of heart failure. Affymetrix U74V2A was used to analyze the gene expression profile of male and female wildtype FVB and TNF-alpha transgenic mice at the time point of compensated hypertrophy and dilated heart failure. 3 week, 13 week and 40 week samples examined.. Date GSE591 Last Updated: May 29 2005 Contributers: Z H Tang Zhong H Tang A M Feldman Arthur M Feldman Includes GDS496. Update date: Mar 02 2004. Dataset description GDS496: Analysis of cardiac-specific tumor necrosis factor alpha (TNF alpha) transgenics at time of compensated hypertrophy and dilated heart failure. Heart tissue from 3, 13 and 40 week animals used. FVB wildtype controls and gender-dependent effects examined.. Mesenchymal Stem Cells 1000 jzo030-rp1-v5_u74av2-met pfc_1045_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 1000 melanoma CNS-SCsev_InjA7d-2A-s2c KPeterson-NonMet-23G110-s2 CNS-SC_CtrB24h-1A-s2 Donor B, pre G-CSF Expression profiling of spinal cord section (T9) extracted from rats 12h following moderate injury Source GEO sample is GSM31520 Last updated (according to GEO): May 27 2005 Blood 861 861 Nerve Coronary artery 901 DR6h(4) The current model to explain the organization of the mammalian nervous system is based on studies of anatomy, embryology, and evolution. To further investigate the molecular organization of the adult mammalian brain, we have built a gene expression-based brain map. We measured gene expression patterns for 24 neural tissues covering the mouse central nervous system and found, surprisingly, that the adult brain bears a transcriptional "imprint" consistent with both embryological origins and classic evolutionary relationships. Embryonic cellular position along the anterior-posterior axis of the neural tube was shown to be closely associated with, and possibly a determinant of, the gene expression patterns in adult structures. We also observed a significant number of embryonic patterning and homeobox genes with region-specific expression in the adult nervous system. The relationships between global expression patterns for different anatomical regions and the nature of the observed region-specific genes suggest that the adult brain retains a degree of overall gene expression established during embryogenesis that is important for regional specificity and the functional relationships between regions in the adult. The complete collection of extensively annotated gene expression data along with data mining and visualization tools have been made available on a publicly accessible web site (www.barlow-lockhart-brainmapnimhgrant.org). total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with fMLP for 120min Source GEO sample is GSM5573 Last updated (according to GEO): May 27 2005 Lymphoblastoid Cell Line for Individual 8170.3 log phase db/db 16 wk 1 1000 Malaria 154 131 ischemic cardiomyopathy 875 Subcutaneous Tissue MGJZ030211002Aadrenalgland Uninjured Control - Epicenter Rep2 19 0 Head and neck cancer NG108 rat neuronal cell culture exposed to 0.25% DMSO (control) for two hours. 10 µg total RNA hybridized per chip. RNA STAT 60 used to extract RNA. Standard Affymetrix chip scaling factors used. No other data transformation. Source GEO sample is GSM1661 Last updated (according to GEO): Oct 28 2005 5 0 brain 15 7 hindbrain M_U133A_63_HC Heart 1000 MO_control_180min_Patient1 5 0 brain of cancers 86 95 1082 1071 in G-protein Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28725 Last updated (according to GEO): May 27 2005 Parkinson Disease 1000 cortex 7 12 of the atrial 647 659 Epithelium 861 Aorta 861 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211295 Last updated (according to GEO): Jul 18 2007 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 18 hours after lights on. Original RNA code = LC50A. Source GEO sample is GSM227365 Last updated (according to GEO): Sep 10 2007 Gene expression data from a neocortex from mouse injected 15 mg/kg kainate Source GEO sample is GSM147405 Last updated (according to GEO): Jan 03 2007 5 0 Spleen 861 Salivary Glands Acetaminophen 6hr Rat 6930 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool 129:30-16-30 choroid plexus 901 Bone Marrow 861 Hippocampus spleen 36 41 GSE8605 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12374 Last updated (according to GEO): May 28 2005 1000 Prostate Category: Serum-response Subcategory: Fibroblasts Scanning Software: unknown Software version: unknown Lot batch = 319 Source GEO sample is GSM2168 Last updated (according to GEO): Nov 21 2005 Nose 1000 brain, frontal cortex: pADX AM S_e1_le1 I_U133A_33_AnCg brain 0 5 Site: University of California, Davis Cohort: Male/Female Control Set Diagnosis: Control pH: 6.71 Subject: 3023 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39050 Last updated (according to GEO): May 27 2005 brain_DLPFC_bipolar B_mr950 9 0 Blood Test Epithelial Cells 1000 861 Dental Pulp brain, contralateral Cortex: Trizol Extraction44_le1 Hyperdip>50-C31 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Endometrium 0 10 in bronchial epithelia 311 332 Gloubus Pallidum Internal 4 Disease Pituitary Gland, Posterior 861 entorhinal cortex layer II stellate island cells Source GEO sample is GSM107541 Last updated (according to GEO): May 01 2006 like glial fibrillary acidic protein 1225 1260 Gene Expression data from the suprachiasmatic nucleus of an animal euthanized 1.5 hours after lights off. Source GEO sample is GSM159296 Last updated (according to GEO): Oct 31 2007 Prostate 861 861 Acquired Immunodeficiency Syndrome Gene expression data from postmorten brain regions Source GEO sample is GSM145151 Last updated (according to GEO): Nov 20 2006 Cerebral cortex 1000 DR6h(3) total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with MIP3-alpha (Macrophage inflammatory protein-3) for 240min Source GEO sample is GSM5695 Last updated (according to GEO): May 27 2005 mouse brain 478 489 Myometrium 18 Normal Standard Affymetrix Protocol Source GEO sample is GSM16485 Last updated (according to GEO): May 28 2005 863 836 of severe autoimmune disease I_U133A_67_AnCg 5.0 mg/kg MeHg forebrain at 1.5h hrs nasal epithelium 1127 1147 plasma cells 50 61 19 0 human frontal cortex NO_KIDNEY_12 861 Blood Arteries 861 GBM/OAC: 60A4 normal testis 54 66 Measles 861 M_U133A_98_HC a specific facial nerve hypomorphism 321 356 prostate Source GEO sample is GSM203389 Last updated (according to GEO): Jun 21 2007 Paravertebral Muscle 5 Disease GSE5285 861 Brain NA11993 Parkinson Disease 861 plasma cells 332 344 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225747 Last updated (according to GEO): Nov 02 2007 Neoplasm 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145171 Last updated (according to GEO): Nov 20 2006 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14949 Last updated (according to GEO): Oct 28 2005 Expression profiling of spinal cord section (T8) extracted from rats 7d following laminectomy (sham) Lot batch = Source GEO sample is GSM4430 Last updated (according to GEO): May 28 2005 23 11 of the kidney Cerebral cortex 861 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202688 Last updated (according to GEO): Jun 20 2007 1000 Mental disorders Stria 861 frontal cortex sprague 3934 I_U133A_109_AnCg Parkinson's disease sample x186 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181167 Last updated (according to GEO): Jul 12 2007 3AJZ02031302_lymphomaburkittsDaudi Myocardial Infarction 1000 Heart 1000 Large-scale analysis of the mouse transcriptome. Spinal cord, upper half C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 284.53 Stdv: 9.02 Min: 266.71 Max: 299.60 Source GEO sample is GSM2919 Last updated (according to GEO): Mar 20 2006 in Peripheral Blood Mononuclear Cells 24 60 from epididymal fat tissues 21 48 Neo6, 48h treatment with 5 AzadC 861 Heart N/A Source GEO sample is GSM96294 Last updated (according to GEO): Feb 13 2006 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5832 Last updated (according to GEO): May 27 2005 brain, cerebral cortex: Co 2 (4/22)_le1 Brain 861 A HID I D044 none Source GEO sample is GSM149525 Last updated (according to GEO): Jan 03 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM144913 Last updated (according to GEO): Nov 20 2006 Mouse Liver AIN Diet 5wk Control, biological replicate F from mouse colon 21 36 Cerebellum 1000 Neoplasm 861 cerebellum 7 16 901 Stem cells Dahl Salt Sensitive Rat Lung- Control 4 1 of 3 replicates in treatment group Source GEO sample is GSM206046 Last updated (according to GEO): Jun 29 2007 comparison of olfactory-bulbectomized and sham-operated rats with depressive-like behaviour Source GEO sample is GSM247201 Last updated (according to GEO): Dec 11 2007 21 0 cerebellum wistar 3888 861 Oocytes the blood 393 402 Keywords = kidney 236 253 Transplant Series 33 , PrimaryTumor Brain 1000 f2#287 versus pool Mouse Brain tissue Nose 1000 1000 Spleen 901 frontal lobe 875 Cerebellar Diseases 091253 HL-60 on Affymetrix GeneChip Human Full Length Array HuGeneFL Expression profiling of spinal cord section (T8) extracted from rats 7d following laminectomy (sham) Source GEO sample is GSM31411 Last updated (according to GEO): May 27 2005 Sample represents the supraoptic nucleus from 5 control animals Source GEO sample is GSM69462 Last updated (according to GEO): Dec 15 2005 Category: Lymphoma Classification Subcategory: Hematopoetic cell lines Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b044 Source GEO sample is GSM1991 Last updated (according to GEO): Nov 21 2005 brain, cerebral cortex: Rat_03-56_NroLep_Lipska_e1_le1 of the colon 28 39 male C57BL6, double amplification Source GEO sample is GSM5415 Last updated (according to GEO): May 27 2005 ISR10 Mouse young brain C5-Br-3 861 Cardiomyopathies 861 Neoplasm THAP24_3 Parkinson Disease 1000 GM18853 olfactory epithelium 194 213 Muscle 645 650 865 Disorder of artery 1000 Liver Transcriptional profiling was done in Hoxb1 mutant E10.5 embryos in tissues primarily consisting of rhombomere 4 and surrounding branchial arches. Source GEO sample is GSM115800 Last updated (according to GEO): Aug 28 2006 of coronary artery disease 317 342 CNS-SCsev_InjA24h-3A-s2 tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44881 Last updated (according to GEO): May 27 2005 Gene expression data from experimental treatment UD = Undifferentiated SH-SY5Y cells, i.e. before PMA induced differentiation (UD). Source GEO sample is GSM102842 Last updated (according to GEO): May 11 2006 Group 1 Control Untreated pool # EP3 vs. reference pool of the postmortem brains 674 698 Uninfected Source GEO sample is GSM34387 Last updated (according to GEO): Oct 16 2006 Cell type specific expression profiles of mouse forebrain neurons 65 49 to cardiomyopathy gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134652 Last updated (according to GEO): Jul 09 2007 AML60 on Affymetrix GeneChip Human Full Length Array HuGeneFL Subcutaneous stromo vascular fraction, rep1 15 0 human cerebellum SN:1007083 Source GEO sample is GSM115364 Last updated (according to GEO): Jun 20 2006 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3340 Last updated (according to GEO): Mar 21 2006 adenoma 861 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11506 Last updated (according to GEO): May 28 2005 072801 Mock 02.00 hr. T-Cell 1581 1566 of HPV+ cancers Heart 1000 988 971 from the hindbrain none Source GEO sample is GSM239916 Last updated (according to GEO): Dec 07 2007 brain, Right Frontal Temporal: Extract68_le2 Arteries 861 CVB3_V-0.5h human caudate nucleus Source GEO sample is GSM86920 Last updated (according to GEO): Feb 08 2006 492 475 in the PCOS oocyte brain, brainstem: LB3_e1_le1 Nose 1000 13 to the nose 599 609 HapMap YRI_parent Male Source GEO sample is GSM159721 Last updated (according to GEO): Feb 01 2007 brain, Right Temporal Lobe: Extract81_le2 1000 Spleen Lymphoblastoid Cell Line for Individual 8149.3 log phase 7 0 Pancreas 861 Colon 19 0 human frontal cortex Hippocampus 8 Normal HC72 CB B PHG-LTM-1aAv2-s2 brain_DLPFC_bipolar C_mr537 Blood 1000 Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.13 Subject: 1871 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39068 Last updated (according to GEO): May 27 2005 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13114.gif Source GEO sample is GSM79976 Last updated (according to GEO): Sep 22 2006 Colon 861 ER negative human primary breast tumor EA02014_41283_H133A_JA-1589 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228634 Last updated (according to GEO): Sep 11 2007 Parkinson Disease 1000 861 Brain none Source GEO sample is GSM239934 Last updated (according to GEO): Dec 07 2007 858 Prostatic Neoplasms Cerebral cortex 861 tTA 7294 Wild type inbred mice Source GEO sample is GSM82997 Last updated (according to GEO): Nov 10 2005 352 347 brain Cerebral cortex 861 Acetaminophen 3hr Rat 3420 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool PLACENTA Source GEO sample is GSM18968 Last updated (according to GEO): Sep 25 2006 Brain 861 112 98 from the kidney 1000 Brain of the colon 28 39 RIIS/J_male_hypothalamus 861 Glioma Skeletal bone 861 Intestines, Small 1000 Lamina 861 256 235 dilated heart failure 1000 frontal lobe 25 7 Right Temporal Lobe Gene expression data from postmorten brain regions Source GEO sample is GSM145311 Last updated (according to GEO): Nov 20 2006 V5-P577 Bladder sample 1065-1 Whole Brain 62 72 Skeletal muscle structure 1000 1000 frontal lobe V5-P176 80 51 in developing sensory ganglia Tissue transferred into RNAlater within 30 minutes of removal, and frozen at -20C Source GEO sample is GSM9100 Last updated (according to GEO): May 28 2005 brain, Right Frontal Temporal: Extract70_le2 DBA/2J Frontal Cortex B 567 548 the descending colon Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID50 5 0 Spleen Expression profiling of spinal cord section (T9) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM4473 Last updated (according to GEO): May 28 2005 2737 tumor cells 2747 PGA-MCR-CR-24h-1aAv2-s1 Brain 1000 Measles 861 the blood 393 402 PBMCs-Type 1 Diabetes-IDDM19_T1D_New Intestines 861 1000 Amygdaloid structure brain, ipsi Cortex: Trizol Extraction1_le1 Gene expression data from dorsal pancreas at e13.5, MG-U74A version2 Source GEO sample is GSM199445 Last updated (according to GEO): Jun 08 2007 NA18552 In Vivo Regulation of Human Skeletal Muscle Gene Expression by Thyroid Hormone Colonic mucous membrane 913 none Source GEO sample is GSM239920 Last updated (according to GEO): Dec 07 2007 Flow cytometry sorted double negative thymocytes from wild type animal #3. Treatment, type=fractionate Source GEO sample is GSM130403 Last updated (according to GEO): Aug 24 2006 Expression profiling of spinal cord section (T10) extracted from rats 30m following mild injury Source GEO sample is GSM31329 Last updated (according to GEO): May 27 2005 Whole Brain 62 72 Biopsy of a colorectal adenoma from patient #11 Mesentery 1000 5 0 Spleen 0 hr Coronary Arteriosclerosis 1000 Nj20: Hippocampus_21PT-AU_rep9 infection 103 112 1000 Coronary Arteriosclerosis Testis 1000 Exp B, Animal #1, control (0mg/kg) CPF Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours Source GEO sample is GSM246145 Last updated (according to GEO): Dec 03 2007 Timepoint3 Ganglia, Spinal 1000 Laser capture lung cancer cells Source GEO sample is GSM191011 Last updated (according to GEO): May 25 2007 f2#143 versus pool Mouse Brain tissue of the tumors 256 268 10 weeks Source GEO sample is GSM147519 Last updated (according to GEO): Dec 01 2006 15_0005_Control_Day1_16 Expression data after reversal of DNA methylation Source GEO sample is GSM230904 Last updated (according to GEO): Sep 20 2007 with some respiratory epithelium. 1039 1072 G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Source GEO sample is GSM9644 Last updated (according to GEO): May 28 2005 Structure of hemidiaphragm 861 B6:19-6 medulla Spleen 1000 Gene expression data from skeletal muscle at baseline Source GEO sample is GSM230453 Last updated (according to GEO): Sep 19 2007 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:343, Count:32 Corner- Avg:35802, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:6.656495,SFGene:All Background:Avg:490.51,Stdev:6.18,Max:507.2,Min:477.7 Noise:Avg:9.41,Stdev:0.30,Max:10.4,Min:8.5 RawQ:14.06 Keywords = ALL Source GEO sample is GSM3408 Last updated (according to GEO): May 28 2005 Wild type inbred mice Source GEO sample is GSM82918 Last updated (according to GEO): Nov 10 2005 1000 Glomerulonephritis umbilical cord_bpd: 1D H129 FC BA4 B 1820 1807 out the liver Spleen 1000 901 Caudate nucleus structure 5 0 brain Myocardial Infarction 1000 1000 Neoplasm 365 348 Spinal cord injury testes_1 Source GEO sample is GSM80868 Last updated (according to GEO): Mar 31 2006 Expression profiling of spinal cord section (T8) extracted from rats 28d following severe injury Source GEO sample is GSM31490 Last updated (according to GEO): May 27 2005 Neoplasm 861 SON - Control Source GEO sample is GSM69839 Last updated (according to GEO): Aug 15 2005 subthalamic_nucleus_9 Source GEO sample is GSM80857 Last updated (according to GEO): Mar 31 2006 Cerebral cortex 861 Exp C, Animal #3, 1mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours Source GEO sample is GSM246162 Last updated (according to GEO): Dec 03 2007 861 Cerebral cortex 0029_1376_H95A2_KF-095_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A MGJZ030212070Bolfactorybulb ALLB-cell55 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Ischemia Leukemia Lymphoblastic (MOLT-4) [JunctionChip 5 of 5] 5 0 brain Multiple Myeloma 1000 861 Oocytes Genome-wide analysis of PPAR? activation in murine small intestine Gene expression data from skeletal muscle following 30 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230442 Last updated (according to GEO): Sep 19 2007 1000 Cerebellum 865 Disorder of artery Prostate 9 Disease Kidney 1000 Gene expression data from a hippocampus of saline-injected mouse Source GEO sample is GSM147415 Last updated (according to GEO): Jan 03 2007 Spleen 1000 Simple annotation: Cell-cycle, Mitotic selection Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16444.gif Source GEO sample is GSM79673 Last updated (according to GEO): Sep 22 2006 PBMCs-Type 1 Diabetes-IDDM45_T1D_4MO Standard affymetrix protocol Source GEO sample is GSM119494 Last updated (according to GEO): Jul 31 2007 Heart failure 1000 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153363 Last updated (according to GEO): Dec 27 2006 Job's patient Source GEO sample is GSM211148 Last updated (according to GEO): Sep 10 2007 147T Brain_MGlio_4_Malignant Glioma on Affymetrix GeneChip Human Full Length Array HuGeneFL Cardiac 523 530 with autism spectrum disorder 37 65 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92362 Last updated (according to GEO): Jan 13 2006 Control, biological rep2 14 days hindlimb suspended, 1 day reloaded RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis Source GEO sample is GSM10060 Last updated (according to GEO): May 28 2005 against malaria 44 59 1000 Brain Autistic Disorder 877 Primary large cell carcinoma 2985 17 7 hippocampus Small Pre-BII cells 8 1000 Cerebral Palsy Total RNA extracted from the forebrain of a stg-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144403 Last updated (according to GEO): Nov 14 2006 plasma cells 50 61 HIGK cells infected with Streptococcus gordonii, biological rep1 Whole blood 0 10 18 Trigeminal Ganglion 0 1000 Cochlear structure Endometrium 1000 Whole Brain 62 72 7 0 prostate CD8+ T Lymphocytes_Healthy donor 2 HLA-matched Time 0_replicate 2 2869 tumor cells 2880 Nose 1000 2N-3-MGU74B 1000 Spleen with myocardial infarction 313 339 Epithelium of bronchus 983 Genome-wide Discovery and Classification of Candidate Ovarian Fertility Genes in the Mouse. Anti-GBM antibody effect on kidney 117 112 Lipids Expression profiling of spinal cord section (T10) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM6654 Last updated (according to GEO): May 28 2005 Brain 1000 HSC_2Months_A B. abortus 2308 replicate 1 1000 hair Muscle 861 p53 +/-, 12 hour, replicate b Source GEO sample is GSM2553 Last updated (according to GEO): May 27 2005 RNA isolated from fetal cerebrum Keywords = trisomy 13 Keywords = brain Keywords = Patau syndrome Source GEO sample is GSM22704 Last updated (according to GEO): May 27 2005 amygdala 25 33 Nervous System; Nucleus Accumbens Keywords = mouse gene expression database Source GEO sample is GSM29423 Last updated (according to GEO): May 27 2005 Microdissected area # 2 of 1761 tumor Gene expression data from postmorten brain regions Source GEO sample is GSM145219 Last updated (according to GEO): Nov 20 2006 1000 Spleen HMEC S1 day 5 sample 1 vehicle treatment, 3 hour time point, biological replicate 2 Coronary Arteriosclerosis 1000 RMS-C5 on NHGRI-6.5k_b Cerebral cortex 861 17 7 hippocampus spinal cord 0 11 Sample represents the Paraventricular nucleus from 5 control animals Source GEO sample is GSM69479 Last updated (according to GEO): Dec 16 2005 none Source GEO sample is GSM210345 Last updated (according to GEO): Jul 16 2007 Brain 1000 861 Heart failure Lymphoblastoid Cell Line for Individual 8155.3 log phase Sham 18 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107507 Last updated (according to GEO): May 01 2006 Medulla Oblongata 861 Neoplasm 861 Replicate3_Voxel G4 peripheral blood-BDCA4DendriticCells Source GEO sample is GSM18714 Last updated (according to GEO): Sep 25 2006 3 Retina 15 22 Examining the effects of tTA expression in mouse hearts Source GEO sample is GSM15071 Last updated (according to GEO): May 28 2005 PGA_MI_nilv_48h_354 from ventral prostate 21 41 Hereditary Malignant Neoplasm 864 bone_marrow_8 Source GEO sample is GSM80602 Last updated (according to GEO): Mar 31 2006 entorhinal cortex layer II stellate island cells Source GEO sample is GSM107522 Last updated (according to GEO): May 01 2006 Transitional epithelium 1000 Neostriatum 1000 GC (HKG2N) Blood 861 atrial septal defects 198 218 /3T3 fibroblasts 743 759 Bone Marrow 1000 between the LAD artery 266 287 1000 Cerebral cortex Tumor__CNS_Glioblastoma_GlioB_2 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Eye 21 0 Mammary Gland @ Preg1 CD3 beads 12.00 hr. T-Cell brain, cerebral cortex: Rat_03-33_NroLep_Lipska_e1_le1 I_U133Plus_36_AnCg dorsal root ganglia 902 920 1_hypothalamus_9hrs_sleep_#12 Femur 1000 Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 0504 left_liver_lobe Trigeminal Ganglion Source GEO sample is GSM53324 Last updated (according to GEO): Jul 06 2005 plasma cells 332 344 Parkinson Disease 1000 Barcode: 251316210240 Source GEO sample is GSM159377 Last updated (according to GEO): Jul 17 2007 n/a Source GEO sample is GSM178055 Last updated (according to GEO): Jun 11 2007 Olfactory Epithelium 901 Large-scale analysis of the human transcriptome. Pancreas Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 131.11 Stdv: 5.76 Min: 119.16 Max: 141.62 Source GEO sample is GSM2845 Last updated (according to GEO): Mar 20 2006 Large-scale analysis of the mouse transcriptome. Salivary gland C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 295.78 Stdv: 17.52 Min: 268.64 Max: 328.63 Source GEO sample is GSM2978 Last updated (according to GEO): Mar 20 2006 bronchial epithelia 224 243 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2781 Source GEO sample is GSM2100 Last updated (according to GEO): Nov 21 2005 none Source GEO sample is GSM244549 Last updated (according to GEO): Nov 23 2007 Autistic Disorder 877 Spinal Cord 1000 129:24-4 cerebellum Malaria resistance main olfactory epithelium 0 24 brain, hippocampus: KA6-II_e1_le1 Parkinson Disease 1000 CNS-SpinalCsev-Adult-7d-2B-s2 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs//27679.gif Source GEO sample is GSM66566 Last updated (according to GEO): Sep 22 2006 Stromo vascular fraction from intraabdominal adipose tissue Source GEO sample is GSM210991 Last updated (according to GEO): Jul 17 2007 acute myeloid leukemia Source GEO sample is GSM227439 Last updated (according to GEO): Sep 12 2007 Acetaminophen 3hr Rat 6474 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool GSE6850 10 7 Left H121 FC BA4 B BRCA2_s1721 on NHGRI-6.5k 1000 Ciliary Body Day 2_L_+RA_Achip GSE1070 1241 CP6_11 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188733 Last updated (according to GEO): Jun 06 2007 12 0 Normal Kidney Brain_MD_7_Medulloblastoma_Classic_D on Affymetrix GeneChip Human Full Length Array HuGeneFL Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:242, Count:32 Corner- Avg:41343, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:8.144650,SFGene:All Background:Avg:497.46,Stdev:4.99,Max:508.4,Min:487.1 Noise:Avg:12.21,Stdev:0.36,Max:13.1,Min:10.9 RawQ:15.49 Keywords = ALL Source GEO sample is GSM3400 Last updated (according to GEO): May 28 2005 rad001 15d, biological rep7 1000 Brain Primary large cell carcinoma 1934 0 32 Testis 1000 Day 1_M_+RA_Achip Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181140 Last updated (according to GEO): Jul 12 2007 putamen_8 Probeset expression data from NA12751 growth 1, replicate 2 Source GEO sample is GSM195204 Last updated (according to GEO): Aug 08 2007 Spleen 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145486 Last updated (according to GEO): Nov 20 2006 stria terminalis 1000 10 7 Left Epithelium 861 CNS-SpinalCsev-Adult-4h-2A-s2 Cerebral cortex 1000 Fibroblasts 1000 from brain 21 30 4h mitotic selection FC 2103113A cerebellum_5 Source GEO sample is GSM80626 Last updated (according to GEO): Mar 31 2006 Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. in tumors 992 1000 Spleen vs CD40 Treated B cell 30min (set2) 330 324 uterus heart sprague1 D13 12h TLR2/1L ileum 0 4 placebo 15d, biological rep8 Epithelium 861 This is replicate 1 of the 0 hours samples from passive avoidance trained rats. Source GEO sample is GSM17396 Last updated (according to GEO): Aug 22 2007 19 0 human frontal cortex NCI60.49_LABEL53EXTRACT52SUB3 Source GEO sample is GSM134239 Last updated (according to GEO): Aug 06 2007 Male 23.4 yr before antibody enrichment scan 1 (U133A) acute myeloid leukemia Source GEO sample is GSM227445 Last updated (according to GEO): Sep 12 2007 NG046_a left 35 38 neurological disease control sample x160 ACTH treated rep1 SR-A mutant olfactory epithlium 0 h replicate3 Gene expression data from postmorten brain regions Source GEO sample is GSM145887 Last updated (according to GEO): Nov 20 2006 Mesenchymal Stem Cells 1000 HC62 FC BA4 B Cerebral cortex 1000 1000 Coronary Arteriosclerosis P24 deprived visual cortex replicate 3 "Sample 6,>5 yr survival(134 months) age 49 erp yes" on vantveer-oligo BAL_37_A1B1 16 6 (transverse Exp 2 Time point 9 861 Thymus Gland MGMH030212060Apancreas Kidney 1000 ATCC number CRL-1502 Source GEO sample is GSM6807 Last updated (according to GEO): May 27 2005 861 Cancer of Neck The most common congenital cardiac abnormalities 50 97 861 Adipose tissue Gene expression data from wild type DAOY cells Source GEO sample is GSM182018 Last updated (according to GEO): Apr 23 2007 Parkinson Disease 861 861 Brain salivary gland Source GEO sample is GSM18692 Last updated (according to GEO): May 27 2005 Spinal Cord 1000 ve_M47 Skeletal muscle structure 1000 starved 27 33 5 0 brain 28 0 Fetal frontal cortex cocaine1 NA12750 growth 3, replicate 4 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201265 Last updated (according to GEO): Jun 14 2007 brain 0 5 Gene expression data from postmorten brain regions Source GEO sample is GSM145739 Last updated (according to GEO): Nov 20 2006 Blood 861 Large-scale analysis of the mouse transcriptome. Heart C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 295.58 Stdv: 6.26 Min: 285.60 Max: 304.11 Source GEO sample is GSM2916 Last updated (according to GEO): Mar 20 2006 861 Cerebral cortex acute myeloid leukemia Source GEO sample is GSM227418 Last updated (according to GEO): Sep 12 2007 E7, hTERT, neural differentiation, bone marrow cell 1 67 40 with coronary artery disease 1000 Hippocampus Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11305 Last updated (according to GEO): May 28 2005 Heart; embryonic_d14.5 wt heart Keywords = mouse gene expression database Source GEO sample is GSM29342 Last updated (according to GEO): May 27 2005 Lymphoblastoid Cell Line for Individual 8125.5 log phase Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68135 Last updated (according to GEO): Jul 07 2006 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211282 Last updated (according to GEO): Jul 18 2007 Leukemia, Lymphocytic, Chronic 1000 /Ovary 15 Disease 11 27 17 7 hippocampus D1_TP-24_I 1000 Prostate Expression profile of genes in mouse brain Source GEO sample is GSM21042 Last updated (according to GEO): May 27 2005 Standard Affymetrix Protocol Source GEO sample is GSM16495 Last updated (according to GEO): May 28 2005 Parkinson Disease 1000 in the cerebral cortex 285 307 12 4 of Kidney Cord Blood T cells;Neonatal Naive I+P Stimulated 861 Cerebral cortex labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156598 Last updated (according to GEO): Jan 22 2007 901 Caudate nucleus structure occipital_lobe_3 Spleen vs Leukotriene B4 (LTB4)Treated B cell 30min (set3) outer medulla 31 43 42 30 Control blood Spinal Cord 1000 865 Disorder of artery Neoplasm 861 Fat RYGB-Success Repl1 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215051 Last updated (according to GEO): Aug 02 2007 861 Stria P1.2A_KIDNEY_5 no additional Source GEO sample is GSM199264 Last updated (according to GEO): Jun 08 2007 Cells isolated from whole bone marrow Source GEO sample is GSM149535 Last updated (according to GEO): Apr 27 2007 21 6 (corpus callosum 52 25 in hereditary breast cancer pfc_1062_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Whole blood from a patient with progressive supranuclear palsy Source GEO sample is GSM153504 Last updated (according to GEO): Jan 11 2007 D_U133Plus_61_Amy 1000 Structure of postcentral gyrus Parkinson Disease 1000 parietal_lobe_3 70 40 without coronary artery disease I_U133A_12_Amy I_U133Plus_115_AnCg P2B_KIDNEY_5 4 0 Brain Skeletal bone 861 from brain 21 30 1000 medulloblastoma spinal cord 70 80 M_U133A_49_nAcc Tacrine 2.7mg/kg/day from 5 weeks Moclobemide 10mg/kg/day Creatine 1%w/v added to wet mash Lot batch = 5253 Source GEO sample is GSM13365 Last updated (according to GEO): May 28 2005 Nasal Epithelium Inhalation Formaldehyde 0ppm 24h ID54 of Parkinson's disease 450 471 861 Brain Expression profiling of somatomotor cortex extracted from rats at 3 months following moderate injury Source GEO sample is GSM41730 Last updated (according to GEO): May 27 2005 Primary tumor 19 32 Time point at 20h post HCMV infection 1000 Spleen Abdominal aorta structure 1000 I_95Av2_2978_DLPFC_0_GS Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma ATCC number CRL-1502 Source GEO sample is GSM6805 Last updated (according to GEO): May 27 2005 861 Brain This is replicate 2 of the 0 hours samples from passive avoidance trained rats. Source GEO sample is GSM17397 Last updated (according to GEO): Aug 22 2007 LPS plus IL-10, 20 min, Rep_1 in blood 16 23 Ta gr2 tumour Source GEO sample is GSM2501 Last updated (according to GEO): May 27 2005 861 Cardiomyopathies f2#199 versus pool Mouse Brain tissue I_U133Plus_36_Amy PBMCs-Healthy-H150_Healthy Primary tumor 19 32 Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Meningioma Primary Grade 2. Source GEO sample is GSM108037 Last updated (according to GEO): Jun 06 2006 biopsy sample obtained from 13-year-old male individual Keywords = gene expression profile of normal human skeletal muscle Keywords = Affymetrix HG-U95A Source GEO sample is GSM15822 Last updated (according to GEO): May 28 2005 of clinical cancers 75 93 38 21 from a hippocampus 30 0 Adult occipital cortex cocaine3 of somatomotor cortex 21 41 hippocampal glutamatergic CA3 pyramidal neurons Source GEO sample is GSM35813 Last updated (according to GEO): May 27 2005 Tumor__Mesothelioma_215_T5 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Macrophage 14smi032 C57L/J Frontal Cortex A VDXIGRU_255627 GIN-Homogenate-CingulateCortex replicate2 Hyperdip>50-C29 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A from Rett Syndrome 84 101 BALB/cByJ Cerebellum A 1000 Spleen Date : 6/12/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 2.5 mg/kg Time : 3 hrs post-injection Intervention : none Risk: NOAEL (no increased risk of malformation) Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AO045 Source GEO sample is GSM12239 Last updated (according to GEO): May 28 2005 Skeletal bone 861 7 cerebral cortex 21 Hereditary Malignant Neoplasm 876 B_AK_Control_ZT 6_2 C3H/HeJ Frontal Cortex F 17 7 hippocampi Expression profiling of naive raphe (T0) in rats Source GEO sample is GSM41560 Last updated (according to GEO): May 27 2005 pooled RNA of the kidney of 36 day old rats Source GEO sample is GSM86647 Last updated (according to GEO): Jun 12 2006 human cerebellum Source GEO sample is GSM87139 Last updated (according to GEO): Feb 08 2006 861 Eye na Source GEO sample is GSM180512 Last updated (according to GEO): Apr 04 2007 no additional Source GEO sample is GSM199093 Last updated (according to GEO): Jun 08 2007 Testes BD Normal Retina 1000 15 0 human cerebellum of mouse brain 9 23 HOXB4const-LSK+ cells_ 1 hour plus TMX (continous exposure) Source GEO sample is GSM228754 Last updated (according to GEO): Sep 13 2007 brain_DLPFC_bipolar C_mr276 861 Neoplasm Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15009.gif Source GEO sample is GSM91604 Last updated (according to GEO): Sep 22 2006 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3279 Last updated (according to GEO): Mar 21 2006 primary hepatocytes 0 19 5 0 Spleen Epithelium 861 Primary tumor 19 32 SN:Human Glioblastoma Biopsy 10457 Dissection of E16.5 cortex for RNA extraction. Cortex Hemispheres of E16.5 mice were divided into the medial (R1), dorsal (R2), ventral (R3), lateral (R4), and occipital regions (R5). Preparation of RNA and Synthesis of cDNA. Poly A+ RNA was obtained through twice column procedures with oligo dT cellulose column (New England Biolabs, Beverly, MA) and was used for synthesis of cDNA. 1ug of polyA+ RNA was converted into double-stranded cDNA by reverse transcription using ReverTra Ace (ToYoBo, Japan) with oligo dT(24) primers containing the T7 RNA polymerase promotor sequence (Amersham Pharmacia Biotech, Japan). The integrity of RNA was confirmed by agarose electrophoresis and RNA contents were analyzed by measuring the optical density at 260 nm. Target preparation and array processing. The following procedures including preparation of cRNA targets, hybridization, washing, staining, and scanning were performed as described in the Expression Analysis Technical Manual (Affymetrix, CA). Briefly, biotin-labeled antisense cRNA targets were synthesized in in vitro transcription reaction system (IVT) using cDNA as template (ENZO BioArrayTM HighYieldTM RNA Transcription Labeling kit with T7 RNA polymerase, Enzo, NY). The cRNA targets were size-fragmented to 35-200 bp in a buffer containing potassium and magnesium acetate at 94 °C for 35 minutes and were used for hybridization as cRNA targets. The hybridization cocktail [containing 10 ug of target cRNA, control oligo BS (Affymetrix), and Eukaryotic Hybridization controls (Affymetrix)] was hybridized with a mouse U74A array at 42 °C for 16 hours in GeneChip Hybridization Oven 640. Washing and staining were performed after hybridization under the fluidics station protocol, EuGE-WS2, on GeneChip Fluidics Station 400. Then, we scanned the array twice on HP GeneArrayTM scanner. Experiments were repeated twice with independent dissection. Data analysis. To quantify the expression level of a transcript, the average difference value (Adv) was calculated from the intensities against the probe cells using the global methods of normalization by Microarray Suite ver. 4.0 (Affymetrix). Keywords = mouse Keywords = cortex Keywords = development Keywords = regional Keywords = gene expression Keywords = medial Keywords = dorsal Keywords = lateral Keywords = rostral Keywords = occipital Source GEO sample is GSM14596 Last updated (according to GEO): Oct 28 2005 Neoplasm 861 4_hypothalamus_12hrs_sleep_deprivation_#105 Ovarian_Tumor_Endometrioid_CHTN-OE-011 Plasma 861 Acute myeloid leukemia 0 21 Gene expression data from postmorten brain regions Source GEO sample is GSM145788 Last updated (according to GEO): Nov 20 2006 5 0 brain 58 30 a severe psychiatric disorder Muscle Fibers 1000 cortex 27 33 Nasal Epithelium 901 78 66 Control blood "Sample 70, <5 yr survival(32 months) age 38 erp yes" on vantveer-oligo Normal human fetal cartilage from 18-22 weeks. Source GEO sample is GSM149651 Last updated (according to GEO): Jul 06 2007 1000 Cardiomyopathy, Alcoholic Mesenchymal Stem Cells 1000 43 0 Chorionic mesoderm-derived mesenchymal cells Primary combined SCLC-AD 4544 Source GEO sample is GSM18312 Last updated (according to GEO): May 27 2005 0 Human Cortex 11 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188799 Last updated (according to GEO): Jun 06 2007 NoCAD_replicate38 Mice sacrificed after swimming twice a day for 1 week. Keywords = exercise induced hypertrophy Source GEO sample is GSM2349 Last updated (according to GEO): May 27 2005 from liver 21 30 bone marrow-CD34 Source GEO sample is GSM18726 Last updated (according to GEO): Sep 25 2006 Nervous system structure 901 Gene expression data from postmorten brain regions Source GEO sample is GSM145535 Last updated (according to GEO): Nov 20 2006 Sum225 1000 Leukemia, Myelocytic, Acute 861 Medulla Lymphoblastoid Cell Line for Individual 8140.4 log phase Cerebral cortex 861 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156561 Last updated (according to GEO): Jan 22 2007 Using breast (cancer) cell lines to measure bortezomib therapy response Epithelium 861 1000 adenoma 23 0 skeletal muscle sprague2 with myocardial infarction 313 339 4535 4527 hepatoma CNS-SpinalCsev-Adult-7d-4A-s2 861 Brain 861 Nerve 58 30 a severe psychiatric disorder 10 Bone marrow 0 HSC_12Months_A 10 7 left neurological disease control sample x107 Cerebellum 1000 Female 65.1 yr after antibody enrichment scan 2 (U133B) 5 0 brain 201 in the frontal cortex 221 n/a Source GEO sample is GSM178000 Last updated (according to GEO): Jun 11 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145513 Last updated (according to GEO): Nov 20 2006 Untreated versus treated (bortezomib) breast cancer cells. Source GEO sample is GSM120360 Last updated (according to GEO): Jul 20 2006 Normal Salivary Gland 861 Acquired Immunodeficiency Syndrome brain, hippocampi, left: ADX PM Hypo b_e1_le1 Prefrontal Cortex Source GEO sample is GSM105457 Last updated (according to GEO): Apr 17 2006 Gene expression data from rat metanephric mesenchymes cultured for 2 days in the presence of the ANX fraction Source GEO sample is GSM126219 Last updated (according to GEO): Dec 08 2006 15 0 human cerebellum 581 566 of breast cancer Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. V5-P171 Mouse Ovary 3 liver_PPARa-knockout_fed_pooled Cerebral cortex 861 PGA-MurLungRag-pbs-72h-1aA-s2 Sph 2, chip MOE430B Spleen vs Lipopolysaccharide (LPS) Treated B cell 120min (set3) Nothing in line. Source GEO sample is GSM154233 Last updated (according to GEO): Jul 05 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145536 Last updated (according to GEO): Nov 20 2006 Gene expression data from aldosterone-producing adenoma Source GEO sample is GSM211451 Last updated (according to GEO): Jul 18 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145663 Last updated (according to GEO): Nov 20 2006 Ta gr3 tumour Source GEO sample is GSM2517 Last updated (according to GEO): Mar 21 2006 General Paralysis 885 Tumor__Melanoma_MGH_11511 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene expression data from postmorten brain regions Source GEO sample is GSM146020 Last updated (according to GEO): Nov 20 2006 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2785 Source GEO sample is GSM2102 Last updated (according to GEO): Nov 21 2005 Epithelium of bronchus 983 In skeletal muscle, the pattern of electrical activity regulates the expression of proteins involved in synaptic transmission, contraction and metabolism. Disruptions in electrical activity, resulting from prolonged bed-rest, cast-immobilization or trauma, inevitably lead to muscle atrophy. The mechanisms that regulate muscle atrophy are poorly understood, but it seems likely that changes in gene expression play a key role in initiating and maintaining a muscle atrophy program. Previously, we found that Runx1, a transcription factor previously termed AML1, was substantially induced in muscle following denervation. More recently, we sought to determine whether this increase in Runx1 expression may be causally related to the morphological changes in skeletal muscle that accompany muscle disuse, notably muscle atrophy. We found that Runx1 is indeed required to sustain muscle and to minimize atrophy following denervation. Experiments described here are designed to identify the genes that are regulated by Runx1 in skeletal muscle with the particular goal of identifying genes that regulate muscle atrophy. We propose to use microarray analysis to identify genes, expressed in skeletal muscle, that are mis-regulated in mice lacking Runx1. We inactivated runx1 selectively in skeletal muscle and found that denervated myofibers in mutant mice atrophy far more (90% atrophy) than in wild-type mice (30% atrophy). We therefore reason that Runx1 activates and/or represses genes that are required to sustain muscle and to minimize atrophy. We generated MCK::cre; runx1f/- and runx1f/- control mice. In normal mice, an increase in runx1 expression is detected by two days after denervation and is maximal by five days after denervation. Muscle atrophy is first evident between one and two weeks after denervation. As we wish to avoid detecting global changes in gene expression that are associated with late stages of muscle atrophy, we plan to denervate muscle for three or five days and to compare gene expression in dissected innervated and denervated muscles from mutant and control mice. We will generate thirty samples for comparison-5 replicates per condition: Samples 1-3 from runx1f/- control mice. (1) innervated tibialis anterior muscles (TA); (2) 3-day-denervated TA; (3) 5-day-denervated TA. Samples 4-6 from MCK::cre; runx1f/- mice. (4) innervated TA; (5) 3-day-denervated TA; (6) 5-day-denervated TA. We obtain sufficient total RNA (10 micrograms) from each dissected muscle to avoid pooling samples. We will analyze adult mice of the same age (~six weeks after birth; most will be littermates) and sex-male. It is difficult to anticipate how many genes will be identified in this screen, as few target genes for Runx1 have been identified in any cell type and none in skeletal muscle. Moreover, although we would prefer to focus our attention on genes that are strongly dependent upon Runx1 expression (e.g. more than 5-fold difference in expression in wild-type and mutant mice), we do not know the extent to which target gene expression will depend upon Runx1. For these reasons, in these experiments, we will analyze expression from five ?identical? samples, so that we can be confident that even small (e.g. three-fold) differences in expression can be reliably determined. Importantly, in order to confirm results obtained from the microarray data, we will use other assays (RNase protection) to measure RNA expression of candidate genes in innervated and denervated muscles of wild-type and mutant mice. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Mar 08 2006 Contributers: Steven J Burden 923 Ventral Tegmental Area 11 0 luo-prostate Parkinson Disease 861 of underlying brain 171 190 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28808 Last updated (according to GEO): May 27 2005 861 Blood M_U133A_106_AnCg This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195283 Last updated (according to GEO): Sep 13 2007 1000 Retinal Diseases Brain 861 861 Fissure V5-P029 1000 Brain We analysed changes in gene expression in the dorsal telencephalon of forebrain-specific FGFR1 mutant mice. Last Updated (by provider): Aug 26 2005 Contributers: Grace Nisbet Frederick J Livesey Steve N Sansom James A Smith Susan K McConnell Jean M Hebert "Sample 100, BRCA1 mutation(24 months) age 48 erp no" on vantveer-oligo of the colon 28 39 352 340 encephalitis Control rat 4 ventral tegmental area Source GEO sample is GSM32164 Last updated (according to GEO): May 27 2005 Fibroblasts 38 48 Adenocarcinoma A1 no additional Source GEO sample is GSM199249 Last updated (according to GEO): Jun 08 2007 Posterior root of spinal nerve 861 To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at ?80C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at ?80°C before routine processing for GeneChip analysis. Source GEO sample is GSM28662 Last updated (according to GEO): Oct 28 2005 Gene expression data from aneurismal tissues obtained from patients with tricuspid valves. Source GEO sample is GSM116795 Last updated (according to GEO): Jun 28 2006 brain 0 5 Tissue Source GEO sample is GSM67222 Last updated (according to GEO): Jan 19 2006 C2C12_5.5_hr Communicable Diseases 1000 ileum 0 4 Macroglia 1000 Fibroblasts 861 430A2_2045_86_control_sham_midbrain Source GEO sample is GSM242709 Last updated (according to GEO): Nov 15 2007 Cultured in DMEM with 10% FBS and penicillin (100U/ml)/streptomycin (100ug/ml). Media changed every other day. 37ºC, 5% CO2. Source GEO sample is GSM15790 Last updated (according to GEO): Oct 28 2005 plasma cells 332 344 Tonsil Source GEO sample is GSM18901 Last updated (according to GEO): Sep 25 2006 Myocardium 861 Cells were either prestimulated (1_X) or not (0_X) for 18h with 100 ng/ml LPS. Media was exchanged and after 2h rest, cells either restimulated (X_1) or not (X_0) with again 100 ng/ml LPS. This resulted in 4 experimental conditions: 0_0, 0_1, 1_0 and 1_1. There were 3 biological replicates done, resulting in 12 arrays altogether. Source GEO sample is GSM213702 Last updated (according to GEO): Aug 01 2007 Type 1 Diabetes patient and the timepoint 1 month after diagnosis. Source GEO sample is GSM228620 Last updated (according to GEO): Sep 11 2007 861 Intestines 84 69 by heart failure ICM pool 1 (n=2) Carcinoma, Large Cell 884 heart 1169 1173 NHF10-hTERT_1.5Gy_2h_C3_21707 Gender differences in brain development and in the prevalence of neuropsychiatric disorders such as depression have been reported. Gender differences in human brain might be related to patterns of gene expression. Microarray technology is one useful method for investigation of gene expression in brain. We investigated gene expression, cell types, and regional expression patterns of differentially expressed sex chromosome genes in brain. We profiled gene expression in male and female dorsolateral prefrontal cortex, anterior cingulate cortex, and cerebellum using the Affymetrix oligonucleotide microarray platform. Differentially expressed genes between males and females on the Y chromosome (DBY, SMCY, UTY, RPS4Y, and USP9Y) and X chromosome (XIST) were confirmed using real-time PCR measurements. In situ hybridization confirmed the differential expression of gender-specific genes and neuronal expression of XIST, RPS4Y, SMCY, and UTY in three brain regions examined. The XIST gene, which silences gene expression on regions of the X chromosome, is expressed in a subset of neurons. Since a subset of neurons express gender-specific genes, neural subpopulations may exhibit a subtle sexual dimorphism at the level of differences in gene regulation and function. The distinctive pattern of neuronal expression of XIST, RPS4Y, SMCY, and UTY and other sex chromosome genes in neuronal subpopulations may possibly contribute to gender differences in prevalence noted for some neuropsychiatric disorders. Studies of the protein expression of these sex-chromosome-linked genes in brain tissue are required to address the functional consequences of the observed gene expression differences. Substantia Nigra Reticulata 4 Normal Primary Neoplasm 1000 Spinal Cord 1000 A dominant negative form of the transcription factor C-jun affects genes that have opposing effects on lipid homeostasis in mice. EOM 28 Day Control rep 1 MGJZ030212070Aolfactorybulb DNA-3W 1st 6hr C-DG Levitiracetam brainstem 3 Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53428 Last updated (according to GEO): Jul 06 2005 N-3_POST Osteoclasts 1000 Replicate1_Voxel E5 autism 0 5 PGA-HMO-MObese-7aUA-s2 304 280 alcoholic cardiomyopathy amygdala long access to cocaine replicate 3 256 235 with HIV encephalitis Gene expression data from postmorten brain regions Source GEO sample is GSM144982 Last updated (according to GEO): Nov 20 2006 control wild-type prostate epithelial cell line maintained in RPMI-1640 medium supplemented with 5% fetal bovine serum Keywords = prostate Keywords = epithelial Source GEO sample is GSM14669 Last updated (according to GEO): May 28 2005 pfc_1059_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 20 0 human caudate nucleus Gene expression data from postmorten brain regions Source GEO sample is GSM145849 Last updated (according to GEO): Nov 20 2006 CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of M?, rhMCSF was added at 1000 U/ml on the same days. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5148 Last updated (according to GEO): Sep 08 2006 To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18434 Last updated (according to GEO): May 27 2005 1000 Ischemia NA12750 growth 1, replicate 2 Cerebellum 1000 1000 Pontine structure 861 Cerebral cortex Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16711.gif Source GEO sample is GSM91490 Last updated (according to GEO): Sep 22 2006 LDMTX_MP-DX-1 861 Blood 84 69 by heart failure 52 40 of human pulp Heart Septal Defects 884 5 0 brain for nicotinic receptors 164 186 spinal cord, ventral spinal cord: D28WTMN2_e1_le1 Laser capture lung cancer cells Source GEO sample is GSM191025 Last updated (according to GEO): May 25 2007 Heart failure 1000 7 frontal cortex 20 mouse brain 478 489 861 Cochlear structure the gap junction protein connexin43 965 999 Blood 861 nostrils 156 164 91 from the bone marrow 72 Colon 1000 Down Syndrome 1000 Ny16: Hippocampus_5T-AI_rep4 861 Cerebellum I_U133A_111_AnCg with related epilepsy 741 762 Gene expression data from postmorten brain regions Source GEO sample is GSM145552 Last updated (according to GEO): Nov 20 2006 7 cerebral cortex 21 Cardiac-specific TNF-alpha transgenic mouse is an excellent model to study the pathologenesis of heart failure. Affytrix U74V2A was used to analyzed the gene expression profile of mice at the time point of compensated hypertrophy and dilated heart failure. Source GEO sample is GSM8997 Last updated (according to GEO): May 28 2005 Vestibular organ at E11, replicate1 thalamus_4 Source GEO sample is GSM80841 Last updated (according to GEO): Mar 31 2006 84 69 by heart failure Fibroblasts 38 48 Nose 1000 AD-276t1(dup b4)-A96-3 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 865 Disorder of artery 861 Blood Levitiracetam hippocampus 2 Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53434 Last updated (according to GEO): Jul 06 2005 low gestational age Source GEO sample is GSM213116 Last updated (according to GEO): Jul 25 2007 74 55 of hyperinsulinaemic Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Globin reduction was performed according to the Affymetrix technical note. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183395 Last updated (according to GEO): Apr 23 2007 human frontal cortex Source GEO sample is GSM86979 Last updated (according to GEO): Feb 08 2006 Expression profiling of moderately injured raphe at 28d in rats Source GEO sample is GSM41598 Last updated (according to GEO): May 27 2005 3AMH02082103_BM_CD105Endothelial folatesufficientAs10ppm2 Mammary Gland @ Preg3, biological rep1 5 0 brain 901 Salivary Glands Spleen vs CD40 Treated B cell 240min (set1) DLCL-0024 || lc8n096 Liver (SF6) 896 Primary Neoplasm Brain 861 nucleus accumbens short access to cocaine replicate 4 Standard affymetrix protocol Source GEO sample is GSM119730 Last updated (according to GEO): Jul 31 2007 Meningioma Primary Grade 1 U133A Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108017 Last updated (according to GEO): Jun 06 2006 1000 Lung Heart 1000 Normal Source GEO sample is GSM175859 Last updated (according to GEO): Apr 09 2007 Spleen 0 5 1000 Infection wilso-affy-rat-132990 CNS-SCsev_InjB14d-3A-s2 901 Myeloid Leukemia HNC2738 H Fast Rep 2 Simple annotation: Cell-line, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3169.gif Source GEO sample is GSM79872 Last updated (according to GEO): Sep 22 2006 The epithelial cells 962 981 156 145 Their livers in the lung 1059 1069 Date : 10/28/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 24 hrs post-injection Intervention : none Risk: estimated 20% increased risk for encephalopathy Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AF623 Source GEO sample is GSM12255 Last updated (according to GEO): May 28 2005 Brain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145399 Last updated (according to GEO): Nov 20 2006 1000 Hippocampus DBA/2J cingulate cortex rep2 brain, hippocampus: PR-CA1-8_e1_le1 Ovary_PD3_Foxo3 Wt_Replica 3 352 340 encephalitis IM-7_PRE Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153441 Last updated (according to GEO): Jan 11 2007 Untreated versus treated (bortezomib), untranformed MCF10A and Transformed (see Adler et al, Nature Gen. 2006) Source GEO sample is GSM120283 Last updated (according to GEO): Jul 20 2006 R644P00804 Olfactory Epithelium 1000 Macrophage 14smi069 861 Blood Trauma 1000 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68224 Last updated (according to GEO): Jul 07 2006 spleen_2 Source GEO sample is GSM80808 Last updated (according to GEO): Mar 31 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withTerbutaline for 120min Source GEO sample is GSM5785 Last updated (according to GEO): May 27 2005 Paravertebral Muscle 8 Disease 0 29 983 Malignant neoplasm of cervix uteri Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:260, Count:32 Corner- Avg:36698, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:5.910607,SFGene:All Background:Avg:337.32,Stdev:12.49,Max:369.9,Min:316.0 Noise:Avg:8.88,Stdev:0.47,Max:10.3,Min:7.8 RawQ:12.15 Keywords = ALL Source GEO sample is GSM3501 Last updated (according to GEO): May 28 2005 Brain 1000 861 Retina Medulla 861 Brain 861 healthy subject Source GEO sample is GSM211029 Last updated (according to GEO): Sep 10 2007 in breast cancer progression. 267 296 Basal 1000 Brain 861 1000 Brain human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195352 Last updated (according to GEO): Jun 04 2007 103T 4 0 Liver SN:Human Glioblastoma Biopsy 10401 Expression data with no treatment Source GEO sample is GSM230909 Last updated (according to GEO): Sep 20 2007 Carcinoma 861 Neoplasm 861 Sample 11 Treatment, type=add, description=low potassium Source GEO sample is GSM53245 Last updated (according to GEO): Jul 06 2005 cells stimulated with lipoprotein prep 1, biological rep1 Epithelium 861 Arteries 861 HMVEC-L stimulated with LPS for 8 hours L08R1 DLCL-0042 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the lv samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12333 Last updated (according to GEO): May 28 2005 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181208 Last updated (according to GEO): Jul 12 2007 Lymphoblastoid Cell Line for Individual 8073.4 log phase 1000 Cerebral cortex "Sample 48, <5 yr survival(12 months) age 30 erp no" on vantveer-oligo Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92286 Last updated (according to GEO): Jan 13 2006 Category: Cell-line Subcategory: HMEC Scanning Software: ScanAlyze Software version: 2.44 Lot batch = 0111-5k Source GEO sample is GSM1934 Last updated (according to GEO): Nov 21 2005 stria terminalis 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145995 Last updated (according to GEO): Nov 20 2006 Liver 861 GSE5516 from the femurs 95 109 861 Anterior 861 Hyperinsulinism acute respiratory distress syndrome 179 214 372 334 of ovarian endometrioid adenocarcinomas of coronary artery disease 258 284 Nasal Epithelium 865 Coronary artery 901 GBM Treatment, type=remove Source GEO sample is GSM99435 Last updated (according to GEO): Apr 21 2006 28 8 large B-cell lymphoma Kidney 1000 Expression profiling of laminectomized raphe at 24h in rats Source GEO sample is GSM41524 Last updated (according to GEO): May 27 2005 This dataset contains the gene expression profile of a CD11c high, CD8 positive splenic dendritic cell population. The cells were processed following 2 hour incubation in tissue culture medium at 37 C. Global scaling was applied to Avg Difference intensity values. Keywords = mouse, dendritic cells, spleen Source GEO sample is GSM4773 Last updated (according to GEO): May 27 2005 processed in batch 2 Source GEO sample is GSM90439 Last updated (according to GEO): Mar 20 2006 Date 3/29/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : headfold Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 2.5 mg/kg Time : 4.5 hrs post-injection Intervention : none Risk: benchmark dose modeled for 5% increased risk of microphthalmia Conditional biomarker: post-injection interval at the time of p53 protein induction Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 16-20 headfolds pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = embryo Keywords = microphthalmia Lot batch = AN962 Source GEO sample is GSM12074 Last updated (according to GEO): May 28 2005 1000 Retina PriG_5%O2_Expt3_Day3_rep1 Normal Source GEO sample is GSM176342 Last updated (according to GEO): Apr 09 2007 Intestines 861 A2780_oxa_IC75_16h_1 Pituitary Gland 861 luo-prostate Brain 1000 /6J mouse cingulate cortex 29 54 Measles 861 861 Neoplasm Whole blood 0 10 Neural tube, treated, GD9:12, T215588 41 36 spleen plasma cells 332 344 2500mg/kg APAP 24Hr rat 3630 blood vs. 3616 PC 24Hr (pool) 1383 1378 glioma 67 40 with coronary artery disease Acetaminophen 24hr Rat 2197 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool ALL-T-cell-23 on Affymetrix GeneChip Human Full Length Array HuGeneFL To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28461 Last updated (according to GEO): May 27 2005 1000 Communicable Diseases M_U133A_96_nAcc Hippocampus VC mice 2 week off dox 1 CNS-SCsev_InjA14d-3A-s2 Brain 861 Hereditary Nonpolyposis Colorectal Neoplasms 947 of the postmortem brains 673 697 Pooled gastroc RNA samples from five 8 wk old male C57BL10 mice Source GEO sample is GSM13677 Last updated (according to GEO): May 28 2005 1000 Muscle 16 7 cerebellum RNA isolated from post-mortem tissues Source GEO sample is GSM6835 Last updated (according to GEO): May 28 2005 C57BL/6J pituitary gland rep1 brain, cerebral cortex: Sham10_e1_le1 78 66 Control blood 1000 Hippocampus AD-043T2-A7-1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Cardiomyopathies Day 11 Mouse #72 - 2nd replicate AD-AD10T1-A389-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Spleen PGA-MFD-CtrPD5-2aAv2-s2 338 333 brain Spinal Cord 1000 Brain_Adult_Salineip_4hr_mouse1 (YP1_#58) 10 0 bone marrow Macrophage 14smi059 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11250 Last updated (according to GEO): May 28 2005 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201303 Last updated (according to GEO): Jun 14 2007 1000 Turner's Syndrome Identification of candidate transcriptional modulators involved in successful regeneration after nerve injury. Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211398 Last updated (according to GEO): Jul 18 2007 Expression profiling of spinal cord section (T9) extracted from rats 30m following laminectomy (sham) Source GEO sample is GSM31262 Last updated (according to GEO): May 27 2005 FormerSmoker 61 15 0 human cerebellum 7 cerebral cortex 21 1000 Brain Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep5 MuscleRegen-ctx12h-1LLAv2-s2 Normal Source GEO sample is GSM176357 Last updated (according to GEO): Apr 09 2007 Levitiracetam hippocampus 4 Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53436 Last updated (according to GEO): Jul 06 2005 Basal 1000 VDXKIU_27C4 D1_TP-0_I 116T Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:308, Count:32 Corner- Avg:38633, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:4.582736,SFGene:All Background:Avg:422.88,Stdev:4.58,Max:441.7,Min:411.8 Noise:Avg:8.65,Stdev:0.46,Max:9.9,Min:7.1 RawQ:12.76 Keywords = ALL Source GEO sample is GSM3430 Last updated (according to GEO): May 28 2005 1000 Malignant neoplasm of breast Bladder sample 1032-1 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.31 Lot batch = lc8n127 Source GEO sample is GSM2051 Last updated (according to GEO): Nov 21 2005 84 69 by heart failure Nose 1000 042601_HF_332FL 861 Hormones Brain 1000 Blood Test (Blinded) Sample Source GEO sample is GSM129938 Last updated (according to GEO): Sep 18 2007 AD-131T1-A15-A200-1* on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Normal Source GEO sample is GSM176225 Last updated (according to GEO): Apr 09 2007 Simple annotation: Reference verification, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9991.gif Source GEO sample is GSM78466 Last updated (according to GEO): Sep 22 2006 Individual LCL vs Pooled control LCLs Source GEO sample is GSM3323 Last updated (according to GEO): Mar 15 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CpG-oligodeoxynucleotide for 60min Source GEO sample is GSM5523 Last updated (according to GEO): May 27 2005 114 101 brains quickly nostrils 156 164 nasal epithelial cells 28 49 1_cerebral_cortex_9hrs_sleep_#13 1000 Oocytes brain 0 5 020502_HF_301FL 221 212 hemorrhage Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 11.75 hours after lights on. Original sample code = CM27A Source GEO sample is GSM227348 Last updated (according to GEO): Sep 10 2007 healthy subject Source GEO sample is GSM211129 Last updated (according to GEO): Sep 10 2007 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68292 Last updated (according to GEO): Jul 07 2006 Sun200_TAV12 group 19 0 human frontal cortex I_U133A_30_Amy 861 Acquired Immunodeficiency Syndrome BT-549 ND012 cardiac 763 769 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11233 Last updated (according to GEO): May 28 2005 Replicate3_Voxel F3 5 0 Spleen Isoflurane 5 exposures-3 none Source GEO sample is GSM244532 Last updated (according to GEO): Nov 23 2007 brain_DLPFC_bipolar B_mr943 Trachea [JunctionChip 4 of 5] Bone Marrow 1000 Gene expression regulated by DACH1-8 Mucous Membrane 861 Nose 1000 39 21 of substantia nigra Caudal 1000 1000 Blood Parkinson Disease 861 WGACON-11 Cerebellum 861 1000 Rectum Lymphoblastoid Cell Line for Individual 8136.4 log phase nasal epithelial cells 28 49 901 frontal lobe Macrophage smi35 43 0 Chorionic mesoderm-derived mesenchymal cells Gene expression data from postmorten brain regions Source GEO sample is GSM145593 Last updated (according to GEO): Nov 20 2006 Epithelium 861 Infected 6 weeks prior with Htt-N171-82Q-expressing recombinant lentivirus Source GEO sample is GSM34378 Last updated (according to GEO): Oct 16 2006 1000 Modiolus anguli oris Sample # 1167-1 Gene expression data from epididymal fat tissues. Source GEO sample is GSM215577 Last updated (according to GEO): Aug 07 2007 861 Neoplasm NCI60.3_LABEL6EXTRACT5SUB3 Source GEO sample is GSM134006 Last updated (according to GEO): Aug 06 2007 Spinal cord tissue from SOD1 mutant mice Treatment, type=linear_amplification, description=T7-based RNA amplification Source GEO sample is GSM113701 Last updated (according to GEO): Jun 09 2006 Infection 1000 861 Muscle of Parkinson's disease 75 97 with some respiratory epithelium. 1039 1072 Wild type 8 wk old male FVB/NJ mouse hypothalamus Source GEO sample is GSM107028 Last updated (according to GEO): Mar 05 2007 110 94 of heart failure 1000 Spinal Cord Saccule 0 6 General Paralysis 885 intermediolateral column motoneurons (IML) 17 4 0 Nasal Adipose tissue 861 plasma cells 50 61 Cerebral cortex 1000 5 0 thymus 1000 Brain n/a Source GEO sample is GSM177912 Last updated (according to GEO): Jun 11 2007 to infection 161 172 VDXOXFU_1183 861 anatomic valve Gene expression data from whole brain infected mouse, day 3 Source GEO sample is GSM189614 Last updated (according to GEO): May 16 2007 18 Trigeminal Ganglion 0 S46 NLS 142Q TG5 F4/1 S46 NLS Htt exon 1 142Q Mouse 10 months Cerebellum Female Source GEO sample is GSM73201 Last updated (according to GEO): Sep 06 2005 AD-136t2-A201-8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A with some respiratory epithelium. 1039 1072 Head and neck cancer Source GEO sample is GSM155725 Last updated (according to GEO): Apr 24 2007 in blood 16 23 low-grade dysplastic liver tissue Source GEO sample is GSM155971 Last updated (according to GEO): Jun 21 2007 1000 Nervous system structure 17 7 hippocampus liver_PPARa-knockout_WY14643_6h_rep2 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Leukotriene B4 (LTB4) for 60min Source GEO sample is GSM5676 Last updated (according to GEO): May 27 2005 41 28 in mouse brain C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 4 hour after the last shock treatment. Source GEO sample is GSM4546 Last updated (according to GEO): May 27 2005 cerebellum wistar ky 3892 858 Mesodermal cell Plasma 861 PAX sample 14 861 Gland structure biopsy sample obtained from a 1-year-old Duchenne Muscular Dystrophy patient Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15838 Last updated (according to GEO): Sep 08 2006 191 181 of ischemia Axon 1000 no additional Source GEO sample is GSM199290 Last updated (according to GEO): Jun 08 2007 1000 Liver Liver 0 4 702 680 combined hyperlipidemia cerebellum 7 16 Pancreas at e12.5, Chip A, rep 2 olfactory epithelium 194 213 Myocardial Infarction 1000 118 from the peritoneal cavity 92 CNS-SC_InjA14d-4A-s2 Simple annotation: Metastatic tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12406.gif Source GEO sample is GSM79828 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145356 Last updated (according to GEO): Nov 20 2006 1000 Tongue ER negative human primary breast tumor EA02014_41247_H133A_JA-120 9 0 Blood Test E2A-PBX1-C4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A PGA-MCR-ctr-0h-2bAv2-s1 septum short access to cocaine replicate 3 of cerebellum 299 312 Thymus_022LACHL_t1b.txt HC69 FC BA4 A D_U133Plus_92_CB COID-COID16t1-A352-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A GM18912 adenoma 861 Normal Source GEO sample is GSM176339 Last updated (according to GEO): Apr 09 2007 Replicate3_Voxel C6 AD control Treatment, type=dissect Source GEO sample is GSM119619 Last updated (according to GEO): Jul 10 2006 Testis 1000 with myocardial infarction 313 339 Kidney 1000 865 Disorder of artery DBA/2J pituitary gland rep1 (430 2.0 Array) 861 Cardiomyopathies High Freezing Source GEO sample is GSM92419 Last updated (according to GEO): Jan 13 2006 228 224 Brain of Parkinson's disease 424 445 WGACON-202 Sample10, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53261 Last updated (according to GEO): Jul 06 2005 of the stria terminalis rep1 21 48 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:285, Count:32 Corner- Avg:33775, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:9.132693,SFGene:All Background:Avg:254.61,Stdev:1.76,Max:260.0,Min:249.4 Noise:Avg:6.85,Stdev:0.19,Max:7.4,Min:6.3 RawQ:9.74 Keywords = ALL Source GEO sample is GSM3478 Last updated (according to GEO): May 28 2005 Expression profiling of spinal cord section (T9) extracted from rats 72h following moderate injury Source GEO sample is GSM31194 Last updated (according to GEO): May 27 2005 208 200 of cancer 1000 Lung of the brain 294 305 Heart 861 NMDA180 (Experiment shortNMDA: Run 19222) Treatment, type=time_course, description=primary cortical neurons were treated with 1 mM NMDA for increasing periods of time (10 to 360 min)., measurement=180.0 m Source GEO sample is GSM96767 Last updated (according to GEO): Feb 14 2006 tibiae 115 120 1000 Coronary Arteriosclerosis 861 Mammary gland The nose 94 101 M_U133Plus_94_HC Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11566 Last updated (according to GEO): May 28 2005 1000 Glaucoma SN:Human Glioblastoma Biopsy 10404 1000 Cerebrum brain 0 5 of mouse brain 9 23 Heart 861 Spleen vs Untreated B cell Time 0 (set11) prostate Source GEO sample is GSM203285 Last updated (according to GEO): Jun 21 2007 very advanced HCC Source GEO sample is GSM155962 Last updated (according to GEO): Jun 21 2007 amygdala short access to cocaine replicate 1 152 117 Keywords = congenital heart disease EWS-T11 on NHGRI-6.5k_b NA Source GEO sample is GSM198918 Last updated (according to GEO): Jun 07 2007 Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 8128 left_liver_lobe PBMCs-Type 1 Diabetes-IDDM22_T1D_New 822 for Turner syndrome 841 wtPrE serumfree 1 from cingulate cortex 12 32 Expression profiling of spinal cord section (T8) extracted from rats 30m following mild injury Source GEO sample is GSM31439 Last updated (according to GEO): May 27 2005 128T Lymphoblastic Leukemia 901 PGA-MurLungRag-rwp-72h-1aC-s2 Cerebral cortex 1000 Dorsal Raphe Source GEO sample is GSM107969 Last updated (according to GEO): Jun 06 2006 The purpose of this study was to develop a method of classifying cancers to specific diagnostic categories based on their gene expression signatures using artificial neural networks (ANNs). We trained the ANNs using the small, round blue-cell tumors (SRBCTs) as a model. These cancers belong to four distinct diagnostic categories and often present diagnostic dilemmas in clinical practice. The ANNs correctly classified all samples and identified the genes most relevant to the classification. Expression of several of these genes has been reported in SRBCTs, but most have not been associated with these cancers. To test the ability of the trained ANN models to recognize SRBCTs, we analyzed additional blinded samples that were not previously used for the training procedure, and correctly classified them in all cases. This study demonstrates the potential applications of these methods for tumor diagnosis and the identification of candidate targets for therapy. medial motoneurons (MMN) 28 861 Blood Macrophage smi50 Adenocarcinoma 10 ALL-B-cell-19 on Affymetrix GeneChip Human Full Length Array HuGeneFL Chromosomes 861 pituitary Source GEO sample is GSM19022 Last updated (according to GEO): Sep 25 2006 861 Basal GSE8514 1000 Spleen from the femurs 95 109 Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep2 15 7 brainstem Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3284 Last updated (according to GEO): Mar 21 2006 901 Pituitary Gland n/a Source GEO sample is GSM178032 Last updated (according to GEO): Jun 11 2007 1000 Muscle DMD muscle 1080 1090 Colon 861 Mitochondrial DNA (mtDNA) mutations may contribute to aging and age-related disorders. Previously, we created mice expressing a proofreading-deficient version of the mtDNA polymerase gamma (Polg) which accumulate age-related mtDNA mutations and display premature aging. Here we performed microarray gene expression profiling to identify mtDNA mutation-responsive genes in the cochlea of aged mitochondrial mutator mice. Age-related accumulation of mtDNA mutations was associated with transcriptional alternations consistent with reduced inner ear function, mitochondrial dysfunction, neurodegeneration, and reduced cell structural modulation. Hearing assessment and histopathological results confirmed that aged PolgD257A/D257A (D257A) mice exhibited moderate hearing loss and severe cochlear degenerations. Age-related accumulation of mtDNA mutations also resulted in alternations in gene expression consistent with induction of apoptosis, proteolysis, stress response, and reduced DNA repair. TUNEL (Terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling) assay confirmed that the cochleae from aged D257A mice showed significantly more TUNEL positive cells compared to wild-type (WT) mice. The levels of cleaved caspase-3 were also found to increase in the cochleae of aged D257A mice. These observations provide evidence that age-related accumulation of mtDNA mutations is associated with apoptotic cell death in aged cochlea. Our results provide the first global view of molecular events associated with mtDNA mutations in postmitotic tissue, and suggest that apoptosis is the major mechanism of mtDNA mediated cell death in the development of age-related hearing disorder. Last Updated (by provider): May 22 2006 Contributers: Richard Weindruch Tatsuya Yamasoba Masaru Tanokura Greg C Kujoth Tom D Pugh Tomas A Prolla Shinichi Someya Barcode: 251316210193 Source GEO sample is GSM159388 Last updated (according to GEO): Jul 17 2007 Abca1 +/- ES cell line was grown on irradiated MEF feeders using standard culture conditions. Feeders were then depleted and ES cells plated on gelatin for ~2 days. RNA was isolated using Trizol/RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol. Data were normalized by AffyMetrix MAS5.0 using defaults. Keywords = embryonic stem cholesterol transport Source GEO sample is GSM9271 Last updated (according to GEO): May 27 2005 Heart 1000 Primary tumor 19 32 Male 69.6 yr before antibody enrichment scan 1 (U133A) 13 0 Nervous System mild cognitive impairment - posterior cingulate cortex 1 468 459 the rectum 901 Nervous system structure Spleen vs Interferon-gamma (IFN gamma) Treated B cell 240min (set1) Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226160 Last updated (according to GEO): Nov 02 2007 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162181 Last updated (according to GEO): Jun 12 2007 30 19 Solid tumor Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181177 Last updated (according to GEO): Jul 12 2007 1000 Hippocampus in muscle 1305 1314 Spinal Cord 861 nasal epithelial cells 28 49 EWS-C8 on NHGRI-6.5k_b Large-scale analysis of the human transcriptome. Thymus Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 118.10 Stdv: 5.33 Min: 107.65 Max: 126.07 Source GEO sample is GSM2826 Last updated (according to GEO): Mar 20 2006 GC (HKG69T) 1340 1327 in adipocytes 14 CN B GM19239 eTat - Noco9hr - 1 GSE8481 early absence seizures 153 174 15 0 human cerebellum Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181125 Last updated (according to GEO): Jul 12 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lipopolysaccharide (LPS) for 120min Source GEO sample is GSM5668 Last updated (according to GEO): May 27 2005 21 0 Mammary Gland @ Lac2 430A2_1945_37_KO_sham_medulla Source GEO sample is GSM242684 Last updated (according to GEO): Nov 15 2007 normal testis 54 66 intestine_PPARa-knockout_control_rep2 Gene expression data from 14B3 BMEL cells cultured under Matrigel conditions. Source GEO sample is GSM160082 Last updated (according to GEO): Jul 11 2007 1000 Retina whole blood_101611 Abdominal aorta 0 14 Tumor__Lymphoma_Large_B-Cell_L_B_CELL_S98_8825_Y on Affymetrix GeneChip Human 35K SubA Array Hu35k-A cerebral cortex sprague 3919 all cortical minus the frontal cortex, individual animal, 10 weeks old, male Sprague Dawley cerebral cortex file:p3919w Source GEO sample is GSM15156 Last updated (according to GEO): Oct 28 2005 gfp pos. sorted cells from 3 disected e14.5 ganglionic eminences Treatment, type=wait Source GEO sample is GSM135769 Last updated (according to GEO): Sep 12 2006 human caudate nucleus Source GEO sample is GSM86794 Last updated (according to GEO): Feb 08 2006 101 61 in pediatric acute lymphoblastic leukemia SN:Human Glioblastoma Biopsy 06728 1000 Cerebral cortex temporal_lobe_10 Expression profiles of HeLa CD4+ cells transfected with epitope-tagged eTat plasmid. Cells are treated with nocodazole and hydroxyurea. Last Updated (by provider): May 29 2005 Contributers: Fatah Kashanchi Anil Maddukuri Includes GDS449. Update date: Nov 18 2003. Dataset description GDS449: Analysis of effect of Tat transactivation during cell cycle. HeLa CD4+ cells transfected with epitope-tagged Tat plasmid or parental vector pCEP4. Cells synchronized with cell cycle blocker hydroxyurea or nocodazole and sampled at 0, 3, 6 and 9 hours.. Expression profiling of somatomotor cortex extracted from rats at T0 naive Source GEO sample is GSM41677 Last updated (according to GEO): May 27 2005 7 Entorhinal Cortex 23 Tumor__Pancreas_Adeno_Pan_16T on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Spleen vs Sphingosine-1-phosphate Treated B cell 30min (set2) 901 frontal lobe Brain 1000 human caudate nucleus Source GEO sample is GSM86901 Last updated (according to GEO): Feb 08 2006 This SuperSeries is composed of the following subset Series: GSE357: Halothane Repetitive Exposure GSE358: Isoflurane Repetitive Exposure GSE752: Halothane/Isoflurane Repetitive Exposures Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Dec 04 2006 1000 Hippocampus Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 8 hours after lights on. Original RNA code = LC42A. Source GEO sample is GSM227372 Last updated (according to GEO): Sep 10 2007 ileum 861 PGA-MLS-Dex-1aAv2-s1 Primary Neoplasm 1000 Brain 1000 16 7 cord blood Date 3/29/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : headfold Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 2.5 mg/kg Time : 6.0 hrs post-injection Intervention : none Risk: benchmark dose modeled for 5% increased risk of microphthalmia Conditional biomarker: post-injection interval beyond p53 protein induction Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 16-20 headfolds pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = embryo Keywords = microphthalmia Lot batch = AN914 Source GEO sample is GSM12077 Last updated (according to GEO): May 28 2005 67 53 in mouse brain 151 126 received fetal liver cells accumbens rattus_norvegicus_strain iNP animal_number 11 +_9959_batch1 on NHGRI-6.7k NCI60.59_LABEL123EXTRACT61SUB3 Source GEO sample is GSM134293 Last updated (according to GEO): Aug 06 2007 of brain 86 93 1406 In Down syndrome 1422 Gene expression data from postmorten brain regions Source GEO sample is GSM145803 Last updated (according to GEO): Nov 20 2006 A2780_oxa_IC90_2h_1 spinal cord, spinal cord: RNA 499_e1_le2 7 0 prostate 39 21 from mammary glands Type 1 Diabetes patient and the timepoint 4 months after diagnosis. Source GEO sample is GSM228618 Last updated (according to GEO): Sep 11 2007 AD control Treatment, type=dissect Source GEO sample is GSM119661 Last updated (according to GEO): Jul 10 2006 D_U133A_67_DLPFC Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48018.gif Developmental Stage: E8 Source GEO sample is GSM229824 Last updated (according to GEO): Nov 06 2007 hypothalamus_3 Source GEO sample is GSM80692 Last updated (according to GEO): Mar 31 2006 Brain 861 70 40 without coronary artery disease Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD14 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD14 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36713 Last updated (according to GEO): May 27 2005 36 21 from whole brain 1000 Eye MGJZ030212009Bfrontalcortex mouse cerebral cortex 0 20 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11528 Last updated (according to GEO): May 28 2005 cortex 7 12 none Source GEO sample is GSM241960 Last updated (according to GEO): Nov 29 2007 Lung 1000 Male 21.5 yr before antibody enrichment scan 1 (U133A) 19 14 (heart Brain 1000 916 Decapitation 1000 Brain Gene expression data from mouse colon Source GEO sample is GSM198109 Last updated (according to GEO): Aug 22 2007 CNS-SCsev_InjB14d-3C-s2 Chronic Lymphocytic Leukemia 19 47 5 0 brain 91 from the bone marrow 72 Brain 1000 983 pM category Synapses 1000 in bronchial epithelia 311 332 pfc_1064_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A RNA isolated from fetal heart (predominantly valve and canal regions) Keywords = trisomy Keywords = heart Keywords = Down syndrome Source GEO sample is GSM22613 Last updated (according to GEO): May 27 2005 with mental retardation 241 263 Brain 1000 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201780 Last updated (according to GEO): Jun 20 2007 STHdhQ7/Q7-3NP-A Normal Source GEO sample is GSM175854 Last updated (according to GEO): Apr 09 2007 MLL-C2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 796 plasma membrane 782 Gene expression data from postmorten brain regions Source GEO sample is GSM145699 Last updated (according to GEO): Nov 20 2006 PGA_IGF1R-dnPI3K_3191 Malignant neoplasm of breast 884 197 176 with coxsackievirus B3 861 Amygdaloid structure The role of mtDNA mutations in age-related hearing loss in mice carrying a mutator DNA polymerase gamma in the retina 47 59 Pressure-Overload Induced Cardiac Hypertrophy Large-scale analysis of the human transcriptome. Brain, caudate nucleus Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 242.86 Stdv: 10.54 Min: 225.27 Max: 258.48 Source GEO sample is GSM2886 Last updated (according to GEO): Mar 20 2006 GC (HKG55T) from the forebrain 20 37 dorsal striatum wistar ky 3972 whole tissue, individual animal, 10 weeks old, male Wistar Kyoto dorsal striatum file:p3978w Source GEO sample is GSM15189 Last updated (according to GEO): Oct 28 2005 A2780_cis_IC90_16h_4 996 in the frontal cortex 1016 no additional Source GEO sample is GSM199147 Last updated (according to GEO): Jun 08 2007 Donor 2 Time point 24 hours Post infection with HIV-1, RF Source GEO sample is GSM2612 Last updated (according to GEO): May 27 2005 861 Hypothalamic structure 100 95 hearts of 2182 tumor 50 62 Cerebral cortex 861 1000 Substantia nigra structure Ta gr2 tumour Source GEO sample is GSM2499 Last updated (according to GEO): May 27 2005 Control Abdominal Aorta Male Pool A with some respiratory epithelium. 1039 1072 Femur 1000 Cerebellum 0 9 Patient2E Spleen vs Neuropeptide Y Treated B cell 120min (set1) CNS-SpinalCsev-Adult-7d-1B-s2 High-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we have generated and analyzed gene expression from a set of samples spanning a broad range of biological conditions. Specifically, we profiled gene expression from 91 human and mouse samples across a diverse array of tissues, organs, and cell lines. Because these samples predominantly come from the normal physiological state in the human and mouse, this dataset represents a preliminary, but substantial, description of the normal mammalian transcriptome. We have used this dataset to illustrate methods of mining these data, and to reveal insights into molecular and physiological gene function, mechanisms of transcriptional regulation, disease etiology, and comparative genomics. Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website (http://expression.gnf.org) that integrates data visualization and curation of current gene annotations.. Date GSE97 Last Updated: May 29 2005 Contributers: M P Cooke J R Walker R G Vega K A Ching L M Sapinoso A I Su T Wiltshire A Patapoutian P G Schultz A P Orth A Moqrich Y Hakak J B Hogenesch G M Hampton Includes GDS182. Update date: May 13 2004. Dataset description GDS182: Gene expression profiles from a diverse array of tissues, organs, and cell lines, from the normal physiological state. Represents a preliminary description of the normal mammalian transcriptome.. 861 Muscle osteoblast 627 637 1000 Spleen Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242056 Last updated (according to GEO): Dec 04 2007 Mouse young brain C5-Br-4 1000 Maxilla I_U133A_9_CB 5 0 brain Kidney; Day 2 postnatal Keywords = mouse gene expression database Source GEO sample is GSM29361 Last updated (according to GEO): May 27 2005 861 Neoplasm 901 Mammary gland of Parkinson's disease 450 471 20 0 Nicotine-hippocampus 7 cerebral cortex 21 osteoblast 627 637 Blood Test (Blinded) Sample Source GEO sample is GSM129951 Last updated (according to GEO): Sep 18 2007 126 CN A Axon 1000 Blood Test (Blinded) Sample Source GEO sample is GSM130010 Last updated (according to GEO): Sep 18 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Bombesin for 240min Source GEO sample is GSM5484 Last updated (according to GEO): May 27 2005 Wild type voxel H1 861 Cerebral cortex AD control Treatment, type=dissect Source GEO sample is GSM119663 Last updated (according to GEO): Jul 10 2006 of atrophied rat soleus muscle 47 77 Day 5_M_-LIF_Achip 861 Asthma Nasal Epithelium Inhalation Formaldehyde 07ppm 19d ID154 Neoplasm 1000 Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit. Source GEO sample is GSM200587 Last updated (according to GEO): Jul 09 2007 Brain after ischemia and antioxidant 136 131 Aortae Spinal Cord 1000 NA Source GEO sample is GSM109472 Last updated (according to GEO): May 22 2006 5 0 brain Parkinson's disease sample x193 arteries 1040 1047 thymus Source GEO sample is GSM18741 Last updated (according to GEO): Sep 25 2006 78 73 rectum 861 Cerebellum 01_0030_SepticShock_Day1_110 AD C+S: Alzheimer's context + shock: Alzheimer's mice were 50% C57BL/6, 50% SJL. Alzheimers animals were the double transgenic models reported by Dineley et al., (2002) J Biol Chem 277(25):22768-22780. Alzheimer's mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 2 hours after the last shock treatment. Source GEO sample is GSM4562 Last updated (according to GEO): May 27 2005 Heart 861 1000 Epithelial Cells Gene expression data from postmorten brain regions Source GEO sample is GSM145891 Last updated (according to GEO): Nov 20 2006 no additional Source GEO sample is GSM199111 Last updated (according to GEO): Jun 08 2007 Transcriptional response of lymphoblastoid cells to ionizing radiation. 660 mesenchymal stem cell 639 Standard Affymetrix Protocal Keywords = microarray Keywords = muscle Source GEO sample is GSM15778 Last updated (according to GEO): May 28 2005 Osteoblasts 1000 embryo_at_day3.5_rep1 Acute lymphoblastic leukemias 0 28 between the LAD artery 225 246 Epithelial Cells 1000 BPH-202 on UMich-10k The epithelial cells 962 981 to the nose 599 609 Gene expression data from colorectal adenoma. Source GEO sample is GSM215105 Last updated (according to GEO): Aug 02 2007 to the nose 599 609 Although immediate early genes (IEGs) such as Bdnf, Arc and Egr1, have been implicated in plasticity, the larger pathways related to memory and memory disorders are not well understood. Here, we combined statistical Affymetrix microarray and behavioral analyses to identify key genes and pathways associated with aging-related cognitive impairment. Aged rats were separated into cognitively unimpaired (AU) or impaired (AI) groups, based on their Morris water maze performance relative to young-adult (Y) animals. Hippocampal gene expression was assessed in Y, AU and AI on the fifth (last) day of maze training or 21 days posttraining, and in non-trained aged and young animals (eight groups, overall n = 78, one chip/animal). ANOVA, linear contrasts, and overrepresentation analyses identified genes and pathways that differed from Y generally with aging (in both AU and AI) or selectively with cognitive status (only in AI or AU). Plasticity pathways, including insulin/cAMP/IEG signaling, and glycogenolytic and lipogenic pathways, were selectively downregulated (5 days) in AI, whereas Notch2 (regulating oligodendrocyte differentiation) and myelination pathways were upregulated (particularly at 21 days). Downregulation with general aging occurred in signal transduction and axonal growth/transport pathways, whereas upegulation occurred in immune/inflammatory, lipid metabolism/transport (e.g., Lxr-Srebf1), and lysosomal pathways. In AU, receptor/signal transduction genes were selectively upregulated, suggesting possible compensatory mechanisms. Immunohistochemistry confirmed and extended results to the protein level. Thus, this study identified novel cognition-linked processes, suggesting a new model in which energy-intensive, plasticity/lipogenic processes and energy-generating pathways necessary for learning are coordinately downregulated during training, while myelinogenic programs that impair cognition are concurrently activated. Last Updated (by provider): Apr 17 2007 Contributers: Eric M Blalock Wayne B Rowe Gregory M Rose Philip W Landfield Daguang Wang Inga Kadish James Barrett Olivier Thibault KueyChu Chen Nada M Porter PriG_5%O2_Expt2_Day7_rep1 Corticotectal Neurons P14 2 Nicotine-neocortex, biological rep5 884 Vestibular ganglion total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with BLC for 60min Source GEO sample is GSM5468 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145716 Last updated (according to GEO): Nov 20 2006 ovarian tumor: endometrioid Source GEO sample is GSM139396 Last updated (according to GEO): Apr 09 2007 Normal__Kidney_KT_3 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A from colorectal adenoma 21 44 Spleen vs NGF (Nerve Growth Factor)Treated B cell 120min (set1) 1000 Mitral Valve Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26117.gif Source GEO sample is GSM81536 Last updated (according to GEO): Sep 22 2006 Medulla Oblongata 861 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 23 hours after lights on. Original sample code = CM17A Source GEO sample is GSM227344 Last updated (according to GEO): Sep 10 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113949 Last updated (according to GEO): Jun 16 2006 no additional Source GEO sample is GSM199237 Last updated (according to GEO): Jun 08 2007 in the retina 437 449 Spleen vs CD27 Treated B cell 30min (set3) 201 in the frontal cortex 221 25 0 Acute cognitive impairment CNS-SCsev_InjA4h-4B-s2 brain, hindbrain and spinal cord: P5KO2_e1_le1 1000 Cornea 1000 frontal lobe 4 0 LIVER 861 Cerebral cortex 101 81 of Mental Retardation hip_1012_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159958 Last updated (according to GEO): Feb 01 2007 brain 0 5 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withSLC (Secondary lymphoid-organ chemokine) for 60min Source GEO sample is GSM5771 Last updated (according to GEO): May 27 2005 HDMTX-2 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD19 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD19 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36697 Last updated (according to GEO): May 27 2005 Mice sacrificed at 12 weeks of age. Can be used as a control for the 3 and 4 week swim mice. Keywords = exercise induced hypertrophy Source GEO sample is GSM2361 Last updated (according to GEO): May 27 2005 I_U133Plus_122_AnCg GSE857 4 0 Heart ovary_8 /HeJ pituitary gland rep2 3 27 heart 119 124 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11303 Last updated (according to GEO): May 28 2005 1000 Cerebral cortex 861 Cerebral cortex Pericardium AB Normal prostate Source GEO sample is GSM203375 Last updated (according to GEO): Jun 21 2007 Nasal Epithelium 901 Epilepsy is a major neurological disorder that affects approximately 1% of the population. The processes that lead to the development of epilepsy (epileptogenesis) are largely unknown. Levetiracetam is a novel antiepileptic drug (AED) that in the kindling model inhibits epileptogenesis in addition to being effective in controlling established epilepsy. The mechanisms of action of levetiracetam as an AED and an antiepileptogenic drug are unknown. By identifying the effect of chronic levetiracetam therapy on gene expression in the brain we hope to be able to identify genes that are involved in epileptogenesis. By comparing the gene expression profiles of levetiracetam and phenytoin treatments, we hope to be able to distinguish between genes that are important for the antiepileptic (anti-seizure) effect and genes that are important for the antiepileptogenic effect of levetiracetam. Phenytoin is a well-established AED; its mechanism of action involves inhibition of sodium channels. In contrast to levetiracetam, available data suggest that phenytoin in certain situations may enhance rather than inhibit the development of epilepsy. We will identify changes in gene expression in the hippocampus, frontal cortex, and brain stem caused by chronic treatment (3 months) with levetiracetam or phenytoin. We will search for differences in the gene expression profiles after chronic treatment with the two drugs, to explain the different clinical effects of the two drugs. We hypothesize that chronic treatment with levetiracetam leads to changes in the expression of genes that are involved in both the antiepileptogenetic and antiepileptic effect of the drug, whereas chronic treatment with phenytoin affects genes that may be related to pro-epileptogenetic as well as antiepileptic effects of that drug. We further hypothesize that i) regional differences in the effects of levetiracetam and phenytoin may reflect important functional differences in the actions of these two drugs, and ii) there may be different mechanisms involved in their anti-seizure effect. Male Wistar rats receive levetiracetam (150 mg/kg x 2), phenytoin (75 mg/kg x 2) or control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Experimental animals and controls are housed together in the same cages in groups of three, facilitating paired comparisons among the three groups in animals that have experienced the same environment throughout the 3 month experimental period. Four hrs after the last dose animals are anesthetized, decapitated, and total RNA is extracted from brain stem, frontal cortex, and hippocampus. RNA will be sent to the TGEN facility for hybridization to the rat U230A chips. The number of chips needed is (2 drugs + 1 control) * (3 brain regions) * (7 animals per group) = 63 chips. We will initially select those genes for analysis that are called ?present? by the Affymetrix software in 4 or more animals for at least one of the 6 experimental groups. Then t-tests with Benjamini & Hochberg correction for protection against multiple comparisons will be used to identify genes that are differentially expressed at a false discovery rate of .05 among any of the six groups. We will be primarily interested in the following expression profiles, analyzed as paired comparisons by the Affymetrix software: 1. phenytoin vs control in hippocampus 2. phenytoin vs control in brain stem 3. levetiracetam vs control in hippocampus 4. levetiracetam vs control in brain stem We will then compare the profiles of both drugs in each brain region (e.g., phenytoin vs levetiracetam in hippocampus) to select genes that are drug-specific. We will also take a Venn diagram approach to identify genes that are drug-specific across both brain regions tested. Last Updated (by provider): Oct 28 2005 Contributers: Ray Dingledine Includes GDS1864. Update date: Dec 05 2006. Dataset description GDS1864: Analysis of the brainstem, frontal cortex, and hippocampus of animals chronically treated for 90 days with levetiracetam or phenytoin. Levetiracetam inhibits epileptogenesis in the kindling model of epilepsy. Phenytoin's antiepileptic activity involves the inhibition of sodium channels.. Kidney 1000 1082 1064 in medulloblastoma Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell 240min (set2) NG036_a Blood 861 Eye 1000 comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247392 Last updated (according to GEO): Dec 11 2007 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc127 Source GEO sample is GSM1906 Last updated (according to GEO): Nov 21 2005 pfc_1033_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A heart 1168 1172 Mammary Neoplasms 1000 453 434 The descending colon NCI60.56_LABEL60EXTRACT59SUB3 Source GEO sample is GSM134275 Last updated (according to GEO): Aug 06 2007 none Source GEO sample is GSM210298 Last updated (according to GEO): Jul 16 2007 Brain Stem 1000 M_U133A_23_CB of parieto-occipital cortex 225 252 Spleen vs CD27 Treated B cell Laser captured visceral sensory neurons. Source GEO sample is GSM63694 Last updated (according to GEO): Dec 21 2005 Medulla Oblongata 861 Normal Source GEO sample is GSM176253 Last updated (according to GEO): Apr 09 2007 GSE411 migraine 104 112 Transcriptional Profiling of Cerebral Malaria from the forebrain 20 37 861 Ovary mild cognitive impairment - entorhinal cortex 6 1000 Communicable Diseases 39 23 of human arteries 5 0 brain 1000 Spleen WGACON-273 n/a Source GEO sample is GSM177991 Last updated (according to GEO): Jun 11 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145658 Last updated (according to GEO): Nov 20 2006 861 Amygdaloid structure Heart 861 Expression profiling of moderately injured raphe at 24h in rats Source GEO sample is GSM41575 Last updated (according to GEO): May 27 2005 Spinal Cord 1000 1240 HP24_11 Brain 1000 Primary Neoplasm 1000 Kidney 1000 70 CB B "Sample 84, BRCA1 mutation(38 months) age 51 erp no" on vantveer-oligo Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153422 Last updated (according to GEO): Jan 11 2007 1000 Coronary Arteriosclerosis Muscle 861 Tumor__Renal_Carcinoma_Carc_614TS on Affymetrix GeneChip Human 35K SubA Array Hu35k-A from brain 21 30 Lymphoblastoid Cell Line for Individual 8145.4 log phase 24 7 Right Frontal Lobe The epithelial cells 962 981 8075_Lung did not develop PGD Lymphoblastoid Cell Line for Individual 8030.3 log phase 1000 Prostate Subcutaneous Fat 1000 with mental retardation 241 263 Brain (corpus callosum) [JunctionChip 3 of 5] 301 287 8 uterine horns Changes in mouse liver mRNA profiles following intra-peritoneal cytokine injection. One of 2 replicates of Interferon-gamma-/- mice, injected with interferon-gamma, and killed after 4h. Source GEO sample is GSM5952 Last updated (according to GEO): May 27 2005 Parkinson Disease 861 hippocampus 400 410 to the nose 599 609 VP16-CREB hippocampus region Source GEO sample is GSM88937 Last updated (according to GEO): Jan 04 2006 Brain 1000 frontal cortex sprague 3933 adipose_tissue_5 Source GEO sample is GSM80588 Last updated (according to GEO): Mar 31 2006 - Source GEO sample is GSM162900 Last updated (according to GEO): Aug 28 2007 plasma cells 50 61 48 29 of bladder carcinoma Occipital lobe 861 Wild type voxel B2 GSE384 318 in nodose ganglia 302 Pancreas; Islets Keywords = mouse gene expression database Source GEO sample is GSM29430 Last updated (according to GEO): May 27 2005 ExpressionLevel:GXN-00531 on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hrs per day, 24 h time point Source GEO sample is GSM159745 Last updated (according to GEO): Apr 23 2007 861 Blood SN:Human Glioblastoma Biopsy 30165 M_U133A_81_DLPFC Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3295 Last updated (according to GEO): Mar 21 2006 Expression profiling of spinal cord section (T10) extracted from rats 30m following mild injury Source GEO sample is GSM31323 Last updated (according to GEO): May 27 2005 frontal lobe 1000 mouse brain contralateral LPS.RU486, biological rep3 12 0 ovarian tumor Brain 1000 Gap Junctions 861 Plasma 861 prostate_gland_4 861 Gland structure B CELLS A on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Pituitary Gland 861 Prostate 861 in the adult nervous system 846 873 25 17 (cerebrum 901 Coronary artery 5 0 brain 6wkA 861 Brain Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n114 Source GEO sample is GSM2047 Last updated (according to GEO): Nov 21 2005 278 255 ischemic cardiomyopathy Gene expression data from biopsy of PBS treated skin of subject with resolver phenotype. (control) Source GEO sample is GSM128954 Last updated (according to GEO): Sep 13 2007 1000 Bronchi 901 Coronary artery Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19206 Last updated (according to GEO): May 27 2005 Mental Retardation 1000 Heart failure 1000 Osteoblasts 1000 normal testis 54 66 of somatomotor cortex 21 41 Brain 861 from colorectal adenoma 21 44 Lmna H222P homozygous male 5 myocardial infarction 383 403 48 30 in HIV encephalitis Endometrium/Ovary-Disease 8 MF_43 small intestine wild type mice, treated with WY14,643 for 5 days. The WY14.643 was present in the diet at 0.1% w/w. Source GEO sample is GSM124313 Last updated (according to GEO): Jun 28 2007 the blood 393 402 Hypothalamus RYGB-Fail Repl1 5 0 brain 5 0 brain tongue_superior_part_w/_papillae_4 Successful regeneration of injured neurons requires a complex molecular response that involves the expression, modification and transport of a large number of proteins. The identity of neuronal proteins responsible for the initiation of regenerative neurite outgrowth is largely unknown. Dorsal root ganglion (DRG) neurons display robust and successful regeneration following lesion of their peripheral neurite, whereas outgrowth of central neurites is weak and does not lead to functional recovery. We have utilized this differential response to gain insight in the early transcriptional events associated with successful regeneration. Surprisingly, our study shows that peripheral and central nerve crushes elicit very distinct transcriptional activation, revealing a large set of novel genes that are differentially regulated within the first 24 h after the lesion. Here we show that Ankrd1, a gene known to act as a transcriptional modulator, is involved in neurite outgrowth of a DRG neuron-derived cell line as well as in cultured adult DRG neurons. This gene, and others identified in this study, may be part of the transcriptional regulatory module that orchestrates the onset of successful regeneration. Neoplasm 861 65 24 from umbilical subcutaneous adipose tissue D_U133A_62_HC 2.5 mg/kg 2CdA embryo at 3.0h rat cortex Treatment, type=time_course, measurement=28.0 d Source GEO sample is GSM53231 Last updated (according to GEO): Jul 06 2005 onto a collagen 71 85 Melanoma xenograft, MEA2_Sub_A (LeiFidler) Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. Moderate controlled cortical impact with pneumatic impactor, 6 m/s impact velocity and 1.5 mm deformation. 72h after surgery, a 4 mm diameter disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44470 Last updated (according to GEO): May 27 2005 Gene expression data from whole brain infected mouse, day 3 Source GEO sample is GSM189651 Last updated (according to GEO): May 16 2007 1000 Neoplasm CCAT Full Length Rep B3 Epithelium 861 HCC (HBV+, HK12) 1000 frontal lobe of coronary artery disease 258 284 Gene expression data from postmorten brain regions Source GEO sample is GSM145626 Last updated (according to GEO): Nov 20 2006 /3T3 fibroblasts 743 759 1000 Hippocampus SkinE16_0222ACI9_036.txt Wild type 8 wk old male 129S6/SvEvTac mouse hippocampus Source GEO sample is GSM74955 Last updated (according to GEO): Feb 27 2007 861 Cardiomyopathies (cortex 19 25 988 980 cerebella no additional Source GEO sample is GSM199260 Last updated (according to GEO): Jun 08 2007 Spleen 0 5 1000 Tricuspid valve structure 40 21 from the hippocampus of Parkinson's disease 450 471 1 of 3 replicates in treatment group Source GEO sample is GSM206045 Last updated (according to GEO): Jun 29 2007 human cerebellum Source GEO sample is GSM87087 Last updated (according to GEO): Feb 08 2006 bone marrow-CD105Endothelial Source GEO sample is GSM18884 Last updated (according to GEO): Sep 25 2006 Type 1 Diabetes patient and the timepoint 1 month after diagnosis. Source GEO sample is GSM228610 Last updated (according to GEO): Sep 11 2007 D_U133A_8_DLPFC in blood 16 23 Muscle Source GEO sample is GSM4304 Last updated (according to GEO): May 27 2005 1000 Uterus Medulla Oblongata 861 858 Mesodermal cell Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15741 Last updated (according to GEO): May 28 2005 1000 Rectum 320 306 Keywords = HIV from ventral prostate 21 41 Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203942 Last updated (according to GEO): Aug 02 2007 Kidney (fetal) [JunctionChip 4 of 5] control 24h, replicate 2 mouse brain contralateral LPS Source GEO sample is GSM149756 Last updated (according to GEO): Mar 15 2007 B6C3Fe-SpinalC-1moM-1bAv2-s2 H109 CN B VDXRHU_1526 mouse brain 478 489 WGACON-254 Healthy patient. Source GEO sample is GSM228577 Last updated (according to GEO): Sep 11 2007 1000 Neoplasm NB-C5 on NHGRI-6.5k_b CNS-RM_Mod28d-2A-s2 lung 191 195 Femur 1000 Pooled total RNA from (3) P27 L3-L5 Egr3-deficient spinal cords Source GEO sample is GSM32060 Last updated (according to GEO): May 27 2005 Sample represents the Neurointermediate lobe of the Pituitary from 5 control animals Source GEO sample is GSM69788 Last updated (according to GEO): Dec 15 2005 10 CN B Putamen 8 Normal Dendritic Cells, Baseline - Repeat #1 91 from the bone marrow 72 Standard Affymetrix Protocol Source GEO sample is GSM15860 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145360 Last updated (according to GEO): Nov 20 2006 861 Malaria putamen_1 1000 Brain BL6: 2-4 motor cortex D_U133A_29_DLPFC Lymphoblastic Leukemia 901 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225683 Last updated (according to GEO): Nov 05 2007 Cardiac-specific TNF-alpha transgenic mouse is an excellent model to study the pathologenesis of heart failure. Affytrix U74V2A was used to analyzed the gene expression profile of mice at the time point of compensated hypertrophy and dilated heart failure. Source GEO sample is GSM8989 Last updated (according to GEO): May 28 2005 KT63_AR2 HC86 FC BA4 A Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68354 Last updated (according to GEO): Jul 07 2006 GSE2882 CC515 nasal epithelial cells 28 49 Sum185 Two 90 minute exposures (3 hr recovery in between) to 1.0% isoflurane every day for 2.5 days, for a total of 5 exposures Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5119 Last updated (according to GEO): Mar 17 2006 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114481 Last updated (according to GEO): Jun 16 2006 Cerebral cortex 861 R7E 1 Chronic leukemia NOS 913 Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep6 1000 Spleen Blood Test (Blinded) Sample Source GEO sample is GSM130051 Last updated (according to GEO): Sep 18 2007 CAD_replicate29 ovary_10 Source GEO sample is GSM80759 Last updated (according to GEO): Mar 31 2006 8 0 leukemia Blood Test (Blinded) Sample Source GEO sample is GSM130022 Last updated (according to GEO): Sep 18 2007 Standard Affymetrix Protocol Keywords = microarray Keywords = muscle Source GEO sample is GSM15846 Last updated (according to GEO): May 28 2005 MO_LB_180min_Patient15 osteoblast 627 637 SN6h(3) Lymphoblastic Leukemia 901 61 42 in neural stem cells Adenocarcinoma 861 ISR16-Fv2E-PERK AP20187 4hr2 RNA from an 2 nm AP20187 treated (4hr) Fv2E-PERK expressing mouse fibroblast cell line in an eIF2 alpha SS (wildtype), PERK-/- background. AP20187 activates the kinase activity of the Fv2E-PERK chimera. The PERK-/- background was used in order to obtain a cell line that expressed high levels of the Fv2E-PERK transgene. (We were unable to obtain clones with high levels of expression in wildtype cells.) The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10899 Last updated (according to GEO): May 28 2005 A HID U D007 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108604 Last updated (according to GEO): Aug 22 2006 Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM Source GEO sample is GSM207689 Last updated (according to GEO): Jul 09 2007 SmIntP145_022JAFB5_173.txt Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68227 Last updated (according to GEO): Jul 07 2006 Gene expression data from hippocampus of one old SAMR1TA mouse Source GEO sample is GSM143756 Last updated (according to GEO): Jan 24 2007 1000 Kidney cortex.1 None Source GEO sample is GSM198097 Last updated (according to GEO): Jul 16 2007 Mesenchymal Stem Cells 1000 Dominant negative cJun VZ19 Whole Brain 73 83 7 0 Melanoma Ventral Tegmental Area 10 Normal Wild-type vs. Rb-/- Prostate Epithelial Cell Lines Vestibular organ at E11, replicate2 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114247 Last updated (according to GEO): Jun 16 2006 Expression profiling of somatomotor cortex extracted from rats at 4h following moderate injury Source GEO sample is GSM41701 Last updated (according to GEO): May 27 2005 Primary small cell lung carcinoma 2243 0 37 Study the transcriptomic effects of the shear stress on cultured osteoblast-like MC3T3 cells Source GEO sample is GSM201207 Last updated (according to GEO): Jun 19 2007 Heart Septal Defects, Atrial 1000 human caudate nucleus Source GEO sample is GSM86878 Last updated (according to GEO): Feb 08 2006 bronchus_4 Source GEO sample is GSM80582 Last updated (according to GEO): Mar 31 2006 human cerebellum Source GEO sample is GSM87072 Last updated (according to GEO): Feb 08 2006 mouse brain ipsilateral control, biological rep4 861 Seizures of coronary artery disease 317 342 Gut 861 Epithelium 861 2nd 4hr C+S-DG 861 Lymph gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134641 Last updated (according to GEO): Jul 09 2007 NH 17172A 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14940 Last updated (according to GEO): Oct 28 2005 V5-P357 3wkB Gene expression data from postmorten brain regions Source GEO sample is GSM144881 Last updated (according to GEO): Nov 20 2006 Neoplasm 861 Ovary 1000 D_U133Plus_113_nAcc MSE_D_516 Type 1 Diabetes patient and the timepoint 4 months after diagnosis. Source GEO sample is GSM228641 Last updated (according to GEO): Sep 11 2007 The use of peripheral blood mononuclear cells (PBMC) for transcriptome analysis has already been proven valuable for assessing disease-associated and drug response related gene signatures. While these proof-of-principle studies have been critically important, the instability of RNA within PBMC prohibits their use in large scale multi-center trials for which samples have to be transported for a prolonged time prior RNA isolation. Therefore, a prerequisite for transcriptome analysis of peripheral blood in clinical trials will be a standardized and valid method to immediately stabilize the RNA profile after blood withdrawal. We demonstrate that the globin mRNA reduction method results in significantly improved data quality of stabilized RNA samples resulting in low intra-group variance and a detection rate of expressed genes similar to PBMC. More important, even small differences in gene expression such as observed between females and males were detected and sufficient to predict gender in whole blood samples. Last Updated (by provider): Apr 20 2007 Contributers: Svenja Debey Joachim L Schultze 67 40 with coronary artery disease brain, retina: 3 Retina at CT 12_e1_le1 Expression profiling of naive raphe (T0) in rats Source GEO sample is GSM41553 Last updated (according to GEO): May 27 2005 hippocampal glutamatergic CA3 pyramidal neurons Source GEO sample is GSM35833 Last updated (according to GEO): May 27 2005 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11246 Last updated (according to GEO): May 28 2005 1124 1103 of the pituitary gland Whole Brain 73 83 putamen_7 Spinal Cord 901 Liver (HBV+, HK37) Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=1 (Acute rejection). One of two samples from the same patient, different visits. Source GEO sample is GSM36433 Last updated (according to GEO): May 27 2005 Muscular Dystrophy, Duchenne 1000 861 Acquired Immunodeficiency Syndrome Epithelium 861 Expression profiling of somatomotor cortex extracted from rats at 28d following moderate injury Source GEO sample is GSM41712 Last updated (according to GEO): May 27 2005 861 Retina SCG_sema3A_40h_rep1 1000 Heart failure Expression profiling of spinal cord section (T8) extracted from rats 7d following laminectomy (sham) Lot batch = Source GEO sample is GSM6629 Last updated (according to GEO): May 28 2005 Specific Phobia 983 Cerebral Cortex 3 Normal 1000 Lung Brain Stem 1000 119 96 in embryonic stem cells KT72_DT CLL-52 861 Trauma Neoplasm 1000 861 Brain human caudate nucleus Source GEO sample is GSM86874 Last updated (according to GEO): Feb 08 2006 861 Cochlear structure 1000 Eye 17 7 hippocampus ovarian tumor: endometrioid Source GEO sample is GSM139409 Last updated (according to GEO): Apr 09 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lipopolysaccharide (LPS) for 60min Source GEO sample is GSM5666 Last updated (according to GEO): May 27 2005 Spleen 0 5 9 0 Blood Test of 10 saccules 5 18 Brain Injuries 1000 Brain Stem 1000 none Source GEO sample is GSM210291 Last updated (according to GEO): Jul 16 2007 brain 0 5 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188806 Last updated (according to GEO): Jun 06 2007 Lung 1000 41 28 in mouse brain 10 Bone marrow 0 Gene expression data from postmorten brain regions Source GEO sample is GSM145659 Last updated (according to GEO): Nov 20 2006 BXD 18_M7SS02080601 Saccule structure 861 1000 Brain Time course of aortic gene expression 225 212 in trisomy 21 of somatomotor cortex 21 41 Arteries 861 Fluid-percussion head injury 83 110 human frontal cortex Source GEO sample is GSM86955 Last updated (according to GEO): Feb 08 2006 brain 0 5 SCG_control_12h_rep1 Expression profiling of somatomotor cortex extracted from rats at 24h following sham surgery Source GEO sample is GSM41641 Last updated (according to GEO): May 27 2005 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156707 Last updated (according to GEO): Jan 22 2007 Mesenchymal stem cells 13 34 901 Nervous system structure 67 40 with coronary artery disease Nasal Epithelium 865 bone marrow Source GEO sample is GSM18909 Last updated (according to GEO): Sep 25 2006 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151998 Last updated (according to GEO): Feb 06 2007 Malignant Neoplasms 861 M_U133A_25_DLPFC 1000 Hippocampus Acetaminophen 3hr Rat 6219 blood vs. Acetaminophen 3hr Rat Pooled Control blood C57BL/6J ACU, Rep2 It was the purpose to analyse the changes in gene expression which occur in the mouse small intestine from the pre-weaning to the post-weaning stage. The gene expression was accordingly followed from postnatal day 4 to postnatal day 32. Last Updated (by provider): Jun 11 2007 Contributers: Jesper T Troelsen Jørgen Olsen brain, cerebral cortex: Rat_03-07_NroLep_Lipska_e1_le1 111T Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n112 Source GEO sample is GSM2058 Last updated (according to GEO): Nov 21 2005 Activity-dependent changes in synapses rely on functional changes in resident proteins and on gene expression. We addressed the relationship between synapse activity and the expression of synaptic genes by comparing RNA levels in the neocortex of normal mice versus secretion-deficient and therefore synaptically silent munc18-1 (mammalian homologue of Caenorhabditis elegans uncoordinated locomotion-18) null mutants, using microarray expression analysis, real-time quantitative PCR and northern blotting. We hypothesized that genes under the control of synaptic activity would be differentially expressed between mutants and controls. We found that few synaptic genes were differentially expressed. However, most neuropeptide genes with detectable expression on the microarray were differentially expressed, being expressed 3-20-fold higher in control cortex. Several other secreted proteins were also differentially expressed, but genes encoding their receptors and many other synaptic components were not. Differential expression was confirmed by real-time quantitative PCR analysis. In situ hybridization indicated that the difference in neuropeptide expression was uniform and not due to the loss of specific cells in the mutant. In primary sensory neurons, which do not depend on synaptic activity for their input, the differential expression of neuropeptides was not observed. These data argue against a general relationship between the activity of synapses and the expression of their resident proteins, but suggest a link between secretion and the expression of genes encoding the secreted products. Expression profiling of somatomotor cortex extracted from rats at 4h following moderate injury Source GEO sample is GSM44449 Last updated (according to GEO): May 27 2005 Primary Neoplasm 1000 WGACON-263 The most common congenital cardiac abnormalities 50 97 Compare the transcriptomes of Cx43 null and Cx43 siRNA treated cortical astrocytes with the transcriptome of the wildtype cortical astrocytes Source GEO sample is GSM200845 Last updated (according to GEO): Jun 19 2007 HapMap CHB Female Source GEO sample is GSM159582 Last updated (according to GEO): Feb 01 2007 Melanoma xenograft, MC1_Lung_B (LeiATCC) Blood Test (Blinded) Sample Source GEO sample is GSM129941 Last updated (according to GEO): Sep 18 2007 PGA-lv_24h_510 Parkinson Disease 861 1000 Heart failure CNS-SCsev_InjB14d-1A-s2 Muscular Dystrophy, Duchenne 923 WGACON-49 CC519 861 Cerebellum Gene expression data from postmorten brain regions Source GEO sample is GSM145732 Last updated (according to GEO): Nov 20 2006 901 frontal lobe Brain 861 1000 Coronary Arteriosclerosis 1000 Kidney Spleen 0 5 This data series contains spotted oligo microarray data from 10 different experiments using Agilent Rat v2 microarrays. This data is being made public in support of Fillon S et al. Journal of Immunology. In Press. Proinflammatory bacterial components are at least partially responsible for causing the clinical features of sepsis, a syndrome that causes >100,000 deaths each year in the US (1). In the case of Gram positive infection, a key bacterial element recognized by the innate immune system is the cell wall, a complex network of peptidoglycan covalently linked to teichoic acids, proteins and lipoproteins. The current model of innate immune recognition of Gram positive bacteria suggests bacterial cell wall interacts with host recognition proteins, such as toll-like receptors (TLR) and Nod proteins. We describe an additional recognition system mediated by the platelet activating factor receptor (PAFr) and directed to the pathogen associated molecular pattern (PAMP) phosphorylcholine that results in uptake of bacterial components into host cells. Intravascular choline-containing cell walls bound to endothelial cells and caused rapid lethality in wild type, Tlr2-/- and Nod2-/- mice, but not in Pafr-/- mice. Cell wall exited the vasculature into the heart and brain, accumulating within endothelial cells, cardiomyocytes and neurons in a PAFr-dependent way. Physiological consequences of the cell wall/PAFr interaction were cell specific, being noninflammatory in endothelial cells and neurons, but causing rapid loss of cardiomyocyte contractility that contributed to death. Thus, PAFr shepherds phosphorylcholine-containing bacterial components such as cell wall into host cells from where the response ranges from quiescence to severe pathophysiology. Last Updated (by provider): Aug 16 2006 Contributers: Deepak Kaushal Sophie Fillon Elaine Tuomanen Head and neck cancer Source GEO sample is GSM155668 Last updated (according to GEO): Apr 24 2007 S2_Muscle_Baseline_0min Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD42 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD42 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36689 Last updated (according to GEO): May 27 2005 1000 Prostate Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy, pathological hypertrophy, rat, heart failure, cardiomyopathy Source GEO sample is GSM12317 Last updated (according to GEO): May 28 2005 fetal_lung Gonadectomized Dahl-Iwai Male LowSalt OuterMedulla rat8 gdahl_medullar_k_GX_8om_rh_051402 Olfactory Epithelium 1000 from ventral prostate 21 41 human caudate nucleus Source GEO sample is GSM86829 Last updated (according to GEO): Feb 08 2006 GM12751 Fibronectins 1000 low gestational age Source GEO sample is GSM213104 Last updated (according to GEO): Jul 25 2007 Wnt (32 h) A on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A MO_DH1c_SON_NCBI A/J Amygdala D 1000 Caudate nucleus structure A2780_oxa_IC90_2h_2 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=700690 LaserPower=2.011.3 Lot batch = LC17N106 Source GEO sample is GSM4826 Last updated (according to GEO): Nov 21 2005 Job's patient Source GEO sample is GSM211115 Last updated (according to GEO): Sep 10 2007 Bone Marrow 1000 +_4981_batch1 on NHGRI-6.7k with mental retardation 241 263 Epithelium 861 39 21 of fast glial cells Brain 1000 for liver 26 35 14 0 Locus Coeruleus 1000 Stem cells 5 0 brain Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225665 Last updated (according to GEO): Nov 02 2007 1000 Rectum +_7225_batch2 on NHGRI-6.7k cerebral cortex 7 21 Basal 1000 M7TW01013179 Normal Source GEO sample is GSM176028 Last updated (according to GEO): Apr 09 2007 Acetaminophen (APAP) Rat Blood Training Gene Expression Data Set 861 Heart 320 291 of human oral epithelial cells Ts1Cje-3-MGU74A frontal_lobe_6 Normal__Prostate_PR_6 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A GC (HKG21T) Effects of SOCS3 on transcriptional response of macrophages to IL-6. Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Replicate 1 unstimulated. Source GEO sample is GSM6075 Last updated (according to GEO): Mar 17 2006 to microbial infection 917 939 PGA_PA-S_281 1820 1807 out the liver Vestibular Nuclei Superior 2 Normal 383 377 Kidneys 5 0 Muscle 18 0 Trigeminal_Ganglion Average value of duplicate experiments of brain neurospheres of BMI-1 knockout mice (postnatal day 0). The cRNAs for hybridization were generated by one round RNA amplifications. Source GEO sample is GSM9242 Last updated (according to GEO): May 27 2005 Lymphoblastoid Cell Line for Individual 8101.6 log phase Rationale: Maternal immune responses can promote allergy development in offspring. Pilot data show that neonates of mother mice exposed during pregnancy to air pollution particles have increased allergic susceptibility. Objective: We investigated whether inflammatory response to titanium dioxide (TiO2) particles earlier considered immunologically ?inert? is enhanced during pregnancy. Methods: Pregnant BALB/c mice (or non-pregnant controls) received particle suspensions intranasally at day 14 of pregnancy. Lung inflammatory responses were evaluated 19 and 48 h after exposure. Results: Pregnant mice showed robust and persistent acute inflammatory responses after exposure to TiO2, while non-pregnant females had the expected minimal responses. Genomic profiling identified genes differentially expressed in pregnant lungs exposed to TiO2. Neonates of mothers exposed to TiO2 (but not PBS) developed increased susceptibility to allergens. Conclusion: Pregnancy enhances lung inflammatory responses to otherwise relatively innocuous inert particles. Last Updated (by provider): Jun 20 2007 Contributers: Alexey V Fedulov Zhiping Yang Thomas J Mariani Lester Kobzik NA19138 from the cerebellum 20 38 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-06/6799.gif Source GEO sample is GSM76462 Last updated (according to GEO): Sep 22 2006 1933 tumor cells 1943 Pooled EDL RNA samples from five 8 wk old male mdx5cv mice Source GEO sample is GSM13666 Last updated (according to GEO): May 28 2005 1000 Brain 12 Temporal Lobe 24 Macrophage smi101 Hippocampus 1997 15 month Old Male 25.1 yr after antibody enrichment scan 2 (U133B) 128 111 uterine leiomyomas 159 139 with HIV encephalitis Vestibular organ at E11.5, replicate2 1000 Skeletal muscle structure human caudate nucleus Source GEO sample is GSM86849 Last updated (according to GEO): Feb 08 2006 42 30 Control blood Brain 1000 Autistic Disorder 1000 28 7 Superior Frontal Gyrus Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 72h. Lot batch = Source GEO sample is GSM1252 Last updated (according to GEO): May 28 2005 1000 Structure of parenchyma of lung Mouse old heart w/ a-tocopherol aT-Ht-5 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120707 Last updated (according to GEO): May 14 2007 3rd 2hr C+S-DG H121 CB B 861 Cerebral cortex CNS-SC_InjA14d-3A-s2 from nose 102 110 901 Caudate nucleus structure 858 Prostatic Neoplasms Primary tumor 19 32 PD brain structures 1110 1129 861 Coxsackievirus Infections 913 Coronary heart disease 1037 of transitional epithelium 1012 MGMH030311038Atongueepidermis the total spinal cord 1675 1696 Gene expression data from postmorten brain regions Source GEO sample is GSM145842 Last updated (according to GEO): Nov 20 2006 901 Coronary artery mRNA was isolated after 12 hours of incubation from IMR-90 cells seeded onto a collagen/chondroitin sulfate tissue engineering scaffold mesh material. Cells were seeded at a density of 1 x 10^6 cells/ mesh, and this chip represents a pooling of cells from 4 meshes. Source GEO sample is GSM6037 Last updated (according to GEO): May 27 2005 brain, Right Temporal Lobe: Extract76_le1 1000 Muscle Mid secretory endometrium from patient with endometriosis Source GEO sample is GSM150213 Last updated (according to GEO): Dec 14 2006 AD control Treatment, type=dissect Source GEO sample is GSM119638 Last updated (according to GEO): Jul 10 2006 Cerebral cortex 861 861 Cerebral cortex Spleen 0 5 human caudate nucleus Source GEO sample is GSM86885 Last updated (according to GEO): Feb 08 2006 91 from the bone marrow 72 Spleen vs ELC Treated B cell 60min (set2) 38 12 of congenital heart disease Epithelium 861 5 0 Spleen 901 frontal lobe Wild-type-hippocampus, biological rep5 (male) 70 40 without coronary artery disease X-ray irradiation (2 Gy) and TGFB added. Source GEO sample is GSM203983 Last updated (according to GEO): Jun 25 2007 1000 Spleen Tumor__Mesothelioma_161_T6 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 2.5 mg/kg 2CdA headfold at 4.5h Cerebral cortex 1000 Brain 861 Heart Septal Defects, Atrial 1000 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10954.gif Source GEO sample is GSM76445 Last updated (according to GEO): Sep 22 2006 Gene expression data from B6xBALB F2 mouse lung Source GEO sample is GSM133467 Last updated (according to GEO): Apr 05 2007 1000 frontal lobe with autism spectrum disorder 37 65 23 14 from lungs Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b105 Source GEO sample is GSM2009 Last updated (according to GEO): Nov 21 2005 1000 Coronary Arteriosclerosis 861 Chromosomes Voxel J4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1460 Last updated (according to GEO): Nov 21 2005 8 0 amygdala stomach_fundus_3 Source GEO sample is GSM80811 Last updated (according to GEO): Mar 31 2006 861 Chromosomes brain, unknown: 03CX_e1_le1 Trachea [JunctionChip 1 of 5] Stem cells 1000 Expression profiling of spinal cord section (T9) extracted from rats 14d following severe injury Source GEO sample is GSM31596 Last updated (according to GEO): May 27 2005 Neostriatum 1000 Blood 861 outer medulla 31 43 1000 Brain DLBC12 on Affymetrix GeneChip Human Full Length Array HuGeneFL Communicable Diseases 1000 GBM Treatment, type=remove Source GEO sample is GSM99565 Last updated (according to GEO): Apr 21 2006 Expression profiling of spinal cord section (T10) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM6650 Last updated (according to GEO): May 28 2005 1000 Neuraxis Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159748 Last updated (according to GEO): Apr 23 2007 Neoplasm 861 10 7 Left Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132491 Last updated (according to GEO): Feb 26 2007 1037 of transitional epithelium 1012 no additional Source GEO sample is GSM199222 Last updated (according to GEO): Jun 08 2007 GC (HKG94T) R6/1 transgenic, brain hemisphere Source GEO sample is GSM83877 Last updated (according to GEO): Apr 20 2007 Spleen vs Sphingosine-1-phosphate Treated B cell 120min (set2) 91 80 from bronchi Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=720630 LaserPower=2.111.28 Lot batch = LC17N110 Source GEO sample is GSM4828 Last updated (according to GEO): Nov 21 2005 BAL_45a_A1B0 D_95Av2_3023_CB_0_GS Spleen vs CD27 Treated B cell 120min (set2) rat kidney at embryonic day 18, rep3 Lymphoblastoid Cell Line for Individual 8081.4 log phase 1439 1417 that cognitive symptoms Cell membrane 901 861 Heart mouse hippocampus 0 16 Superior Frontal Gyrus_10y_normal Epithelial Cells 1000 of Parkinson's disease 450 471 Down Syndrome 1000 Unfertilized egg replication 2 Keywords = preimplantation Keywords = development Source GEO sample is GSM14660 Last updated (according to GEO): May 28 2005 Lymphoblastoid Cell Line for Individual 8028.3 log phase 171 158 of metastasis plasma cells 332 344 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28803 Last updated (according to GEO): May 27 2005 861 Cardiomyopathies 861 Brain 19 0 Human breast tumours Nose 1000 UO-31 hgu95b metanephric mesenchyme, LIF, 5 days, biological rep2 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225733 Last updated (according to GEO): Nov 02 2007 A39 WT5 F1/1 A39 wild type Mouse 10.5 months Cerebellum Male Source GEO sample is GSM73186 Last updated (according to GEO): Sep 06 2005 19 0 Head and neck cancer spleen_2 7 0 prostate frontal cortex wistar ky 3926 whole tissue, individual animal, 10 weeks old, male Wistar Kyoto frontal cortex file:p3926w Source GEO sample is GSM15163 Last updated (according to GEO): Oct 28 2005 brain, hippocampus: PR-DG-9_e1_le1 1000 Palatine Tonsil 861 Cerebellum control 2 weeks C Treatment, type=time_course, measurement=2.0 weeks Source GEO sample is GSM107858 Last updated (according to GEO): Jun 06 2006 HapMap YRI_parent Male Source GEO sample is GSM159672 Last updated (according to GEO): Feb 01 2007 Encephalopathies 861 861 Lymphoblastic Leukemia 901 Epithelial Cells Nose 1000 Anterior interpositus nucleus-centered deep cerebellar nuclei were sampled using syringe needles Source GEO sample is GSM84988 Last updated (according to GEO): Mar 29 2006 of human neurodegenerative diseases 9 43 MLL__5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Standard Affymetrix procedure Source GEO sample is GSM133021 Last updated (according to GEO): Aug 28 2007 1601 1578 to IR-induced DNA damage Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184720 Last updated (according to GEO): Apr 26 2007 PGA-swim_2.5d_s1000 0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point, biological rep 2 Entorhinal Cortex 7 23 861 Substantia nigra structure 330 324 uterus 11 0 Normal Heart Heart Septal Defects, Atrial 1000 Recurrent Squamous cell carcinoma 7 14 6 (thalamus MLL-#1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 6 (cerebral cortex 21 861 Cerebral cortex C3H/HeJ Cerebellum A Prostate 4 Disease Nasal Epithelium 865 861 Cardiomyopathies Leukemia, Lymphocytic, Acute 1000 865 Disorder of artery Normal Source GEO sample is GSM176419 Last updated (according to GEO): Apr 09 2007 High-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we have generated and analyzed gene expression from a set of samples spanning a broad range of biological conditions. Specifically, we profiled gene expression from 91 human and mouse samples across a diverse array of tissues, organs, and cell lines. Because these samples predominantly come from the normal physiological state in the human and mouse, this dataset represents a preliminary, but substantial, description of the normal mammalian transcriptome. We have used this dataset to illustrate methods of mining these data, and to reveal insights into molecular and physiological gene function, mechanisms of transcriptional regulation, disease etiology, and comparative genomics. Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website (http://expression.gnf.org) that integrates data visualization and curation of current gene annotations. 861 Coxsackievirus Infections n/a Source GEO sample is GSM177890 Last updated (according to GEO): Jun 11 2007 1205 1190 in PCOS oocytes Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3505.gif Source GEO sample is GSM76429 Last updated (according to GEO): Sep 22 2006 experiment XI, hTERT Pool of total RNA from 3 euploid cerebella at P0 postnatal stage Keywords = Down syndrome Keywords = Chromosome 21 Keywords = Transcriptome Keywords = Microarray Keywords = Brain Keywords = Cerebellum Keywords = Development Source GEO sample is GSM27473 Last updated (according to GEO): May 27 2005 mammary gland ; females with E18 embryos Source GEO sample is GSM18685 Last updated (according to GEO): May 27 2005 Cochlear nucleus structure 901 Lymphoblastoid Cell Line for Individual 8126.3 log phase GSE5078 Gene expression data from dorsal pancreas at e15.5, MG-U74C version2 Source GEO sample is GSM199470 Last updated (according to GEO): Jun 08 2007 by liver progenitor cells 329 354 1000 Lung Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35378 Last updated (according to GEO): May 27 2005 gene expression data from melanoma xenografts following ILI with melphalan Source GEO sample is GSM213628 Last updated (according to GEO): Jul 27 2007 Medulla 861 Rat SCN Sample 11 (Technical replicate - 12 hr) 15 0 human cerebellum CF knockout HMCF CHN537 M4 biol repl 1 24M_B22103 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68187 Last updated (according to GEO): Jul 07 2006 337 323 with adiposity PC 12Hr rat 4126 blood vs. 2500mg/kg APAP 12Hr rat 4136 blood processed in batch 2 Source GEO sample is GSM90434 Last updated (according to GEO): Mar 20 2006 861 Blood 41 36 spleen Primary large cell lung carcinoma 1485 Source GEO sample is GSM18308 Last updated (according to GEO): May 27 2005 Early secretory endometrium from patient with endometriosis Source GEO sample is GSM150206 Last updated (according to GEO): Dec 14 2006 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 0613 left_liver_lobe 76 65 from bronchi 3AMH02030602_LymphomaRaji none Source GEO sample is GSM210293 Last updated (according to GEO): Jul 16 2007 CNS-SpinalCmod-Adult-4h-1B-s2 Gene expression data from postmorten brain regions Source GEO sample is GSM145369 Last updated (according to GEO): Nov 20 2006 brain 0 5 1000 melanoma Rett Syndrome 1000 metanephric mesenchyme, LIF, 5 days, biological rep1 Olanzapine vs. Saline rat pfc Whole blood from a patient with progressive supranuclear palsy Source GEO sample is GSM153426 Last updated (according to GEO): Jan 11 2007 B6:21-3 spinal cord 24 0 human prostate PC3 tumors 727 721 spleens RNA3 Exp1 TSA treated B2-2 on NCI-7.6k 1000 Alzheimer's Disease Macrophage smi124 Epithelium of bronchus 983 no additional Source GEO sample is GSM199257 Last updated (according to GEO): Jun 08 2007 861 Cerebral cortex Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15748 Last updated (according to GEO): May 28 2005 Small Intestine; d1 small intestine Keywords = mouse gene expression database Source GEO sample is GSM29294 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM176132 Last updated (according to GEO): Apr 09 2007 9 0 Blood Test P21 cochlear nuclei 0 18 Small cell carcinoma of lung 901 nmda5 (Experiment Neuroprotection4- Run 21823) Treatment, type=timepoint, description=Same sample used for Experiment Neuroprotection4-Run 14985, samples were rerun due to oven failure, measurement=0.0 h Source GEO sample is GSM96697 Last updated (according to GEO): Feb 14 2006 Spleen 0 5 861 Heart Blastocyst replication 3 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3343 Last updated (according to GEO): Mar 21 2006 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM80003 Last updated (according to GEO): Oct 26 2005 GSE8150 GBM Treatment, type=remove Source GEO sample is GSM99446 Last updated (according to GEO): Apr 21 2006 BL-C4 on NHGRI-6.5k_b from lateral geniculate nucleus 12 42 Chronic leukemia NOS 853 A/J Olfactory Bulb F at the Human Brain 745 762 Effects of SOCS3 on transcriptional response of macrophages to IL-6. Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Replicate 3 after stimulation for 400 minutes with 10 ng/ml IL-6. Source GEO sample is GSM6085 Last updated (according to GEO): Mar 17 2006 with autism spectrum disorder 37 65 A2780_oxa_IC90_6h_2 Array representing the response of Human foreskin fibroblasts at 30 min post HCMV infection Source GEO sample is GSM10357 Last updated (according to GEO): May 27 2005 Temporal expression profiling was utilized to define transcriptional regulatory pathways in vivo in a mouse muscle regeneration model. Potential downstream targets of MyoD were identified by temporal expression, promoter data base mining, and gel shift assays; Slug and calpain 6 were identified as novel MyoD targets. Slug, a member of the snail/slug family of zinc finger transcriptional repressors critical for mesoderm/ectoderm development, was further shown to be a downstream target by using promoter/reporter constructs and demonstration of defective muscle regeneration in Slug null mice. 861 Cornea 861 Fissure 861 Pancreas 1000 Hippocampus 126 107 in rat neuroblastoma Testis 861 Gene expression data from postmorten brain regions Source GEO sample is GSM144992 Last updated (according to GEO): Nov 20 2006 Expression profiling of moderately injured raphe at 4h in rats Source GEO sample is GSM41614 Last updated (according to GEO): May 27 2005 SJL/J_male_hypothalamus Source GEO sample is GSM184218 Last updated (according to GEO): Apr 26 2007 615 602 resident glia DLCL-0032 || lc8n110 Brain 861 Expression profiling of spinal cord section (T9) extracted from rats 12h following moderate injury Source GEO sample is GSM31518 Last updated (according to GEO): May 27 2005 Sample Type: human total RNA Sample User: dpatel Experiment User: dpatel Algorithm: Statistical Corner+ Avg:354, Count:32 Corner- Avg:32797, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:6.210512,SFGene:All Background:Avg:294.21,Stdev:4.75,Max:307.6,Min:284.7 Noise:Avg:7.86,Stdev:0.23,Max:8.5,Min:7.2 RawQ:12.32 Keywords = ALL Source GEO sample is GSM3467 Last updated (according to GEO): May 27 2005 Co 3 (Experiment Nic 15 - Run 23145) Treatment, type=timepoint, measurement=0.0 m Source GEO sample is GSM96705 Last updated (according to GEO): Feb 14 2006 1414 1382 of a systemic autoimmune disease 88 68 with bicuspid valves /Ovary 17 Disease 11 27 D_U133Plus_1_DLPFC_R 1000 Skeletal muscle structure Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11313 Last updated (according to GEO): May 28 2005 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28826 Last updated (according to GEO): May 27 2005 453 434 The descending colon Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2664.gif Source GEO sample is GSM72135 Last updated (according to GEO): Sep 22 2006 CNS-SpinalCmod-Adult-7d-1C-s2 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68131 Last updated (according to GEO): Jul 07 2006 1000 Neoplasm 861 Dislocations DCIS183 on harvard-12k HeLa CD4+ cells were transfected with an epitope-tagged eTat plasmid and selected with hygromycin. Cells were treated with hydroxyurea and collected @0 hours. Source GEO sample is GSM8695 Last updated (according to GEO): May 27 2005 Parkinson Disease 1000 1000 Mammary gland 861 Blood 239 233 Retinas Sensitized on days 0 and 3 with ragweed pollen protein and alum, challenged intratrecheally on days 10 and 17 with ragweed pollen protein and sacrificed after 72h. Lot batch = Source GEO sample is GSM1271 Last updated (according to GEO): May 28 2005 861 Eye Cerebral cortex 861 10 week mutant OMN rep 2 Communicable Diseases 861 CNS-RM_Mod24h-4C-s2 020102_HF_289FL GC (HKG10N) 901 Caudate nucleus structure Fibroblasts 861 DLBC58 on Affymetrix GeneChip Human Full Length Array HuGeneFL Unfertilized egg replication 3 Skeletal bone 861 2500 mg/kg X 6 hr Source GEO sample is GSM129835 Last updated (according to GEO): Sep 18 2007 Chronic Obstructive Airway Disease 1000 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228598 Last updated (according to GEO): Sep 11 2007 long access to cocaine, nucleus accumbens, 6 hrs/day access to cocaine Source GEO sample is GSM93821 Last updated (according to GEO): Jan 26 2006 09_0001_SepticShock_Day3_77 V5-P043 BALB/cByJ_male_hypothalamus 154 133 autonomic motoneurons Brain 1000 NHF3-hTERT_1.5Gy_2h_C5_21397 AdrenalCortex Source GEO sample is GSM18836 Last updated (according to GEO): Sep 25 2006 gfp pos. sorted cells from 3 disected e14.5 ganglionic eminences Treatment, type=wait Source GEO sample is GSM135783 Last updated (according to GEO): Sep 12 2006 Gene expression profiling of circulating plasma RNA is a valuable tool to detect cancer and a potential clinical instrument to study tumor progression and therapy responsiveness. In this study, differential gene expression analysis was used to identify genes specifically increased in cancer patients. Last Updated (by provider): Jun 06 2006 GM12707 in bronchial epithelia 311 332 NFIA E18WT2 1000 Liver 861 Glioblastoma Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202675 Last updated (according to GEO): Jun 20 2007 2_hypothalamus_12hrs_sleep_#99 PGA_MI_nilv_4h_391 cerebellum_10 Source GEO sample is GSM80639 Last updated (according to GEO): Mar 31 2006 HeLa CD4+ cells were transfected with an epitope-tagged eTat plasmid and selected with hygromycin. Cells were treated with hydroxyurea and collected @0 hours. Source GEO sample is GSM8694 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T9) extracted from rats 48h following laminectomy (sham) Source GEO sample is GSM31260 Last updated (according to GEO): May 27 2005 861 Cerebellum 14 days hindlimb suspended, 1 day reloaded RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis. Source GEO sample is GSM10059 Last updated (according to GEO): May 28 2005 B361 on Affymetrix GeneChip Human Full Length Array HuGeneFL brain, Entorhinal Cortex: Sample3_e1_le1 861 Heart failure 20 0 hypothalamus sprague2 brain 0 5 hc3 between the LAD artery 266 287 Brain 861 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM80014 Last updated (according to GEO): Oct 26 2005 #4 (isolate 55 rich media VEGF-A 24hours) in several common carcinomas 1286 1314 660 mesenchymal stem cell 639 from colonic normal mucosa 21 47 861 Brain brain, cerebral cortex: Co5_le1 from rat hippocampus 14 33 cortex Source GEO sample is GSM38979 Last updated (according to GEO): May 27 2005 Bone structure of tibia 1000 Human Sural Nerve Schwann Cell Donor 317 Passage 1 Treatment, type=add, description=growth factors heregulin and forskolin added Source GEO sample is GSM92232 Last updated (according to GEO): Jan 13 2006 from colonic normal mucosa 21 47 1000 Asthma MGMH030311010Bdigits Primary Neoplasm 1000 861 Cerebral cortex Oi2: Hippocampus_5T-Y_rep6 1037 of transitional epithelium 1012 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs//7302.gif Source GEO sample is GSM79711 Last updated (according to GEO): Sep 22 2006 VDXKIU_87A79 Gene expression data from human prostate tissue with 90 percent tumor content Source GEO sample is GSM119308 Last updated (according to GEO): Feb 23 2007 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213507 Last updated (according to GEO): Jul 31 2007 330 324 uterus brain, hippocampus: PR-CA1-A3_e1_le1 861 Cerebral cortex Primary tumor 19 32 15 0 human cerebellum Brain_nAChRbeta4SubunitDeficent_MiceNob4365 Synapses 1000 AD-275t1-A95-3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Brain 1000 Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 1550 left_liver_lobe 1000 Spinal Cord of the colon 28 39 Control, 00.00 hr. T-Cell Skeletal bone 861 NCI60.7_LABEL10EXTRACT9SUB3 Source GEO sample is GSM134029 Last updated (according to GEO): Aug 06 2007 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198634 Last updated (according to GEO): Jun 06 2007 928 Endometrium GC (HKG40T) 7 Entorhinal Cortex 23 Bone Marrow 1000 Voxel E2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1416 Last updated (according to GEO): Nov 21 2005 476 453 oligodendroglial tumors Category: Tissue Rejection Subcategory: Kidney UTI/Pyelonephritis also Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=690660 LaserPower=2.121.29 Lot batch = LC17N112 Source GEO sample is GSM4830 Last updated (according to GEO): Nov 21 2005 Nose 1000 brain, cerebellum: RNA #1_le1 1037 of transitional epithelium 1012 Assay of baseline expression in the cerebellum of an alcohol-naive Inbred Short Sleep mouse Source GEO sample is GSM67193 Last updated (according to GEO): Oct 28 2005 with some respiratory epithelium. 1039 1072 Sample 2 at Time 2 Source GEO sample is GSM113088 Last updated (according to GEO): Jun 06 2006 Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35388 Last updated (according to GEO): May 27 2005 2 Retina 13 20 Normal epithelial cells were removed by dissection and digestion from bronchi of donor long tissue from normal subject. Source GEO sample is GSM3916 Last updated (according to GEO): May 27 2005 PGA-Band_8w_1-m5 Heart 1000 Whole Brain 62 72 Brain 861 none Source GEO sample is GSM149627 Last updated (according to GEO): Jan 03 2007 MGJZ030228005Abone Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:351, Count:32 Corner- Avg:36252, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:10.785266,SFGene:All Background:Avg:323.88,Stdev:5.02,Max:340.4,Min:313.2 Noise:Avg:7.64,Stdev:0.27,Max:8.6,Min:7.0 RawQ:11.43 Keywords = ALL Source GEO sample is GSM3480 Last updated (according to GEO): May 27 2005 63 50 Striatum C57BL Cortex Treatment, type=pharmacogenomic_treatment, description=Handled (no stress) control Source GEO sample is GSM53315 Last updated (according to GEO): Jul 06 2005 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc134 Source GEO sample is GSM1858 Last updated (according to GEO): Nov 21 2005 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225764 Last updated (according to GEO): Nov 02 2007 Synovial Membrane 11 Disease Medulla 861 20 0 human caudate nucleus adipose_tissue_omental_2 Parkinson Disease 861 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:318, Count:32 Corner- Avg:40188, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:5.120892,SFGene:All Background:Avg:521.89,Stdev:28.41,Max:587.8,Min:478.3 Noise:Avg:9.78,Stdev:0.69,Max:11.9,Min:8.4 RawQ:14.30 Keywords = ALL Source GEO sample is GSM3441 Last updated (according to GEO): May 27 2005 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211385 Last updated (according to GEO): Jul 18 2007 Normal and diseased human tissues were profiled for gene expression using the Affymetrix U133 plus 2.0 array In total 677 samples were processed , representing over 90 distinct tissue types Some tissue samples were purchased from Stratagene (SG), Ambion (AB), and Becton-Dickinson (BD) Last Updated (by provider): Apr 09 2007 Contributers: Richard Roth brain, cochlea: [1] Sample #1_le1 Lung_6wk_FVB_Female 861 Malignant Neoplasms Control rats 1h after injection with PBS Treatment, type=time_course, description=Control animals are treated with PBS, measurement=1.0 h Source GEO sample is GSM32070 Last updated (according to GEO): May 27 2005 GSE6503 861 medulloblastoma 861 Cerebral cortex 1000 Brain Adipocytes 861 Pressure-overload induced hypertrophy model. Mouse was sacrificed 1 week after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2261 Last updated (according to GEO): May 27 2005 2062 2043 in sporadic cancers 1000 Leukemia, Myelocytic, Acute processed in batch 5 Source GEO sample is GSM90410 Last updated (according to GEO): Mar 20 2006 CNS-SpinalC-30mAdult-5A-s2 861 Cerebral cortex CAMA_1_Untreated_10% Untreated Control 12weeks AffyGC RMA rep5 cardiac 763 769 brain 0 5 861 Muscle M7TW00121851 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184721 Last updated (according to GEO): Apr 26 2007 from mouse brain 20 35 913 Coronary heart disease 52 8 in docetaxel-refractory prostate cancer_docet Heart 1000 10 0 Normal Skin 1000 Brain 43 0 Chorionic mesoderm-derived mesenchymal cells Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9974.gif Source GEO sample is GSM79832 Last updated (according to GEO): Sep 22 2006 of Parkinson's disease 450 471 BALB/c_OVA Replicate 2 Trigeminal_Ganglion Source GEO sample is GSM19006 Last updated (according to GEO): Sep 25 2006 901 Coronary artery SUDHL5 || lc4b040 Plasma 861 5 0 brain Heart 861 Blastocyst replication 4 Keywords = preimplantation Keywords = development Source GEO sample is GSM14694 Last updated (according to GEO): May 28 2005 339 298 from primary conjunctival epithelial cells Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28771 Last updated (according to GEO): May 27 2005 Arteries 861 1000 Brain 913 Coronary heart disease B6 day 1, biological rep 4, tech rep 2 Richard Almon-5-1133800608870 Mesenchymal Stem Cells 1000 Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 72h. Lot batch = Source GEO sample is GSM1251 Last updated (according to GEO): May 28 2005 fetal lung fibroblast #1, serum starved 1000 Amygdaloid structure 1000 Cerebral cortex ALL-B-cell-24 on Affymetrix GeneChip Human Full Length Array HuGeneFL VDXRHU_1919 1000 adenoma infection 436 445 14 NT C4 Treatment, type=add, description=10ng/mL Ciliary neurotrophiic factor, 4d Source GEO sample is GSM92493 Last updated (according to GEO): Jan 13 2006 Skeletal bone 861 Female 66.6 yr before antibody enrichment scan 1 (U133B) 861 Lung Epithelium 861 Pituitary Gland 861 C57BL/6J SAL, Rep3 of coronary artery disease 258 284 C57BL10 EDL sample 2 Hypothalamic structure 861 861 Blood Brain 1000 51 25 that pluripotent stem cells the blood 393 402 861 Lung 0 Human Cortex 11 Plasma 861 861 Blood 2.5 mg/kg 2CdA headfold at 3.0h post infection 36 49 Wild type P46 (dark reared to P42) mouse visual cortex ipsilateral to monocular enucleation Source GEO sample is GSM97225 Last updated (according to GEO): Feb 17 2006 of caudal 93 101 Gene expression data from aldosterone-producing adenoma Source GEO sample is GSM211453 Last updated (according to GEO): Jul 18 2007 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201257 Last updated (according to GEO): Jun 14 2007 1000 Hippocampus Transitional epithelium 1000 Disease Source GEO sample is GSM176375 Last updated (according to GEO): Apr 09 2007 19 0 human frontal cortex D_U133Plus_37_DLPFC +_10444_batch1 on NHGRI-6.7k Myocardium 861 D_U133A_15_nAcc 1000 Neoplasm 5 0 Spleen with Parkinson's disease 27 50 7650 on TGRI-6.5k Normal Source GEO sample is GSM176322 Last updated (according to GEO): Apr 09 2007 Epithelium 861 no additional Source GEO sample is GSM199196 Last updated (according to GEO): Jun 08 2007 This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques P. Tremblay (jacques-p.tremblay@crchul.ulaval.ca; 2705 boulevard Laurier) for analysis. Stembase Experiment ID: E205 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205 SCGP Sample ID: S269 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205#SAMPLE_246 Short description: Adult mouse muscle was enzymatically dissociated. Muscle derived stem cells proliferate unattached, in spheres, in the proliferation medium. Analysis requested: mouse genechips RNA concentration: 0.336ug/uL Sample volume: 14uL total Source GEO sample is GSM93608 Last updated (according to GEO): Jan 23 2006 Brain 1000 TEL-AML1-C12 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A nostrils 156 164 1000 Cerebral cortex Richard Almon-46-1133800610182 Spleen 0 5 NeverSmoker 46 GSE758 in the cerebral cortex 522 543 PBMCs-Type 1 Diabetes-IDDM52_T1D_4MO D_U133Plus_55_HC 2525 CP6_32 Myocardium 861 LiverAdult_022TACHH.txt 319-00MT2_Adeno Plasma 861 1000 Solid tumor NCI60.51_LABEL55EXTRACT54SUB3 Source GEO sample is GSM134251 Last updated (according to GEO): Aug 06 2007 Mental disorders 901 muscle weakness 1501 1516 Liver 1000 kidney 37 43 1000 Retina 091220 OVR15 on Affymetrix GeneChip Human Full Length Array HuGeneFL 861 Neoplasm Primary Neoplasm 1000 heart 1169 1173 Parkinson's model voxel D1 Rostral #1 Wild type 8 wk old male A/J mouse cingulate cortex Source GEO sample is GSM74945 Last updated (according to GEO): Feb 27 2007 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201270 Last updated (according to GEO): Jun 14 2007 PHA, 00.00 hr. T-Cell, Repeat. D_U133Plus_61_CB in adenocarcinoma 29 45 Muscle Source GEO sample is GSM4268 Last updated (according to GEO): May 27 2005 Skeletal bone 861 C57BL/6J female number 3, DNFB-treated allergic ear (#6_Wt-Tr-7) 6 (cerebral cortex 21 Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14341.gif Source GEO sample is GSM79694 Last updated (according to GEO): Sep 22 2006 na Source GEO sample is GSM181268 Last updated (according to GEO): Apr 10 2007 861 Blood Brain (cerebral cortex) [JunctionChip 2 of 5] Epithelium 865 Primary Neoplasm 1000 MuscleRegen-ctx7.5d-1LLAv2-s2 f2#272 versus pool Mouse Brain tissue Spleen vs Tumor necrosis factor-alpha Treated B cell 120min (set1) kidney 37 43 prostate Source GEO sample is GSM203286 Last updated (according to GEO): Jun 21 2007 7 0 prostate Communicable Diseases 1000 Mislabeled (was labeled Heart (interventricular septum)) [JunctionChip 4 of 5] Cultured_osteoblast-like_control_MC3T3-E1_cells_rep2 HUVEC isolate 9 low serum media control for #14 Source GEO sample is GSM12906 Last updated (according to GEO): May 28 2005 Spleen 1000 Inflammatory myopathy specimen GEIM16 567 548 the descending colon of the postmortem brains 676 700 1000 Cerebrovascular accident NA18970 lung_3 Source GEO sample is GSM80707 Last updated (according to GEO): Mar 31 2006 Brain 1000 WHOLEBLOOD Source GEO sample is GSM18868 Last updated (according to GEO): Sep 25 2006 86 FC BA9 A 1000 Coronary Arteriosclerosis 21 0 Mammary Gland @ Preg3 with mental retardation 241 263 861 Neoplasm 861 frontal lobe of a colorectal adenoma 7 29 brain 0 5 Malignant Neoplasms 1000 AD-363t1-A283-10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 988 980 cerebella of parieto-occipital cortex 229 256 1000 Amygdaloid structure Mesenchymal Stem Cells 1000 jazaeri-breast Expression profiling of somatomotor cortex extracted from rats at 72h following sham surgery Source GEO sample is GSM41665 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM176058 Last updated (according to GEO): Apr 09 2007 861 Cerebral cortex 191 181 of ischemia at the Human Brain 743 760 liver_PPARa-knockout_WY14643_6h_rep5 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68348 Last updated (according to GEO): Jul 07 2006 Colorectal cancer patient SC15_vs_Pool 43 0 Chorionic mesoderm-derived mesenchymal cells HapMap JPT Male Source GEO sample is GSM159644 Last updated (according to GEO): Feb 01 2007 Subject code A19 Heart 1000 1000 Prostate of parieto-occipital cortex 226 253 861 Infection This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195292 Last updated (according to GEO): Sep 13 2007 Normal__Breast_BR_4 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A of regenerating Dorsal Root Ganglia 21 55 Communicable Diseases 1000 plasma cells 50 61 Brain_MD_53_Medulloblastoma_Desmoplastic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL T47D_Untreated_10% 1000 Descending colon lateral hypothalamus no access to cocaine replicate 1 M_U133A_49_HC 1000 Coronary Arteriosclerosis Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P18, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3219 Last updated (according to GEO): May 28 2005 by ALS 47 52 Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for twelve weeks. Source GEO sample is GSM148658 Last updated (according to GEO): Dec 12 2006 between the LAD artery 266 287 901 Bone Marrow Alzheimer's Disease 1000 Starvation 916 Laser capture lung cancer cells Source GEO sample is GSM191055 Last updated (according to GEO): May 25 2007 913 Acute leukemia Brain 861 Coronary artery 901 Gene expression patterns of testicular seminoma were analysed applying oligonucleotide microarrays in 40 specimens of different tumour stages (pT1, pT2, pT3) and in 3 normal testes. Last Updated (by provider): Jul 31 2007 Contributers: Isabella Gashaw Ludger Klein-Hitpass Elke Winterhager Spleen 1000 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113973 Last updated (according to GEO): Jun 16 2006 Epithelium 861 Mesenchymal Stem Cells 1000 BALB-cByJ_male_hypothalamus Source GEO sample is GSM138577 Last updated (according to GEO): Apr 18 2007 brain, hippocampus: Ctr-72h-P15-I_e1_le1 302 288 8 uterine horns 1000 Trachea Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68040.gif Source GEO sample is GSM137415 Last updated (according to GEO): Sep 26 2006 5 0 brain hippocampus 7 17 M_U133A_26_nAcc 5_hypothalamus_time_0_#131 M_U133A_18_AnCg 861 Immune system Expression profiling of somatomotor cortex extracted from rats at 4h following sham surgery Source GEO sample is GSM41659 Last updated (according to GEO): May 27 2005 SN:1007096 Source GEO sample is GSM115371 Last updated (according to GEO): Jun 20 2006 none Source GEO sample is GSM210336 Last updated (according to GEO): Jul 16 2007 brain, cerebral cortex: Rat_03-48_NroLep_Lipska_e1_le1 NB4+ATRA osteoblast 627 637 0029_1485_H95A2_T96-136_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Communicable Diseases brain 0 5 0.1hr Hela Double Thymidine 75 CB A Gene expression data from postmorten brain regions Source GEO sample is GSM145568 Last updated (according to GEO): Nov 20 2006 plasma cells 50 61 12 0 ovarian tumor 5 0 brain 24 0 human prostate PC3 tumors of somatomotor cortex 21 41 cortex 7 12 Semeralul_PFC_Development_Week5_Batch1_Animal_2 umbilical cord; E18 embryos Source GEO sample is GSM18656 Last updated (according to GEO): May 27 2005 brain, cerebral cortex: Control 3_le1 48 44 Lungs Neoplasm 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145767 Last updated (according to GEO): Nov 20 2006 24 19 (Brain HC69 CN B 46 8 in docetaxel-refractory prostate cancer human cerebellum Source GEO sample is GSM87128 Last updated (according to GEO): Feb 08 2006 913 Fetal Diseases Melanoma xenograft, MC1_Sub_A (LeiATCC) Whole Brain 73 83 PMN_control_0min_Patient11 Expression profiling of spinal cord section (T9) extracted from rats 7d following moderate injury Source GEO sample is GSM31585 Last updated (according to GEO): May 27 2005 901 Prostate carcinoma Gene expression data from postmorten brain regions Source GEO sample is GSM145318 Last updated (according to GEO): Nov 20 2006 mild cognitive impairment - hippocampus 1 1hr S-CA1 DBA/2J Basal Ganglia A prostate Source GEO sample is GSM203377 Last updated (according to GEO): Jun 21 2007 1000 Descending colon 43 29 from the kidney cardiac 746 752 Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. Moderate controlled cortical impact with pneumatic impactor, 6 m/s impact velocity and 1.5 mm deformation. 8h after surgery, a 4 mm diameter disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44487 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM146034 Last updated (according to GEO): Nov 20 2006 90 81 in stroke Normal Source GEO sample is GSM176394 Last updated (according to GEO): Apr 09 2007 1500 mg/kg X 24 hr Source GEO sample is GSM129889 Last updated (according to GEO): Sep 18 2007 Primary Neoplasm 1000 1000 Brain Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 8897 left_liver_lobe Classification of Antipsychotic Drugs by Gene Expression in the Frontal Cortex of Mice AO Treatment, type=remove Source GEO sample is GSM99511 Last updated (according to GEO): Apr 21 2006 snout epidermis; vibrissa epidermal region Source GEO sample is GSM18645 Last updated (according to GEO): May 27 2005 V5-P276 B cell chronic lymphocytic leukemia 34 68 MLL_18 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Plasma 861 gene expression of 1 day RA differentiated ESCs Source GEO sample is GSM181963 Last updated (according to GEO): Apr 12 2007 Aortic Aneurysm 901 large-cell carcinoma 1260 1280 M_U133A_75_nAcc mouse left hemi-diaphragm 0 24 901 Coronary artery Primary Carcinoma 876 S3_IL6_2 TK-10 hgu95e Chronic inflammation during placental malaria (PM) is most frequent in first time mothers and is associated with poor maternal and fetal outcomes. In the first genome-wide analysis of the local human response to sequestered malaria parasites, we identified genes associated with chronic PM and then localized the corresponding proteins and immune cell subsets in placental cryosections. B cell-related genes were among the most highly up-regulated transcripts in inflamed tissue. The B cell chemoattractant CXCL13 was up-regulated >1,000-fold, and B cell-activating factor was also detected. Both proteins were expressed by intervillous macrophages. Ig L and H chain transcription increased significantly, and heavy depositions of IgG3 and IgM were observed in intervillous spaces. The B cell phenotype was heterogenous, including naive (CD27-negative), mature (CD138-positive), and cycling (Ki-67-positive) cells. B cells expressed T-bet but not Bcl-6, suggesting T cell-independent activation without germinal center formation. Genes for the Fc binding proteins FcgammaRIa, FcgammaRIIIa, and C1q were highly up-regulated, and the proteins localized to intervillous macrophages. Birth weight was inversely correlated with transcript levels of CXCL13, IgG H chain, and IgM H chain. The iron regulatory peptide hepcidin was also expressed but was not associated with maternal anemia. The results suggest that B cells and macrophages contribute to chronic PM in a process resembling lymphoid neogenesis. We propose a model where the production of Ig during chronic malaria may enhance inflammation by attracting and activating macrophages that, in turn, recruit B cells to further produce Ig in the intervillous spaces. 5 0 brain n/a Source GEO sample is GSM177943 Last updated (according to GEO): Jun 11 2007 660 mesenchymal stem cell 639 VDXIGRU_246381 C57BL10 quadriceps sample 2 NHF1-hTERT_M_C5_16180 861 Anterior Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228645 Last updated (according to GEO): Sep 11 2007 Olfactory Epithelium 1000 GBM Treatment, type=remove Source GEO sample is GSM99456 Last updated (according to GEO): Apr 21 2006 brain, hippocampus: KA-240h-P15-III_e1_le1 Brain 1000 Pool of 10 cochlear tissues at E10.5 Source GEO sample is GSM182570 Last updated (according to GEO): Aug 14 2007 RNA of Kidney was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 biological replicates were analyzed. Keywords = db/m mice Keywords = kidney Source GEO sample is GSM9920 Last updated (according to GEO): May 27 2005 125 103 of early osteoarthritis 1000 Communicable Diseases DLCL-0033 1000 leukemia mouse hippocampus 0 16 1000 Coronary Arteriosclerosis Acetaminophen 24hr Rat 9537 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool CNS-SCsev_InjA28d-2B-s2b between the LAD artery 266 287 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160200 Last updated (according to GEO): Feb 08 2007 in cerebellum 564 576 32 CB A To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132978 Last updated (according to GEO): Sep 12 2006 453 434 The descending colon Sph 2, chip MOE430A 901 frontal lobe 1000 Cerebral cortex Female 65.9 yr before antibody enrichment scan 1 (U133B) Met. Colon Cancer (SF10) Cochlea 0 6 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11526 Last updated (according to GEO): May 28 2005 Thalamus Subthalamic Nucleus 3 Normal Gene expression data from postmorten brain regions Source GEO sample is GSM145283 Last updated (according to GEO): Nov 20 2006 hrs nasal epithelium 1126 1146 of coronary artery disease 317 342 17 7 hippocampus Expression profiling of spinal cord section (T9) extracted from rats 4h following laminectomy (sham) Source GEO sample is GSM31270 Last updated (according to GEO): May 27 2005 Nasal Epithelium 865 335 325 The jejunum TestiLeydigCell Source GEO sample is GSM18984 Last updated (according to GEO): Sep 25 2006 Myocardial Infarction 1000 Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7472 Last updated (according to GEO): May 27 2005 TS21 sample 1 (heart) Probeset expression data from NA12740 growth 3 Source GEO sample is GSM201525 Last updated (according to GEO): Aug 08 2007 Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2673.gif Source GEO sample is GSM72169 Last updated (according to GEO): Sep 22 2006 Expression profiling of spinal cord section (T9) extracted from rats 24h following severe injury Lot batch = Source GEO sample is GSM7568 Last updated (according to GEO): May 28 2005 152 117 Keywords = congenital heart disease Motor neurons obtained from a SOD1 mutant mouse by laser capture microdissection. Source GEO sample is GSM113720 Last updated (according to GEO): Jun 09 2006 Olfactory Epithelium 1000 884 Intestinal Diseases Nasal Epithelium 865 cerebellum Source GEO sample is GSM18606 Last updated (according to GEO): May 27 2005 24 7 Right Frontal Lobe T25__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Kidney yeoh-leukemia Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b102 Source GEO sample is GSM1986 Last updated (according to GEO): Nov 21 2005 Myocardial Infarction 1000 123 102 of lepromatous leprosy PGA-Band_Sham_8w_5-m5 Cochlear Nerve 1000 Blood 1000 55 37 in prostate cancer CNS-SC_InjB4h-2B-s2 Plasma 861 olfactory bulb Source GEO sample is GSM18605 Last updated (according to GEO): May 27 2005 of infected skin 33 48 Infection 1000 315-99_SCLC E10.5 craniofacial tissue, first branchial arch: KO_MXA-2_e1_le1 nipple_cross-section_1 Source GEO sample is GSM80740 Last updated (according to GEO): Mar 31 2006 cerebellum 7 16 1000 Hippocampus M7TW00121823 A/J hippocampus rep2 Central Nervous System 86 108 Tacrine 2.7mg/kg/day from 5 weeks Moclobemide 10mg/kg/day Creatine 1%w/v added to wet mash Lot batch = 5197 Source GEO sample is GSM13360 Last updated (according to GEO): May 28 2005 861 Nicotinic Receptors saphenous_vein_2 Source GEO sample is GSM80788 Last updated (according to GEO): Mar 31 2006 Spleen vs TGF-beta (transforming growth factor-beta) Treated B cell 30min (set3) 5 0 brain Bone Marrow 1000 of mouse brain 9 23 Heart Septal Defects, Atrial 1000 brainstem 7 15 "20 hr Hela Double Thymidine, exp3" 11 0 Hypothalamus brain, hindbrain and spinal cord: P0KO3_e1_le1 Muscular Dystrophy, Duchenne 1000 923 Organ of Corti gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134614 Last updated (according to GEO): Jul 09 2007 gfp pos. sorted cells from 3 disected e14.5 cortecies Treatment, type=wait Source GEO sample is GSM135773 Last updated (according to GEO): Sep 12 2006 861 Lumbar Region U251(2)_CL12009_CNS on Affymetrix GeneChip Human Full Length Array HuGeneFL Spleen 1000 at the Human Brain 726 743 e_M45B 39 21 from mammary glands Keywords = kidney 149 166 1000 Amygdaloid structure Collagen 1000 1593 1565 of medulloblastoma metastasis Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225662 Last updated (according to GEO): Nov 02 2007 FNH (SF33) Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3278 Last updated (according to GEO): Mar 17 2006 Lymphoblastoid Cell Line for Individual 8016.4 log phase brain, hindbrain and spinal cord: N1 cDNA Heart Septal Defects, Atrial 1000 GSE446 673 659 by decapitation 1000 Brain SN:1006728 Source GEO sample is GSM115353 Last updated (according to GEO): Jun 20 2006 of 1919 tumor 24 36 1000 Cerebral cortex Normal human tissue:Normal Ovary Keywords = Human, Normal Tissue, Normal Ovary Source GEO sample is GSM44674 Last updated (according to GEO): May 27 2005 Gene expression data from hippocampus of one young SAMR1TA mouse Source GEO sample is GSM143759 Last updated (according to GEO): Jan 24 2007 5 0 brain no additional Source GEO sample is GSM199167 Last updated (according to GEO): Jun 08 2007 861 Blood Muscle 1000 Brain 1000 Standard Affymetrix Protocol Source GEO sample is GSM15859 Last updated (according to GEO): May 28 2005 f2#77 versus pool Mouse Brain tissue R7N 1 to the nose 599 609 24 skeletal muscle 10 this sample is from a 16-week-old male normal mouse gastrocnemius muscle Source GEO sample is GSM4372 Last updated (according to GEO): May 28 2005 0 Frontal Cortex 13 brain, hippocampus: PR-CA3-A25_e1_le1 Breast Carcinoma 983 Small cell carcinoma of lung 937 Testis 1000 Normal Source GEO sample is GSM176451 Last updated (according to GEO): Apr 09 2007 Arteries 1000 352 340 encephalitis 4016 0a Seminoma 1000 707 in the motor cortex 725 Gastrointestinal Stromal Tumors 1000 5 0 brain cardiac 763 769 human melanoma metastatic cell line A375 Source GEO sample is GSM155029 Last updated (according to GEO): Jun 04 2007 /Ovary 13 Disease 11 27 861 Muscle Osteoblasts 1000 with autism spectrum disorder 37 65 Skeletal bone 861 30 19 Solid tumor Blood 1000 129S6/SvEvTac hypothalamus rep2 Mouse model of congenital heart disease in Csx/Nkx2.5 mutant embryos. Heterozygous embyronic day 9.5 mouse. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2278 Last updated (according to GEO): May 27 2005 Abdominal Aortic Aneurysm Male Pool A plasma cells 332 344 Nose 1000 18 month oculomotor nucleus rep 1 Lymph Nodes 3 Normal Normal Source GEO sample is GSM175877 Last updated (according to GEO): Apr 09 2007 Cerebral cortex 861 Parkinson Disease 861 Temporal neocortex mTLE 5 Coronary heart disease 913 15 0 human cerebellum Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132542 Last updated (according to GEO): Feb 26 2007 Normal__Colon_CR_3 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A M_U133A_17_nAcc Laser captured visceral sensory neurons. Source GEO sample is GSM63691 Last updated (according to GEO): Dec 21 2005 Multiclass cancer diagnosis using tumor gene expression signatures. Gene expressions affected by TNF alpha Source GEO sample is GSM189819 Last updated (according to GEO): May 21 2007 Parkinson Disease 861 marsh-affy-mouse-232749 with autism spectrum disorder 37 65 Voxel D3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1410 Last updated (according to GEO): Nov 21 2005 Mouse ileum 0 10 D_U133Plus_56_CB 1000 Coronary Arteriosclerosis EWS-T7 on NHGRI-6.5k_b Neoplasm 861 5 0 Muscle BC2 Mouse Liver Male 2 brain 0 5 152T Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging and comparing calorie restricted-fed 30-month-old to control-fed 30-month-old to investigate effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7461 Last updated (according to GEO): May 27 2005 Medulla Oblongata 861 Frontal Cortex Source GEO sample is GSM107899 Last updated (according to GEO): Jun 06 2006 f2#156 versus pool Mouse Brain tissue the mitochondrion 416 433 1000 Solid tumor 861 Cardiomyopathies Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17328.gif Source GEO sample is GSM91588 Last updated (according to GEO): Sep 22 2006 861 Cartilage in the mammalian nervous system 110 141 Large cell carcinoma of lung 901 Anterior nares 1000 Gene expression data from PD1 Foxo3 Null ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203845 Last updated (according to GEO): Aug 02 2007 DLCL-0030 PGA-Band_Sham_1w_6-m5 rad001 12h, biological rep3 1000 Communicable Diseases 1000 Pancreas Prosencephalon 1000 Lymphoblastoid Cell Line for Individual 8085.3 log phase CNS-SpinalCmod-Adult-24h-2C-s2 "Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers." 1000 Structure of dentate gyrus 58 41 with endometriosis 1000 Brain Stem NA Source GEO sample is GSM198898 Last updated (according to GEO): Jun 07 2007 21 adrenal medulla 7 1000 Brain 331 307 in central nervous system Gene expression data from postmorten brain regions Source GEO sample is GSM146072 Last updated (according to GEO): Nov 20 2006 1000 Uterine Fibroids Chronic contusion spinal cord injury in rats A2780_cis_IC90_2h_1 Adenovirus Infections 1000 M_U133A_13_nAcc ER negative human primary breast tumor EA02014_41293_H133A_JA-1966 C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P10 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM24816 Last updated (according to GEO): May 27 2005 WGACON-115 adenoma 861 amygdala_8 Transitional epithelium 1000 Brain 861 Control total RNA was pooled from the kidney of five normal BALB/c mice. Total RNA was extracted from the kidney of BALB/c mice injected with anti-GBM antibody for 11 day. Source GEO sample is GSM15081 Last updated (according to GEO): May 28 2005 1177 1163 with neurotoxic Hemisphere #2 GC (HKG87T) Simple annotation: FNH, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10017.gif Source GEO sample is GSM79844 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145559 Last updated (according to GEO): Nov 20 2006 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 30 minutes following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10952 Last updated (according to GEO): May 27 2005 Blood Test (Blinded) Sample Source GEO sample is GSM130007 Last updated (according to GEO): Sep 18 2007 Male 23.4 yr after antibody enrichment scan 2 (U133A) TONGUE Source GEO sample is GSM19018 Last updated (according to GEO): Sep 25 2006 36 15 from whole bone marrow 56 32 out of mouse bone marrow Acetaminophen 3hr Rat 0246 blood vs. Acetaminophen 3hr Rat Pooled Control blood 1000 Ectrodactyly 2N-6-MGU74B Study of in vitro granulocyte differentiation Source GEO sample is GSM137446 Last updated (according to GEO): Jun 06 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145907 Last updated (according to GEO): Nov 20 2006 kidney_medulla_1 Source GEO sample is GSM80731 Last updated (according to GEO): Mar 31 2006 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153374 Last updated (according to GEO): Dec 27 2006 1000 Hypothalamic structure During Measles 62 76 1000 Brain 10.0 mg/kg MeHg at 3.0h 1000 Intestines, Small 1000 Cerebrovascular accident 091234 OVR27 on Affymetrix GeneChip Human Full Length Array HuGeneFL Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231042 Last updated (according to GEO): Sep 26 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145977 Last updated (according to GEO): Nov 20 2006 NoCAD_replicate18 CNS-SC_InjA14d-4B-s2 16-2 olfactory bulbs 3 22 0 Human Cortex 11 mouse brain 478 489 GSE8057 Cervix carcinoma 1000 1000 Lipids Expression profiling of spinal cord section (T9) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM4474 Last updated (according to GEO): May 28 2005 Gene expression data from microdissected area # 3 of 2182 tumor Source GEO sample is GSM182305 Last updated (according to GEO): Apr 16 2007 Voxel I1 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1446 Last updated (according to GEO): Nov 21 2005 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5464.gif Source GEO sample is GSM93126 Last updated (according to GEO): Sep 22 2006 1000 Coronary Arteriosclerosis brain 0 5 PBMCs-Type 1 Diabetes-IDDM8_T1D_New Primary Neoplasm 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11220 Last updated (according to GEO): May 28 2005 sensorimotor cortex 404 422 /Ovary 1 Disease 11 26 1000 Hippocampus Keywords = Heart 505 521 AML_19 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Cerebral cortex Brain 1000 Parkinson Disease 1000 This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis. Stembase Experiment ID: E189 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189 SCGP Sample ID: S240 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_198 Short description: RNA isolated from primary retinal sphere cells. Estimated purity: > 90% RNA concentration: > 0.7 ug/ul Num cells for RNA prep: ~600,000 Sample volume: 5.0 ul Source GEO sample is GSM87202 Last updated (according to GEO): Jan 19 2006 PGA_PA-S_224 DLCL-0036;OCT || lc5b087 20 0 human caudate nucleus 61 50 Spinal cord brain, Right Frontal Temporal: Extract69_le2 Spleen 1000 Primary Neoplasm 1000 1000 Aorta 861 medulloblastoma Muscular Dystrophy, Duchenne 913 The sample is a part of a series describing gene expression changes during postnatal development of the small intestine Source GEO sample is GSM198879 Last updated (according to GEO): Jun 11 2007 861 Breast 861 Dislocations SN:Human Glioblastoma Biopsy 29150 1000 Hippocampus Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184758 Last updated (according to GEO): Apr 26 2007 1000 Brain Joint Tissue Synovium 2 Normal 1000 Brain OltactoryEpithelium_mutant_biolrepli1 n/a Source GEO sample is GSM177968 Last updated (according to GEO): Jun 11 2007 Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68041.gif Source GEO sample is GSM137416 Last updated (according to GEO): Sep 26 2006 Epithelium of bronchus 983 Wnt (16 h) B on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A adenocarcinoma 3863 1000 Uterus Synovial Cell Sarcoma 0 20 166-96_SCC Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203999 Last updated (according to GEO): Aug 02 2007 of Parkinson's disease 450 471 MCF7 human breast cancer cells treated with DMSO and used as a control in a 2 platform, three replicate experiment Source GEO sample is GSM188013 Last updated (according to GEO): May 11 2007 The genomic influcence of the combination of four reagents on cultured cortical neurons (9-11 DIV). Bursts of action potential firing were induced by the treatment of cultured cortical neurons with 50 ?M bicuculline (Bic) and 5 ?M 4-aminopyridine (4AP), which were significantly affected by the addition of 10 ?M MK801 and 5 ?M nifedipine (Nif). Source GEO sample is GSM144060 Last updated (according to GEO): Nov 24 2006 ovary 45 50 Voxel H2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1440 Last updated (according to GEO): Nov 21 2005 1000 Communicable Diseases Spleen vs Terbutaline Treated B cell 30min (set2) of the postmortem brains 665 689 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181138 Last updated (according to GEO): Jul 12 2007 1 of 3 replicates in treatment group Source GEO sample is GSM206049 Last updated (according to GEO): Jun 29 2007 H104 FC BA4 A 861 Muscle TUMOR 17 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Spleen vs Untreated B cell Time 0 (set2) 1000 Brain Layer 6 pyramidal neurons in cigulate cortex which project to medial dorsal thalamus. Source GEO sample is GSM63033 Last updated (according to GEO): Dec 01 2005 Cocaine Addiction 1000 Parkinson Disease 861 Spinal Cord 901 In this time course pregnant CD-1 (outbred) dams were exposed to the 2-chloro analogue of 2'-deoxyadenosine (a metabolic toxin) on 8 d.p.c. The test dose of 2.5 mg/kg 2CdA was modeled for a 5% increased risk of microphthalmia in term fetuses. Sampling intervals were anchored to the conditional biomarker (p53 protein induction) expressed in 2CdA-treated embryos between 3.0- and 4.5h post-exposure. Since p53 protein induction has been defined as a critical event in 2CdA-induced micropthalmia, these sampling intervals represent times before (3.0h), during (4.5h), and after (6.0h) this critical event. All measurements were on RNA from the embryonic headfold.. Date GSE1069 Last Updated: May 29 2005 Contributers: Kimberly R Nemeth Jeffrey H Charlap Amar V Singh Thomas B Knudsen Includes GDS631. Update date: Jul 14 2004. Dataset description GDS631: Temporal analysis of ocular teratogen 2-chloro-2'deoxyadenosine (2CdA) exposure and induction of microphthalmia (small eye syndrome). Pregnant 8 days post coitum CD-1 dams exposed to 2.5 mg/kg 2CdA, and embryonic headfold examined at 3, 4.5, and 6 hours.. CAD_replicate25 /SvEvTac mouse pituitary gland 29 58 of human cancers 38 53 331 307 in central nervous system vehicle #3 513 500 in leg muscle of coronary artery disease 258 284 MP-DX-2 Schizophrenia 1000 Liver 0 4 Blood Test (Blinded) Sample Source GEO sample is GSM129947 Last updated (according to GEO): Sep 18 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lysophosphatidic Acid for 60min Source GEO sample is GSM5652 Last updated (according to GEO): May 27 2005 none Source GEO sample is GSM149611 Last updated (according to GEO): Jan 03 2007 1000 Heart Epithelial Cells 1000 PMN_LB_360min_Patient10 Plasma 861 Small cell carcinoma of lung 867 90 81 in stroke Communicable Diseases 1000 Hippocampus 1000 7 cortex 12 E7.75_rep1 M_U133A_93_DLPFC Study of in vitro granulocyte differentiation Source GEO sample is GSM137451 Last updated (according to GEO): Jun 06 2007 Gene expression data from embryos at day 1.5. Source GEO sample is GSM176484 Last updated (according to GEO): Mar 19 2007 901 Heart failure Gene expression data from a hippocampus from mouse injected 15 mg/kg kainate Source GEO sample is GSM147421 Last updated (according to GEO): Jan 03 2007 Wild type inbred mice Source GEO sample is GSM82944 Last updated (according to GEO): Nov 10 2005 Otic vesicle at E9.5, replicate2 brain, Right Temporal Lobe: Extract81_le1 Cerebellum_nontransgenic control S25_3 months_replicate 3 Leukemia, Lymphocytic, Chronic 1000 Biopsy of a colorectal adenoma from patient #7 GBM: 76A34 #7 Sample 113 on vantveer-oligo 454 425 of the vastus lateralis muscle Spleen 1000 in follicular thyroid carcinoma 1105 1135 This is 8-week-old mouse untreated gastrocnemius muscle Source GEO sample is GSM4246 Last updated (according to GEO): May 27 2005 28 20 (cerebrum 901 Caudate nucleus structure Parkinson's disease sample x174 1000 Brain SN:1006485 Source GEO sample is GSM115343 Last updated (according to GEO): Jun 20 2006 5 0 brain Cardiac 523 530 CHIPEXP_NAME: 230_2_050531tpj_4h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Vehicle_Control TREAT_TOX_MECHANISM1: Liver_Non_Toxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0 SAMPLING_TIME: 1 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197604 Last updated (according to GEO): Jun 01 2007 Temporal Cortex Alzheimer's disease 6 brain, cerebral cortex: Sham20_e1_le1 Whole blood 0 10 Wild type 8 wk old male FVB/NJ mouse bed nucleus of the stria terminalis Source GEO sample is GSM107004 Last updated (according to GEO): Mar 05 2007 VDXKIU_282C51 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7432.gif Source GEO sample is GSM79829 Last updated (according to GEO): Sep 22 2006 861 Blood 12 0 Blood B cells Epithelium 861 pfc_1006_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A of regenerating Dorsal Root Ganglia 21 55 Sample details: Three pools of rostral (R1-3), three pools of middle (M1-3), and three pools of caudal (C1-3) E13.5 MF1 neocortex were collected from 4 embryos. All possible 18 comparisons were carried out. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. Source GEO sample is GSM62819 Last updated (according to GEO): Aug 26 2005 Coronary heart disease 913 Mouse old heart w/ a-tocopherol aT-Ht-4 1000 Coronary Arteriosclerosis CNS-SCsev_InjA14d-2C-s2 41 30 PCOS oocytes Primary tumor 19 32 853 Refractory Carcinoma Communicable Diseases 1000 Left hemidiaphragm 923 Breast 3 Disease 7 0 Amygdala of the human frontal cortex 228 254 Seminoma 1000 Control brainstem 7 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53446 Last updated (according to GEO): Jul 06 2005 Liver Test (Blinded) Sample Source GEO sample is GSM130076 Last updated (according to GEO): Sep 18 2007 19 0 human frontal cortex Kainate-neocortex, biological rep4 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Anti-IgM for 240min Source GEO sample is GSM5450 Last updated (according to GEO): May 27 2005 923 Mesenchymal Stem Cells 40 21 from skeletal muscle 1000 Cerebellum Cerebral cortex 1000 Blood Test (Blinded) Sample Source GEO sample is GSM129982 Last updated (according to GEO): Sep 18 2007 Substantia Nigra Pars Compacta 3 Disease 1000 Brain Estrogen induction of uterine wet weight provides an excellent model to investigate relationships between changes in global gene expression and well-characterized physiological responses. In this study, time course microarray GeneChip data were analyzed using a novel approach to identify temporal changes in uterine gene expression following treatment of immature ovariectomized C57BL/6 mice with 0.1 mg/kg 17alpha-ethynylestradiol. Functional gene annotation information from public databases facilitated the association of changes in gene expression with physiological outcomes, which allowed detailed mechanistic inferences to be drawn regarding cell cycle control and proliferation, transcription and translation, structural tissue remodeling, and immunologic responses. These systematic approaches confirm previously established responses, identify novel estrogen-regulated transcriptional effects, and disclose the coordinated activation of multiple modes of action that support the uterotrophic response elicited by estrogen. In particular, it was possible to elucidate the physiological significance of the dramatic induction of arginase, a classic estrogenic response, by elucidating its mechanistic relevance and delineating the role of arginine and ornithine utilization in the estrogen-stimulated induction of uterine wet weight. 1000 Brain DRG003_c 11 CN A occipital_lobe_4 Source GEO sample is GSM80775 Last updated (according to GEO): Mar 31 2006 Replicate1_Voxel F6 Abdominal aortic aneurysm 0 24 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225670 Last updated (according to GEO): Nov 02 2007 NoCAD_replicate24 747 tumor cells 757 GSE3248 1000 Solid tumor none Source GEO sample is GSM244631 Last updated (according to GEO): Nov 23 2007 1000 Parietal Lobe 858 Prostatic Neoplasms in fibroblasts 1222 1236 D_U133A_42_Amy We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201737 Last updated (according to GEO): Jun 20 2007 of prostate cancer 67 84 488 462 neurological manifestations Epithelium of bronchus 983 SN:Human Glioblastoma Biopsy 12376 458 449 infection During kidney development segmented epithelia of the nephron derive from progenitor cells in the metanephric mesenchyme after induction by secreted molecules from the ureteric bud. We have identified three distinct inductive activities from a ureteric bud cell line. These include leukemia inhibitory factor (LIF), neutrophil gelatinase-associated lipocalin (NGAL) and an active fraction currently referred to as ANX. Each of these activities induces segmented nephron epithelia in isolated rat metanephric mesenchyme over a time period of 7 days. This study was designed to characterize the temporal sequence of gene expression in the course of the conversion process induced by each of the distinct inducers. Last Updated (by provider): Dec 08 2006 Contributers: Abby Sarkar Jun Yang Kai M Schmidt-Ott Benjamin J Hirsh Xia Chen Jonathan Barasch Gene expression data from postmorten brain regions Source GEO sample is GSM145444 Last updated (according to GEO): Nov 20 2006 DND41 DMSO control 24h rep2 GSE1978 1000 Hippocampus 901 Hepatocyte Expression profiling of spinal cord section (T10) extracted from rats 4h following severe injury Source GEO sample is GSM31378 Last updated (according to GEO): May 27 2005 CH2121 for liver 26 35 Menstrual phase - Follicular Source GEO sample is GSM175777 Last updated (according to GEO): Apr 09 2007 PC 17 Treatment, type=incubate, description=Hypoxic preconditioning Source GEO sample is GSM107501 Last updated (according to GEO): May 01 2006 Whole Brain 62 72 brain 0 5 Spleen 1000 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141274 Last updated (according to GEO): Oct 26 2006 1000 Spleen Hereditary Nonpolyposis Colorectal Neoplasms 947 of insulin resistance 1708 1728 Spleen 0 5 BRCA2_s1936 on NHGRI-6.5k 12M_A31103 NB-C10 on NHGRI-6.5k_b Paravertebral Muscle 10 Disease 0 30 Lymphoblastoid Cell Line for Individual 8062.3 log phase Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles. PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity. Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence. To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips. Source GEO sample is GSM136525 Last updated (according to GEO): Jun 05 2007 Substantia Nigra Pars Compacta 5 Normal Malignant neoplasm of breast 1000 Spleen vs Neuropeptide Y Treated B cell 60min (set1) 091233 OVR26 on Affymetrix GeneChip Human Full Length Array HuGeneFL Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15564.gif Source GEO sample is GSM84155 Last updated (according to GEO): Sep 22 2006 8 uterine horns 421 435 12hr time point after 3 Gy of IR exposure Source GEO sample is GSM10970 Last updated (according to GEO): May 28 2005 Whole Brain 62 72 Spleen vs Untreated B cell 120min (set1) Brain 861 AT2-hTERT_sham_6h_C3_26742 17 6 (hippocampus from progenitor satellite cells 36 66 Isograft 70 days No.2 Myocardial Infarction 1000 Expression profiling of spinal cord section (T9) extracted from rats 28d following severe injury Source GEO sample is GSM31606 Last updated (according to GEO): May 27 2005 Aged hematopoietic stem cells, p53 mutants 0 Human Cortex 11 Simple annotation: aging, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17027.gif Source GEO sample is GSM81530 Last updated (according to GEO): Sep 22 2006 Whole brain 0 10 Nasal Epithelium 901 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134604 Last updated (according to GEO): Jul 09 2007 1000 Pituitary Gland 0 Human Cortex 11 Gene expression data from postmorten brain regions Source GEO sample is GSM145298 Last updated (according to GEO): Nov 20 2006 amygdala_4 spinal cord, spinal cord: RNA 500_e1_le1 The epithelial cells 962 981 cardiac 763 769 JMR-RatInj21d-3aA-s2 5 0 Spleen /NJ mouse pituitary gland 27 51 -_5691_batch2 on NHGRI-6.7k C_C6 of the postmortem brains 675 699 Muscle Fibers 1000 444 435 infection 27 11 /Ovary-Disease 10 861 Retina HapMap JPT Male Source GEO sample is GSM159654 Last updated (according to GEO): Feb 01 2007 Nervous system structure 861 T-cell co-stimulation GM19138_technical_rep_2 of Parkinson's disease 450 471 MO_control_180min_Patient9 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM79059 Last updated (according to GEO): Oct 24 2005 A HID B D057 gene expression of undifferentiated ESCs Source GEO sample is GSM181940 Last updated (according to GEO): Apr 12 2007 447 438 infection 901 Temporal Lobe C57 whole brain 1 1000 Hippocampus Sham 14 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107498 Last updated (according to GEO): May 01 2006 Mesenchymal stem cells 13 34 M_U133A_35_nAcc Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141318 Last updated (according to GEO): Oct 26 2006 1551 to neurodegenerative diseases 1579 Posterior root of spinal nerve 861 663 mesenchymal stem cell 642 PGA-MCR-CR-12h-1bAv2-s1 1000 Hippocampus HOXB4ERT-LSK+ cells_ 1 hour after TMX withdrawal Source GEO sample is GSM228748 Last updated (according to GEO): Sep 13 2007 Brn3a Wildtype TG e13.5 U74Av2 2 f2#170 versus pool Mouse Brain tissue Gene expression data from skeletal muscle at baseline Source GEO sample is GSM230438 Last updated (according to GEO): Sep 19 2007 between the LAD artery 266 287 umbilical cord_nobpd: 5D WGACON-154 5 0 brain 12 0 ovarian tumor 50 43 jejunum Intestines 861 861 Brain OVAR_IGROV1 on Affymetrix GeneChip Human Full Length Array HuGeneFL brain_Down_syndrome_sampleid_jg1738 brain 0 5 Leukemia, Lymphocytic, Chronic 1000 Medulla_Oblongata Source GEO sample is GSM18767 Last updated (according to GEO): Sep 25 2006 Plasma 861 f2#71 versus pool Mouse Brain tissue Spinal Cord 901 99 FC BA9 A ODG: 80A25 858 Mesodermal cell 17 7 hippocampus dorsal root ganglia 329 347 DBA/2J Acute morphine treated, striatum, biological replicate 1 Source GEO sample is GSM187986 Last updated (according to GEO): Jun 14 2007 HMVEC-L stimulated without LPS for 4 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114565 Last updated (according to GEO): Sep 20 2006 MGMH030211062Aamygdala The nose 94 101 Cerebral cortex 861 HT29 hgu95a 861 Cerebral cortex 1000 Cerebrum spinal cord 13 23 Protein complex 861 C3H/HeJ Hippocampus A from ventral prostate 21 41 MCF7 human breast cancer cells treated with 100 nM of dioxin to quantify RNA differences in a 2 platform, three replicate experiment Source GEO sample is GSM188023 Last updated (according to GEO): May 11 2007 Epithelium 861 Brain 1000 wholebrain Source GEO sample is GSM18922 Last updated (according to GEO): Sep 25 2006 HDMTX_MP-2 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2786 Source GEO sample is GSM2103 Last updated (according to GEO): Nov 21 2005 Egr3 is a zinc-finger transcription factor involved in growth and development. Egr3-deficient mice have severe sensory ataxia due to failed development of muscle spindle stretch receptors. Sensory and motor neurons that normally innervate spindles are absent in Egr3-deficient mice, presumably as a secondary consequence to the loss of trophic signals produced by spindles during development that are required for innervation and neuron survival. The molecular mechanisms involving motor neuron fate specification, target derived growth factor dependencies, and specification of target innervation have been difficult to study since select markers for functionally specific motor neurons are very poorly characterized. A more thorough understanding of the molecular mediators of motor neuron biology will be important to evaluate the efficacy of new strategies devised to thwart neuron death that occurs in a variety of human motor neuronopathies and neuropathies. To identify genes specifically expressed by spinal cord fusimotor neurons: Many motor neuron specific genes have been described over the years. However, none have been described that distinguish fusimotor neurons from skeletomotor neurons despite the fact that they have distinct muscle targets (muscle spindle stretch receptors) and comprise 25-30% of the spinal motor neuron populations. Since these motor neurons have remarkably different target innervation and function, we hypothesize that they express genes that establish their specific phenotypes during development. We hypothesize that fusimotor neurons can be distinguished in the spinal cord by characterizing fusimotor neuron specific gene expression. Once fusimotor neuron specific genes are identified, they will be used as markers to identify fusimotor neurons in complex neuroglial cell populations in vivo and in vitro. We hypothesize that by characterizing fusimotor neuron specific genes, unique marker molecules will be identified for in vivo and in vitro study of this functionally distinct and important motor neuron subtype. Moreover, we hypothesize that many of the genes that are specifically expressed by fusimotor neurons will be involved in mechanisms related to their fate specification, target innervation and growth factor dependent biology. We will use the Affymetrix microarray platform to identify genes that are specifically expressed by fusimotor neurons in mouse spinal cord. The differential expression analysis will be performed on microdissected segments of spinal cord (L3-L5) from wild type and Egr3-deficient mice. Postnatal Egr3-deficient mice lack muscle spindles and fusimotor neurons in their spinal cords. By comparing gene expression from microdissected segments of spinal cord (L3-L5) between wild type and Egr3-deficient mice, we hypothesize that fusimotor neuron selective genes can be identified. We will microdissect L3-L5 segments of spinal cord using precise anatomical landmarks to ensure that comparable spinal cord regions are anlayzed from each animal. For each microarray experiment, total RNA will be extracted from L3-L5 cords (approximately 2 mm length of spinal cord). The integrity of each RNA sample will be verified by gel electrophoresis. The intact RNA samples from mice of similar genotype will be pooled from three (3) 27-day old animals. The intact cord dissection is easier in young animals (eg: 27-day old) and the phenotype is known to exist at this developmental stage. The RNA from each animal of a similar genotype will be pooled into a single sample to minimize false positive gene calls that may represent genes related to the specific state of vigilance of a particular animal at the time of sacrifice (eg: activity dependent genes). Thus, each of the two RNA samples to be analyzed for a particular microarray experiment will represent RNA from three (3) spinal cords of each genotype. RNA amplification for probe synthesis should not be necessary since we will provide 7 ug of intact pooled total RNA for each sample. For statistical analysis, the experiment will be performed twice. Since the RNA samples are precious, they will be provided to the Array Consortium in two shipments with each of the experiments performed independently. Last Updated (by provider): May 29 2005 Contributers: Warren G Tourtellotte f2#260 versus pool Mouse Brain tissue Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28734 Last updated (according to GEO): May 27 2005 D_95Av2_3023_Cg_0_GS 1000 Cerebellum 61 45 from 12 cochleas 1000 Hypothalamic structure 901 frontal lobe subthalamic_nucleus_6 Source GEO sample is GSM80850 Last updated (according to GEO): Mar 31 2006 Normal Source GEO sample is GSM175941 Last updated (according to GEO): Apr 09 2007 28 15 of Endometrium Hippocampus VC mice 5 weeks off dox 1000 Brain Blood 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM144994 Last updated (according to GEO): Nov 20 2006 Brain 1000 Hepatocyte 913 Brain 861 rad001 12h, biological rep2 Knockout saline, biological replicate 1 bronchial epithelia 224 243 91 from the bone marrow 72 Expression profiling of spinal cord section (T8) extracted from rats 28d following severe injury Source GEO sample is GSM31482 Last updated (according to GEO): May 27 2005 M_U133A_74_nAcc 154 147 in lung Exp B, Animal #4, 0.5mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 0.5mg/kg of CPF for 96 hours Source GEO sample is GSM246152 Last updated (according to GEO): Dec 03 2007 human frontal cortex Source GEO sample is GSM87021 Last updated (according to GEO): Feb 08 2006 ISR19-Fv2E-PERK UT1, RNA from an untreated Fv2E-PERK expressing fibroblast cell line in an eIF2 alpha AA (mutant) background. The eIF2 alpha AA background was used in order to determine whether genes activated through Fv2E-PERK required eIF2alpha phosphorylation. The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules. Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10902 Last updated (according to GEO): May 28 2005 9 0 Blood Test heart failure 583 595 1000 Cerebral cortex Balb/c day 3, biological rep 2, tech rep 2 NA19193 NA18526 dorsal skin 11 21 Coronary artery 901 Epithelial Cells 901 304 280 alcoholic cardiomyopathy Lymphoblastoid Cell Line for Individual 8125.4 log phase na Source GEO sample is GSM181261 Last updated (according to GEO): Apr 10 2007 ER negative human primary breast tumor EA02014_41292_H133A_JA-1949 BAL_46_A2B0 Gene expression data from postmorten brain regions Source GEO sample is GSM145436 Last updated (according to GEO): Nov 20 2006 861 Cerebral cortex 19 0 Head and neck cancer Disease Source GEO sample is GSM175805 Last updated (according to GEO): Apr 09 2007 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8837.gif Source GEO sample is GSM76412 Last updated (according to GEO): Sep 22 2006 In pevious research we have shown that the disruption of the normal development of the ventral hippocampus in rodents leads to cellular abnormalities in the frontal cortex and behavioral deficits related to schizophenia (Neurotox Res. 2002, 4(5-6):469-475). We propose the use of gene expression analysis to investigate the molecular underpinnings of these processes which may shed light on the molecular processes relevant to human schizophrenia. In addition, we seek to characterize expression differences induced by chronic administration of antipsychotic medications, which may give insight into the molecular processes involved in ameliorating psychotic symptoms. Using both surgical and drug interventions, we aim to examine experimentally induced expression differences in the rodent brain that are relevant to human neuropsychiatric disorders. Disruption of the normal development of the vental hippocampus or chronic neuroleptic administration, will result in gene expression changes in the frontal cortex of rats. Elucidation of the molecular cascades underlying these treatments will shed light on both the pathoetiology (from the lesion experiments) and theurapeutic processes (from the antipsychotic treatment experiments) involved in human schizophrenia. We have developed 3 groups of samples: 1] Ventral hippocampal lesion in neonatal rats (treatment and controls, total N=22) 2] Tetrodotoxin disruption of the ventral hippocampus (treatment and controls, total N=20) 3] Chronic administration of neuroleptics (multiple drugs, multiple doses, and controls, total N=63) Grand Total N=105 161T TNFTG-3w-f-3 HBEC Source GEO sample is GSM18974 Last updated (according to GEO): Sep 25 2006 Day 2_L_+RA_Bchip Examining the effects of tTA expression in mouse hearts Source GEO sample is GSM15059 Last updated (according to GEO): May 28 2005 MP-8 ileum 1000 Calorie restriction, followed by ad libitum refeeding, results, respectively, in loss and regeneration of pulmonary alveoli. We now show 35% of alveoli are lost within 72 h of onset of calorie restriction ((2/3) decreased daily chow intake), and an additional 12% of alveoli are lost over a subsequent 12 days of calorie restriction. Tissue necrosis was not seen. Within 72 h of refeeding, after 15 days of calorie restriction, the number of alveoli returns to precalorie restriction values. Microarray lung gene profiling, in conjunction with Western and RNase protection assay, demonstrate an increase of granzyme and caspase gene expression 2-3 h after onset of calorie restriction. By 12 h, granzyme and caspase expression is no longer increased, but tumor necrosis factor death receptor expression is elevated. At 336 h, Fas death receptor expression is increased. Because granzymes are found only in cytotoxic lymphocytes (CTLs) and natural killer (NK) cells, we suggest calorie restriction activates these cells, initiating a series of molecular events that results in alveolar destruction. The evidence of involvement of CTLs and NK cells and the absence of necrosis are similar to alveolar destruction in chronic obstructive pulmonary disease. Anterior nares 1000 M_U133A_100_DLPFC from colonic normal mucosa 21 47 Primary tumor 19 32 Pituitary Gland 861 placebo 12h, biological rep3 Gene expression data from postmorten brain regions Source GEO sample is GSM145141 Last updated (according to GEO): Nov 20 2006 PGA-E12.5_3 Myocardial Infarction 1000 5 0 brain plasma cells 332 344 cingulate cortex 1000 of a colorectal adenoma 7 29 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=720640 LaserPower=2.161.29 Lot batch = LC17N113 Source GEO sample is GSM4831 Last updated (according to GEO): Nov 21 2005 cerebral cortex 7 21 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-beta (IFN beta) for 30min Source GEO sample is GSM5591 Last updated (according to GEO): May 27 2005 ME cells transduced with hTERT Source GEO sample is GSM5160 Last updated (according to GEO): May 27 2005 861 Cardiomyopathies rat hippocampus Treatment, type=pharmacogenomic_treatment, description=Fetal alcohol exposed Source GEO sample is GSM35873 Last updated (according to GEO): May 27 2005 plasma cells 332 344 Expression profiling of spinal cord section (T8) extracted from rats 14d following mild injury Source GEO sample is GSM31428 Last updated (according to GEO): May 27 2005 Septum Source GEO sample is GSM107948 Last updated (according to GEO): Jun 06 2006 Spleen 1000 brain, Right Parietal Occipital: Extract75_le2 Neuraxis 923 Expression profiling of somatomotor cortex extracted from rats at 3 months following sham surgery Source GEO sample is GSM41655 Last updated (according to GEO): May 27 2005 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:248, Count:32 Corner- Avg:43803, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:17.496950,SFGene:All Background:Avg:346.00,Stdev:4.31,Max:359.2,Min:337.0 Noise:Avg:9.84,Stdev:0.35,Max:10.9,Min:8.9 RawQ:14.73 Keywords = ALL Source GEO sample is GSM3498 Last updated (according to GEO): May 28 2005 318 of Down syndrome 303 none Source GEO sample is GSM239861 Last updated (according to GEO): Dec 07 2007 10 0 fibroblasts none Source GEO sample is GSM244555 Last updated (according to GEO): Nov 23 2007 Prostate 14 Disease Spleen 1000 PGA-MurLungRag-pbs-72h-1aAv2-s2 PCA-48 on UMich-10k NCI60.9_LABEL12EXTRACT11SUB3 Source GEO sample is GSM134036 Last updated (according to GEO): Aug 06 2007 brainstem 7 15 304 280 alcoholic cardiomyopathy 1000 Dermatomyositis Gene expression data from postmorten brain regions Source GEO sample is GSM145341 Last updated (according to GEO): Nov 20 2006 whole blood_101726 Cerebral cortex 1000 1000 Rectum Nidogen 1000 between the two eyes 190 209 GM18521 Control Source GEO sample is GSM176470 Last updated (according to GEO): Apr 09 2007 The orphan nuclear receptor Nurr1 has been shown to be critical for the development of ventral midbrain dopaminergic neurons. Consequently, the development of ES cells overexpressing Nurr1 has raised hope for the development of cell replacement therapies for Parkinson's Disease to replace degenerated dopaminergic neurons. However, the molecular consequences of Nurr1 on gene expression in these cells remain unknown. To address this, stable, clonal, c17.2 neural stem cell lines were established that overexpressed the orphan nuclear receptor Nurr1 (clone 42 & clone 48) or parental control cell line (puroB & puroD, respectively). Last Updated (by provider): Nov 08 2005 Contributers: Helena Mira Moriake Kusakabe Anita C Hall Kyle M Sousa Ernest Arenas Lottie J Sjostrand Expression profiling of somatomotor cortex extracted from rats at 7d following moderate injury Lot batch = Source GEO sample is GSM44719 Last updated (according to GEO): May 27 2005 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134623 Last updated (according to GEO): Jul 09 2007 27 week Pre Natal Human lung tissue Source GEO sample is GSM107826 Last updated (according to GEO): May 04 2006 AO Treatment, type=remove Source GEO sample is GSM99515 Last updated (according to GEO): Apr 21 2006 To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18424 Last updated (according to GEO): May 27 2005 Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. 1000 Spleen NCI60.1_LABEL124EXTRACT63SUB3 Source GEO sample is GSM133998 Last updated (according to GEO): Aug 06 2007 Dendritic Cells, Baseline - Repeat #2 OCI Ly10 || lc8n086 Blood 1000 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141327 Last updated (according to GEO): Oct 26 2006 861 Cerebral cortex 1000 Mammary gland human cerebellum Source GEO sample is GSM87071 Last updated (according to GEO): Feb 08 2006 for liver 26 35 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27035 Last updated (according to GEO): May 27 2005 Blood 1000 Brain 861 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11300 Last updated (according to GEO): May 28 2005 Femur 1000 Expression data after reversal of DNA methylation Source GEO sample is GSM230902 Last updated (according to GEO): Sep 20 2007 of postmortem skeletal muscle 24 53 spleen 214 220 the ventricular 1095 1109 m1-adenoma2 olfactory epithelium 194 213 Duchenne muscular dystrophy 0 26 727 721 spleens Diet Induced Obese rat C2 in fibroblasts 1222 1236 Parkinson's disease sample x149 0 30 861 Neoplasm SCG_sema3A_2h_rep2 intraabdominal adipose tissue 75 103 NO_KIDNEY_4 cy5:SHR treated w/ nifedipine, biological rep 2r; cy3:pool of 6 WKY control rats Blood Test (Blinded) Sample Source GEO sample is GSM129989 Last updated (according to GEO): Sep 18 2007 1672 1658 the hippocampus Gene expression data from postmorten brain regions Source GEO sample is GSM145562 Last updated (according to GEO): Nov 20 2006 /J Cingulate Cortex A 4 24 Blood Test (Blinded) Sample Source GEO sample is GSM130032 Last updated (according to GEO): Sep 18 2007 5 0 brain Renal Cell Carcinoma 875 Hippocampus 1000 Male 13-week-old ddY mice (Japan SLC Co., Hamamatsu, Japan) weighing 38-43 g were used. Dose of 18.75 mg/kg quetiapine fumarate (gift from AstraZeneca, Macclesfield, UK) was used in the study. The drug was dissolved in acetic anhydride and diluted with 0.9% saline, resulting in a final concentration of acetic acid of 0.5%. The drugs were injected intraperitoneally once daily for 28 consecutive days in a volume of 0.1 ml/10 g body weight. Microarray experiments were performed using an Agilent G4121A Mouse Oligo Microarray Kit as per the manufacturer?s instructions. The frontal cortex was immediately removed and the RNA was stabilized in RNAlater RNA Stabilization Reagent (Qiagen, Valencia, CA) and stored at -80°C until use. Total RNA was extracted using the RNeasy Mini Kit (Qiagen). The RNA was amplified and labeled by the Low RNA Input Fluorescent Linear Amplification Kit (Agilent). To synthesize cDNA, 200 ng total RNA was used. Vehicle-injected controls were labeled by cyanine 3 (PerkinElmer Life Sciences, Inc., Boston, MA) and drug-injected mice were labeled by cyanine 5. Hybridizations to the microarray were performed using the In situ Hybridization Kit Plus (Agilent). Doses of 750 ng cyanine 3-labeled cRNA, 750 ng cyanine 5-labeled cRNA, and control targets were mixed and fragmented in the kit?s fragmentation buffer, and then hybridized to the microarrays for 17 hours at 60°C in a hybridization rotator (Agilent) set to rotate at 4 rpm. Microarrays were washed in 6×SSC with 0.005% Triton X-102 at RT for 10 min, followed by 0.1×SSC with 0.005% Triton X-102 at 4°C for 5 min. The slides were dried, and then scanned by the Agilent G2565BA Microarray Scanner System. Data were analyzed using the Agilent Feature Extraction Software version 7.1. A rank consistency filter and LOWESS were used for dye normalization. Control mice and drug-injected mice were processed in parallel. Keywords = quetiapine Lot batch = US22502606_16011978017255 Source GEO sample is GSM25982 Last updated (according to GEO): Oct 28 2005 healthy subject Source GEO sample is GSM211074 Last updated (according to GEO): Sep 10 2007 Standard Affymetrix Protocol Source GEO sample is GSM16473 Last updated (according to GEO): May 28 2005 spinal cord, ventral spinal cord: D60WTSPMN2_e1_le1 Primary tumor 19 32 Mouse ileum 0 10 Normal__Colon_CR_8 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Cerebral cortex 861 1000 Turner's Syndrome UET-13TR-EWS/FLI1 24hr 0029_1209_H95Av2_KF0077_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A to the nose 599 609 A HID I D052 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108598 Last updated (according to GEO): Aug 22 2006 39 12 of congenital heart disease Subject code A42 160 144 of the cerebellum 8 0 lymphnode Cortex Source GEO sample is GSM53378 Last updated (according to GEO): Jul 06 2005 861 Amygdaloid structure bone marrow-CD34 Source GEO sample is GSM18885 Last updated (according to GEO): Sep 25 2006 D_U133Plus_116_DLPFC Neoplasm 861 Prefrontal Cortex 0 16 24 0 human prostate PC3 tumors HMVEC-L stimulated with LPS for 4 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114553 Last updated (according to GEO): Sep 20 2006 1000 Brain 660 mesenchymal stem cell 639 M_U133A_84_AnCg 5 0 brain 1000 frontal lobe total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CpG-oligodeoxynucleotide for 60min Source GEO sample is GSM5524 Last updated (according to GEO): May 27 2005 The transition from pregnancy to lactation is a critical event in the survival of the newborn since all the nutrient requirements of the infant are provided by milk. While milk contains numerous components, including proteins, that aid in maintaining the health of the infant, lactose and milk fat represent the critical energy providing elements of milk. Much of the research to date on mammary epithelial differentiation has focused upon expression of milk protein genes, providing a somewhat distorted view of alveolar differentiation and secretory activation. While expression of milk protein genes increases during pregnancy and at secretory activation, the genes whose expression is more tightly regulated at this transition are those that regulate lipid biosynthesis. The sterol regulatory element binding protein (SREBP) family of transcription factors is recognized as regulating fatty acid and cholesterol biosynthesis. We propose that SREBP1 is a critical regulator of secretory activation with regard to lipid biosynthesis, in a manner that responds to diet, and that the serine/threonine protein kinase Akt influences this process, resulting in a highly efficient lipid synthetic organ that is able to support the nutritional needs of the newborn. Last Updated (by provider): Jun 20 2007 Contributers: M C Rudolph S M Anderson J L McManaman M C Neville 152 117 Keywords = congenital heart disease 1000 Communicable Diseases Gene expression data from older female during 1 week of adequate protein intake Source GEO sample is GSM209821 Last updated (according to GEO): Jul 11 2007 40 21 from dorsal pancreas Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD33 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD33 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36684 Last updated (according to GEO): May 27 2005 Heart 861 CNS-SpinalC-4hAdult-1C-s2 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213474 Last updated (according to GEO): Jul 31 2007 None Source GEO sample is GSM214181 Last updated (according to GEO): Aug 01 2007 X50 WT3 F2/33 X50 wild type Mouse 16 months Cerebellum Male Source GEO sample is GSM73192 Last updated (according to GEO): Sep 06 2005 B322 on Affymetrix GeneChip Human Full Length Array HuGeneFL Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. 129S6/SvEvTac periaqueductal gray rep2 Liver (HBV+, HK9) Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162186 Last updated (according to GEO): Jun 12 2007 OVCAR-8 hgu95b 607 599 /- retina 1000 Carcinoma, Embryonal Cortex_reserpine_treated_rep5 HD4a Mouse neuroblastoma 0 18 Small Pre-BII cells 1 mouse brain ipsilateral LPS.RU486 Source GEO sample is GSM149779 Last updated (according to GEO): Mar 15 2007 cingulate cortex 861 f2#171 versus pool Mouse Brain tissue Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27742.gif Source GEO sample is GSM66590 Last updated (according to GEO): Sep 22 2006 1223 1215 gelsolin NCI60.18_LABEL22EXTRACT21SUB3 Source GEO sample is GSM134082 Last updated (according to GEO): Aug 06 2007 n/a Source GEO sample is GSM177993 Last updated (according to GEO): Jun 11 2007 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n108 Source GEO sample is GSM2074 Last updated (according to GEO): Nov 21 2005 Richard Almon-49-1138200270899 Hippocampus 1000 1000 Liver MAS 5.0, scaled to 500; Affymetrix data Mining Tool 3.0; dChip was used to determine differentially expressed genes (MBEI); Statistical Analysis of Microarrays(SAM), as described in Miller et al. 2004. Source GEO sample is GSM108084 Last updated (according to GEO): Sep 12 2006 1000 Brain TEL-AML1-C30 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Samp8 Retina Old Sample 1 Myometrium 4 Normal Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:364, Count:32 Corner- Avg:36544, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:15.267480,SFGene:All Background:Avg:408.40,Stdev:5.81,Max:426.0,Min:399.9 Noise:Avg:9.27,Stdev:0.43,Max:10.8,Min:8.4 RawQ:13.27 Keywords = ALL Source GEO sample is GSM3489 Last updated (according to GEO): May 28 2005 n/a Source GEO sample is GSM178079 Last updated (according to GEO): Jun 11 2007 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28467 Last updated (according to GEO): May 27 2005 human peripheral blood derived monocytes, 24 hour LPS stimulation, biological rep2 Source GEO sample is GSM127010 Last updated (according to GEO): Aug 15 2006 CVB3_S-3h-3 no additional Source GEO sample is GSM199096 Last updated (according to GEO): Jun 08 2007 250 236 their cerebella 91 from the bone marrow 72 liver_PPARa-knockout_control_6h_rep3 1000 Hippocampus CNS-SpinalCmod-Adult-48h-2C-s2 Cerebral cortex 1000 Mammary Neoplasms 901 healthy control sample x169 Posterior root of spinal nerve 861 5 0 brain of tumor cells 96 109 of the stria terminalis 46 68 Gene Expression data from the suprachiasmatic nucleus of an animal euthanized 1.5 hours after lights off. Source GEO sample is GSM159297 Last updated (according to GEO): Oct 31 2007 Spleen 1000 4 0 Brain 1000 Amyotrophic Lateral Sclerosis 496_11d tibiae 115 120 cocaine naive, nucleus accumbens, 0 hrs access to cocaine Source GEO sample is GSM93815 Last updated (according to GEO): Jan 26 2006 Recurrent Squamous cell carcinoma 2 0 34 UBOC1 Exp A Day 6 (b) Midbrain 9 Normal 861 frontal lobe aggressive meningiomas 1002 1024 Gene expression data from postmorten brain regions Source GEO sample is GSM145476 Last updated (according to GEO): Nov 20 2006 SN:1012380 Source GEO sample is GSM115411 Last updated (according to GEO): Jun 20 2006 of mouse brain 9 23 The role of the Wnt-signaling antagonist DKK1 in the development of osteolytic lesions in multiple myeloma. 1000 Colon Normal Source GEO sample is GSM176177 Last updated (according to GEO): Apr 09 2007 0029_1238_H95A2_KF0128_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 5 0 TONGUE C57BL/6 benchmark dataset: Embryonic day 10.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stage 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25150 Last updated (according to GEO): May 27 2005 of somatomotor cortex 21 41 AD-172t2-A213-8 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Disease Source GEO sample is GSM176111 Last updated (according to GEO): Apr 09 2007 from liver 21 30 Normal human tissue:Normal Uterus Keywords = Human, Normal Tissue, Normal Uterus Source GEO sample is GSM44684 Last updated (according to GEO): May 27 2005 Gene expression data from brain of adult rats Source GEO sample is GSM101053 Last updated (according to GEO): Feb 20 2007 HC53 CB B Liver 0 4 Whole blood 0 10 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15779.gif Source GEO sample is GSM91504 Last updated (according to GEO): Sep 22 2006 MLL__4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A D_U133A_25_DLPFC hTERT, cord blood total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Tumor necrosis factor-alpha for 60min Source GEO sample is GSM5804 Last updated (according to GEO): May 27 2005 plasma cells 332 344 Brain 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11331 Last updated (according to GEO): May 28 2005 of chronic heart failure 67 90 20 week!Sample_source_name_ch1 = Pre Natal Human lung tissue Source GEO sample is GSM107828 Last updated (according to GEO): May 04 2006 12 Temporal Lobe 24 7 0 prostate 901 Nervous system structure Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11318 Last updated (according to GEO): May 28 2005 1366 1348 in the hypothalamus Cerebellum Control (AD) 7 5 0 brain Comparison between cell lines from 9 different cancer tissue (NCI-60) (U95 platform) brain_DLPFC_bipolar B_mr281 1000 Brain A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke. Standard Affymetrix Protocol Source GEO sample is GSM16450 Last updated (according to GEO): May 28 2005 Polyamide 2 treated LNCaP cells not stimulated with DHT, biological replicate 3 Source GEO sample is GSM187382 Last updated (according to GEO): May 04 2007 PERA/EiJ_male_hypothalamus Source GEO sample is GSM184213 Last updated (according to GEO): Apr 26 2007 0 Human Cortex 11 Hippocampus 2006 2 month Old Astrocytomas are heterogeneous intracranial glial neoplasms ranging from the highly aggressive malignant glioblastoma multiforme (GBM) to the indolent, low-grade pilocytic astrocytoma. We have investigated whether DNA microarrays can identify gene expression differences between high-grade and low-grade glial tumors. We compared the transcriptional profile of 45 astrocytic tumors including 21 GBMs and 19 pilocytic astrocytomas using oligonucleotide-based microarrays. Of the approximately 6800 genes that were analyzed, a set of 360 genes provided a molecular signature that distinguished between GBMs and pilocytic astrocytomas. Many transcripts that were increased in GBM were not previously associated with gliomas and were found to encode proteins with properties that suggest their involvement in cell proliferation or cell migration. Microarray-based data for a subset of genes was validated using real-time quantitative reverse transcription-PCR. Immunohistochemical analysis also localized the protein products of specific genes of interest to the neoplastic cells of high-grade astrocytomas. Our study has identified a large number of novel genes with distinct expression patterns in high-grade and low-grade gliomas. 1791 1786 livers brain, hippocampus: C6-I_e1_le1 Recommended Affymetrix protocols were followed. Source GEO sample is GSM148468 Last updated (according to GEO): May 01 2007 PC 15 Treatment, type=incubate, description=Hypoxic preconditioning Source GEO sample is GSM107494 Last updated (according to GEO): May 01 2006 9 0 Blood Test Prosencephalon 861 1000 Brain Medulla 10 Normal 1000 Left Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4982.gif Source GEO sample is GSM93114 Last updated (according to GEO): Sep 22 2006 from brains 17 27 biopsy sample obtained from a 1.5-year-old male Duchenne Muscular Dystrophy patient Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15834 Last updated (according to GEO): Sep 08 2006 1000 Hippocampus Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28823 Last updated (according to GEO): May 27 2005 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 18 hours after lights on. Original sample code = CM14A Source GEO sample is GSM227337 Last updated (according to GEO): Sep 10 2007 heart_ventricle_2 DLCL-0026 16 7 cerebellum Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153505 Last updated (according to GEO): Jan 11 2007 NCI60.30_LABEL34EXTRACT33SUB3 Source GEO sample is GSM134140 Last updated (according to GEO): Aug 06 2007 GSE9046 Secondary malignant neoplasm of lymph node 1000 7 0 prostate Macrophage smi61 Neoplasm 861 from nose 96 104 Tissue fiber 861 processed in batch 5 Source GEO sample is GSM90412 Last updated (according to GEO): Mar 20 2006 901 Bone Marrow GM18516_technical_rep_2 VDXOXFU_157 KPeterson-NonMet-22G110-s2 214 176 for cutaneous contact hypersensitivity Gene expression data from PD7 Foxo3 null ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203829 Last updated (according to GEO): Aug 02 2007 Immune; normal adult(2X+) Keywords = mouse gene expression database Source GEO sample is GSM29355 Last updated (according to GEO): May 27 2005 Liver 1000 3 hrs Pre-clamp sample 6 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113910 Last updated (according to GEO): Jun 16 2006 861 Brain SN:Human Glioblastoma Biopsy 06712 Donor 1 Time point 24 hours post infection with HIV-1, RF Source GEO sample is GSM2602 Last updated (according to GEO): May 27 2005 B358 on Affymetrix GeneChip Human Full Length Array HuGeneFL Plasma 861 10 Bone marrow 0 Gene expression data from postmorten brain regions Source GEO sample is GSM145909 Last updated (according to GEO): Nov 20 2006 of somatomotor cortex 21 41 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16016.gif Source GEO sample is GSM91567 Last updated (according to GEO): Sep 22 2006 M_U133Plus_124_CB Mesenchymal Stem Cells 1000 olfactory epithelium 194 213 406 395 whose hearts GM19152 Heart failure 1000 adACN7 Standard Affymetrix Protocol Source GEO sample is GSM16492 Last updated (according to GEO): May 28 2005 1000 Brain CAD_replicate38 CNS-SC_CtrB4h-2C-s2 950 929 in the infected brains 361 335 hypertrophic cardiomyopathy Epithelial Cells 901 Leukemia, Lymphocytic, Chronic 1000 901 Caudate nucleus structure Cerebellum_nontransgenic control A39_4 months_replicate 3 CNS-SpinalCsev-Adult-14d-2A-s2 5 0 Spleen none Source GEO sample is GSM239939 Last updated (according to GEO): Dec 07 2007 Mammary epithelial cell transduction 14 0 thymus sprague2 16 0 Fetal fibroblast Hippocampus 861 Gene expression affected by TNFa and SB203580 901 frontal lobe pfc_1063_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Autistic Disorder 1000 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc132 Source GEO sample is GSM1849 Last updated (according to GEO): Nov 21 2005 "0_1 hr Hela Double Thymidine, exp3" 1000 Cerebral cortex 0 Human Cortex 11 1000 Coronary Arteriosclerosis 335 325 The jejunum Control 3 Cerebellum_nontransgenic control A39_8 months_replicate 4 /3T3 fibroblasts 295 310 160 125 Keywords = Congestive heart failure HMEC X BC2-2 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11509 Last updated (according to GEO): May 28 2005 Blood 861 C3H/HeJ amygdala rep1 430A2_1945_59_control_neuropath_medulla Source GEO sample is GSM242688 Last updated (according to GEO): Nov 15 2007 Plasma 861 Neoplasm 861 na Source GEO sample is GSM181253 Last updated (according to GEO): Apr 10 2007 3 hrs Pre-clamp sample 1 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211267 Last updated (according to GEO): Jul 18 2007 Colon 1000 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141311 Last updated (according to GEO): Oct 26 2006 1000 Structure of parenchyma of lung CT34-1 Ptdsr-/- fibroblast_rep3 1000 Brain mouse hippocampus from COX-2 WT Source GEO sample is GSM121442 Last updated (according to GEO): Jan 31 2007 spinal_cord_3 Liver 0 4 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120706 Last updated (according to GEO): May 14 2007 861 Cardiomyopathies 1000 Brain 55 39 from 12 cochleas with Parkinson's disease 27 50 Human Cell Line, adrenal medulla: RNA614_le1 BTBR T+ tf/tf Cerebellum B Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68229 Last updated (according to GEO): Jul 07 2006 Brain 1000 Skeletal bone 861 Liver 1000 Cardiac-specific TNF-alpha transgenic mouse is an excellent model to study the pathologenesis of heart failure. Affytrix U74V2A was used to analyzed the gene expression profile of mice at the time point of compensated hypertrophy and dilated heart failure. Source GEO sample is GSM8994 Last updated (according to GEO): May 28 2005 Parkinson's disease sample x103 84 69 Cervical Cancers Gene expression data from postmorten brain regions Source GEO sample is GSM144971 Last updated (according to GEO): Nov 20 2006 Saccule structure 1000 CNS-SpinalCsev-Adult-7d-1A-s2 430A2_1945_64_control_neuropath_midbrain Source GEO sample is GSM242691 Last updated (according to GEO): Nov 15 2007 The mammalian neocortex develops layer organizations with regional differences represented by expression of multiple genes at embryonic stages. These genes could play important roles in the formation of areal cyto-architecture, yet, the number of genes identified so far is not sufficient to explain such intricate processes. Here we collected five regions; the medial, dorsal, lateral, rostral, and occipital, from the dissected E16.5 mouse cerebral cortex and performed extensive gene expression analysis using the Affymetrix U74Av2 array.. Date GSE929 Last Updated: May 29 2005 Contributers: Shun Nakamura Takayoshi Inoue Nobuo Funatsu Includes GDS615. Update date: Jul 09 2004. Dataset description GDS615: Analysis of medial, dorsal, lateral, rostral, and occipital regions from strain ICR embryo day 16.5 cerebral cortex provides insight into molecular mechanisms of neocortical area and layer formation.. M_U133Plus_55_HC Myocardial Infarction 1000 Brain 1000 Primary Neoplasm 1000 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201277 Last updated (according to GEO): Jun 14 2007 966 Hippocampus cerebral cortex 7 21 913 Blood Cells 25 CB A Parkinson Disease 1000 1000 Spleen BREAST_T47D on Affymetrix GeneChip Human Full Length Array HuGeneFL "39 hr Hela Double Thymidine, exp3" Primary Neoplasm 1000 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68255 Last updated (according to GEO): Jul 07 2006 Testis 1000 Whole blood 0 10 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181128 Last updated (according to GEO): Jul 12 2007 Adenocarcinoma 1000 in livers 1104 1112 Gene expression data from postmorten brain regions Source GEO sample is GSM145110 Last updated (according to GEO): Nov 20 2006 MuscleRegen-ctx2d-2LLAv2-s2 healthy subject Source GEO sample is GSM211063 Last updated (according to GEO): Sep 10 2007 1000 jejunum Communicable Diseases 1000 331 307 in central nervous system Recurrent Squamous cell carcinoma 4 Whole brain 0 10 3AJZ02052318_WHOLEBLOOD(JJV) hippocampus Source GEO sample is GSM36009 Last updated (according to GEO): May 27 2005 TAp63 alpha 24h induction s1 bladder 0 6 Wild type olfactory epithlium 2 hpO replicate3 experiment IV, BABE transduced, replicate 2 T47D_Treated 1000 Cerebral cortex Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 1 hour following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM11032 Last updated (according to GEO): May 28 2005 861 Cardiomyopathies 861 Brain Prefrontal Cortex 0 16 4016 12a AML cDNA hybridization-ID48-L 1000 Spleen zhang-affy-mouse-200705 Cerebral cortex 1000 Normal Source GEO sample is GSM175895 Last updated (according to GEO): Apr 09 2007 SK-OV-3 hgu95c 1000 Spleen 32 12 frontal temporal lobe Spleen vs Untreated B cell 60min (set2) placebo 48h, biological rep2 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225932 Last updated (according to GEO): Nov 02 2007 NoCAD_replicate43 Replicate1_Voxel E7 B2-8 on NCI-7.6k 649 differentiating embryonic stem cells 614 left 35 38 Plasma 861 Cerebellum Control (AD) 9 1000 Brain Epithelium 865 Normal Source GEO sample is GSM176181 Last updated (according to GEO): Apr 09 2007 Assay of baseline expression in the cerebellum of an alcohol-naive Inbred Short Sleep mouse Source GEO sample is GSM67185 Last updated (according to GEO): Oct 28 2005 Nasal Epithelium 865 Investigation into murine dermal burn wound. Mouse thermal injury induced, and skin excised at different times post-injury. Source GEO sample is GSM7478 Last updated (according to GEO): May 27 2005 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92378 Last updated (according to GEO): Jan 13 2006 901 theca cell Blood 1000 1000 Brain Primary tumor 19 32 na Source GEO sample is GSM181305 Last updated (according to GEO): Apr 10 2007 3AJZ02051606_ParietalLobe Control total RNA was pooled from the kidney of five normal BALB/c mice. Total RNA was extracted from the kidney of BALB/c mice injected with anti-GBM antibody for 16 day. Source GEO sample is GSM15092 Last updated (according to GEO): May 28 2005 Olfactory Epithelium 1000 #9 (isolate 22 low serum media control) 1000 Pituitary Gland PBMC Media 1 Resting OBJECTIVE: To describe the use of large-scale gene expression profiles to distinguish broad categories of myopathy and subtypes of inflammatory myopathies (IM) and to provide insight into the pathogenesis of inclusion body myositis (IBM), polymyositis, and dermatomyositis. METHODS: Using Affymetrix GeneChip microarrays, the authors measured the simultaneous expression of approximately 10,000 genes in muscle specimens from 45 patients in four major disease categories (dystrophy, congenital myopathy, inflammatory myopathy, and normal). The authors separately analyzed gene expression in 14 patients limited to the three major subtypes of IM. Bioinformatics techniques were used to classify specimens with similar expression profiles based on global patterns of gene expression and to identify genes with significant differential gene expression compared with normal. RESULTS: Ten of 11 patients with IM, all normals and nemaline myopathies, and 10 of 12 patients with Duchenne muscular dystrophy were correctly classified by this approach. The various subtypes of inflammatory myopathies have distinct gene expression signatures. Specific sets of immune-related genes allow for molecular classification of patients with IBM, polymyositis, and dermatomyositis. Analysis of differential gene expression identifies as relevant to disease pathogenesis previously reported cytokines, major histocompatibility complex class I and II molecules, granzymes, and adhesion molecules, as well as newly identified members of these categories. Increased expression of actin cytoskeleton genes is also identified. CONCLUSIONS: The molecular profiles of muscle tissue in patients with inflammatory myopathies are distinct and represent molecular signatures from which diagnostic insight may follow. Large numbers of differentially expressed genes are rapidly identified. M7TW01013180 Group 4 PEITC + NMBA treated, pool # EP 17 vs. reference pool Aortic Aneurysm, Abdominal 923 Brain 1000 with Alzheimer's disease 27 50 Pancreas at e13.5, Chip C, rep 1 Spinal Cord 1000 Mesenchymal Stem Cells 1000 small intestine sprague1 low gestational age Source GEO sample is GSM213092 Last updated (according to GEO): Jul 25 2007 aml-aml8_883_ab_hu68_abms on Affymetrix GeneChip Human Full Length Array HuGeneFL no additional Source GEO sample is GSM199077 Last updated (according to GEO): Jun 08 2007 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132523 Last updated (according to GEO): Feb 26 2007 Obesity 1000 Large-scale analysis of the human transcriptome. Promyelocytic leukemia Source: ATCC Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 125.16 Stdv: 6.21 Min: 111.43 Max: 135.41 Source GEO sample is GSM2902 Last updated (according to GEO): Mar 20 2006 Brain 861 Tissue Source GEO sample is GSM67239 Last updated (according to GEO): Jan 19 2006 JP(BT) DLCL-0052 || lc4b060 46 8 in docetaxel-refractory prostate cancer 1000 Hippocampus Skeletal bone 861 G2 Macula (rep) DND41 DMSO control 24h rep1 1215 1210 tumors mouse brains 187 198 Fibroblasts 1000 Standard Affymetrix Protocol on total RNA extracted from brain tissue Source GEO sample is GSM101412 Last updated (according to GEO): Mar 28 2006 Coronary artery 901 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118338 Last updated (according to GEO): Jul 11 2006 tibiae 115 120 THAP24_2 no additional Source GEO sample is GSM199136 Last updated (according to GEO): Jun 08 2007 GSE6575 8 0 G1 Retina 861 Neoplasm no additional Source GEO sample is GSM199107 Last updated (according to GEO): Jun 08 2007 experiment II, untransduced, replicate 2 861 Cerebral cortex Normal Source GEO sample is GSM175825 Last updated (according to GEO): Apr 09 2007 short access to cocaine, nucleus accumbens, 1 hr/day access to cocaine Source GEO sample is GSM93819 Last updated (according to GEO): Jan 26 2006 1000 Prosencephalon GC (HKG26T) Infection 1176 1185 M_U133A_47_HC We used the default settings of GCOS software to scan the chips. Source GEO sample is GSM148489 Last updated (according to GEO): Apr 16 2007 NA18501 Exp 4 (+TNFa) 663 mesenchymal stem cell 642 11 0 Hypothalamus Homozygous O377 mutant mouse line versus wildtype mice Source GEO sample is GSM86411 Last updated (according to GEO): Dec 08 2005 861 Heart 1000 Lung TS21 sample 3 (cerebellum) We analyzed the lumbar spinal cord tract of transplanted nmd mice (n=3), untransplanted nmd mice (n=3) and wild-type mice (n=3) (all mice are of male gender). The latter groups underwent surgical procedure with vehicle. The surgical procedure and spinal cord-derived neural stem cell transplantation (intratechal injection) were done at P1 and the animals were sacrificed at 6 weeks of age. Source GEO sample is GSM67525 Last updated (according to GEO): Dec 21 2005 mouse brain 478 489 Occipital lobe 983 67 40 with coronary artery disease Liver (HBV+, HK30) 21 0 cerebellum wistar 3887 PNS WT Chip B Probeset expression data from NA12742 growth 1 Source GEO sample is GSM201527 Last updated (according to GEO): Aug 08 2007 Mouse ileum Germ-free_B_5554 Spleen vs fMLP Treated B cell 240min (set2) kidney_medulla_1 Spinal Cord 1000 T13__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Cerebral cortex 861 Leukemic fractions of ID13 AML patient have been hybridized. Source GEO sample is GSM103100 Last updated (according to GEO): Feb 26 2007 20 0 human caudate nucleus Cerebral cortex 861 Gene expression data Source GEO sample is GSM183182 Last updated (according to GEO): Jul 30 2007 of the small intestine 97 118 Coronary artery 901 Gene expression data from postmorten brain regions Source GEO sample is GSM144902 Last updated (according to GEO): Nov 20 2006 901 Caudate nucleus structure low gestational age Source GEO sample is GSM213095 Last updated (according to GEO): Jul 25 2007 Testis 1000 110 FC BA9 A nostrils 156 164 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211380 Last updated (according to GEO): Jul 18 2007 MSS-Spa-M6moF-1aAv2-s2 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 4 hours after lights on. Original RNA code = LC40A. Source GEO sample is GSM227393 Last updated (according to GEO): Sep 10 2007 1000 Hippocampus Brain 861 Expression data after reversal of DNA methylation Source GEO sample is GSM230906 Last updated (according to GEO): Sep 20 2007 1000 ovarian neoplasm 5 0 brain Gene expression data from a hippocampus from mouse injected 10 mg/kg nicotine Source GEO sample is GSM147429 Last updated (according to GEO): Jan 03 2007 453 434 The descending colon Nose 1000 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92339 Last updated (according to GEO): Jan 13 2006 corpus_callosum_10 Source GEO sample is GSM80647 Last updated (according to GEO): Mar 31 2006 861 Cerebellum Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35374 Last updated (according to GEO): May 27 2005 Brain 861 Testis 861 861 Oocytes Gene expression data from epididymal fat tissues. Source GEO sample is GSM215576 Last updated (according to GEO): Aug 07 2007 1000 Hippocampus ALLB-cell71 on Affymetrix GeneChip Human Full Length Array HuGeneFL MDA-MB-435_CL5011__BREAST 43 29 from the kidney Brain 1000 Stria 861 Expression profiling of moderately injured raphe at 4h in rats Source GEO sample is GSM41611 Last updated (according to GEO): May 27 2005 D_U133A_74_nAcc Brain 1000 Brain 861 32h-DMSO replication 1 pineal sprague2 Ischemia-reperfusion with AEOL 10150 #14 1000 Brain MGJZ030211004Bbladder Disease Source GEO sample is GSM176443 Last updated (according to GEO): Apr 09 2007 1000 Brain Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68219 Last updated (according to GEO): Jul 07 2006 Heart 1000 6 0 trachea Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11591 Last updated (according to GEO): May 28 2005 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13094.gif Source GEO sample is GSM79904 Last updated (according to GEO): Sep 22 2006 brain, cortex: 7dexp1_e1_le1 Pool of 15 vestibular tissues at E11.5 Source GEO sample is GSM182594 Last updated (according to GEO): Aug 14 2007 NCI/ADR-RES hgu95a Gene expression was measured in trisomy 21 and trisomy 13 human fetal samples. For TS21, regions assayed were cerebrum, cerebellum, heart, and cerebrum-derived astrocyte cell lines. Last Updated (by provider): Mar 28 2006 Contributers: Jonathan Pevsner Rong Mao total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells cultured for 120min Source GEO sample is GSM5845 Last updated (according to GEO): May 27 2005 NCI60.45_LABEL49EXTRACT48SUB3 Source GEO sample is GSM134221 Last updated (according to GEO): Aug 06 2007 Expression profiling of spinal cord section (T10) extracted from rats 24h following laminectomy (sham) Lot batch = Source GEO sample is GSM4434 Last updated (according to GEO): May 28 2005 M7TW01010684 Backskin_WT_P6_rep4 1000 Heart normal testis 54 66 LDMTX_MP-DX-12 MO_control_180min_Patient15 MP-9 Medulla 861 1000 Left Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153365 Last updated (according to GEO): Dec 27 2006 1129 1115 in the oocytes Left 1000 1000 Amygdaloid structure 861 Cerebral cortex NCI60.8_LABEL11EXTRACT10SUB3 Source GEO sample is GSM134032 Last updated (according to GEO): Aug 06 2007 Heart 1000 1000 Spleen Parkinson 0 8 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155053 Last updated (according to GEO): Jun 04 2007 brain, brainstem: LB7_e1_le1 Compare the transcriptomes of Cx43 null and Cx43 siRNA treated cortical astrocytes with the transcriptome of the wildtype cortical astrocytes Source GEO sample is GSM200854 Last updated (according to GEO): Jun 19 2007 1000 frontal lobe 1000 Cerebral cortex human peripheral blood derived monocytes, 24 hour LPS stimulation, biological rep1 Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153773 Last updated (according to GEO): Jan 19 2007 Disease Source GEO sample is GSM175915 Last updated (according to GEO): Apr 09 2007 human cerebellum Source GEO sample is GSM87184 Last updated (according to GEO): Feb 08 2006 spinal cord 13 23 Brain 861 accumbens_1 ALL_16 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Heart 1000 Lung 861 Immune system Melanoma metastatic cell line A375, biological rep3 (LeiFidler) NCI60.39_LABEL43EXTRACT42SUB3 Source GEO sample is GSM134187 Last updated (according to GEO): Aug 06 2007 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159955 Last updated (according to GEO): Feb 01 2007 Epithelium of bronchus 983 166 156 of retinal Primary tumor 19 32 umbilical cord_bpd: 4I human frontal cortex Source GEO sample is GSM87050 Last updated (according to GEO): Feb 08 2006 Neural tube, control, GD8:15, C216799 89 68 with tricuspid valves Skeletal bone 861 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181188 Last updated (according to GEO): Jul 12 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145266 Last updated (according to GEO): Nov 20 2006 M_U133A_74_AnCg Head and neck cancer Source GEO sample is GSM155689 Last updated (according to GEO): Apr 24 2007 861 Muscle 1000 Left VIIcCA1_Signal on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B 861 Hippocampus CNS-SC_InjA24h-1B-s2 Bronchus 2 Normal To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28466 Last updated (according to GEO): May 27 2005 M_U133A_67_DLPFC Cardiac-specific TNF-alpha transgenic mouse is an excellent model to study the pathologenesis of heart failure. Affytrix U74V2A was used to analyzed the gene expression profile of mice at the time point of compensated hypertrophy and dilated heart failure. Source GEO sample is GSM8990 Last updated (according to GEO): May 28 2005 Cerebral cortex 861 24 0 Proliferative endometrium PP164_uninfected_DC mouse brains 187 198 1000 ovarian neoplasm Gene expression data from postmorten brain regions Source GEO sample is GSM145312 Last updated (according to GEO): Nov 20 2006 1000 Hypertrophic Cardiomyopathy Coronary Arteriosclerosis 1000 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188805 Last updated (according to GEO): Jun 06 2007 tongue epidermis 0 15 Myeloid Leukemia 901 Transplant Series 25 Left, PrimaryTumor from femur 21 30 861 Chromosomes no additional Source GEO sample is GSM199393 Last updated (according to GEO): Jun 08 2007 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184694 Last updated (according to GEO): Apr 26 2007 Primary Neoplasm 1000 Renal carcinoma 875 861 Brain Acetaminophen 24hr Rat 5999 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool AD-201t1-A138-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1BJZ02072563_Hypothalamus allander-gist NA12760 1000 Liver Cirrhosis Starvation 916 with some respiratory epithelium. 1039 1072 HP(BT) Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 9434 blood CAD_replicate8 Cerebral cortex 1000 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:215, Count:32 Corner- Avg:35328, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:11.352031,SFGene:All Background:Avg:320.18,Stdev:5.90,Max:336.6,Min:306.8 Noise:Avg:7.65,Stdev:0.20,Max:8.2,Min:6.7 RawQ:11.39 Keywords = ALL Source GEO sample is GSM3456 Last updated (according to GEO): May 28 2005 80 68 Control blood Eye 861 of underlying brain 171 190 Oat cell carcinoma 867 golub-leukemia Mouse Liver AIN Diet 5wk Control, biological replicate D Subcutaneous Fat 1000 CO_sham_med_1 Nrl ko samples were compared to wt at postnatal 2. Source GEO sample is GSM227448 Last updated (according to GEO): Sep 07 2007 Blood 1000 post HCMV infection 69 87 Gene expression data from postmorten brain regions Source GEO sample is GSM145248 Last updated (according to GEO): Nov 20 2006 NA Source GEO sample is GSM198932 Last updated (according to GEO): Jun 07 2007 MGMH030212051Bsmallintestine 136 131 Aortae Voxel B3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1396 Last updated (according to GEO): Nov 21 2005 Myometrium 35 Disease 50 43 jejunum Ovary_PD3_Foxo3 Wt_Replica 2 TEL-AML1-C45 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Normal Source GEO sample is GSM175981 Last updated (according to GEO): Apr 09 2007 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15383.gif Source GEO sample is GSM84148 Last updated (according to GEO): Sep 22 2006 Bone Marrow 1000 H132 FC BA4 A CNS-RM_Ctr3mo-1C-s2 brain, Superior Frontal Gyrus: Sample52_e1_le1 NH 17374A 1000 Prostate GC (HKG38T) Measles 861 standard Affymetrix protocol, MAS 5.0 Source GEO sample is GSM9139 Last updated (according to GEO): May 28 2005 5 0 brain 1000 Descending colon Category: Lymphoma Classification Subcategory: Chronic Lymphocytic Leukemia Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n117 Source GEO sample is GSM2064 Last updated (according to GEO): Nov 21 2005 Expression profiling of spinal cord section (T9) extracted from rats 4h following severe injury Lot batch = Source GEO sample is GSM7588 Last updated (according to GEO): May 28 2005 Primary Neoplasm 1000 7 0 prostate Standard Affymetrix Protocal Keywords = microarray Keywords = muscle Source GEO sample is GSM15774 Last updated (according to GEO): May 28 2005 liver_wildtype_WY14643_5d_rep1 1000 Structure of entorhinal cortex Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12827.gif Source GEO sample is GSM76410 Last updated (according to GEO): Sep 22 2006 na Source GEO sample is GSM181295 Last updated (according to GEO): Apr 10 2007 5 0 brain 67 40 with coronary artery disease Wild type inbred mice Source GEO sample is GSM82990 Last updated (according to GEO): Nov 10 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL10 for 60min Source GEO sample is GSM5635 Last updated (according to GEO): May 27 2005 4 0 Brain from whole tumor 21 36 Untreated LNCaP cells not stimulated with DHT, biological replicate 1 Source GEO sample is GSM187369 Last updated (according to GEO): May 04 2007 olfactory epithelium 194 213 low gestational age Source GEO sample is GSM213114 Last updated (according to GEO): Jul 25 2007 1000 Malignant Neoplasms Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188814 Last updated (according to GEO): Jun 06 2007 5.0 mg/kg MeHg forebrain at 6.0h of the stria terminalis rep2 26 53 NA Source GEO sample is GSM198930 Last updated (according to GEO): Jun 07 2007 Gene expression data from colorectal adenoma. Source GEO sample is GSM215104 Last updated (according to GEO): Aug 02 2007 861 Neoplasm Wild type olfactory epithelium 48 hpO replicate1 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68265 Last updated (according to GEO): Jul 07 2006 Nothing in line. Source GEO sample is GSM154226 Last updated (according to GEO): Jul 05 2007 human cerebellum Source GEO sample is GSM87066 Last updated (according to GEO): Feb 08 2006 861 Brain Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 11.75 hours after lights on. Original sample code = CM45A Source GEO sample is GSM227327 Last updated (according to GEO): Sep 10 2007 hippocampus_3 Source GEO sample is GSM80662 Last updated (according to GEO): Mar 31 2006 CNS-RM_Mod28d-4B-s2 UACC-62 hgu95e Control Abdominal Aorta 3-M Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.43 Subject: 2846 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39034 Last updated (according to GEO): May 27 2005 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114387 Last updated (according to GEO): Jun 16 2006 human caudate nucleus Source GEO sample is GSM86797 Last updated (according to GEO): Feb 08 2006 Mouse Expression DB 2001 CHMC Medulla 861 Gene expression data from colorectal adenoma. Source GEO sample is GSM215100 Last updated (according to GEO): Aug 02 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113909 Last updated (according to GEO): Jun 16 2006 Brain 861 861 Spinal Cord 0 Human Cortex 11 Cerebral cortex 861 1000 Temporal Lobe ovarian tumor: serous Source GEO sample is GSM139473 Last updated (according to GEO): Apr 09 2007 865 Disorder of artery 1000 Cerebrovascular accident Z4 biol repl 3 none Source GEO sample is GSM239899 Last updated (according to GEO): Dec 07 2007 861 Blood GSE7784 CH1803 Low Freezing Source GEO sample is GSM92412 Last updated (according to GEO): Jan 13 2006 Muscle 861 Fibroblasts 1000 brain 0 5 P2B_KIDNEY_10 olfactory epithelium 194 213 Healthy patient. Source GEO sample is GSM228573 Last updated (according to GEO): Sep 11 2007 120 cortex 126 Liver 1000 1000 Creutzfeldt-Jakob Syndrome 901 frontal lobe 865 Disorder of artery 24h -TGF-beta pulp tissue Gene expression data from postmorten brain regions Source GEO sample is GSM145583 Last updated (according to GEO): Nov 20 2006 TUMOR 5 0 6 Femur 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CpG-oligodeoxynucleotide for 60min Source GEO sample is GSM5525 Last updated (according to GEO): May 27 2005 Spinal Cord Injuries 1000 normal testis 54 66 Communicable Diseases 1000 Coronary artery 901 901 Mental disorders RNA isolated from fetal cerebellum Keywords = trisomy Keywords = brain Keywords = Down syndrome Source GEO sample is GSM22586 Last updated (according to GEO): May 27 2005 experimental autoimmune encephalomyelitis 73 113 Left 1000 MDA Mb231 2 Control NCI60.60_LABEL122EXTRACT62SUB3 Source GEO sample is GSM134297 Last updated (according to GEO): Aug 06 2007 1000 Muscle 4 0 Brain 861 Blood testis 52 58 Heart 861 1000 Brain n/a Source GEO sample is GSM178067 Last updated (according to GEO): Jun 11 2007 mouse brains 187 198 The insulin-like growth factor 1 receptor induces physiological heart growth via the phosphoinositide 3-kinase(p110alpha) pathway. Seminoma 1000 With the sequencing and assembly of the rat genome comes the difficult task of assigning functions to genes. Tissue localization of gene expression gives some information about the potential role of a gene in physiology. Various examples of the utility of multiple tissue gene expression data sets are illustrated here. First, we highlight their use in finding genes that might play an important role in a particular tissue on the basis of exclusive expression in that tissue or coexpression with a gene or genes with known function. Second, we show how this data might be used to explain known phenotypic differences between strains. Third, we show how expression patterns of genes in a genomic interval might identify candidate genes in quantitative trait loci (QTL) mapping studies. Lastly, we show how multiple tissue and species data can help researchers prioritize follow up studies to microarray experiments. All of these applications of multiple tissue gene expression data sets will play a role in functionally annotating the rat genome. Primary tumor 19 32 315 312 left Structure of parenchyma of lung 901 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114439 Last updated (according to GEO): Jun 16 2006 BC213A-AF Gene expression data from postmorten brain regions Source GEO sample is GSM146079 Last updated (according to GEO): Nov 20 2006 brain 1507 1511 to the nose 599 609 1000 Cerebral cortex 117 99 of the hypothalamus of the prefrontal cortex 21 44 brain 0 5 EP-3W brain, unknown: 3317-99_e1_le1 none Source GEO sample is GSM161907 Last updated (according to GEO): Feb 16 2007 861 Malignant Neoplasms Gene expression data from hippocampus of one young SAMP8/Ta mouse Source GEO sample is GSM143755 Last updated (according to GEO): Jan 24 2007 36 21 from whole brain Bone Marrow 1000 1000 Hippocampus cortex from B6 mice at ZT9 rep1 Source GEO sample is GSM160455 Last updated (according to GEO): Feb 05 2007 Hippocampal pathways in cognitive impairment 66 42 out of mouse bone marrow Gene expression profile of the cell line UB/OC-1 grown for 8 days under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1525 Last updated (according to GEO): May 27 2005 861 Brain 5 0 brain 5 0 Spleen 143T Heart 1000 pituitary sprague2 whole tissue, pool of 5 animals, 10 weeks old, male Sprague Dawley pituitary file:R3JBH02100404 Source GEO sample is GSM15196 Last updated (according to GEO): May 28 2005 43 0 Chorionic mesoderm-derived mesenchymal cells plus_1440_2 Hippocampus 861 Arteries 861 from a primary branch 21 41 Stem cells 913 The goal of these experiments was to identify the genes that are regulated by CCAT, a novel transcription factor derived from the C-terminus of CaV1.2. Neuro2A neuroblastoma cells were transfected with the last 503 AA of CaV1.2 which is full length CCAT (CCAT FL) or with the last 280 AA of CaV1.2, a form of CCAT that lacks the transcriptional activation domain (CCAT DTA). The mRNA from either CCAT FL or CCAT DTA expressing cells was hybridized to Agilent mouse genome microarrays along with mRNA from untransfected neuro2A cells. The microarray data was subsequently analyzed with the Rossetta Luminator gene expression data analysis system. Subsequent investigation revealed that CCAT DTA can still activate transcription albeit at much lower levels than CCAT FL. Source GEO sample is GSM95630 Last updated (according to GEO): Feb 07 2006 Arteries 861 H9RGV00111005 brain, hippocampus: PR-CA3-11_e1_le1 plasma cells 50 61 D1_TP-72_I 1000 Mitral Valve medial prefrontal cortex cocaine naive replicate 3 HapMap YRI_parent Female Source GEO sample is GSM159669 Last updated (according to GEO): Feb 01 2007 246 219 of parieto-occipital cortex Nose 1000 hippocampal glutamatergic CA1 pyramidal neurons Source GEO sample is GSM35830 Last updated (according to GEO): May 27 2005 brain, Posterior Singulate: Sample48_e1_le1 1000 Brain 1BRS02080873b_ciliary_ganglion Simple annotation: Normal tissue, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27745.gif Source GEO sample is GSM66558 Last updated (according to GEO): Sep 22 2006 1000 Endometrium normal lung 2266 Source GEO sample is GSM17301 Last updated (according to GEO): May 28 2005 from Job's Syndrome 41 59 A HID U D007 Gene expression data from skeletal muscle following 240 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230434 Last updated (according to GEO): Sep 19 2007 n/a Source GEO sample is GSM177983 Last updated (according to GEO): Jun 11 2007 Cerebellum 0 9 TGFBd8_13 Dominant negative cJun VZ18 brain 0 5 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b056 Source GEO sample is GSM2000 Last updated (according to GEO): Nov 21 2005 none Source GEO sample is GSM149554 Last updated (according to GEO): Jan 03 2007 NHE1 null mutation cortex-2 Normal Source GEO sample is GSM176335 Last updated (according to GEO): Apr 09 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Leukotriene B4 (LTB4) for 120min Source GEO sample is GSM5681 Last updated (according to GEO): May 27 2005 36 21 from whole brain ER negative human primary breast tumor EA02014_41294_H133A_JA-1967 10 7 Left Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35373 Last updated (according to GEO): May 27 2005 CNS-SC_CtrB14d-2C-s2 A HID B D092 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108591 Last updated (according to GEO): Aug 22 2006 24 7 Right Frontal Lobe SCG explant cultured for 48 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246056 Last updated (according to GEO): Dec 03 2007 brain_DLPFC_bipolar C_mr521 Pool of 6 cochlear tissues at E14.5 Source GEO sample is GSM182587 Last updated (according to GEO): Aug 14 2007 Normal Source GEO sample is GSM176142 Last updated (according to GEO): Apr 09 2007 Exp C_1, 10mg/kg CPF 41 29 Control blood Colonic mucous membrane 913 "Sample 94, BRCA2 mutation(51 months) age 38 erp yes" on vantveer-oligo adenoma 861 861 Encephalitis Brain 861 Richard Almon-40-1133800610026 MA/MyJ_male_hypothalamus Source GEO sample is GSM184207 Last updated (according to GEO): Apr 26 2007 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132535 Last updated (according to GEO): Feb 26 2007 MGMH030402089Boocyte f2#300 versus pool Mouse Brain tissue Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10414.gif Source GEO sample is GSM79935 Last updated (according to GEO): Sep 22 2006 1000 Descending colon CO (Experiment 4Rlong: Run 19283) Treatment, type=timepoint, measurement=0.0 m Source GEO sample is GSM96678 Last updated (according to GEO): Feb 14 2006 Gene expression data from liver Source GEO sample is GSM243396 Last updated (according to GEO): Nov 16 2007 Keywords = kidney 236 253 Gene expression data from postmorten brain regions Source GEO sample is GSM144921 Last updated (according to GEO): Nov 20 2006 Brain 1000 pfc_1027_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 861 Cerebral cortex Immunoglobulins 861 Gene expression data from mammary glands of lactating mice Source GEO sample is GSM202701 Last updated (according to GEO): Jun 20 2007 in bronchial epithelia 311 332 Lymphoblastoid Cell Line for Individual 8066.4 log phase 861 Blood ve_M63B Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181145 Last updated (according to GEO): Jul 12 2007 861 Brain 861 Brain 94 68 dorsal tongue surface C57BL Epithelium 861 CNS-SpinalCsev-Adult-14d-1C-s2 150mg/kg APAP 6Hr rat 3588 blood vs. PC 6Hr rat 3586 blood 1000 Cerebral cortex FSCC6 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1037 of transitional epithelium 1012 leukemia 861 AML_7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A M_95A_1905_DLPFC_1_GS 861 Neurites Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153349 Last updated (according to GEO): Dec 27 2006 7 0 Pancreas 15478 on TGRI-6.5k Altered hippocampal transcript profile accompanies an age-related spatial memory deficit in mice. Cultured_cortical_astrocyte_Cx43_null_rep4 CH2120 Cicardian regulation in rat liver Gene expression data from postmorten brain regions Source GEO sample is GSM145274 Last updated (according to GEO): Nov 20 2006 1000 Liver Gene expression data from postmorten brain regions Source GEO sample is GSM145422 Last updated (according to GEO): Nov 20 2006 prostate Source GEO sample is GSM203370 Last updated (according to GEO): Jun 21 2007 5 0 brain Brain 1000 861 Colon 19 0 human frontal cortex 1000 ovarian neoplasm 861 Medulla 861 Brain MDA Mb231 3 Control Myopathy 875 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113951 Last updated (according to GEO): Jun 16 2006 amygdala long access to cocaine replicate 1 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114451 Last updated (according to GEO): Jun 16 2006 Primary Neoplasm 1000 5 0 brain Liver (HBV+, HK11) GSE63 1000 Retina PGA_PA-N_112 between the LAD artery 266 287 Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2653.gif Source GEO sample is GSM72205 Last updated (according to GEO): Sep 22 2006 HC81 FC BA4 A muscle 669 675 861 Brain Brain 1000 C57 whole brain 5A Gene expression profile of conjunctival epithelial cell lines CAD_replicate64 7 cerebral cortex 21 Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16864.gif Source GEO sample is GSM91503 Last updated (according to GEO): Sep 22 2006 L_D2_SleepDep_ZT 6_2 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:173, Count:32 Corner- Avg:38236, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:10.340834,SFGene:All Background:Avg:635.33,Stdev:20.39,Max:681.8,Min:583.2 Noise:Avg:11.21,Stdev:0.55,Max:13.1,Min:9.7 RawQ:16.42 Keywords = ALL Source GEO sample is GSM3436 Last updated (according to GEO): May 27 2005 Subject code A49 Prosencephalon 861 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Leukotriene B4 (LTB4) for 60min Source GEO sample is GSM5677 Last updated (according to GEO): May 27 2005 Tongue Superior With Papillae 1 Normal 1012 1006 seizure Expression profiling of spinal cord section (T9) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM6669 Last updated (according to GEO): May 28 2005 Mouse_E13.5_Front_Middle_Back_8 of the colon 28 39 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=2 and B=0 (Acute rejection). Source GEO sample is GSM36453 Last updated (according to GEO): May 27 2005 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188742 Last updated (according to GEO): Jun 06 2007 10 Bone marrow 0 Cerebral cortex 861 861 Alzheimer's Disease osteoblast 627 637 Brain 1000 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy, pathological hypertrophy, rat, heart failure, cardiomyopathy Source GEO sample is GSM12314 Last updated (according to GEO): May 28 2005 in the amygdala 802 816 141 106 Keywords = Congestive heart failure 9 0 Blood Test Epithelium 861 HMEC 184 day 3 sample 2 HapMap CEU_parent Female Source GEO sample is GSM159550 Last updated (according to GEO): Feb 01 2007 Macrophage smi112 861 Neoplasm Nasal Epithelium Instilation Formaldehyde 0mM 6h ID355 Brain_C57 Wildtype_affs275-1100 Control rat 5 substantia nigra Source GEO sample is GSM32165 Last updated (according to GEO): May 27 2005 GSE7999 Sample is skeletal muscle from morbidly obese patient undergoing elective abdominal surgery Source GEO sample is GSM3981 Last updated (according to GEO): May 28 2005 5 0 brain brain, cerebral cortex: Rat_03-58_NroLep_Lipska_e1_le1 to the nose 599 609 Macrophage 14smi024 Menstrual phase - Follicular Source GEO sample is GSM175782 Last updated (according to GEO): Apr 09 2007 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188694 Last updated (according to GEO): Jun 06 2007 Neural tube, control, GD8:15, C216801 Small Pre-BII cells 9b Corticospinal Motor Neurons P6 2 386 0a 1000 Amyotrophic Lateral Sclerosis 1000 Brain adult cerebellum 549 564 5 0 brain Frontal Cortex Source GEO sample is GSM107898 Last updated (according to GEO): Jun 06 2006 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P14, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3218 Last updated (according to GEO): May 28 2005 5 0 brain 1000 Brain Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs//7275.gif Source GEO sample is GSM79726 Last updated (according to GEO): Sep 22 2006 human frontal cortex Source GEO sample is GSM87007 Last updated (according to GEO): Feb 08 2006 1000 Rectum 5 0 brain Nasal Epithelium Instilation Formaldehyde 400mM 6h ID369 447 438 infection CNS-SCsev_InjB28d-3A-s2 Gene expression data from postmorten brain regions Source GEO sample is GSM145140 Last updated (according to GEO): Nov 20 2006 in which neocortical progenitor cells 63 99 25 7 Right Temporal Lobe 3 0 Skin brain, unknown: 00ZP_e1_le1 Malignant neoplasm of prostate 861 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188700 Last updated (according to GEO): Jun 06 2007 rotenone 1 week C Treatment, type=time_course, measurement=1.0 weeks Source GEO sample is GSM107855 Last updated (according to GEO): Jun 06 2006 TK-10 hgu95c Cerebral cortex 1000 R3 jzo022-rp1-v5-u74av2-met Brain 1000 A HID I D055 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108599 Last updated (according to GEO): Aug 22 2006 861 Brain 4hr S-CA1 Time point at 16h post HCMV infection DRG026_a 239 233 Retinas Aortic Aneurysm 861 to the nose 599 609 1000 Brain 1388 1363 in anatomical compartments CNS-SMTC_CtrT0-3C-s2 D2_TP-24_C Communicable Diseases 861 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 22 hours after lights on. Original RNA code = LC52A. Source GEO sample is GSM227392 Last updated (according to GEO): Sep 10 2007 Expression profiling of somatomotor cortex extracted from rats at T0 naive Source GEO sample is GSM41679 Last updated (according to GEO): May 27 2005 Muscular Dystrophy, Duchenne 913 BACKGROUND: Abdominal aortic aneurysms are a common disorder with an incompletely understood etiology. We used Illumina and Affymetrix microarray platforms to generate global gene expression profiles for both aneurysmal (AAA) and non-aneurysmal abdominal aorta, and identified genes that were significantly differentially expressed between cases and controls. RESULTS: Affymetrix and Illumina arrays included 18,057 genes in common; 11,542 (64%) of these genes were considered to be expressed in either aneurysmal or normal abdominal aorta. There were 3,274 differentially expressed genes with a false discovery rate (FDR) </= 0.05. Many of these genes were not previously known to be involved in AAA, including SOST and RUNX3, which were confirmed using Q-RT-PCR (Pearson correlation coefficient for microarray and Q-RT-PCR data = 0.89; p-values for differences in expression between AAA and controls for SOST: 4.87 x 10-4 and for RUNX3: 4.33 x 10-5). Analysis of biological pathways, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), indicated extreme overrepresentation of immune related categories. The enriched categories included the GO category Immune Response (GO:0006955; FDR = 2.1 x 10-14), and the KEGG pathways natural killer cell mediated cytotoxicity (hsa04650; FDR = 5.9 x 10-6) and leukocyte transendothelial migration (hsa04670; FDR = 1.1 x 10-5). CONCLUSION: Previous studies have provided evidence for the involvement of the immune system in AAA. The current expression analysis extends these findings by demonstrating broad coordinate gene expression in immunological pathways. A large number of genes involved in immune function were differentially expressed in AAA, and the pathway analysis gave these results a biological context. The data provide valuable insight for future studies to dissect the pathogenesis of human AAA. These pathways might also be used as targets for the development of therapeutic agents for AAA. 33 17 tibialis anterior DBA/2J Cingulate Cortex C Plasma 861 olfactory epithelium 194 213 Normal Source GEO sample is GSM175812 Last updated (according to GEO): Apr 09 2007 14 NT B4 Treatment, type=add, description=10ng/mL Bonemorphogentic Protein, 4d Source GEO sample is GSM92492 Last updated (according to GEO): Jan 13 2006 A2780_oxa_IC10_16h_2 CNS-SMTC_Mod28d-2C-s2 861 Neoplasm 2869 tumor cells 2880 41 30 PCOS oocytes PBMCs-Type 1 Diabetes-IDDM24_T1D_New 861 Pancreas 673 659 by decapitation ernst-affy-mouse-264940 928 Endometrium 5 0 brain Small cell carcinoma of lung 867 DMN-NF1Hippo28d-1aAv2-s2 26 0 cerebral cortex wistar 3902 brain, hippocampus: C6-II_e1_le1 Brain 1000 Neoplasm 861 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153502 Last updated (according to GEO): Jan 11 2007 861 Tract Brain 861 Epithelial Cells 1000 ADH191 on harvard-12k brain, cerebral cortex: 4R-3(1/29)_le1 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=740610 LaserPower=2.071.29 Lot batch = LC17N096 Source GEO sample is GSM4819 Last updated (according to GEO): Nov 21 2005 an adenovirus 57 69 260 256 Lungs CNS-SC_CtrA30m-1B-s2 39 21 of substantia nigra Epithelial Cells 901 H109 FC BA4 A I_U133Plus_124_Amy Mouse ileum with L.monocytogenes(delta-inlA)_A_5545 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68306 Last updated (according to GEO): Jul 07 2006 Medulla 861 Breast Carcinoma 1000 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153353 Last updated (according to GEO): Dec 27 2006 1000 Encephalitis Mouse Hypothalamus Female 3 (technical replicate) Brain 1000 20 0 human caudate nucleus 5 0 brain SK-MEL-28 hgu95c PGA-MFD-CtrPD1-1aBv2-s2 861 Blood 861 Heart Parkinson's model voxel D2 MGJZ030211001Badiposetissue GSE460 Muscle Source GEO sample is GSM4269 Last updated (according to GEO): May 27 2005 MeHg: PK11195 intervention at 3.0h Liver 1000 mod096_Con-3 70 cortex 76 861 Cerebral cortex Normal Source GEO sample is GSM176153 Last updated (according to GEO): Apr 09 2007 This is a wildtype littermate at postnatal day 5 pool of 5 animals Lot batch = Source GEO sample is GSM4065 Last updated (according to GEO): May 28 2005 CS-B cell UVC-irradiated (12hour) replicate 1 U133A 861 Hippocampus brain, cerebellum: RNA#1S_le1 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210386 Last updated (according to GEO): Jul 16 2007 mouse brains 187 198 outer medulla 31 43 1000 Heart B239 Monocytes treated with isotype control antibody for 24 hrs Universal Mouse Reference RNA Source GEO sample is GSM93435 Last updated (according to GEO): Jan 23 2006 brain 0 5 brain, hippocampus: Hippocampus 3_le1 Adenocarcinoma 861 GSE9770 626 615 PCOS oocytes 15 7 brainstem Regional and strain-specific gene expression mapping in the adult mouse brain. 1000 Brain 21 0 Mammary Gland @ Preg1 Muscle_inadequate protein_female_rep5 Sample is skeletal muscle from a morbidly obese patient undergoing elective abdominal surgery Source GEO sample is GSM3984 Last updated (according to GEO): May 28 2005 Autistic Disorder 877 1_cerebral_cortex_6hrs_sleep_deprivation_#46 Cerebral cortex 861 osteoblast 627 637 high-grade dysplastic liver tissue Source GEO sample is GSM155982 Last updated (according to GEO): Jun 21 2007 with mental retardation 241 263 TEL-AML1-C42 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A MuscleRegen-ctx2d-6LLA-s2 Transitional epithelium 1000 CNS-SC_InjB4h-3C-s2 865 Disorder of artery none Source GEO sample is GSM210292 Last updated (according to GEO): Jul 16 2007 114 101 brains quickly total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withSLC (Secondary lymphoid-organ chemokine) for 240min Source GEO sample is GSM5778 Last updated (according to GEO): May 27 2005 Neoplasm 861 Mucous Membrane 861 861 Acquired Immunodeficiency Syndrome Tissue Source GEO sample is GSM67263 Last updated (according to GEO): Jan 19 2006 858 Prostatic Neoplasms hippocampus rattus_norvegicus_strain iP animal_number 6 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n057 Source GEO sample is GSM2085 Last updated (according to GEO): Nov 21 2005 Heart Septal Defects, Atrial 1000 5 0 brain Melanoma (G361) [JunctionChip 2 of 5] 10 0 hippocampus 861 Skeletal muscle structure 11 0 Fetal brains to hypertension 1744 1758 These studies address temporal changes in gene expression during spontaneous sleep and extended wakefulness in the mouse cerebral cortex, a neuronal target for processes that control sleep; and the hypothalamus, an important site of sleep regulatory processes. We determined these changes by comparing expression in sleeping animals sacrificed at different times during the lights on period, to that in animals sleep deprived and sacrificed at the same diurnal time. Last Updated (by provider): Jan 03 2007 Contributers: S T Jensen J E Zimmerman M Mackiewicz G A Churchill A I Pack D A Baldwin M A Romer K R Shockley N Naidoo R J Galante MP-DX-4 CNS-SC_CtrA24h-2A-s2 Whole blood from a healthy control Source GEO sample is GSM153452 Last updated (according to GEO): Jan 11 2007 Substantia nigra PD rep12 901 frontal lobe Replicate2_Voxel G4 BPH-22 on NHGRI-6.5k_c 1000 Amygdaloid structure Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15750 Last updated (according to GEO): May 28 2005 Stromal Vascular Cells B on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 0861 blood A2780_control_16h_3 Parkinson Disease 1000 PGA-lv_8w_339 1321 1299 by cervical dislocation Expression profiling of spinal cord section (T10) extracted from rats 7dh following severe injury Source GEO sample is GSM31387 Last updated (according to GEO): May 27 2005 Brain 1000 Brain 861 1000 Encephalitis mouse brains 187 198 spinal cord, spinal cord: G2C_le1 85 65 with HIV encephalitis at the Human Brain 746 763 in the striatum 1019 1033 15 0 human cerebellum This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12340 Last updated (according to GEO): May 28 2005 Alzheimer's Disease 861 Caudate P5 Normal na Source GEO sample is GSM181293 Last updated (according to GEO): Apr 10 2007 Prosencephalon 861 30 0 Fetal occipital cortex cocaine5 1000 Retina of coronary artery disease 258 284 MO_control_0min_Patient13 1000 Brain Brain_MD_30_Medulloblastoma_Desmoplastic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Muscle with myocardial infarction 313 339 861 Cerebral cortex Carcinoma, Large Cell 867 Metastatic tumor 19 35 brain_Down_syndrome_sampleid_jg1741 2046 2018 of adhering connective tissue 1150 1131 CA3 pyramidal cells 10 7 Left Wild type 8 wk old male FVB/NJ mouse bed nucleus of the stria terminalis Source GEO sample is GSM74939 Last updated (according to GEO): Feb 27 2007 Eminence 861 brain 0 5 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15700.gif Source GEO sample is GSM84140 Last updated (according to GEO): Sep 22 2006 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18217.gif Source GEO sample is GSM91526 Last updated (according to GEO): Sep 22 2006 663 mesenchymal stem cell 642 NCI60.13_LABEL16EXTRACT15SUB3 Source GEO sample is GSM134059 Last updated (according to GEO): Aug 06 2007 Hypothalamus Source GEO sample is GSM107951 Last updated (according to GEO): Jun 06 2006 Neostriatum 1000 884 Structure of intestinal epithelium adipose_tissue_omental_4 Brain of P10 wildtype C57Bl/6j mouse, replica W4 Standard affymetrix protocol Source GEO sample is GSM119714 Last updated (according to GEO): Jul 31 2007 Utricle and 3 ampullae at E13, replicate1 1000 Cerebrovascular accident Standard Affymetrix Protocol Source GEO sample is GSM16453 Last updated (according to GEO): May 28 2005 861 medulloblastoma brain, brainstem: CB5_e1_le1 OVAR_OVCAR8 on Affymetrix GeneChip Human Full Length Array HuGeneFL at the Human Brain 724 741 Cerebellum 1000 61 41 from postmortem brain Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68130 Last updated (according to GEO): Jul 07 2006 901 lymph nodes from mouse brain 20 35 Spleen 262 267 T-ALL-C14 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Sample47, Post Injury 24 hours Treatment, type=wait Source GEO sample is GSM53297 Last updated (according to GEO): Jul 06 2005 prostate Source GEO sample is GSM203405 Last updated (according to GEO): Jun 21 2007 retina 5 10 Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183414 Last updated (according to GEO): Apr 23 2007 861 Neoplasm brain, frontal cortex: Sample59_e1_le1 1978 1973 muscle Male Sprague-Dawley albino rats (Charles River) initially weighting approximately 200 grams were randomly assigned to one of the following: 1) olanzapine (2 mg/kg/day, I.P.) (N=20) or 2) Saline (N=20) and administered olanzapine or saline for 21 days. Frontal cortex (N=4/group) was dissected and homogenized for microarray, QPCR and western blotting following previous methods (Fatemi et al. 2003; Brooks et al. 2003). RNA isolation, cDNA preparation, microarray hybridization and QPCR followed previous methods (Brooks et al. 2003). Keywords = olanzapine Keywords = frontal cortex Source GEO sample is GSM48581 Last updated (according to GEO): Apr 10 2006 Tumor__Pancreas_Adeno_95_I_298_(I) on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Glial Fibrillary Acidic Protein 1000 Coronary heart disease 913 861 Diabetes Mellitus no additional Source GEO sample is GSM199179 Last updated (according to GEO): Jun 08 2007 no additional Source GEO sample is GSM199086 Last updated (according to GEO): Jun 08 2007 1000 Left Muscle 861 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b064 Source GEO sample is GSM1981 Last updated (according to GEO): Nov 21 2005 of mouse brain 9 23 Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit. Source GEO sample is GSM200584 Last updated (according to GEO): Jul 09 2007 1000 Kidney Pituitary Gland 861 TEL-AML1-2M#5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A N18__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 0 Human Cortex 11 Wild type inbred mice Source GEO sample is GSM82977 Last updated (according to GEO): Nov 10 2005 of somatomotor cortex 21 41 19 0 human frontal cortex Liver (HBV+, HK62) Heart; Atrium Keywords = mouse gene expression database Source GEO sample is GSM29339 Last updated (according to GEO): May 27 2005 129P3/J SAL, Rep1 Ischemia-reperfusion #1 Normal Source GEO sample is GSM176104 Last updated (according to GEO): Apr 09 2007 kidney_cortex_3 HC80 FC BA4 A brain, Right Frontal Lobe: Extract64_le1 SK-MEL-2_CL10005_MELANOMA Normal Source GEO sample is GSM176367 Last updated (according to GEO): Apr 09 2007 in blood 16 23 Disorder of artery 865 C57BL/6ByJ strain, brain hemisphere, biological rep3 1000 Neoplasm Metastasis brain 0 5 Cerebellum_nontransgenic control S46_3.5 months_replicate 4 Spleen vs MIP3-alpha Treated B cell 240min (set2) total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-beta (IFN beta) for 120min Source GEO sample is GSM5597 Last updated (according to GEO): May 27 2005 67 40 with coronary artery disease Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed 6 h to hydrostatic pressure (HP6), pressure experiment # 1 (PE1). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11387 Last updated (according to GEO): Dec 15 2006 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210380 Last updated (according to GEO): Jul 16 2007 Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 9540 left_liver_lobe Sprague-Dawley Female HighSalt Cortex rat704 sd_cortexr_k_704c_020802 Substantia nigra PD rep6 HapMap CEU_parent Male Source GEO sample is GSM159516 Last updated (according to GEO): Feb 01 2007 91 from the bone marrow 72 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13421.gif Source GEO sample is GSM79658 Last updated (according to GEO): Sep 22 2006 7 cortex 12 YFP labeled neurons in amygdala. Source GEO sample is GSM63047 Last updated (according to GEO): Dec 01 2005 the ventricular 1095 1109 10 0 spinal cord Total RNA extracted from mouse brain Source GEO sample is GSM103428 Last updated (according to GEO): Sep 21 2006 0 Human Cortex 11 Cochlea at E11.5, replicate2 GM11830 plasma cells 50 61 Epithelium 865 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225361 Last updated (according to GEO): Aug 31 2007 Ovarian_Tumor_Serous_KU-OS-005 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10149.gif Source GEO sample is GSM79635 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145565 Last updated (according to GEO): Nov 20 2006 Hep2_42_rep3 1509 1499 of diabetes Infection 861 Melanoma xenograft, MA2_Sub_A (LeiATCC) 901 Coronary artery 1000 Descending colon /2J mouse pituitary gland 27 51 861 Epithelium Femur 1000 high gestational age Source GEO sample is GSM213087 Last updated (according to GEO): Jul 25 2007 1000 Brain 1000 Brain muscle 713 719 RNAtotC_23, ZT6 Gene expression data from retinas of two old SAMP8/Ta mice Source GEO sample is GSM143739 Last updated (according to GEO): Jan 24 2007 Spleen 1000 861 Neoplasm 110 94 of heart failure from the femurs 95 109 GSE108 We analyzed the lumbar spinal cord tract of transplanted nmd mice (n=3), untransplanted nmd mice (n=3) and wild-type mice (n=3) (all mice are of male gender). The latter groups underwent surgical procedure with vehicle. The surgical procedure and spinal cord-derived neural stem cell transplantation (intratechal injection) were done at P1 and the animals were sacrificed at 6 weeks of age. Source GEO sample is GSM67533 Last updated (according to GEO): Dec 21 2005 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10130.gif Source GEO sample is GSM79701 Last updated (according to GEO): Sep 22 2006 25 0 frontal cortex wistar 3923 SK-MEL-2 hgu95b Oj5: Hippocampus_21PT-AI_rep9 ER-/LN+/Nevins9 on Affymetrix GeneChip Human Full Length Array HuGeneFL whole blood_101872 none Source GEO sample is GSM244540 Last updated (according to GEO): Nov 23 2007 /3T3 fibroblasts 478 493 large intestine sprague2 Brain 861 Laser capture lung cancer cells Source GEO sample is GSM191019 Last updated (according to GEO): May 25 2007 Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 1987 blood Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15387.gif Source GEO sample is GSM84159 Last updated (according to GEO): Sep 22 2006 Anterior nares 1000 Arteries 861 NCI60.12_LABEL15EXTRACT14SUB3 Source GEO sample is GSM134053 Last updated (according to GEO): Aug 06 2007 I + P T-Cell 48.00 hr. 861 Cerebral cortex Male 27.1 yr after antibody enrichment scan 2 (U133A) DLBC19 on Affymetrix GeneChip Human Full Length Array HuGeneFL 32h-Control replication 2 Keywords = preimplantation Keywords = development Source GEO sample is GSM14699 Last updated (according to GEO): May 28 2005 H9SGK99091504 HapMap JPT Male Source GEO sample is GSM159623 Last updated (according to GEO): Feb 01 2007 Lymphoma (Burkitts Daudi) [JunctionChip 3 of 5] 5 0 brain KidAd_022RAFIO_105.txt nasal epithelial cells 28 49 110 94 of heart failure none Source GEO sample is GSM210310 Last updated (according to GEO): Jul 16 2007 315 312 left 1000 Brain 901 Bone Marrow MCF7/ADRr_CL5002_Breast on Affymetrix GeneChip Human Full Length Array HuGeneFL Infected 6 weeks prior with GFP-expressing recombinant lentivirus Source GEO sample is GSM34389 Last updated (according to GEO): Oct 16 2006 Wild type 8 wk old male DBA/2J mouse amygdala Source GEO sample is GSM74922 Last updated (according to GEO): Feb 27 2007 with benign prostatic hyperplasia 134 166 NoCAD_replicate11 Gene expression data from human colon tumor tissue Source GEO sample is GSM173325 Last updated (according to GEO): Apr 20 2007 The nose 94 101 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211401 Last updated (according to GEO): Jul 18 2007 861 Blood 79 67 Normal Spleen mouse brains 187 198 brain, frontal cortex: Sham AM DR_e1_le1 1000 Heart failure Parkinson Disease 1000 861 Medulla Oblongata Mouse Liver AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate E Brain 861 Femur 1000 Lymphoblastic Leukemia 901 61 50 Spinal cord zhang-affy-mouse-217286 Plasma 861 mouse brain 478 489 human cerebellum Source GEO sample is GSM87136 Last updated (according to GEO): Feb 08 2006 865 Disorder of artery 13 0 Nervous System 361 335 hypertrophic cardiomyopathy Whole blood 0 10 1BJZ02052311_HUMANCULTUREDADIPOCYTE Among the multiple mechanisms that control the intensity and duration of macrophage activation, the development of a state of refractoriness to a second stimulation in cells treated with LPS has long been recognized. Release of inhibitory cytokines and alterations in intracellular signaling pathways may be involved in the development of LPS tolerance. Although a number of molecules have been implicated, a detailed picture of the molecular changes in LPS tolerance is still missing. We have used a genome-wide gene expression analysis approach to (i) define which fraction of LPS target genes are subject to tolerance induction and (ii) identify genes that are expressed at high levels in tolerant macrophages. Our data show that in LPS tolerant macrophages the vast majority of LPS-induced gene expression is abrogated. The extent of tolerance induction varies for individual genes, and a small subset appears to be excepted. Compared to other negative control mechanisms of macrophages, e.g. IL-10-induced deactivation, LPS-tolerance inhibits a much wider range of transcriptional targets. Some previously described negative regulators of TLR-signaling (e.g. IRAK-M) were confirmed as expressed at higher levels in LPS-tolerant macrophages. In addition, we discuss other potential players in LPS tolerance identified in this group of genes. Last Updated (by provider): Aug 01 2007 Contributers: Roland Lang Jörg Mages Plasma 861 1000 Solid tumor Expression profiling of spinal cord section (T9) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31251 Last updated (according to GEO): May 27 2005 VDXIGRU_171150 E2A-PBX1-#11 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Control hippocampus 1 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53447 Last updated (according to GEO): Jul 06 2005 Brain 1000 osteoblast 627 637 FETALTHYROID Source GEO sample is GSM18964 Last updated (according to GEO): Sep 25 2006 CNS-SC_InjB14d-2C-s2 salivary_gland_2 Source GEO sample is GSM80821 Last updated (according to GEO): Mar 31 2006 human cerebellum Source GEO sample is GSM87115 Last updated (according to GEO): Feb 08 2006 Sample28, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53279 Last updated (according to GEO): Jul 06 2005 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27037 Last updated (according to GEO): May 27 2005 39 21 from mammary glands Superior_Cervical_Ganglion Source GEO sample is GSM19012 Last updated (according to GEO): Sep 25 2006 913 Coronary heart disease 1000 Aorta hip_1059_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A MeHg: PK11195 intervention at 6.0h 73 54 of hyperinsulinaemic Muscular Atrophy 1000 Sample 1 at Time 1 Source GEO sample is GSM113087 Last updated (according to GEO): Jun 06 2006 28 0 Amyotrophic lateral sclerosis COID-COID12t1-A349-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Nasal Epithelium 865 1000 Brain Primary Neoplasm 1000 GSE2856 Myometrium 38 Disease OVCAR-8 hgu95e no additional Source GEO sample is GSM199110 Last updated (according to GEO): Jun 08 2007 Wild type voxel D1 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Prostaglandin E2 for 120min Source GEO sample is GSM5737 Last updated (according to GEO): May 27 2005 861 Cerebral cortex of somatomotor cortex 21 41 the infection 46 58 Nasal Epithelium 901 268 251 across donor lungs brain, contralateral HC: Trizol Extraction32_le1 3AJZ02022218_leukemia lymphoblastic (MOLT-4) Brain 1000 152 123 with inflammatory myopathies. Approximately 10 pairs of the most anterior dorsal root ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until sufficient tissue was harvested to be pooled by genotype. Ganglia from 5 embryos were pooled for a single analysis and RNA extracted using the RNeasy system (Qiagen). Source GEO sample is GSM132428 Last updated (according to GEO): Aug 30 2006 Cerebellum_transgenic nuclear localization signal Htt exon1 18Q x50_16 months_replicate 3 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181210 Last updated (according to GEO): Jul 12 2007 Small Pre-BII cells 9 T47D MGMH030228087Aembryoday9.5 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188738 Last updated (according to GEO): Jun 06 2007 Nrf2 +/+ mice (C57B6/SJL) were crossed with nrf2 -/- mice (C57B6/129SVJ) to generate mice heterozygous for nrf2. Interbreeding these heterozygotes generated the double-knockout mice (nrf2 -/-) as well as the corresponding littermate controls (nrf2 +/+). Mice were housed in plastic cages on a bedding of wood chips and maintained at ~22C, ~60% relative humidity, and a 12 hr light/dark cycle. The animals were fed with mouse diet 5015, which includes 30 IU/g of vitamin A and 35 IU/kg of vitamin E, (LabDiet, Richmond, IN) and drinking water ad libitum. All animal protocols were approved by the Institutional Animal Use and Care Committee at the University of Wisconsin-Madison. Total RNA was extracted from livers and spleens isolated from male and female nrf2 wildtype and knockout mice at 5 months of age (prior to the development of severe autoimmune disease). Keywords = Nrf2 Keywords = liver Source GEO sample is GSM13438 Last updated (according to GEO): May 28 2005 Array representing the response of Human foreskin fibroblasts at 4h post HCMV infection Source GEO sample is GSM10371 Last updated (according to GEO): May 27 2005 Disease Source GEO sample is GSM176229 Last updated (according to GEO): Apr 09 2007 67 with bipolar disorder 87 WGACON-43 Hs578T-NCI 861 Brain 281 in the prefrontal cortex 304 861 Cerebral cortex Gene expression data from male mice. Source GEO sample is GSM115537 Last updated (according to GEO): Jun 13 2007 in bronchial epithelia 311 332 cardiac 445 451 Hypothalamus response to LPS and restraint stress B61 on NCI-7.6k CNS-RM_Mod24h-4B-s2 Colorectal cancer patient SC8_vs_Pool Posterior root of spinal nerve 861 Con (16 h) A on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A myocardial infarction 383 403 M_U133A_107_AnCg HapMap JPT Female Source GEO sample is GSM159645 Last updated (according to GEO): Feb 01 2007 H118 CB A Wild type inbred mice Source GEO sample is GSM83020 Last updated (according to GEO): Nov 10 2005 HT29 hgu95e Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120687 Last updated (according to GEO): May 14 2007 861 Occipital lobe WGACON-145 1000 Structure of superior cervical ganglion 5 0 brain Normal gene expression in male and female Sprague-Dawley rat nasal respiratory and olfactory epithelium with some respiratory epithelium. 1039 1072 1000 frontal lobe Isolated adipocytes from subcutaeous adipose tissue Source GEO sample is GSM210981 Last updated (according to GEO): Jul 17 2007 Parkinson's disease sample x017a 0 31 R461P00322 20 0 human caudate nucleus 15 0 human cerebellum the ventricular 1095 1109 in bronchial epithelia 311 332 Sample details: We analysed changes in gene expression in the dorsal telencephalon of forebrain-specific FGFR1 mutant mice. Gene expression was compared between the dorsal telencephalons of single E12.5 embryos of two genotypes: FGFR1 heterozygous (HET1,3,8) and homozygous mutants (HOM2,4,7) that were both heterozygous for the FoxG1 transcription factor, as Cre recombinase expression is driven off the endogenous FoxG1 locus in these animals (Hebert, J. M., Lin, M., Partanen, J., Rossant, J. and McConnell, S. K. (2003b). FGF signaling through FGFR1 is required for olfactory bulb morphogenesis. Development 130, 1101-11. & Hebert, J. M. and McConnell, S. K. (2000). Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures. Dev Biol 222, 296-306. Source GEO sample is GSM62846 Last updated (according to GEO): Aug 26 2005 913 Coronary heart disease 502 481 of human malignancies Autistic Disorder 877 plasma cells 332 344 5 0 brain 875 Acute leukemia nostrils 156 164 Gene expression data from whole brain of uninfected mouse Source GEO sample is GSM189599 Last updated (according to GEO): May 16 2007 861 Alzheimer's Disease Stomach on chromosome 8 716 731 12 4 of Kidney HNC2887 913 Coronary heart disease 5 0 brain Spleen vs Lysophosphatidic Acid Treated B cell 60min (set2) total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CGS for 240min Source GEO sample is GSM5517 Last updated (according to GEO): May 27 2005 861 Acquired Immunodeficiency Syndrome 24 skeletal muscle 10 Sham 2 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107476 Last updated (according to GEO): May 01 2006 Cerebellum 1000 913 Coronary heart disease Low-Density Lipoproteins 884 1767 1752 small intestine Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181200 Last updated (according to GEO): Jul 12 2007 mouse brains 187 198 C57BL/6 benchmark dataset: Embryonic day 10.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25151 Last updated (according to GEO): May 27 2005 D_U133Plus_83_HC 875 Refractory Carcinoma 329 306 valvular cardiomyopathy Keywords = muscle 188 205 of early distant metastases 1579 1606 DNA variation and brain-region specific expression profiles show different relationships between inbred mouse strains: implications for eQTL mapping studies. Parkinson Disease 861 Testis 861 Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for twelve weeks. Source GEO sample is GSM148662 Last updated (according to GEO): Dec 12 2006 1000 Brain the heart 987 996 80 68 Control blood retina 7 12 1000 Spleen Epithelium of bronchus 983 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with NGF (Nerve Growth Factor) for 120min Source GEO sample is GSM5704 Last updated (according to GEO): May 27 2005 Gene expression data from human colon tumor tissue Source GEO sample is GSM173352 Last updated (according to GEO): Apr 20 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with BLC for 30min Source GEO sample is GSM5465 Last updated (according to GEO): May 27 2005 striatum_wt_3m_436 1000 Rectum human frontal cortex Source GEO sample is GSM87016 Last updated (according to GEO): Feb 08 2006 low gestational age Source GEO sample is GSM213108 Last updated (according to GEO): Jul 25 2007 aml8-aml8_549_ab_hu68_abms on Affymetrix GeneChip Human Full Length Array HuGeneFL LDa1a 0 Human Cortex 11 81 70 mouse brains CNS-SC_InjB7d-2C-s2 Mesenchymal Stem Cells 1000 Expression profiling of spinal cord section (T8) extracted from rats 14d following mild injury Source GEO sample is GSM31427 Last updated (according to GEO): May 27 2005 2596 2581 from brain stem adLacZ4 Cochlear nuclei pooled from 20 pups to generate one sample for one replicate hybridization out of 5. Cohybridized with P7_cy3_2. Source GEO sample is GSM44985 Last updated (according to GEO): Jun 08 2005 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16877.gif Source GEO sample is GSM81526 Last updated (according to GEO): Sep 22 2006 Sample is skeletal muscle from obese patient undergoing elective abdominal surgery Source GEO sample is GSM3995 Last updated (according to GEO): May 28 2005 9 0 Blood Test KT9_CAN of the atrial 647 659 14 0 Locus Coeruleus 1000 Myositis osteoblast 627 637 Lymphoblastoid Cell Line for Individual 8202.3 log phase Vestibular organ 0 15 Primary Neoplasm 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Prostaglandin E2 for 60min Source GEO sample is GSM5736 Last updated (according to GEO): May 27 2005 861 Cerebral cortex Gene expression data from postmorten brain regions Source GEO sample is GSM146068 Last updated (according to GEO): Nov 20 2006 HC61 CN A Transplant Series 33 , Transplant # 3 HDMTX_MP-DX-2 TestiLeydigCell Source GEO sample is GSM18825 Last updated (according to GEO): Sep 25 2006 62 29 a genetic, neurocutaneous syndrome 5 0 brain Cerebral cortex 861 substantia_nigra_5 embryonic hearts 1064 1079 Olfactory Epithelium 1000 Spleen vs Lysophosphatidic Acid Treated B cell 30min (set3) Brain 1000 G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Source GEO sample is GSM9647 Last updated (according to GEO): May 28 2005 Lymphoblastoid Cell Line for Individual 8088.4 log phase "Sample 86, BRCA1 mutation(15 months) age 30 erp yes" on vantveer-oligo S1P2-KO-hippocampus, biological rep5 (male) Liver (SF5) Gene expression data from postmorten brain regions Source GEO sample is GSM145745 Last updated (according to GEO): Nov 20 2006 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14972 Last updated (according to GEO): Oct 28 2005 3 0 lung Hippocampus 861 Hereditary Malignant Neoplasm 876 no doxycycline, mutant Source GEO sample is GSM213385 Last updated (according to GEO): Jul 26 2007 /J mouse pituitary gland 25 48 of fibers 969 977 21 0 acute myeloid leukemia Liver 1000 Parkinson Disease 1000 Cerebellum 1000 Spleen vs Platelet activating factor Treated B cell 60min (set2) Blood Test (Blinded) Sample Source GEO sample is GSM129994 Last updated (according to GEO): Sep 18 2007 Hyperdip>50-C23 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 7 cerebral cortex 21 vehicle treatment, 72 hour time point, biological replicate 1 Untreated Control 4weeks AffyGC RMA rep3 brain, Left frontal Lobe: Extract9_le2 587 569 activated microglia Sprague-Dawley Female LowSalt Cortex rat702 sd_cortexr_k_702c_020802 727 721 spleens 861 Cerebral cortex Epithelial Cells 901 N/A Source GEO sample is GSM96291 Last updated (according to GEO): Feb 13 2006 861 Prostate Basal Ganglia 901 1000 Liver Cirrhosis Primary Neoplasm 1000 Infection 1000 Fetal frontal cortex cocaine1 /3T3 fibroblasts 478 493 1000 Spleen Adipose tissue 884 9 0 Blood Test kidney_cortex_2 Source GEO sample is GSM80687 Last updated (according to GEO): Mar 31 2006 1284 HP48_12 2730 2709 with neurite outgrowth 1000 Cerebral cortex Plasma 861 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc123 Source GEO sample is GSM1853 Last updated (according to GEO): Nov 21 2005 Duchenne muscular dystrophy (DMD) patient?s skeletal muscle sample 10 Whole Brain 62 72 Keywords = Heart 505 521 7 0 prostate Disorder of artery 865 Job's patient Source GEO sample is GSM211131 Last updated (according to GEO): Sep 10 2007 Mesenchymal Stem Cells 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28795 Last updated (according to GEO): May 27 2005 41 28 in mouse brain Seminoma 1000 Brain 1000 NA18966 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM80010 Last updated (according to GEO): Oct 26 2005 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120696 Last updated (according to GEO): May 14 2007 Bone Marrow 1000 rat cortex Treatment, type=time_course, measurement=7.0 d Source GEO sample is GSM53215 Last updated (according to GEO): Jul 06 2005 Cerebral cortex 861 Rat frontal cortex RNA - VH TTX Experiment Source GEO sample is GSM92304 Last updated (according to GEO): Jan 13 2006 parietal_lobe_2 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132536 Last updated (according to GEO): Feb 26 2007 1000 Spleen COLON_HCT15 on Affymetrix GeneChip Human Full Length Array HuGeneFL GC (HKG31N) spinal Source GEO sample is GSM67254 Last updated (according to GEO): Jan 19 2006 1000 Brain 1000 frontal lobe 41 28 in mouse brain plasma cells 50 61 Category: Cell-line Subcategory: HMEC This experiment was an out file converted from rana. The original files were not provided to load this experiment in Oracle. Category and Subcategories were made by curators. Scanning Software: unknown Software version: unknown Lot batch = 0374-5k Source GEO sample is GSM1928 Last updated (according to GEO): Nov 21 2005 Brain 861 Metastatic tumor 19 35 80 68 Control blood CHIPEXP_NAME: 230_2_050531tpj_35h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Isoproterenol TREAT_TOX_MECHANISM1: Heart_Cardiotoxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0.5 SAMPLING_TIME: 1 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197609 Last updated (according to GEO): Jun 01 2007 of somatomotor cortex 21 41 Y SIT D075 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108644 Last updated (according to GEO): Aug 22 2006 Mouse Liver LRD Diet 5wk 10ppb As Food Exposure, biological replicate F RNAtotSD_21, ZT6 Cerebral cortex 861 Liver (HBV+, HK63) (AML 23 26 861 Ribosomal RNA Primary tumor 19 32 Normal Source GEO sample is GSM176170 Last updated (according to GEO): Apr 09 2007 Overexpression of the EGFR/FKBP12/HIF-2alpha pathway identified in childhood astrocytomas by angiogenesis gene profiling. Neoplasm 861 1000 Amygdaloid structure adenocarcinoma 3420 0 18 Gene expression data from older female during 1 week of adequate protein intake Source GEO sample is GSM209823 Last updated (according to GEO): Jul 11 2007 Primary tumor 19 32 WT 3 CVB3_S-0.5h-2 cardiac 763 769 Blood 7 11 n/a Source GEO sample is GSM178029 Last updated (according to GEO): Jun 11 2007 Cochlear structure 1000 1000 Hippocampus Cockayne syndrome B cell Source GEO sample is GSM226608 Last updated (according to GEO): Sep 04 2007 1000 Cardiomyopathy, Alcoholic 1000 Cerebral cortex cingulate cortex 861 Locus Coeruleus Source GEO sample is GSM107934 Last updated (according to GEO): Jun 06 2006 human cerebellum Source GEO sample is GSM87149 Last updated (according to GEO): Feb 08 2006 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15521.gif Source GEO sample is GSM84139 Last updated (according to GEO): Sep 22 2006 Expression profiling of moderately injured raphe at 3 months in rats Source GEO sample is GSM41610 Last updated (according to GEO): May 27 2005 M_U133Plus_119_AnCg Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198627 Last updated (according to GEO): Jun 06 2007 The nose 94 101 Uterus 861 41 28 in mouse brain brain, cerebral cortex: Sham17_e1_le1 091215 OVR13 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Skin 1000 Hippocampus D_U133A_49_HC Nasal Epithelium Inhalation Formaldehyde 2ppm 19d ID230 in the brain 150 162 392 368 in secondary glioblastoma Aorta 1000 22 0 Mammary Gland @ Invo2 in human skeletal muscle 111 135 from subcutaneous adipose tissue 25 56 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25505.gif Source GEO sample is GSM81557 Last updated (according to GEO): Sep 22 2006 Ventral Tegmental Area 1000 SF-539 hgu95c Brain 1000 OBX Day 7,# 1 865 Disorder of artery Expression profiling of spinal cord section (T9) extracted from rats 24h following severe injury Lot batch = Source GEO sample is GSM7577 Last updated (according to GEO): May 28 2005 Liver 1000 AD control Treatment, type=dissect Source GEO sample is GSM119642 Last updated (according to GEO): Jul 10 2006 53 26 benign prostatic hyperplasia KT1008a_N the spinal cords 144 159 Circadian Time Treatment, type=time_course, measurement=12.0 h Source GEO sample is GSM53338 Last updated (according to GEO): Jul 06 2005 861 Mammary gland 3rd 1hr C+S-DG 1000 Brain Macrophage smi103 NCI60.15_LABEL19EXTRACT18SUB3 Source GEO sample is GSM134066 Last updated (according to GEO): Aug 06 2007 IFN_PBS_2 Genome wide analysis of placental malaria B_B6_SleepDep_ZT 6_1 C2C12_6.0_hr 861 Retina 15 on NHGRI-13.8k Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc18 Source GEO sample is GSM1902 Last updated (according to GEO): Nov 21 2005 0029_1344_H95A2_KF-188_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11274 Last updated (according to GEO): May 28 2005 Central gray substance of midbrain 861 278 255 ischemic cardiomyopathy 1000 Heart 406 395 whose hearts EWS-C7 on NHGRI-6.5k_b Primary Neoplasm 1000 Neostriatum 1000 Ganglia, Sensory 901 10 0 Endometrium Epithelial Cells 1000 Blood 1000 Whole blood 0 10 Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep7 19 0 human frontal cortex Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28741 Last updated (according to GEO): May 27 2005 M_U133A_93_nAcc with Parkinson's disease 27 50 1000 Cochlear structure I_U133A_42_CB CNS-SpinalC-conAdult-48h-2B-s2 "Sample 8,>5 yr survival(106 months) age 48 erp no" on vantveer-oligo Sun188_BAV13 group 7 0 prostate Chronic leukemia NOS 913 Sun206_TAV12 group 2500mg/kg APAP 24Hr rat 3628 blood vs. 3616 PC 24Hr (pool) of the stria terminalis rep2 19 46 ipsi Cortex 7 17 721_Blymphoblasts Source GEO sample is GSM18731 Last updated (according to GEO): Sep 25 2006 Structure of zygote 861 n/a Source GEO sample is GSM177895 Last updated (according to GEO): Jun 11 2007 Bone Marrow 1000 Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep8 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3736.gif Source GEO sample is GSM76450 Last updated (according to GEO): Sep 22 2006 Chronic leukemia NOS 853 within the hippocampus 789 811 1000 Cochlear structure Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202687 Last updated (according to GEO): Jun 20 2007 Lymphoblastoid Cell Line for Individual 8111.4 log phase Primary small cell lung carcinoma 4271 0 37 CSCC7 sample 2 19 0 human frontal cortex H115 CN B Lg19: Hippocampus_5T-AU_rep6 brain, forebrain: WCx4w#3_e1_le1 D04 3h Media from liver 21 30 ovarian tumor: mucinous Source GEO sample is GSM139430 Last updated (according to GEO): Apr 09 2007 1000 Brain in these tumors 1214 1228 489 472 in the hippocampus Male Sprague-Dawley albino rats (Charles River) initially weighting approximately 200 grams were randomly assigned to one of the following: 1) olanzapine (2 mg/kg/day, I.P.) (N=20) or 2) Saline (N=20) and administered olanzapine or saline for 21 days. Frontal cortex (N=4/group) was dissected and homogenized for microarray, QPCR and western blotting following previous methods (Fatemi et al. 2003; Brooks et al. 2003). RNA isolation, cDNA preparation, microarray hybridization and QPCR followed previous methods (Brooks et al. 2003). Keywords = olanzapine Keywords = frontal cortex Source GEO sample is GSM48583 Last updated (according to GEO): Apr 10 2006 1000 Carcinoma HME-CC_2 1000 Structure of locus ceruleus Hippocampus 861 Frontal Cortex Source GEO sample is GSM107895 Last updated (according to GEO): Jun 06 2006 CAD_replicate81 44 26 of gliomas strongly 92 38 of nicotinic acetylcholine receptor subunit mutant mice Olfactory Epithelium 901 Organ 861 in the cerebellum 29 45 Primary small cell lung carcinoma 3105 0 37 Site: University of California, Davis Cohort: Male/Female Control Set Diagnosis: Control pH: 6.43 Subject: 2846 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39032 Last updated (according to GEO): May 27 2005 mouse hippocampus 0 16 M_U133A_10_AnCg Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152009 Last updated (according to GEO): Feb 06 2007 -_8398_batch1 on NHGRI-6.7k 1000 Cerebral cortex Mental Retardation 1000 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n104 Source GEO sample is GSM2043 Last updated (according to GEO): Nov 21 2005 617 603 the cerebellum Epithelium 861 These data were used as preliminary results for paper: Maternal Cocaine Administration Alters DNA Methylation in Hippocampal Neurons of Neonatal and Prepubertal Mice Svetlana I. Novikova, Fang He, Jie Bai, Nicholas J. Cutrufello, Ashiwel S. Undie and Michael S. Lidow Source GEO sample is GSM154050 Last updated (according to GEO): Jan 19 2007 Abdominal aorta 0 14 331 in nodose ganglia 314 361 335 hypertrophic cardiomyopathy Heart 1000 WGACON-161 brain, unknown: 03DD_e1_le1 CH2128 Knockout saline, technical replicate 1 Bone Marrow 1000 5 0 Uterus Brain 861 19 0 Head and neck cancer Hyperdip>50-#4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Prostate DBA/2J Cerebellum C dorsal striatum wistar ky 3970 whole tissue, individual animal, 10 weeks old, male Wistar Kyoto dorsal striatum file:p3966w Source GEO sample is GSM15186 Last updated (according to GEO): Oct 28 2005 Cerebral cortex 1000 1000 Basal Ganglia Blood 1000 Brain 861 1000 Cerebellum Prostate 16 Disease 0 18 82 53 with congestive heart failure WT P10 replicate 3 of the diaphragm 562 577 861 Intestines P104 non-deprived visual cortex replicate 3 275_1 M_U133Plus_59_HC Relationships among murine CD11c(high) dendritic cell subsets as revealed by baseline gene expression patterns. HapMap YRI_parent Female Source GEO sample is GSM159680 Last updated (according to GEO): Feb 01 2007 healthy subject Source GEO sample is GSM211052 Last updated (according to GEO): Sep 10 2007 112 98 from the kidney Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc88 Source GEO sample is GSM1914 Last updated (according to GEO): Nov 21 2005 Experiment comparing Low-density, CCg derived, progenitors (LDP) with high-density progenitors (HDP), and neurons (LDN) and astrocytes (LDA) derived from the LDP condition Last Updated (by provider): Jul 21 2005 Contributers: Alysson R Muotri Vi T Chu Fred H Gage Includes GDS1396. Update date: Aug 23 2006. Dataset description GDS1396: Analysis of multipotent neural progenitor cells (NPCs) propagated by growth on media containing cystatin C and fibroblast growth factor-2. NPCs isolated from hippocampus neural stem cells. Results provide insight into the frequency of L1 element retrotransposition events in multipotent NPCs.. 1000 Brain brain, unknown: 03DO_e1_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM145947 Last updated (according to GEO): Nov 20 2006 AML-34 on Affymetrix GeneChip Human Full Length Array HuGeneFL N2_d5 #2(16012165010080) trigeminal_ganglia_1 0 Human Cortex 11 Parkinson Disease 861 Parkinson Disease 861 Spleen vs Anti-IgM Treated B cell 120min (set2) 861 Cerebral cortex Anaplastic astrocytoma 875 Gene expression data from postmorten brain regions Source GEO sample is GSM144903 Last updated (according to GEO): Nov 20 2006 1000 Left 861 Trachea 861 Brain Myocardium 861 Phenytoin brainstem 4 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53415 Last updated (according to GEO): Jul 06 2005 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells cultured for 60min Source GEO sample is GSM5842 Last updated (according to GEO): May 27 2005 Brain 1000 Mouse_E13.5_Front_Middle_Back_4 Oi6: Hippocampus_5T-Y_rep10 MCF10A_Untreated_#1 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28804 Last updated (according to GEO): May 27 2005 5 0 Muscle 913 Muscular Dystrophy, Duchenne cirrhotic liver tissue from patients without HCC Source GEO sample is GSM155951 Last updated (according to GEO): Jun 21 2007 Parkinson Disease 1000 AK_SleepDep_ZT 18_2 R664P01207 Gene expression data from postmorten brain regions Source GEO sample is GSM145397 Last updated (according to GEO): Nov 20 2006 Coronary Arteriosclerosis 1000 leukemia 1000 00291187H95A2-T00-0064v2p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Whole Genome array hippocampus_cocaine3 Cell Adhesion Molecules 1000 D_U133Plus_84_nAcc CNS-RM_Mod24h-3A-s2 from mouse brain 14 29 healthy subject Source GEO sample is GSM211071 Last updated (according to GEO): Sep 10 2007 Brain 861 24 19 (Brain Murine_NK_Resting_3 Dendritic Cells, Exposed to Mycobacterium tuberculosis - Repeat #1 with myocardial infarction 313 339 brain_DLPFC_bipolar C_mr423 D_U133A_12_DLPFC 1000 Skeletal muscle structure brain, forebrain: Stg-/-_FB2_le1 Hemisphere #1 Mental Retardation 1000 Brain 861 Integumentary system 861 84 69 by heart failure Knockout saline, biological replicate 3 563 544 of the anterior horn Pituitary Gland 861 1000 Organ of Corti 67 40 with coronary artery disease Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2833 Source GEO sample is GSM2120 Last updated (according to GEO): Nov 21 2005 Skeletal Muscle 3 Normal Gene expression data from postmorten brain regions Source GEO sample is GSM146022 Last updated (according to GEO): Nov 20 2006 no additional Source GEO sample is GSM199063 Last updated (according to GEO): Jun 08 2007 human caudate nucleus Source GEO sample is GSM86918 Last updated (according to GEO): Feb 08 2006 Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19203 Last updated (according to GEO): May 27 2005 none Source GEO sample is GSM123276 Last updated (according to GEO): Jul 27 2006 Spleen vs TGF-beta (transforming growth factor-beta) Treated B cell 30min (set2) 861 Brain occipital_lobe_3 Source GEO sample is GSM80774 Last updated (according to GEO): Mar 31 2006 1000 Liver Duchenne muscular dystrophy (DMD) patient?s skeletal muscle sample 11 129:24-6 pons Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16599.gif Source GEO sample is GSM91573 Last updated (according to GEO): Sep 22 2006 Meningioma Recurrent Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108001 Last updated (according to GEO): Jun 06 2006 SCG explant cultured for 2 hours in vitro Source GEO sample is GSM246032 Last updated (according to GEO): Dec 03 2007 Keywords = kidney 113 130 Stem cells 901 Structure of dentate gyrus 901 Melanocytes, 48h treatment with 5 AzadC HC76 CN A heart failure 583 595 G1E_21_B M7TW00121821 24 0 human prostate PC3 tumors Thyroid Source GEO sample is GSM18962 Last updated (according to GEO): Sep 25 2006 from brains 17 27 228 219 Hippocampi Macrophage 14smi080 Stem cells 901 LT-Hematopoietic stem cell isolated by flow cytometry Source GEO sample is GSM149536 Last updated (according to GEO): Apr 27 2007 923 Congestive heart failure Brain 1000 Sobel-1R01NS046414-01 4 0 Colon of the saphenous artery 43 65 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181091 Last updated (according to GEO): Jul 12 2007 PGA-MurLungRag-pbs-24h-1aBv2-s2 119 96 in embryonic stem cells G9a-H1093K Primary tumor 19 32 1187 1175 In the brain 191 181 of ischemia 1000 Nervous system structure Blood Cells 875 5 0 Spleen brain, cerebral cortex: Rat_03-09_NroLep_Lipska_e1_le1 Brain 861 ISR21-Fv2E-PERK AP20187 4hr2 RNA from an 2nm AP20187 treated (4hr) Fv2E expressing fibroblast cell line in an eIF2 alpha AA (mutant) background. AP20187 activates the kinase activity of the Fv2E-PERK chimera. The eIF2 alpha AA background was used in order to determine whether genes activated through Fv2E-PERK required eIF2alpha phosphorylation. The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules. Source GEO sample is GSM10908 Last updated (according to GEO): May 28 2005 Brain 1000 D_U133A_57_DLPFC 24 0 Proliferative endometrium with Parkinson's disease 27 50 V5-P155 Epithelial Cells 901 Mouse old heart w/ a-tocopherol aT-Ht-2 5 0 brain Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour.This animal was sacrificed at 6 hours after lights on.Original sample code = CM23A Source GEO sample is GSM227341 Last updated (according to GEO): Sep 10 2007 1000 Brain 2500 mg/kg X 24 hr Source GEO sample is GSM129853 Last updated (according to GEO): Sep 18 2007 1000 Familial cancer of breast NOS exp1 NMDA We will separately dissect the maxillary and mandibular branches of the E10.5 first branchial arch from wild type, dlx2, dlx1/2 and Dlx5/6 mutants. The tissues wil be flash frozen within 1 min of removal.We have not performed the dissections yet so we dont know how much RNA will be get from each sample, but previous experience suggests that we will need ~10 branchial arches/experiment. Treatment, type=nucleic_acid_extraction, description=We anticipate using this method as it was recommended by TGEN for small amounts of tissue. Source GEO sample is GSM107887 Last updated (according to GEO): Jun 06 2006 22 0 Mammary Gland @ Preg17 100 FC BA9 B 91 from the bone marrow 72 no additional Source GEO sample is GSM199272 Last updated (according to GEO): Jun 08 2007 Muscle Source GEO sample is GSM4286 Last updated (according to GEO): May 27 2005 Plasma 861 Primary Carcinoma 876 Circadian Time Treatment, type=time_course, measurement=6.0 h Source GEO sample is GSM53330 Last updated (according to GEO): Jul 06 2005 Meningioma Source GEO sample is GSM108020 Last updated (according to GEO): Jun 06 2006 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68271 Last updated (according to GEO): Jul 07 2006 901 Spinal Cord human caudate nucleus Source GEO sample is GSM86808 Last updated (according to GEO): Feb 08 2006 brain, contralateral Cortex: Trizol Extraction14_le1 R743P00701 74 55 of hyperinsulinaemic to distant metastasis 764 784 164 136 of the middle cerebral artery Bone Marrow 1000 The most common congenital cardiac abnormalities 50 97 utricle 895 901 Cochlea at E14.5, replicate1 in blood 16 23 M7TW00121458 healthy subject Source GEO sample is GSM211124 Last updated (according to GEO): Sep 10 2007 861 Epithelial Cells thalamus 567 575 This is the mutant littermate at postnatal day 1 pooled 5 animals Lot batch = Source GEO sample is GSM4079 Last updated (according to GEO): May 28 2005 Blood 1000 Normal Source GEO sample is GSM176347 Last updated (according to GEO): Apr 09 2007 Seminoma 1000 PBMCs-Healthy-HIDDM4_Healthy nasal epithelial cells 28 49 Blood Test (Blinded) Sample Source GEO sample is GSM129959 Last updated (according to GEO): Sep 18 2007 861 Neoplasm Heart 1000 Osteoblasts 1000 861 Cerebral cortex 119 96 in embryonic stem cells Total RNA extracted from the cerebellum of a stg+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144415 Last updated (according to GEO): Nov 14 2006 861 Brain Medulla 861 HMVEC-L stimulated with LPS for 4 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114552 Last updated (according to GEO): Sep 20 2006 Cerebellum BD Normal Con (0 h) A on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A 1000 Prostate SM/J_male_hypothalamus Brain 861 1377 1359 of the cytoskeleton Liver 0 4 Wild type inbred mice Source GEO sample is GSM82955 Last updated (according to GEO): Nov 10 2005 of 1761 tumor 24 36 Leg 23 Day mdx rep 1 brain 0 5 Pooled Total Prefrontal cortex RNA from 4 female FVB/N mice. Source GEO sample is GSM14621 Last updated (according to GEO): May 28 2005 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113957 Last updated (according to GEO): Jun 16 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CpG-oligodeoxynucleotide for 240min Source GEO sample is GSM5529 Last updated (according to GEO): May 27 2005 Layer 5 pyramidal neurons in cigulate cortex. Source GEO sample is GSM63036 Last updated (according to GEO): Dec 01 2005 Hep2_43_rep2 Replicate2_Voxel E7 Job's patient Source GEO sample is GSM211090 Last updated (according to GEO): Sep 10 2007 861 Blood Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151981 Last updated (according to GEO): Feb 06 2007 of Parkinson's disease 450 471 12mo APPSw #1 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211416 Last updated (according to GEO): Jul 18 2007 861 Cardiomyopathies Gene expression data from postmorten brain regions Source GEO sample is GSM145420 Last updated (according to GEO): Nov 20 2006 RENAL_A498 on Affymetrix GeneChip Human Full Length Array HuGeneFL Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26623.gif Source GEO sample is GSM81547 Last updated (according to GEO): Sep 22 2006 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11461 Last updated (according to GEO): May 28 2005 M_U133A_54_DLPFC Skeletal bone 861 none Source GEO sample is GSM241965 Last updated (according to GEO): Nov 29 2007 901 Caudate nucleus structure The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160207 Last updated (according to GEO): Feb 08 2007 Whole Brain 62 72 81 66 mesenteric C57BL Job's patient Source GEO sample is GSM211094 Last updated (according to GEO): Sep 10 2007 hippocampus 7 17 Gene expression data from postmorten brain regions Source GEO sample is GSM145244 Last updated (according to GEO): Nov 20 2006 NCI60.48_LABEL52EXTRACT51SUB3 Source GEO sample is GSM134237 Last updated (according to GEO): Aug 06 2007 Wild type inbred mice Source GEO sample is GSM82999 Last updated (according to GEO): Nov 10 2005 GM19204 Neuraxis 1000 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160212 Last updated (according to GEO): Feb 08 2007 RNA isolated from fetal cerebrum Keywords = trisomy Keywords = brain Keywords = Down syndrome Source GEO sample is GSM22511 Last updated (according to GEO): May 27 2005 primary hepatocytes 0 19 lg_NY57 15 0 human cerebellum Normal Source GEO sample is GSM176208 Last updated (according to GEO): Apr 09 2007 901 Caudate nucleus structure Donor C, prior to G-CSF Source GEO sample is GSM178551 Last updated (according to GEO): Aug 09 2007 The rearranged immunoglobulin 184 212 57 39 with endometriosis Donarum-3R01NS040270-03S1 aml-aml8_644_ab_hu68_abms on Affymetrix GeneChip Human Full Length Array HuGeneFL NA Source GEO sample is GSM198893 Last updated (according to GEO): Jun 07 2007 Voxel F3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1426 Last updated (according to GEO): Nov 21 2005 Skeletal muscle structure 901 We will separately dissect the maxillary and mandibular branches of the E10.5 first branchial arch from wild type, dlx2, dlx1/2 and Dlx5/6 mutants. The tissues wil be flash frozen within 1 min of removal.We have not performed the dissections yet so we dont know how much RNA will be get from each sample, but previous experience suggests that we will need ~10 branchial arches/experiment. Treatment, type=nucleic_acid_extraction, description=We anticipate using this method as it was recommended by TGEN for small amounts of tissue. Source GEO sample is GSM107894 Last updated (according to GEO): Jun 06 2006 Liver 1000 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells cultured for 60min Source GEO sample is GSM5841 Last updated (according to GEO): May 27 2005 Total RNA from iPS clone was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations. Source GEO sample is GSM230267 Last updated (according to GEO): Nov 22 2007 brain, cerebellum: RNA#36_le1 NA12763 59 35 out of mouse bone marrow BREAST_MCF7 on Affymetrix GeneChip Human Full Length Array HuGeneFL CS 3143145A Primary tumor 19 32 Medulla 861 Liver Test (Blinded) Sample Source GEO sample is GSM130169 Last updated (according to GEO): Sep 18 2007 Wild type 8 wk old male A/J mouse hippocampus Source GEO sample is GSM74958 Last updated (according to GEO): Feb 27 2007 11_0029_SepticShock_Day3_29 Blood Test (Blinded) Sample Source GEO sample is GSM129973 Last updated (according to GEO): Sep 18 2007 Nose 1000 from colonic normal mucosa 21 47 861 Cerebral cortex Job's patient Source GEO sample is GSM211133 Last updated (according to GEO): Sep 10 2007 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198648 Last updated (according to GEO): Jun 06 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113915 Last updated (according to GEO): Jun 16 2006 Normal Source GEO sample is GSM176401 Last updated (according to GEO): Apr 09 2007 Epithelial Cells 1000 N/A Source GEO sample is GSM96296 Last updated (according to GEO): Feb 13 2006 I_U133A_28_AnCg 1000 frontal lobe 352 340 encephalitis Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13103.gif Source GEO sample is GSM79936 Last updated (according to GEO): Sep 22 2006 Pooled gastroc RNA samples from five 8 wk old male mdx mice Source GEO sample is GSM13681 Last updated (according to GEO): May 28 2005 hippocampus_9 Source GEO sample is GSM80681 Last updated (according to GEO): Mar 31 2006 Plasma 861 66 55 in the uteri 861 Liver HNN013 Gene expression data from postmorten brain regions Source GEO sample is GSM145800 Last updated (according to GEO): Nov 20 2006 NeverSmoker 43 Neoplasm Metastasis 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11343 Last updated (according to GEO): May 28 2005 861 Muscle Date 11/30/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : embryo proper Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 0.625 mg/kg Time : 3 hrs post-injection Intervention : none Risk: subNOAEL (no increased risk of malformation) Conditional biomarker: p53 protein induction not observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 8-10 embryos pooled from same litter Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = embryo Lot batch = AI057 Source GEO sample is GSM12052 Last updated (according to GEO): May 28 2005 We hypothesized that broad-scale expression profiling would provide insight into the regulatory pathways that control gene expression in response to stress, and potentially identify novel heat-responsive genes. HEp2 cells were heated at 37 to 43 °C for 60 min to gauge the heat shock response, using as a proxy inducible HSP-70 quantified by western blot analysis. Based on these results, microarray experiments were conducted at 37, 40, 41, 42 and 43°C (3 replicates/temperature x 5 groups = 15 U95Aver2 GeneChips). Using linear modeling, we compared the sets of microarrays at 40, 41, 42 and 43°C with the 37°C baseline temperature and took the union of the genes exhibiting differential gene expression signal to create two sets of ?heat shock response? genes, each set reflecting either increased or decreased RNA abundance. Leveraging human and mouse orthologous alignments, we used the two lists of co-expressed genes to predict transcription factor binding sites in silico, including those for heat shock factor 1 (HSF1) and heat shock factor 2 (HSF2) transcription factors. We discovered HSF1 and HSF2 binding sites in 15 genes not previously associated with the heat shock response. We conclude that microarray experiments coupled with upstream promoter analysis can be used to identify novel genes that respond to heat shock. Additional experiments are required to validate these putative heat shock proteins and facilitate a deeper understanding of the mechanisms involved during the stress response. Last Updated (by provider): Apr 04 2007 Contributers: Perren Cobb Jason M Laramie Gary D Stormo Philip Chung Buddy Brownstein MuscleRegen-ctx12h-1LLA-s2 219-97_normal 861 Leukemia, Lymphocytic, Acute Total RNA was extracted from olfactory epithelium tissue from male C57Bl/6 mice (6 week old). Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol. Keywords = olfaction Keywords = neurogenesis Keywords = apoptosis Keywords = gene silencing Keywords = microarray, transcription factor Source GEO sample is GSM45677 Last updated (according to GEO): Oct 28 2005 Spleen vs Sphingosine-1-phosphate Treated B cell 30min (set3) f2#242 versus pool Mouse Brain tissue with Alzheimer's disease 27 50 Heart 1000 Mid secretory endometrium from normal patient Source GEO sample is GSM150226 Last updated (according to GEO): Dec 14 2006 WT-Nrf2-Female-1 n/a Source GEO sample is GSM177899 Last updated (according to GEO): Jun 11 2007 4wkC 25 0 frontal cortex wistar 3925 861 Muscle HapMap JPT Male Source GEO sample is GSM159635 Last updated (according to GEO): Feb 01 2007 with autism spectrum disorder 37 65 Epithelium 861 31 0 Conventional Descending colon 2 1000 Brain 861 Malignant Neoplasms M_U133A_34_CB Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection). Source GEO sample is GSM36428 Last updated (according to GEO): May 27 2005 13 0 Nervous System Rat vestibular ganglia stained with calretinin. Tissue is LCM captured, calretinin positive cells Source GEO sample is GSM100182 Last updated (according to GEO): Mar 13 2006 Alzheimer's Disease 861 0.625 mg/kg 2CdA embryo at 3.0h 54h-AM replication 1 Parkinson Disease 861 high gestational age Source GEO sample is GSM213125 Last updated (according to GEO): Jul 25 2007 brain, Right Parietal Lobe: Extract71_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM145250 Last updated (according to GEO): Nov 20 2006 in seminoma 28 38 metastasize 1467 1478 660 mesenchymal stem cell 639 103 87 of left ventricle PriG_5%O2_Expt3_Day21_rep1 B467 on Affymetrix GeneChip Human Full Length Array HuGeneFL Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225685 Last updated (according to GEO): Nov 05 2007 1000 Microphthalmos A HID U D016 Human lung tissue 55 71 from subcutaeous adipose tissue 20 50 GSE558 ER+/LN+/Nevins4 on Affymetrix GeneChip Human Full Length Array HuGeneFL Subject code A15 Probeset expression data from NA12751 growth 3, replicate 4 Source GEO sample is GSM195216 Last updated (according to GEO): Aug 08 2007 plasma cells 332 344 1000 Mammary gland 861 Blood Fat RYGB-Fail Repl2 M_U133Plus_59_AnCg Cerebellum 1000 Gene expression data from the right forebrain of C57BL mouse received Haloperidol oral treatment for twelve weeks. Source GEO sample is GSM148669 Last updated (according to GEO): Dec 12 2006 myocardial infarction 383 403 913 frontal lobe Olfactory Epithelium 861 Gap Junctions 861 no_pre_no_restimulation_rep_B Infection 1000 myocardial infarction 383 403 Normal Source GEO sample is GSM175881 Last updated (according to GEO): Apr 09 2007 861 Encephalitis Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD8 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD8 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36675 Last updated (according to GEO): May 27 2005 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 10 hours after lights on. Original sample code = CM43A Source GEO sample is GSM227332 Last updated (according to GEO): Sep 10 2007 healthy subject Source GEO sample is GSM211045 Last updated (according to GEO): Sep 10 2007 DBA whole brain 3B AD control Treatment, type=dissect Source GEO sample is GSM119673 Last updated (according to GEO): Jul 10 2006 Gene expression data from a hippocampus of saline-injected mouse Source GEO sample is GSM147416 Last updated (according to GEO): Jan 03 2007 of the stria terminalis 46 68 Mortal human skin fibroblast cell line ATCC number CRL-1502 Source GEO sample is GSM6799 Last updated (according to GEO): May 27 2005 Mouse Liver LRD Diet 5wk Control, biological replicate C HC52 CN A 1000 Retina "Sample 28,>5 yr survival(75 months) age 40 erp no" on vantveer-oligo Normal Source GEO sample is GSM176076 Last updated (according to GEO): Apr 09 2007 Bone Marrow 1000 901 Caudate nucleus structure P21_cy5_4 CT30-1 ovarian tumor: serous Source GEO sample is GSM139443 Last updated (according to GEO): Apr 09 2007 Brain 861 24 0 human prostate PC3 tumors WGACON-205 Liver Test (Blinded) Sample Source GEO sample is GSM130182 Last updated (according to GEO): Sep 18 2007 Spleen vs TGF-beta (transforming growth factor-beta) Treated B cell 30min (set1) Ventral tegmental area 0 22 midbrain_1 Source GEO sample is GSM80699 Last updated (according to GEO): Mar 31 2006 1000 Brain 19 0 human frontal cortex Spleen 0 5 CNS-SC_Inj7d-1C-s2c plasma cells 50 61 Ovary_PD14_Foxo3 Null_Replica 1 Expression profiling of somatomotor cortex extracted from rats at 24h following moderate injury Source GEO sample is GSM41699 Last updated (according to GEO): May 27 2005 prostate Source GEO sample is GSM203394 Last updated (according to GEO): Jun 21 2007 1000 Seizures The epithelial cells 962 981 cy3:SHR control, biological rep 6g; cy5:pool of 6 WKY control rats PGA-HMO-NonObese-6aUA-s2 41 36 spleen lung 107 111 61 50 Kidney C57BL mouse hippocampus, cox-1 WT, rep2 14 7 amygdala osteoblast 627 637 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198659 Last updated (according to GEO): Jun 06 2007 256 235 dilated heart failure Fibroid_2192 Hippocampal development in fetal alcohol exposed rats. Perrone-Bizzozero-5R01NS030255-12-3 Gene expression differences over a critical period of afferent-dependent neuron survival in the mouse auditory brainstem. 430A2_2045_32_KO_neuropath_midbrain Source GEO sample is GSM242695 Last updated (according to GEO): Nov 15 2007 from the femurs 95 109 Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14346.gif Source GEO sample is GSM79699 Last updated (according to GEO): Sep 22 2006 861 Cerebral cortex thyroid_gland_4 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188830 Last updated (according to GEO): Jun 06 2007 "Sample 69, <5 yr survival(25 months) age 41 erp yes" on vantveer-oligo Autistic Disorder 1000 Bone structure of tibia 1000 861 Brain 1251 1211 in chronic obstructive pulmonary disease NCI60.21_LABEL25EXTRACT24SUB3 Source GEO sample is GSM134098 Last updated (according to GEO): Aug 06 2007 Exp B, Animal #4, control (0mg/kg) CPF Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours Source GEO sample is GSM246148 Last updated (according to GEO): Dec 03 2007 1230 1221 of tumours 29 DNA damage 20 Spinal Cord 1000 17 7 hippocampus 304 280 alcoholic cardiomyopathy Myocardium 861 16 6 (cerebellum Posterior root of spinal nerve 861 of uterine horns 375 390 Heart Ventricle 1000 DNA Damage 861 GBM Treatment, type=remove Source GEO sample is GSM99571 Last updated (according to GEO): Apr 21 2006 E8.5b_rep1 1000 Left 861 Mammary gland Adipose tissue 901 3AJZ02050802_AdrenalCortex Universal Mouse Reference RNA Source GEO sample is GSM93428 Last updated (according to GEO): Jan 23 2006 5 0 brain Dendrites 1000 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 0.25 hours after lights on. Original RNA code = LC19A. Source GEO sample is GSM227395 Last updated (according to GEO): Sep 10 2007 Brain 1000 Brain 1000 7 frontal cortex 20 B226 Immature DCs treated with inflammatory cytokines for 24 hrs NHF10-hTERT_G0_C3_26581 1000 Communicable Diseases Nose 1000 in many human cancers 68 89 112 98 from the kidney D_U133A_23_HC in the mammalian nervous system 110 141 913 Bipolar Disorder testis 52 58 PC2 Treatment, type=incubate, description=Hypoxic preconditioning Source GEO sample is GSM107471 Last updated (according to GEO): May 01 2006 1115 1102 cardiomyopathy Brain 1000 I_U133Plus_119_Amy brain_DLPFC_bipolar B_mr288 D03 3h Media Adult frontal cortex cocaine1 884 Intestinal Diseases tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44891 Last updated (according to GEO): May 27 2005 HC103 CB B Male 25.2 yr before antibody enrichment scan 1 (U133A) CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of M?, rhM-CSF was added at 1000 U/ml on the same days. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5146 Last updated (according to GEO): Sep 08 2006 brain, cerebral cortex: Rat_03-40_NroLep_Lipska_e1_le1 Spleen 1000 Oi1: Hippocampus_5T-Y_rep5 239 233 Retinas DLBC22 on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211395 Last updated (according to GEO): Jul 18 2007 from the cerebellum 20 38 8 0 G3 Macula 1000 Kidney retina 5 10 NO_KIDNEY_5 MO_control_180min_Patient17 C3H/HeJ bed nucleus of the stria terminalis rep3 (430 2.0 Array) 366 350 in the amygdala. total RNA from biosource CC#11* Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92476 Last updated (according to GEO): Jan 13 2006 CurrentSmoker 109 Brain 1000 HMEC X BC790 Epithelium 861 129 16:4-6 CA3 Coronary Arteriosclerosis 1000 Primary small cell lung carcinoma 2425 Source GEO sample is GSM17340 Last updated (according to GEO): May 28 2005 Macrophage smi70 #13 (isolate 9 low serum media control) R6/1 18 week transgenic_BC91 HC72 FC BA4 B Simple annotation: Reference verification, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9992.gif Source GEO sample is GSM78467 Last updated (according to GEO): Sep 22 2006 human melanoma metastatic cell line A375 Source GEO sample is GSM195326 Last updated (according to GEO): Jun 04 2007 861 Skeletal bone Anterior interpositus nucleus-centered deep cerebellar nuclei were sampled using syringe needles Source GEO sample is GSM84980 Last updated (according to GEO): Mar 29 2006 to the nose 599 609 RNA samples extracted from astrocytes cultured from wild type and Cx43 null neonatal mice were dye labeled and individually co-hybridized with a reference of labeled cDNAs pooled from a variety of tissues on eight gene arrays containing 8975 mouse DNA sequences Lot batch = 4 Source GEO sample is GSM8896 Last updated (according to GEO): May 27 2005 PERA/EiJ_male_hypothalamus Whole blood 0 10 663 mesenchymal stem cell 642 4 0 Brain Brain 861 Bipolar affective disorder is a severe psychiatric disorder with a strong genetic component but unknown pathophysiology. We used microarray technology (Affymetrix HG-U133A GeneChips) to determine the expression of approximately 22 000 mRNA transcripts in post-mortem brain tissue (orbitofrontal cortex) from patients with bipolar disorder and matched healthy controls. Orbitofrontal cortex tissue from a cohort of 30 subjects was investigated and the final analysis included 10 bipolar and 11 control subjects. Differences between disease and control groups were identified using a rigorous statistical analysis with correction for confounding variables and multiple testing. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Jul 27 2006 Contributers: Sabine Bahn Margaret M Ryan Matthew T Wayland Maree J Webster Stephen J Huffaker Helen E Lockstone Includes GDS2191. Update date: Aug 28 2006. Dataset description GDS2191: Analysis of postmortem orbitofrontal cortex from 10 adults with bipolar disorder. Results provide insight into the pathophysiology of the disease.. brain, Entorhinal Cortex: 99-28 tangle_e1_le1 1000 Brain FBooth-MDX-2Av2-s2 12 0 basal ganglia brain, cerebral cortex: PC17_e1_le1 112 98 from the kidney SNB-75_CL12005_RENAL D08 12h Media Postnatal day 3corticospinal motor neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription. Source GEO sample is GSM37092 Last updated (according to GEO): May 27 2005 E9.0_rep2 15 0 human cerebellum Heart 861 Brain 1000 The left hippocampus was dissected out of a male, 12 month-old nontransgenic control mouse (C57B6/SJL). Total RNA was extracted and the data were analyzed with MAS 5.0 and scaled to 2500. Source GEO sample is GSM26707 Last updated (according to GEO): May 27 2005 Mid secretory endometrium from normal patient Source GEO sample is GSM150221 Last updated (according to GEO): Dec 14 2006 1000 Brain brain 0 5 Total RNA from brain sample of NR3B knockout mice at P5. Treatment, type=purify, measurement=0.0 years Source GEO sample is GSM113689 Last updated (according to GEO): Jun 09 2006 emphysema. 257 267 from brain 21 30 NCI60.4_LABEL7EXTRACT6SUB3 Source GEO sample is GSM134012 Last updated (according to GEO): Aug 06 2007 Normal Source GEO sample is GSM176025 Last updated (according to GEO): Apr 09 2007 cardiomyopathy 190 203 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211339 Last updated (according to GEO): Jul 18 2007 Blood Test (Blinded) Sample Source GEO sample is GSM129971 Last updated (according to GEO): Sep 18 2007 20 0 human caudate nucleus Gene expression data from postmorten brain regions Source GEO sample is GSM145015 Last updated (according to GEO): Nov 20 2006 MO_DH3a_SON_NCBI 196 161 Keywords = Congestive heart failure Brain (thalamus) [JunctionChip 1 of 5] Medulla 861 Bilateral olfactory bulbectomies were performed on male C57Bl/6 mice(6 week old) and olfactory epithelium tissue collected 5 days post-bulbectomy. Total RNA was extracted from the olfactory epithelium tissue. Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol. Keywords = olfaction Keywords = neurogenesis Keywords = apoptosis Keywords = gene silencing Keywords = microarray, transcription factor Source GEO sample is GSM45685 Last updated (according to GEO): Oct 28 2005 Small cell carcinoma of lung 901 91 from the bone marrow 72 Primary tumor 19 32 with myocardial infarction 313 339 340 334 kidney Sample is skeletal muscle from nonobese patient undergoing elective abdominal surgery Source GEO sample is GSM3987 Last updated (according to GEO): May 28 2005 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201795 Last updated (according to GEO): Jun 20 2007 861 Anemia 1000 Amygdaloid structure 22 7 bone marrow cell 5 0 Spleen LymphomaRaji Source GEO sample is GSM18733 Last updated (according to GEO): Sep 25 2006 Cerebral cortex 861 Infected with B. abortus 2308 BA41 and euthanized 3 days post-infection Source GEO sample is GSM155252 Last updated (according to GEO): Aug 08 2007 805-1 Brain 1000 plasma cells 332 344 Spinal Cord Injuries 1000 Gene expression data from colorectal adenoma. Source GEO sample is GSM215113 Last updated (according to GEO): Aug 02 2007 Human prostate cancer and benign prostatic hyperplasia: molecular dissection by gene expression profiling. 62 38 out of mouse bone marrow CNS-RM_CtrT0-3B-s2 NCI60.5_LABEL8EXTRACT7SUB3 Source GEO sample is GSM134016 Last updated (according to GEO): Aug 06 2007 utricle 334 341 nucleus accumbens long access to cocaine replicate 2 (heart 1229 1235 Whole blood from a patient with progressive supranuclear palsy Source GEO sample is GSM153473 Last updated (according to GEO): Jan 11 2007 421 412 infection 7 frontal cortex 20 Chronic Lymphocytic Leukemia 19 47 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68205 Last updated (according to GEO): Jul 07 2006 Brain_PNET_1_PNET on Affymetrix GeneChip Human Full Length Array HuGeneFL brain 0 5 Expression profiling of moderately injured raphe at 3 months in rats Source GEO sample is GSM41602 Last updated (according to GEO): May 27 2005 Occipital lobe 861 Coronary heart disease 913 of mouse brain 9 23 V5-P598 Neoplasm 861 Obesity 1000 trigeminal_ganglia_10 Source GEO sample is GSM80895 Last updated (according to GEO): Mar 31 2006 Brain 1000 91 from the bone marrow 72 228 224 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145971 Last updated (according to GEO): Nov 20 2006 1BRS02081536e_DRG none Source GEO sample is GSM123183 Last updated (according to GEO): Jul 26 2006 H9RGV00102604 Platelet activating receptor factor and innate immunity: 251186821694 9 0 Blood Test 865 Disorder of artery Brain 1000 no additional Source GEO sample is GSM199209 Last updated (according to GEO): Jun 08 2007 Cerebral cortex 861 913 Coronary heart disease prostate Source GEO sample is GSM203267 Last updated (according to GEO): Jun 21 2007 Malignant Neoplasms 861 12 0 ovarian tumor 245 240 Autism 43 0 Chorionic mesoderm-derived mesenchymal cells 1000 Brain 43h-Control replication 2 12 frontal Lobe 23 We analyzed the lumbar spinal cord tract of transplanted nmd mice (n=3), untransplanted nmd mice (n=3) and wild-type mice (n=3) (all mice are of male gender). The latter groups underwent surgical procedure with vehicle. The surgical procedure and spinal cord-derived neural stem cell transplantation (intratechal injection) were done at P1 and the animals were sacrificed at 6 weeks of age. Source GEO sample is GSM67531 Last updated (according to GEO): Dec 21 2005 5 0 brain 138T 361 335 hypertrophic cardiomyopathy Gene expression data from mouse primary visual cortex Source GEO sample is GSM101718 Last updated (according to GEO): Jun 15 2006 1124 1117 tubulin human melanoma metastatic cell line A375 Source GEO sample is GSM195322 Last updated (according to GEO): Jun 04 2007 Gene expression data from rat metanephric mesenchymes cultured for 1 day in the presence of LIF Source GEO sample is GSM126193 Last updated (according to GEO): Dec 08 2006 Hippocampus 1000 24 skeletal muscle 10 prostate Source GEO sample is GSM203261 Last updated (according to GEO): Jun 21 2007 WBM_2Months_B I_U133A_89_AnCg PP149_infected_Skin biopsy Expression profiling of spinal cord section (T8) extracted from rats 14d following severe injury Source GEO sample is GSM31461 Last updated (according to GEO): May 27 2005 of spindle cell tumors 620 641 CAD_replicate55 B388 on Affymetrix GeneChip Human Full Length Array HuGeneFL CNS-SMTC_Mod4h-2A-s2 Gene expression data from experimental treatment D-MD = differentiated and MeCP2 decoy transfected cells. Source GEO sample is GSM102879 Last updated (according to GEO): May 11 2006 Wild type inbred mice Source GEO sample is GSM82994 Last updated (according to GEO): Nov 10 2005 Mesenchymal Stem Cells 1000 129/SvImJ Frontal Cortex C amygdala wistar ky 3946 19 0 human frontal cortex Anterior interpositus nucleus (AIN) is a proposed site of memory formation of eyeblink conditioning. A large part of the underlying molecular events, however, remains unknown. To elucidate molecular mechanisms, we examined transcriptional changes in the AIN of mice trained with delayed-type eyeblink conditioning Last Updated (by provider): Mar 29 2006 Contributers: Shin-ichi Nishimura Shigeyoshi Itohara Jin-Sung Park Prosencephalon 1000 1000 Leukemia, Myelocytic, Acute Cerebral cortex 861 1000 Liver 1000 Breast Carcinoma Accumbens P4 Disease DBA/2J CHR, Rep2 Hippocampal transcript profile in young and middle-aged mice plasma cells 50 61 "35 hr Hela Double Thymidine, exp3" Gene expression data from postmorten brain regions Source GEO sample is GSM144914 Last updated (according to GEO): Nov 20 2006 in the striatum 1034 1049 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Platelet activating factor for 120min Source GEO sample is GSM5726 Last updated (according to GEO): May 27 2005 large intestine 0 14 CD28 beads 06.00 hr. T-Cell Laser capture lung cancer cells Source GEO sample is GSM191058 Last updated (according to GEO): May 25 2007 HapMap CEU_parent Female Source GEO sample is GSM159520 Last updated (according to GEO): Feb 01 2007 0 Human Cortex 11 brain_DLPFC_bipolar B_mr425 909 893 of endometriosis Aorta 861 Gene expression data from postmorten brain regions Source GEO sample is GSM144885 Last updated (according to GEO): Nov 20 2006 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188737 Last updated (according to GEO): Jun 06 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11239 Last updated (according to GEO): May 28 2005 861 Cerebellum 1000 Liver 582 565 of the spinal cord 1000 Cerebellum high-grade dysplastic liver tissue Source GEO sample is GSM155981 Last updated (according to GEO): Jun 21 2007 Papillary thyroid carcinoma 0 26 Brain 861 1000 Brain 366 349 in the hippocampus 861 Brain entorhinal cortex layer II stellate island cells Source GEO sample is GSM107530 Last updated (according to GEO): May 01 2006 Pressure-overload induced hypertrophy model. Mouse was sacrificed 4 hours after aortic banding. Keywords = Cardiac hypertrophy Source GEO sample is GSM2233 Last updated (according to GEO): May 27 2005 1000 Muscle 430_1 MuscleRegen-ctx3.5d-2RLAv2-s2 Mouse ileum 0 10 striatum_Q92_18m_66 Cerebral cortex 861 1000 Communicable Diseases starved 143 149 Epithelial Cells 901 brain_OFC_control C_mr231 5 0 Spleen Carcinoma, Large Cell 884 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211366 Last updated (according to GEO): Jul 18 2007 Bladder sample 1083-2 10 7 Left 89 72 with endometriosis Rat frontal cortex RNA - VH TTX Experiment Source GEO sample is GSM92302 Last updated (according to GEO): Jan 13 2006 Large-scale analysis of the mouse transcriptome. Stomach C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 218.04 Stdv: 7.29 Min: 206.42 Max: 231.90 Source GEO sample is GSM2906 Last updated (according to GEO): Mar 20 2006 Rats 24h after injection with dose kainate. Treatment, type=time_course, description=KA animals are treated with kainate., measurement=24.0 h Source GEO sample is GSM32080 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 5 0 Muscle 17 0 Cord Blood B cells SUDHL6 liver 0 5 Prostate [JunctionChip 1 of 5] 901 Heart failure PrimaryConj2 Keywords = Infectious diseases 1069 1099 GC (HKG46T) Squamous cell carcinoma 2 0 24 normal lung 2841 Source GEO sample is GSM17302 Last updated (according to GEO): May 28 2005 Contralateral 1 18 0 Neurofibromatosis 1 Total RNA from brain sample of wild type mice at P5. Treatment, type=purify, measurement=0.0 years Source GEO sample is GSM113687 Last updated (according to GEO): Jun 09 2006 Macrophage 14smi122 BladdAd_22DAFAY_087.txt Gene expression data from postmorten brain regions Source GEO sample is GSM146063 Last updated (according to GEO): Nov 20 2006 BALB-c mice were given intratracheal bleomycin (1.5U per kg). Lungs were harvested and frozen at 72h. Lot batch = Source GEO sample is GSM4152 Last updated (according to GEO): May 28 2005 Lymphoblastoid Cell Line for Individual 8197.4 log phase Expression profiling of laminectomized raphe at 4h in rats Source GEO sample is GSM41543 Last updated (according to GEO): May 27 2005 Liver (HBV+, HK5) Osteoblasts 1000 Viscera 1000 352 340 encephalitis 264 284 of ovarian follicles Down syndrome (DS) is the most common chromosomally caused form of mental retardation and is caused by trisomy of chromosome 21. The over-expression of genes located on the trisomic region has been assumed to be responsible for the phenotypic abnormalities of DS, but this hypothesis has not been confirmed fully and the very existence of gene dosage effects has been called into question. We have therefore investigated global gene expression profiles in Ts1Cje, a mouse model for DS that displays learning deficits and has a segmental trisomy of chromosome 16 orthologous to a segment of human chromosome 21 spanning from Sod1 to Znf295. DNA microarray analyses of six Ts1Cje and six normal littermate (2N) mouse brains at postnatal day 0 with probe sets representing approximately 11,300 genes revealed that the number of expressed genes and their identities in Ts1Cje mice were almost same in 2N mice. Notably, the expression levels of most genes in the trisomic region were increased approximately 1.5-fold, and the top 24 most consistently over-expressed genes in the Ts1Cje mice were all located in the trisomic region. In contrast, the expression levels of genes on other chromosomes or the euploid region of chromosome 16 were largely the same (1.0-fold) in Ts1Cje and 2N mice. These results indicate that the genes in the trisomic region of Ts1Cje are over-expressed in a dosage-dependent manner and are implicated in the molecular pathogenesis of DS. 923 Subcutaneous Fat 1000 Pituitary Gland, Posterior Spleen 0 5 Primary large cell carcinoma 1997 0 32 Epithelial Cells 901 DBA:2-1-2 entorhinal cortex metanephric mesenchyme, NGAL, 5 days, biological rep2 861 Brain brain 0 5 days nasal epithelium 1127 1148 1 of 3 replicates in treatment group Source GEO sample is GSM206028 Last updated (according to GEO): Jun 29 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CpG-oligodeoxynucleotide for 120min Source GEO sample is GSM5528 Last updated (according to GEO): May 27 2005 861 Breast Leg 56 Day control rep 2 Spleen vs TGF-beta Treated B cell 240min (set1) gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134625 Last updated (according to GEO): Jul 09 2007 Spleen vs Untreated B cell 60min (set1) tTA +Doxy 7424 heart_ventricle_1 Nose 1000 NCI60.11_LABEL14EXTRACT13SUB3 Source GEO sample is GSM134049 Last updated (according to GEO): Aug 06 2007 I_U133A_109_CB 901 Bronchiolitis Obliterans CNS-SMTC_CtrT0-1A-s2 ISR4-WT TM2 RNA from 2ug/ml tunicamycin treated (6 hr) wildtype cells. The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules. Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10887 Last updated (according to GEO): May 27 2005 PE_D_647 metanephric mesenchyme, LIF, 3 days, biological rep1 huang-breast 0 Human Cortex 11 Neurosphere cultures were established from individually isolated E 14.5 forebrains of mouse embryos that carry a bcl2 transgene. Single-cell suspensions were prepared, seeded at 1x105 cells/ml and treated for two days with 150 nM Trichostatin A (TSA), 500 nM 5-Aza-2?-deoxycytidine (AzaC) or both compounds, or left untreated. Two independent experiments were performed. Source GEO sample is GSM8902 Last updated (according to GEO): Oct 28 2005 MGMH030212060Bpancreas bronchial epithelia 224 243 Mouse model of congenital heart disease in Csx/Nkx2.5 mutant embryos. Homozygous mutant mouse at embyronic day 9.5. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2275 Last updated (according to GEO): May 27 2005 Parkinson's disease sample x100 129:4-1 + 4-2 BNST Disease Source GEO sample is GSM175966 Last updated (according to GEO): Apr 09 2007 861 Retina 913 Coronary heart disease 331 307 in central nervous system Prostate 8 Disease C57BL/6J Cingulate Cortex D BL-C7 on NHGRI-6.5k_b 0 Human Cortex 11 1000 Rectum 861 Cerebral cortex 14 7 amygdala Immune; Lymph Node_unstimulated Keywords = mouse gene expression database Source GEO sample is GSM29353 Last updated (according to GEO): May 27 2005 RXF 393 hgu95c 26 week Pre Natal Human lung tissue Source GEO sample is GSM107827 Last updated (according to GEO): May 04 2006 7 0 prostate D_U133A_5_Amy 1000 Cerebrum D_U133A_29_HC Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226049 Last updated (according to GEO): Nov 02 2007 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153373 Last updated (according to GEO): Dec 27 2006 CS 3151152A with myocardial infarction 313 339 Muscular Dystrophies 901 Gene expression data from human prostate tissue with 90 percent tumor content Source GEO sample is GSM119313 Last updated (according to GEO): Feb 23 2007 1000 Thalamic structure Liver 1000 whole blood_101234 Gene expression from Dendritic cells from human subject with pustule former phenotype uninfected. Source GEO sample is GSM128973 Last updated (according to GEO): Sep 13 2007 of regenerating Dorsal Root Ganglia 21 55 861 Heart SynovCTRL_022HACIZ_150.txt Brain 1000 osteoblast 627 637 LOX_IMVI_CL10001_Melanoma on Affymetrix GeneChip Human Full Length Array HuGeneFL 861 Blood 1000 Prostate 861 Cardiomyopathies metanephric mesenchyme, ANX, 1 day, biological rep2 Large cell neuroendocrine carcinoma 901 Brain 861 1000 Structure of superior frontal gyrus Cancers; Colon Tumor Keywords = mouse gene expression database Source GEO sample is GSM29265 Last updated (according to GEO): May 27 2005 Myopathy 875 plasma cells 332 344 2hr time point after 10 Gy of IR exposure Source GEO sample is GSM10973 Last updated (according to GEO): May 28 2005 Expression profiling of spinal cord section (T10) extracted from rats 30m following laminectomy (sham) (sham) Source GEO sample is GSM31279 Last updated (according to GEO): May 27 2005 Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174520 Last updated (according to GEO): Mar 14 2007 Testis 1000 Approximately 10 pairs of the most anterior dorsal root ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until sufficient tissue was harvested to be pooled by genotype. Ganglia from 5 embryos were pooled for a single analysis and RNA extracted using the RNeasy system (Qiagen). Source GEO sample is GSM132429 Last updated (according to GEO): Aug 30 2006 frontal lobe 1000 BALB-c mice were given intratracheal bleomycin (1.5U per kg) or saline control. Lungs were harvested and frozen at 24h. Lot batch = Source GEO sample is GSM4155 Last updated (according to GEO): May 28 2005 983 Cervix carcinoma The left hippocampus was dissected out of a male, 12 month-old nontransgenic control mouse (C57B6/SJL). Total RNA was extracted and the data were analyzed with MAS 5.0 and scaled to 2500. Source GEO sample is GSM26706 Last updated (according to GEO): May 27 2005 2035 2025 for livers 1000 Brain Malignant Neoplasms 861 Nasal Epithelium 865 from epididymal fat tissues 21 48 865 Disorder of artery Malignant Neoplasms 1000 Exploiting the power of high-density gene arrays, the simultaneous expression analysis of 5600 cellular genes was executed on proliferating peripheral blood mononuclear cells (PBMCs) from three normal human donors that were infected in vitro with the T cell tropic laboratory strain of HIV-1, RF. Profiles of expressed genes were assessed at 1, 12, 24, 48, and 72 hr postinfection and compared with those of matched uninfected PBMCs. Viral infection resulted in an overall increase in the number of genes expressed with peaks of expression at 1, 12, and 48 hr postinfection. Functional clustering of genes whose expression level in infected PBMCs varied by 2-fold or greater from levels in the controls indicated that cellular activation markers, proteins associated with immune cell function and with transcription and translation, exhibited increased expression subsequent to viral infection. Gene families exhibiting a decline in gene expression were confined to the 72 hr time point and included genes associated with catabolism and a subset of genes involved with cell signaling and synthetic pathways. Self-organizing map (SOM) cluster analysis identified temporal patterns of coordinated gene expression in infected PBMCs including genes associated with the immune response, the cytoskeleton, and ribosomal subunit structural proteins required for protein synthesis. 7 cerebral cortex 21 mouse brain 478 489 0.5 mg/kg/ml Isoproterenol treatment, 3 hour time point, biological rep 2 Whole Brain 62 72 Stomach 861 gene expression of 3 day LIF differentiated ESCs Source GEO sample is GSM181949 Last updated (according to GEO): Apr 12 2007 Nasal Epithelium 865 Replicate3_Voxel B4 Anterior nares 1000 1000 Cerebral cortex 38 21 from a hippocampus 126 CN B brain, cortex: 7dexp2_e1_le1 7 frontal cortex 20 The most common congenital cardiac abnormalities 50 97 Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep1 plasma cells 50 61 Gene expression data from the right forebrain of C57BL mouse received Haloperidol oral treatment for twelve weeks. Source GEO sample is GSM148676 Last updated (according to GEO): Dec 12 2006 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114230 Last updated (according to GEO): Jun 16 2006 None Source GEO sample is GSM214200 Last updated (according to GEO): Aug 01 2007 of primary fibroblast 136 156 Whole Brain 62 72 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b066 Source GEO sample is GSM1973 Last updated (according to GEO): Nov 21 2005 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11283 Last updated (according to GEO): May 28 2005 Primary Neoplasm 1000 M_U133A_80_AnCg brain 0 5 DBA/2J Basal Ganglia C Ovary_Normal_UM-NO-4 umbilical cord_nobpd: 8B Nose 1000 H85 CN B Heart 861 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc79 Source GEO sample is GSM1870 Last updated (according to GEO): Nov 21 2005 Localized Carcinoma 853 Cardiac 523 530 Skin 1000 Cultured_osteoblast-like_shear-stressed_MC3T3-E1_cells_rep2 Gene expression data from whole tumor Source GEO sample is GSM182299 Last updated (according to GEO): Apr 16 2007 none Source GEO sample is GSM245999 Last updated (according to GEO): Dec 03 2007 Whole Brain 62 72 Wild type 8 wk old male 129S6/SvEvTac mouse bed nucleus of the stria terminalis Source GEO sample is GSM106992 Last updated (according to GEO): Mar 05 2007 Nervous system structure 901 SN48h(2) Gene expression data from whole brain infected mouse, day 6 Source GEO sample is GSM189625 Last updated (according to GEO): May 16 2007 spinal cord, spinal cord: G6F_le1 Assay of baseline expression in the cerebellum of an alcohol-naive Inbred Short Sleep mouse Source GEO sample is GSM67184 Last updated (according to GEO): Oct 28 2005 ProstateCancer-5 on NHGRI-6.5k_c of the postmortem brains 654 678 CD rep 1 901 theca cell from the right forebrain 21 44 at the Human Brain 726 743 1000 Brain 1000 Kidney Arteries 861 NoCAD_replicate20 of the cortex 243 256 Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Meningioma Primary Grade 2. Source GEO sample is GSM108047 Last updated (according to GEO): Jun 06 2006 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16013.gif Source GEO sample is GSM91556 Last updated (according to GEO): Sep 22 2006 Cochlea_WT_9mo_5 Liver 1000 1000 Brain frontal cortex wistar 3658 Gene expression data from postmorten brain regions Source GEO sample is GSM145682 Last updated (according to GEO): Nov 20 2006 861 Mammary gland Nasal Epithelium 901 T265_Mock_2 901 Polycystic Ovary Syndrome 1000 Substantia nigra structure Wild type 8 wk old male 129S6/SvEvTac mouse bed nucleus of the stria terminalis Source GEO sample is GSM106993 Last updated (according to GEO): Mar 05 2007 with Parkinson's disease 27 50 G30-Amygdala-replicate2 A/J Cerebellum E brain, frontal cortex: pADX PM S b_e1_le1 myocardial infarction 383 403 AK_Control_ZT 12_2 Female 71.4 yr before antibody enrichment scan 1 (U133A) Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM Source GEO sample is GSM207680 Last updated (according to GEO): Jul 09 2007 865 Disorder of artery Structure of trigeminal ganglion 1000 861 Brain 256 235 dilated heart failure Head and neck cancer Source GEO sample is GSM155664 Last updated (according to GEO): Apr 24 2007 Brain 861 Whole Brain 73 83 Hippocampus 1000 a_NY36 861 Cerebral cortex 09_0002_SepticShock_Day1_76 56 37 with chronic malaria Ta gr2 tumour Source GEO sample is GSM2532 Last updated (according to GEO): Mar 21 2006 Gender dependent expression of Parkinson's disease 450 471 20 0 human caudate nucleus Medulla Oblongata 861 1000 Cerebrovascular accident Diaphragm 112 Day control rep 2 brain, Entorhinal Cortex: 98-18 tangle_e1_le1 901 Caudate nucleus structure 1000 Glioma brain, hippocampus: KA1-II_e1_le1 Huntington?s disease is a genetic disease caused by a single mutation. It is characterised by progressive movement, emotional and cognitive deficits. R6/2 transgenic mice carrying the Huntington?s disease mutation have a progressive neurological phenotype, including deterioration in cognitive function. The mechanism underlying the cognitive deficits in R6/2 mice is unknown, but dysregulated gene expression, reduced neurotransmitter levels and abnormal synaptic function are present before the cognitive decline becomes pronounced. Our goal here was to ameliorate the cognitive phenotype in R6/2 mice using a combination drug therapy (tacrine, moclobemide and creatine) aimed boosting neurotransmitter levels in the brain. Treatment from 5 weeks of age prevented deterioration in two different cognitive tasks until at least 12 weeks. However, motor deterioration continued unabated. Microarray analysis of global gene expression revealed that many genes significantly up- or down-regulated in untreated R6/2 mice had returned towards normal levels after treatment. Thus dysregulated gene expression was reversed by the combination treatment in the R6/2 mice and probably underlies the observed improvements in cognitive function. Our study shows that cognitive decline caused by a genetic mutation can be slowed by a combination drug treatment, and gives hope that cognitive symptoms in HD can be treated.. Date GSE857 Last Updated: Dec 21 2005 Contributers: Angela K Hodges Lesley Jones Paul D Lewis A J Morton Stephen B Dunnett Mark J Hunt Includes GDS717. Update date: Sep 09 2004. Dataset description GDS717: Whole brain hemispheres from Huntingtons disease model R6/2 transgenic mice treated with creatine, tacrine and moclobemide from 5 weeks of age. Drug therapy was aimed at boosting neurotransmitter levels and improve cognitive functions.. 715 702 After the eyes Frontal_Cerebrocortex_Vehicle_6hr_rep8 rat hippocampus Treatment, type=time_course, measurement=24.0 h Source GEO sample is GSM32140 Last updated (according to GEO): May 27 2005 Control, 01.00 hr. T-Cell Macrophage smi92 of the Brain 70 81 1000 Coronary Arteriosclerosis 288 of alcohol abuse 272 Seizures 861 adenoma 861 Lung Neoplasms 896 8 0 pituitary 1000 Schizophrenia 5 0 Spleen M_U133A_61_nAcc 6 0 Cancers f2#8 versus pool Mouse Brain tissue C57BL/6 benchmark dataset: Embryonic day 15.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25174 Last updated (according to GEO): May 27 2005 5 0 brain Gene expression data from postmorten brain regions Source GEO sample is GSM145280 Last updated (according to GEO): Nov 20 2006 3 days, repeat 2 Posterior root of spinal nerve 861 GSE2031 1000 Left 861 Cerebral cortex GBM Treatment, type=remove Source GEO sample is GSM99539 Last updated (according to GEO): Apr 21 2006 1000 Cerebral cortex 13 0 Nervous System Human muscle cultures were prepared from progenitor satellite cells isolated from a muscle biopsy of a 16-donor subject through an explant-reexplant technique (5). Biopsies were obtained with informed consent and approval of the Human Use Committee of the Hospital Vall d?Hebrón, Barcelona. A batch of cells isolated after 1 explant and 4 consecutive subcultures at dilution (1:3) were induced to differentiate for 15 days and then weekly monitored for the stated parameters. Growth medium was DMEM:MEM-199 3:1, supplemented with 10 % fetal bovine serum (FBS), 10 µg/ml insulin, 2 mM glutamine, 25 ng/ml fibroblast growth factor (FGF) and 10 ng/ml epidermal growth factor (EGF). Differentiating medium had the same composition except FGF and EGF. Cultures were kept at 37ºC in a humidified 5% CO2 atmosphere. Source GEO sample is GSM19164 Last updated (according to GEO): Oct 28 2005 Cochlear nucleus structure 1000 1000 Brain VDXKIU_15C5 1000 Infection Gene expression data from the hippocampus of S1P2-knockout mouse Source GEO sample is GSM172967 Last updated (according to GEO): Mar 08 2007 1000 Brain Myomatous neoplasm 896 7 Entorhinal Cortex 23 Spleen 0 5 WGACON-252 1000 Coronary Arteriosclerosis 2869 tumor cells 2880 To investigate the global effects of vitamin E supplementation on heart aging, we used high-density oligonucleotide arrays to measure transcriptional alterations in 30-month-old B6C3F1 mice supplemented with ?- and ?-tocopherol since middle age (15 months). Last Updated (by provider): Jun 20 2007 Contributers: Tomas A Prolla Richard Weindruch Kyoungmi Kim Sang-Kyu Park David B Allison Mohsen Meydani Grier P Page osteoblast 627 637 Epithelial Cells 861 Baseline comparison of global gene expression in ILS and ISS cerebellum to find differences in the naive state. Source GEO sample is GSM69521 Last updated (according to GEO): Oct 28 2005 of parieto-occipital cortex 64 90 135 116 by CO2 asphyxiation Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11608 Last updated (according to GEO): May 28 2005 female mhm chip 41 Hypothalamus RYGB-Success Repl2 Cy3-labeled cDNA from brains of neonatal C57BL/6j wildtype mice was compared to Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice. Keywords = wildtype mouse brain Source GEO sample is GSM34858 Last updated (according to GEO): Jun 19 2007 GSE8316.1 CD3 + CD28 beads 12.00 hr. T-Cell untransduced mammary epithelial cells passage 9 Source GEO sample is GSM5157 Last updated (according to GEO): May 27 2005 1000 Malignant Neoplasms Control Source GEO sample is GSM175969 Last updated (according to GEO): Apr 09 2007 901 Bone Marrow C118 on NCI-7.6k 104 in the prefrontal cortex 127 from mouse liver 16 31 7 0 Pancreas Gene expression data from liver Source GEO sample is GSM243356 Last updated (according to GEO): Nov 16 2007 Substantia Nigra Control Sample3 RMA, MAS 5, dChip PGA-HMO-MObese-1aUA-s2 75 50 Dorsal root ganglion C57BL 15 0 skeletal muscle Global gene expression information that can be used to identify pathways involved in the pathophysiology of disease. We used microarrays to identify which genes are expressed in either the abdominal aorta (control) or in abdominal aortic aneurysms (case), and also which genes may be differential between the two tissue states. Last Updated (by provider): Jul 26 2007 Contributers: Gerard Tromp Shantel Weinsheimer Guy M Lenk Helena Kuivaniemi 861 Brain Mouse retinal sphere RNA-4, chip MOE430A Primary tumor 19 32 Gene expression data from postmorten brain regions Source GEO sample is GSM145769 Last updated (according to GEO): Nov 20 2006 CNS-SpinalCmod-Adult-72h-4B-s2 1000 Myositis brain, cerebellum: KCb4w#1_e1_le1 Whole blood 0 10 861 Cerebellum Plasma 861 Carcinoma, Large Cell 867 Type 2 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228668 Last updated (according to GEO): Sep 11 2007 5-Hydroxytryptamine 2A receptor 307 337 Oat cell carcinoma 867 Mesenchymal Stem Cells 1000 SK-OV-3 hgu95e 1000 Heart Spinal Cord 901 430A2_2045_4_KO_sham_midbrain Source GEO sample is GSM242701 Last updated (according to GEO): Nov 15 2007 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153354 Last updated (according to GEO): Dec 27 2006 861 Brain 41 29 Control blood A/J Olfactory Bulb D Parkinson Disease 861 Richard Almon-45-1133800610151 Pooled gastroc RNA samples from five 8 wk old male C57BL10 mice Source GEO sample is GSM13674 Last updated (according to GEO): May 28 2005 Substantia nigra normal rep3 1000 Intestines, Small Brain 1000 Development of the pancreas from the endoderm is initiated at embryonic day 9 of mouse development and over the following days several different cell types develop from pancreas progenitor cells. A distinct phase of pancreas development, known as the secondary transition, is initiated at day 13 of development and one of the key features of this transition is a massive increase in the number of mature endocrine cells. To study gene expression in pancreas during the secondary transition we performed high-density oligonucleotide microarray experiments on dorsal pancreas tissue isolated from NMRI embryos on consecutive days from e12.5 to e16.5. Last Updated (by provider): Jun 08 2007 Contributers: Andreas Petri Ganglia 861 Day 7 Mouse #53 - 2nd replicate H129 CN A c_NY104 Nasal Epithelium Inhalation Formaldehyde 0ppm 5d ID62 Pool of total RNA from 2 euploid cerebella at P30 postnatal stage Keywords = Down syndrome Keywords = Chromosome 21 Keywords = Transcriptome Keywords = Microarray Keywords = Brain Keywords = Cerebellum Keywords = Development Source GEO sample is GSM27476 Last updated (according to GEO): May 27 2005 Cortex 0 5 Nose 1000 gfp pos. sorted cells from 3 disected e14.5 cortecies Treatment, type=wait Source GEO sample is GSM135785 Last updated (according to GEO): Sep 12 2006 in the mammalian nervous system 110 141 Normal Source GEO sample is GSM175827 Last updated (according to GEO): Apr 09 2007 The source of aldosterone in 30 to 40 % of patients with primary hyperaldosteronism (PA) is unilateral aldosterone-producing adenoma (APA). The mechanisms causing elevated aldosterone production in APA are unknown. Herein, we examined expression of G-protein coupled receptors (GPCR) in APA and demonstrate that compared to normal adrenals there is a general elevation of certain GPCR in many APA and/or ectopic expression of GPCR in others. RNA samples from normal adrenals (n = 5), APAs (n = 10), and cortisol-producing adenomas (CPAs) (n=13) were used on 15 genomic expression arrays, each of which included 223 GPCR transcripts presented in at least one out of 15 of the independent microarrays. The array results were confirmed using real-time RT-PCR (qPCR). Four GPCR transcripts exhibited a statistically significant increase that was greater than 3-fold compared to normal adrenals, suggesting a general increase in expression compared to normal adrenal glands. Four GPCR transcripts exhibited a greater than 15-fold increase of expression in one or more of the APA samples compared to normal adrenals. qPCR analysis confirmed array data and found the receptors with the highest fold increase in APA expression to be luteinizing hormone receptor (LH-R), serotonin receptor 4 (HTR4), gonadotropin-releasing hormone receptor (GnRHR), glutamate receptor metabotropic 3 (GRM3), endothelin receptor type B-like protein (GPR37), and ACTH receptor (MC2R). There are also sporadic increased expressions of these genes in the CPAs. Together, these findings suggest a potential role of altered GPCR expression in many cases of PA and provide candidate GPCR for further study. Last Updated (by provider): Jul 18 2007 Contributers: William Rainey Ping Ye 1000 Brain NHF10-hTERT_1.5Gy_6h_C3_21764 1358 1350 in brains AO Treatment, type=remove Source GEO sample is GSM99523 Last updated (according to GEO): Apr 21 2006 Parkinson Disease 861 of the atrial 647 659 human frontal cortex Source GEO sample is GSM87011 Last updated (according to GEO): Feb 08 2006 TGFbeta added. Source GEO sample is GSM203978 Last updated (according to GEO): Jun 25 2007 20 0 human caudate nucleus Prosencephalon 1000 Tumor__CNS_Medulloblastoma_M20_A56 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Central gray substance of midbrain 861 NA07022 in the brain 500 511 Intestines, Small 1000 Neoplasm 861 Fluid-percussion head injury 83 110 Hyperdip>50-C17 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A NCI60.17_LABEL21EXTRACT20SUB3 Source GEO sample is GSM134078 Last updated (according to GEO): Aug 06 2007 P14 cochlear nuclei pooled from 5 pups for one replicate hybridization out of 2 replicates. Source GEO sample is GSM44853 Last updated (according to GEO): Jun 08 2005 The nose 94 101 Assay of baseline expression in the cerebellum of an alcohol-naive Inbred Short Sleep mouse Source GEO sample is GSM67194 Last updated (according to GEO): Oct 28 2005 Brain 861 brain, ipsi HC: Trizol Extraction21_le1 Lymphoma (Burkitts Daudi) [JunctionChip 2 of 5] 61 41 from postmortem brain 11 0 spinal cord I_95Av2_3108_CB_0_GS M_U133A_51_DLPFC Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2794 Source GEO sample is GSM2106 Last updated (according to GEO): Nov 21 2005 ovarian tumor: endometrioid Source GEO sample is GSM139418 Last updated (according to GEO): Apr 09 2007 "4h Thy-Noc, Exp4" kidney 37 43 I_U133A_48_AnCg spinal cord 37 47 Blood Test (Blinded) Sample Source GEO sample is GSM130050 Last updated (according to GEO): Sep 18 2007 no additional Source GEO sample is GSM199384 Last updated (according to GEO): Jun 08 2007 Hippocampus 1000 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16366.gif Source GEO sample is GSM91531 Last updated (according to GEO): Sep 22 2006 SN:1011115;Fetal Cartilage, U133B validation of the stria terminalis 78 101 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Insulin-like growth factor 1 for 30min Source GEO sample is GSM5615 Last updated (according to GEO): May 27 2005 The nose 94 101 in the frontal cortex 268 289 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22188.gif Source GEO sample is GSM93132 Last updated (according to GEO): Sep 22 2006 Disorder of artery 865 Rett Syndrome 861 Oi5: Hippocampus_5T-Y_rep9 17 7 hippocampus Liver 1000 starved 22 28 Hyperdip>50-C21 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A "Sample 37,>5 yr survival(88 months) age 54 erp missing" on vantveer-oligo Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10146.gif Source GEO sample is GSM79631 Last updated (according to GEO): Sep 22 2006 861 Coxsackievirus Infections Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P21, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3239 Last updated (according to GEO): May 28 2005 We will separately dissect the maxillary and mandibular branches of the E10.5 first branchial arch from wild type, dlx2, dlx1/2 and Dlx5/6 mutants. The tissues wil be flash frozen within 1 min of removal.We have not performed the dissections yet so we dont know how much RNA will be get from each sample, but previous experience suggests that we will need ~10 branchial arches/experiment. Treatment, type=nucleic_acid_extraction, description=We anticipate using this method as it was recommended by TGEN for small amounts of tissue. Source GEO sample is GSM107883 Last updated (according to GEO): Jun 06 2006 Ventral Tegmental Area 2 Normal B6By.C.132.54 strain, brain hemisphere, biological rep2 25 7 Right Parietal Lobe Mental Retardation 1000 2 hrs Pre-clamp sample 5 42 22 of ciliary epithelium 91 from the bone marrow 72 nodose_nucleus_5 7 0 prostate 861 Intestines a_B35B total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD40 for 30min Source GEO sample is GSM5492 Last updated (according to GEO): May 27 2005 Skeletal bone 861 m1-carcinoma4 bronchial epithelia 224 243 ER+/LN+/Marks206 on Affymetrix GeneChip Human Full Length Array HuGeneFL Retina 861 Brain_MD_18_Medulloblastoma_Classic_D on Affymetrix GeneChip Human Full Length Array HuGeneFL Hypothalamic structure 861 outer medulla 31 43 Large cell carcinoma of lung 901 The temporal program of gene expression during a model physiological response of human cells, the response of fibroblasts to serum, was explored with a complementary DNA microarray representing about 8600 different human genes. Genes could be clustered into groups on the basis of their temporal patterns of expression in this program. Many features of the transcriptional program appeared to be related to the physiology of wound repair, suggesting that fibroblasts play a larger and richer role in this complex multicellular response than had previously been appreciated. Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68302 Last updated (according to GEO): Jul 07 2006 Neoplasm 861 Normal Source GEO sample is GSM176430 Last updated (according to GEO): Apr 09 2007 1037 of transitional epithelium 1012 RNA sample 1 from motor neurons of SOD1 mice Treatment, type=double_round_amplification, description=T7-based two round of RNA amplification Source GEO sample is GSM92521 Last updated (according to GEO): Jan 13 2006 Timed pregnant C57Bl6 mice were exposed to ethanol during gestational day 15 to day 18 and ethanol exposed fetuses were delivered by cessarian section on gestational day 19. Alcohol exposed fetuses were compared to control timed preg Source GEO sample is GSM116858 Last updated (according to GEO): Jul 03 2006 human cerebellum Source GEO sample is GSM87183 Last updated (according to GEO): Feb 08 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL4 for 240min Source GEO sample is GSM5640 Last updated (according to GEO): May 27 2005 928 Endometrium Gene expression data from postmorten brain regions Source GEO sample is GSM144923 Last updated (according to GEO): Nov 20 2006 AD-221t1-A148-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A DBA/2J hypothalamus rep1 (430 2.0 Array) 1000 Amygdaloid structure PriG_5%O2_Expt2_Day5_rep1 1000 Pituitary Gland 24 0 human prostate PC3 tumors Structure of superior frontal gyrus 1000 173 150 to cognitive impairment spinal cords 265 276 A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism Source GEO sample is GSM5981 Last updated (according to GEO): Nov 21 2005 861 Cardiomyopathies Skeletal bone 861 JMR-RatSham4h-1aA-s2 1st 1hr C+S-CA1 WGACON-199 861 Occipital lobe Gene expression data from brain of adult rats Source GEO sample is GSM101009 Last updated (according to GEO): Feb 20 2007 Cancers; Prox.Jejunum tumor Keywords = mouse gene expression database Source GEO sample is GSM29282 Last updated (according to GEO): May 27 2005 no additional Source GEO sample is GSM199114 Last updated (according to GEO): Jun 08 2007 Expression profiling of moderately injured raphe at 28d in rats Source GEO sample is GSM41588 Last updated (according to GEO): May 27 2005 Plasma 861 CAD_replicate14 SynovCTRL_0227ACID_150.txt 861 Skeletal bone Gene expression data Source GEO sample is GSM183177 Last updated (according to GEO): Jul 30 2007 nucleus accumbens long access to cocaine replicate 3 Total RNA extracted from the forebrain of a stg-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144383 Last updated (according to GEO): Nov 14 2006 228 219 Hippocampi Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13107.gif Source GEO sample is GSM79941 Last updated (according to GEO): Sep 22 2006 TUMOR 9 0 6 195 with coxsackievirus B3 174 BCR-ABL-#1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Neoplasm 861 861 Neoplasm 1000 Brain 091221 OVR16 on Affymetrix GeneChip Human Full Length Array HuGeneFL HMVEC-L stimulated with LPS for 24 hours L24R2 The sample is a part of a series describing gene expression changes during postnatal development of the small intestine Source GEO sample is GSM198856 Last updated (according to GEO): Jun 11 2007 1000 Chromatin Ng2: Hippocampus_NT-Y_rep8 Ganglia 861 spinal cord injury 141 158 PCA28_localized prostate cancer 54h-Control replication 3 plasma cells 332 344 Parkinson?s disease (PD) progresses relentlessly and affects five million people worldwide. Laboratory tests for PD are critically needed for developing treatments designed to slow or prevent progression of the disease. We performed a transcriptome-wide scan in 105 individuals to interrogate the molecular processes perturbed in cellular blood of patients with early-stage PD. The molecular marker here identified is strongly associated with risk of PD in 66 samples of the training set (third tertile cross-validated odds ratio of 5.7 {P for trend 0.005}). It is further validated in 39 independent test samples (third tertile odds ratio of 5.1 {P for trend 0.04}). The genes differentially expressed in patients with PD, or Alzheimer?s or progressive supranuclear palsy offer unique insights into disease-linked processes detectable in peripheral blood. Combining gene expression scans in blood and linked clinical data will facilitate the rapid characterization of candidate biomarkers as demonstrated here with respect to PD. Last Updated (by provider): Jan 23 2007 Contributers: Clemens R Scherzer Ventral Tegmental Area 9 Normal COLON_SW620 on Affymetrix GeneChip Human Full Length Array HuGeneFL 5 0 brain Gene expression data of substantia nigra from postmortem brain of PD patients Source GEO sample is GSM184376 Last updated (according to GEO): May 29 2007 1000 Hippocampus Wild-type 5 months old, male Source GEO sample is GSM154349 Last updated (according to GEO): Jan 09 2007 Basal 1000 into squamous, large cell 270 295 126 123 (ALS nasal epithelial cells 28 49 284 274 in cancer. f2#47 versus pool Mouse Brain tissue Microarray analyses during adipogenesis: understanding the effects of Wnt signaling on adipogenesis and the roles of liver X receptor alpha in adipocyte metabolism. B55 on NCI-7.6k Nose 1000 100210 Cerebral cortex 861 Liver 1000 1000 Encephalitis Whole blood 0 10 1868 1854 adhering blood 884 Vestibular ganglion 1000 Caudate nucleus structure Control total RNA was pooled from the kidney of five normal BALB/c mice. Total RNA was extracted from the kidney of BALB/c mice injected with anti-GBM antibody for 11 day. Source GEO sample is GSM15086 Last updated (according to GEO): May 28 2005 Spleen vs fMLP Treated B cell 240min (set1) Substantia Nigra MML Sample1 RMA, MAS 5, dChip Acetaminophen 24hr Rat 6954 blood vs. Acetaminophen 24hr Rat Pooled Control blood CLL-55 50 43 jejunum Medulla Oblongata 861 AMM_0_0_Female7_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111837 Last updated (according to GEO): Nov 21 2006 Neoplasm 861 Cortex_Bulbectomized_rep5 Gene expression data from the neocortex of wild-type mouse Source GEO sample is GSM172932 Last updated (according to GEO): Mar 08 2007 Brain 861 huang-papillary 861 Liver nostrils 156 164 NA11832 12 0 ovarian tumor Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35390 Last updated (according to GEO): May 27 2005 Occipital lobe 861 CS 105h the blood 393 402 Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 4678 left_liver_lobe Gene expression data from postmorten brain regions Source GEO sample is GSM146083 Last updated (according to GEO): Nov 20 2006 Response of murine splenocytes to infection with wild type or virB mutant Brucella strains 861 Brain Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211316 Last updated (according to GEO): Jul 18 2007 Mesenchymal Stem Cells 1000 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132519 Last updated (according to GEO): Feb 26 2007 in seminoma 28 38 wt mouse number 1 Source GEO sample is GSM186666 Last updated (according to GEO): Jun 11 2007 DMN-NF1Hippo20d-1aAv2-s2 0 Human Cortex 11 f2#94 versus pool Mouse Brain tissue HBEC Source GEO sample is GSM18814 Last updated (according to GEO): Sep 25 2006 Normal human fetal cartilage from 18-22 weeks. Source GEO sample is GSM149644 Last updated (according to GEO): Jul 06 2007 I_U133Plus_121_Amy 36 21 from whole brain Hippocampus 0 10 861 Cerebral cortex The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159977 Last updated (according to GEO): Feb 01 2007 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120705 Last updated (according to GEO): May 14 2007 n/a Source GEO sample is GSM178066 Last updated (according to GEO): Jun 11 2007 5 0 Spleen Recommended Affymetrix protocols were followed. Source GEO sample is GSM148474 Last updated (according to GEO): May 01 2007 B220Low sIgM+ immature B cells sorted out of mouse bone marrow, sort no. 8 Source GEO sample is GSM640 Last updated (according to GEO): Mar 20 2006 leukemia, chronic Myelogenous K-562 Source GEO sample is GSM18898 Last updated (according to GEO): Sep 25 2006 193 160 that transformed neural stem cells Expression profiling of spinal cord section (T9) extracted from rats 24h following severe injury Lot batch = Source GEO sample is GSM7569 Last updated (according to GEO): May 28 2005 nmd untreated 3 985 953 in more posterior sensory ganglia Attenuation of allergic contact dermatitis through the endocannabinoid system. 861 Brain Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11279 Last updated (according to GEO): May 28 2005 861 Malignant neoplasm of prostate Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:364, Count:32 Corner- Avg:36544, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:15.267480,SFGene:All Background:Avg:408.40,Stdev:5.81,Max:426.0,Min:399.9 Noise:Avg:9.27,Stdev:0.43,Max:10.8,Min:8.4 RawQ:13.27 Keywords = ALL Source GEO sample is GSM3490 Last updated (according to GEO): May 28 2005 /3T3 fibroblasts 743 759 C57BL/6 benchmark dataset: Embryonic day 14.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25173 Last updated (according to GEO): May 27 2005 1000 Brain human caudate nucleus Source GEO sample is GSM86911 Last updated (according to GEO): Feb 08 2006 cingulate cortex 861 Transitional epithelium 1000 GSE372 Flow cytometry sorted double negative thymocytes from Egr1/Egr3 double knockout animal #3. Treatment, type=fractionate Source GEO sample is GSM130406 Last updated (according to GEO): Aug 24 2006 Epithelium of bronchus 983 Neoplasm 861 9 0 Blood Test Epithelial Cells 901 Corpus Callosum 5 Normal human frontal cortex Source GEO sample is GSM87035 Last updated (according to GEO): Feb 08 2006 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113925 Last updated (according to GEO): Jun 16 2006 Whole Brain 62 72 of regenerating Dorsal Root Ganglia 21 55 Osteoblasts 1000 1533 Stem cells 1524 91 from the bone marrow 72 MGJZ030212025Aprostate Adrenal Medulla 1000 215 199 of neural retinas 21 7 adrenal medulla UBOC1 Exp B Day 2 (a) Heart 861 21 CN A Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68118 Last updated (according to GEO): Jul 07 2006 Gene expression data from human colon tumor tissue Source GEO sample is GSM173360 Last updated (according to GEO): Apr 20 2007 cerebellum 7 16 1238 CP24_11 660 mesenchymal stem cell 639 (1 utricle 10 19 Brain 861 1000 Communicable Diseases Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n092 Source GEO sample is GSM2034 Last updated (according to GEO): Nov 21 2005 contralateral Cortex 7 27 Epithelium 865 Sample details: We analysed changes in gene expression in the dorsal telencephalon of forebrain-specific FGFR1 mutant mice. Gene expression was compared between the dorsal telencephalons of single E12.5 embryos of two genotypes: FGFR1 heterozygous (HET1,3,8) and homozygous mutants (HOM2,4,7) that were both heterozygous for the FoxG1 transcription factor, as Cre recombinase expression is driven off the endogenous FoxG1 locus in these animals (Hebert, J. M., Lin, M., Partanen, J., Rossant, J. and McConnell, S. K. (2003b). FGF signaling through FGFR1 is required for olfactory bulb morphogenesis. Development 130, 1101-11. & Hebert, J. M. and McConnell, S. K. (2000). Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures. Dev Biol 222, 296-306. Source GEO sample is GSM62849 Last updated (according to GEO): Aug 26 2005 na Source GEO sample is GSM181302 Last updated (according to GEO): Apr 10 2007 in the brain 150 162 human caudate nucleus Source GEO sample is GSM86818 Last updated (according to GEO): Feb 08 2006 901 Bone Marrow C57BL/6J female number 2, DNFB-treated allergic ear (#5_Wt-Tr-4) brain_DLPFC_bipolar C_mr801 129P3/J Chronic morphine treated, striatum, biological replicate 2 Source GEO sample is GSM187972 Last updated (according to GEO): Jun 14 2007 MSE_D_33A 1000 Cardiomyopathy, Alcoholic BXD38_M7SS02042213 1000 Communicable Diseases **** Source GEO sample is GSM4285 Last updated (according to GEO): May 27 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68245 Last updated (according to GEO): Jul 07 2006 913 Coronary heart disease Transcriptional profiling of the human frontal cortex from individuals ranging from 26 to 106 years of age. The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Last Updated (by provider): May 29 2005 Contributers: Shyan-Yuan Kao Tao Lu Bruce A Yankner Ying Pan Jennifer Chan Cheng Li Isaac Kohane Includes GDS707. Update date: Sep 09 2004. Dataset description GDS707: Analysis of gene expression profiles obtained from the postmortem frontal cortex of 18 normal males and 12 normal females at 26 to 106 years of age. Results provide insight into molecular events underlying the onset of brain aging.. Spleen 1000 e_2m51 Head and neck cancer Source GEO sample is GSM155692 Last updated (according to GEO): Apr 24 2007 hippocampus_10 Source GEO sample is GSM80682 Last updated (according to GEO): Mar 31 2006 20 0 human caudate nucleus Neuroglia 901 Heart 1000 88 68 with bicuspid valves 7 0 prostate nasal epithelial cells 28 49 Heart 861 Disease Source GEO sample is GSM175921 Last updated (according to GEO): Apr 09 2007 17 0 Normal Bone Marrow Olfactory Epithelium 1000 cortex from B6 mice at ZT3 rep2 Source GEO sample is GSM160453 Last updated (according to GEO): Feb 05 2007 Cerebral cortex 861 Parkinson Disease 861 stria terminalis 901 Non-inner ear tissues pooled from E9.5 to E10.5, replicate2 Plasma 861 against malaria 1759 1774 brain, unknown: Sample61_e1_le1 334 320 Keywords = HIV 858 Prostatic Neoplasms H9LMS00111503 Mesenchymal Stem Cells 1000 from rat lungs 21 34 intestine_wildtype_treated_rep1 Individual array of a bladder cancer expression experiment. Source GEO sample is GSM180994 Last updated (according to GEO): Apr 12 2007 Control Abdominal Aorta 2-M 31 M arm fibroblast LS7, serum starved 7 0 prostate Mutant striatal cells Source GEO sample is GSM82449 Last updated (according to GEO): Jun 26 2007 Brain 861 M_U133Plus_115_CB Ileum_022CAFB4_067.txt 861 Anterior Mesenchymal Stem Cells 1000 Backskin_WT_P6_rep3 1000 Cerebellum none Source GEO sample is GSM149564 Last updated (according to GEO): Jan 03 2007 118 95 Glioblastoma multiforme CNS-RM_Mod24h-1C-s2 for hereditary non-polyposis colon cancer 340 380 mouse brain 478 489 Cerebral cortex 1000 CS 23139A 1 of 3 replicates in treatment group Source GEO sample is GSM206024 Last updated (according to GEO): Jun 29 2007 I_U133A_101_Amy 1000 Descending colon nostrils 156 164 0 Frontal Cortex 13 days nasal epithelium 1126 1147 100 95 hearts embryo day 9.5 Source GEO sample is GSM18632 Last updated (according to GEO): May 27 2005 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14936 Last updated (according to GEO): Oct 28 2005 Replicate1_Voxel D2 CAD_replicate76 Hyperdip>50-C20 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expressions affected by TNF alpha Source GEO sample is GSM189811 Last updated (according to GEO): May 21 2007 901 Salivary Glands GSE1997 ileum 0 4 adrenal_gland_cortex_2 Source GEO sample is GSM80606 Last updated (according to GEO): Mar 31 2006 Normal Source GEO sample is GSM175851 Last updated (according to GEO): Apr 09 2007 DMN-NF1Hippo15d-2dAv2-s2 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26116.gif Source GEO sample is GSM81532 Last updated (according to GEO): Sep 22 2006 1688 1687 Ig plasma cells 332 344 1000 Liver brain, cerebral cortex: Total RNA extraction_le1 261199 1000 Tricuspid valve structure Muscle 861 RNA7 Exp2 TSA treated 901 Pituitary Gland spinal cord, spinal cord: G5C_le1 Expression profiling of moderately injured raphe at 14d in rats Source GEO sample is GSM41574 Last updated (according to GEO): May 27 2005 tumors 853 858 GSE1145 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12349 Last updated (according to GEO): May 28 2005 Mesenchymal Stem Cells 1000 861 Spinal Cord 17 7 hippocampus total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5834 Last updated (according to GEO): May 27 2005 cingulate cortex 861 Cerebellum 1000 17 7 hippocampus 1st 4hr C-DG mouse brain 478 489 brain, Right Frontal Lobe: Extract59_le2 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12680.gif Source GEO sample is GSM79790 Last updated (according to GEO): Sep 22 2006 Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181982 Last updated (according to GEO): Apr 13 2007 901 Epithelial Cells 1000 Hippocampus GM19200 Lymphoblastoid Cell Line for Individual 8164.3 log phase Male; Epididymis-tail Keywords = mouse gene expression database Source GEO sample is GSM29395 Last updated (according to GEO): May 27 2005 335 325 The jejunum Autistic Disorder 877 1000 Hippocampus RNA isolated from spinal cord of human fetus aborted due to causes not related to Lethal Congenital Contracture Syndrome Source GEO sample is GSM25312 Last updated (according to GEO): May 27 2005 Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183419 Last updated (according to GEO): Apr 23 2007 Disease Source GEO sample is GSM176236 Last updated (according to GEO): Apr 09 2007 ventral tegmental area sprague2 brain_DLPFC_bipolar C_mr539 1000 Coronary Arteriosclerosis CNS-SMTC_Mod7d-3A-s2 1000 Brain 0 Human Cortex 11 861 Cerebral cortex 983 Cervix carcinoma Tumor__Lymphoma_Large_B-Cell_L_B_CELL_S98_1217_R on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Malignant Neoplasms 861 MDA-MB-231 transfected with EGRE3-VgRXR and pIND-DACH1, selected by Zeocin and G418. Induced DACH1 expression was confirmed by western blot. Source GEO sample is GSM11364 Last updated (according to GEO): May 28 2005 Study of in vitro granulocyte differentiation Source GEO sample is GSM137434 Last updated (according to GEO): Jun 06 2007 brain, brainstem: LB4_e1_le1 brain, frontal cortex: Sample45_e1_le1 Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231040 Last updated (according to GEO): Sep 26 2007 1958 1945 out the liver for nicotinic receptors 158 180 994 974 on several autosomes HapMap JPT Male Source GEO sample is GSM159659 Last updated (according to GEO): Feb 01 2007 19 0 primary hepatocytes Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11293 Last updated (according to GEO): May 28 2005 for assigning tumors 159 178 1000 Skeletal muscle structure 18 Trigeminal Ganglion 0 Interatrial septum 865 901 Caudate nucleus structure 1000 Amygdaloid structure Primary tumor 19 32 901 frontal lobe 1396 1386 the cornea human frontal cortex Source GEO sample is GSM86960 Last updated (according to GEO): Feb 08 2006 1000 Brain Lamina Propria 1000 Effer/Affer Interaction in Vestibular Caliceal vs. Dimorphic and Bouton Primary Afferent Neurons 1209 1191 in skeletal muscle Saccule at E14, replicate2 Skeletal muscle structure 1000 Retina 861 brain 162 167 cortex 27 33 Primary small cell lung carcinoma 2243 0 37 Coronary heart disease 913 913 Acute leukemia with other neurodegenerative diseases 883 919 Nerve Tissue 884 Sensitized on days 0 and 3 with ragweed pollen protein and alum, challenged intratrecheally on days 10 and 17 with ragweed pollen protein and sacrificed after 72h. Lot batch = Source GEO sample is GSM1275 Last updated (according to GEO): May 28 2005 "4 hr Hela Double Thymidine, exp3" Retina 1000 D_U133A_32_nAcc CNS-RM_Mod3mo-3C-s2 1000 Malignant Glioma Gene expression data from postmorten brain regions Source GEO sample is GSM145404 Last updated (according to GEO): Nov 20 2006 HDMTX-DX-5 ovarian tumor: serous Source GEO sample is GSM139442 Last updated (according to GEO): Apr 09 2007 Muscle 861 Malignant neoplasm of prostate 1000 brain, hippocampus: CON-DG-19_e1_le1 normal lung 1074 Source GEO sample is GSM17290 Last updated (according to GEO): May 28 2005 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181099 Last updated (according to GEO): Jul 12 2007 Normal Source GEO sample is GSM176403 Last updated (according to GEO): Apr 09 2007 Myometrium 36 Disease 861 Hippocampus outer medulla 31 43 Cerebral cortex 861 Infection 1000 Heritability of alternative splicing in the human genome 5 0 brain Molecular profiles of muscle tissue in patients with inflammatory myopathies Last Updated (by provider): Jun 15 2005 Contributers: A A Amato I S Kohane S A Greenberg D Sanoudou L M Kunkel A H Beggs J N Haslett Includes GDS198. Update date: Apr 08 2003. Dataset description GDS198: Molecular profiles of muscle tissue in patients with inflammatory myopathies.. MGJZ030212069Bumbilicalcord Gene expression data from whole brain infected mouse, day 6 Source GEO sample is GSM189624 Last updated (according to GEO): May 16 2007 861 Cerebral cortex Parkinson Disease 861 Stem cells 901 111 102 from lungs Voxel H4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1444 Last updated (according to GEO): Nov 21 2005 Parkinson Disease 861 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195272 Last updated (according to GEO): Sep 13 2007 17 7 hippocampus Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging and comparing calorie restricted-fed 30-month-old to control-fed 30-month-old to investigate effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7460 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145897 Last updated (according to GEO): Nov 20 2006 V5-P127 D_U133A_14_HC A549/ATCC hgu95a 114 101 brains quickly Primary tumor 19 32 91 from the bone marrow 72 D_U133Plus_108_HC 4-cell embryo replication 2 Stem cells 901 Expression profiling of spinal cord section (T10) extracted from rats 14d following severe injury Source GEO sample is GSM31351 Last updated (according to GEO): May 27 2005 1.25 mg/kg 2CdA embryo at 3.0h for Marfan syndrome 233 251 7 0 Amygdala 20 0 human caudate nucleus Spleen vs Lysophosphatidic Acid Treated B cell 240min (set1) Testis 861 no additional Source GEO sample is GSM199161 Last updated (according to GEO): Jun 08 2007 Sham 9 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107488 Last updated (according to GEO): May 01 2006 NINDS-RNP-VTA-1aA-s2 Neurites 861 1000 Brain 0 Human Cortex 11 D_U133A_48_HC 118 101 anterior commisure Whole ganglioneuroma tumor_1172 outer medulla 31 43 1000 Malignant Neoplasms 34 CB A 5_hypothalamus_12hrs_sleep_deprivation_#106 1000 Spleen Infected with PBS and euthanized 3 days post-infection Source GEO sample is GSM155248 Last updated (according to GEO): Aug 08 2007 Neuroglia 901 901 frontal lobe Exp C, Animal #2, 30mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 30mg/kg of CPF for 96 hours Source GEO sample is GSM246173 Last updated (according to GEO): Dec 03 2007 901 Caudate nucleus structure Plasma 861 160 125 Keywords = Congestive heart failure skin 125 129 ALS model Source GEO sample is GSM75472 Last updated (according to GEO): Mar 06 2006 KPeterson-NonMet-15G110-s2 201 197 liver Keywords = Heart 505 521 P14 cochlear nuclei 0 18 861 Bone Marrow Whole Brain 62 72 Liver (HBV+, SF35) TUMOR 24 0 7 PMN_control_180min_Patient18 Malignant Neoplasms 861 Parkinson Disease 861 from the spinal cord 14 33 NCI60.2_LABEL125EXTRACT64SUB3 Source GEO sample is GSM134004 Last updated (according to GEO): Aug 06 2007 Spleen vs fMLP Treated B cell 30min (set3) Spleen 1000 NeverSmoker 5 brain 0 5 1000 Lung NoCAD_replicate9 SKBR3_untreated_10% small cell lung carcinoma 4271 Source GEO sample is GSM17346 Last updated (according to GEO): May 28 2005 Phenytoin hippocampus 5 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53423 Last updated (according to GEO): Jul 06 2005 15 0 human cerebellum total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Platelet activating factor for 30min Source GEO sample is GSM5722 Last updated (according to GEO): May 27 2005 NA18529 SK-OV-3 hgu95b Structure of aggregated lymphoid follicle of small intestine 983 19 0 human frontal cortex G1E_3_A brain 0 5 DBA whole brain 3 HNC2748 brain_DLPFC_bipolar B_mr676 Gene expression data from postmorten brain regions Source GEO sample is GSM145012 Last updated (according to GEO): Nov 20 2006 human peripheral blood derived monocytes, no stimulation, biological rep2 Replicate3_Voxel B7 1000 Adrenal Medulla 1000 Mammary gland in the brain 150 162 Gene expression data from mouse primary visual cortex Source GEO sample is GSM101713 Last updated (according to GEO): Mar 27 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145210 Last updated (according to GEO): Nov 20 2006 Gene expression data from brain of adult rats Source GEO sample is GSM101001 Last updated (according to GEO): Feb 20 2007 Nasal Epithelium Inhalation Formaldehyde 6ppm 19d ID309 CLL-51 36 21 from whole brain 901 Mammary gland mouse left hemi-diaphragm 0 24 GC (HKG75T) 861 Cerebral cortex DLBC24 on Affymetrix GeneChip Human Full Length Array HuGeneFL Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15739 Last updated (according to GEO): May 28 2005 SR hgu95d Cerebellum 1000 861 Ganglia Date : 4/5/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 6.0 hrs post-injection Intervention : none Risk: 20% increased risk for encephalopathy Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AE319 Source GEO sample is GSM12251 Last updated (according to GEO): May 28 2005 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181203 Last updated (according to GEO): Jul 12 2007 at the Human Brain 724 741 Diaphragm 112 Day mdx rep 3 lymph node Source GEO sample is GSM18904 Last updated (according to GEO): Sep 25 2006 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181155 Last updated (according to GEO): Jul 12 2007 in primary tumors 321 338 Cerebral cortex 1000 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162155 Last updated (according to GEO): Jun 12 2007 Head and neck cancer Source GEO sample is GSM155710 Last updated (according to GEO): Apr 24 2007 1000 Brain 848 819 of the pubertal mammary gland Endometrium 0 10 from the femurs 95 109 Mouse Liver LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate F OBJECTIVE: To analyze genome-wide changes in chondrocyte gene expression in a surgically induced model of early osteoarthritis (OA) in rats, to assess the similarity of this model to human OA, and to identify genes and mechanisms leading to OA pathogenesis. METHODS: OA was surgically induced in 5 rats by anterior cruciate ligament transection and partial medial meniscectomy. Sham surgery was performed in 5 additional animals, which were used as controls. Both groups underwent 4 weeks of forced mobilization, 3 times per week. RNA was extracted directly from articular chondrocytes in the OA (operated), contralateral, and sham-operated knees. Affymetrix GeneChip expression arrays were used to assess genome-wide changes in gene expression. Expression patterns of selected dysregulated genes, including Col2a1, Mmp13, Adamts5, Ctsc, Ptges, and Cxcr4, were validated by real-time polymerase chain reaction, immunofluorescence, or immunohistochemistry 2, 4, and 8 weeks after surgery. RESULTS: After normalization, comparison of OA and sham-operated samples showed 1,619 differentially expressed probe sets with changes in their levels of expression > or = 1.5-fold, 722 with changes > or = 2-fold, 135 with changes > or = 4-fold, and 20 with changes of 8-fold. Dysregulated genes known to be involved in human OA included Mmp13, Adamts5, and Ptgs2, among others. Several dysregulated genes (e.g., Reln, Phex, and Ltbp2) had been identified in our earlier microarray study of hypertrophic chondrocyte differentiation. Other genes involved in cytokine and chemokine signaling, including Cxcr4 and Ccl2, were identified. Changes in gene expression were also observed in the contralateral knee, validating the sham operation as the appropriate control. CONCLUSION: Our results demonstrate that the animal model mimics gene expression changes seen in human OA, supporting the relevance of newly identified genes and pathways to early human OA. We propose new avenues for OA pathogenesis research and potential targets for novel OA treatments, including cathepsins and cytokine, chemokine, and growth factor signaling pathways, in addition to factors controlling the progression of chondrocyte differentiation. olfactory epithelium 194 213 7 cerebral cortex 21 Cerebral cortex 861 660 mesenchymal stem cell 639 1000 Rectum VDXRHU_1970 1000 Brain 861 Cerebellum Tumor__Pancreas_Adeno_Pan_29T on Affymetrix GeneChip Human 35K SubA Array Hu35k-A nasal epithelial cells 28 49 22 7 Right Cerebellum 861 Glioblastoma n/a Source GEO sample is GSM177956 Last updated (according to GEO): Jun 11 2007 /2J periaqueductal gray rep1 3 30 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 13 hours after lights on. Original RNA code = LC29A. Source GEO sample is GSM227356 Last updated (according to GEO): Sep 10 2007 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68321 Last updated (according to GEO): Jul 07 2006 Pooled soleus RNA samples from five 8 wk old male C57BL10 mice Source GEO sample is GSM13735 Last updated (according to GEO): May 28 2005 43 29 from the kidney mouse cerebral cortex from COX-2 WT Source GEO sample is GSM121429 Last updated (according to GEO): Jan 31 2007 663 mesenchymal stem cell 642 1000 Muscle 406 395 whose hearts Primary Neoplasm 1000 4535 4527 hepatoma 861 Kidney Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 9934 left_liver_lobe 861 Lung R6/1 18 week transgenic_5D42 Wild type 8 wk old male A/J mouse pituitary gland Source GEO sample is GSM74999 Last updated (according to GEO): Feb 27 2007 Gene expression analysis of the late embryonic mouse cerebral cortex using DNA microarray: identification of several region- and layer-specific genes. Parkinson's disease sample x175 0 30 nucleus accumbens short access to cocaine replicate 1 Amygdaloid structure 861 to the nose 599 609 Rat SCN Sample 5b (Exp 1 - 24 hr b) 861 Neoplasm 861 Occipital lobe Epithelium 861 T146 1000 ovarian neoplasm Parkinson Disease 861 1388 1375 in endometrium Head and neck cancer Source GEO sample is GSM155723 Last updated (according to GEO): Apr 24 2007 f2#257 versus pool Mouse Brain tissue Bone Marrow 1000 AKR/J Frontal Cortex E Malaria 1000 park_1144_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A brain, cerebellum: WCb4w#2_e1_le1 BL6:4-3 + 4-4 PAG P24 deprived visual cortex replicate 2 Sample details: We analysed changes in gene expression in the dorsal telencephalon of forebrain-specific FGFR1 mutant mice. Gene expression was compared between the dorsal telencephalons of single E12.5 embryos of two genotypes: FGFR1 heterozygous (HET1,3,8) and homozygous mutants (HOM2,4,7) that were both heterozygous for the FoxG1 transcription factor, as Cre recombinase expression is driven off the endogenous FoxG1 locus in these animals (Hebert, J. M., Lin, M., Partanen, J., Rossant, J. and McConnell, S. K. (2003b). FGF signaling through FGFR1 is required for olfactory bulb morphogenesis. Development 130, 1101-11. & Hebert, J. M. and McConnell, S. K. (2000). Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures. Dev Biol 222, 296-306. Source GEO sample is GSM62851 Last updated (according to GEO): Aug 26 2005 Hereditary Nonpolyposis Colorectal Neoplasms 947 PGA-MFD-MutantPD5-1aBv2-s2 of somatomotor cortex 21 41 Coronary heart disease 913 Group 4 PEITC + NMBA treated, pool # EP 18 vs. reference pool 20 0 human caudate nucleus GC (HKG42L) Control 2 Exp C, Animal #4, 5mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 5mg/kg of CPF for 96 hours Source GEO sample is GSM246167 Last updated (according to GEO): Dec 03 2007 0h mitotic selection, test 1000 melanoma 320 306 Keywords = HIV 1000 Brain to the central nervous system 149 179 1000 Substantia nigra structure 1000 Encephalitis A VIS D032 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108619 Last updated (according to GEO): Aug 22 2006 Wild type 8 wk old male 129S6/SvEvTac mouse pituitary gland Source GEO sample is GSM107042 Last updated (according to GEO): Mar 05 2007 brain, cerebellum: 3 hrs B GW_e1_le1 Gene expression data from liver Source GEO sample is GSM243361 Last updated (according to GEO): Nov 16 2007 36 21 from whole brain Aorta 1000 Cerebral cortex 861 1000 Left SCG explant cultured for 12 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246028 Last updated (according to GEO): Dec 03 2007 40 21 from skeletal muscle D_U133A_52_DLPFC 1000 jejunum M_U133Plus_118_nAcc m1-adenoma5 Osteoblasts 1000 nostrils 156 164 The ability of dendritic cells (DCs) to activate immunity is linked to their maturation status. In prior studies, we have shown that selective antibody-mediated blockade of inhibitory FcgammaRIIB receptor on human DCs in the presence of activating immunoglobulin (Ig) ligands leads to DC maturation and enhanced immunity to antibody-coated tumor cells. We show that Fcgamma receptor (FcgammaR)-mediated activation of human monocytes and monocyte-derived DCs is associated with a distinct gene expression pattern, including several inflammation-associated chemokines, as well as type 1 interferon (IFN) response genes, including the activation of signal transducer and activator of transcription 1 (STAT1). FcgammaR-mediated STAT1 activation is rapid and requires activating FcgammaRs. However, this IFN response is observed without a detectable increase in the expression of type I IFNs themselves or the need to add exogenous IFNs. Induction of IFN response genes plays an important role in FcgammaR-mediated effects on DCs, as suppression of STAT1 by RNA interference inhibited FcgammaR-mediated DC maturation. These data suggest that the balance of activating/inhibitory FcgammaRs may regulate IFN signaling in myeloid cells. Manipulation of FcgammaR balance on DCs and monocytes may provide a novel approach to regulating IFN-mediated pathways in autoimmunity and human cancer. Primary Neoplasm 1000 40 21 from dorsal pancreas none Source GEO sample is GSM239952 Last updated (according to GEO): Dec 07 2007 Brain 1000 660 mesenchymal stem cell 639 none Source GEO sample is GSM244598 Last updated (according to GEO): Nov 23 2007 Spleen 0 5 861 Muscle total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lysophosphatidic Acid for 30min Source GEO sample is GSM5650 Last updated (according to GEO): May 27 2005 Osteoblasts 1000 Female 67.9 yr before antibody enrichment scan 1 (U133B) Gene expression data from the neocortex of S1P2-knockout mouse Source GEO sample is GSM172944 Last updated (according to GEO): Mar 08 2007 A39 NES 142Q TG7 F2/13 A39 NES Htt exon 1 142Q Mouse 10 months Cerebellum Male Source GEO sample is GSM73190 Last updated (according to GEO): Sep 06 2005 oral_mucosa_2 Cerebral cortex 861 Intestine Carcinoma, Papillary 902 Expression data from normal adrenal gland and aldosterone-producing adenoma 1000 Brain plasma cells 332 344 Brain 50 55 Malignant Neoplasms 861 HC62 CB B 5 0 brain Spleen vs Prostaglandin E2 Treated B cell 30min (set3) 923 Congestive heart failure 901 Epithelial Cells 68 CB B from epididymal fat tissues 21 48 Gene expression data from postmorten brain regions Source GEO sample is GSM145616 Last updated (according to GEO): Nov 20 2006 HUMANCULTUREDADIPOCYTE Source GEO sample is GSM18976 Last updated (according to GEO): Sep 25 2006 Infection 861 Mucous Membrane 861 KHG-LG-2Av2-s2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A KHG-LG-6Av2-s2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A from liver 21 30 861 Neoplasm 861 Carcinoma 75 CB B Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174522 Last updated (according to GEO): Mar 14 2007 adenoma 861 CNS-SpinalCsev-Adult-28d-4C-s2 2763 2755 28S rRNA 41 28 in mouse brain Epithelial Cells 901 CNS-SpinalCsev-Adult-28d-2C-s2 1BJZ02081483a_Trigeminal_Ganglion 164 141 hematopoietic stem cells Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153368 Last updated (according to GEO): Dec 27 2006 Spleen 0 5 Muscle 861 Spinal Cord 861 brain_DLPFC_bipolar B_mr678 Basal- 0 5 Whole Brain 73 83 Cerebral cortex 861 Brain 861 Brain 1000 D_U133Plus_110_Amy I_U133Plus_122_CB M_U133Plus_117_nAcc of the heart 842 854 861 Blood to the nose 599 609 C2C12_1.0_hr GSE775 mouse_hepatocytes_WY24h_pooled 861 Cancer of Neck Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hour time point Source GEO sample is GSM159807 Last updated (according to GEO): Apr 23 2007 Ganglia, Spinal 923 Lymphoblastoid Cell Line for Individual 8130.3 log phase Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188827 Last updated (according to GEO): Jun 06 2007 human frontal cortex Source GEO sample is GSM86939 Last updated (according to GEO): Feb 08 2006 032801_HF_330FL 1000 Cerebral cortex Plasma 861 1000 Brain Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n077 Source GEO sample is GSM2068 Last updated (according to GEO): Nov 21 2005 5 0 brain AML_4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A none Source GEO sample is GSM239895 Last updated (according to GEO): Dec 07 2007 Vector, bone marrow cell The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169483 Last updated (according to GEO): Feb 21 2007 901 Coronary artery Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28828 Last updated (according to GEO): May 27 2005 Gene expression data from the right forebrain of C57BL mouse received no treatment for twelve weeks. Source GEO sample is GSM148685 Last updated (according to GEO): Dec 12 2006 /3T3 fibroblasts 743 759 210 195 atherosclerosis NCI60.27_LABEL31EXTRACT30SUB3 Source GEO sample is GSM134128 Last updated (according to GEO): Aug 06 2007 in seminoma 28 38 Gene expression data from postmorten brain regions Source GEO sample is GSM145948 Last updated (according to GEO): Nov 20 2006 dorsal_root_ganglia_9 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114411 Last updated (according to GEO): Jun 16 2006 Neoplasm 861 1000 Lipids Myocardium 861 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47536 Last updated (according to GEO): May 29 2005 Squamous cell carcinoma 9 Gene expression data from postmorten brain regions Source GEO sample is GSM145449 Last updated (according to GEO): Nov 20 2006 Nasal Epithelium 865 Fibroblasts 38 48 Laser captured visceral sensory neurons. Source GEO sample is GSM63661 Last updated (according to GEO): Dec 21 2005 81 68 Normal Stomach Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. 861 Blood Normal Source GEO sample is GSM175935 Last updated (according to GEO): Apr 09 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11265 Last updated (according to GEO): May 28 2005 none Source GEO sample is GSM149513 Last updated (according to GEO): Jan 03 2007 with mental retardation 241 263 between the LAD artery 266 287 Heart 861 esophagus.1 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201812 Last updated (according to GEO): Jun 20 2007 Diaphragm 14 Day control rep 2 Integumentary system 861 1000 Spleen from the femurs 95 109 Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160707 Last updated (according to GEO): Sep 24 2007 Neoplasm 861 Cerebral cortex 1000 Testi_LeydigCell Source GEO sample is GSM18824 Last updated (according to GEO): Sep 25 2006 Arteries 861 pfc_1019_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Brain 861 brain 0 5 17 0 Normal hippocampus NHF1-hTERT_G1_C5_13865 gene expression data from ODC mouse skin samples Source GEO sample is GSM216655 Last updated (according to GEO): Aug 09 2007 NL-268n1-A92-3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Lymphoblastoid Cell Line for Individual 8203.3 log phase bc-ZT15-3 liver 0 5 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184803 Last updated (according to GEO): Apr 26 2007 with some respiratory epithelium. 1039 1072 Universal Mouse Reference RNA Source GEO sample is GSM93430 Last updated (according to GEO): Jan 23 2006 607 597 the rectum 1000 Cardiomyopathies Seminoma 1000 Blood 1000 9 0 Blood Test 901 frontal lobe Skeletal bone 861 CNS-SMTC_Ctr4h-2Bs2 of the hypothalamus 131 149 Whole brain 0 10 nasal epithelial cells 28 49 Coronary heart disease 913 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211352 Last updated (according to GEO): Jul 18 2007 Sum185_2 BACKGROUND: There is no known biochemical basis for the adverse neurological events attributed to mefloquine. Identification of genes modulated by toxic agents using microarrays may provide sufficient information to generate hypotheses regarding their mode of action. However, this utility may be compromised if sample sizes are too low or the filtering methods used to identify differentially expressed genes are inappropriate. METHODS: The transcriptional changes induced in rat neuroblastoma cells by a physiological dose of mefloquine (10 micro-molar) were investigated using Affymetrix arrays. A large sample size was used (total of 16 arrays). Genes were ranked by P-value (t-test). RT-PCR was used to confirm (or reject) the expression changes of several of the genes with the lowest P-values. Different P-value filtering methods were compared in terms of their ability to detect these differentially expressed genes. A retrospective power analysis was then performed to determine whether the use of lower sample sizes might also have detected those genes with altered transcription. RESULTS: Based on RT-PCR, mefloquine upregulated cJun, IkappaB and GADD153. Reverse Holm-Bonferroni P-value filtering was superior to other methods in terms of maximizing detection of differentially expressed genes but not those with unaltered expression. Reduction of total microarray sample size (< 10) impaired the capacity to detect differentially expressed genes. CONCLUSIONS: Adequate sample sizes and appropriate selection of P-value filtering methods are essential for the reliable detection of differentially expressed genes. The changes in gene expression induced by mefloquine suggest that the ER might be a neuronal target of the drug. na Source GEO sample is GSM181301 Last updated (according to GEO): Apr 10 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28711 Last updated (according to GEO): May 27 2005 D_U133A_86_DLPFC between the LAD artery 266 287 129S6/SvEvTac cingulate cortex rep2 brainstem 7 15 Utricle and 3 ampullae at E15, replicate2 Proliferative endometrium from patient with endometriosis Source GEO sample is GSM150190 Last updated (according to GEO): Dec 14 2006 26 0 Bone marrow [JunctionChip 3 Polyglutamine-expanded ataxin-7 decreases nuclear translocation of NF-kappaB p65 and impairs NF-kappaB activity by inhibiting proteasome activity of cerebellar neurons. 1000 Heart failure Epithelium of bronchus 983 brain, Left Temporal Lobe: Extract49_le2 Control, 06.00 hr. T-Cell LCM 800 biological rep4 NCI60.3_LABEL6EXTRACT5SUB3 Source GEO sample is GSM134007 Last updated (according to GEO): Aug 06 2007 control lean rat A5 Fetal brains were obtained from 3 pregnant rats at pregnant day 17. Primary cortical neurons were isolated and pooled separately from each mother and plated onto 100mm ´ dishes, for a total of 4 plates from each pregnant rat. At Day in Vitro (DIV) 16, 3 of the 4 platesfrom the same mother, were exposed to either 1 or 3 MAC halothane (about 1% or 3%) or 3 MAC isoflurane (about 4%) in a gas tight chamber inside the culture incubator for 6 hr. The 4th plate from each mother treated with air were used (inside the same incubator, but outside the chamber) as controls. Isoflurane at 1 MAC was not conducted because of the complete lack of transcriptional response in the animals exposed to 1 MAC of isoflurane. The cells were recovered for an additional 6 hr, harvested, frozen by liquid nitrogen, and stored at ?80oC. Source GEO sample is GSM61805 Last updated (according to GEO): Oct 28 2005 17 7 hippocampi GC (HKG11T) Brain 1000 17 7 hippocampus human frontal cortex Source GEO sample is GSM87026 Last updated (according to GEO): Feb 08 2006 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n098 Source GEO sample is GSM2079 Last updated (according to GEO): Nov 21 2005 at the Human Brain 746 763 1000 Hippocampus KT1023a_CAN 69 CB A Expression profiling of somatomotor cortex extracted from rats at T0 naive Source GEO sample is GSM41678 Last updated (according to GEO): May 27 2005 Myocardial Infarction 1000 Nrl ko P2 replicate 2 00291048H95A2-T01514v2p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 12 0 ovarian tumor 570 cortex 576 Exp C, Animal #3, 5mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 5mg/kg of CPF for 96 hours Source GEO sample is GSM246166 Last updated (according to GEO): Dec 03 2007 19 0 Head and neck cancer 901 Epithelial Cells Heart 1000 Malignant neoplasm of urinary bladder 901 1000 Mammary gland 861 Cardiomyopathies healthy control sample x192 1820 1807 out the liver human frontal cortex Source GEO sample is GSM86957 Last updated (according to GEO): Feb 08 2006 platelets 63 72 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162150 Last updated (according to GEO): Jun 12 2007 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226167 Last updated (according to GEO): Nov 02 2007 NA12750 growth 3, replicate 5 Date 9/12/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : embryo proper Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 2.5 mg/kg Time : 3 hrs post-injection Intervention : none Risk: benchmark dose modeled for 5% increased risk of microphthalmia Conditional biomarker: weak p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 8-10 embryos pooled from same litter Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = embryo Keywords = threshold Lot batch = AG680 Source GEO sample is GSM12059 Last updated (according to GEO): May 28 2005 Skeletal bone 861 /J Olfactory Bulb D1 3 22 from liver 21 30 Myocardium 861 FVB-3wk-m-2 Control2 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141291 Last updated (according to GEO): Oct 26 2006 11 0 Normal Colon VDXRHU_1568 1000 Structure of entorhinal cortex Plasma 861 Parkinson 0 8 to the nose 599 609 Skeletal bone 861 5 0 brain 129/SvImJ Basal Ganglia B 1000 Brain Cockayne syndrome B cell Source GEO sample is GSM225190 Last updated (according to GEO): Sep 04 2007 Gene expression data from whole tumor Source GEO sample is GSM182288 Last updated (according to GEO): Apr 16 2007 100330 NCI60.53_LABEL57EXTRACT56SUB3 Source GEO sample is GSM134263 Last updated (according to GEO): Aug 06 2007 acute myeloid leukemia Source GEO sample is GSM227441 Last updated (according to GEO): Sep 12 2007 Cortex Source GEO sample is GSM53363 Last updated (according to GEO): Jul 06 2005 Biopsy of a colorectal adenoma from patient #3 stria terminalis 901 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68275 Last updated (according to GEO): Jul 07 2006 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195240 Last updated (according to GEO): Sep 13 2007 Brain 861 SK-MEL-5 hgu95d 901 Caudate nucleus structure nasal epithelial cells 28 49 healthy subject Source GEO sample is GSM211076 Last updated (according to GEO): Sep 10 2007 1000 melanoma total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with NGF (Nerve Growth Factor) for 30min Source GEO sample is GSM5685 Last updated (according to GEO): May 27 2005 1000 Brain Stem Liver 0 4 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188794 Last updated (according to GEO): Jun 06 2007 Infection 1000 15 0 human cerebellum 28 7 Superior Frontal Gyrus 861 Cancer of Neck Epithelium of bronchus 983 pfc_1051_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A ileum 0 4 (cortex 19 25 GBM Treatment, type=remove Source GEO sample is GSM99463 Last updated (according to GEO): Apr 21 2006 Heart 861 Epithelium of bronchus 983 Day 3 Mouse #32 - 2nd replicate prostate Source GEO sample is GSM203402 Last updated (according to GEO): Jun 21 2007 TUMOR 11 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Plasma 861 Animal models represent a very useful tool for the study of depressive-like behaviour and for the evaluation of the therapeutic efficacy of antidepressants. Nevertheless, gene expression patterns of these different animal models and whether genes classically associated to human major depression are present in these genetic profiles remain unknown. Gene expression was evaluated in an animal model of depression: acute treatment with reserpine. Gene expression analyses were carried out using the Affymetrix® GeneChip® technology. Last Updated (by provider): Dec 11 2007 Contributers: Javier Meana Angel Pazos David Arteta Rebeca Diez-Alarcia Marcel Ferrer-Alcon Alvaro Diaz Leyre Uriguen Osteoblasts 1000 1000 Brain ovary 45 50 Cerebral cortex 861 DBA/2J Olfactory Bulb C 78 66 Control blood Mesenchymal Stem Cells 1000 Y HID D002 Parkinson Disease 1000 Melanoma xenograft, MC1_Lung_C (LeiATCC) in the brain 150 162 Eye 1000 Standard Affymetrix Protocol Source GEO sample is GSM16452 Last updated (according to GEO): May 28 2005 865 Disorder of artery 192 basal ganglia 179 Cardiac-specific TNF-alpha transgenic mouse is an excellent model to study the pathologenesis of heart failure. Affytrix U74V2A was used to analyzed the gene expression profile of mice at the time point of compensated hypertrophy and dilated heart failure. Source GEO sample is GSM8992 Last updated (according to GEO): May 28 2005 /3T3 fibroblasts 743 759 CNS-SCsev_InjB24h-3B-s2 ER+/LN+/Nevins20 on Affymetrix GeneChip Human Full Length Array HuGeneFL Laser captured visceral sensory neurons. Source GEO sample is GSM63671 Last updated (according to GEO): Dec 21 2005 of human fibroblasts 131 150 Hair; Awn Hair (back) anagen Keywords = mouse gene expression database Source GEO sample is GSM29336 Last updated (according to GEO): May 27 2005 2N-2-MGU74A 861 Ovary neurological disease control sample x161 Neoplasm 861 Sample 102 on vantveer-oligo Liver 1000 Parkinson Disease 861 hypothalamus_2 Source GEO sample is GSM80691 Last updated (according to GEO): Mar 31 2006 from primary carcinoma 2271 2292 FBX15-iPS MEF4-7 (rep2) 114 101 brains quickly HUVEC isolate 52 rich media VEGF-A 24hours cf. #1 Source GEO sample is GSM12895 Last updated (according to GEO): May 28 2005 861 Cerebral cortex M_U133A_9_DLPFC PBMCs-Type 1 Diabetes-IDDM43_T1D_4MO Rat Retina- chip number 251186834925; 20 weeks vs 5 weeks labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156714 Last updated (according to GEO): Jan 22 2007 1BRS02080877b_subthalamic_nucleus SN14d(1) 1000 Brain 0 Human Cortex 11 amygdala long access to cocaine replicate 2 Lung [JunctionChip 3 of 5] 861 Oocytes DLBC42 on Affymetrix GeneChip Human Full Length Array HuGeneFL Suprachiasmatic Nucleus after 30-min dark pulse rep3 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Source GEO sample is GSM28449 Last updated (according to GEO): May 27 2005 1000 Cerebral cortex Pooled total RNA from (3) P27 L3-L5 Egr3-deficient spinal cords Treatment, type=acclimatization Source GEO sample is GSM32064 Last updated (according to GEO): May 27 2005 Spinal muscular atrophy 0 22 Plasma 861 3T3-L1 Adipocytes B on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A NA18555 Gene expression data from postmorten brain regions Source GEO sample is GSM145592 Last updated (according to GEO): Nov 20 2006 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188698 Last updated (according to GEO): Jun 06 2007 Ny5: Hippocampus_5T-AU_rep9 M1 biol repl 1 861 Pancreas Transplant Series 42 , Transplant # 3 in the brain 150 162 Prosencephalon 861 Malignant Neoplasms 861 334 320 Keywords = HIV 1000 Kidney bronchial epithelia 224 243 1000 Structure of entorhinal cortex 119 96 in embryonic stem cells SynovChrAr_022OACJ1_152.txt Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM80004 Last updated (according to GEO): Oct 26 2005 Osteoblasts 1000 mefloquine-treated NG108 neuronal cells 1 none Source GEO sample is GSM190786 Last updated (according to GEO): Jun 25 2007 1000 Descending colon 1000 Retina 113 103 of myopathy Olfactory Epithelium 1000 Rat frontal cortex RNA - VH TTX Experiment Source GEO sample is GSM92317 Last updated (according to GEO): Jan 13 2006 1000 Brain Melanoma xenograft, MA1_Lung_C (LeiATCC) CAD_replicate53 Parkinson's disease sample x106 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188860 Last updated (according to GEO): Jun 06 2007 of Parkinson's disease 450 471 5 0 brain RNA from Lymphoblastoid Cell Line from this individual Source GEO sample is GSM213298 Last updated (according to GEO): Jul 26 2007 brain 0 5 cerebellum 7 16 in seminoma 28 38 Epithelium 861 Neoplasm 861 Spinal Cord 901 in blood 16 23 1000 Cerebellum 1000 ovarian neoplasm brain, cerebral cortex: NMDA 60 4_le1 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 4 hours after lights on. Original RNA code = LC22A. Source GEO sample is GSM227371 Last updated (according to GEO): Sep 10 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145074 Last updated (according to GEO): Nov 20 2006 1000 decorin I_U133Plus_116_AnCg 1283 1269 in the cochleae 14 days hindlimb suspended, 1 day reloaded RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis. Source GEO sample is GSM10057 Last updated (according to GEO): May 28 2005 69 53 in mouse stomach 972 Structure of middle temporal gyrus 9 0 Blood Test Expression profiling of spinal cord section (T9) extracted from rats 7d following moderate injury Source GEO sample is GSM31595 Last updated (according to GEO): May 27 2005 Spleen vs CpG-oligodeoxynucleotide Treated B cell 240min (set3) spinal cord, ventral spinal cord: D60WTSP3_e1_le1 183 158 the ventral tegmental area We describe the most comprehensive study to date on gene expression during mouse inner ear (IE) organogenesis. Samples were micro-dissected from mouse embryos at E9 to E15 in half day intervals; a period that spans all of IE organogenesis. These included separate dissections of all discernible IE sub-structures such as the cochlea, utricle, and saccule. All samples were analyzed on high density expression microarrays under strict statistical filters. Extensive confirmatory tests were performed, including RNA in situ-hybridizations. Over 5,000 genes significantly varied in expression according to developmental stage, tissue, or both and defined 28 distinct expression patterns. For example, up-regulation of 315 genes provided a clear-cut "signature" of early events in IE specification. Additional, clear-cut, gene expression "signatures" marked specific structures such as the cochlea, utricle or saccule throughout late IE development. Pathway analysis identified 53 signaling cascades enriched within the 28 patterns. Many novel pathways, not previously implicated in IE development, including beta adrenergic, amyloid, estrogen receptor, circadian rhythm, and immune system pathways, were identified. Finally, we identified positional candidate genes in 54 un-cloned non-syndromic human deafness intervals. This detailed analysis provides many new insights into the spatial and temporal genetic specification of this complex organ system. Blood 861 Coronary Arteriosclerosis 1000 1BRS02080873a_ciliary_ganglion Job's patient Source GEO sample is GSM211085 Last updated (according to GEO): Sep 10 2007 1000 Rectum Universal Mouse Reference RNA Source GEO sample is GSM93437 Last updated (according to GEO): Jan 23 2006 Brain 1000 contralateral Cortex 7 27 1000 frontal lobe Communicable Diseases 1000 5 0 brain PBMCs-Type 1 Diabetes-IDDM34_T1D_1MO with autism spectrum disorder 37 65 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160205 Last updated (according to GEO): Feb 08 2007 EWS-C4 on NHGRI-6.5k_b Dystrophin 1000 Epithelium 861 cerebral cortex 7 21 HDMTX-DX-19 of muscle fibers 1608 1624 CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of DC, recombinant human (rh) IL-4 and rhGMCSF were added to the culture at 50 ng/ml on days 1, 3, and 5 of culture. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5141 Last updated (according to GEO): Mar 21 2006 at the synapse 193 207 U937+HRF+antibody H126 CN A 1000 Spleen DU-145 hgu95b Abdominal aorta structure 865 C57BL/6J hypothalamus rep2 (430 2.0 Array) in the mouse brain 77 94 Brain 861 Brain 1000 7 0 prostate 1000 Brain Expression profiling of spinal cord section (T10) extracted from rats 4h following severe injury Source GEO sample is GSM31377 Last updated (according to GEO): May 27 2005 0 Epithelial cells 15 GM19211 Renal Cell Carcinoma 923 41 30 PCOS oocytes Squamous cell carcinoma 923 861 Cerebral cortex 1000 Brain Tumor, Primary 7 0 Lymphoma 1000 Coronary Arteriosclerosis Brain 1000 1000 Brain Blood Test (Blinded) Sample Source GEO sample is GSM130042 Last updated (according to GEO): Sep 18 2007 GC (HKG32T) Osteosarcoma TE85 cell tissue culture study Cerebellum 1000 VDXGUYU_4087 tongue epidermis; dorsal tongue surface Source GEO sample is GSM18647 Last updated (according to GEO): May 27 2005 NCI/ADR-RES hgu95b H111 CN A Osteoblasts 1000 1000 Structure of locus ceruleus Cultured_osteoblast-like_control_MC3T3-E1_cells_rep4 Seizures 861 1000 Prostate 383 370 in the cochlea 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114461 Last updated (according to GEO): Jun 16 2006 Affymetrix RGU34A Naive A Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118558 Last updated (according to GEO): Jul 11 2006 R523P00585 901 Coronary artery 1000 Amygdaloid structure Primary tumor 19 32 4 0 Brain Biopsy of a colorectal adenoma from patient #26 Normal Prostate cingulate cortex 1000 ma-breast 15_0004_SepticShock_Day3_17 Heart failure 1000 HOXB4const-LSK+ cells_ 1 hour plus TMX (continous exposure) Source GEO sample is GSM228755 Last updated (according to GEO): Sep 13 2007 1BJZ02030679_LEUKEMIALYMPHOBLASTIC(MOLT4) neurological disease control sample x167 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc96 Source GEO sample is GSM1860 Last updated (according to GEO): Nov 21 2005 24 0 human prostate PC3 tumors Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3316 Last updated (according to GEO): Mar 21 2006 7 0 Pancreas Disorder of artery 865 folatesufficientAs0ppm2 5 0 Spleen CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of M?, rhMCSF was added at 1000 U/ml on the same days. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5150 Last updated (according to GEO): Sep 08 2006 of coronary artery disease 317 342 Endometrium 1000 of coronary artery disease 258 284 14 0 globus_pallidus Disorder of artery 865 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Tumor necrosis factor-alpha for 60min Source GEO sample is GSM5805 Last updated (according to GEO): May 27 2005 Saccule 0 6 MGMH030228091Aembryoday10.5 329 306 valvular cardiomyopathy outer medulla 31 43 Colonic mucous membrane 913 Untreated Control 12weeks AffyGC RMA rep8 1000 Muscular Atrophy Wild type 8 wk old male A/J mouse bed nucleus of the stria terminalis Source GEO sample is GSM74930 Last updated (according to GEO): Feb 27 2007 5 0 Spleen spinal_cord_3 Source GEO sample is GSM80786 Last updated (according to GEO): Mar 31 2006 1204 1194 hippocampus Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12416.gif Source GEO sample is GSM79861 Last updated (according to GEO): Sep 22 2006 Mesenchymal Stem Cells 1000 17 7 hippocampus NA Source GEO sample is GSM84309 Last updated (according to GEO): Dec 01 2005 861 Cancer of Neck Pancreas at e16.5, Chip B, rep 2 1000 Adrenal Medulla olfactory epithelium 194 213 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188762 Last updated (according to GEO): Jun 06 2007 to the nose 599 609 70 40 without coronary artery disease T-ALL-C20 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Osteoblasts 1000 1000 Hippocampus the blood 393 402 156 145 Their livers GSE3630 from rat lungs 21 34 901 frontal lobe 861 Communicable Diseases 9 0 Blood Test R707P01302 Exp C_2, 10mg/kg CPF, 1st repeat GSE2864 663 mesenchymal stem cell 642 V5-P535 Lung; Fetal Day 16.5 Keywords = mouse gene expression database Source GEO sample is GSM29388 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM144930 Last updated (according to GEO): Nov 20 2006 Pool of 9 (1 utricle and 3 ampullae) at E12.5 Source GEO sample is GSM182599 Last updated (according to GEO): Aug 14 2007 GSE8665 Date : 3/21/2002 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 3.0 hrs post-injection Intervention : 4.0 mg/kg PK11195 co-administered Risk: anticipated remediation to <10% malformations Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots Keywords = methylmercury Keywords = PK11195 Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = SC857 Source GEO sample is GSM12260 Last updated (according to GEO): May 28 2005 nic 2 (Experiment Neuroprotection4- Run 14985) Treatment, type=timepoint, description=primary cortical neurons were treated for 18 h with nicotine 10uM , agonist was then washed out and the cells were harvested 24h later, measurement=18.0 h Source GEO sample is GSM96726 Last updated (according to GEO): Feb 14 2006 26 15 endometrioid GM19137 The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76962 Last updated (according to GEO): Oct 11 2005 brain 0 5 Coronary artery 901 Spinal Cord Injuries 1000 brain 0 5 Primary Neoplasm 1000 861 Cerebellum n/a Source GEO sample is GSM177994 Last updated (according to GEO): Jun 11 2007 brain 0 5 Cerebellum Alzheimer's disease 5 Mid secretory endometrium from patient with endometriosis Source GEO sample is GSM150216 Last updated (according to GEO): Dec 14 2006 Brain 1000 Exp 2 Time point 1 901 Cerebral cortex Macrophage 14smi105 Nasal Epithelium Inhalation Formaldehyde 6ppm 5d ID296 Brain 861 NINDS-RNP-VTA-3aA-s2 Male 73.5 yr before antibody enrichment scan 1 (U133B) Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=680640 LaserPower=1.991.3 Lot batch = LC17N030 Source GEO sample is GSM4782 Last updated (according to GEO): Nov 21 2005 Brain 861 GSE8168 Neoplasm 1000 human frontal cortex Source GEO sample is GSM86975 Last updated (according to GEO): Feb 08 2006 Stomach Cardiac 3 Normal DNA Damage 1000 19 0 human frontal cortex Bone marrow [JunctionChip 5 of 5] Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed 48 h to hydrostatic pressure (HP48), pressure experiment # 1 (PE1). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11422 Last updated (according to GEO): Dec 15 2006 0029_1242_H95A2_KF0149_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A NCI60.38_LABEL42EXTRACT41SUB3 Source GEO sample is GSM134180 Last updated (according to GEO): Aug 06 2007 865 Disorder of artery 5 0 Spleen 861 Cancer of Neck Abdominal aorta collected during autopsy within 24 hours post mortem Source GEO sample is GSM170563 Last updated (according to GEO): Jul 26 2007 Expression profiling of somatomotor cortex extracted from rats at 7d following sham surgery Source GEO sample is GSM41671 Last updated (according to GEO): May 27 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68339 Last updated (according to GEO): Jul 07 2006 158 152 rectum The epithelial cells 962 981 of parieto-occipital cortex 223 250 1000 Amygdaloid structure nasal epithelial cells 28 49 Normal__Peripheral_Blood_Poly_POLY3 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A ovarian tumor: mucinous Source GEO sample is GSM139422 Last updated (according to GEO): Apr 09 2007 Epithelium 861 spinal cord, spinal cord: RNA 499_e1_le1 PGA-MPF-BALB-bleo-72h-1bAv2-s2 19 0 human frontal cortex 36 21 from whole brain Communicable Diseases 1000 JMR-MurSham4h-1bAv2-s2 Bipolar Disorder 1000 216 200 of neural retinas Female 71.4 yr before antibody enrichment scan 1 (U133B) prostate Source GEO sample is GSM203371 Last updated (according to GEO): Jun 21 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11486 Last updated (according to GEO): May 28 2005 5 0 Spleen of the heart 842 854 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-beta (IFN beta) for 60min Source GEO sample is GSM5593 Last updated (according to GEO): May 27 2005 Clone 3.3 chip 1 AKR/J Hippocampus A Diaphragm 28 Day control rep 2 HapMap CEU_parent Male Source GEO sample is GSM159532 Last updated (according to GEO): Feb 01 2007 1000 Communicable Diseases Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n084 Source GEO sample is GSM2070 Last updated (according to GEO): Nov 21 2005 Structure of trigeminal ganglion 1000 DBA whole brain 2 HUVEC isolate 22 low serum media control for #10 Source GEO sample is GSM12902 Last updated (according to GEO): May 28 2005 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156597 Last updated (according to GEO): Jan 22 2007 861 Cerebral cortex PMN_LB_180min_Patient5 ovary_3 starved 32 38 Brain 861 Biopsy of a colorectal adenoma from patient #28 875 Blood Cells Endometrium 1000 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2828 Source GEO sample is GSM2132 Last updated (according to GEO): Nov 21 2005 Brain 861 Biopsy of a colorectal adenoma from patient #8 660 mesenchymal stem cell 639 Liver 1000 Wild type P46 mouse visual cortex ipsilateral to monocular enucleation Source GEO sample is GSM97217 Last updated (according to GEO): Feb 17 2006 Fat RYGB-Fail Repl1 1414 1402 HPV- cancers Gene expression data from postmorten brain regions Source GEO sample is GSM145371 Last updated (according to GEO): Nov 20 2006 Primary tumor 19 32 TUMOR 7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 901 Contact hypersensitivity Brain 50 55 ATCC number CRL-1502 Source GEO sample is GSM6808 Last updated (according to GEO): May 27 2005 Retina 861 Whole Brain 73 83 Keywords = kidney 149 166 304 280 alcoholic cardiomyopathy neurological disease control sample x164 3 0 Hair Mouse neuroblastoma 0 18 RNA isolated from spinal cord of human fetus suffering from Lethal Congenital Contracture Syndrome Source GEO sample is GSM25308 Last updated (according to GEO): May 27 2005 Neoplasm 861 mRNA expression profiles of resting and IL-15 activated murine NK cells 861 Brain Affymetrix RGU34A 6HB NCI60.40_LABEL44EXTRACT43SUB3 Source GEO sample is GSM134193 Last updated (according to GEO): Aug 06 2007 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210395 Last updated (according to GEO): Jul 16 2007 BACKGROUND: Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH) and microsatellite marker analysis for the detection of loss of heterozygosity (LOH). Currently, high throughput methods such as array comparative genomic hybridization (array CGH), single nucleotide polymorphism array (SNP array) and gene expression arrays are available to study genome-wide alterations. Integration of these 3 platforms allows detection of genomic alterations at high resolution and investigation of an association between copy number changes and expression. RESULTS: Genome-wide copy number and genotype analysis of 10 cervical cancer cell lines by array CGH and SNP array showed highly complex large-scale alterations. A comparison between array CGH and SNP array revealed that the overall concordance in detection of the same areas with copy number alterations (CNA) was above 90%. The use of SNP arrays demonstrated that about 75% of LOH events would not have been found by methods which screen for copy number changes, such as array CGH, since these were LOH events without CNA. Regions frequently targeted by CNA, as determined by array CGH, such as amplification of 5p and 20q, and loss of 8p were confirmed by fluorescent in situ hybridization (FISH). Genome-wide, we did not find a correlation between copy-number and gene expression. At chromosome arm 5p however, 22% of the genes were significantly upregulated in cell lines with amplifications as compared to cell lines without amplifications, as measured by gene expression arrays. For 3 genes, SKP2, ANKH and TRIO, expression differences were confirmed by quantitative real-time PCR (qRT-PCR). CONCLUSION: This study showed that copy number data retrieved from either array CGH or SNP array are comparable and that the integration of genome-wide LOH, copy number and gene expression is useful for the identification of gene specific targets that could be relevant for the development and progression in cervical cancer. 00291092H95A2-T01838v2p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 0 cortex 5 78 73 rectum from epididymal fat tissues 21 48 Identifying the neuronal cell types that comprise the mammalian forebrain is a central unsolved problem in neuroscience. Global gene expression profiles offer a potentially unbiased way to assess functional relationships between neurons. Here, we carried out microarray analysis of 12 populations of neurons in the adult mouse forebrain. Five of these populations were chosen from cingulate cortex and included several subtypes of GABAergic interneurons and pyramidal neurons. The remaining seven were derived from the somatosensory cortex, hippocampus, amygdala and thalamus. Using these expression profiles, we were able to construct a taxonomic tree that reflected the expected major relationships between these populations, such as the distinction between cortical interneurons and projection neurons. The taxonomic tree indicated highly heterogeneous gene expression even within a single region. This dataset should be useful for the classification of unknown neuronal subtypes, the investigation of specifically expressed genes and the genetic manipulation of specific neuronal circuit elements. Disease Source GEO sample is GSM176088 Last updated (according to GEO): Apr 09 2007 Parkinson Disease 1000 HC74 CN A PGA_IGF1R-caPI3K_1401 ovary.2 Control 1 (Experiment Neuroprotection4- Run 14985) Treatment, type=timepoint, measurement=0.0 h Source GEO sample is GSM96669 Last updated (according to GEO): Feb 14 2006 #3 (isolate 55 rich media control) Untreated versus treated (bortezomib), untranformed MCF10A and Transformed (see Adler et al, Nature Gen. 2006) Source GEO sample is GSM120225 Last updated (according to GEO): Jul 20 2006 126 101 with chronic renal disease Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120686 Last updated (according to GEO): May 14 2007 1000 Cerebral cortex GTP-Binding Proteins 1000 40 21 from skeletal muscle Normal__Prostate_PR_3 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 19 0 Head and neck cancer 361 335 hypertrophic cardiomyopathy Primary tumor 19 32 0 Human Cortex 11 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92352 Last updated (according to GEO): Jan 13 2006 cortex 7 12 Primary tumor 19 32 Blood B cells;anti-IgM+CD40L low 48h Structure of horn of uterus 983 I_U133A_62_AnCg Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200627 Last updated (according to GEO): Jun 12 2007 Cancers; Prox.Jejunum tumor Keywords = mouse gene expression database Source GEO sample is GSM29279 Last updated (according to GEO): May 27 2005 861 Gland structure A2780_cis_IC10_16h_2 19 0 Head and neck cancer none Source GEO sample is GSM123233 Last updated (according to GEO): Jul 26 2006 JMR-MurInj24h-1cAv2-s2 Interatrial septum 865 42 30 Control blood "44 hr Hela Double Thymidine, exp3" Coronary Arteriosclerosis 1000 861 Nerve Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD5 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD5 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36711 Last updated (according to GEO): May 27 2005 The nose 94 101 mouse brain 478 489 Adenocarcinoma 1000 normal ovaries 541 554 frontal cortex wistar 3659 whole tissue, individual animal, 10 weeks old, male Wistar frontal cortex file:p3659w Source GEO sample is GSM15118 Last updated (according to GEO): Oct 28 2005 05_0006_SepticShock_Day3_98 Amplified RNA from lungs of ovalbumen sensitized and challenged C3H 2 mouse vs. pool of amplified RNA from lungs of control C3H mice. Source GEO sample is GSM6739 Last updated (according to GEO): Nov 21 2005 Primary Neoplasm 896 GM19154 861 Adipose tissue Replicate2_Voxel D7 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228622 Last updated (according to GEO): Sep 11 2007 Primary Carcinoma 876 human caudate nucleus Source GEO sample is GSM86926 Last updated (according to GEO): Feb 08 2006 Standard Affymetrix Protocol Source GEO sample is GSM16489 Last updated (according to GEO): May 28 2005 3AMH02030701_Whole Brain 514 487 before the cognitive decline 1000 ovarian neoplasm Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16368.gif Source GEO sample is GSM91532 Last updated (according to GEO): Sep 22 2006 D_U133A_41_HC Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 2105 left_liver_lobe Nerve 1000 in the developing hindbrain 800 827 PGA-MCR-CR-96h-1aAv2-s1 Samp8 Hippocampus Old Sample 3 Macrophage smi96 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211399 Last updated (according to GEO): Jul 18 2007 brain, hippocampi, left: pADX AM Hypo b_e1_le1 331 307 in central nervous system 100208 HMVEC-L stimulated without LPS for 8 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114570 Last updated (according to GEO): Sep 20 2006 testis 52 58 brain, Left frontal Lobe: Extract13_le2 Tumor__Prostate_Adeno_94_I_052 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene expression data from postmorten brain regions Source GEO sample is GSM145347 Last updated (according to GEO): Nov 20 2006 MOLT3 DMSO control 24h rep2 GBM Treatment, type=remove Source GEO sample is GSM99551 Last updated (according to GEO): Apr 21 2006 861 Blood 660 mesenchymal stem cell 639 Brain 861 Salivary Gland [JunctionChip 3 of 5] Whole Brain 62 72 Wildtype (untreated) 5176 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228593 Last updated (according to GEO): Sep 11 2007 of brain neurospheres 39 59 Normal Source GEO sample is GSM176018 Last updated (according to GEO): Apr 09 2007 Primary Neoplasm 1000 Control 1 (Experiment Neuroprotection4- Run 21823) Treatment, type=timepoint, description=Same sample used for Experiment Neuroprotection4-Run 14985, samples were rerun due to oven failure, measurement=0.0 h Source GEO sample is GSM96683 Last updated (according to GEO): Feb 14 2006 861 Neoplasm human cerebellum Source GEO sample is GSM87109 Last updated (according to GEO): Feb 08 2006 Spleen 1000 M_U133A_92_nAcc ventral striatum wistar ky 3960 Penis 6 Normal M_U133A_50_AnCg 5 0 brain 1000 Hippocampus D03 0h Media Lymphoblastoid Cell Line for Individual 8060.3 log phase Clozapine treated 12weeks AffyGC RMA rep9 901 Coronary artery 861 Neoplasm Gene expression data from liver Source GEO sample is GSM243408 Last updated (according to GEO): Nov 16 2007 Acute leukemia 896 FormerSmoker 34 of the postmortem brains 674 698 1000 Kidney human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195346 Last updated (according to GEO): Jun 04 2007 Ng11: Hippocampus_NT-Y_rep6 PBMCs-Type 1 Diabetes-IDDM56_T1D_New Myometrium 2 Normal Serotonin 1000 Liver 1000 OBX Day 5,# 1 Normal Source GEO sample is GSM176223 Last updated (according to GEO): Apr 09 2007 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:364, Count:32 Corner- Avg:38122, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:5.656439,SFGene:All Background:Avg:510.04,Stdev:16.15,Max:569.6,Min:474.6 Noise:Avg:12.10,Stdev:0.85,Max:16.1,Min:10.6 RawQ:15.05 Keywords = ALL Source GEO sample is GSM3414 Last updated (according to GEO): May 27 2005 1000 Lung 26 11 /Ovary-Disease 2 15 0 human cerebellum Osteoclasts 1000 healthy subject Source GEO sample is GSM211103 Last updated (according to GEO): Sep 10 2007 Polyamide1_1 1000 Bregma I_95Av2_2672_Cg_0_GS 1000 Brain 625 for the orbitofrontal cortex 653 Macrophage smi41 brain, cerebral cortex: 15004_e2_le1 Adrenal Medulla 1000 NHE1 null mutation hippocampus-2DS Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11556 Last updated (according to GEO): May 28 2005 brain, contralateral HC: Trizol Extraction27_le1 Hippocampus Source GEO sample is GSM107965 Last updated (according to GEO): Jun 06 2006 in the brain 150 162 Nrl ko P10 replicate 4 Connexins 884 Brain (fetal) [JunctionChip 1 of 5] Sprague-Dawley Male HighSalt Cortex rat711 sd_cortexr_k_711c_020802 Ta gr2 tumour Source GEO sample is GSM2491 Last updated (according to GEO): Mar 21 2006 CNS-SpinalC-conAdult-30m-1C-s2 861 Cerebellum Transcriptional response of lymphoblastoid cells to ionizing radiation 1000 ovarian neoplasm Brain 1000 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50645.gif Developmental Stage: E8.75 Source GEO sample is GSM229815 Last updated (according to GEO): Nov 06 2007 the metastasis 808 821 healthy subject Source GEO sample is GSM211127 Last updated (according to GEO): Sep 10 2007 A control group consisting of nine C57/BL/6J mice was maintained on a normal diet consisting of Purina Rodent Chow (Harlan Teklad, catalog #5008, 6.5% fat, 49% carbohydrate, 23% protein, 3.5 kcal/ g). The experimental group consisted of nine mice grown on a specialty high-fat diet (Harlan Teklad, catalog #TD88137, 42.16% fat, 42.81% carbohydrate, 15.02% protein, 4.53 kcal/ g). Mice were maintained for ten weeks on their respective diets in a controlled environment with standard light and feeding schedule. Two days before tissue harvest, the experimental group on the high-fat diet was divided into one group of five and one group of four mice. The first group continued on the high-fat diet for the final two days, while the second group fasted. Mouse weights were recorded two days prior, and the day of tissue harvest. At the end of the fasting period liver tissue samples were harvested from each mouse. RNA was purified from the liver tissue samples. Each tissue was homogenized in 1 mL of STAT-60 (Tel-Test, Inc., Friendswood, TX) and the homogenate was mixed with 200 uL of chloroform. The aqueous phase was removed, and mixed with 500 uL of isopropanol to precipitate the RNA. The resulting RNA pellet was washed with 500 uL of 70% ethanol and allowed to air dry. The pellet was dissolved in RNase free water (Ambion, TX), quantified by UV spectroscopy, and stored at -80C. Total RNA control samples (Universal Mouse Reference RNA, catalog # 740100, Stratagene) were labeled using Cy3 dCTP (Perkin-Elmer), and liver total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). The control RNA samples were additionally mixed with 2 uL of random hexamers. The reaction mixtures were incubated at 42 C for two hours. After the reverse transcription reactions, the RNA templates were degraded by addition of 2 uL of 1 N NaOH and incubation at 65 C for 10 minutes. The alkaline conditions were neutralized by addition of 2 uL of 1 N HCl. Liver cDNA samples were then mixed with a control cDNA sample, and the mixtures were cleaned using a QIAquick Nucleotide Removal kit (Qiagen) as described by the manufacturer's instructions. The cleaned samples were concentrated in a speed vacufuge (Eppendorf) for 20 minutes at 65 C, and were dissolved in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), quantified, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 C using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), then in 1X SSC, and finally in 0.1X SSC. The arrays were dried by centrifugation and scanned using a GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and analyzed using Matlab (The MathWorks, Inc.). Microarrays were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). Arrays contained 16,847 features, printed from a synthesized oligonucleotide mouse library (Operon). The library was suspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed at approximately 50% humidity. Once printed, the probes were crosslinked using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride (Fluka AG), 239 mL 1-methyl-2-pyrrolidinone (EM Science), and 10.7 mL of 1 M boric acid (Fisher), pH 8.0. They were cleaned by rinsing twice in 250 mL of milli-Q water, followed by 250 mL of 95% ethanol (Pharmco Products). After blocking, they were dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, energy homeostasis, gene expression, microarrays Source GEO sample is GSM6592 Last updated (according to GEO): Nov 21 2005 brain, unknown: Sample60_e1_le1 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 19 day time point Source GEO sample is GSM159742 Last updated (according to GEO): Apr 23 2007 Mental Retardation 1000 Kidney 1000 861 Cerebral cortex 1603 1586 in the PCOS oocyte Gene expression data from brain of adult rats Source GEO sample is GSM101050 Last updated (according to GEO): Feb 20 2007 olfactory epithelium wild type mouse 2 hpO Source GEO sample is GSM80187 Last updated (according to GEO): Oct 26 2005 of the postmortem brains 674 698 Cells captured via Arcturus LCM system, amplified (RiboAmp, 2 rounds) and labeled (Enzo) for hybridizaton to Affymetrix MG_U74Av2 arrays, using manufacturers protocols in each step. Source GEO sample is GSM6200 Last updated (according to GEO): Mar 17 2006 in mouse hearts 40 54 Disease Source GEO sample is GSM176287 Last updated (according to GEO): Apr 09 2007 913 Coronary heart disease Spleen vs Untreated B cell Time 0 (set9) 41 29 Control blood Experimental Autoimmune Encephalomyelitis 901 861 Skeletal bone cancer 81 86 15 0 human cerebellum Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151988 Last updated (according to GEO): Feb 06 2007 901 frontal lobe none Source GEO sample is GSM244635 Last updated (according to GEO): Nov 23 2007 Normal human tissue:Normal Lung Keywords = Human, Normal Tissue, Normal Lung Source GEO sample is GSM44704 Last updated (according to GEO): May 27 2005 Malignant neoplasm of prostate 901 Congenital Abnormality 853 Gene expression data from postmorten brain regions Source GEO sample is GSM145609 Last updated (according to GEO): Nov 20 2006 176 166 bone marrow 861 Stem cells Spleen 3 Normal Saccule structure 1000 FormerSmoker 40 the infection 46 58 osteoblast 630 640 MuscleRegen-ctx16d-2RLAv2-s2-2 901 Autoimmune Diseases MSE_N_617 1000 Brain 861 Blood 861 Substantia nigra structure Lymphoblastoid Cell Line for Individual 8109.4 log phase 861 Cerebellum 1000 Cardiomyopathy, Alcoholic 1000 ovarian neoplasm JMR-RatSham30m-1aA-s2 endothelial cells 1323 1339 PGA-Band_Sham_8w_7-m5 797 778 in the rodent brain FBooth-CON-4Av2-s2 /2J mouse periaqueductal gray 27 55 901 Polycystic Ovary Syndrome TestiGermCell Source GEO sample is GSM18827 Last updated (according to GEO): Sep 25 2006 LT-Hematopoietic stem cell isolated by flow cytometry Source GEO sample is GSM149530 Last updated (according to GEO): Apr 27 2007 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211264 Last updated (according to GEO): Jul 18 2007 CNS-SCsev_InjB24h-1B-s2 518 491 before the cognitive decline EWS-T3 on NHGRI-6.5k_b 99 81 to childhood asthma Epithelial Cells 901 052401_HF_298CB MPTP 1 Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 5102 blood GSE8000 Expression profiling of spinal cord section (T10) extracted from rats 24h following severe injury Source GEO sample is GSM31358 Last updated (according to GEO): May 27 2005 5 0 brain 21h-Control replication 3 1000 Liver 1000 Tubulin atrial septal defects 198 218 of trauma 592 601 1000 frontal lobe 901 Kidney Diseases C3H/HeJmale_hypothalamus 1000 Maxilla Seminoma 1000 brain 162 167 Blood 1000 of mouse brain 9 23 8 hr EE repl 1 861 Oocytes Normal Source GEO sample is GSM176074 Last updated (according to GEO): Apr 09 2007 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181051 Last updated (according to GEO): Jul 12 2007 Mouse Liver LRD Diet 5wk 10ppb As Food Exposure, biological replicate C brain 0 5 0 Alzheimer's disease 18 ovarian tumor: serous Source GEO sample is GSM139435 Last updated (according to GEO): Apr 09 2007 Aldosterone-producing adenoma (APA11) B6 day 6, biological rep 3, tech rep 1 Expression profiling of spinal cord section (T8) extracted from rats 24h following laminectomy (sham) Source GEO sample is GSM31400 Last updated (according to GEO): May 27 2005 human caudate nucleus Source GEO sample is GSM86860 Last updated (according to GEO): Feb 08 2006 865 Disorder of artery Brain 861 1000 Hypertrophic Cardiomyopathy I_U133Plus_108_CB 251 239 polymyositis 117 93 of hindlimb gastrocnemius Gene expression data from whole brain of uninfected mouse Source GEO sample is GSM189631 Last updated (according to GEO): May 16 2007 embryonic hearts 1063 1078 1000 Amygdaloid structure Ovarian_Tumor_Endometrioid_KU-OE-007 n/a Source GEO sample is GSM178019 Last updated (according to GEO): Jun 11 2007 Amygdada Source GEO sample is GSM107915 Last updated (according to GEO): Jun 06 2006 861 Intestines Lung 1000 1000 Schizophrenia brain 1191 1195 Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum.. Date GSE1392 Last Updated: Oct 28 2005 Contributers: Irène Corthésy-Theulaz Rainer Simmering David M Mutch Dominique Donnicola James Holzwarth Gary Williamson Grigorios Fotopoulos Includes GDS640. Update date: Jul 14 2004. Dataset description GDS640: Analysis of germ-free and conventional corpus, jejunum, descending colon and rectum. Findings identify important interaction between commensal microbiota and gastrointestinal tract transcriptome.. of the acetylcholine receptor 1877 1906 Ventral Tegmental Area 1000 CA01-103A plasma cells 50 61 Study of in vitro granulocyte differentiation Source GEO sample is GSM137479 Last updated (according to GEO): Jun 06 2007 Gene expression data from dorsal pancreas at e14.5, MG-U74B version2 Source GEO sample is GSM199457 Last updated (according to GEO): Jun 08 2007 BABE empty vector transduced mammary epithelial cells Source GEO sample is GSM5168 Last updated (according to GEO): May 27 2005 The nose 94 101 Skeletal bone 861 normal 1546 5 0 brain Expression profiling of spinal cord section (T9) extracted from rats 72h following moderate injury Source GEO sample is GSM31577 Last updated (according to GEO): May 27 2005 Blood Test (Blinded) Sample Source GEO sample is GSM130028 Last updated (according to GEO): Sep 18 2007 Expression profiling of spinal cord section (T9) extracted from rats 24h following moderate injury Source GEO sample is GSM31536 Last updated (according to GEO): May 27 2005 NA Source GEO sample is GSM198922 Last updated (according to GEO): Jun 07 2007 1000 Retina Brain 861 861 Blood AKR/J Olfactory Bulb D1 Fibroblasts 861 Lung 1000 To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at ?80C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at ?80°C before routine processing for GeneChip analysis. Source GEO sample is GSM28671 Last updated (according to GEO): Oct 28 2005 Olfactory Epithelium 1000 901 Epithelial Cells WGACON-270 mouse brain 478 489 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Sphingosine-1-phosphate labeled with Cy5- time course with repeats. Date GSE396 Last Updated: May 29 2005 Contributers: Zhen Yan Angela Alexander Jong-Woo Kim Mi Sook Chang Robert Hsueh Rebecca Hart Yun Anna Cao Sun Young Lee Joella Grossoehme Sangdun Choi Includes GDS317. Update date: Nov 18 2003. Dataset description GDS317: Temporal analysis of effects induced by 0.3 uM sphingosine-1-phosphate in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. Ovarian_Tumor_Serous_KU-OS-001 the axons 199 207 Category: Serum-response Subcategory: Fibroblasts Scanning Software: unknown Software version: unknown Lot batch = 408 Source GEO sample is GSM2160 Last updated (according to GEO): Nov 21 2005 901 Coronary artery VDXKIU_1000 Brain 1000 10 7 Left Cy3-labeled cDNA from brains of neonatal Cx43 null C57BL mice was compared to Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice. Keywords = Cx43 null neonatal mouse brain Source GEO sample is GSM34871 Last updated (according to GEO): Jun 19 2007 Metastatic tumor 19 35 in some fibres 1817 1830 total RNA from biosource CC#1 Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92467 Last updated (according to GEO): Jan 13 2006 BXD 2_M7SS02080611 Gene expression data from postmorten brain regions Source GEO sample is GSM145545 Last updated (according to GEO): Nov 20 2006 UBOC1 Exp B Day 2 (b) 1209 frontal cortex 1223 cingulate cortex 861 of regenerating Dorsal Root Ganglia 21 55 1000 Prostate GSE9105 Rett Syndrome 1000 11 Bone marrow 0 Individual array of a bladder cancer expression experiment. Source GEO sample is GSM180991 Last updated (according to GEO): Apr 12 2007 The nose 94 101 Gene expression data from brain of adult rats Source GEO sample is GSM101022 Last updated (according to GEO): Feb 20 2007 Medulla Oblongata 861 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15704 Last updated (according to GEO): May 28 2005 Normal Source GEO sample is GSM176380 Last updated (according to GEO): Apr 09 2007 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210402 Last updated (according to GEO): Jul 16 2007 RNA was amplified and converted into cDNA with the NuGEN Ovation? Biotin RNA Amplification and Labeling System {http://www.nugentechnologies.com/html/03_products2.html} Source GEO sample is GSM82891 Last updated (according to GEO): Jun 22 2006 334 320 Keywords = HIV none Source GEO sample is GSM244537 Last updated (according to GEO): Nov 23 2007 5 0 brain Heart Ventricle 1000 plasma cells 50 61 MCF7_Untreated_0.1% Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P14, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3232 Last updated (according to GEO): May 28 2005 Brain 861 Gene expression data from aldosterone-producing adenoma Source GEO sample is GSM211458 Last updated (according to GEO): Jul 18 2007 141 118 in the rat hypothalamus From naive male Sprague-Dawley rats (400Ã?±25 g), a 7 mm disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44496 Last updated (according to GEO): Oct 28 2005 CC553 HC68 CN A Primary tumor 19 32 nodose_nucleus_10 Source GEO sample is GSM80755 Last updated (according to GEO): Mar 31 2006 Substantia Nigra Reticulata 1 Disease Blood 861 Medulla Oblongata 861 NL-6853-A336-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Posterior root of spinal nerve 901 Category: Cell-line Subcategory: Breast isolate obtained from ATCC Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc71 Source GEO sample is GSM1886 Last updated (according to GEO): Nov 21 2005 PGA-Band_48h_7-m5 Muscle_adequate protein_female_rep3 none Source GEO sample is GSM210351 Last updated (according to GEO): Jul 16 2007 16 7 cerebellum Spinal Cord 1000 human caudate nucleus Source GEO sample is GSM86866 Last updated (according to GEO): Feb 08 2006 PMN_LB_360min_Patient9 Gene expression data from postmorten brain regions Source GEO sample is GSM145169 Last updated (according to GEO): Nov 20 2006 BALB/c_OVA Replicate 3 Normal Source GEO sample is GSM176071 Last updated (according to GEO): Apr 09 2007 Peripheral Nerves 851 total RNA from biosource CC#35 Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92480 Last updated (according to GEO): Jan 13 2006 T04__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 10 7 Left ventral spinal cord 13 31 Blood 861 umbilical cord_bpd: 1C NHF1-hTERT_Basal_C5_53956 659 639 of vascular structure NG014_b I_U133Plus_125_CB Autistic Disorder 877 Whole Brain 62 72 1000 Endometrium nerves 236 242 901 Bone Marrow Nasal Epithelium Inhalation Formaldehyde 2ppm 5d ID218 brain, left frontal temporal lobe: Extract3_le2 M_U133Plus_121_nAcc 1000 Hippocampus Retinas 1036 1042 RNA isolated from post-mortem tissues Source GEO sample is GSM6829 Last updated (according to GEO): May 28 2005 607 597 the rectum total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells cultured for 120min Source GEO sample is GSM5847 Last updated (according to GEO): May 27 2005 NCI60.47_LABEL51EXTRACT50SUB3 Source GEO sample is GSM134230 Last updated (according to GEO): Aug 06 2007 Cockayne syndrome B cell Source GEO sample is GSM226289 Last updated (according to GEO): Sep 04 2007 6 on NHGRI-13.8k PBMCs-Type 1 Diabetes-IDDM53_T1D_4MO 20 0 human caudate nucleus 1000 Basal of somatomotor cortex 21 41 1BJZ02052321_WHOLEBLOOD(JJV) The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76939 Last updated (according to GEO): Oct 11 2005 "31 hr Hela Double Thymidine, exp3" Gene expression data from postmorten brain regions Source GEO sample is GSM145629 Last updated (according to GEO): Nov 20 2006 Coronary artery 901 the ventricular 1095 1109 861 medulloblastoma 1000 Brain f2#262 versus pool Mouse Brain tissue Ovary 1000 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132529 Last updated (according to GEO): Feb 26 2007 pharyngeal_mucosa_3 Coronary artery 901 1000 Cerebrovascular accident Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 1 - Pair 5 - LMN Source GEO sample is GSM49893 Last updated (according to GEO): Dec 20 2005 Primary Neoplasm 1000 KT28c_CAN brain 0 5 Ventral tegmental area, male 10.5 week old c57bl/6J mouse, UNSUSCEPTIBLE group Source GEO sample is GSM224754 Last updated (according to GEO): Aug 31 2007 1000 Brown Fat /3T3 fibroblasts 295 310 Dorsal root ganglion 277 296 of anatomy 98 108 Brain_MD_55_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL Liver 0 4 Brain 861 park_1155_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 129P3/J Saline treated, striatum, biological replicate 2 Source GEO sample is GSM187966 Last updated (according to GEO): Jun 14 2007 CNS-RM_Mod14d-1A-s2 Wild type 8 wk old male DBA/2J mouse pituitary gland Source GEO sample is GSM107050 Last updated (according to GEO): Mar 05 2007 7 frontal cortex 20 Breast Carcinoma 901 7 cortex 12 with some respiratory epithelium. 1039 1072 rat cortex Treatment, type=time_course, measurement=14.0 d Source GEO sample is GSM53226 Last updated (according to GEO): Jul 06 2005 Simple annotation: Metastatic tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5173.gif Source GEO sample is GSM79795 Last updated (according to GEO): Sep 22 2006 Brain 861 1000 Infection 861 Cerebral cortex total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Bombesin for 60min Source GEO sample is GSM5477 Last updated (according to GEO): May 27 2005 861 Cerebral cortex 9 0 Blood Test normal human skeletal muscle sample 11 142 130 In the brain Cerebellum 1000 A HID U D053 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108583 Last updated (according to GEO): Aug 22 2006 B220Low sIgM+ immature B cells sorted out of mouse bone marrow, sort no. 1 Source GEO sample is GSM637 Last updated (according to GEO): Mar 20 2006 no additional Source GEO sample is GSM199208 Last updated (according to GEO): Jun 08 2007 for liver 26 35 osteoblast 627 637 Cerebral cortex 861 of mouse brain 9 23 human frontal cortex Source GEO sample is GSM87038 Last updated (according to GEO): Feb 08 2006 Liver Test (Blinded) Sample Source GEO sample is GSM130061 Last updated (according to GEO): Sep 18 2007 HMVEC-L stimulated with LPS for 8 hours L08R4 1000 Hippocampus 82 56 of anovulatory infertility Brain_MD_38_Medulloblastoma_Desmoplastic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL the blood 393 402 PGA-swim_4w1w_s1123 Whole brain 0 10 Gonadectomized Dahl-Iwai Male HighSalt Cortex rat10 gdahl_cortexr_k_GX_10c_051702 PAX sample 1 AD-330t2-A279-10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Brain 7 Entorhinal Cortex 23 1110 1093 in the hippocampus This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12357 Last updated (according to GEO): May 28 2005 in DMD muscle 1265 1278 1000 Soleus muscle structure Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184702 Last updated (according to GEO): Apr 26 2007 R6/1 27 week transgenic_OE41 1000 Skeletal muscle structure Infection 1000 1000 Large Intestine adLacZ5 Plasma 861 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210387 Last updated (according to GEO): Jul 16 2007 N/A Source GEO sample is GSM6685 Last updated (according to GEO): May 28 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68360 Last updated (according to GEO): Jul 07 2006 Total RNA extracted from the cerebellum of a Tg-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144413 Last updated (according to GEO): Nov 14 2006 ventral spinal cord 13 31 VP16-CREB hippocampus region Source GEO sample is GSM88940 Last updated (according to GEO): Jan 04 2006 Replicate1_Voxel G2 PGA-E12.5_1 Gene expression data from postmorten brain regions Source GEO sample is GSM145896 Last updated (according to GEO): Nov 20 2006 to fibroblasts 174 187 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114224 Last updated (according to GEO): Jun 16 2006 WGACON-104 olfactory epithelium SR-A mutant mouse 2 hpO Source GEO sample is GSM80202 Last updated (according to GEO): Oct 26 2005 1000 Infection from colorectal adenoma 21 44 V5-P492-2 PGA-RnSalt_e_3w_3-m5 1000 Brain 1000 Tenascin Neurodegenerative Disorders 901 Skeletal bone 861 67 40 with coronary artery disease Control Abdominal Aorta 1-M GM18504_technical_rep_1 long access to cocaine, lateral hypothalamus, 6 hrs/day access to cocaine Source GEO sample is GSM93848 Last updated (according to GEO): Jan 26 2006 Tumor__Renal_Carcinoma_Carc_623TS on Affymetrix GeneChip Human 35K SubA Array Hu35k-A A SIT D099 spleen 164 170 Gene expression data from postmorten brain regions Source GEO sample is GSM145396 Last updated (according to GEO): Nov 20 2006 CAD_replicate36 84 69 by heart failure S25 NLS 142Q TG3 F4/34 S25 NLS Htt exon 1 142Q Mouse 3 months Cerebellum Male Source GEO sample is GSM73207 Last updated (according to GEO): Sep 06 2005 Mesenchymal Stem Cells 1000 with mental retardation 241 263 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134630 Last updated (according to GEO): Jul 09 2007 Skeletal bone 861 cerebral cortex 7 21 Expression profiling of spinal cord section (T8) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM6643 Last updated (according to GEO): May 28 2005 Laser captured visceral sensory neurons. Source GEO sample is GSM63677 Last updated (according to GEO): Dec 21 2005 1000 Liver Cerebral cortex 1000 Cerebral cortex 1000 1000 Neuraxis CF control DMW CHN313 Nose 1000 (cortex 19 25 Panic Disorder 1000 Muscle Fibers 1000 Plasma 861 Brain 1000 1000 Liver 4 0 Liver Gene expression data from postmorten brain regions Source GEO sample is GSM145883 Last updated (according to GEO): Nov 20 2006 901 frontal lobe D_U133Plus_59_HC of coronary artery disease 317 342 861 Cardiomyopathies Study of in vitro granulocyte differentiation Source GEO sample is GSM137477 Last updated (according to GEO): Jun 06 2007 in the mammalian nervous system 110 141 SkelMusc_0224AFC2_086.txt 1000 Retina M1 biol repl 2 Acute cognitive impairment (i.e., delirium) is common in elderly emergency department patients and frequently results from infections that are unrelated to the central nervous system. Since activation of the peripheral innate immune system induces brain microglia to produce inflammatory cytokines that are responsible for behavioral deficits, we investigated if aging exacerbated neuroinflammation and sickness behavior after peripheral injection of lipopolysaccharide (LPS). Microarray analysis revealed a transcriptional profile indicating the presence of primed or activated microglia and increased inflammation in the aged brain. Furthermore, aged mice had a unique gene expression profile in the brain after an intraperitoneal injection of LPS, and the LPS-induced elevation in the brain inflammatory cytokines and oxidative stress was both exaggerated and prolonged compared with adults. Aged mice were anorectic longer and lost more weight than adults after peripheral LPS administration. Moreover, reductions in both locomotor and social behavior remained 24 h later in aged mice, when adults had fully recovered, and the exaggerated neuroinflammatory response in aged mice was not reliably paralleled by increased circulating cytokines in the periphery. Taken together, these data establish that activation of the peripheral innate immune system leads to exacerbated neuroinflammation in the aged as compared with adult mice. This dysregulated link between the peripheral and central innate immune system is likely to be involved in the severe behavioral deficits that frequently occur in older adults with systemic infections.. Date GSE3253 Last Updated: Oct 28 2005 Contributers: Johnathan P Godbout Jing Chen Amy F Richwine Brian M Berg Keith K Kelley Rodney W Johnson Jayne Abraham Includes GDS1311. Update date: Nov 04 2005. Dataset description GDS1311: Analysis of aged brain after activation of the peripheral innate immune system by intraperitoneal injection of E. coli lipopolysaccharide (LPS). Results provide insight into molecular events underlying severe behavioral deficits (delirium) common in older adults with systemic infections.. Skeletal muscle structure 1000 R601P01083 Replicate1_Voxel D7 Heart 1000 Lymphoblastoid Cell Line for Individual 8186.4 log phase 5 0 brain Dissection of E16.5 cortex for RNA extraction. Cortex Hemispheres of E16.5 mice were divided into the medial (R1), dorsal (R2), ventral (R3), lateral (R4), and occipital regions (R5). Preparation of RNA and Synthesis of cDNA. Poly A+ RNA was obtained through twice column procedures with oligo dT cellulose column (New England Biolabs, Beverly, MA) and was used for synthesis of cDNA. 1ug of polyA+ RNA was converted into double-stranded cDNA by reverse transcription using ReverTra Ace (ToYoBo, Japan) with oligo dT(24) primers containing the T7 RNA polymerase promotor sequence (Amersham Pharmacia Biotech, Japan). The integrity of RNA was confirmed by agarose electrophoresis and RNA contents were analyzed by measuring the optical density at 260 nm. Target preparation and array processing. The following procedures including preparation of cRNA targets, hybridization, washing, staining, and scanning were performed as described in the Expression Analysis Technical Manual (Affymetrix, CA). Briefly, biotin-labeled antisense cRNA targets were synthesized in in vitro transcription reaction system (IVT) using cDNA as template (ENZO BioArrayTM HighYieldTM RNA Transcription Labeling kit with T7 RNA polymerase, Enzo, NY). The cRNA targets were size-fragmented to 35-200 bp in a buffer containing potassium and magnesium acetate at 94 °C for 35 minutes and were used for hybridization as cRNA targets. The hybridization cocktail [containing 10 ug of target cRNA, control oligo BS (Affymetrix), and Eukaryotic Hybridization controls (Affymetrix)] was hybridized with a mouse U74A array at 42 °C for 16 hours in GeneChip Hybridization Oven 640. Washing and staining were performed after hybridization under the fluidics station protocol, EuGE-WS2, on GeneChip Fluidics Station 400. Then, we scanned the array twice on HP GeneArrayTM scanner. Experiments were repeated twice with independent dissection. Data analysis. To quantify the expression level of a transcript, the average difference value (Adv) was calculated from the intensities against the probe cells using the global methods of normalization by Microarray Suite ver. 4.0 (Affymetrix). Keywords = mouse Keywords = cortex Keywords = development Keywords = regional Keywords = gene expression Keywords = medial Keywords = dorsal Keywords = lateral Keywords = rostral Keywords = occipital Source GEO sample is GSM14592 Last updated (according to GEO): Oct 28 2005 Gap junction 0 11 Normal__Bladder_BL_2 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Spinal Cord 1000 M_U133A_5_DLPFC Brain 1000 Normal Source GEO sample is GSM175974 Last updated (according to GEO): Apr 09 2007 Expression profiling of spinal cord section (T8) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM4449 Last updated (according to GEO): May 28 2005 in seminoma 28 38 Spleen 1000 Ovarian Diseases 877 M_U133A_89_nAcc 861 Cerebral cortex 40 21 from skeletal muscle A HID B D014 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108581 Last updated (according to GEO): Aug 22 2006 UET-13TR-EWS/FLI1 0hr NA18852 61 41 from postmortem brain Cerebellum Control (AD) 5 LT-Hematopoietic stem cell isolated by flow cytometry Source GEO sample is GSM149528 Last updated (according to GEO): Apr 27 2007 Brain 1000 ventral_tegmental_area_8 Source GEO sample is GSM80907 Last updated (according to GEO): Mar 31 2006 Spleen vs Anti-IgM Treated B cell 30min (set1) Spleen vs Anti-IgM Treated B cell 240min (set3) 091205 OVR5 on Affymetrix GeneChip Human Full Length Array HuGeneFL 23 3 /BnJmale_hypothalamus Brain_MD_19_Medulloblastoma_Classic_D on Affymetrix GeneChip Human Full Length Array HuGeneFL Contusion - 35 Day Epicenter Rep3 Gene expression data from hippocampus of one old SAMP8/Ta mouse Source GEO sample is GSM143753 Last updated (according to GEO): Jan 24 2007 Aortic aneurysm without mention of rupture NOS 901 447 438 infection 36 from the facial nucleus 14 liver, wild-type mice, control conditions Source GEO sample is GSM205804 Last updated (according to GEO): Jul 24 2007 Plasma 861 mdx quadriceps sample 2 /2J mouse periaqueductal gray 27 55 1000 frontal lobe Lymphoblastoid Cell Line for Individual 8008.4 log phase UBOC1 Exp A Day 6 (a) 1000 Ischemia GC (HKG55L) Aortic Aneurysm, Abdominal 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Anti-IgM for 240min Source GEO sample is GSM5451 Last updated (according to GEO): May 27 2005 Male; Epididymis-tail Keywords = mouse gene expression database Source GEO sample is GSM29394 Last updated (according to GEO): May 27 2005 Control 11 The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat "Western" diet from 8-24 weeks of age. These have been genotyped for QTL mapping, and various phenotypes measured. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Jul 27 2006 Contributers: Susanna Wang Hui Wang Xia Yang Eric E Schadt Leslie Ingram-Drake Arthur P Arnold Aldons J Lusis Thomas A Drake Macrophage smi73 skeletal muscle, tibialis anterior: Denervated 3-day Control 3_e1_le1 Primary tumor 19 32 AKR/J_male_hypothalamus Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242067 Last updated (according to GEO): Dec 04 2007 1000 Brain Control (Experiment NMDA2-Run 9600) Treatment, type=time_course, measurement=0.0 m Source GEO sample is GSM96665 Last updated (according to GEO): Feb 14 2006 skin 48 51 cingulate cortex 861 VDXIGRU_245392 5 0 brain 1768 1763 livers Lymphoblastoid Cell Line for Individual 8057.4 log phase human caudate nucleus Source GEO sample is GSM86896 Last updated (according to GEO): Feb 08 2006 Primary tumor 19 32 "28h Thy-Noc, Exp4" Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 3942 left_liver_lobe trigeminal_ganglia_9 Medulla 861 in hypothalamus 117 131 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68243 Last updated (according to GEO): Jul 07 2006 Brain 861 56 32 out of mouse bone marrow 1000 Cerebral cortex GSE7638 prostate Source GEO sample is GSM203277 Last updated (according to GEO): Jun 21 2007 Dahl-Iwai Male LowSalt OuterMedulla rat109 dahl_medullar_109_1_OM_053001 861 Malignant Neoplasms Chronic leukemia NOS 913 at the Human Brain 724 741 in the liver 91 102 ColonTum_022AAFC8_cta.txt brain 0 5 861 Oocytes 5 0 Spleen Female mice used were SvJ/129, 10-16 weeks of age, with both copies of the Hoxa-10 gene (GenBank # NM_008263) disrupted. These mice were littermates of Hoxa-10+/+ mice used in parallel experiments. 14 days after ovariectomy, mice were injected subcutaneously with progesterone dissolved in sesame oil (Sigma; 0.2mg/0.1mL/mouse), followed by sacrifice and removal of uterine horns at 6 hours after injection. 8 uterine horns from 4 mice were pooled to form one sample. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix. Source GEO sample is GSM3048 Last updated (according to GEO): May 27 2005 NHF10-hTERT_1.5Gy_6h_C5_21708 Gene expression data from postmorten brain regions Source GEO sample is GSM145666 Last updated (according to GEO): Nov 20 2006 plasma cells 332 344 1000 Coronary Arteriosclerosis Type 1 Diabetes patient and the timepoint 1 month after diagnosis. Source GEO sample is GSM228650 Last updated (according to GEO): Sep 11 2007 10 7 Left GM12802 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL10 for 30min Source GEO sample is GSM5632 Last updated (according to GEO): May 27 2005 WGACON-225 Mesenchymal Stem Cells 1000 UBOC1 Exp A Day 11 (a) Neurodegenerative Disorders 1000 660 mesenchymal stem cell 639 VDXKIU_219C42 5 0 brain Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47523 Last updated (according to GEO): May 29 2005 B220Low sIgM+ immature B cells sorted out of mouse bone marrow, sort no. 8 Source GEO sample is GSM614 Last updated (according to GEO): Mar 17 2006 brain 0 5 Plasma 861 eTat - Noco3hr - 2 90 74 Fetal liver cells NCI60.38_LABEL42EXTRACT41SUB3 Source GEO sample is GSM134184 Last updated (according to GEO): Aug 06 2007 331 307 in central nervous system Wild type inbred mice Source GEO sample is GSM83044 Last updated (according to GEO): Nov 10 2005 Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14355.gif Source GEO sample is GSM79624 Last updated (according to GEO): Sep 22 2006 1000 Prostate Gene expression data from postmorten brain regions Source GEO sample is GSM146058 Last updated (according to GEO): Nov 20 2006 Wild type inbred mice Source GEO sample is GSM83021 Last updated (according to GEO): Nov 10 2005 Mesenchymal Stem Cells 1000 Spleen vs Lipopolysaccharide (LPS) Treated B cell 240min (set3) Low-density CCg progenitors treated with FBS to derive Astrocytes Source GEO sample is GSM47556 Last updated (according to GEO): Jun 10 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Sphingosine-1-phosphate for 120min Source GEO sample is GSM5750 Last updated (according to GEO): May 27 2005 Central gray substance of midbrain 861 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201797 Last updated (according to GEO): Jun 20 2007 Endometrium-Normal 6 DM(LL) 1000 Brain RNA characterization of tissue from the injury location (~T8) in an uninjured animal. From the Christopher Reeve Paralysis Foundation Research Consortium microarray study (www.crpf.org/microarray) Source GEO sample is GSM49937 Last updated (according to GEO): May 27 2005 pooled RNA of the kidney of 36 day old rats Source GEO sample is GSM86648 Last updated (according to GEO): Jun 12 2006 1000 Maxilla Gene profiling of VP16-CREB transgenic mice 1000 Cerebral cortex WGACON-188 shipp-dlbcl gene expression data from melanoma xenografts following ILI with saline Source GEO sample is GSM213632 Last updated (according to GEO): Jul 27 2007 RIIIS-J_male_hypothalamus Source GEO sample is GSM138584 Last updated (according to GEO): Apr 18 2007 human frontal cortex Source GEO sample is GSM86970 Last updated (according to GEO): Feb 08 2006 7 cerebral cortex 21 ER+/LN+/Nevins5 on Affymetrix GeneChip Human Full Length Array HuGeneFL Skin 1000 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211260 Last updated (according to GEO): Jul 18 2007 2_cerebral_cortex_9hrs_sleep_#14 CNS-SMTC_Ctr7d-2A-s2 6,18,30 month oculomotor nucleus and spinal cord Source GEO sample is GSM74338 Last updated (according to GEO): Sep 16 2005 Large-scale analysis of the mouse transcriptome. Hippocampus C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 229.96 Stdv: 6.90 Min: 220.30 Max: 241.73 Source GEO sample is GSM2929 Last updated (according to GEO): May 27 2005 plasma cells 50 61 Blood 861 320 306 Keywords = HIV brain, cerebral cortex: Rat_02-46_VHL_Lipska_e1_le1 Sham 12 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107496 Last updated (according to GEO): May 01 2006 spinal cord, ventral spinal cord: D60SODSPMN2_e1_le1 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155058 Last updated (according to GEO): Jun 04 2007 amygdala sprague 3950 whole tissue, individual animal, 10 weeks old, male Sprague Dawley amygdala file:R3KJF02021179 Source GEO sample is GSM15221 Last updated (according to GEO): Oct 28 2005 Ta gr2 tumour Source GEO sample is GSM2482 Last updated (according to GEO): May 27 2005 small Source GEO sample is GSM67251 Last updated (according to GEO): Jan 19 2006 Epithelial Cells 1000 HapMap CEU_parent Male Source GEO sample is GSM159515 Last updated (according to GEO): Feb 01 2007 Wild type inbred mice Source GEO sample is GSM82963 Last updated (according to GEO): Nov 10 2005 Primary tumor 19 32 59 35 out of mouse bone marrow Brain 1000 1000 Rectum of postmortem brains 657 676 972 Structure of middle temporal gyrus Tissue fiber 861 Gene expression data from liver Source GEO sample is GSM243409 Last updated (according to GEO): Nov 16 2007 M1 juvenile biol repl 2 Measles 861 Mouse model of congenital heart disease in Csx/Nkx2.5 mutant embryos. Homozygous mutant mouse at embyronic day 9.5. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2277 Last updated (according to GEO): May 27 2005 861 Occipital lobe Nose 1000 nasal epithelial cells 28 49 with some respiratory epithelium. 1039 1072 Plasma 861 mouse brain ipsilateral control, biological rep2 Category: Serum-response Subcategory: Fibroblasts Scanning Software: unknown Software version: unknown Lot batch = 129 Source GEO sample is GSM1727 Last updated (according to GEO): Nov 21 2005 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16207.gif Source GEO sample is GSM84125 Last updated (according to GEO): Sep 22 2006 GSE511 Heart 1000 913 frontal lobe 5 0 brain 588 565 normal epithelial cells from brain 21 30 64 47 that whole ovaries no additional Source GEO sample is GSM199189 Last updated (according to GEO): Jun 08 2007 Primary small cell lung carcinoma 4271 227 200 in cardiac differentiation. Osteoblasts 1000 7 cortex 12 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 1 - Pair 5 - MMN Source GEO sample is GSM49895 Last updated (according to GEO): Dec 20 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145048 Last updated (according to GEO): Nov 20 2006 Malignant Neoplasms 1000 Transplant Series 34 , Transplant # 2 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11455 Last updated (according to GEO): May 28 2005 in the brain 150 162 861 Medulla Oblongata no additional Source GEO sample is GSM199164 Last updated (according to GEO): Jun 08 2007 861 Cardiomyopathies Gene expression data from liver Source GEO sample is GSM243381 Last updated (according to GEO): Nov 16 2007 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153352 Last updated (according to GEO): Dec 27 2006 /J mouse pituitary gland 25 48 U87 glioblastoma cell, clone 3.1 (neo-resistant negative control) Keywords = bioinformatics Keywords = gene expression Keywords = cancer Keywords = platelet-derived growth factor Keywords = sterol regulatory element binding protein Keywords = glioblastoma multiformae Keywords = microarray Source GEO sample is GSM34582 Last updated (according to GEO): May 27 2005 SN:1030150 Source GEO sample is GSM115422 Last updated (according to GEO): Jun 20 2006 contralateral Cortex 7 27 791 775 /rhabdoid tumours GSE2599 brain, cerebral cortex: NMDA 8/30_le1 861 Cerebral cortex Liver 861 CLL-25 CNS-SpinalCsev-Adult-28d-1B-s2b 10 Bone marrow 0 Liver 1000 Kp6: Hippocampus_5T-Y_rep1 Neural tube, treated, GD9:00, T215581 Tissue Source GEO sample is GSM67257 Last updated (according to GEO): Jan 19 2006 Brain 1000 Expression profiling of somatomotor cortex extracted from rats at 7d following sham surgery Source GEO sample is GSM41673 Last updated (according to GEO): May 27 2005 /NJ mouse pituitary gland 27 51 Brain 1000 901 Parkinson Disease Ovarian_Tumor_Endometrioid_CHTN-OE-017 plasma cells 332 344 Laser capture lung cancer cells Source GEO sample is GSM191020 Last updated (according to GEO): May 25 2007 salivarygland Source GEO sample is GSM18833 Last updated (according to GEO): Sep 25 2006 BALB/cByJ_female_hypothalamus Source GEO sample is GSM138565 Last updated (according to GEO): Apr 18 2007 Ovarian_Tumor_Endometrioid_CHTN-OE-014 861 Liver 1000 Spleen Replicate3_Voxel E7 1000 Medulla Oblongata olfactory epithelium wild type mouse 2 hpO Source GEO sample is GSM80188 Last updated (according to GEO): Oct 26 2005 Disorder of artery 865 861 Brain Sample46, Post Injury 24 hours Treatment, type=wait Source GEO sample is GSM53296 Last updated (according to GEO): Jul 06 2005 901 frontal lobe Use of genetic profiling in leprosy to discriminate clinical forms of the disease. Tumor__Mesothelioma_228_T4 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A NHE1 null mutation cerebellum-1 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 0.25 hours after lights on. Original sample code = CM1A. Source GEO sample is GSM227289 Last updated (according to GEO): Sep 10 2007 C2C12_4.0_hr Medulla 861 of normal colonic epithelium 376 404 Gene expression data from microdissected area # 2 of 2182 tumor Source GEO sample is GSM182304 Last updated (according to GEO): Apr 16 2007 Primary tumor 19 32 1000 Hippocampus Transitional epithelium 1000 1000 Lung Gene expression data from postmorten brain regions Source GEO sample is GSM145329 Last updated (according to GEO): Nov 20 2006 Tumor__Melanoma_MGH_10427 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene expression data from whole brain of uninfected mouse Source GEO sample is GSM189635 Last updated (according to GEO): May 16 2007 trachea_3 Source GEO sample is GSM80888 Last updated (according to GEO): Mar 31 2006 901 Nervous system structure 5 0 Spleen 80 68 Control blood 1000 Hypothalamic structure in the mammalian nervous system 110 141 Spleen vs Terbutaline Treated B cell 120min (set2) Cochlea at E10.5, replicate1 1000 Adrenal Medulla Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68272 Last updated (according to GEO): Jul 07 2006 Primary tumor 19 32 liver_PPARa-knockout_control_6h_rep4 Gene expression data from mammary glands of lactating mice Source GEO sample is GSM202700 Last updated (according to GEO): Jun 20 2007 Cerebral cortex 861 Coronary Arteriosclerosis 1000 VDXIGRU_271982 We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7. Source GEO sample is GSM200756 Last updated (according to GEO): Jul 12 2007 Trisomy 21 sample 2 (cerebrum) 5 0 Spleen Neoplasm 861 861 Cerebral cortex labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156695 Last updated (according to GEO): Jan 22 2007 Heart 1000 CONTROL_3 13 7 cochlea Spleen vs TGF-beta (transforming growth factor-beta) Treated B cell 60min (set2) spinal cord 0 11 1000 Brain Brain 861 HeartAtrium22HAFI9_080.txt 861 Fibroblasts Cerebral cortex 861 NoCAD_replicate4 5 0 brain /SvEvTac mouse periaqueductal gray 29 62 Heart 861 1000 Neoplasm Liver (fetal) [JunctionChip 5 of 5] 22-oct-2002-liverD-Mu11KsubAsc This is the second replicate for the SNc neurons which were captured using LCM. Source GEO sample is GSM19315 Last updated (according to GEO): May 27 2005 cartilage 1813 1822 Blood 1000 Spleen 1000 Spleen vs Terbutaline Treated B cell 240min (set1) HDMTX_MP-9 plasma cells 332 344 861 Brain Mammary Gland @ Preg1, biological rep4 91 from the bone marrow 72 7 0 prostate Myocardium 861 CNS-SpinalCmod-Adult-12h-4A-s2 14 0 globus_pallidus Blood B cells;anti-IgM+IL-4 6h 107 FC BA9 A cardiac 746 752 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134647 Last updated (according to GEO): Jul 09 2007 Tumor__Pancreas_Adeno_97_I_077 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Nose 1000 Coronary Arteriosclerosis 1000 PGA_IGF1R-dnPI3K_3190 welsh-ovarian brain, left frontal temporal lobe: Extract37_le1 112 98 from the kidney /cByJ Olfactory Bulb A 4 25 Anterior nares 1000 The goal of these experiments was to identify the genes that are regulated by CCAT, a novel transcription factor derived from the C-terminus of CaV1.2. Neuro2A neuroblastoma cells were transfected with the last 503 AA of CaV1.2 which is full length CCAT (CCAT FL) or with the last 280 AA of CaV1.2, a form of CCAT that lacks the transcriptional activation domain (CCAT DTA). The mRNA from either CCAT FL or CCAT DTA expressing cells was hybridized to Agilent mouse genome microarrays along with mRNA from untransfected neuro2A cells. The microarray data was subsequently analyzed with the Rossetta Luminator gene expression data analysis system. Subsequent investigation revealed that CCAT DTA can still activate transcription albeit at much lower levels than CCAT FL. Source GEO sample is GSM95629 Last updated (according to GEO): Feb 07 2006 Monocular deprivation left cortex, biological rep1 861 Brain Brain_MD_56_Medulloblastoma_Desmoplastic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL Alzheimer's Disease 861 67 52 descending colon 091200 CtrlMix on Affymetrix GeneChip Human Full Length Array HuGeneFL OVCAR-3_CL6001_OVARIAN brain, frontal cortex: ADX PM S_e1_le1 1000 Organ of Corti 4 0 Heart Coronary Arteriosclerosis 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145655 Last updated (according to GEO): Nov 20 2006 Human Hypothalamus Female 4 FC 35h NH 111h Dark rearing, biological rep3 CHB DR-3 mild cognitive impairment - primary visual cortex 5 mouse_hepatocytes_control_pooled Homozygous O377 mutant mouse line versus wildtype mice Source GEO sample is GSM86291 Last updated (according to GEO): Dec 08 2005 861 Ribosomal RNA adACN9 Expression profiling of somatomotor cortex extracted from rats at 7d following moderate injury Lot batch = Source GEO sample is GSM44715 Last updated (according to GEO): May 27 2005 GSE61 Small Intestine; ileum short bowel resection Keywords = mouse gene expression database Source GEO sample is GSM29302 Last updated (according to GEO): May 27 2005 Fibroblasts 1000 Central gray substance of midbrain 861 Normal Source GEO sample is GSM175890 Last updated (according to GEO): Apr 09 2007 no additional Source GEO sample is GSM199244 Last updated (according to GEO): Jun 08 2007 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18926.gif Source GEO sample is GSM84124 Last updated (according to GEO): Sep 22 2006 heart 1169 1173 1000 Hippocampus umbilical cord_nobpd: 3I Colon 861 M_U133A_18_DLPFC_R Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15742 Last updated (according to GEO): May 28 2005 brain, cerebral cortex: 15002_e2_le1 42 in skeletal muscle 25 928 Hyperinsulinism 1000 Adrenal Medulla Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141320 Last updated (according to GEO): Oct 26 2006 Tumor__Leukemia_ALL-B_ALL_(23953)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A CAD_replicate109 kidney 37 43 Cerebral cortex 861 Nasal Epithelium 865 660 mesenchymal stem cell 639 HDMTX-DX-1 C57BL/6 benchmark dataset: Embryonic day 11.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25155 Last updated (according to GEO): May 27 2005 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141270 Last updated (according to GEO): Oct 26 2006 Primary Neoplasm 1000 I_U133A_98_CB DBA/2J Cingulate Cortex A Parkinson Disease 1000 Spleen vs SDF1 alpha (Stromal cell derived factor-1) Treated B cell 60min (set3) Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151962 Last updated (according to GEO): Feb 06 2007 Parkinson Disease 861 409 379 of multiple joint contractures Occipital Lobe 10 Normal 861 Dislocations M7TW00121475 Spleen vs fMLP Treated B cell 60min (set1) SynovChrAr_022LACIF_152.txt 67 40 with coronary artery disease SR-A mutant olfactory epithlium 16 hpO replicate2 Squamous cell carcinoma 884 Lymphoblastoid Cell Line for Individual 8039.4 log phase brain 0 5 Colon 1000 Plasma 861 861 Parkinson Disease Hereditary Nonpolyposis Colorectal Neoplasms 947 7 0 prostate M_U133A_52_nAcc Experimental Autoimmune Encephalomyelitis 1000 861 Occipital lobe total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with TGF-beta (transforming growth factor-beta) for 60min Lot batch = Source GEO sample is GSM5795 Last updated (according to GEO): May 28 2005 none Source GEO sample is GSM244579 Last updated (according to GEO): Nov 23 2007 Parkinson Disease 1000 458 449 infection ileum (pool of 4 animals)_72h monoassociation with L.innocua(hly)_B_5556 Source GEO sample is GSM161585 Last updated (according to GEO): Apr 23 2007 1000 Heart failure H9RGV00111502 Samp10 Hippocampus Young Sample 2 corpus_callosum_5 Standard affymetrix protocol Source GEO sample is GSM119723 Last updated (according to GEO): Jul 31 2007 Prefrontal Cortex Source GEO sample is GSM105469 Last updated (according to GEO): Apr 17 2006 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184710 Last updated (according to GEO): Apr 26 2007 dentate granule cells Source GEO sample is GSM35820 Last updated (according to GEO): May 27 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68145 Last updated (according to GEO): Jul 07 2006 umbilical cord_nobpd: 4C Infection 1000 1000 Neoplasm 861 Nerve VDXKIU_440 Heart 861 human cerebellum Source GEO sample is GSM87105 Last updated (according to GEO): Feb 08 2006 861 Heart Diseases 1000 Retina Medulla Oblongata 861 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 20 hours after lights on. Original sample code = CM15A Source GEO sample is GSM227312 Last updated (according to GEO): Sep 10 2007 M_95Av2_3023_DLPFC_0_GS from ventral prostate 21 41 861 Substantia nigra structure Liver 1000 Abdominal aorta 0 14 of the small intestine 51 72 901 frontal lobe 861 Blood None Source GEO sample is GSM214243 Last updated (according to GEO): Aug 01 2007 Lymphoblastoid Cell Line for Individual 8037.3 log phase PGA_PA-D_102 Blood Test (Blinded) Sample Source GEO sample is GSM130002 Last updated (according to GEO): Sep 18 2007 seminoma specimen, pT1, patient age: 35y; W00 222 epidermis 0 8 156 145 Their livers Occipital lobe 983 VDXRHU_5235 contralateral Cortex 7 27 cerebral cortex 7 21 Cerebellum 1000 HapMap JPT Female Source GEO sample is GSM159660 Last updated (according to GEO): Feb 01 2007 Macrophage 14smi013 Communicable Diseases 1000 423 an autoimmune disease 443 Spleen 1000 from whole tumor 21 36 SAMR1 Retina Young Sample 1 0 Many neurodegenerative disorders 31 Collagen 1000 Hippocampus 1000 of the developing cortex 25 48 A HID B D010 Ovary 50 55 14 9 tumour Monocytes Resting 30h 2 Resting in blood 16 23 16 7 cerebellum S4_1, mouse, SW, control (non-infected), 4 day time matched control_rep 1 Skeletal bone 861 1000 Skin Brain Injuries 901 Pool of 13 (1 utricle and 3 ampullae) at E14 Source GEO sample is GSM182605 Last updated (according to GEO): Aug 14 2007 GISTs 160 164 901 frontal lobe Anterior nares 1000 CNS-RM_Mod7d-1A-s2 Human Cell Line, adrenal medulla: RNA613_le1 Brain (postcentral gyrus) [JunctionChip 5 of 5] 67 52 descending colon tibiae 115 120 1000 Neoplasm 1056 1049 muscles Testis 1000 ileum (pool of 4 animals)_Germ-free_B_5554 Source GEO sample is GSM161582 Last updated (according to GEO): Apr 23 2007 Liver 1000 Expression data in native lipoprotein-stimulated human THP-1 macrophages in hepatocellular carcinoma 1243 1269 1000 frontal lobe 444 435 infection Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188748 Last updated (according to GEO): Jun 06 2007 901 Mammary gland prostate Source GEO sample is GSM203341 Last updated (according to GEO): Jun 21 2007 Comprehensive analysis of PPARa-dependent regulation of hepatic lipid metabolism by expression profiling - Mus musculus 41 30 PCOS oocytes Forebrain 229 237 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.71 Subject: 3023 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39056 Last updated (according to GEO): May 27 2005 Lmna H222P homozygous male 2 Hippocampus 0 10 MF-24 785 770 of chromosome 6 1000 Hippocampus Frontal cortex 254 267 Large-scale analysis of the mouse transcriptome. Large intestine, cecum C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 211.32 Stdv: 7.51 Min: 198.57 Max: 224.94 Source GEO sample is GSM2932 Last updated (according to GEO): May 27 2005 HNC2714 67 40 with coronary artery disease in the mammalian nervous system 110 141 normal human skeletal muscle sample 6 bronchial epithelia 224 243 medulla_1 Source GEO sample is GSM80708 Last updated (according to GEO): Mar 31 2006 Transplant Series 13 , Transplant # 4 Normal human tissue:Normal hippocampus Keywords = Human, Normal Tissue, Normal hippocampus Source GEO sample is GSM44697 Last updated (according to GEO): May 27 2005 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159982 Last updated (according to GEO): Feb 01 2007 The nose 94 101 7 0 Synovium HCC (HBV+, HK57) Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 0.25 hours after lights on. Original sample code = CM37A. Source GEO sample is GSM227309 Last updated (according to GEO): Sep 10 2007 Gene expression data from mouse primary visual cortex Source GEO sample is GSM101708 Last updated (according to GEO): Mar 27 2006 Spleen vs CGS Treated B cell 240min (set1) 1000 Cerebrovascular accident the gap junction protein connexin43 960 994 Prosencephalon 1000 Tissue Source GEO sample is GSM67202 Last updated (according to GEO): Jan 19 2006 462 cortex 467 Bone structure of tibia 1000 Spleen 0 5 861 Ganglia to muscle 2308 2316 Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. All patients were considered sporadic cases on the basis that no clinical antecedents of familial adenomatous polyposis were reported, and those that met the clinical criteria for hereditary non-polyposis colon cancer (Amsterdam criteria) were excluded. Source GEO sample is GSM112299 Last updated (according to GEO): Jun 06 2006 Parkinson Disease 861 C102 on NCI-7.6k 861 pars compacta above anterior commisure 17 41 8984 on TGRI-6.5k Transcriptional profiling of the transition from normal intestinal epithelia to adenomas and carcinomas in the APCMin/+ mouse. Expression profiling of spinal cord section (T8) extracted from rats 0h following laminectomy (naive) Source GEO sample is GSM31415 Last updated (according to GEO): May 27 2005 1000 Brain Control male 6 Brain 861 Primary Neoplasm 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11238 Last updated (according to GEO): May 28 2005 ER negative human primary breast tumor EA02014_41255_H133A_JA-838 12 0 ovarian tumor 28 0 Adult frontal cortex cocaine4 Lymphoblastoid Cell Line for Individual 8013.4 log phase testis 52 58 1000 Heart human frontal cortex Source GEO sample is GSM86958 Last updated (according to GEO): Feb 08 2006 none Source GEO sample is GSM149619 Last updated (according to GEO): Jan 03 2007 Skeletal muscle biopsy was obtained after a two-hours of hyperinsulinaemic (40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172130 Last updated (according to GEO): Feb 28 2007 Heart Septal Defects 884 post infection 66 79 NoCAD_replicate48 Gene expression profile of the cell line UB/OC-1 grown for 9 days under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1542 Last updated (according to GEO): May 27 2005 129:23-7,8,9 inferior colliculi Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184823 Last updated (according to GEO): Apr 26 2007 1000 Microglia The most common congenital cardiac abnormalities 50 97 901 Heart failure 861 Uterus 358 348 in melanoma NA11829 of the stria terminalis 56 78 Infection 1176 1185 861 Colon D_U133A_52_CB - Source GEO sample is GSM216541 Last updated (according to GEO): Aug 09 2007 131 121 cerebellum Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188820 Last updated (according to GEO): Jun 06 2007 Ldn1 C57 whole brain 4A Gene expression data from postmorten brain regions Source GEO sample is GSM145154 Last updated (according to GEO): Nov 20 2006 1000 Prostate normal testis 54 66 861 Stomach fetalliver Source GEO sample is GSM18746 Last updated (according to GEO): Sep 25 2006 Neuroglia 901 861 Muscle with myocardial infarction 313 339 Gene expression data from the neocortex of S1P3-knockout mouse Source GEO sample is GSM172948 Last updated (according to GEO): Mar 08 2007 na Source GEO sample is GSM180463 Last updated (according to GEO): Apr 04 2007 normal 2911 brain, cerebral cortex: Rat_03-52_NroLep_Lipska_e1_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM145095 Last updated (according to GEO): Nov 20 2006 5 0 kidney Inherited mutations of calcium ion channels exhibit neurological defects, such as epilepsy, ataxia, and migraine, and these phenotypes are shared among humans and mouse models. Absence epilepsy and ataxic phenotypes are present in the calcium channelopathy mutants stargazer (stg-gamma2 subunit), tottering (tg-alpha1 subunit), and lethargic (lh-beta4 subunit). These mutations of high-voltage-activated (HVA) calcium channel subunits initiate increases in membrane excitability of low-voltage-activated (LVA) calcium channels in thalamic neurons, thus enhancing LVA currents. Elevated LVA currents, produced from T-type calcium channels, induce rhythmic thalamocortical burst firing and spike-wave seizures. The changes in gene expression originating from the different mutations result in similar T-type channel function; however, the network of gene modifications causing altered molecular plasticity and the emergence of pathological phenotypes remain unknown. We would like to understand how loss of 3 different subunits of a calcium ion channel differentially alter gene expression in the brain. Characterizing the gene expression profiles of the mutant stg, tg, and lh mice will provide evidence of the epileptic and ataxic mechanisms, which may identify potential therapeutic targets. We will compare the gene expression profiles among adult mutant stg, tg, and lh mice, which display the ataxic and epileptic phenotypes, along with their wildtype, litter-mate controls, in the cerebellum and brain (without cerebellum). We propose that the neuronal dysfunction associated with the ataxic and epileptic phenotypes develops from a common network of interacting gene alterations within the mutant stg, tg, and lh brain. The changes dictated by the initial mutations leading to the ataxic and epileptic phenotypes are hypothesized to be localized to the cerebellum and the remaining areas of the brain, including the thalamus and cortex, respectively. Adult mutant stg, tg, and lh mice, between 2 and 5 months of age, along with wildtype, litter-mate controls, will be sacrificed. Two brain regions responsible for two phenotypes will be examined. The cerebellum (ataxia) will be dissected from remainder of the forebrain (generalized epilepsy). Each tissue set will be collected in triplicate (3 separate mice per set) to account for biological variance, and total RNA isolated via standard Trizol procedure (Invitrogen) and purified with the RNeasy cleanup kit (Qiagen). RNA samples will be stored at -80 C until sent for analysis using the Affymetrix GeneChip Mouse Genome 430 2.0 whole genome array. Last Updated (by provider): Nov 14 2006 Contributers: Wayne L Ernst 861 Infection MGJZ030312081Bcd4+Tcell 1000 Spleen CNS-SMTC_Mod4h-1B-s2 HC57 CB A Expression profiling of spinal cord section (T10) extracted from rats 14d following mild injury Source GEO sample is GSM31310 Last updated (according to GEO): May 27 2005 olfactory epithelium tissue 54 80 M_U133A_22_DLPFC Alzheimer's Disease 1000 N33__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Non-defeated Control Group, Nucleus accumbens, Biological Replicate 1 Total RNA from iPS clone was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations. Source GEO sample is GSM231508 Last updated (according to GEO): Nov 22 2007 Gene expression data from rat metanephric mesenchymes cultured for 5 days in the presence of NGAL Source GEO sample is GSM126214 Last updated (according to GEO): Dec 08 2006 1000 Rectum Whole brain 0 10 Mitochondria 1000 of the colon 28 39 Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. Moderate controlled cortical impact with pneumatic impactor, 6 m/s impact velocity and 1.5 mm deformation. 72h after surgery, a 4 mm diameter disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44472 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T8) extracted from rats 4h following laminectomy (sham) Lot batch = Source GEO sample is GSM4429 Last updated (according to GEO): May 28 2005 NeverSmoker 44 1000 Neoplasm Metastasis Neuroglia 901 eye, retina: Pineal at CT 6_e1_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM145491 Last updated (according to GEO): Nov 20 2006 Kidney; Adult Keywords = mouse gene expression database Source GEO sample is GSM29359 Last updated (according to GEO): May 27 2005 14 days hindlimb suspended, 1 day reloaded RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis Source GEO sample is GSM10061 Last updated (according to GEO): May 28 2005 1000 ovarian neoplasm Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198631 Last updated (according to GEO): Jun 06 2007 D_U133Plus_118_Amy Communicable Diseases 901 91 from the bone marrow 72 eTat - Hu0hr - 2 n/a Source GEO sample is GSM177911 Last updated (according to GEO): Jun 11 2007 1000 Muscle Gene expression data from whole tumor Source GEO sample is GSM182306 Last updated (according to GEO): Apr 16 2007 Unfertilized egg replication 3 0 29 HCT-15 hgu95c 5 0 brain none Source GEO sample is GSM239886 Last updated (according to GEO): Dec 07 2007 Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14343.gif Source GEO sample is GSM79696 Last updated (according to GEO): Sep 22 2006 36 21 from hippocampus Lymphoblastoid Cell Line for Individual 8130.4 log phase Neoplasm 861 Donor A, after G-CSF Source GEO sample is GSM178554 Last updated (according to GEO): Aug 09 2007 PGA-HMO-NonObese-2aUA-s2 large intestine sprague1 whole tissue, individual animal, 10 weeks old, male Sprague Dawley large intestine file:R3JW02103013 Source GEO sample is GSM15211 Last updated (according to GEO): May 28 2005 SN:Human Glioblastoma Biopsy 12382 305 291 in spinal cord 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201286 Last updated (according to GEO): Jun 14 2007 Nose 1000 22 0 Mammary Gland @ Preg17 Hereditary Malignant Neoplasm 876 861 Blood 861 Breast in somatosensory cortex 1564 1586 HMEC X BC23 : 0090-5k Lung tissue from C57BL/6 mice calorie restricted by 2/3 and sacrificed 72hrs after the onset of calorie restriction. Lot batch = Source GEO sample is GSM4030 Last updated (according to GEO): May 28 2005 A498_CL9013_Renal on Affymetrix GeneChip Human Full Length Array HuGeneFL 7 cerebral cortex 21 67 52 descending colon 138 125 other cancers brain, hippocampus: CH3_e1_le1 Expression profiling of somatomotor cortex extracted from rats at 14d following sham surgery Source GEO sample is GSM41638 Last updated (according to GEO): May 27 2005 of somatomotor cortex 21 41 Gene expression data from liver Source GEO sample is GSM243407 Last updated (according to GEO): Nov 16 2007 Malignant neoplasm of prostate 1000 low gestational age Source GEO sample is GSM213096 Last updated (according to GEO): Jul 25 2007 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188787 Last updated (according to GEO): Jun 06 2007 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18168.gif Source GEO sample is GSM91598 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145641 Last updated (according to GEO): Nov 20 2006 Brain 1000 1000 Rectum Richard Almon-52-1138200270977 1000 Brain D_U133Plus_120_Amy 983 Malignant neoplasm of cervix uteri 1000 Spleen 280 254 Allergic contact dermatitis processed in batch 2 Source GEO sample is GSM90453 Last updated (according to GEO): Mar 20 2006 BALB-c mice were given intratracheal bleomycin (1.5U per kg). Lungs were harvested and frozen at 14d. Lot batch = Source GEO sample is GSM4147 Last updated (according to GEO): May 28 2005 Exp A_4, control (0mg/kg) CPF testis 52 58 Brain 861 Nose 1000 Accumbens P6 Normal 48h -TGF-beta pulp tissue Alzheimer's Disease 1000 proteoglycans 563 576 Spleen 0 5 Exp C, Animal #3, 10mg/kg CPF, 1st repeat Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours Source GEO sample is GSM246170 Last updated (according to GEO): Dec 03 2007 Saccule 0 6 D_U133A_11_Amy 2058 2020 in aging-related cognitive dysfunction C57L/J Hippocampus C C57BL/6J Chronic morphine treated, striatum, biological replicate 2 Source GEO sample is GSM187981 Last updated (according to GEO): Jun 14 2007 Keywords = Infectious diseases 1070 1100 GSE3114 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD40 for 240min Source GEO sample is GSM5508 Last updated (according to GEO): May 27 2005 966 955 HPV+ cancers Brain 861 medulla_2 Source GEO sample is GSM80711 Last updated (according to GEO): Mar 31 2006 901 Caudate nucleus structure PGA-MurLungRag-rwp-72h-1aCv2-s2 cervix_9 Source GEO sample is GSM80634 Last updated (according to GEO): Mar 31 2006 Nasal Epithelium Inhalation Formaldehyde 0ppm 5d ID61 Large-scale analysis of the mouse transcriptome. Kidney C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 351.75 Stdv: 15.51 Min: 323.03 Max: 372.32 Source GEO sample is GSM2930 Last updated (according to GEO): Mar 20 2006 Total RNA extracted from mouse brain Source GEO sample is GSM103429 Last updated (according to GEO): Sep 21 2006 Gene expression data from mouse colon Source GEO sample is GSM198118 Last updated (according to GEO): Aug 22 2007 Biopsy of the normal mucosa of the colon from patient #6 GC (HKG90N) of somatomotor cortex 21 41 C105 on NCI-7.6k GBM Treatment, type=remove Source GEO sample is GSM99591 Last updated (according to GEO): Apr 21 2006 brain 0 5 N-7_PRE Primary Neoplasm 1000 tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44867 Last updated (according to GEO): May 27 2005 66 42 out of mouse bone marrow Mental Retardation 1000 Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep1 cerebral_cortex_3 Neoplasm 861 Leukemic fractions of ID29 AML patient have been hybridized. Source GEO sample is GSM103102 Last updated (according to GEO): Feb 26 2007 from the right forebrain 21 44 B6 2000-2 Liver CVB3-infected HeLa cells (multiple time points and triplicate sample per time point) We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201805 Last updated (according to GEO): Jun 20 2007 Expression profiling of spinal cord section (T8) extracted from rats 7d following severe injury Source GEO sample is GSM31496 Last updated (according to GEO): May 27 2005 Female infertility syndromes are among the most prevalent chronic health disorders in women, but their genetic basis remains unknown because of uncertainty regarding the number and identity of ovarian factors controlling the assembly, preservation, and maturation of ovarian follicles. To systematically discover ovarian fertility genes en masse, we employed a mouse model (Foxo3), in which follicles are assembled normally but then undergo synchronous activation. We developed a microarray-based approach for the systematic discovery of tissue-specific genes and, by applying it to Foxo3 ovaries and other samples, defined a surprisingly large set of ovarian factors (n=348, about 1% of the mouse genome). This set included the vast majority of known ovarian factors, 44% of which when mutated produce female sterility phenotypes, but most were novel. Comparative profiling of other tissues including microdissected oocytes and somatic cells revealed distinct gene classes and provided new insights into oogenesis and ovarian function, demonstrating the utility of our approach for tissue-specific gene discovery. This study will thus facilitate comprehensive analyses of follicle development, ovarian function, and female infertility. Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=770640 LaserPower=4.263.93 Lot batch = LC17N130 Source GEO sample is GSM4839 Last updated (according to GEO): Nov 21 2005 from ventral prostate 21 41 Coxsackievirus Infections 861 kidney.2 41 CB A Gene expression data from postmorten brain regions Source GEO sample is GSM145859 Last updated (according to GEO): Nov 20 2006 1000 Brain n/a Source GEO sample is GSM178027 Last updated (according to GEO): Jun 11 2007 TEL-AML1-C32 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Mammary gland Cerebral cortex 861 928 Endometrium Epithelium 861 Epithelial Cells 901 5 0 Spleen Neoplasm 861 of spermatogonia 938 953 Coronary heart disease 913 4 0 Colon 861 Cerebral cortex 861 Brain PC 6Hr rat 3586 blood vs. 1500mg/kg APAP 6Hr rat 3591 blood 9 0 Blood Test Expression profiling of somatomotor cortex extracted from rats at 14d following moderate injury Source GEO sample is GSM41687 Last updated (according to GEO): May 27 2005 1188 1174 in the amygdala M7TW00122048 Chronic inflammation during placental malaria (PM) caused by Plasmodium falciparum is most frequent in first-time mothers and is associated with poor maternal and fetal outcomes. In the first genome wide analysis of the local human response to sequestered malaria parasites, we identified genes associated with chronic PM, then localized the corresponding proteins and immune cell subsets in placental cryosections. Last Updated (by provider): Jun 30 2007 Contributers: Patrick E Duffy Theonest K Mutabingwa Michal Fried Atis Muehlenbachs #14 (isolate 9 low serum media VEGF-A 24hours) 114 101 brains quickly Pool of 8 cochlear tissues at E13.5 Source GEO sample is GSM182583 Last updated (according to GEO): Aug 14 2007 Parkinson Disease 861 1000 Hippocampus Expression profiling of brain tissue from (C57BL/6J X C3H/HeJ)F2 mice on ApoE null backgrounds Medulla Oblongata 861 Parkinson's disease sample x014 ventral spinal cord 13 31 861 Cardiomyopathies 258 245 from 6 brains Wild type voxel C2 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181148 Last updated (according to GEO): Jul 12 2007 cerebral cortex 7 21 total RNA from biosource CC#41 Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92470 Last updated (according to GEO): Jan 13 2006 jzo014-rp1-v5-u74av2-met KT138b_AR1 the ventricular 1095 1109 78 73 rectum labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156591 Last updated (according to GEO): Jan 22 2007 1000 Brain R494P00442 Voxel B4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1398 Last updated (according to GEO): Nov 21 2005 plasma cells 50 61 B220Low sIgM+ immature B cells sorted out of mouse bone marrow, sort no. 2 Source GEO sample is GSM613 Last updated (according to GEO): Mar 17 2006 Expression profiling of laminectomized raphe at 28d in rats Source GEO sample is GSM41532 Last updated (according to GEO): May 27 2005 the blood 393 402 Female 66.6 yr after antibody enrichment scan 2 (U133A) PMN_control_360min_Patient13 1000 Spleen brain 0 5 basal ganglia Source GEO sample is GSM38977 Last updated (according to GEO): May 27 2005 Nidogen 861 913 Left ventricular structure Gene expression data from postmorten brain regions Source GEO sample is GSM144940 Last updated (according to GEO): Nov 20 2006 MDA Mb231 6h + 10 nM Cxcl12 3 Treated NG108 rat neuronal cell culture exposed to 4400 ng/ml mefloquine (treated) for two hours. 10 µg total RNA hybridized per chip. RNA STAT 60 used to extract RNA. Standard Affymetrix chip scaling factors used. No other data transformation. Source GEO sample is GSM1665 Last updated (according to GEO): Oct 28 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with BAFF for 240min Source GEO sample is GSM5461 Last updated (according to GEO): May 27 2005 39 0 endothelial cells sprague2 whole tissue Primary large cell neuroendocrine carcinoma 2144 Source GEO sample is GSM17328 Last updated (according to GEO): May 28 2005 from aorta 150 160 mouse brain contralateral RU486 Source GEO sample is GSM149757 Last updated (according to GEO): Mar 15 2007 HCC (HK55) none Source GEO sample is GSM244562 Last updated (according to GEO): Nov 23 2007 brain, cerebral cortex: Rat_02-44_VHL_Lipska_e1_le1 Pancreas [JunctionChip 1 of 5] Spinal Cord 1000 966 Esophagus Brain 1000 that the adult brain 1023 1042 41 36 spleen Cochlea at E15, replicate1 for developing lung metastasis 606 636 1000 Aorta none Source GEO sample is GSM123227 Last updated (according to GEO): Jul 26 2006 AD-240t1-A159-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Bone Marrow 1000 Heart 1000 n/a Source GEO sample is GSM177916 Last updated (according to GEO): Jun 11 2007 Heart 1000 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50644.gif Developmental Stage: E8.5 Source GEO sample is GSM229813 Last updated (according to GEO): Nov 06 2007 1037 of transitional epithelium 1012 1000 Cerebrovascular accident Head and neck cancer Source GEO sample is GSM155705 Last updated (according to GEO): Apr 24 2007 plasma cells 50 61 FC 3148150A Hoxb1 mutant E10.5, rep 3 (M8) BC308B-BE Spleen 1000 Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14342.gif Source GEO sample is GSM79695 Last updated (according to GEO): Sep 22 2006 1000 Hippocampus 28 13 from spinal cord 7 cerebral cortex 21 BPH-201 on UMich-10k none Source GEO sample is GSM239871 Last updated (according to GEO): Dec 07 2007 1000 Brain Occipital region 983 wild-type control 901 Mammary gland 26 0 Bone marrow [JunctionChip 4 Nose 1000 DBA/2J hippocampus rep1 (430 2.0 Array) NCI60.28_LABEL32EXTRACT31SUB3 Source GEO sample is GSM134134 Last updated (according to GEO): Aug 06 2007 1000 Prostate T-ALL-C22 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A osteoblast 627 637 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 4h after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44498 Last updated (according to GEO): May 27 2005 Squamous cell carcinoma 1 ME16C2 Brain 861 TEL-AML1-C24 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Pineal gland 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM144890 Last updated (according to GEO): Nov 20 2006 none Source GEO sample is GSM244551 Last updated (according to GEO): Nov 23 2007 PGA_IGF1R-caPI3K_1057 Gene expression data from postmorten brain regions Source GEO sample is GSM145196 Last updated (according to GEO): Nov 20 2006 20 0 Human prostate cancer Ovarian_Tumor_Serous_CHTN-OS-003 Gene expression data from postmorten brain regions Source GEO sample is GSM145900 Last updated (according to GEO): Nov 20 2006 115 cortex 121 19 0 Head and neck cancer E8.0b_rep1 CNS-SMTC_Ctr72h-1A-s2 1000 Uterus rotenone 2 weeks A Treatment, type=time_course, measurement=2.0 weeks Source GEO sample is GSM107859 Last updated (according to GEO): Jun 06 2006 none Source GEO sample is GSM239940 Last updated (according to GEO): Dec 07 2007 human frontal cortex Source GEO sample is GSM86987 Last updated (according to GEO): Feb 08 2006 Timecourse of TLR2/1 stimulated human dendritic cells with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225885 Last updated (according to GEO): Aug 31 2007 Epithelium of bronchus 983 human frontal cortex Source GEO sample is GSM87014 Last updated (according to GEO): Feb 08 2006 Timecourse of TLR2/1 stimulated human dendritic cells with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225871 Last updated (according to GEO): Aug 31 2007 rad001 15d, biological rep3 none Source GEO sample is GSM241958 Last updated (according to GEO): Nov 29 2007 124 115 from liver blood 0 5 Thalamus 4 Normal brain, hippocampus: PR-CA1-15_e1_le1 brain 0 5 Ischemia-reperfusion with AEOL 10150 #2 Cerebellum_naive_ISS56_A Nerve 861 5 0 brain hrs nasal epithelium 1127 1147 660 mesenchymal stem cell 639 Total RNA extracted from the cerebellum of a Lh-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144397 Last updated (according to GEO): Nov 14 2006 lymph node Source GEO sample is GSM18903 Last updated (according to GEO): Sep 25 2006 Liver Test (Blinded) Sample Source GEO sample is GSM130099 Last updated (according to GEO): Sep 18 2007 Superficial 1000 Ta gr2 tumour Source GEO sample is GSM2479 Last updated (according to GEO): May 27 2005 861 Cardiomyopathies 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114203 Last updated (according to GEO): Jun 16 2006 Gene expression data from a primary branch of the saphenous artery of 16 week old male Wistar-Kyoto rats Source GEO sample is GSM198859 Last updated (according to GEO): Nov 28 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CpG-oligodeoxynucleotide for 240min Source GEO sample is GSM5530 Last updated (according to GEO): May 27 2005 brain, cochlea: [11] Sample #11_le1 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228594 Last updated (according to GEO): Sep 11 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Neuropeptide Y for 30min Source GEO sample is GSM5710 Last updated (according to GEO): May 27 2005 861 Oocytes 1000 Cardiomyopathy, Alcoholic Subject code A38 Replicate2_Voxel D1 GC (HKG72T) Spinal cord [JunctionChip 1 of 5] 44 21 during placental malaria Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11330 Last updated (according to GEO): May 28 2005 Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19204 Last updated (according to GEO): May 27 2005 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92340 Last updated (according to GEO): Jan 13 2006 12 0 ovarian tumor 262 226 in the substantia nigra pars compacta Richard Almon-38-1138200270602 1000 Coronary Arteriosclerosis 861 Skeletal bone mouse brains 187 198 Liver 1000 Whole blood from a healthy control Source GEO sample is GSM153419 Last updated (according to GEO): Jan 11 2007 1000 Brain We build a model for the molecular and cellular events underlying phenotypic discordance in glycine receptor defects (beta subunit). Some mice progress and die, while their littermates recover and get better, despite the same mutation on an inbred genetic background. We find evidence for glycine neurotransmitter toxicity and loss of glycinergic interneurons early in the disease, but some mice are able to keep things going until they can over-express homomeric alpha1 channels, whereupon they recover. In the mice progressing towards lethality, neurotransmitter toxicity too quickly extends to GABAergic interneurons and motorneurons, and they lose their window of time to upregulate the alpha1 glycine receptor, and they crash and burn. Importantly, human patients with glycine receptor defects typically show a resolution of their phenotype with age, and we propose that the same remodeling events are occuring in human patients. Source GEO sample is GSM31006 Last updated (according to GEO): May 27 2005 M_U133A_60_DLPFC Gene expression data Source GEO sample is GSM183178 Last updated (according to GEO): Jul 30 2007 Nervous system structure 901 Brain_PNET_3_PNET on Affymetrix GeneChip Human Full Length Array HuGeneFL 861 HIV Infections This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12364 Last updated (according to GEO): May 28 2005 B6_SleepDep_ZT 18_1 10 squamous cell carcinomas 208 234 knockin mouse forebrain Treatment, type=time_course, measurement=11.0 weeks Source GEO sample is GSM53358 Last updated (according to GEO): Jul 06 2005 C57BL/6J Cerebellum C Brain 1000 Primary tumor 19 32 M7TW00121460 Cerebral cortex 861 5.0 mg/kg MeHg forebrain at 4.5h Bone Marrow 10 Normal spinal cord, ventral spinal cord: D28WTSP2 e1_le1 -_test-7_batch5 on NHGRI-6.7k mouse brains 187 198 GSE3895 861 Cardiomyopathies 1000 Secondary malignant neoplasm of lymph node 1000 Cerebrum Sample represents the supraoptic nucleus from 5 control animals Source GEO sample is GSM69461 Last updated (according to GEO): Dec 15 2005 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 1 - Pair 4 - IML Source GEO sample is GSM49891 Last updated (according to GEO): Dec 20 2005 11_0001_SepticShock_Day1_56 collagen 302 310 ovarian tumor: serous Source GEO sample is GSM139470 Last updated (according to GEO): Apr 09 2007 1 of 3 replicates in treatment group Source GEO sample is GSM206040 Last updated (according to GEO): Jun 29 2007 KT1009a_DT/IN Spinal cord [JunctionChip 2 of 5] 868 850 of medulloblastoma brain, cortex: Sample21_e1_le1 Gap Junctions 861 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118540 Last updated (according to GEO): Jul 11 2006 NA18940 Adipose tissue 901 cerebellum 7 16 Infection 1000 1000 Spinal Cord We will separately dissect the maxillary and mandibular branches of the E10.5 first branchial arch from wild type, dlx2, dlx1/2 and Dlx5/6 mutants. The tissues wil be flash frozen within 1 min of removal.We have not performed the dissections yet so we dont know how much RNA will be get from each sample, but previous experience suggests that we will need ~10 branchial arches/experiment. Treatment, type=nucleic_acid_extraction, description=We anticipate using this method as it was recommended by TGEN for small amounts of tissue. Source GEO sample is GSM107884 Last updated (according to GEO): Jun 06 2006 50 41 mouse lung OccipitalLobe Source GEO sample is GSM18931 Last updated (according to GEO): Sep 25 2006 Liver 1000 Primary tumor 19 32 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68222 Last updated (according to GEO): Jul 07 2006 133 111 in the optic nerve head Epithelial Cells 1000 NZB-BlNJ_male_hypothalamus P1_KIDNEY_3 Plasma 861 41 36 spleen Gene expression data from postmorten brain regions Source GEO sample is GSM145310 Last updated (according to GEO): Nov 20 2006 Brain (occipital) Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184794 Last updated (according to GEO): Apr 26 2007 CNS-SMTC_Ctr4h-1A-s2 4 0 Brain VDXIGRU_219873 861 Cardiomyopathies cortex 7 12 1000 Maxilla Oj9: Hippocampus_5T-AI_rep10 36 21 from whole brain NFIA E18KO1 861 Cerebral cortex tibiae 115 120 Epithelium 861 Primary small cell lung carcinoma 3170 in the brain 150 162 Blood 861 Gene expression data from rat metanephric mesenchymes cultured for 4 days in the presence of the ANX fraction Source GEO sample is GSM126223 Last updated (according to GEO): Dec 08 2006 db/m 16 wk1 70 40 without coronary artery disease 861 Thymus Gland CNS-SCsev_InjB4h-3C-s2 Entorhinal Cortex 7 23 These studies adress differential changes in gene expression between 6h sleep deprived and control mice in the brain and the liver. We profiled gene expression in three different inbred strains to understand the influence of genetic background. Last Updated (by provider): Dec 07 2007 Contributers: Mehdi Tafti Brice Petit Didier Chollet Sylvain Pradervand ALL-T-cell-3 on Affymetrix GeneChip Human Full Length Array HuGeneFL Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28827 Last updated (according to GEO): May 27 2005 Normal ovary Source GEO sample is GSM139477 Last updated (according to GEO): Apr 09 2007 Arteries 1000 low dose 24h, replicate 1 RPMI-8226 hgu95a 861 Milk 1000 Rectum 861 Amygdaloid structure DNA-EP-4HRS_1 861 Cerebral cortex Neuraxis 1000 22 14 (cerebrum Dissection of E16.5 cortex for RNA extraction. Cortex Hemispheres of E16.5 mice were divided into the medial (R1), dorsal (R2), ventral (R3), lateral (R4), and occipital regions (R5). Preparation of RNA and Synthesis of cDNA. Poly A+ RNA was obtained through twice column procedures with oligo dT cellulose column (New England Biolabs, Beverly, MA) and was used for synthesis of cDNA. 1ug of polyA+ RNA was converted into double-stranded cDNA by reverse transcription using ReverTra Ace (ToYoBo, Japan) with oligo dT(24) primers containing the T7 RNA polymerase promotor sequence (Amersham Pharmacia Biotech, Japan). The integrity of RNA was confirmed by agarose electrophoresis and RNA contents were analyzed by measuring the optical density at 260 nm. Target preparation and array processing. The following procedures including preparation of cRNA targets, hybridization, washing, staining, and scanning were performed as described in the Expression Analysis Technical Manual (Affymetrix, CA). Briefly, biotin-labeled antisense cRNA targets were synthesized in in vitro transcription reaction system (IVT) using cDNA as template (ENZO BioArrayTM HighYieldTM RNA Transcription Labeling kit with T7 RNA polymerase, Enzo, NY). The cRNA targets were size-fragmented to 35-200 bp in a buffer containing potassium and magnesium acetate at 94°C for 35 minutes and were used for hybridization as cRNA targets. The hybridization cocktail [containing 10 ug of target cRNA, control oligo BS (Affymetrix), and Eukaryotic Hybridization controls (Affymetrix)] was hybridized with a mouse U74A array at 42°C for 16 hours in GeneChip Hybridization Oven 640. Washing and staining were performed after hybridization under the fluidics station protocol, EuGE-WS2, on GeneChip Fluidics Station 400. Then, we scanned the array twice on HP GeneArrayTM scanner. Experiments were repeated twice with independent dissection. Data analysis. To quantify the expression level of a transcript, the average difference value (Adv) was calculated from the intensities against the probe cells using the global methods of normalization by Microarray Suite ver. 4.0 (Affymetrix). Source GEO sample is GSM14602 Last updated (according to GEO): Oct 28 2005 frontal cortex wistar 3924 whole tissue, individual animal, 10 weeks old, male Wistar frontal cortex file:p3924w Source GEO sample is GSM15161 Last updated (according to GEO): Oct 28 2005 in bronchial epithelia 311 332 Gene expression in papillary thyroid carcinoma reveals highly consistent profiles. B_AK_Control_ZT 6_3 861 Cancer of Neck Macrophage 14smi101 UBOC1 Exp A Day 3 (a) septum short access to cocaine replicate 1 Obesity, especially central obesity, is a hereditable trait associated with a high risk for development of diabetes and metabolic disorders. Combined gene expression analysis of adipocyte- and preadipocyte-containing fractions from intraabdominal and subcutaneous adipose tissue of mice revealed coordinated depot-specific differences in expression of multiple genes involved in embryonic development and pattern specification. These differences were intrinsic and persisted during in vitro culture and differentiation. Similar depot-specific differences in expression of developmental genes were observed in human subcutaneous versus visceral adipose tissue. Furthermore, in humans, several genes exhibited changes in expression that correlated closely with body mass index and/or waist/hip ratio. Together, these data suggest that genetically programmed developmental differences in adipocytes and their precursors in different regions of the body play an important role in obesity, body fat distribution, and potential functional differences between internal and subcutaneous adipose tissue. mouse brains 187 198 278 255 ischemic cardiomyopathy Paresis 861 D_U133Plus_61_HC Foreskin Microarray data set (Sample 1) Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 0644 left_liver_lobe brain, cortex: norm2_e1_le1 Tissue Source GEO sample is GSM67208 Last updated (according to GEO): Jan 19 2006 913 Coronary heart disease 1000 Epidermis of endemic malaria 520 538 GSE464 15 0 human cerebellum Wild type 8 wk old male 129S6/SvEvTac mouse hypothalamus Source GEO sample is GSM74971 Last updated (according to GEO): Feb 27 2007 Muscular Dystrophies 901 D_U133Plus_77_Amy Large-scale analysis of the mouse transcriptome. Small intestine, duodenum C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 269.23 Stdv: 8.45 Min: 259.01 Max: 286.06 Source GEO sample is GSM2905 Last updated (according to GEO): Mar 20 2006 Stomach Carcinoma 901 10 7 left Brain 861 (Ig 214 216 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with ELC for 240min Source GEO sample is GSM5556 Last updated (according to GEO): May 27 2005 HC71 CN B 861 Pituitary Gland 453 434 The descending colon M_U133A_87_DLPFC Skin 1000 GSE97 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11248 Last updated (according to GEO): May 28 2005 Plasma 861 Spleen 1000 Brain 50 55 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3497.gif Source GEO sample is GSM76468 Last updated (according to GEO): Sep 22 2006 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P7, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3226 Last updated (according to GEO): May 28 2005 n/a Source GEO sample is GSM177945 Last updated (according to GEO): Jun 11 2007 Hyperdip>50-C18 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Cerebral cortex 861 Subcutaneous Tissue 913 olfactory epithelium wild type mouse 2 hpO Source GEO sample is GSM80186 Last updated (according to GEO): Oct 26 2005 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13127.gif Source GEO sample is GSM79638 Last updated (according to GEO): Sep 22 2006 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28739 Last updated (according to GEO): May 27 2005 901 Cerebral cortex eye 0 3 of somatomotor cortex 21 41 1000 Hyperlipidemia, Familial Combined 1000 Cerebral cortex 861 Brain Total RNA extracted from the forebrain of a Tg-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144405 Last updated (according to GEO): Nov 14 2006 901 Caudate nucleus structure +_6294_batch3 on NHGRI-6.7k N41__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from postmorten brain regions Source GEO sample is GSM146002 Last updated (according to GEO): Nov 20 2006 Plasma 861 Hereditary Nonpolyposis Colorectal Neoplasms 947 brain, unknown: 9708-99_e1_le1 17 0 Trigeminal ganglia 861 Brain 0 Human Cortex 11 ovarian tumor: endometrioid Source GEO sample is GSM139415 Last updated (according to GEO): Apr 09 2007 Female7, Respiratory RNA_Nasal respiratory epithelium_Tissue was preserved in RNA Later and collected from nose Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16019.gif Source GEO sample is GSM91574 Last updated (according to GEO): Sep 22 2006 biopsy sample obtained from a 7-year-old male Duchenne Muscular Dystrophy patient Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15835 Last updated (according to GEO): May 28 2005 processed in batch 6 Source GEO sample is GSM90413 Last updated (according to GEO): Mar 20 2006 14 7 amygdala no additional Source GEO sample is GSM199141 Last updated (according to GEO): Jun 08 2007 proteoglycans 548 561 216 204 glioblastoma Communicable Diseases 901 1000 Brain 7 cerebral cortex 21 STHdhQ7/Q7-B 1000 Hippocampus Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181186 Last updated (according to GEO): Jul 12 2007 278 255 ischemic cardiomyopathy Trigeminal Ganglia 10 Normal GSE1095 epithelia 36 44 358 332 the articular chondrocytes from the forebrain 20 37 861 Asthma Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hour time point Source GEO sample is GSM159740 Last updated (according to GEO): Apr 23 2007 1000 Integumentary system 1000 Cerebral cortex These data were used as preliminary results for paper: Maternal Cocaine Administration Alters DNA Methylation in Hippocampal Neurons of Neonatal and Prepubertal Mice Svetlana I. Novikova, Fang He, Jie Bai, Nicholas J. Curtufello, Ashiwel S. Undie and Michael S. Lidow Source GEO sample is GSM154047 Last updated (according to GEO): Jan 19 2007 901 Mammary gland Prefrontal Cortex Source GEO sample is GSM105464 Last updated (according to GEO): Apr 17 2006 861 Liver 861 Blood Whole blood 0 10 Testis [JunctionChip 4 of 5] Alzheimer's Disease 861 Hepatocellular carcinoma is characterized by hypervascularity and a propensity for vascular invasion. Detailed analysis of complementary DNA (cDNA) microarray global gene expression data and further validation on a smaller independent sample set by reverse transcription-polymerase chain reaction established the presence of two endothelial gene clusters in hepatocellular carcinoma. Cluster I, consists of 20 cDNA clones, representing 15 unique genes. Cluster II consists of nine unique genes. The expression of the cluster I genes appeared to be significantly upregulated in hepatocellular carcinoma compared with normal liver, cirrhotic liver, or nontumor liver tissues adjacent to the hepatocellular carcinoma. The pattern of gene expression of cluster I genes correlated positively with the 'proliferation gene cluster' and 'stromal cells cluster 2'. Expression of cluster II genes, in contrast, was not significantly different between hepatocellular carcinoma and non-neoplastic liver tissues. Studies conducted to localize the protein products of these genes by immunohistochemical staining of tissue arrays with up to 350 cores of tissues, and by in situ hybridization led to the discovery of novel sinusoidal endothelial cell markers in hepatocellular carcinoma: podocalyxin-like and regulator of G protein signaling-5. Our results underscore fundamental differences not only between neoplastic vs non-neoplastic liver cells but also between the hepatic sinusoidal endothelium of hepatocellular carcinoma and normal liver. striatum 22 30 striatum rattus_norvegicus_strain iNP animal_number 12 TP53 does not fully comply with the Knudson model [Knudson, A. G., Jr. (1971) Proc. Natl. Acad. Sci. USA 68, 820-823] in that a reduction of constitutional expression of p53 may be sufficient for tumor predisposition. This finding suggests a gene-dosage effect for p53 function. To determine whether TP53 gene dosage affects the transcriptional regulation of target genes, we performed oligonucleotide-array gene expression analysis by using human cells with wild-type p53 (p53 +/+), or with one (p53 +/-), or both (p53 -/-) TP53 alleles disrupted by homologous recombination. We identified 35 genes whose expression is significantly correlated to the dosage of TP53. These genes are involved in a variety of cellular processes including signal transduction, cell adhesion, and transcription regulation. Several of them are involved in neurogenesis and neural crest migration, developmental processes in which p53 is known to play a role. Motif search analysis revealed that of the genes highly expressed in p53 +/+ and +/- cells, several contain a putative p53 consensus binding site (bs), suggesting that they could be directly regulated by p53. Among those genes, we chose CSPG2 (which encodes versican) for further study because it contains a bona fide p53 bs in its first intron and its expression highly correlates with TP53 dosage. By using in vitro and in vivo assays, we showed CSPG2 to be directly transactivated by p53. In conclusion, we developed a strategy to demonstrate that many genes are affected by TP53 gene dosage for their expression. We report several candidate genes as potential downstream targets of p53 in nonstressed cells. Among them, CSPG2 is validated as being directly transactivated by p53. Our method provides a useful tool to elucidate additional mechanisms by which p53 exerts its functions. Pharyngeal Mucosa 2 Normal Alzheimer's Disease 861 Normal Source GEO sample is GSM176340 Last updated (according to GEO): Apr 09 2007 PBMCs-Type 1 Diabetes-IDDM46_T1D_New bronchial epithelia 224 243 M_U133A_91_HC DCIS178 on harvard-12k Divergence between motoneurons: gene expression profiling provides a molecular characterization of functionally discrete somatic and autonomic motoneurons. Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10171.gif Source GEO sample is GSM79713 Last updated (according to GEO): Sep 22 2006 5 0 brain 1000 Cerebral cortex Brain_MGlio_6_Malignant Glioma on Affymetrix GeneChip Human Full Length Array HuGeneFL 1529 1524 muscle 153 128 of inflammatory myopathies Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68310 Last updated (according to GEO): Jul 07 2006 endothelium 613 624 25 CB B hippocampal glutamatergic CA1 pyramidal neurons Source GEO sample is GSM35835 Last updated (according to GEO): May 27 2005 7124_Lung developed PGD Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 24h. Lot batch = Source GEO sample is GSM1234 Last updated (according to GEO): May 28 2005 Normal human tissue:Normal Heart Keywords = Human, Normal Tissue, Normal Heart Source GEO sample is GSM44671 Last updated (according to GEO): May 27 2005 from benign astrocytoma 90 113 Cerebral cortex 861 /HeJ mouse pituitary gland 27 52 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68301 Last updated (according to GEO): Jul 07 2006 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13229.gif Source GEO sample is GSM76476 Last updated (according to GEO): Sep 22 2006 216 Ganglia 210 Brain 861 Bladder sample 679-1 V5-P391 375 367 of brains Richard Almon-24-1138200270196 Gene expression data from postmorten brain regions Source GEO sample is GSM145601 Last updated (according to GEO): Nov 20 2006 of brain neurospheres 40 60 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11458 Last updated (according to GEO): May 28 2005 healthy control sample x004 Breast Diseases 913 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=750660 LaserPower=2.121.29 Lot batch = LC17N058 Source GEO sample is GSM4800 Last updated (according to GEO): Nov 21 2005 Backskin_WT_P23_rep3 901 Stem cells Measles 1000 Myometrium 30 Disease 861 Neoplasm an adenovirus 57 69 brain, unknown: 3090-00_e1_le1 C57L/J_male_hypothalamus Source GEO sample is GSM184199 Last updated (according to GEO): Apr 26 2007 BAL_44b_A0B0 1000 Cerebral cortex 1321 1299 by cervical dislocation 861 Neoplasm f2#175 versus pool Mouse Brain tissue of the heart 842 854 966 Amygdaloid structure 1000 Encephalitis Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 12 Brain 861 Basal- 0 5 Gene expression data from postmorten brain regions Source GEO sample is GSM145614 Last updated (according to GEO): Nov 20 2006 861 Epithelial Cells hTERT transduced mammary epithelial cells Source GEO sample is GSM5170 Last updated (according to GEO): May 27 2005 1000 Left 1000 Encephalitis 1000 Myeloid Leukemia, Chronic GSE5327 plasma cells 332 344 Cardiac 523 530 Aorta 1000 100341 na Source GEO sample is GSM181267 Last updated (according to GEO): Apr 10 2007 Blood Test (Blinded) Sample Source GEO sample is GSM129993 Last updated (according to GEO): Sep 18 2007 Pressure-overload induced hypertrophy model. Mouse was sacrificed 1 hour after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2249 Last updated (according to GEO): May 27 2005 Liver [JunctionChip 2 of 5] 315 312 left Spleen 0 5 1000 ovarian neoplasm I_U133A_68_Amy The epithelial cells 962 981 Control (7/8RC) (Experiment NMDA1 (Run 9136)) Treatment, type=time_course, measurement=0.0 m Source GEO sample is GSM96664 Last updated (according to GEO): Feb 14 2006 Replicate No 2 of 3 (same genotype, same age), all replicates were individual animals. Source GEO sample is GSM138267 Last updated (according to GEO): Sep 29 2006 156 145 Their livers Gene expression data from a neocortex of saline-injected mouse Source GEO sample is GSM147401 Last updated (according to GEO): Jan 03 2007 Mesenchymal Stem Cells 1000 ProstateCancer-16 on NHGRI-6.5k_c "Sample 75, <5 yr survival(27 months) age 52 erp no" on vantveer-oligo FVB/NJ Cingulate Cortex A 964 Attention deficit hyperactivity disorder f2#115 versus pool Mouse Brain tissue 861 Ovary 1000 Cerebral cortex b220+bcell Source GEO sample is GSM18670 Last updated (according to GEO): May 27 2005 OVCAR-8 hgu95d 141 115 of parieto-occipital cortex 1000 Brain striatum_Q92_3m_440 636 618 with endometriosis GSE409 Gene expression data from postmorten brain regions Source GEO sample is GSM145991 Last updated (according to GEO): Nov 20 2006 901 frontal lobe Primary Neoplasm 1000 CNS-SMTC_Mod14d-2C-s2 T-ALL-C8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 923 Leukemia, Lymphocytic, Acute mouse cerebral cortex from COX-2 knockout Source GEO sample is GSM121430 Last updated (according to GEO): Jan 31 2007 brain, cerebral cortex: NMDA30 7/8RC_le1 Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22562 Last updated (according to GEO): May 27 2005 70 40 without coronary artery disease D_U133A_80_nAcc 406 395 whose hearts 861 Cerebellum WGACON-68 Expression profiling of spinal cord section (T8) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM4448 Last updated (according to GEO): May 28 2005 endometrium_3 Source GEO sample is GSM80685 Last updated (according to GEO): Mar 31 2006 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13105.gif Source GEO sample is GSM79937 Last updated (according to GEO): Sep 22 2006 Parietal Lobe 5 Normal Neoplasm 861 1000 Hypertrophic Cardiomyopathy 861 Blood CNS-SC_InjB7d-4B-s2 200 in the frontal cortex 220 Primary small cell lung carcinoma 2942 861 Malignant neoplasm of prostate R531P00647 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228619 Last updated (according to GEO): Sep 11 2007 brain, hippocampus: Wt #3405 Cereb_e1_le1 prostate Source GEO sample is GSM203361 Last updated (according to GEO): Jun 21 2007 Age-related transcriptional changes and the effect of dietary supplementation of vitamin E in the mouse heart 12mo Control #1 1000 Atherosclerosis Cerebral cortex 1000 Mouse ileum with L.innocua(hly)_B_5556 ISR19 28 20 (cerebrum of a colorectal adenoma 7 29 Sample 120 on vantveer-oligo Testis 1000 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25503.gif Source GEO sample is GSM81555 Last updated (according to GEO): Sep 22 2006 I_U133A_68_CB Spleen vs Dimaprit Treated B cell 240min (set1) MO_control_180min_Patient12 901 Stem cells Communicable Diseases 901 for liver 26 35 Integumentary system 1000 to the nose 599 609 1000 Left G1E_21_A 1000 Mitral Valve CNS-SC_InjB24h-4B-s2 216 200 of neural retinas brain, cerebral cortex: Control 8/30_le1 Liver (HCV+, SF28, 2) Hereditary Malignant Neoplasm 876 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156713 Last updated (according to GEO): Jan 22 2007 Nrl ko samples were compared to wt at postnatal 10. Source GEO sample is GSM227462 Last updated (according to GEO): Sep 07 2007 Liver 1000 the blood 393 402 Basal-like breast tumor cell line ME16C2 Keywords = Agilent microarray, Expression analysis, EGFR, Breast cancer growth Source GEO sample is GSM29522 Last updated (according to GEO): Dec 13 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145703 Last updated (according to GEO): Nov 20 2006 1000 Coronary Arteriosclerosis Intestines 861 GSE685 human caudate nucleus Source GEO sample is GSM86856 Last updated (according to GEO): Feb 08 2006 858 Prostatic Neoplasms 660 mesenchymal stem cell 639 3 days, repeat 1 5 0 brain 1BJZ02052324_FETALTHYROID Trisomy 21 sample 4 (cerebrum) of coronary artery disease 317 342 EAE, placebo-treated #1 PAX sample 12 Brain 861 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181204 Last updated (according to GEO): Jul 12 2007 1000 Brain brain 0 5 SN:Human Glioblastoma Biopsy 06731 913 Coronary heart disease Rb-/- prostate epithelial cell line maintained in RPMI-1640 medium without fetal bovine serum for 48 hours Keywords = prostate Keywords = epithelial Source GEO sample is GSM14675 Last updated (according to GEO): May 28 2005 Cerebral cortex 861 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151993 Last updated (according to GEO): Feb 06 2007 ileum 861 Utricle structure 861 jzo009-rp1-v5-u74av2-met 91 from the bone marrow 72 Small cell carcinoma of lung 867 Female 29.8 yr before antibody enrichment scan 1 (U133A) brain, Primary Visual Cortex: Sample63_e1_le1 no additional Source GEO sample is GSM199051 Last updated (according to GEO): Jun 08 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145715 Last updated (according to GEO): Nov 20 2006 861 Modiolus anguli oris Nasal Epithelium 901 5 0 brain from ventral prostate 21 41 Primary adenocarcinoma Source GEO sample is GSM16567 Last updated (according to GEO): May 28 2005 7 0 Pancreas 990 980 under basal Thalamus 2 Normal 1000 Multiple Sclerosis 1000 Endometriosis, site unspecified Gene expression data from postmorten brain regions Source GEO sample is GSM145188 Last updated (according to GEO): Nov 20 2006 plasma cells 50 61 ileum 1000 WT 4 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.84 Subject: 2835 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39026 Last updated (according to GEO): May 27 2005 15_0007_SepticShock_Day3_14 573 544 of nonsensory epithelial cells NIA-NEUROARRAY_CT3 Nose 1000 D_U133A_5_HC Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26115.gif Source GEO sample is GSM81527 Last updated (according to GEO): Sep 22 2006 long access to cocaine ,medial prefrontal cortex, 6 hrs/day access to cocaine Source GEO sample is GSM93873 Last updated (according to GEO): Jan 26 2006 Anterior nares 1000 5 0 Spleen 861 Blood P7 cochlear nuclei 0 17 Female 29.8 yr after antibody enrichment scan 2 (U133B) Bone Marrow 1000 SWR/J_male_hypothalamus Source GEO sample is GSM184221 Last updated (according to GEO): Apr 26 2007 Blood 1000 of the nasal epithelium 475 497 Baseline comparison of global gene expression in ILS and ISS cerebellum to find differences in the naive state. Source GEO sample is GSM69522 Last updated (according to GEO): Oct 28 2005 Sample details: Three pools of rostral (R1-3), three pools of middle (M1-3), and three pools of caudal (C1-3) E13.5 MF1 neocortex were collected from 4 embryos. All possible 18 comparisons were carried out. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. Source GEO sample is GSM62836 Last updated (according to GEO): Aug 26 2005 27 17 (Cerebellum 12 frontal Lobe 23 861 Bone Marrow fetal buttock-thigh fibroblast #1, asynch 1BJZ02022223_spinalcord Primary large cell neuroendocrine carcinoma 6042 0 47 861 Muscle Y VIS D064 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108648 Last updated (according to GEO): Aug 22 2006 1000 Spleen Aortic Aneurysm, Abdominal 1000 7 0 Pancreas Nasal Epithelium 865 Bone Marrow 1000 To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at ?80C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at ?80°C before routine processing for GeneChip analysis. Source GEO sample is GSM28669 Last updated (according to GEO): Oct 28 2005 at the Human Brain 725 742 ciliary_ganglion Source GEO sample is GSM19004 Last updated (according to GEO): Sep 25 2006 MeHg: PK11195 intervention at 4.5h Cerebral cortex 1000 myocardial infarction 383 403 161 134 by progressive lung disease Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28790 Last updated (according to GEO): May 27 2005 GSE8671 cerebral cortex 7 21 no additional Source GEO sample is GSM199363 Last updated (according to GEO): Jun 08 2007 Alzheimer's Disease 861 WGACON-231 brain, cerebral cortex: Rat_02-142_TTX_Lipska_e1_le1 7 cerebral cortex 21 GRP sample 10 Normal__Germinal_Center_GC38 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A mild cognitive impairment - hippocampus 6 nasal epithelial cells 28 49 1BMH02083001_BM_CD71EarlyErythroid parietal_lobe_1 of the stria terminalis 49 71 1000 medulloblastoma Gene expression data from mouse primary visual cortex Source GEO sample is GSM101717 Last updated (according to GEO): Jun 15 2006 HCC (HBV+, HK45) Hippocampus 861 Skeletal bone 861 of the saphenous artery 43 65 /6J mouse pituitary gland 29 53 1000 Brain Brain 1000 Brain 1000 Spleen vs Interferon-gamma (IFN gamma) Treated B cell 240min (set2) Gene expression data from postmorten brain regions Source GEO sample is GSM145179 Last updated (according to GEO): Nov 20 2006 861 Blood Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD18 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD18 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36693 Last updated (according to GEO): May 27 2005 91 from the bone marrow 72 875 Nicotinic Receptors 26 0 Spinal cord [JunctionChip 2 Blood 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145743 Last updated (according to GEO): Nov 20 2006 of the stria terminalis 51 73 M4 juvenile biol repl 3 Creatine increases health and life span in mice Brain 1000 MuscleRegen-ctx9.5d-2RLAv2-s2 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201292 Last updated (according to GEO): Jun 14 2007 Gene expression data from a placenta with chronic malaria Source GEO sample is GSM183614 Last updated (according to GEO): Apr 23 2007 Expression profiling of spinal cord section (T8) extracted from rats 24h following mild injury Source GEO sample is GSM31431 Last updated (according to GEO): May 27 2005 SNB-75 hgu95d Unfertilized egg replication 2 0 29 Muscle Source GEO sample is GSM4299 Last updated (according to GEO): May 27 2005 ProstateCancer-8 on NHGRI-6.5k_c Lymphoblastoid Cell Line for Individual 8142.4 log phase 1000 Bipolar Disorder 5 0 brain 5 0 Spleen 156 145 Their livers of a colorectal adenoma 7 29 prostate Source GEO sample is GSM203313 Last updated (according to GEO): Jun 21 2007 Liver Test (Blinded) Sample Source GEO sample is GSM130134 Last updated (according to GEO): Sep 18 2007 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 24 h time point Source GEO sample is GSM159804 Last updated (according to GEO): Apr 23 2007 24 7 Right Frontal Lobe gene expression of 2 day RA differentiated ESCs Source GEO sample is GSM181970 Last updated (according to GEO): Apr 12 2007 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html. Date GSE775 Last Updated: Jun 15 2005 Contributers: Jeffrey Brown Martina Schinke Seigo Izumo Includes GDS488. Update date: Mar 22 2004. Dataset description GDS488: Temporal analysis of acute myocardial infarction (AMI) induced by left coronary artery ligation. Left ventricle above and below left anterior descending (LAD) artery examined at 1 hour to 8 week time points.. 972 Structure of middle temporal gyrus Melanotransferrin (MTf) or melanoma tumor antigen p97 is an iron (Fe)-binding transferrin homolog expressed highly on melanomas and at lower levels on normal tissues. It has been suggested that MTf is involved in a variety of processes such as Fe metabolism and cellular differentiation. Considering the crucial role of Fe in many metabolic pathways e.g., DNA synthesis, it is important to understand the function of MTf. To define the roles of MTf, a MTf knockout (MTf -/-) mouse model was developed. Examination of the MTf -/- mice demonstrated no phenotypic differences compared to wild-type littermates. However, microarray analysis showed differential expression of molecules involved in proliferation such as Mef2a, Tcf4, Gls and Apod in MTf -/- mice compared to MTf +/+ littermates, suggesting a role for MTf in proliferation and tumorigenesis.. Date GSE4523 Last Updated: Jun 13 2006 Contributers: Louise L Dunn Yohan Suryo Rahmanto Eric O Sekyere Des R Richardson Includes GDS1964. Update date: Jun 14 2006. Dataset description GDS1964: Analysis of brain from melanotransferrin (MTf) knockout mutants. MTf or melanoma tumor antigen p97 is a membrane bound iron binding transferrin homolog highly expressed in melanomas and at lower levels in normal tissues. Results provide insight into the function of MTf.. Parkinson Disease 1000 12 0 ovarian tumor P2A_KIDNEY_2 CNS-SMTC_Ctr30m-1A-s2 14h mitotic selection Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211370 Last updated (according to GEO): Jul 18 2007 861 Neoplasm Nose 1000 Proliferative endometrium from patient with endometriosis Source GEO sample is GSM150191 Last updated (according to GEO): Dec 14 2006 B6 day 1, biological rep 1, tech rep 2 NCI60.18_LABEL22EXTRACT21SUB3 Source GEO sample is GSM134084 Last updated (according to GEO): Aug 06 2007 Semeralul_PFC_Development_Week5_Batch2_Animal_4 no additional Source GEO sample is GSM199082 Last updated (according to GEO): Jun 08 2007 24 19 (Brain Cerebral cortex 861 from SVG-A glial cells 21 43 861 Gland structure 5 0 brain PrSC A on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A n/a Source GEO sample is GSM178015 Last updated (according to GEO): Jun 11 2007 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225681 Last updated (according to GEO): Nov 05 2007 Fibroblasts 861 1000 Left from nose 96 104 Plasma 861 1000 Pancreas Normal Source GEO sample is GSM176410 Last updated (according to GEO): Apr 09 2007 913 Coronary heart disease small intestine; duodenum Source GEO sample is GSM18690 Last updated (according to GEO): May 27 2005 Medulla 861 861 Breast M_95Av2_2978_DLPFC_0_GS 1000 Liver 861 Neoplasm Neoplasm 861 HMEC 184 day 3 sample 1 brain, cortex: 28dexp4_e1_le1 Ventral Tegmental Area 1000 /2J Hippocampus A 3 19 GC (HKG8T) Rett Syndrome 1000 GC (HKG4N) 32h-AM replication 3 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 18 hours after lights on. Original RNA code = LC32A. Source GEO sample is GSM227375 Last updated (according to GEO): Sep 10 2007 Bladder sample 1133-1 Plasma 861 Five different human MPNST cell lines, mock treated or infected with G207. Source GEO sample is GSM215810 Last updated (according to GEO): Aug 07 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11278 Last updated (according to GEO): May 28 2005 f2#50 versus pool Mouse Brain tissue processed in batch 3 Source GEO sample is GSM90437 Last updated (according to GEO): Mar 20 2006 Epithelium 861 Mucous Membrane 861 1000 Hippocampus M_U133Plus_73_CB Prognostic and predictive factors are indispensable tools in the treatment of patients with neoplastic disease. For the most part, such factors rely on a few specific cell surface, histological, or gross pathologic features. Gene expression assays have the potential to supplement what were previously a few distinct features with many thousands of features. We have developed Bayesian regression models that provide predictive capability based on gene expression data derived from DNA microarray analysis of a series of primary breast cancer samples. These patterns have the capacity to discriminate breast tumors on the basis of estrogen receptor status and also on the categorized lymph node status. Importantly, we assess the utility and validity of such models in predicting the status of tumors in crossvalidation determinations. The practical value of such approaches relies on the ability not only to assess relative probabilities of clinical outcomes for future samples but also to provide an honest assessment of the uncertainties associated with such predictive classifications on the basis of the selection of gene subsets for each validation analysis. This latter point is of critical importance in the ability to apply these methodologies to clinical assessment of tumor phenotype. 861 Infertility small intestine PPARalpha knockout mice, treated with WY14,643 for 5 days. The WY14.643 was present in the diet at 0.1% w/w. Source GEO sample is GSM124320 Last updated (according to GEO): Jun 28 2007 from whole tumor 21 36 HCC (HBV+, HK67, T1) Primary Neoplasm 1000 12 0 Blood T cells no additional Source GEO sample is GSM199391 Last updated (according to GEO): Jun 08 2007 AD-AD2T1-A384-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Kidney 1000 Primary Neoplasm 1000 with mental retardation 241 263 25 7 Right Parietal Lobe from hematopoietic stem cells 118 146 PBMCs-Type 1 Diabetes-IDDM32_T1D_1MO 329 306 valvular cardiomyopathy outer medulla 31 43 from the right forebrain 21 44 861 Cerebral cortex Parkinson Disease 861 amygdala_5 12 0 ovarian tumor Occipital lobe 861 Myocardium 861 CNS-SCsev_InjA24h-4C-s2 hindbrain 1000 129:3-1-2 entorhinal cortex Gene expression data from postmorten brain regions Source GEO sample is GSM144961 Last updated (according to GEO): Nov 20 2006 This SuperSeries is composed of the following subset Series: GSE4263: P18 mouse non-deprived vs. deprived visual cortex GSE4264: P24 mouse non-deprived vs. deprived visual cortex GSE4265: P46 mouse non-deprived vs. deprived visual cortex GSE4266: P104 mouse non-deprived vs. deprived visual cortex GSE4267: P46DR (dark reared) mouse non-deprived vs. deprived visual cortex Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Apr 20 2006 BXD 19_M7SS02080606 861 Blood Liver Test (Blinded) Sample Source GEO sample is GSM130188 Last updated (according to GEO): Sep 18 2007 Bladder sample 937-1 ILS/ISS cerebellum baseline comparison OVCAR-4 hgu95b 0029_1221_H95A2_KF0144_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 89 FC BA9 B with mental retardation 241 263 N13__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A T1 gr3 tumour Source GEO sample is GSM2540 Last updated (according to GEO): May 27 2005 1000 Brain spinal cord, ventral spinal cord: D60WTSPMN3_e1_le1 1000 Uterus Neoplasm 861 901 Pilocytic Astrocytoma Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.98 Subject: 2672 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39008 Last updated (according to GEO): May 27 2005 JMR-MurSham4h-1cAv2-s2 M_U133A_48_DLPFC To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132972 Last updated (according to GEO): Sep 12 2006 ProstateCancer-4 on NHGRI-6.5k_c Bone Marrow 1000 861 Cerebral cortex Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11308 Last updated (according to GEO): May 28 2005 18 on NHGRI-13.8k spinal cord 13 23 1000 frontal lobe Effects of SOCS3 on transcriptional response of macrophages to IL-6. Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Replicate 3 after stimulation for 400 minutes with 10 ng/ml IL-6. Source GEO sample is GSM6088 Last updated (according to GEO): Mar 17 2006 Effect of serotonergic hallucinogen in mouse somatosensory cortex M_U133A_52_HC osteoblast 627 637 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14941 Last updated (according to GEO): Oct 28 2005 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153366 Last updated (according to GEO): Dec 27 2006 Neoplasm 861 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11543 Last updated (according to GEO): May 28 2005 GC (HKG96N) Skeletal bone 861 1000 Descending colon 1000 Rectum Hypothalamus Pair-Fed Repl2 148 132 cervical cancers FSCC11 on Affymetrix GeneChip Human Full Length Array HuGeneFL The most common congenital cardiac abnormalities 50 97 Epithelium 861 healthy subject Source GEO sample is GSM211050 Last updated (according to GEO): Sep 10 2007 human cerebellum Source GEO sample is GSM87068 Last updated (according to GEO): Feb 08 2006 Lymphoblastoid Cell Line for Individual 8115.5 log phase 1000 Uterus Brain 861 of lipid 1308 1316 Whole Brain 73 83 brain, cerebral cortex: NMDA 30 3_le1 1000 Hypothalamic structure NA12234 73 60 (gastrocnemius total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with fMLP for 240min Source GEO sample is GSM5575 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145278 Last updated (according to GEO): Nov 20 2006 with myocardial infarction 148 173 Large-scale analysis of the mouse transcriptome. Epidermis, dorsal skin without fur C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 282.13 Stdv: 23.65 Min: 251.03 Max: 321.08 Source GEO sample is GSM2964 Last updated (according to GEO): May 27 2005 NA Source GEO sample is GSM84320 Last updated (according to GEO): Dec 01 2005 heart_atrium_4 Source GEO sample is GSM80656 Last updated (according to GEO): Mar 31 2006 1000 Congestive heart failure Normal Source GEO sample is GSM176122 Last updated (according to GEO): Apr 09 2007 with autism spectrum disorder 37 65 Osteoblasts 1000 Gene expression data from human colon tumor tissue Source GEO sample is GSM173377 Last updated (according to GEO): Apr 20 2007 MGMH030228088Bfertilizedegg from brain 21 30 brain_OFC_control C_mr217 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n126 Source GEO sample is GSM2046 Last updated (according to GEO): Nov 21 2005 Coronary Arteriosclerosis 1000 Mouse neuroblastoma (N2a) cells are available from the American Tissue Culture Collection (ATCC, number CCL-131). To generate cells expressing 3F4-tagged PrP, cells were stably transfected with Mo3F4 PrP in a pcDNA3.1/Zeo vector (Invitrogen, Leek, The Netherlands) and stable transfectants selected using Zeozine 300 ug/ml medium (Gilch et al, 2001, EMBO 20: 3957-3966). RNA was isolated from control and infected cell lines by the Trizol method. 20µg total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 30µl hybridisation buffer (6x SSC, 0,5% SDS 5 fold Denhardt's solution and 50% formamide) and mixed with 30µl of reference cDNA solution labelled with the second dye. This hybridisation mixture was placed on a pre hybriddised microarray, covered with cover slip, placed into a hybridisation chamber (Genomatix) and immersed in a thermostatic bath at 42°C for at least 16 hours. Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Maen intensities with substracted background were normalised so that the median of their rations has became 1 Keywords = prion Keywords = neuroblastoma Keywords = N2a Source GEO sample is GSM31104 Last updated (according to GEO): Oct 28 2005 Abnormal development of the prefrontal cortex (PFC) is associated with a number of neuropsychiatric disorders that have an onset in childhood or adolescence. Although the basic laminar structure of the PFC is established in utero, extensive remodeling continues into adolescence. To map the overall pattern of changes in cortical gene transcripts during postnatal development, we made serial measurements of mRNA levels in mouse PFC using oligonucleotide microarrays. We observed changes in mRNA transcripts consistent with known postnatal morphological and biochemical events. Overall, most transcripts that changed significantly showed a progressive decrease in abundance after birth, with the majority of change between postnatal weeks 2 and 4. Genes with cell proliferative, cytoskeletal, extracellular matrix, plasma membrane lipid/transport, protein folding, and regulatory functions had decreases in mRNA levels. Quantitative PCR verified the microarray results for six selected genes: DNA methyltransferase 3A (Dnmt3a), procollagen, type III, alpha 1 (Col3a1), solute carrier family 16 (monocarboxylic acid transporters), member 1 (Slc16a1), MARCKS-like 1 (Marcksl1), nidogen 1 (Nid1) and 3-hydroxybutyrate dehydrogenase (heart, mitochondrial) (Bdh). cerebral cortex 7 21 "Sample 99, BRCA2 mutation(8 months) age 31 erp yes" on vantveer-oligo 1000 Brain 901 Heart Diseases Replicate3_Voxel D6 total RNA from biosource CC#6S Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92484 Last updated (according to GEO): Jan 13 2006 Occipital region 983 1000 frontal lobe Mesenchymal Stem Cells 1000 1000 Spleen no additional Source GEO sample is GSM199027 Last updated (according to GEO): Jun 08 2007 Cerebral cortex 1000 from colonic normal mucosa 21 47 Normal Source GEO sample is GSM176152 Last updated (according to GEO): Apr 09 2007 healthy subject Source GEO sample is GSM211057 Last updated (according to GEO): Sep 10 2007 861 Bladder 1000 Glioma 406 395 whose hearts Nose 1000 Localized Carcinoma 853 Brain 861 88 68 with bicuspid valves We build a model for the molecular and cellular events underlying phenotypic discordance in glycine receptor defects (beta subunit). Some mice progress and die, while their littermates recover and get better, despite the same mutation on an inbred genetic background. We find evidence for glycine neurotransmitter toxicity and loss of glycinergic interneurons early in the disease, but some mice are able to keep things going until they can over-express homomeric alpha1 channels, whereupon they recover. In the mice progressing towards lethality, neurotransmitter toxicity too quickly extends to GABAergic interneurons and motorneurons, and they lose their window of time to upregulate the alpha1 glycine receptor, and they crash and burn. Importantly, human patients with glycine receptor defects typically show a resolution of their phenotype with age, and we propose that the same remodeling events are occuring in human patients. Source GEO sample is GSM30996 Last updated (according to GEO): May 27 2005 Abdominal aorta structure 1000 Femur 1000 861 Colon 12 frontal Lobe 23 Brain 861 "Sample 20,>5 yr survival(61 months) age 34 erp no" on vantveer-oligo ER negative human primary breast tumor EA02014_41245_H133A_JA-123 Lymphoblastoid Cell Line for Individual 8062.4 log phase 861 Prosencephalon Small cell carcinoma of lung 901 MGJZ030207054Bheart This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195269 Last updated (according to GEO): Sep 13 2007 brain, hippocampi, left: Sham PM Hypo b_e1_le1 D_U133A_31_Amy NA12750 growth 2, replicate 3 30 CB B brain, contralateral Cortex: Trizol Extraction45_le1 453 434 The descending colon 1000 Brain Stem 1000 Hippocampus 660 mesenchymal stem cell 639 861 Neoplasm Gene expression data from a placenta without malaria Source GEO sample is GSM183609 Last updated (according to GEO): Apr 23 2007 hrs nasal epithelium 1127 1147 Hypothalamus 9 Normal 91 from the bone marrow 72 Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231052 Last updated (according to GEO): Sep 26 2007 1000 Brain from the olfactory epithelium tissue 171 207 901 Caudate nucleus structure 901 Coronary artery 22 0 Normal epithelial cells 966 Hippocampus /HeJ cingulate cortex rep1 3 28 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n113 Source GEO sample is GSM2054 Last updated (according to GEO): Nov 21 2005 Ovary 1000 861 Communicable Diseases 257 242 of uterine horns 2N-4-MGU74B T01__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A HDMTX-DX-7 no additional Source GEO sample is GSM199262 Last updated (according to GEO): Jun 08 2007 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22197.gif Source GEO sample is GSM93116 Last updated (according to GEO): Sep 22 2006 901 Coronary artery 1000 Bone Marrow 861 Intestines 1000 Polymyositis CCRF-CEM hgu95b Neoplasm Metastasis 1000 1000 Stomach 1000 Brain 861 Muscle Heart 1000 952 of the pituitary gland 929 10 7 Left 1000 Cerebrovascular accident 715 705 from livers Halothane 5 exposures-3 Gene expression data from human colon tumor tissue Source GEO sample is GSM173329 Last updated (according to GEO): Apr 20 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145775 Last updated (according to GEO): Nov 20 2006 4 0 Ovary Small cell carcinoma of lung 867 Nucleus Accumbends, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231034 Last updated (according to GEO): Sep 26 2007 Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21273.gif Source GEO sample is GSM91565 Last updated (according to GEO): Sep 22 2006 Infection 1112 1121 19 0 human frontal cortex Osteoblasts 1000 Epithelium 861 1115 1102 cardiomyopathy Congenital Abnormality 873 N2_d5 #1(16012165010071) Expression profiling of spinal cord section (T9) extracted from rats 28d following moderate injury Source GEO sample is GSM31544 Last updated (according to GEO): May 27 2005 9 0 Blood Test none Source GEO sample is GSM244618 Last updated (according to GEO): Nov 23 2007 Control, 24.00 hr. T-Cell 16 0 Bone marrow cell 901 Coronary artery brain 0 5 Replicate1_Voxel C4 R7N 11 Infected with B. abortus 2308 ADH4.2 and euthanized 3 days post-infection Source GEO sample is GSM155255 Last updated (according to GEO): Aug 08 2007 Cockayne syndrome B cell Source GEO sample is GSM226292 Last updated (according to GEO): Sep 04 2007 Ta gr3 tumour Source GEO sample is GSM2511 Last updated (according to GEO): Mar 21 2006 BC24 861 Cerebral cortex M_U133A_49_AnCg mouse brain 478 489 Mouse ileum with L.monocytogenes_A_5543 Day 7 Mouse #54 - 3rd replicate Control, biological rep2 CHC Con-1 seminoma specimen, pT2, patient age: 45y; W99 037 901 Connective Tissue plasma cells 50 61 1000 Coronary Arteriosclerosis f2#214 versus pool Mouse Brain tissue Heart 1000 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114453 Last updated (according to GEO): Jun 16 2006 42 30 Control blood Keywords = Heart 505 521 chronic allograft nephropathy 786 815 cingulate cortex 861 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113979 Last updated (according to GEO): Jun 16 2006 entorhinal cortex layer II stellate island cells Source GEO sample is GSM107532 Last updated (according to GEO): May 01 2006 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181226 Last updated (according to GEO): Jul 12 2007 Lung 1000 I_U133A_107_AnCg Gene expression data Source GEO sample is GSM183167 Last updated (according to GEO): Jul 30 2007 Triple treatment R6/2 mice Brain 861 cortex rattus_norvegicus_strain iNP animal_number 9 Plasma 861 Glucosephosphate Dehydrogenase 901 Primary Neoplasm 1000 Cerebral cortical contusion in rat, 1 dpi #3 Interatrial septum 865 9 DNA damage 0 Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Lymph Node [JunctionChip 1 of 5] Brain 861 Brain 861 861 Brain nasal epithelial cells 28 49 from colorectal adenoma 21 44 861 Cerebral cortex nasal epithelial cells 28 49 Spleen vs Untreated B cell 30min (set3) Dendritic Cells, Exposed to Leishmania major - Repeat #1 Malignant neoplasm of cervix uteri 901 7 frontal cortex 20 59 35 out of mouse bone marrow Kidney OC-1B 14 days age control RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis. Source GEO sample is GSM10049 Last updated (according to GEO): May 28 2005 the ventricular 1095 1109 NA06993 VIIcSC_Signal on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B 255 234 with HIV encephalitis 430A2_1945_42_KO_sham_midbrain Source GEO sample is GSM242687 Last updated (according to GEO): Nov 15 2007 Ovarian_Tumor_Mucinous_KU-OM-007 NA Source GEO sample is GSM84322 Last updated (according to GEO): Dec 01 2005 197 176 with coxsackievirus B3 of the atrial 647 659 1000 Skeletal muscle structure Cocaine Addiction 1000 Skeletal bone 861 Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108006 Last updated (according to GEO): Jun 06 2006 Gene expression data from liver Source GEO sample is GSM243376 Last updated (according to GEO): Nov 16 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with MIP3-alpha (Macrophage inflammatory protein-3) for 60min Source GEO sample is GSM5690 Last updated (according to GEO): May 27 2005 Fat RYGB-Fail Repl3 Coronary heart disease 913 This is the seventh replicate for the SNc neurons which were captured using LCM. Source GEO sample is GSM19325 Last updated (according to GEO): May 27 2005 Dendritic Cells, Exposed to Brugia malayi (50) - Repeat #1 Osteoblasts 1000 CNS-RM_Mod28d-2C-s2 Plasma 861 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n103 Source GEO sample is GSM2059 Last updated (according to GEO): Nov 21 2005 3 bone 0 1000 Spleen The nose 94 101 Seminoma 1000 Compare the transcriptomes of Cx43 null and Cx43 siRNA treated cortical astrocytes with the transcriptome of the wildtype cortical astrocytes Source GEO sample is GSM202235 Last updated (according to GEO): Jun 19 2007 Ganglia 861 Pons AB Normal 605 581 in the brain hippocampus human frontal cortex Source GEO sample is GSM86930 Last updated (according to GEO): Feb 08 2006 68 49 salivary gland C57BL Spleen vs BLC Treated B cell 30min (set1) GM10857_technical_rep_2 1000 Liver 861 Cerebellum r3 Brain_MD_26_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL Polyamide1_3 HCC (SF4) 1250 1231 persistent infection Gene expression data from postmorten brain regions Source GEO sample is GSM145381 Last updated (according to GEO): Nov 20 2006 Intestines, Small 1000 N-2_POST MP-DX-7 Cerebral cortex 1000 tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44897 Last updated (according to GEO): May 27 2005 Spleen 1000 cerebral cortex wistar 3903 C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P18 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25121 Last updated (according to GEO): May 27 2005 lg_NY24 Thalamus 5 Normal Sample is skeletal muscle from obese patient undergoing elective abdominal surgery Source GEO sample is GSM4000 Last updated (according to GEO): May 28 2005 hip_1039_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Expression profiling of spinal cord section (T8) extracted from rats 14d following mild injury Source GEO sample is GSM31422 Last updated (according to GEO): May 27 2005 ovarian tumor: endometrioid Source GEO sample is GSM139402 Last updated (according to GEO): Apr 09 2007 in the hippocampus. 346 365 Paravertebral Muscle 3 Disease 1000 Spleen 1000 ovarian neoplasm as Neuroblastoma 362 377 Vestibular organ 0 15 Tumor__Leukemia_ALL-B_ALL_(14749)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 124 115 to bregma Skeletal muscle structure 1000 LDMTX_MP-DX-8 861 Cerebral cortex Epithelium 861 meningioma 1000 In our original grant we proposed to use the NR3B-null mouse model to study the role of NR3B subunit in motor neuron function. We have now successfully generated NR3B null mice. Interestingly, NR3B-null mice invariably die at age P4-P8. Our preliminary examination indicates that the motor strength of these mice is severely impaired prior to death. As we continue to explore the cause of death in NR3B null mice, we propose to conduct gene profiling experiments to search for transcription changes in the brain related to ablation of the NR3B gene. We have used the facility provided by the NINDS/NIMH Microarray Consortium to identify genes that show abnormal expression patterns in these mice. We would like to compare these changes with that opccured in SOD1 mice, a mouse model of motor neuron diseases. Analysis of these genes will help to identify changes in networks and pathways that may cause the death of NR3B-null mice. These studies will further help to elucidate the functional role of NR3B in motor neurons. We will compare samples from motor neurons of wild type and SOD1 mice to identify genes that show abnormal expression patterns, which may be implicated in the death of SOD1 mice and shared with the same changes in NR3B-null mice. We hypothesize that genes with their transcription level changing significantly by ablation of NR3B will be associated with the molecular mechanism underlying the death of motor neurons in NR3B null mice. As NR3B is expressed primarily in the motor neurons of hindbrain and spinal cord, we have first collected and analyzed the spinal cord samples from NR3B null mice and wild-type controls in P4, an age of disease onset. We like to compare motor neuron smaples from SOD1 mice at the age around the disease onset. Total RNA from total 6 samples will be purified from ~200 motor neurons obtained by Laser Capture Microdissection. Extracted RNAs will be subjected to two rounds of amplification and the obtained cRNA will be biotinylated. The purified cRNA will be sent to the NINDS/NIMH Microarray Consortium be used to hybridize the GeneChip Mouse Genome 430 2.0 Array. The hybridization, scanning, and initial data analysis of these GeneChips will be conducted by the Consortium staff. We will analyze the collected data further after data collection. We will first identify genes that show significant changes between wild-type and SOD1 mice and then compare that with the result from NR3B null mice. Last Updated (by provider): Jan 13 2006 Contributers: Dongxian Zhang Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68335 Last updated (according to GEO): Jul 07 2006 861 Brain C57 whole brain 5 B78 on NCI-7.6k 1_hypothalamus_6hrs_sleep_#139 of Parkinson's disease 450 471 Cortex_Bulbectomized_rep3 Substantia nigra PD rep2 Brain 861 brain 0 5 small Source GEO sample is GSM67252 Last updated (according to GEO): Jan 19 2006 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213472 Last updated (according to GEO): Jul 31 2007 R570P00762 Molecular signature of late-stage human ALS revealed by expression profiling of postmortem spinal cord gray matter. Autoimmune Diseases 913 Affymetrix RGU34A 2HB Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198651 Last updated (according to GEO): Jun 06 2007 1000 Cardiomyopathies 202 165 with premature coronary heart disease 901 Bone Marrow Neural tube, control, GD9:00, C215579 1000 Hippocampus Parkinson's disease sample x199 Parkinson Disease 861 861 Glioblastoma Primary tumor 19 32 BC23 861 lymph nodes 861 Basal Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181146 Last updated (according to GEO): Jul 12 2007 6 0 Stomach Communicable Diseases 1000 41 29 Control blood brain 0 5 Malignant neoplasm of ovary 901 Spleen vs NGF (Nerve Growth Factor)Treated B cell 60min (set2) Cervix 10 Normal heart failure 583 595 none Source GEO sample is GSM239898 Last updated (according to GEO): Dec 07 2007 cerebellum 7 16 from the right forebrain 21 44 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132518 Last updated (according to GEO): Feb 26 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145107 Last updated (according to GEO): Nov 20 2006 D_U133A_84_DLPFC AML_15 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 0184 blood e14-1 1000 Lung spinal cord 37 47 9 0 Blood Test Motor neurons from the spinal cord of SOD1 mutant mice Treatment, type=linear_amplification, description=T7-based RNA amplification Source GEO sample is GSM113707 Last updated (according to GEO): Jun 09 2006 Leukemic fractions of ID71 AML patient have been hybridized. Source GEO sample is GSM154056 Last updated (according to GEO): Feb 26 2007 human caudate nucleus Source GEO sample is GSM86824 Last updated (according to GEO): Feb 08 2006 Large-scale analysis of the human transcriptome. Prostate Source: University of Virginia, see PMID 11507037 Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 143.82 Stdv: 6.74 Min: 127.68 Max: 154.07 Source GEO sample is GSM2865 Last updated (according to GEO): Mar 20 2006 control 6h, replicate 1 12 frontal Lobe 23 67 52 descending colon A HID U D020 SN:Human Glioblastoma Biopsy 10429 Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35380 Last updated (according to GEO): May 27 2005 Neoplasm 861 IOBA2 from nose 102 110 Facial nerve nucleus 1000 Tumor__Pancreas_Adeno_Pan_1T on Affymetrix GeneChip Human 35K SubA Array Hu35k-A HapMap CHB Female Source GEO sample is GSM159600 Last updated (according to GEO): Feb 01 2007 861 Prostate Gene expression data from postmorten brain regions Source GEO sample is GSM145854 Last updated (according to GEO): Nov 20 2006 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28787 Last updated (according to GEO): May 27 2005 1000 Liver The nose 94 101 GTP-Binding Proteins 901 f2#350 versus pool Mouse Brain tissue Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211303 Last updated (according to GEO): Jul 18 2007 no additional Source GEO sample is GSM199221 Last updated (according to GEO): Jun 08 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145428 Last updated (according to GEO): Nov 20 2006 19 0 human frontal cortex Gene expression data from postmorten brain regions Source GEO sample is GSM144871 Last updated (according to GEO): Nov 20 2006 39 12 of congenital heart disease Liver 0 4 Collagen 1000 10 7 Left 14 6 (thalamus Female mice used were 129/SvImJ wildtype (Jackson Lab), 10-16 weeks of age. 14 days after ovariectomy, mice were injected subcutaneously with progesterone dissolved in sesame oil (Sigma; 0.2mg/0.1mL/mouse), followed by sacrifice and removal of uterine horns at 6 hours after injection. 8 uterine horns from 4 mice were pooled to form one sample. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix. Source GEO sample is GSM3056 Last updated (according to GEO): May 27 2005 19 0 Head and neck cancer 1000 Rectum a severe psychiatric disorder 30 58 SN:1012376 Source GEO sample is GSM115409 Last updated (according to GEO): Jun 20 2006 The nose 94 101 Brain 861 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114469 Last updated (according to GEO): Jun 16 2006 brain, cerebral cortex: Total RNA extraction_le1 261215 none Source GEO sample is GSM244542 Last updated (according to GEO): Nov 23 2007 Blood 1000 Primary tumor 19 32 Heart Ventricle 1000 37 0 skeletal muscle sprague1 whole tissue Colo 668 SCLC cell line Gene expression data from aldosterone-producing adenoma Source GEO sample is GSM211460 Last updated (according to GEO): Jul 18 2007 In vertebrates, paralogous Hox genes play diverse biological roles. We examined the interchangeability of Hoxa1 and Hoxb1 in mouse development by swapping their protein-coding regions. Remarkably, the mice expressing the Hox-B1 protein from the Hoxa1 locus, and vice versa, are essentially normal. We noted, nonetheless, a specific facial nerve hypomorphism in hemizygous Hoxb1(A1/-) mice and decreased viability in homozygous Hoxa1(B1/B1) embryos. Further, we established a mouse line in which we have inserted the 107 bp Hoxb1 autoregulatory enhancer into the Hoxa1 promoter. Strikingly, the newly generated autoregulatory Hoxa1 gene can deliver the functionality of both paralogs in these mice, providing normal viability as well as proper facial nerve formation even in the Hoxb1 mutant background. This study affirms that subfunctionalization of the transcriptional regulatory elements has a principal role in the diversification of paralogous Hox genes. Moreover, we show that the ancestral vertebrate Hox1 gene can still be experimentally reconstructed. 4 0 Brain Expression profiling of spinal cord section (T10) extracted from rats 4h following severe injury Source GEO sample is GSM31375 Last updated (according to GEO): May 27 2005 Parkinson Disease 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145642 Last updated (according to GEO): Nov 20 2006 Blood Test (Blinded) Sample Source GEO sample is GSM129992 Last updated (according to GEO): Sep 18 2007 203 185 the early skeleton 660 mesenchymal stem cell 639 SN:1007084 Source GEO sample is GSM115365 Last updated (according to GEO): Jun 20 2006 H132 CB B Brain 861 Epithelium of bronchus 983 Spleen 0 5 Gene expression data from postmorten brain regions Source GEO sample is GSM146075 Last updated (according to GEO): Nov 20 2006 brain 0 5 Prostate 23 Normal 901 Heart failure Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28772 Last updated (according to GEO): May 27 2005 none Source GEO sample is GSM241962 Last updated (according to GEO): Nov 29 2007 Multiple sclerosis (MS) is a debilitating autoimmune disease of the central nervous system (CNS) that develops in genetically susceptible individuals who are exposed to undefined environmental risk factors. Epidemiological, genetic, and biological evidence suggests that insufficient vitamin D may be an MS risk factor. However, little is known about how vitamin D might be protective in MS. We hypothesized that 1,25-dihydroxyvitamin D3 [1,25-(OH)2D3] might regulate gene expression patterns in a manner that would resolve inflammation. To test this hypothesis, experimental autoimmune encephalomyelitis (EAE) was induced in mice, 1,25-(OH)2D3 or a placebo was administered, and 6 h later, DNA microarray hybridization was performed with spinal cord RNA to analyze the gene expression patterns. At this time, clinical, histopathological, and biological studies showed that the two groups did not differ in EAE disease, but changes in several 1,25-(OH)2D3-responsive genes indicated that the 1,25-(OH)2D3 had reached the CNS. Compared with normal mice, placebo-treated mice with EAE showed increased expression of many immune system genes, confirming the acute inflammation. When 1,25-(OH)2D3 was administered, several genes like glial fibrillary acidic protein and eukaryotic initiation factor 2alpha kinase 4, whose expression increased or decreased with EAE, returned to homeostatic levels. Also, two genes with pro-apoptotic functions, calpain-2 and caspase-8-associated protein, increased significantly. A terminal deoxynucleotidyl transferase-mediated dUTP nicked end labeling study detected increased nuclear fragmentation in the 1,25-(OH)2D3-treated samples, confirming increased apoptosis. Together, these results suggest that sensitization of inflammatory cells to apoptotic signals may be one mechanism by which the 1,25-(OH)2D3 resolved EAE. PGA-MPF-C57-bleo-72h-1aAv2-s2 ALL_1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A in seminoma 28 38 Sample14, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53265 Last updated (according to GEO): Jul 06 2005 NA Source GEO sample is GSM198889 Last updated (according to GEO): Jun 07 2007 19 0 human frontal cortex 861 Lung Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 5 day time point Source GEO sample is GSM159736 Last updated (according to GEO): Apr 23 2007 Wild type 8 wk old male FVB/NJ mouse hypothalamus Source GEO sample is GSM74980 Last updated (according to GEO): Feb 27 2007 Colon 1000 (No additional Information) Source GEO sample is GSM114426 Last updated (according to GEO): Jun 19 2006 (No additional Information) Source GEO sample is GSM114437 Last updated (according to GEO): Jun 19 2006 Job's patient Source GEO sample is GSM211083 Last updated (according to GEO): Sep 10 2007 19 0 Human ovarian tumors 468 459 the rectum 1000 Spleen Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92293 Last updated (according to GEO): Jan 13 2006 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134650 Last updated (according to GEO): Jul 09 2007 M7TW00121817 acute lymphoblastic leukemia 729 756 CNS-SC_InjB14d-3B-s2 ovary 45 50 14 0 Small Intestine Nasal Epithelium Inhalation Formaldehyde 15ppm 6h ID342 Liver Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188732 Last updated (according to GEO): Jun 06 2007 Paresis 861 861 Retina ILS/ISS_cerebellum_naive_437 of these adult retinal stem cells 331 363 /6J Olfactory Bulb A 5 24 human frontal cortex Source GEO sample is GSM87002 Last updated (according to GEO): Feb 08 2006 865 Ovarian Diseases of regenerating Dorsal Root Ganglia 21 55 1000 medulloblastoma Muscle 861 5 0 brain 1000 Cerebrovascular accident with acute measles 20 37 Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3887 Last updated (according to GEO): May 27 2005 1000 Heart failure Gene expression data from a neocortex from mouse injected 15 mg/kg kainate Source GEO sample is GSM147404 Last updated (according to GEO): Jan 03 2007 NCI60.4_LABEL7EXTRACT6SUB3 Source GEO sample is GSM134014 Last updated (according to GEO): Aug 06 2007 with acute measles 20 37 4 0 Ovary brain, forebrain: Sample15_e1_le1 in human mammary epithelial cells 37 69 15 0 human cerebellum 5 0 brain 1000 frontal lobe Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92350 Last updated (according to GEO): Jan 13 2006 Voxel D1 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1405 Last updated (according to GEO): Nov 21 2005 V5-P418 Human Cell Line, adrenal medulla: RNA615_le1 1000 Cerebral cortex 861 Liver C57BL/6J_male_hypothalamus Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153498 Last updated (according to GEO): Jan 11 2007 861 Blood Tumor__Leukemia_AML_AML_(6,PK)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 hair 861 Cardiomyopathies 5 0 Spleen Cortex_Control_rep7 (06SE469) Gene expression data from postmorten brain regions Source GEO sample is GSM145961 Last updated (according to GEO): Nov 20 2006 Brain 1000 Epithelium 861 861 Cancer of Neck Liver 1000 ATCC number CRL-1502 Source GEO sample is GSM6811 Last updated (according to GEO): May 27 2005 R652P01186 1000 Cerebrovascular accident 1000 Malaria, Cerebral Fibroblasts 1000 Mice sacrificed after swimming twice a day for 2.5 days. Keywords = exercised induced hypertrophy Source GEO sample is GSM2346 Last updated (according to GEO): May 27 2005 Normal Fetal Liver mefloquine-treated NG108 neuronal cells 7 Coronary heart disease 913 VDXOXFU_662 1000 Heart failure 1000 Nervous system structure Normal Source GEO sample is GSM175862 Last updated (according to GEO): Apr 09 2007 Fi4_2, mouse, FVB, infected, 4 days post infection_rep 2 Cockayne syndrome B cell Source GEO sample is GSM226294 Last updated (according to GEO): Sep 04 2007 The mitochondrial membrane potential slightly 558 602 to the nose 599 609 Gene expression data from the hippocampus of wild-type mouse Source GEO sample is GSM172955 Last updated (according to GEO): Mar 08 2007 R7E 6 Bladder sample 1238-1 Endometrium 0 10 861 Blood 1000 Cerebellum Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 4h after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44667 Last updated (according to GEO): May 27 2005 1000 Brain 5 0 Spleen 66 42 out of mouse bone marrow C3H/HeJ Olfactory Bulb D 861 Cerebral cortex Liver 0 4 Gene expression data Source GEO sample is GSM183180 Last updated (according to GEO): Jul 30 2007 Colon 861 aRNA probe from T7-based amplification Source GEO sample is GSM113694 Last updated (according to GEO): Jun 09 2006 43 28 Alzheimer's mice Neostriatum 1000 f2#17 versus pool Mouse Brain tissue Plasma 861 901 frontal lobe Lung Neoplasms 876 Spleen vs Anti-IgM Treated B cell 120min (set3) 27 0 dorsal root ganglion fisher2 GSE3110 NoCAD_replicate39 GSE396 861 medulloblastoma Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 7404 blood 626 615 PCOS oocytes Cerebral cortex 861 Total RNA was extracted from umbilical subcutaneous adipose tissue from an individual affected with FCHL and exhibiting the USF1 protective haplotype Source GEO sample is GSM9049 Last updated (according to GEO): May 28 2005 cingulate cortex 901 Parahippocampal Gyrus 913 104 89 in Rat Esophagus 40 21 from skeletal muscle Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11547 Last updated (according to GEO): May 28 2005 40 21 from skeletal muscle KM12__CL4017_COLON 3 min exposure to halothane, sacrificed by cold saline perfusion. Keywords = Eckenhoff anesthetics Source GEO sample is GSM5082 Last updated (according to GEO): May 27 2005 Nephrons 1000 861 Cardiomyopathies 861 Cerebral cortex brain, frontal cortex: Sample46_e1_le1 brain 0 5 41 36 spleen Bladder sample 625-1 Identification of oscillatory genes in somitogenesis from functional genomic analysis of a human mesenchymal stem cell model. 1000 Spinal Cord NA18997 Saline control-hippocampus, biological rep4 Kidney [JunctionChip 4 of 5] Replicate two: differential expression analysis of CW treatment on RBEC6 cells Source GEO sample is GSM128923 Last updated (according to GEO): Aug 16 2006 Prostate carcinoma 861 Gene expression data from the hippocampus of S1P2-knockout mouse Source GEO sample is GSM172971 Last updated (according to GEO): Mar 08 2007 Epithelial Cells 1000 Heart; HyperdynamicControl Keywords = mouse gene expression database Source GEO sample is GSM29344 Last updated (according to GEO): May 27 2005 966 Hippocampus mod088_Con1 HapMap JPT Male Source GEO sample is GSM159625 Last updated (according to GEO): Feb 01 2007 865 Disorder of artery from intraabdominal adipose tissue 25 58 329 306 valvular cardiomyopathy 1000 Brain blood, Blood: 2253_0103_le1 wild-type mouse cerebellum Treatment, type=time_course, measurement=11.0 weeks Source GEO sample is GSM53356 Last updated (according to GEO): Jul 06 2005 861 Colon 861 Cerebral cortex 861 Cerebral cortex 5 0 brain HapMap CEU_parent Male Source GEO sample is GSM159536 Last updated (according to GEO): Feb 01 2007 B296b on Affymetrix GeneChip Human Full Length Array HuGeneFL Sun199_TAV12 group Myometrium 44 Disease CNS-SC_Inj14d-4A-s2 G2 Sup. Retina allander-gist Chronic Lymphocytic Leukemia 19 47 C Fed Rep 3 67 40 with coronary artery disease with acute measles 20 37 278 265 from 6 brains Brain 861 11_0012_Control_Day1_48 901 Mammary Neoplasms 542 527 among the tumors 12 frontal Lobe 23 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection). Source GEO sample is GSM36448 Last updated (according to GEO): May 27 2005 VDXKIU_309C49 1000 Hippocampus 1000 Rectum C57/BL6 to C57/BL6 Source GEO sample is GSM8927 Last updated (according to GEO): May 28 2005 901 Spinal Cord ovary 197 201 Mk1: Hippocampus_21PT-AU_rep4 CLL-52 || lc7b069 M_U133A_92_DLPFC Gene expression data from postmorten brain regions Source GEO sample is GSM145752 Last updated (according to GEO): Nov 20 2006 Gene expression data from microdissected area # 1 of 1761 tumor Source GEO sample is GSM182294 Last updated (according to GEO): Apr 16 2007 Myocardium 861 Primary adenocarcinoma Source GEO sample is GSM16565 Last updated (according to GEO): May 28 2005 16 0 Bone marrow cell 1000 Coronary Arteriosclerosis 13 0 Lung carcinoma whole blood_101621 Plasma 861 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68148 Last updated (according to GEO): Jul 07 2006 Balb/c day 0, biological rep 3, tech rep 1 adenocarcinoma 189 203 861 Cerebral cortex 861 Medulla Oblongata 861 Alzheimer's Disease ovarian tumor: mucinous Source GEO sample is GSM139424 Last updated (according to GEO): Apr 09 2007 91 from the bone marrow 72 ALL_24 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A f2#215 versus pool Mouse Brain tissue brain, forebrain: Sample3_e1_le1 Neoplasm 861 Leg 14 Day Control rep 2 Parkinson's disease sample x014 0 30 7 cortex 12 in hepatocellular carcinoma 574 600 1000 Brain human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195347 Last updated (according to GEO): Jun 04 2007 1000 Prostate 1_hypothalamus_9hrs_sleep_deprivation_#81 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:248, Count:32 Corner- Avg:43803, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:17.496950,SFGene:All Background:Avg:346.00,Stdev:4.31,Max:359.2,Min:337.0 Noise:Avg:9.84,Stdev:0.35,Max:10.9,Min:8.9 RawQ:14.73 Keywords = ALL Source GEO sample is GSM3499 Last updated (according to GEO): May 28 2005 WGACON-98 Cerebellum Control (AD) 4 in the Rat Nasal Epithelium 24 50 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181161 Last updated (according to GEO): Jul 12 2007 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10133.gif Source GEO sample is GSM79704 Last updated (according to GEO): Sep 22 2006 61 50 Spinal cord brain, left frontal temporal lobe: Extract3_le1 CLL-57 brain, contralateral Cortex: Trizol Extraction46_le1 Parkinson Disease 1000 Hereditary Nonpolyposis Colorectal Neoplasms 947 Normal Source GEO sample is GSM176127 Last updated (according to GEO): Apr 09 2007 Spleen 1000 17 7 hippocampus GSE2871 Gene expression data from postmorten brain regions Source GEO sample is GSM144901 Last updated (according to GEO): Nov 20 2006 HUVEC isolate 8 low serum media control for #30 Source GEO sample is GSM12921 Last updated (according to GEO): May 28 2005 ISR15-Fv2E-PERK AP20187 8hr2, RNA from an 2nm AP20187 treated (8hr) Fv2E-PERK expressing fibroblast cell line in an eIF2 alpha SS (wildtype), PERK-/- background. AP20187 activates the kinase activity of the Fv2E-PERK chimera. The PERK-/- background was used in order to obtain a cell line that expressed high levels of the Fv2E-PERK transgene. (We were unable to obtain clones with high levels of expression in wildtype cells.) The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules. Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10901 Last updated (according to GEO): May 28 2005 11 0 Fetal brains Lymphoblastoid Cell Line for Individual 8145.3 log phase Communicable Diseases 1000 Tumor__Uterus_Adeno_92_I_073 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Bilateral olfactory bulbectomies were performed on male C57Bl/6 mice(6 week old) and olfactory epithelium tissue collected 7 days post-bulbectomy. Total RNA was extracted from the olfactory epithelium tissue. Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol. Keywords = olfaction Keywords = neurogenesis Keywords = apoptosis Keywords = gene silencing Keywords = microarray, transcription factor Source GEO sample is GSM45689 Last updated (according to GEO): Oct 28 2005 1000 Uterus to the nose 599 609 39 21 from mammary glands Primary small cell lung carcinoma 1926 brain 0 5 12 Temporal Lobe 24 cy5:WKY control, biological rep 6r; cy3:pool of 6 WKY control rats of a colorectal adenoma 7 29 rat hippocampus Treatment, type=time_course, measurement=240.0 h Source GEO sample is GSM32147 Last updated (according to GEO): May 27 2005 The cardiac-specific tetracycline-regulated gene expression system (tet-system) is a powerful tool using double-transgenic mice. The cardiac alpha-myosin heavy chain promoter (alphaMHC) drives lifetime expression of a tetracycline-inhibited transcription activator (tTA). Crossing alphaMHC-tTA mice with mice containing a tTA-responsive promoter linked to a target gene yields double-transgenic mice having tetracycline-repressed expression of the target gene in the heart. Using the tet-system, some studies use nontransgenic mice for the control group, whereas others use single-transgenic alphaMHC-tTA mice. However, previous studies found that high-level expression of a modified activator protein caused cardiomyopathy. Therefore, we tested whether cardiac expression of tTA was associated with altered function of alphaMHC-tTA mice compared with wild-type (WT) littermates. We monitored in vivo and in vitro function and gene expression profiles for myocardium from WT and alphaMHC-tTA mice. Compared with WT littermates, alphaMHC-tTA mice had a greater heart-to-body weight ratio (approximately 10%), ventricular dilation, and decreased ejection fraction, suggesting mild cardiomyopathy. In vitro, submaximal contractions were greater compared with WT and were associated with greater myofilament Ca2+ sensitivity. Gene expression profiling revealed that the expression of 153 genes was significantly changed by >20% when comparing alphaMHC-tTA with WT myocardium. These findings demonstrate that introduction of the alphaMHC-tTA construct causes significant effects on myocardial gene expression and major functional abnormalities in vivo and in vitro. For studies using the tet-system, these results suggest caution in the use of controls, since alphaMHC-tTA myocardium differs appreciably from WT. Furthermore, the results raise the possibility that the phenotype conferred by a target gene may be influenced by the modified genetic background of alphaMHC-tTA myocardium. left hemi-diaphragm 27 45 1000 Cartilage ColTum_022NAFD9_g8.txt Normal__Colon_9912c071_CC on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 443_1 HC53 FC BA4 B Squamous cell carcinoma 8 0 24 spinal cord, spinal cord: G2F_le1 Gene expression of organ of Corti of newborn rats_repeat 1 inner ear Brain 1000 Nervous system structure 901 Prefrontal Cortex 0 16 858 Prostatic Neoplasms Parkinson Disease 1000 Coronary artery 901 Integumentary system 1000 Blood 861 brain, Right Frontal Lobe: Extract59_le1 12 0 ovarian tumor 35 15 in spinal cord injury Expression data from heart failure vs control peripheral blood mononuclear cells. 861 Thymus Gland Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92338 Last updated (according to GEO): Jan 13 2006 Epithelium 861 GSE391 Cerebral cortex 1000 the blood 393 402 Myopathy 875 Hippocampus Source GEO sample is GSM53361 Last updated (according to GEO): Jul 06 2005 Cerebral cortex 1000 91 from the bone marrow 72 of the colon 28 39 CNS-SC_InjB7d-3A-s2 1000 Blood 1994 1985 hippocampi 861 Brain CAD_replicate44 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 30min after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44500 Last updated (according to GEO): May 27 2005 Cerebral cortex 1000 Structure of dentate gyrus 861 autism 0 5 H113 CN B Sample represents the Neurointermediate lobe of the Pituitary from 5 control animals Source GEO sample is GSM69789 Last updated (according to GEO): Dec 15 2005 Endometrium/Ovary 3 Disease Expression profiling of spinal cord section (T10) extracted from rats 14d following mild injury Source GEO sample is GSM31311 Last updated (according to GEO): May 27 2005 brain, Right Frontal Parietal: Extract65_le2 Ovarian_Tumor_Serous_CHTN-OS-038 no additional Source GEO sample is GSM199037 Last updated (according to GEO): Jun 08 2007 Sample represents the supraoptic nucleus from 5 control animals Source GEO sample is GSM69463 Last updated (according to GEO): Dec 15 2005 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11327 Last updated (according to GEO): May 28 2005 1000 Brain in the hippocampus 1561 1578 858 Mesodermal cell in fibroblasts 1222 1236 86 70 Fetal liver cells Spleen 1000 Effects of SOCS3 on the transcriptional response of macrophages to IL-6. Fetal liver cells from SOCS3+/+ embryos were used to reconstitute irradiated mice. Donor derived cells from the bone marrow were differentiated to macrophages. Replicate 1 of unstimulated macrophages. Keywords = macrophage, SOCS3, IL-6, interferon Source GEO sample is GSM6072 Last updated (according to GEO): May 27 2005 258_1 Renal Cell Carcinoma 923 Blood 1000 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228649 Last updated (according to GEO): Sep 11 2007 Cochlear nuclei pooled from 20 pups to generate one sample for one replicate hybridization out of 5. Cohybridized with P7_cy3_1. Source GEO sample is GSM44984 Last updated (according to GEO): Jun 08 2005 Gene expression data from the hippocampus of wild-type mouse Source GEO sample is GSM172959 Last updated (according to GEO): Mar 08 2007 HCC (HBV+, HK5) Laser captured visceral sensory neurons. Source GEO sample is GSM63658 Last updated (according to GEO): Dec 21 2005 Head and neck cancer Source GEO sample is GSM155676 Last updated (according to GEO): Apr 24 2007 Femur 1000 Blood 1000 150 mg/kg X 6 hr Source GEO sample is GSM129866 Last updated (according to GEO): Sep 18 2007 from Duchenne muscular dystrophy 39 70 901 Caudate nucleus structure prostate Source GEO sample is GSM203408 Last updated (according to GEO): Jun 21 2007 7 cerebral cortex 21 901 frontal lobe 19 on NHGRI-13.8k Mouse Liver LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate D Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198626 Last updated (according to GEO): Jun 06 2007 7 0 Pancreas 24 hr EE repl 1 Dissection of E16.5 cortex for RNA extraction. Cortex Hemispheres of E16.5 mice were divided into the medial (R1), dorsal (R2), ventral (R3), lateral (R4), and occipital regions (R5). Preparation of RNA and Synthesis of cDNA. Poly A+ RNA was obtained through twice column procedures with oligo dT cellulose column (New England Biolabs, Beverly, MA) and was used for synthesis of cDNA. 1ug of polyA+ RNA was converted into double-stranded cDNA by reverse transcription using ReverTra Ace (ToYoBo, Japan) with oligo dT(24) primers containing the T7 RNA polymerase promotor sequence (Amersham Pharmacia Biotech, Japan). The integrity of RNA was confirmed by agarose electrophoresis and RNA contents were analyzed by measuring the optical density at 260 nm. Target preparation and array processing. The following procedures including preparation of cRNA targets, hybridization, washing, staining, and scanning were performed as described in the Expression Analysis Technical Manual (Affymetrix, CA). Briefly, biotin-labeled antisense cRNA targets were synthesized in in vitro transcription reaction system (IVT) using cDNA as template (ENZO BioArrayTM HighYieldTM RNA Transcription Labeling kit with T7 RNA polymerase, Enzo, NY). The cRNA targets were size-fragmented to 35-200 bp in a buffer containing potassium and magnesium acetate at 94 °C for 35 minutes and were used for hybridization as cRNA targets. The hybridization cocktail [containing 10 ug of target cRNA, control oligo BS (Affymetrix), and Eukaryotic Hybridization controls (Affymetrix)] was hybridized with a mouse U74A array at 42 °C for 16 hours in GeneChip Hybridization Oven 640. Washing and staining were performed after hybridization under the fluidics station protocol, EuGE-WS2, on GeneChip Fluidics Station 400. Then, we scanned the array twice on HP GeneArrayTM scanner. Experiments were repeated twice with independent dissection. Data analysis. To quantify the expression level of a transcript, the average difference value (Adv) was calculated from the intensities against the probe cells using the global methods of normalization by Microarray Suite ver. 4.0 (Affymetrix). Keywords = mouse Keywords = cortex Keywords = development Keywords = regional Keywords = gene expression Keywords = medial Keywords = dorsal Keywords = lateral Keywords = rostral Keywords = occipital Source GEO sample is GSM14591 Last updated (according to GEO): Oct 28 2005 861 Neoplasm endothelial cells sprague1 whole tissue, individual animal, 10 weeks old, male Sprague Dawley endothelial cells file:R3JW02103021 Source GEO sample is GSM15217 Last updated (according to GEO): May 28 2005 Primary Neoplasm 886 This study was conducted using affymetrix microarrays. We were interested in determining the effects of tTA expression in the hearts of FVBN mice. We compared expression to wild type mice.. Date GSE986 Last Updated: May 29 2005 Includes GDS591. Update date: May 12 2004. Dataset description GDS591: Determination of effects of tetracycline transactivator (tTA) expression in cardiac ventricle of FVBN mice.. biopsy sample obtained from a 4-year-old male Duchenne Muscular Dystrophy patient Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15843 Last updated (according to GEO): Sep 08 2006 brain 0 5 none Source GEO sample is GSM161912 Last updated (according to GEO): Feb 16 2007 Sun211_TAV12 group 928 Hyperinsulinism Primary Carcinoma 876 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15755 Last updated (according to GEO): May 28 2005 Heart; tg - hyperdynamic Keywords = mouse gene expression database Source GEO sample is GSM29346 Last updated (according to GEO): May 27 2005 Liver Test (Blinded) Sample Source GEO sample is GSM130093 Last updated (according to GEO): Sep 18 2007 1000 Ectodermal Dysplasia Replicate2_Voxel D6 gene expression from allergen stimulated mouse lung Source GEO sample is GSM158135 Last updated (according to GEO): Jan 25 2007 Temporal Cortex Control (AD) 1 VDXGUYU_4045 Expression profiling of spinal cord section (T10) extracted from rats 24h following laminectomy (sham) Lot batch = Source GEO sample is GSM6630 Last updated (according to GEO): May 28 2005 Substantia Nigra 3 Normal Kidney 40 45 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188734 Last updated (according to GEO): Jun 06 2007 Dissection of temporal gene expression signatures of affected and spared muscle groups in dystrophin-deficient (mdx) mice. 1000 Cardiomyopathy, Alcoholic Richard Almon-18-1133800609323 BC710B-AF 861 Malignant neoplasm of prostate 10 0 Endometrium of regenerating Dorsal Root Ganglia 21 55 Epithelial Cells 901 1768 1763 livers DBA/2J Amygdala A Transplant Series 25 Right, PrimaryTumor 1000 Uterus Cerebral cortex 1000 091250 MDAH2774 on Affymetrix GeneChip Human Full Length Array HuGeneFL control lean rat A3 10 0 Endometrium Brain 861 Hippocampus 1000 1000 Brain 40 21 from the hippocampus Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141306 Last updated (according to GEO): Oct 26 2006 CON(SN)(2) M_U133A_114_DLPFC Gene expression data from postmorten brain regions Source GEO sample is GSM145279 Last updated (according to GEO): Nov 20 2006 SON control Source GEO sample is GSM69860 Last updated (according to GEO): Dec 02 2005 Nodose Nucleus 10 Normal 64 47 that whole ovaries Chronic leukemia NOS 913 861 Cancer of Neck /J mouse periaqueductal gray 25 52 BC16 between the LAD artery 266 287 Heart Ventricle 1000 1000 Brain Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118545 Last updated (according to GEO): Jul 11 2006 FVB/NJ Cerebellum B Primary Carcinoma 876 I_U133A_17_CB mouse cerebral cortex, cox-2 knockout, rep2 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b060 Source GEO sample is GSM2013 Last updated (according to GEO): Nov 21 2005 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195234 Last updated (according to GEO): Sep 13 2007 1000 Benign prostatic hypertrophy 1.25 mg/kg MeHg forebrain at 3.0h Normal Source GEO sample is GSM175875 Last updated (according to GEO): Apr 09 2007 Amygdaloid structure 1000 Tonsil Memory B 901 Stem cells Group 3 NMBA treated, pool #EP5 vs. reference pool VDXGUYU_4002 861 Hypersensitivity Bone Marrow 1000 The frontal cortex 543 560 R483P00305 Primary Neoplasm 1000 Huntington Disease 1000 (cortex 19 25 Untreated versus treated (bortezomib) breast cancer cells. Source GEO sample is GSM120358 Last updated (according to GEO): Jul 20 2006 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181209 Last updated (according to GEO): Jul 12 2007 GFP labeled neurons in amygdala. Source GEO sample is GSM63050 Last updated (according to GEO): Dec 01 2005 "Sample 66, <5 yr survival(49 months) age 47 erp yes" on vantveer-oligo 3 0 Pons Saline control-hippocampus, biological rep2 H7 Human Embryonic Stem cell (H7 ESC) d5 1000 Endoplasmic Reticulum the blood 393 402 PBMC_022WAFD0_096.txt Heart failure sample 3 Embryonic day 18 callosal projection neurons purified by fluorescence-activated cell sorting. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription. Source GEO sample is GSM37083 Last updated (according to GEO): May 27 2005 HapMap CHB Male Source GEO sample is GSM159613 Last updated (according to GEO): Feb 01 2007 1000 Infection testis 52 58 brain, Right Parietal Lobe: Extract73_le1 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11268 Last updated (according to GEO): May 28 2005 myocardial infarction 383 403 subsequent progenitor cell proliferation 335 374 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15399.gif Source GEO sample is GSM84180 Last updated (according to GEO): Sep 22 2006 Parkinson Disease 861 A HID I D008 5 0 brain D_95Av2_2822_CB_1_GS M_U133A_68_AnCg Neoplasm Metastasis 1000 Subject code A17 hippocampus 174 184 Brain 1000 Papillary thyroid carcinoma 1000 COLO 205 hgu95a MOLT4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 43 0 Chorionic mesoderm-derived mesenchymal cells Brain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145067 Last updated (according to GEO): Nov 20 2006 FC 89h between the LAD artery 225 246 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27038 Last updated (according to GEO): May 27 2005 17 7 hippocampus 5 0 Muscle 861 Neoplasm liver_wildtype_WY14643_6h_rep2 117 112 Lipids 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114440 Last updated (according to GEO): Jun 16 2006 AML 52 on Affymetrix GeneChip Human Full Length Array HuGeneFL NA19222 Seminoma 1000 Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231043 Last updated (according to GEO): Sep 26 2007 257 251 trauma Nasal Epithelium 901 1000 Cerebral cortex 660 mesenchymal stem cell 639 GM19238 Myocardium 861 Osteoblasts 1000 Female mice used were 129/SvImJ wildtype (Jackson Lab), 10-16 weeks of age. 14 days after ovariectomy, mice were injected subcutaneously with progesterone dissolved in sesame oil (Sigma; 0.2mg/0.1mL/mouse), followed by sacrifice and removal of uterine horns at 3 hours after injection. 8 uterine horns from 4 mice were pooled to form one sample. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix. Source GEO sample is GSM3055 Last updated (according to GEO): May 27 2005 HUVEC isolate 52 rich media control for #2 Source GEO sample is GSM12894 Last updated (according to GEO): May 28 2005 Coronary heart disease 913 Wild type inbred mice Source GEO sample is GSM82921 Last updated (according to GEO): Nov 10 2005 Primary Neoplasm 1000 9 0 Blood Test Lymphoblastic Leukemia 901 Normal Source GEO sample is GSM175900 Last updated (according to GEO): Apr 09 2007 Intestines 861 Semeralul_PFC_Development_Week10_Batch1_Animal_7 861 hair HapMap JPT Female Source GEO sample is GSM159653 Last updated (according to GEO): Feb 01 2007 913 Acute leukemia NA18976 Macrophage 14smi056 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with fMLP for 240min Source GEO sample is GSM5577 Last updated (according to GEO): May 27 2005 1000 Spleen corpus_callosum_4 Laser captured visceral sensory neurons. Source GEO sample is GSM63675 Last updated (according to GEO): Dec 21 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with MIP3-alpha (Macrophage inflammatory protein-3) for 120min Source GEO sample is GSM5693 Last updated (according to GEO): May 27 2005 AML-37 on Affymetrix GeneChip Human Full Length Array HuGeneFL The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27023 Last updated (according to GEO): May 27 2005 3AJZ02060604_CardiacMyocytes AO Treatment, type=remove Source GEO sample is GSM99519 Last updated (according to GEO): Apr 21 2006 Nasal Epithelium 901 Mesenchymal Stem Cells 923 GM19192 CT6-CingulateCortex-replicate3 adipose_tissue_subcutaneous_4 Source GEO sample is GSM80584 Last updated (according to GEO): Mar 31 2006 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184750 Last updated (according to GEO): Apr 26 2007 Epithelium 861 Femur 1000 Gene expression data from microdissected area # 1 of 1589 tumor Source GEO sample is GSM182290 Last updated (according to GEO): Apr 16 2007 1000 Heart failure no additional Source GEO sample is GSM199127 Last updated (according to GEO): Jun 08 2007 Liver 1000 P18 non-deprived visual cortex replicate 4 Whole Brain 62 72 Gene expression data from whole brain of uninfected mouse Source GEO sample is GSM189597 Last updated (according to GEO): May 16 2007 brain, Entorhinal Cortex: 97-01 tangle_e1_le1 Timecourse of TLR2/1 stimulated human dendritic cells with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225887 Last updated (according to GEO): Aug 31 2007 Primary Neoplasm 1000 320 306 Keywords = HIV ER negative human primary breast tumor EA02014_41287_H133A_JA-1858 Cerebellum 861 Epithelium 861 hrs nasal epithelium 1127 1147 -_6388_batch3 on NHGRI-6.7k 113 FC BA9 A 2hr S-CA1 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15396.gif Source GEO sample is GSM84178 Last updated (according to GEO): Sep 22 2006 SQ-5897-A328-5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A A_3 BT-474 861 Gastrocnemius muscle structure M_U133A_89_AnCg Left ventricular structure 1000 M_U133A_10_HC T53__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 901 frontal lobe long access to cocaine, amygdala, 6 hrs/day access to cocaine Source GEO sample is GSM93836 Last updated (according to GEO): Jan 26 2006 Gene expression data from liver Source GEO sample is GSM243379 Last updated (according to GEO): Nov 16 2007 1000 Pancreas BALB/cByJ Basal Ganglia C S1P3-KO-hippocampus, biological rep5 (female) Probeset expression data from NA12750 growth 1, replicate 4 Source GEO sample is GSM195194 Last updated (according to GEO): Aug 08 2007 4525 4520 liver Brain 1000 MDA-N hgu95a MGMH030212040Atrigeminal 1000 Infection Acetaminophen 3hr Rat 6622 blood vs. Acetaminophen 3hr Rat Pooled Control blood Spleen vs Interferon-gamma (IFN gamma) Treated B cell 60min (set1) 12 0 basal ganglia Bone Marrow 1000 865 Disorder of artery Pool Eu_P30_hyb1 Basal Ganglia 901 NA18995 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114183 Last updated (according to GEO): Jun 16 2006 M_U133A_48_AnCg Autistic Disorder 877 366 354 encephalitis no additional Source GEO sample is GSM199030 Last updated (according to GEO): Jun 08 2007 tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44882 Last updated (according to GEO): May 27 2005 to JCV infection 249 265 Normal Source GEO sample is GSM176180 Last updated (according to GEO): Apr 09 2007 Tumor__Lymphoma_Follicular_FSCC_S93_20082 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene expression data from rat metanephric mesenchymes cultured for 7 days in the presence of LIF Source GEO sample is GSM126203 Last updated (according to GEO): Dec 08 2006 Disease Source GEO sample is GSM175917 Last updated (according to GEO): Apr 09 2007 M_U133A_40_DLPFC testis 0 5 1000 Brain 861 Coxsackievirus Infections cingulate cortex 1000 RXF 393 hgu95b Study of in vitro granulocyte differentiation Source GEO sample is GSM137455 Last updated (according to GEO): Jun 06 2007 128 113 such as dementia Transplant Series 17 , PrimaryTumor 32h-DMSO replication 3 C57BL/6J hypothalamus rep2 Acetaminophen 6hr Rat 6034 blood vs. Acetaminophen 6hr Rat Pooled Control blood n/a Source GEO sample is GSM178069 Last updated (according to GEO): Jun 11 2007 in the brain 150 162 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184731 Last updated (according to GEO): Apr 26 2007 257 230 of activating immunoglobulin of somatomotor cortex 21 41 Endometrium 1000 mouse brain 478 489 1000 Brain peripheral nervous system 169 194 861 Hemidesmosomes mouse brain 478 489 Epithelium 861 Primary small cell lung carcinoma 2212 Spinocerebellar Ataxias 861 91 from the bone marrow 72 Parkinson Disease 861 Sprague-Dawley Female LowSalt Cortex rat701 sd_cortexr_k_701c_020802 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184814 Last updated (according to GEO): Apr 26 2007 Phenytoin brainstem 7 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53418 Last updated (according to GEO): Jul 06 2005 acute myeloid leukemia Source GEO sample is GSM227430 Last updated (according to GEO): Sep 12 2007 NHF10-hTERT_1.5Gy_24h_C3_21766 913 Spinal Injuries Structure of dentate gyrus 901 Type 2 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228670 Last updated (according to GEO): Sep 11 2007 Cell Culture: Hippocampal cells from E18 rat embryos were plated at a density of 500,000 cells per 60 mm poly-L-lysine (1mg/ml; Sigma) coated dish. Cultures were maintained at 37 C in 5% CO2 humidified incubator and used for experiments at 21 day in vitro (DIV). Control and experimental group cultures were incubated with 10 micro M TTX for 15 min followed by addition of 100 micro M baclofen or vehicle. Total RNA preparation: Each experimental group was compared as replicates of three. For each replicate cultured hippocampal neurones were harvested after 2 hours incubation +/- baclofen and total RNA was isolated using RNeasy Mini kit (Qiagen, UK) according to the manufacturer's protocol. Microarray Target Labelling and Hybridisation: Targets for cDNA microarrays were generated using 5 micro g of total RNA in a standard reverse transcription (RT) reaction. RNA was annealed, in 16 micro l water, with 1 micro g of 24-mer poly(dT) primer (Invitrogen, UK), by heating at 65oC for 10 min and cooling on ice for 2 min. The RT reaction was performed by adding 8 micro l of 5X first strand RT buffer (Life technologies, MD), 4 micro l of 20mM dNTPs minus dCTP (Pharmacia, UK), 4 micro l of 0.1M DTT, 40U of RNAse OUT (Life Technologies, MD), 6 micro l of 3000 Ci/mmol 33P-dCTP (ICN Biomedicals, UK) to the RNA/primer mixture to a final volume of 40 micro l. Two micro l (400 U) of Superscript II reverse transcriptase (Life Technologies, MD) was then added and the sample incubated for 30 min at 42oC followed by additional 2 micro l of Superscript II reverse transcriptase and another 30 min incubation. The reaction was stopped by addition of 5 micro l 0.5 M EDTA. Samples were incubated at 65oC for 30 min after addition of 10 micro l of 0.1M NaOH to hydrolyse and remove RNA. Samples were pH neutralized with 45 micro l 0.5M Tris, pH 8.0 and purified using Bio-Rad 6 purification columns (BioRad, UK). The NIA NeuroArray consists of 1152 cDNAs printed on nylon membrane in duplicate. The arrays were hybridised with alpha-33P-dCTP labelled cDNA probes overnight at 50oC in 4ml of hybridisation solution. Hybridised arrays were rinsed in 50ml of 2XSSC and 1%SDS twice at 55oC followed by two washes in 2X SSC and 1% SDS at 55oC for 15 min each. The microarrays were exposed to phosphorimager screens for 1-3 days. The screens were then scanned with Molecular Dynamics STORM PhosphorImager (Sunnyvale, CA) at 25 micro m resolution. Source GEO sample is GSM28537 Last updated (according to GEO): May 27 2005 1000 Brain Salivary GBM Treatment, type=remove Source GEO sample is GSM99524 Last updated (according to GEO): Apr 21 2006 putamen_5 Source GEO sample is GSM80586 Last updated (according to GEO): Mar 31 2006 Expression profiling of moderately injured raphe at 7d in rats Source GEO sample is GSM41630 Last updated (according to GEO): May 27 2005 Eye 1000 no additional Source GEO sample is GSM199369 Last updated (according to GEO): Jun 08 2007 NCI60.28_LABEL32EXTRACT31SUB3 Source GEO sample is GSM134131 Last updated (according to GEO): Aug 06 2007 42 30 Control blood 861 Glioma 25 7 Right Temporal Lobe 901 Bone Marrow UBOC1 Exp A Day 2 (b) ALS model Source GEO sample is GSM75465 Last updated (according to GEO): Mar 06 2006 225 210 atherosclerosis To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28464 Last updated (according to GEO): May 27 2005 control 24h, replicate 1 Brain 861 small intestine PPARa knockout mice, fasted for 24 hours Source GEO sample is GSM154797 Last updated (according to GEO): Jul 04 2007 brain, cerebral cortex: NMDA 10 4_le1 brain, hippocampus: KA-72h-P15-II_e1_le1 S1P3-KO-neocortex, biological rep1 (male) 1037 of transitional epithelium 1012 Gene expression data from postmorten brain regions Source GEO sample is GSM145198 Last updated (according to GEO): Nov 20 2006 7 cerebral cortex 21 We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7. Source GEO sample is GSM200754 Last updated (according to GEO): Jul 12 2007 The nose 94 101 Richard Almon-15-1133800609182 5 0 brain Nose 1000 5 0 Spleen Some of the most common neurodegenerative disorders have a strong association with aging. Curiously, these conditions tend to involve specific areas of the central and peripheral nervous system, at least initially. For example, amyotrophic lateral sclerosis preferentially targets spinal motor neurons and spares oculomotor neurons. This suggests that aging has divergent effects on brain stem and spinal cord, a factor that may explain differential susceptibility to certain neurodegenerative disorders. Therefore, for this study we asked whether aging induces a change in the evolution of the transcriptome of oculomotor nucleus (OMN) throughout the lifespan which would be different than that of the spinal cord aging. Age induced a transcriptome shift to a pattern consistent with inflammation/immune response in both OMN and spinal cord. However, the response was more dramatic in the spinal cord. On the other hand, age repressed genes coding ion channels and transporters in OMN and cytoskeletal proteins in the spinal cord. The results indicate that OMN and spinal cord transcriptomes change differently with age. The results give an initial glimpse of how tissue-specific gene expression patterns may underlie the differential susceptibility to age-related neuromuscular dysfunction. Last Updated (by provider): Oct 28 2005 Contributers: Francisco H Andrade Jorge Gamboa Colleen A McMullen Includes GDS1280. Update date: Nov 08 2005. Dataset description GDS1280: Comparison of gene expression in the oculomotor nucleus (OMN) to that in the spinal cord. Animals 6, 18, and 30 months of age examined. Provides insight into the mechanisms underlying the divergent effects of age on the central and peripheral nervous systems. Osteoblasts 1000 CNS-SpinalCsev-Adult-4h-4C-s2 1000 Spleen Lymphoblastoid Cell Line for Individual 8136.5 log phase plasma cells 50 61 901 Cervical sympathetic ganglion A HID U D042 Generation of germ-line competent induced pluripotent stem cells 1000 Spleen CS-B wt-rescued cell unirradiated replicate 3 U133A Multiple Myeloma 861 861 Cerebral cortex lipoproteins 602 614 seminoma specimen, pT1, patient age: 29y; W03 022 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181124 Last updated (according to GEO): Jul 12 2007 Lymphoblastoid Cell Line for Individual 8166.3 log phase Parkinson Disease 1000 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188804 Last updated (according to GEO): Jun 06 2007 50 43 jejunum Lamina 861 colon.1 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152007 Last updated (according to GEO): Feb 06 2007 Myocardial Infarction 901 Gene expression data from postmorten brain regions Source GEO sample is GSM145175 Last updated (according to GEO): Nov 20 2006 /3T3 fibroblasts 295 310 Cerebral cortex 861 mRNA was isolated after 12 hours of incubation from IMR-90 cells seeded onto a collagen/chondroitin sulfate tissue engineering scaffold mesh material. Cells were seeded at a density of 1 x 10^6 cells/ mesh, and this chip represents a pooling of cells from 4 meshes. Keywords = tissue engineering mesh, collagen, chondroitin sulfate, biomaterials design Source GEO sample is GSM6038 Last updated (according to GEO): May 27 2005 Neurites 861 beta Thalassemia 1000 262_1 mouse brain contralateral saline.RU486, biological rep2 Gene expression data from postmorten brain regions Source GEO sample is GSM145561 Last updated (according to GEO): Nov 20 2006 A2780_oxa_IC90_0h_2 1000 Hypertrophic Cardiomyopathy osteoblast 627 637 1000 Brain MGMH030212052Astomach SCN2.2 Sample 3 (Exp#1-6 hr) trachea Source GEO sample is GSM18619 Last updated (according to GEO): May 27 2005 CNS-SCsev_InjA24h-1A-s2 Total RNA extracted from mouse brain Source GEO sample is GSM103427 Last updated (according to GEO): Sep 21 2006 12 0 ovarian tumor brain, Left frontal Lobe: Extract17_le2 Ventral Tegmental Area 1000 1000 Intestines 1000 Brain 1000 Hypothalamic structure 861 Brain Normal Source GEO sample is GSM175956 Last updated (according to GEO): Apr 09 2007 Cultured_cortical_astrocyte_Cx43_null_rep2 13 0 Nervous System none Source GEO sample is GSM244590 Last updated (according to GEO): Nov 23 2007 901 Structure of olfactory bulb HEART Source GEO sample is GSM18951 Last updated (according to GEO): Sep 25 2006 n/a Source GEO sample is GSM177970 Last updated (according to GEO): Jun 11 2007 Cerebral cortex 1000 Transcriptional profiling was done in Hoxb1 mutant E10.5 embryos in tissues primarily consisting of rhombomere 4 and surrounding branchial arches. Source GEO sample is GSM115799 Last updated (according to GEO): Aug 28 2006 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour.This animal was sacrificed at 2 hours after lights on.Original sample code = CM39A Source GEO sample is GSM227334 Last updated (according to GEO): Sep 10 2007 Fertilized egg replication 3 0 27 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225368 Last updated (according to GEO): Aug 31 2007 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24272.gif Source GEO sample is GSM66580 Last updated (according to GEO): Sep 22 2006 1000 Coronary Arteriosclerosis with Parkinson's disease 27 50 Brain 1000 Cerebellar astrocyte chip 2. CHIP ID 10490 Source GEO sample is GSM130363 Last updated (according to GEO): Mar 14 2007 none Source GEO sample is GSM123259 Last updated (according to GEO): Jul 26 2006 at the Human Brain 746 763 1000 Prostate ileum 0 4 335 325 The jejunum C3H/HeJ hypothalamus rep2 none Source GEO sample is GSM210337 Last updated (according to GEO): Jul 16 2007 BXD12_M7SS02042207 861 Cardiomyopathies 175 161 8 uterine horns 28 0 Fetal frontal cortex cocaine3 the axons 199 207 Lung tissue from C57BL/6 mice calorie restricted by 2/3 and sacrificed 2hrs after the onset of calorie restriction. Lot batch = Source GEO sample is GSM4024 Last updated (according to GEO): May 28 2005 from brain 21 30 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202672 Last updated (according to GEO): Jun 20 2007 armstrong-mll HMEC-C Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120670 Last updated (according to GEO): May 14 2007 972 Structure of middle temporal gyrus infection 278 287 none Source GEO sample is GSM161906 Last updated (according to GEO): Feb 16 2007 SCN2.2 Sample 22 (Exp#3-12 hr) BL-C-TEST-15 on NHGRI-6.5k_b 901 Connective Tissue bladder Source GEO sample is GSM18628 Last updated (according to GEO): May 27 2005 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Source GEO sample is GSM28451 Last updated (according to GEO): May 27 2005 278 255 ischemic cardiomyopathy 901 Autoimmune Diseases The nose 94 101 Disease Source GEO sample is GSM176089 Last updated (according to GEO): Apr 09 2007 The epithelial cells 962 981 17 CN B of the postmortem brains 673 697 acute myeloid leukemia Source GEO sample is GSM227429 Last updated (according to GEO): Sep 12 2007 19 0 human frontal cortex D_U133A_48_nAcc Voxel J3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1458 Last updated (according to GEO): Nov 21 2005 Non-inner ear tissue at E9, replicate2 Down Syndrome 1000 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156699 Last updated (according to GEO): Jan 22 2007 brain 0 5 Plasma 861 660 mesenchymal stem cell 639 37 18 frontal cortex [BA4 AEOL 10150 control #3 Wild type P18 mouse visual cortex contralateral to monocular enucleation Source GEO sample is GSM97198 Last updated (according to GEO): Feb 17 2006 brain, Entorhinal Cortex: Sample12_e1_le1 861 Retina Prefrontal Cortex 0 16 Male 21.5 yr before antibody enrichment scan 1 (U133B) Healthy patient. Source GEO sample is GSM228564 Last updated (according to GEO): Sep 11 2007 1000 Coronary Arteriosclerosis 30 19 Solid tumor for hereditary non-polyposis colon cancer 340 380 1000 Coronary Arteriosclerosis Brain 861 none Source GEO sample is GSM123262 Last updated (according to GEO): Jul 26 2006 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3326 Last updated (according to GEO): Mar 21 2006 7 0 prostate no additional Source GEO sample is GSM199265 Last updated (according to GEO): Jun 08 2007 BPH-204 on UMich-10k 5 0 brain vulva_3 human frontal cortex Source GEO sample is GSM86991 Last updated (according to GEO): Feb 08 2006 forebrain 1133 1141 cy3:WKY treated w/ angtiotensin, biological rep 3g; cy5:pool of 6 WKY control rats Neoplasm 861 1000 Brain Brain 861 NHF10-hTERT_G1_C5_26582 embryonic hearts 1064 1079 GSE1147 ER +/LN+/Nevins46 on Affymetrix GeneChip Human Full Length Array HuGeneFL 3AJZ02082987A_TONGUE Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy, pathological hypertrophy, rat, heart failure, cardiomyopathy Source GEO sample is GSM12311 Last updated (according to GEO): May 28 2005 Replicate2_Voxel F7 Replicate1_Voxel C1 from the right forebrain 21 44 Proteoglycan 1000 Monocular deprivation right cortex, biological rep1 CHC MD-4 endometrium_9 103 85 of a past infection Spleen 0 5 brain, Left frontal Lobe: Extract16_le1 mouse brain contralateral control, biological rep2 Gene expression data from postmorten brain regions Source GEO sample is GSM146021 Last updated (according to GEO): Nov 20 2006 Lymphoblastoid Cell Line for Individual 8100.5 log phase to the viscera 501 515 861 jejunum Tumor__Leukemia_ALL-T_ALL_(19881)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A MA/MyJ_male_hypothalamus Medulla Oblongata 861 ALLSIL DMSO control 24h rep2 DMN-CtrHippo32d-1bAv2-s2 1000 Colon Gene expression data from SVGR2 glial cells. Source GEO sample is GSM189713 Last updated (according to GEO): May 16 2007 1000 Glioma Liver 1000 Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200614 Last updated (according to GEO): Jun 12 2007 CNS-RM_Ctr4h-1C-s2 1000 Brain with autism spectrum disorder 37 65 1000 Liver 308 294 8 uterine horns Gene array profiles of alcohol and aldehyde metabolizing enzymes in brains of C57BL/6 and DBA/2 mice. Kidney 1000 26 0 cerebral cortex wistar 3902 cerebral cortex sprague 3918 all cortical minus the frontal cortex, individual animal, 10 weeks old, male Sprague Dawley cerebral cortex file:p3918w Source GEO sample is GSM15155 Last updated (according to GEO): Oct 28 2005 DBA/2J Cerebellum B Expression profiling of laminectomized raphe at 28d in rats Source GEO sample is GSM41530 Last updated (according to GEO): May 27 2005 whole blood_101339 Replicate 3 of 3 (same genotype, same age). All replicates were individual animals. Source GEO sample is GSM138279 Last updated (according to GEO): Sep 29 2006 DLBC7 on Affymetrix GeneChip Human Full Length Array HuGeneFL COLON_HT29 on Affymetrix GeneChip Human Full Length Array HuGeneFL in the brain 150 162 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225716 Last updated (according to GEO): Nov 05 2007 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181061 Last updated (according to GEO): Jul 12 2007 NA19128 1000 Liver 861 Prostate carcinoma 861 Cerebral cortex 84 FC BA9 B salivarygland Source GEO sample is GSM18991 Last updated (according to GEO): Sep 25 2006 861 Mammary gland hippocampus 541 552 923 Congestive heart failure 123 96 into gastrocnemius muscle to 1037 of transitional epithelium 1012 26 0 Spinal cord [JunctionChip 1 Neoplasm 861 Fluid-percussion head injury 86 113 Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153762 Last updated (according to GEO): Jan 19 2007 brain, Left frontal Lobe: Extract12_le1 from liver 21 30 Neoplasm Metastasis 1000 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92328 Last updated (according to GEO): Jan 13 2006 putamen_10 Source GEO sample is GSM80596 Last updated (according to GEO): Mar 31 2006 1000 hindbrain Cerebellum 1000 Craniocerebral Trauma 861 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:325, Count:32 Corner- Avg:40125, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:4.084172,SFGene:All Background:Avg:636.91,Stdev:54.68,Max:958.1,Min:573.4 Noise:Avg:12.64,Stdev:5.61,Max:47.9,Min:9.0 RawQ:15.96 Keywords = ALL Source GEO sample is GSM3406 Last updated (according to GEO): May 27 2005 CurrentSmoker 75 Chromosomes 861 Date : 8/23/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 1.5 hrs post-injection Intervention : none Risk: estimated 20% increased risk for encephalopahy Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AF619 Source GEO sample is GSM12244 Last updated (according to GEO): May 28 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL4 for 30min Source GEO sample is GSM5626 Last updated (according to GEO): May 27 2005 KO_IL-6_100_rep3 ileum 1000 G30 neurons from cingulate cortex Source GEO sample is GSM63026 Last updated (according to GEO): Dec 01 2005 pfc_1049_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A olfactory epithelium 194 213 pfc_1015_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Brain 861 Nose 1000 NCI60.40_LABEL44EXTRACT43SUB3 Source GEO sample is GSM134194 Last updated (according to GEO): Aug 06 2007 13 0 Lung carcinoma 100333 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132487 Last updated (according to GEO): Feb 26 2007 928 Hyperinsulinism 23 CB A 5 0 brain Brain 1000 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153346 Last updated (according to GEO): Dec 27 2006 SCLC cell line SBC-2 1000 Cerebral cortex Primary Carcinoma 875 GCP.1 in the Frontal Cortex 57 77 808 799 cirrhosis Normal Source GEO sample is GSM176422 Last updated (according to GEO): Apr 09 2007 Fertilized egg replication 1 Keywords = preimplantation Keywords = development Source GEO sample is GSM14663 Last updated (according to GEO): May 28 2005 IGR-OV1 hgu95b Macrophage 14smi109 low gestational age Source GEO sample is GSM213082 Last updated (according to GEO): Jul 25 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11448 Last updated (according to GEO): May 28 2005 D3_TP-0_I U87 glioblastoma cell, parent Keywords = bioinformatics Keywords = gene expression Keywords = cancer Keywords = platelet-derived growth factor Keywords = sterol regulatory element binding protein Keywords = glioblastoma multiformae Keywords = microarray Source GEO sample is GSM34594 Last updated (according to GEO): May 27 2005 Mesenchymal Stem Cells 1000 865 Disorder of artery 78 66 Control blood Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:260, Count:32 Corner- Avg:36698, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:5.910607,SFGene:All Background:Avg:337.32,Stdev:12.49,Max:369.9,Min:316.0 Noise:Avg:8.88,Stdev:0.47,Max:10.3,Min:7.8 RawQ:12.15 Keywords = ALL Source GEO sample is GSM3502 Last updated (according to GEO): May 28 2005 Pharyngeal Mucosa 1 Normal plasma cells 50 61 I_U133A_89_Amy infection 34 42 normal 2266 Expression profiling of spinal cord section (T9) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM1327 Last updated (according to GEO): May 28 2005 Knockout 3 months old, female Source GEO sample is GSM154339 Last updated (according to GEO): Jan 09 2007 Brain 861 Abdominal aortic aneurysm obtained from surgery to correct. Source GEO sample is GSM170550 Last updated (according to GEO): Jul 26 2007 Disease Source GEO sample is GSM175919 Last updated (according to GEO): Apr 09 2007 Gene expression data from human colon tumor tissue Source GEO sample is GSM173321 Last updated (according to GEO): Apr 20 2007 gene expression data from melanoma xenografts following ILI with melphalan Source GEO sample is GSM213639 Last updated (according to GEO): Jul 27 2007 154 143 Spinal cords Nasal Epithelium 901 1000 Prostate carcinoma 1000 Heart failure Blood 1000 SCG_reference_pool Epithelium 861 Lymphoblastoid Cell Line for Individual 8141.3 log phase Normal__Uterus_UT_3 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene expression data from embryos at day 3.5. Source GEO sample is GSM176487 Last updated (according to GEO): Mar 19 2007 901 Structure of entorhinal cortex 56 37 with chronic malaria M_U133A_34_AnCg Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151985 Last updated (according to GEO): Feb 06 2007 KO_IL-6_400_rep3 CD28 beads 48.00 hr. T-Cell 861 Neoplasm Seminoma 861 Intestines 861 17 7 hippocampus Retina 1000 VDXGUYU_4088 Myometrium 48 Disease Melanoma metastatic cell line A375, biological rep6 (LeiFidler) nmda3 (Experiment Neuroprotection4- Run 14985) Treatment, type=timepoint, description=primary cortical neurons were treated for 30 min with NMDA 1mM, the agonist was then washed out and the cells were harvested 24h later, measurement=30.0 m Source GEO sample is GSM96751 Last updated (according to GEO): Feb 14 2006 VIIIcCA3_Signal on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B Primary Carcinoma 875 Ovarian_Tumor_Endometrioid_CHTN-OE-077 Gene expression data from a primary branch of the saphenous artery of 16 week old spontaneously hypertensive (SHR) rats Source GEO sample is GSM198863 Last updated (according to GEO): Nov 28 2007 NHF3-hTERT_sham_6h_C3_21247 mouse cerebral cortex 0 21 Caudal 1000 861 Malignant Neoplasms Wild type inbred mice Source GEO sample is GSM83005 Last updated (according to GEO): Nov 10 2005 Cytoskeleton 861 Duchenne muscular dystrophy (DMD) patient?s skeletal muscle sample 7 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68239 Last updated (according to GEO): Jul 07 2006 ISR21 Heart; embryonic_d14.5 wt heart Keywords = mouse gene expression database Source GEO sample is GSM29341 Last updated (according to GEO): May 27 2005 brain, cortex: 3dexp2_e1_le1 from liver 21 30 RNA sample 3 from motor neurons of wild type mice Treatment, type=double_round_amplification, description=T7-based two round of RNA amplification Source GEO sample is GSM92520 Last updated (according to GEO): Jan 13 2006 1000 Pancreas RNAtotSD_18, ZT6 Gene expression data from postmorten brain regions Source GEO sample is GSM146061 Last updated (according to GEO): Nov 20 2006 Endometrium-Normal 3 861 Blood Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 1580 blood 1931 1923 maxillary Endometrium/Ovary 15 Disease 29/OVX/P4/6h/UTX 129 Hoxa-10+/+ Trasnsformed Lymphocytes Bipolar Disorder 0 40 Large-scale analysis of the human transcriptome. Testis Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 205.42 Stdv: 7.66 Min: 192.17 Max: 217.78 Source GEO sample is GSM2824 Last updated (according to GEO): Mar 20 2006 Brain 861 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184712 Last updated (according to GEO): Apr 26 2007 in blood 16 23 Adenocarcinoma 861 Neoplasm 861 M_U133A_12_DLPFC Total RNA from brain sample of NR3B knockout mice at P5. Treatment, type=purify, measurement=0.0 years Source GEO sample is GSM113688 Last updated (according to GEO): Jun 09 2006 kidney 178 184 Gene expression data from whole brain infected mouse, day 3 Source GEO sample is GSM189612 Last updated (according to GEO): May 16 2007 of somatomotor cortex 21 41 LT-Hematopoietic stem cell isolated by flow cytometry Source GEO sample is GSM149527 Last updated (according to GEO): Apr 27 2007 Coronary artery 901 M_U133A_46_AnCg Total RNA extracted from the cerebellum of a stg-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144393 Last updated (according to GEO): Nov 14 2006 Two 90 minute exposures (3 hr recovery in between) to 1.0% isoflurane every day for 5 days, for a total of 10 exposures Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5115 Last updated (according to GEO): Mar 17 2006 1000 Heart failure jzo008-rp1-v5-u74av2-met Medulla 861 1000 Primary carcinoma of the liver cells Replicate2_Voxel F4 Gene expression data from 14B3 BMEL cells cultured under basal conditions. Source GEO sample is GSM160073 Last updated (according to GEO): Jul 11 2007 Mice sacrificed after swimming twice a day for 2.5 days. Keywords = exercise induced hypertrophy Source GEO sample is GSM2347 Last updated (according to GEO): May 27 2005 Lymphoblastoid Cell Line for Individual 8072.4 log phase 877 Down Syndrome 1000 Hippocampus ventral tegmental area] 900 923 Wild type P24 mouse visual cortex ipsilateral to monocular enucleation Source GEO sample is GSM97203 Last updated (according to GEO): Feb 17 2006 Blood 7 11 plasma cells 332 344 M_95Av2_2835_DLPFC_1_GS I_U133A_57_AnCg /3T3 fibroblasts 778 794 Wild type inbred mice Source GEO sample is GSM82943 Last updated (according to GEO): Nov 10 2005 Ovarian_Tumor_Serous_UM-OS-09 Whole blood 0 10 experiment VIII, BABE empty vector 1000 Spinal Cord Injuries 129S6/SvEvTac hypothalamus rep1 Brain 861 1000 Cerebral cortex Large Pre-BII cells 2b with mental retardation 241 263 1000 Spleen 5 0 brain Abdominal aorta 0 14 stomach_pyloric_4 Source GEO sample is GSM80816 Last updated (according to GEO): Mar 31 2006 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68351 Last updated (according to GEO): Jul 07 2006 for hereditary non-polyposis colon cancer 340 380 108 76 of a spinal cord contusion injury Gene expression data from SVG-A glial cells. Source GEO sample is GSM189709 Last updated (according to GEO): May 16 2007 1000 Hippocampus Lymphoblastoid Cell Line for Individual 8181.3 log phase trigeminal_ganglia_1 Source GEO sample is GSM80875 Last updated (according to GEO): Mar 31 2006 KT1006c_DT Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181228 Last updated (according to GEO): Jul 12 2007 WGACON-143 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12347 Last updated (according to GEO): May 28 2005 Recurrent Carcinoma 875 P46DR (dark reared) deprived visual cortex replicate 1 NCI60.52_LABEL56EXTRACT55SUB3 Source GEO sample is GSM134254 Last updated (according to GEO): Aug 06 2007 1000 ovarian neoplasm cy3:WKY control, biological rep 1g; cy5:pool of 6 WKY control rats Plasma 861 Carcinoma, Large Cell 884 plasma cells 50 61 Muscle Fibers 861 acute myeloid leukemia Source GEO sample is GSM227432 Last updated (according to GEO): Sep 12 2007 Muscle 861 Whole Brain 73 83 1000 frontal lobe CNS-SpinalC-28dAdult-1A-s2 14 0 Bladder tumours nidogen 1 1182 1190 861 Occipital lobe Plasma 861 Nasal Epithelium 901 Spleen vs CD40 Treated B cell 240min (set3) brain, Right Parietal Occipital: Extract75_le1 MGMH030401084Bembryoday6.5 928 Hyperinsulinism Testis 861 D2_SleepDep_ZT 0_2 Colon 1000 ovary Source GEO sample is GSM18622 Last updated (according to GEO): May 27 2005 MuscleRegen-ctx11d-2RLAv2-s2 14 0 spleen sprague2 none Source GEO sample is GSM123209 Last updated (according to GEO): Jul 26 2006 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection). Source GEO sample is GSM36444 Last updated (according to GEO): May 27 2005 cy3:SHR treated w/ nifedipine and then washed out, biological rep 5g; cy5:pool of 6 WKY control rats Interatrial septum 865 healthy subject Source GEO sample is GSM211147 Last updated (according to GEO): Sep 10 2007 1BJZ02081479a_Medulla_Oblongata PMN_control_360min_Patient2 CD3 beads 06.00 hr. T-Cell Adenocarcinoma 861 brain, unknown: 00HK_e1_le1 with some respiratory epithelium. 1039 1072 10 7 Left Wild type 8 wk old male FVB/NJ mouse hippocampus Source GEO sample is GSM107016 Last updated (according to GEO): Mar 05 2007 Mammary Neoplasms 1000 Dioxin treated MCF7 breast cancer cells [HG-U133B] Exp 1 GSE7191 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141304 Last updated (according to GEO): Oct 26 2006 GSE8077 CAD_replicate103 1000 Hippocampus brain, Superior Frontal Gyrus: Sample62_e1_le1 GM07022 Lymphoblastoid Cell Line for Individual 8013.3 log phase LungE185_022CAF6X_079.txt 901 Hepatocyte 24 0 human prostate PC3 tumors OAC:_36A8 Blood supply aspects 896 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201799 Last updated (according to GEO): Jun 20 2007 GM12874 The epithelial cells 962 981 Parkinson Disease 861 861 Neoplasm Metastasis Estrogen reduces brain injury after experimental cerebral ischemia in part through a genomic mechanism of action. Using DNA microarrays, we analyzed the genomic response of the brain to estradiol, and we identified a transcript, cocaine- and amphetamine-regulated transcript (CART), that is highly induced in the cerebral cortex by estradiol under ischemic conditions. Using in vitro and in vivo models of neural injury, we confirmed and characterized CART mRNA and protein up-regulation by estradiol in surviving neurons, and we demonstrated that i.v. administration of a rat CART peptide is protective against ischemic brain injury in vivo. We further demonstrated binding of cAMP response element (CRE)-binding protein to a CART promoter CRE site in ischemic brain and rapid activation by CART of ERK in primary cultured cortical neurons. The findings suggest that CART is an important player in estrogen-mediated neuroprotection and a potential therapeutic agent for stroke and other neurodegenerative diseases. Last Updated (by provider): Sep 22 2006 MGJZ030228005Bbone 7 0 prostate Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132522 Last updated (according to GEO): Feb 26 2007 Cerebellum Alzheimer's disease 1 Neoplasm 861 Wild type 8 wk old male 129S6/SvEvTac mouse periaqueductal gray Source GEO sample is GSM107029 Last updated (according to GEO): Mar 05 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11607 Last updated (according to GEO): May 28 2005 Primary tumor 19 32 Brain 861 Spleen 1000 Brain Injuries 901 861 Neoplasm Cortex_Control_rep9 (06SE471) labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156603 Last updated (according to GEO): Jan 22 2007 Transplant Series 10 , PrimaryTumor Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell 120min (set1) Epithelium 861 Seminoma 1000 861 Ovary Malignant neoplasm of thyroid 901 na Source GEO sample is GSM181263 Last updated (according to GEO): Apr 10 2007 1000 Brain brain, Left frontal Lobe: Extract27_le1 Compare the transcriptomes of Cx43 null and Cx43 siRNA treated cortical astrocytes with the transcriptome of the wildtype cortical astrocytes Source GEO sample is GSM200960 Last updated (according to GEO): Jun 19 2007 of somatomotor cortex 21 41 1000 Kidney NA Source GEO sample is GSM198916 Last updated (according to GEO): Jun 07 2007 NA18953 organs 496 502 na Source GEO sample is GSM181306 Last updated (according to GEO): Apr 10 2007 1000 Infection Acetaminophen 3hr Rat 3426 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 2hr after experimental mice received their last shock treatment. Source GEO sample is GSM4498 Last updated (according to GEO): May 27 2005 PBMCs-Type 1 Diabetes-IDDM30_T1D_4MO D_U133A_91_CB 861 Occipital lobe thymocytes_DN4_4 Sample 6 Treatment, type=pharmacogenomic_treatment, description=Neuronal cultures from cultures of rat cerebellar granule neurons will be treated with the chemical compound GW5074. Source GEO sample is GSM53244 Last updated (according to GEO): Jul 06 2005 hip_1066_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Brain 861 MGMH030312008Acortex VDXIGRU_219587 861 Cerebellum of mouse brain 9 23 21 7 adrenal medulla Cerebral cortex 1000 TEL-AML1-#11 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A of brain 955 962 Brain_MD_12_Medulloblastoma_Classic_D on Affymetrix GeneChip Human Full Length Array HuGeneFL from mouse colon 21 36 3AJZ02060502_Pancreas Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181194 Last updated (according to GEO): Jul 12 2007 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10020.gif Source GEO sample is GSM79865 Last updated (according to GEO): Sep 22 2006 Mouse ileum Germ-free_A_5553 plasma cells 332 344 pancreas 0 7 Infection 1000 Brain 861 PBMCs-Type 1 Diabetes-IDDM32_T1D_New total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Prostaglandin E2 labeled with Cy5- time course with repeats. Date GSE395 Last Updated: May 29 2005 Contributers: Robert Hsueh Angela Alexander Yun Anna Cao Jong-Woo Kim Rebecca Hart Zhen Yan Sun Young Lee Mi Sook Chang Sangdun Choi Joella Grossoehme Includes GDS316. Update date: Nov 18 2003. Dataset description GDS316: Temporal analysis of effects induced by 10 uM prostaglandin E2 in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. 14 0 pineal sprague1 Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 4550 left_liver_lobe 1000 Liver Gene expression data from UET-13TR-EWS/FLI1 cells incubated in the absence of tetracycline for 0 hours Source GEO sample is GSM214917 Last updated (according to GEO): Aug 02 2007 Whole Brain 62 72 Sample details: We analysed changes in gene expression in the dorsal telencephalon of forebrain-specific FGFR1 mutant mice. Gene expression was compared between the dorsal telencephalons of single E12.5 embryos of two genotypes: FGFR1 heterozygous (HET1,3,8) and homozygous mutants (HOM2,4,7) that were both heterozygous for the FoxG1 transcription factor, as Cre recombinase expression is driven off the endogenous FoxG1 locus in these animals (Hebert, J. M., Lin, M., Partanen, J., Rossant, J. and McConnell, S. K. (2003b). FGF signaling through FGFR1 is required for olfactory bulb morphogenesis. Development 130, 1101-11. & Hebert, J. M. and McConnell, S. K. (2000). Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures. Dev Biol 222, 296-306. Source GEO sample is GSM62850 Last updated (according to GEO): Aug 26 2005 Polyamide 1 treated LNCaP cells not stimulated with DHT, biological replicate 1 Source GEO sample is GSM187377 Last updated (according to GEO): May 04 2007 with acute measles 9 26 Skeletal bone 861 Bone Marrow 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145617 Last updated (according to GEO): Nov 20 2006 861 Acquired Immunodeficiency Syndrome 1933 tumor cells 1943 Cell Culture Exposure (1MAC Halo3) 1000 medulloblastoma Epithelium 861 with some respiratory epithelium. 1039 1072 Corticospinal Motor Neurons P3 1 Expression profiling by p53 status AML-32 on Affymetrix GeneChip Human Full Length Array HuGeneFL human frontal cortex Source GEO sample is GSM86945 Last updated (according to GEO): Feb 08 2006 Heart 1000 brain, frontal cortex: pADX PM LC_e1_le1 71 year old female 1000 Bipolar Disorder CAD_replicate83 Plasma 861 MOLT4 861 Cerebral cortex mouse brain ipsilateral control Source GEO sample is GSM149766 Last updated (according to GEO): Mar 15 2007 na Source GEO sample is GSM181287 Last updated (according to GEO): Apr 10 2007 +_4538_batch4 on NHGRI-6.7k NICM pool 1 (n=2) 944 Nail plate 1444 1429 of human cancer 901 frontal lobe Disorder of artery 865 Wild type 8 wk old male C57BL/6J mouse bed nucleus of the stria terminalis Source GEO sample is GSM106997 Last updated (according to GEO): Mar 05 2007 NA18990 B6 day 0, biological rep 3, tech rep 2 861 Asphyxia Heart 861 Gene expression data from colorectal adenoma. Source GEO sample is GSM215107 Last updated (according to GEO): Aug 02 2007 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210398 Last updated (according to GEO): Jul 16 2007 "Sample 89, BRCA1 mutation(7 months) age 50 erp no" on vantveer-oligo Spleen 0 5 966 Hippocampus HC53 CN A Wild type inbred mice Source GEO sample is GSM83014 Last updated (according to GEO): Nov 10 2005 CurrentSmoker 79 Gene expression data from human prostate tissue with 90 percent tumor content Source GEO sample is GSM119320 Last updated (according to GEO): Feb 23 2007 Ovarian_Tumor_Serous_CHTN-OS-093 Normal Source GEO sample is GSM176096 Last updated (according to GEO): Apr 09 2007 Saccule 0 6 olfactory epithelium 194 213 from the right forebrain 21 44 Infection 861 Gene expression data from postmorten brain regions Source GEO sample is GSM144975 Last updated (according to GEO): Nov 20 2006 Epithelium of bronchus 983 730 711 in the mammary gland C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 2hr after experimental mice received their last shock treatment. Source GEO sample is GSM4516 Last updated (according to GEO): May 27 2005 Wildtype saline, biological replicate 4 ALS gray matter 2 Familial Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. Moderate controlled cortical impact with pneumatic impactor, 6 m/s impact velocity and 1.5 mm deformation. 72h after surgery, a 4 mm diameter disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44504 Last updated (according to GEO): May 27 2005 Hyperdip>50-C15 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Meningioma Primary Grade 1. Source GEO sample is GSM108012 Last updated (according to GEO): Jun 06 2006 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153492 Last updated (according to GEO): Jan 11 2007 Epithelial Cells 1000 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7705.gif Source GEO sample is GSM79990 Last updated (according to GEO): Sep 22 2006 1000 Liver 129:3-2 hippocampus Femur 1000 15 0 human cerebellum in the metastasis 709 725 103 FC BA9 A post HCMV infection 69 87 Standard affymetrix protocol Source GEO sample is GSM119498 Last updated (according to GEO): Jul 31 2007 Transcriptional profiling was utilized to define the biological pathways of gingival epithelial cells modulated by co-culture with the oral commensal S. gordonii and the opportunistic commensal F. nucleatum. We used microarrays to detail the global programme of gene expression underlying infection and identified distinct classes of up- and down-regulated genes during this process. Last Updated (by provider): Jun 21 2007 Contributers: Richard J Lamont Yoshiaki Hasegawa Martin Handfield Jeffrey J Mans Henry V Baker 1000 Brain 2_hypothalamus_6hrs_sleep_#140 Wild type inbred mice Source GEO sample is GSM82962 Last updated (according to GEO): Nov 10 2005 Identification of a cluster of X-linked imprinted genes in mice. AML_21 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Mouse Kidney Female 1 Hippocampus 1984 15 month Old Normal Source GEO sample is GSM175899 Last updated (according to GEO): Apr 09 2007 NHF3-hTERT_M_C3_26573 HMVEC-L stimulated without LPS for 8 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114568 Last updated (according to GEO): Sep 20 2006 Heart 861 Nasal Epithelium 865 Nose 1000 96 FC BA9 A Y HID D040 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108635 Last updated (according to GEO): Aug 22 2006 7 frontal cortex 20 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225738 Last updated (according to GEO): Nov 02 2007 /progenitor cells 127 144 PGA-MPF-BALB-bleo-24h-2aAv2-s2 D_U133Plus_77_HC GSE5715 DBA/2J Saline treated, striatum, biological replicate 3 Source GEO sample is GSM187985 Last updated (according to GEO): Jun 14 2007 Brain 861 Day 1_H_-LIF_Bchip_rep1 91 from the bone marrow 72 PMN_LB_180min_Patient4 36 21 from whole brain 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114465 Last updated (according to GEO): Jun 16 2006 f2#292 versus pool Mouse Brain tissue 901 Coronary artery 2786 2778 28S rRNA 269802DC_4 Bone Marrow 1000 ALL B-cell43 on Affymetrix GeneChip Human Full Length Array HuGeneFL 27 7 Medial Temporal Gyrus brain, hippocampus: CH4_e1_le1 whole blood_101062 with Parkinson's disease 27 50 NCI60.17_LABEL21EXTRACT20SUB3 Source GEO sample is GSM134075 Last updated (according to GEO): Aug 06 2007 Tumor__Bladder_TCC_B_0004 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene expression data from postmorten brain regions Source GEO sample is GSM144894 Last updated (according to GEO): Nov 20 2006 CNS-SMTC_Ctr28d-1A-s2 GSE1397 human caudate nucleus Source GEO sample is GSM86886 Last updated (according to GEO): Feb 08 2006 9 0 Blood Test brain, adrenal medulla: Sample#A3 (Exp pt 3)_e1_le1 f2#329 versus pool Mouse Brain tissue 5 0 brain Bladder sample 533-1 Muscle 861 Our recent study indicated that polyglutamine-expanded ataxin-7-Q75 induced apoptotic death of cultured cerebellar neurons by downregulating Bcl-x(L) expression and activating mitochondrial apoptotic cascade. Mutant polyglutamine-expanded proteins are believed to impair the proteolytic function of ubiquitin-proteasome system by sequestering components of proteasomes. Proteasome degradation of IkappaBalpha permits nuclear translocation of NF-kappaB and is required for continuous NF-kappaB activity, which supports the survival of cultured cerebellar neurons by inducing Bcl-x(L) expression. Thus, we tested the hypothesis that mutant ataxin-7-Q75 causes proteasome dysfunction and impairs NF-kappaB activity, leading to reduced Bcl-x(L) expression, caspase activation and cerebellar neuronal death. EMSA assays indicate that DNA-binding activity of NF-kappaB was significantly decreased in cerebellar neurons expressing ataxin-7-Q75. Similar to mutant ataxin-7-Q75, NF-kappaB inhibitor APEQ induced cerebellar neuronal death by decreasing Bcl-x(L) expression and activating caspase-9. Mutant ataxin-7-Q75 inhibited the proteolytic activity of proteasomes in cerebellar neurons. Proteasome inhibitor MG132 also caused cerebellar neuronal death by decreasing Bcl-x(L) expression and activating caspase-9. Both ataxin-7-Q75 and MG132 caused the cytosolic accumulation of IkappaBalpha in cerebellar neurons. Mutant ataxin-7-Q75 or MG132 increased the cytosolic level of NF-kappaB p65 and decreased the nuclear NF-kappaB p65 level. Our study provides the evidence that polyglutamine-expanded ataxin-7-Q75 decreases nuclear translocation of NF-kappaB p65 and impairs NF-kappaB activity by inhibiting proteasome activity of cerebellar neurons. 861 Brain A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism Source GEO sample is GSM5987 Last updated (according to GEO): Nov 21 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145183 Last updated (according to GEO): Nov 20 2006 Frontal cortex 254 267 Myocardial Infarction 1000 none Source GEO sample is GSM210323 Last updated (according to GEO): Jul 16 2007 Nose 1000 19 0 amygdala wistar 3942 KidP2_0228ACJ9_107.txt Plasma 861 861 Dorsum of tongue Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12511.gif Source GEO sample is GSM79923 Last updated (according to GEO): Sep 22 2006 M14 hgu95a db/m 8wk 2 41 28 in mouse brain UACC-257_CL10021_Prostate on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Hippocampus Cells captured via Arcturus LCM system, amplified (RiboAmp, 2 rounds) and labeled (Enzo) for hybridizaton to Affymetrix MG_U74Av2 arrays, using manufacturers protocols in each step. Source GEO sample is GSM6204 Last updated (according to GEO): Mar 17 2006 Striat_022ZAFBQ_004.txt Keywords = Heart 505 521 Sample 119 on vantveer-oligo plasma cells 332 344 ramaswamy-cancer Sham 5 Blood 1000 865 Disorder of artery Cerebral cortex 1000 861 Encephalitis HapMap CEU_parent Male Source GEO sample is GSM159568 Last updated (according to GEO): Feb 01 2007 Cerebellum Alzheimer's disease 7 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202682 Last updated (according to GEO): Jun 20 2007 Kainate-neocortex, biological rep3 4 0 Ovary Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13156.gif Source GEO sample is GSM79728 Last updated (according to GEO): Sep 22 2006 NCI60.47_LABEL51EXTRACT50SUB3 Source GEO sample is GSM134229 Last updated (according to GEO): Aug 06 2007 Congenital Abnormality 853 between arteries 829 844 VDXGUYU_4074 901 Ciliary Body Spleen 0 5 brain_DLPFC_bipolar B_mr430 H129 CN B Spleen vs Untreated B cell Time 0 (set25) Mucous Membrane 861 861 Spinal Cord kidney 37 43 RENAL_ACHN on Affymetrix GeneChip Human Full Length Array HuGeneFL Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep1 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211307 Last updated (according to GEO): Jul 18 2007 of the postmortem brains 676 700 1000 Prostate 12 frontal Lobe 23 Structure of olfactory bulb 1000 1000 Liver Expression profiling of spinal cord section (T9) extracted from rats 72h following laminectomy (sham) Source GEO sample is GSM31508 Last updated (according to GEO): May 27 2005 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225755 Last updated (according to GEO): Nov 02 2007 GBM Treatment, type=remove Source GEO sample is GSM99469 Last updated (according to GEO): Apr 21 2006 51 37 without malaria HairAnag_022TACIB_038.txt 21 7 adrenal medulla Primary small cell lung carcinoma 3105 861 Epithelium 3 0 Lung brain_Down_syndrome_sampleid_jg1739 Male C57Bl/6 mice (6 week old) were sham-operated and olfactory epithelium tissue collected 5 days post-operation. Total RNA was extracted from the olfactory epithelium tissue. Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol. Keywords = olfaction Keywords = neurogenesis Keywords = apoptosis Keywords = gene silencing Keywords = microarray, transcription factor Source GEO sample is GSM45679 Last updated (according to GEO): Oct 28 2005 40 35 stroke 1000 Cerebellum Human Hypothalamus Female 2 /NJ pituitary gland rep2 3 26 861 Cerebral cortex D_U133A_62_CB This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis. Stembase Experiment ID: E189 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189 SCGP Sample ID: S231 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_189 Short description: RNA isolated from first passage retinal sphere cells. Estimated purity: > 90% RNA concentration: > 30.0 ng Num cells for RNA prep: ~160,000 Sample volume: 5.0 ul Source GEO sample is GSM87191 Last updated (according to GEO): Jan 19 2006 of cerebella 88 99 1000 Brain Squamous cell carcinoma 884 Cerebral cortex 1000 Category: Serum-response Subcategory: Fibroblasts Scanning Software: unknown Software version: unknown Lot batch = 417 Source GEO sample is GSM2166 Last updated (according to GEO): Nov 21 2005 15 7 brainstem brain 0 5 738 727 in the skin outer medulla 31 43 GM19160 Comparison of gene expression in SVG-A glial cells and SVGR2 glial cells Female 65.9 yr before antibody enrichment scan 1 (U133A) Nervous System; Day 2 postnatal whole brain Keywords = mouse gene expression database Source GEO sample is GSM29414 Last updated (according to GEO): May 27 2005 129 120 of keratin Lymphoblastoid Cell Line for Individual 8070.3 log phase HMEC X BC1257 Osteoblasts 1000 brain 0 5 Cochlea 0 6 36 21 from whole brain Brain 861 cerebral cortex 7 21 Lymphoblastic Leukemia 901 VDXRHU_1721 Sensitized on days 0 and 3 with ragweed pollen protein and alum, challenged intratrecheally on days 10 and 17 with ragweed pollen protein and sacrificed after 72h. Lot batch = Source GEO sample is GSM1272 Last updated (according to GEO): May 28 2005 Muscle Source GEO sample is GSM4311 Last updated (according to GEO): May 27 2005 1100 1077 of Medulloblastoma - 8 - We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201733 Last updated (according to GEO): Jun 20 2007 brain, cerebral cortex: Co 7/8_le1 of the striatum 256 270 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113923 Last updated (according to GEO): Jun 16 2006 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202683 Last updated (according to GEO): Jun 20 2007 Lymphoblastoid Cell Line for Individual 8027.4 log phase NHF3-hTERT_sham_6h_C5_21395 MDA Mb231 1h + 10 nM Cxcl12 2 Treated 861 Brain human cerebellum Source GEO sample is GSM87075 Last updated (according to GEO): Feb 08 2006 78 73 rectum of somatomotor cortex 21 41 human cerebellum Source GEO sample is GSM87171 Last updated (according to GEO): Feb 08 2006 Expression profiling of spinal cord section (T10) extracted from rats 30m following mild injury Source GEO sample is GSM31326 Last updated (according to GEO): May 27 2005 5 0 brain Brain 861 Backskin_WT_P6_rep5 parietal_lobe_8 Neoplasm 861 Large-scale analysis of the mouse transcriptome. Snout epidermis, vibrissa epidermal region C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 285.27 Stdv: 8.04 Min: 273.58 Max: 300.96 Source GEO sample is GSM2955 Last updated (according to GEO): Mar 20 2006 861 Brain Htt-N171 HD in vitro Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211350 Last updated (according to GEO): Jul 18 2007 Gene expression data from rat metanephric mesenchymes cultured for 3 days in the presence of the ANX fraction Source GEO sample is GSM126222 Last updated (according to GEO): Dec 08 2006 Control total RNA was pooled from the kidney of five normal BALB/c mice. Total RNA was extracted from the kidney of BALB/c mice injected with anti-GBM antibody for 1 day. Source GEO sample is GSM15088 Last updated (according to GEO): May 28 2005 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188690 Last updated (according to GEO): Jun 06 2007 Subcutaneous Tissue 913 Neuroglia 901 1000 ovarian neoplasm metanephric mesenchyme, LIF, 1 day, biological rep2 brain 0 5 Left 1000 Nose 1000 We analyzed the lumbar spinal cord tract of transplanted nmd mice (n=3), untransplanted nmd mice (n=3) and wild-type mice (n=3) (all mice are of male gender). The latter groups underwent surgical procedure with vehicle. The surgical procedure and spinal cord-derived neural stem cell transplantation (intratechal injection) were done at P1 and the animals were sacrificed at 6 weeks of age. Frozen tissue was stored at -80°C. Total RNA was purified from tissue, using the EUROZol Kit (EuroClone Ltd., United Kingdom) following the manufacturer?s instructions. Total RNA (5 ug) was reverse-transcribed with a cDNA synthesis kit in the presence of SuperScript II RT (Invitrogen-Life Technologies, Inc.) and an oligo dT-T7 primer (Affymetrix Inc., Santa Clara, CA). After phenol/chloroform extraction and ethanol precipitation, the cDNA pellet was air-dried and re-suspended in 12 uL of diethyl pyrocarbonate-treated water and quantified by spectrophotometer measurement. An aliquot of each sample was conserved for gel electrophoresis and for inspection of RNA quality (i.e., 28S:18S RNA ratio). 10 ul was used for the IVT (In Vitro Transcription) amplification reaction, in the presence of biotinylated nucleotides (Enzo Biochem Inc.). Labeled cRNA (15 ug) was fragmented by incubation at 94°C for 35 minutes in fragmentation buffer (GeneChip Sample Cleanup, Qiagen) and the fragmented cRNA was then hybridized competitively against the Affymetrix 430 2.0 Array oligonucleotide array. Hybridization occurred at 47°C overnight. The arrays were scanned using a GeneArray 2500 Scanner (Affymetrix) and analyzed using MicroArray Suite 5.0 (Affymetrix). All experiments were validated after direct measures of cRNA quality: 5':3' ratios for beta-actin and for GAPDH (determined from Affymetrix chip hybridization analysis) are indirect indicators of overall RNA preservation. The default parameters were used for the statistical algorithm and for probe set scaling. The target intensity was set to 1,000 to normalize expression levels across all samples. Source GEO sample is GSM67523 Last updated (according to GEO): Dec 21 2005 Brain 861 as a sole abnormality 151 171 Spleen 1000 Primary Neoplasm 1000 Epithelium of bronchus 983 861 Hepatocyte 17 0 Spinal cord injury Osteoblasts 1000 f2#163 versus pool Mouse Brain tissue Ta gr2 tumour Source GEO sample is GSM2485 Last updated (according to GEO): May 27 2005 C57BL-6J mice were given intratracheal saline control and sacrificed at 24 hrs. Source GEO sample is GSM4167 Last updated (according to GEO): May 27 2005 Kidney 1000 NCI60.10_LABEL13EXTRACT12SUB3 Source GEO sample is GSM134044 Last updated (according to GEO): Aug 06 2007 duodenum 17 24 This is the mutant littermate at postnatal day 1 pooled 4 animals Lot batch = Source GEO sample is GSM4069 Last updated (according to GEO): May 28 2005 NCI60.4_LABEL7EXTRACT6SUB3 Source GEO sample is GSM134010 Last updated (according to GEO): Aug 06 2007 Coronary heart disease 913 Summary: Brain trauma is a major cause of morbidity and mortality, both in adult and pediatric populations. Much of the functional deficit derives from delayed cell death resulting from induction of neurotoxic factors that overwhelm endogenous neuroprotective responses. Hypothesis: Gene expression profiling across species and models may help identify candidate molecular pathways induced by brain injury, some of which may provide novel targets for therapeutic intervention. Specific Aim: To identify the potential molecular mechanisms underlying such delayed responses, we compared gene expression patterns using high-density oligonucleotide arrays at 4, 8, 24 and 72 hours after moderate levels of lateral fluid percussion-induced brain injury in rats and lateral controlled cortical impact injury in mice. Last Updated (by provider): Contributers: JoAnne Natale Includes GDS2851. Update date: Aug 20 2007. Dataset description GDS2851: Analysis of brain at various time points up to 21 days following lateral fluid percussion-induced brain injury. Delayed cell death following trauma results in brain damage. Results provide insight into the mechanisms underlying brain damage after traumatic injury.. Parkinson Disease 1000 KT15_DT Mouse Liver Male 2 (technical replicate) 1000 Brain 1000 Spleen Two 90 minute exposures (3 hr recovery in between) to 0.8% halothane every day for 2.5 days, for a total of 5 exposures Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5113 Last updated (according to GEO): May 27 2005 7 0 prostate Melanoma xenograft, MEA3_Lung_A (LeiFidler) 861 Cerebral cortex Anterior nares 1000 861 Blood stria terminalis 901 91 from the bone marrow 72 Blood 861 Mouse Liver AIN Diet 8hr 1mg/kg As Injection, biological replicate E Plasma 861 786-0 hgu95c cingulate cortex 1000 Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.71 Subject: 3023 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39058 Last updated (according to GEO): May 27 2005 Replicate1_Voxel G7 121 114 synaptic 1000 Left CNS-SpinalCmod-Adult-7d-4A-s2 50 43 jejunum autism 252 258 hearts 35 40 Whole Brain 62 72 304 280 alcoholic cardiomyopathy Neoplasm 1000 processed in batch 5 Source GEO sample is GSM90419 Last updated (according to GEO): Mar 20 2006 f2#180 versus pool Mouse Brain tissue Molecular evidence for two-stage learning and partial laterality in eyeblink conditioning of mice. Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14345.gif Source GEO sample is GSM79698 Last updated (according to GEO): Sep 22 2006 861 Neoplasm 102 CN B Nrl ko samples were compared to wt at postnatal 2. Source GEO sample is GSM227453 Last updated (according to GEO): Sep 07 2007 7 0 prostate Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200622 Last updated (according to GEO): Jun 12 2007 Nic 2 (Experiment Nic 15 - Run 23145) Treatment, type=timepoint, description=primary cortical neurons were treated with nicotine 10 microMolar for 15 minutes, medium was then changed to remove the agonist and cells were harvested 45 min later, measurement=15.0 m Source GEO sample is GSM96720 Last updated (according to GEO): Feb 14 2006 NCI60.5_LABEL8EXTRACT7SUB3 Source GEO sample is GSM134018 Last updated (according to GEO): Aug 06 2007 861 Brain Frontal Cortex Source GEO sample is GSM107942 Last updated (according to GEO): Jun 06 2006 medial motoneurons (MMN) 9 Gene expression data from liver Source GEO sample is GSM243370 Last updated (according to GEO): Nov 16 2007 Gene expression data from the right forebrain of C57BL mouse received no treatment for twelve weeks. Source GEO sample is GSM148683 Last updated (according to GEO): Dec 12 2006 Expression profiling of spinal cord section (T10) extracted from rats 14d following mild injury Source GEO sample is GSM31309 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145094 Last updated (according to GEO): Nov 20 2006 Normal Source GEO sample is GSM176031 Last updated (according to GEO): Apr 09 2007 PGA_PA-N_300 Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92279 Last updated (according to GEO): Jan 13 2006 M7TW00121353 Brain 861 mammary epithelial cells transduced with BABE empty vector Source GEO sample is GSM5167 Last updated (according to GEO): May 27 2005 Brain_Melanotransferrin Knockout_affs275-1098 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184732 Last updated (according to GEO): Apr 26 2007 total RNA from biosource CC#2S Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92482 Last updated (according to GEO): Jan 13 2006 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:480, Count:32 Corner- Avg:33296, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:8.668220,SFGene:All Background:Avg:772.79,Stdev:31.84,Max:891.5,Min:725.7 Noise:Avg:22.39,Stdev:2.11,Max:30.3,Min:19.6 RawQ:22.98 Keywords = ALL Source GEO sample is GSM3431 Last updated (according to GEO): May 27 2005 PGA_MI_nilv_8w_311 EWSR1-POU5F1 chimera, Undifferentiated bone tumor GST6 rad001 6d, biological rep3 f2#201 versus pool Mouse Brain tissue Liver Test (Blinded) Sample Source GEO sample is GSM130106 Last updated (according to GEO): Sep 18 2007 Ld1b nasal epithelial cells 28 49 Occipital lobe 861 Pre-BI cells 8 1000 Amygdaloid structure Brain_MD_54_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL Subject code A27 865 Disorder of artery Squamous cell carcinoma 923 329 306 valvular cardiomyopathy in cigulate cortex 26 44 Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Globin reduction was performed according to the Affymetrix technical note. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM63224 Last updated (according to GEO): Apr 20 2007 252_2 Small cell carcinoma of lung 1000 CNS-SpinalCsev-Adult-24h-4C-s2 10 0 whole brain Spinal Cord 1000 Skeletal bone 861 913 Mitral Valve CAD_replicate1 human frontal cortex Source GEO sample is GSM87024 Last updated (according to GEO): Feb 08 2006 Hormones 861 861 Cerebral cortex brain, cerebral cortex: Rat_02-57_VHL_Lipska_e1_le1 Diaphragm 28 Day mdx rep 1 HC80 FC BA4 B hip_1069_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A brain, hippocampus: ADX AM Hip_e1_le1 Plasma 861 of the normal mucosa 7 26 /2J Olfactory Bulb A 3 22 10 7 Left umbilical cord_bpd: 9F Biopsy of the normal mucosa of the colon from patient #23 The ability of dendritic cells (DCs) to activate immunity is linked to their maturation status. In prior studies we have shown that selective antibody-mediated blockade of inhibitory FcgRIIB receptor on human DCs in the presence of activating immunoglobulin (Ig) ligands leads to DC maturation and enhanced immunity to antibody-coated tumor cells. Here we show that Fcg receptor (FcgR) mediated activation of human monocytes and monocyte-derived DCs is associated with a distinct gene expression pattern, including several inflammation associated chemokines as well as type 1 interferon (IFN) response genes including the activation of signal transducer and activator of transcription 1 (STAT1). Last Updated (by provider): May 16 2007 PMN_control_360min_Patient6 COID-4385-A301-5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 91 from the bone marrow 72 Spleen 1000 Array representing the response of Human foreskin fibroblasts at 18h post HCMV infection Source GEO sample is GSM10351 Last updated (according to GEO): May 27 2005 Blood Test (Blinded) Sample Source GEO sample is GSM129943 Last updated (according to GEO): Sep 18 2007 Epithelial Cells 1000 1000 Muscle 861 Cerebellum f2#234 versus pool Mouse Brain tissue nasal epithelial cells 28 49 mouse brains 187 198 12 0 ovarian tumor Expression profiling of spinal cord section (T9) extracted from rats 28d following moderate injury Source GEO sample is GSM31547 Last updated (according to GEO): May 27 2005 Disease Source GEO sample is GSM176304 Last updated (according to GEO): Apr 09 2007 Head and neck cancer Source GEO sample is GSM155716 Last updated (according to GEO): Apr 24 2007 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195293 Last updated (according to GEO): Sep 13 2007 D_U133A_80_Amy 36 21 from mouse brain Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11580 Last updated (according to GEO): May 28 2005 Analysis of prefrontal cortex from 3 biological replicates of C57BL/6J mice at four Zeitgeber Times (ZT 3, 9, 15, and 21). Source GEO sample is GSM240425 Last updated (according to GEO): Oct 30 2007 brain, cerebral cortex: Co4 (2/5CG)_le1 f2#76 versus pool Mouse Brain tissue human cerebellum Source GEO sample is GSM87127 Last updated (according to GEO): Feb 08 2006 of the most anterior dorsal root ganglia 23 62 Large-scale analysis of the mouse transcriptome. Gall bladder C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 241.90 Stdv: 8.17 Min: 228.80 Max: 256.08 Source GEO sample is GSM2927 Last updated (according to GEO): Mar 20 2006 hypothalamus la hypo 1BJZ02081479b_Medulla_Oblongata rat model organism with depression left untreated or treated with reserpine Source GEO sample is GSM247182 Last updated (according to GEO): Dec 11 2007 901 Bone Marrow with acute measles 20 37 UterViDi_0225ACHT_112a.txt cerebellum 7 16 861 Spinal Cord 1092 with the bone 1080 4 0 Brain 1000 Coronary Arteriosclerosis 7 frontal cortex 20 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213492 Last updated (according to GEO): Jul 31 2007 Brain 861 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188719 Last updated (according to GEO): Jun 06 2007 861 Cancer of Neck comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247382 Last updated (according to GEO): Dec 11 2007 Hyperdip>50-#7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Osteoblasts 1000 Papillary thyroid carcinoma 1000 Nerve Tissue 884 1693 1668 in the contralateral knee 861 Ventral Tegmental Area 858 Mesodermal cell Cardiac 523 530 1000 Kidney 10 7 Left 901 Mammary gland 52 CN B Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3288 Last updated (according to GEO): Mar 21 2006 1000 Nervous system structure Spleen 0 5 Egr1/Egr3 double knockout #1 Source GEO sample is GSM107467 Last updated (according to GEO): May 01 2006 (cortex 19 25 Laser capture lung cancer cells Source GEO sample is GSM191053 Last updated (according to GEO): May 25 2007 913 Coronary heart disease Compare the transcriptomes of Cx43 null and Cx43 siRNA treated cortical astrocytes with the transcriptome of the wildtype cortical astrocytes Source GEO sample is GSM202233 Last updated (according to GEO): Jun 19 2007 LPS, 30 min, Rep_3 Ovum 861 ci_NY37 15 0 human cerebellum 1000 Mammary gland To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18478 Last updated (according to GEO): May 27 2005 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18921.gif Source GEO sample is GSM84189 Last updated (according to GEO): Sep 22 2006 prostate Source GEO sample is GSM203382 Last updated (according to GEO): Jun 21 2007 1000 Endometrium 7 frontal cortex 20 HA96-112A GBM Treatment, type=remove Source GEO sample is GSM99464 Last updated (according to GEO): Apr 21 2006 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 4 hours after lights on. Original RNA code = LC4A. Source GEO sample is GSM227368 Last updated (according to GEO): Sep 10 2007 83 69 Normal Prostate 861 Cerebral cortex 858 Mesodermal cell Brain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145153 Last updated (according to GEO): Nov 20 2006 861 Neoplasm Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174523 Last updated (according to GEO): Mar 14 2007 119 76 with sporadic amyotrophic lateral sclerosis HeLa CD4+ cells were transfected with an epitope-tagged eTat plasmid and selected with hygromycin. Cells were treated with nocodazole and collected @6 hours. Source GEO sample is GSM8706 Last updated (according to GEO): May 27 2005 0 Human Cortex 11 mouse cerebral cortex 0 21 Analysis of prefrontal cortex from 3 biological replicates of C57BL/6J mice at four Zeitgeber Times (ZT 3, 9, 15, and 21). Source GEO sample is GSM240424 Last updated (according to GEO): Oct 30 2007 Epithelium 861 NoCAD_replicate29 Cerebral cortex 861 CHIPEXP_NAME: 230_2_050531tpj_19h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Vehicle_Control TREAT_TOX_MECHANISM1: Liver_Non_Toxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0 SAMPLING_TIME: 72 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197626 Last updated (according to GEO): Jun 01 2007 Brain 1000 Inflammatory myopathy specimen GEIM7 ALS model Source GEO sample is GSM75469 Last updated (according to GEO): Mar 06 2006 1000 Neuronal Ceroid-Lipofuscinosis I_U133A_66_AnCg CNS-SCsev_InjA28d-4C-s2 Normal Source GEO sample is GSM176124 Last updated (according to GEO): Apr 09 2007 106 95 from kidneys FL-10;CD19+ cy5:SHR control, biological rep 3r; cy3:pool of 6 WKY control rats GBM Treatment, type=remove Source GEO sample is GSM99580 Last updated (according to GEO): Apr 21 2006 NA Source GEO sample is GSM198906 Last updated (according to GEO): Jun 07 2007 Liver 0 4 PBMCs-Healthy-INF301_Healthy 1000 Cerebral cortex 92 38 of nicotinic acetylcholine receptor subunit mutant mice Macrophage 14smi055 AD control Treatment, type=dissect Source GEO sample is GSM119656 Last updated (according to GEO): Jul 10 2006 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16311.gif Source GEO sample is GSM81524 Last updated (according to GEO): Sep 22 2006 Brain 1000 Bone Marrow 1000 MO_control_180min_Patient5 Kidney 861 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:239, Count:32 Corner- Avg:38822, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:7.316926,SFGene:All Background:Avg:371.14,Stdev:5.69,Max:385.0,Min:359.1 Noise:Avg:10.15,Stdev:0.33,Max:11.2,Min:9.4 RawQ:12.76 Keywords = ALL Source GEO sample is GSM3494 Last updated (according to GEO): May 28 2005 GM10856 Gap Junction 0 11 Laser captured visceral sensory neurons. Source GEO sample is GSM63660 Last updated (according to GEO): Dec 21 2005 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118330 Last updated (according to GEO): Jul 11 2006 Spleen vs ELC Treated B cell V5-P283 Untreated versus treated (bortezomib), untranformed MCF10A and Transformed (see Adler et al, Nature Gen. 2006) Source GEO sample is GSM120228 Last updated (according to GEO): Jul 20 2006 Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174507 Last updated (according to GEO): Mar 14 2007 COLON 18 22 PCA17_localized prostate cancer 0 30 medial motoneurons (MMN) 16 ExpressionLevel:GXN-00536 on Affymetrix GeneChip Mouse Expression Array 430A and Mouse Genome 430A 2.0 Array CNS-SpinalC-conAdult-T0-1B-s2 Medulla 861 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118562 Last updated (according to GEO): Jul 11 2006 1000 Descending colon frontal lobe 901 Primary Neoplasm 1000 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/9630.gif Source GEO sample is GSM79880 Last updated (according to GEO): Sep 22 2006 Spleen 0 5 Gene expression data from brain of adult rats Source GEO sample is GSM101016 Last updated (according to GEO): Feb 20 2007 3 0 Lung Gene expression data from mouse primary visual cortex Source GEO sample is GSM101714 Last updated (according to GEO): Mar 27 2006 The nose 94 101 VDXGUYU_4008 861 Blood Parkinson Disease 1000 Myocardial Infarction 1000 Female9, Respiratory RNA_Nasal respiratory epithelium_Tissue was preserved in RNA later and collected from nose Structure of olfactory bulb 1000 "12 hr Hela Double Thymidine, exp3" AcB61 #12249620 Anterior nares 1000 1000 Brain NCI60.6_LABEL9EXTRACT8SUB3 Source GEO sample is GSM134021 Last updated (according to GEO): Aug 06 2007 to UVC-induced DNA damage 210 234 HMVEC-L stimulated without LPS for 24 hours c24R1 Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_4 months_replicate 1 0 Prefrontal cortex 16 LivReSham6h22EAFIH_181.txt B220Low sIgM+ immature B cells sorted out of mouse bone marrow, sort no. 2 Source GEO sample is GSM639 Last updated (according to GEO): May 27 2005 Normal__Prostate_PR_5 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A cerebral_cortex_7 spinal cord injury 141 158 Liver (HBV+, HK64) 0029_1250_H95A2_KF0129_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A brain, cerebral cortex: Nic 2_le1 KPeterson-Met-21G110-s2 Nasal Epithelium 901 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211320 Last updated (according to GEO): Jul 18 2007 brain 0 5 Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 8385 blood 1000 Rectum Brain 861 Total RNA from brain sample of NR3B knockout mice at P0. Treatment, type=purify, measurement=0.0 years Source GEO sample is GSM113682 Last updated (according to GEO): Jun 09 2006 GM18872 Pancreas at e14.5, Chip A, rep 2 trachea Source GEO sample is GSM18834 Last updated (according to GEO): Sep 25 2006 Stem cells 901 of mouse brain 9 23 brain 0 5 Wild type inbred mice Source GEO sample is GSM83031 Last updated (according to GEO): Nov 10 2005 Brain 861 Neurosphere cultures were established from individually isolated E 14.5 forebrains of mouse embryos that carry a bcl2 transgene. Single-cell suspensions were prepared, seeded at 1x105 cells/ml and treated for two days with 150 nM Trichostatin A (TSA), 500 nM 5-Aza-2?-deoxycytidine (AzaC) or both compounds, or left untreated. Two independent experiments were performed. Source GEO sample is GSM8898 Last updated (according to GEO): Oct 28 2005 861 Mammary gland 375 358 in small intestine Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118541 Last updated (according to GEO): Jul 11 2006 1226 1218 of tumors no additional Source GEO sample is GSM199198 Last updated (according to GEO): Jun 08 2007 cerebral cortex 7 21 Nucleus Accumbends, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231031 Last updated (according to GEO): Sep 26 2007 Normal__Cerebellum_Brain_Ncer_S-51 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A nucleus accumbens_shell sprague1 Half-moon-shaped NAc shell samples were obtained with a 12 gauge punch of the remaining ventromedial shell tissue, pool of 5 animals, 20 weeks old, male Sprague Dawley nucleus accumbens shell file:R3MH01110601 Source GEO sample is GSM15225 Last updated (according to GEO): Oct 28 2005 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141302 Last updated (according to GEO): Oct 26 2006 Wild type 8 wk old male DBA/2J mouse bed nucleus of the stria terminalis Source GEO sample is GSM107002 Last updated (according to GEO): Mar 05 2007 Normal Source GEO sample is GSM175822 Last updated (according to GEO): Apr 09 2007 865 Disorder of artery brain 0 5 913 Spinal Injuries GIN-Hippocampus replicate2 D_U133A_51_nAcc Keywords = Infectious diseases 1133 1163 brain, Right Parietal Lobe: Extract72_le1 ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes(delta-inlAB)_B_5552 Source GEO sample is GSM161579 Last updated (according to GEO): Apr 23 2007 frontal cortex wistar ky 3927 whole tissue, individual animal, 10 weeks old, male Wistar Kyoto frontal cortex file:p3927w Source GEO sample is GSM15164 Last updated (according to GEO): Oct 28 2005 430A2_2045_40_KO_neuropath_midbrain Source GEO sample is GSM242698 Last updated (according to GEO): Nov 15 2007 PGA-HMO-Obese-3aUA-s2 5 0 Uterus Cerebral cortex 861 Prosencephalon 1000 Nrl ko P10 replicate 3 olfactory.bulb.2 OVCAR-8 hgu95a 923 Organ of Corti Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13407.gif Source GEO sample is GSM79727 Last updated (according to GEO): Sep 22 2006 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68117 Last updated (according to GEO): Jul 07 2006 lung.3 #17 (isolate 36 low serum media control) Brain 1000 ISR17-Fv2E-PERK AP20187 8hr1 RNA from an 2nm AP20187 treated (8hr) Fv2E-PERK expressing fibroblast cell line in an eIF2 alpha SS (wildtype), PERK-/- background. AP20187 activates the kinase activity of the Fv2E-PERK chimera. The PERK-/- background was used in order to obtain a cell line that expressed high levels of the Fv2E-PERK transgene. (We were unable to obtain clones with high levels of expression in wildtype cells.) The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules. Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10900 Last updated (according to GEO): May 28 2005 V5-P285 Muscular Dystrophies 901 Neoplasm 861 1090 1065 of inflammatory myopathies Gene expression data from the right forebrain of C57BL mouse received no treatment for twelve weeks. Source GEO sample is GSM148684 Last updated (according to GEO): Dec 12 2006 861 HIV Infections brain, Entorhinal Cortex: Sample11_e1_le1 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13431.gif Source GEO sample is GSM79687 Last updated (according to GEO): Sep 22 2006 1000 Hippocampus IDC131 on harvard-12k RNA was obtained from vastus lateralis muscle biopsies taken from 8 healthy men, 21-24 years old. RNA was pooled before cDNA synthesis. Analysis done with Affymetrix Microarray Suite 5.0 software. Source GEO sample is GSM2394 Last updated (according to GEO): May 27 2005 Primary Neoplasm 1000 NA11882 I_U133A_12_AnCg 3AJZ02052312_HUMANCULTUREDADIPOCYTE PHA, 24.00 hr. T-cell Plasma 861 371 355 glioma invasion. Muscle 861 of the atrial 647 659 thymocytes_DN2_1 Macrophage 14smi114 Epithelium 861 Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22576 Last updated (according to GEO): May 27 2005 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188842 Last updated (according to GEO): Jun 06 2007 Nose 1000 KT1003d_CAN 9 0 Blood Test Myocardium 861 Primary tumor 19 32 MSE_N_G98A Epithelial Cells 901 5 0 brain cortex 7 12 Starvation 916 GBM Treatment, type=remove Source GEO sample is GSM99433 Last updated (according to GEO): Apr 21 2006 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19240 Last updated (according to GEO): May 27 2005 between the LAD artery 266 287 901 Temporal Lobe WGACON-139 HapMap YRI_parent Male Source GEO sample is GSM159723 Last updated (according to GEO): Feb 01 2007 Blood B cells;anti-IgM+CD40L high 48h 57 39 with endometriosis Fibroblasts 1000 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210391 Last updated (according to GEO): Jul 16 2007 kidney 172 178 amygdala wistar 3724 Microarray analysis of NL and PCOS oocytes Putamen 10 Normal wild-type mouse forebrain Treatment, type=time_course, measurement=11.0 weeks Source GEO sample is GSM53360 Last updated (according to GEO): Jul 06 2005 Gene expression data Source GEO sample is GSM183166 Last updated (according to GEO): Jul 30 2007 1000 Communicable Diseases 5 0 Spleen Gene expression data from postmorten brain regions Source GEO sample is GSM146078 Last updated (according to GEO): Nov 20 2006 7 cerebral cortex 21 saphenous_vein_1 Source GEO sample is GSM80793 Last updated (according to GEO): Mar 31 2006 Alzheimer's Disease 861 HapMap CEU_parent Female Source GEO sample is GSM159545 Last updated (according to GEO): Feb 01 2007 Normal Source GEO sample is GSM176256 Last updated (according to GEO): Apr 09 2007 8065_Lung developed PGD Tumor__Ovary_Adeno_mOVT1_(8691) on Affymetrix GeneChip Human 35K SubA Array Hu35k-A low gestational age Source GEO sample is GSM213094 Last updated (according to GEO): Jul 25 2007 983 Primary Glioblastoma P46 deprived visual cortex replicate 1 osteoblast 627 637 5 0 Muscle 861 Retina Mental Retardation 1000 Cochlear nucleus structure 901 861 Encephalitis 164 136 of the middle cerebral artery outer medulla 31 43 901 frontal lobe 1953 1937 mandibular branch Melanoma xenograft, MEC2_Sub_A (LeiFidler) NG012_c Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Englow 2 Pooled diaphragm RNA samples from five 8 wk old male mdx5cv mice Source GEO sample is GSM13567 Last updated (according to GEO): May 28 2005 Expression profiling of spinal cord section (T8) extracted from rats 4h following laminectomy (sham) Lot batch = Source GEO sample is GSM6627 Last updated (according to GEO): May 28 2005 of dystrophin 132 144 14 7 Thalamus Cerebral cortex 901 10785 on TGRI-6.5k M_U133Plus_87_HC with autism spectrum disorder 37 65 proteoglycans 563 576 747 tumor cells 757 CVB3-S-0h-2 KPeterson-NonMet-18G110-s2 Epithelium 865 Pain 861 of Parkinson's disease 450 471 2219 2202 in the hippocampus colan-affy-rat-89421 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28748 Last updated (according to GEO): May 27 2005 Parkinson Disease 1000 Liver Test (Blinded) Sample Source GEO sample is GSM130080 Last updated (according to GEO): Sep 18 2007 1000 Prostate carcinoma RNA isolated from fetal cerebrum Keywords = trisomy 13 Keywords = brain Keywords = Patau syndrome Source GEO sample is GSM22703 Last updated (according to GEO): May 27 2005 of neurite outgrowth 682 701 1000 Spinal Cord brain, cerebral cortex: Nic5_le1 12 frontal Lobe 23 PMN_LB_180min_Patient10 MO_LB_180min_Patient1 472-1 mouse brain 478 489 BXD 19_M7SS02080605 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs//7270.gif Source GEO sample is GSM76467 Last updated (according to GEO): Sep 22 2006 Coordinated regulation of gene expression by Brn3a in developing sensory ganglia. Utricle structure 861 861 Neoplasm Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153443 Last updated (according to GEO): Jan 11 2007 Whole blood from a healthy control Source GEO sample is GSM153500 Last updated (according to GEO): Jan 11 2007 Brain 1000 The Mg-delta strain of fibrillin-1 deficient mice display an early defect in alveolar septation. This study attempts to identify expression patterns in the mutant mouse lung compared to their wild-type littermates that suggest pathways that are critical for normal septation. This experiment focuses on postnatal days 1 and 5. Other time points will be added at a later date.. Date GSE479 Last Updated: Jul 27 2006 Contributers: Enid R Neptune Includes GDS243. Update date: Jul 27 2006. Dataset description GDS243: Study of alveolar septation using the Mg-delta strain of fibrillin-1 deficient mice which display an early defect in alveolar septation, and serve as a model for Marfan syndrome and emphysema.. Includes GDS244. Update date: Jul 27 2006. Dataset description GDS244: Study of alveolar septation using the Mg-delta strain of fibrillin-1 deficient mice which display an early defect in alveolar septation, and serve as a model for Marfan syndrome and emphysema.. Includes GDS242. Update date: Jul 27 2006. Dataset description GDS242: Study of alveolar septation using the Mg-delta strain of fibrillin-1 deficient mice which display an early defect in alveolar septation, and serve as a model for Marfan syndrome and emphysema.. Blood 7 11 660 mesenchymal stem cell 639 Standard Affymetrix Protocol Keywords = microarray Keywords = muscle Source GEO sample is GSM15940 Last updated (according to GEO): May 28 2005 67 50 Gall bladder C57BL of the postmortem brains 674 698 1000 Rectum Gene expression data from normal adrenal gland Source GEO sample is GSM211450 Last updated (according to GEO): Jul 18 2007 861 Encephalitis Small cell carcinoma of lung 901 Blood 861 26 15 endometrioid of the digestive tract 76 98 2nd 1hr C+S-CA1 Nose 1000 in primary cancer 1362 1378 nodose_nucleus_5 Source GEO sample is GSM80753 Last updated (according to GEO): Mar 31 2006 H9RGV00061304 6 week mutant OMN rep 2 Gene expression data from retinas of two old SAMR1TA mice Source GEO sample is GSM143742 Last updated (according to GEO): Jan 24 2007 total RNA from biosource CC#21* Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92478 Last updated (according to GEO): Jan 13 2006 Gene expression data from hippocampus of one old SAMP8/Ta mouse Source GEO sample is GSM143751 Last updated (according to GEO): Jan 24 2007 A control group consisting of nine C57/BL/6J mice was maintained on a normal diet consisting of Purina Rodent Chow (Harlan Teklad, catalog #5008, 6.5% fat, 49% carbohydrate, 23% protein, 3.5 kcal/ g). The experimental group consisted of nine mice grown on a specialty high-fat diet (Harlan Teklad, catalog #TD88137, 42.16% fat, 42.81% carbohydrate, 15.02% protein, 4.53 kcal/ g). Mice were maintained for ten weeks on their respective diets in a controlled environment with standard light and feeding schedule. Two days before tissue harvest, the experimental group on the high-fat diet was divided into one group of five and one group of four mice. The first group continued on the high-fat diet for the final two days, while the second group fasted. Mouse weights were recorded two days prior, and the day of tissue harvest. At the end of the fasting period liver tissue samples were harvested from each mouse. RNA was purified from the liver tissue samples. Each tissue was homogenized in 1 mL of STAT-60 (Tel-Test, Inc., Friendswood, TX) and the homogenate was mixed with 200 uL of chloroform. The aqueous phase was removed, and mixed with 500 uL of isopropanol to precipitate the RNA. The resulting RNA pellet was washed with 500 uL of 70% ethanol and allowed to air dry. The pellet was dissolved in RNase free water (Ambion, TX), quantified by UV spectroscopy, and stored at -80C. Total RNA control samples (Universal Mouse Reference RNA, catalog # 740100, Stratagene) were labeled using Cy3 dCTP (Perkin-Elmer), and liver total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). The control RNA samples were additionally mixed with 2 uL of random hexamers. The reaction mixtures were incubated at 42 C for two hours. After the reverse transcription reactions, the RNA templates were degraded by addition of 2 uL of 1 N NaOH and incubation at 65 C for 10 minutes. The alkaline conditions were neutralized by addition of 2 uL of 1 N HCl. Liver cDNA samples were then mixed with a control cDNA sample, and the mixtures were cleaned using a QIAquick Nucleotide Removal kit (Qiagen) as described by the manufacturer's instructions. The cleaned samples were concentrated in a speed vacufuge (Eppendorf) for 20 minutes at 65 C, and were dissolved in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), quantified, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 C using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), then in 1X SSC, and finally in 0.1X SSC. The arrays were dried by centrifugation and scanned using a GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and analyzed using Matlab (The MathWorks, Inc.). Microarrays were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). Arrays contained 16,847 features, printed from a synthesized oligonucleotide mouse library (Operon). The library was suspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed at approximately 50% humidity. Once printed, the probes were crosslinked using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride (Fluka AG), 239 mL 1-methyl-2-pyrrolidinone (EM Science), and 10.7 mL of 1 M boric acid (Fisher), pH 8.0. They were cleaned by rinsing twice in 250 mL of milli-Q water, followed by 250 mL of 95% ethanol (Pharmco Products). After blocking, they were dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, energy homeostasis, gene expression, microarrays Source GEO sample is GSM6599 Last updated (according to GEO): Nov 21 2005 GSE8646 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2830 Source GEO sample is GSM2118 Last updated (according to GEO): Nov 21 2005 3074 HP6_43 Bone Marrow 1000 cerebral cortex 7 21 corticosterone_treated_rep3 (06SE458) 1000 Liver I_U133A_90_AnCg SQ-3529-A324-5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A olfactory epithelium 194 213 Spleen 1000 Stomach Pyloric 2 Normal Affymetrix GeneChip® Mouse Genome 430 2.0 Array Source GEO sample is GSM197117 Last updated (according to GEO): May 31 2007 Recurrent Adenocarcinoma 6 Primary tumor 19 32 HDMTX-16 50 43 jejunum 1000 Brain B6Cerebellum(1)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B Aging of skeletal muscle tissue is characterized by loss of metabolic and contractile competence. It is thought that this phenomenon is driven via extrinsic and intrinsic factors. In order to identify age-dependent changes intrinsic to the muscle cell, microarray transcriptional profiles and measurements of glucose metabolism were performed in primary cultured human myotubes at different time points over seven weeks. Aging in culture tended to reduce myotube glucose metabolism, oxidative and storage capacities, despite elevation of glucose transport. The mitochondrial membrane potential slightly increased, whereas peroxidation of cell membrane lipids declined and membrane integrity was preserved. Transcriptional analysis revealed a fall in genes involved in glucose metabolism and oxidative phosphorylation, while stress defense genes were elevated. Expression of numerous genes coding for muscle contractile proteins and calcium-regulating proteins, was gradually decreased during aging of cultured myotubes. Transcripts of genes involved in cell growth, matrix and motility markedly rose while those involved in cell adhesion dropped. In conclusion, aging myotubes in culture exhibit a loss of glucose metabolic capacity. They are characterized by a shift from a contractile to a growth-survival, matrix-remodeling phenotype. This pattern of changes, linked to intrinsic factors, displays significant similarities with aging of muscle from primates and human subjects.. Date GSE1144 Last Updated: Oct 28 2005 Contributers: Katherine Macé Eulàlia Montell Robert Mansourian Anna M Gómez-Foix Andreu Ferrer-Martínez Matthew A Roberts Includes GDS647. Update date: Jul 21 2004. Dataset description GDS647: Examination of aging myotubes from a muscle biopsy incubated in glucose. Myotubes in 25 mM glucose at 2, 3, 4, 5, and 7 weeks, and in 10 mM glucose at 4 weeks examined in reference to 0 mM glucose control at 1 week.. NoCAD_replicate47 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3298 Last updated (according to GEO): Mar 21 2006 Communicable Diseases 1000 Expression profiling of spinal cord section (T8) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM6647 Last updated (according to GEO): May 28 2005 Brain [JunctionChip 4 of 5] Primary tumor 19 32 n/a Source GEO sample is GSM178024 Last updated (according to GEO): Jun 11 2007 Trigeminal ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until enough tissue was harvested to be pooled by genotype. Approximately 10-12 ganglia were pooled for a single analysis, which was extracted using the RNeasy system (Qiagen). Source GEO sample is GSM89133 Last updated (according to GEO): Dec 23 2005 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 13 hours after lights on. Original sample code = CM11A Source GEO sample is GSM227318 Last updated (according to GEO): Sep 10 2007 plasma cells 332 344 KM12 hgu95b PGA-MurLungRag-pbs-72h-1aC-s2 human caudate nucleus Source GEO sample is GSM86917 Last updated (according to GEO): Feb 08 2006 673 659 by decapitation PWK/Ph_male_hypothalamus FNH (SF16) 36 22 caudate nucleus no additional Source GEO sample is GSM199342 Last updated (according to GEO): Jun 08 2007 from neuroepithelial stem cells 1086 1116 Gene expression data from postmorten brain regions Source GEO sample is GSM146014 Last updated (according to GEO): Nov 20 2006 GSE466 7 cerebral cortex 21 Primary Neoplasm 901 ProstateCancer-7 on NHGRI-6.5k_c ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes(delta-inlA)_A_5545 Source GEO sample is GSM161566 Last updated (according to GEO): Feb 14 2007 Spleen 0 5 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp3324 Source GEO sample is GSM2116 Last updated (according to GEO): Nov 21 2005 striatum 22 30 Zeitgeber Time Treatment, type=time_course, measurement=12.0 h Source GEO sample is GSM53336 Last updated (according to GEO): Jul 06 2005 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 13 hours after lights on. Original sample code = CM47A Source GEO sample is GSM227329 Last updated (according to GEO): Sep 10 2007 Adenocarcinoma 1000 Epithelium of bronchus 983 cerebral cortex 7 21 GBM: 38K Arteries 861 frontal cortex wistar ky 3931 whole tissue, individual animal, 10 weeks old, male Wistar Kyoto frontal cortex file:p3931w Source GEO sample is GSM15168 Last updated (according to GEO): Oct 28 2005 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3522.gif Source GEO sample is GSM93134 Last updated (according to GEO): Sep 22 2006 Compare the transcriptomes of Cx43 null and Cx43 siRNA treated cortical astrocytes with the transcriptome of the wildtype cortical astrocytes Source GEO sample is GSM200840 Last updated (according to GEO): Jun 19 2007 861 Oocytes Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213469 Last updated (according to GEO): Jul 31 2007 Cerebral cortex 861 Muscle Fibers 1000 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202666 Last updated (according to GEO): Jun 20 2007 Whole Brain 73 83 bone_marrow_8 478_4d with Parkinson's disease 27 50 20 0 human caudate nucleus This is replicate 3 of the 6 hour sample from passive avoidance trained rats. Source GEO sample is GSM17403 Last updated (according to GEO): Aug 22 2007 RNA isolated from astrocyte cell lines derived from fetal cerebrum Keywords = trisomy Keywords = brain Keywords = Down syndrome Source GEO sample is GSM22608 Last updated (according to GEO): May 27 2005 M_U133A_1_DLPFC NB-C4 on NHGRI-6.5k_b 5 0 Spleen 983 Structure of horn of uterus 1037 of transitional epithelium 1012 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201242 Last updated (according to GEO): Jun 14 2007 none Source GEO sample is GSM239918 Last updated (according to GEO): Dec 07 2007 861 HIV Infections PMN_LB_360min_Patient8 from liver 21 30 Job's patient Source GEO sample is GSM211123 Last updated (according to GEO): Sep 10 2007 Normal human tissue:Normal Breast Keywords = Human, Normal Tissue, Normal Breast Source GEO sample is GSM44683 Last updated (according to GEO): May 27 2005 858 Mesodermal cell D_U133Plus_115_HC 44 minus the frontal cortex 68 Stomach Carcinoma 901 1000 Muscle Squamous cell carcinoma 1 0 24 861 Cerebral cortex Untreated Control 4weeks AffyGC RMA rep2 1000 Seizures CNS-SCsev_InjB24h-4C-s2 M_U133A_26_CB of the normal mucosa 7 26 Prostate 861 Expression profiling of moderately injured raphe at 7d in rats Source GEO sample is GSM41627 Last updated (according to GEO): May 27 2005 10 bone marrow 0 905 Lung Diseases, Obstructive cingulate cortex 1000 obesity 604 610 ovary 45 50 The aged mouse was injected intraperitoneal (ip) with saline (~100ul/mouse) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use. Source GEO sample is GSM73017 Last updated (according to GEO): Sep 07 2005 the blood 393 402 CD8+ T Lymphocytes_Healthy donor 3 HLA-matched Time 0_replicate 2 Primary Carcinoma 1000 861 Ovary 1037 of transitional epithelium 1012 frontal_lobe_7 Source GEO sample is GSM80675 Last updated (according to GEO): Mar 31 2006 brain, hippocampus: CON-CA1-13_e1_le1 NA19144 Spinal cord 1243 1253 24 0 human prostate PC3 tumors Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162168 Last updated (according to GEO): Jun 12 2007 Utricle structure 1000 Pooled quad RNA samples from five 8 wk old male C57BL10 mice Source GEO sample is GSM13720 Last updated (according to GEO): May 28 2005 testes_5 Source GEO sample is GSM80853 Last updated (according to GEO): Mar 31 2006 115 98 with Endometriosis Normal Source GEO sample is GSM175976 Last updated (according to GEO): Apr 09 2007 861 Cerebellum I-12_PRE 861 Soleus muscle structure 8 brown fat 0 of motor neuron diseases 784 808 human caudate nucleus Source GEO sample is GSM86898 Last updated (according to GEO): Feb 08 2006 861 Brain 90-8_Mock_1 5 0 brain Plasma 861 striatum 24 32 Gene expression data from mouse colon Source GEO sample is GSM198101 Last updated (according to GEO): Aug 22 2007 Liver 1000 MO_control_180min_Patient16 Primary Neoplasm 1000 Liver Test (Blinded) Sample Source GEO sample is GSM130186 Last updated (according to GEO): Sep 18 2007 1000 Brain Osteoblasts 1000 Neuraxis 1000 Liver 1000 1000 Mammary Neoplasms Gene expression data from postmorten brain regions Source GEO sample is GSM145387 Last updated (according to GEO): Nov 20 2006 Expression profiling of spinal cord section (T9) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM6660 Last updated (according to GEO): May 28 2005 D_U133A_70_DLPFC 41 29 Control blood none Source GEO sample is GSM123268 Last updated (according to GEO): Jul 27 2006 Brain 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145830 Last updated (according to GEO): Nov 20 2006 /3T3 fibroblasts 478 493 Large-scale gene expression differences across brain regions and inbred strains correlate with a behavioral phenotype. Mesenchymal Stem Cells 1000 Medulla 861 5 0 brain 76 65 from bronchi post HCMV infection 69 87 Testis 861 861 Structure of blastomere HYDROXYACYL-CoA DEHYDROGENASE 1000 Placenta, primary PL112 Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep8 Ky3: Hippocampus_21PT-Y_rep3 23 0 Murine Neurofibromatosis Gap junctions and purinergic P2 receptors (P2Rs) can be regarded as belonging to a common functional unit, given that they are involved in the transmission of calcium signals between cells. We have previously shown that deletion of the Gja1 gene alters expression levels of numerous genes encoding proteins with diverse functions, including purinergic, P2Rs, and have found that genes synergistically or antagonistically expressed in wildtype tissues are more prone to be similarly or oppositely regulated in Cx43-nulls. We have now explored the use of coordination analysis of gene expression as a strategy to identify interlinked genes encoding functionally related proteins and used pull-downs to evaluate their interlinkage. Our findings indicate that, in brain and in cultured astrocytes, several of these co-expressed genes encode proteins that are components of P2R signal transduction pathways and/or directly interact with these receptors, including the gap junction protein connexin43 (Cx43) and connexin45 (Cx45), as well as pannexins. It is proposed that coordination analysis of gene expression may provide a novel unbiased strategy for the identification of proteins belonging to supramolecular complexes. Note: 10 samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: GSM200854, GSM200840, GSM200845, GSM200843, GSM200960, GSM200839, GSM200855, GSM200841, GSM200842, GSM200844, Last Updated (by provider): Sep 19 2007 Contributers: Christina Chrisman David C Spray Michal Cohen Sanda Iacobas Sylvia O Suadicani Dumitru A Iacobas Eliana Scemes 1000 Prostate of 2182 tumor 24 36 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68289 Last updated (according to GEO): Jul 07 2006 Fibroblasts 861 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184685 Last updated (according to GEO): Apr 26 2007 AD-AD15T1-A390-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A SON 3d dehydrated Source GEO sample is GSM69863 Last updated (according to GEO): Dec 02 2005 brain, hippocampus: Hippocampus 12_le1 2869 tumor cells 2880 D_U133Plus_118_CB 1000 Liver 1394 1379 medulloblastomas khatua-astrocytoma 0 17 Spleen 0 5 GSE1803 46 13 cutaneous contact hypersensitivity 901 Large Intestine Cultured in DMEM with 10% FBS and penicillin (100U/ml)/streptomycin (100ug/ml). Media changed every other day. 37ºC, 5% CO2. Source GEO sample is GSM15786 Last updated (according to GEO): Oct 28 2005 81 53 with congestive heart failure Ovarian Diseases 877 f2#207 versus pool Mouse Brain tissue Metastatic tumor 19 35 Myocardium 861 96 13 from fetal cerebrum Keywords = trisomy 13 Keywords = brain Keywords = Patau syndrome no additional Source GEO sample is GSM199317 Last updated (according to GEO): Jun 08 2007 NA Source GEO sample is GSM84326 Last updated (according to GEO): Dec 01 2005 D_U133Plus_88_nAcc Acetaminophen 24hr Rat 7393 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool Mouse ileum 0 10 PGA-Band_Sham_1h_5-m5 Olfactory Epithelium 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with MIP3-alpha (Macrophage inflammatory protein-3) for 120min Source GEO sample is GSM5694 Last updated (according to GEO): May 27 2005 Brain 861 Normal Source GEO sample is GSM175867 Last updated (according to GEO): Apr 09 2007 16 0 Embryonal tumours Probeset expression data from NA12750 growth 2, replicate 2 Source GEO sample is GSM195196 Last updated (according to GEO): Aug 08 2007 caudate-putamen 374 388 Nose 1000 1000 Cornea n/a Source GEO sample is GSM177930 Last updated (according to GEO): Jun 11 2007 N8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Acetaminophen 24hr Rat 9398 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool 861 Cardiomyopathies 9 0 Blood Test cardiac 763 769 Bone Marrow 1000 Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S25_3 months_replicate 1 cerebral cortex 7 21 Neoplasm 861 A2780_cis_IC90_pre_1 Gene expression data from postmorten brain regions Source GEO sample is GSM145469 Last updated (according to GEO): Nov 20 2006 Wild-type-hippocampus, biological rep4 (male) 1000 Basal Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198643 Last updated (according to GEO): Jun 06 2007 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc99 Source GEO sample is GSM1916 Last updated (according to GEO): Nov 21 2005 D_U133Plus_33_DLPFC Asthma is caused by a combination of poorly understood genetic and environmental factors. We found multiple markers on chromosome 17q21 to be strongly and reproducibly associated with childhood onset asthma in family and case-referent panels with a combined P < 10-12. In independent replication studies the 17q21 locus showed strong association with diagnosis of childhood asthma in 2,320 subjects from a cohort of German children (P = 0.0003) and in 3,301 subjects from the British 1958 Birth Cohort (P = 0.0005). We systematically evaluated the relationships between markers of the 17q21 locus and transcript levels of genes in EBV-transformed lymphoblastoid cell lines from children in the asthma family panel used in our association study. The SNPs associated with childhood asthma were consistently and strongly associated (P <10-22) in cis with transcript levels of ORMDL3, a member of a gene family that encode transmembrane proteins anchored in the endoplasmic reticulum. The results indicate that genetic variants regulating ORMDL3 expression are determinants of susceptibility to childhood asthma. Last Updated (by provider): Jun 08 2007 Contributers: Ivo G Gut Simon Heath William O Cookson Albrecht Bufe Anna L Dixon Andrea von Berg Saffron A Willis-Owen Liming Liang David Strachan Michael Kabesch Gonçalo R Abecasis Christian Vogelberg Martin Farrall Andrea Heinzmann Martin Depner G Lathrop Erika von Mutius Kenny C Wong Stephan K Weiland Miriam F Moffatt Ernst Rietschel Thomas Frischer Thomas Illig Burkard Simma Gene expression data from postmorten brain regions Source GEO sample is GSM145233 Last updated (according to GEO): Nov 20 2006 CAD_replicate51 Testi_GermCell Source GEO sample is GSM18826 Last updated (according to GEO): Sep 25 2006 Eye 861 1000 Lung Liver Test (Blinded) Sample Source GEO sample is GSM130198 Last updated (according to GEO): Sep 18 2007 1000 Cerebral cortex 10 7 Left Female 67.3 yr after antibody enrichment scan 2 (U133B) Susceptible Group, Ventral tegmental area, Biological Replicate 3 41 28 in mouse brain Monocular deprivation right cortex, biological rep2, CHB MD-2 Nasal Epithelium Inhalation Formaldehyde 07ppm 6h ID130 DU-145_CL11003_CNS on Affymetrix GeneChip Human Full Length Array HuGeneFL at the Human Brain 726 743 607 597 the rectum olfactory epithelium 194 213 processed in batch 3 Source GEO sample is GSM90454 Last updated (according to GEO): Mar 20 2006 Epithelial Cells 901 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 21d after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44497 Last updated (according to GEO): May 27 2005 ALL_11 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Endometrium 15 Normal Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211428 Last updated (according to GEO): Jul 18 2007 861 Bone Marrow Immature B cells 8b Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=720630 LaserPower=2.061.3 Lot batch = LC17N095 Source GEO sample is GSM4818 Last updated (according to GEO): Nov 21 2005 Mesenchymal Stem Cells 1000 1000 Spleen ovarian tumor: endometrioid Source GEO sample is GSM139398 Last updated (according to GEO): Apr 09 2007 n/a Source GEO sample is GSM177888 Last updated (according to GEO): Jun 11 2007 Muscular Dystrophies 901 Gene expression data from male mice. Source GEO sample is GSM115528 Last updated (according to GEO): Jun 13 2007 Urethra 1 Normal 39 27 the maxillary Mucous Membrane 861 Nose 1000 Normal Source GEO sample is GSM176112 Last updated (according to GEO): Apr 09 2007 plasma cells 332 344 Adipose tissue 901 Expression profiling of laminectomized raphe at 7d in rats Source GEO sample is GSM41549 Last updated (according to GEO): May 27 2005 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210363 Last updated (according to GEO): Jul 16 2007 total RNA extracted from mouse brain Source GEO sample is GSM103421 Last updated (according to GEO): Sep 21 2006 Branch 861 304 280 alcoholic cardiomyopathy 1000 Structure of locus ceruleus GC (HKG36T) The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169499 Last updated (according to GEO): Feb 21 2007 Muscle 861 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 24h after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44482 Last updated (according to GEO): May 27 2005 GM12056 1327 1306 if their initial tumor 1000 Structure of middle cerebral artery G30 neurons from cingulate cortex Source GEO sample is GSM63024 Last updated (according to GEO): Dec 01 2005 gene expression data from melanoma xenografts following ILI with saline Source GEO sample is GSM213629 Last updated (according to GEO): Jul 27 2007 dentate granule cells Treatment, type=behavioral_stimulus, description=These are untreated animals. Source GEO sample is GSM35845 Last updated (according to GEO): May 27 2005 Heart 1000 Seminoma 1000 of mouse brain 9 23 Structure of trigeminal ganglion 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28750 Last updated (according to GEO): May 27 2005 A2780_cis_IC90_6h_2 1000 Bipolar Disorder Brain 1000 Cerebellum 1000 GSE485 of regenerating Dorsal Root Ganglia 21 55 the blood 393 402 1000 Brain 901 Caudate nucleus structure Neoplasm 861 1381 1361 with maternal anemia Epithelium 861 1000 Brain Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. All patients were considered sporadic cases on the basis that no clinical antecedents of familial adenomatous polyposis were reported, and those that met the clinical criteria for hereditary non-polyposis colon cancer (Amsterdam criteria) were excluded. Source GEO sample is GSM112302 Last updated (according to GEO): Jun 06 2006 875 Cerebellar Diseases Gene expression of organ of Corti of newborn rats_cultivation_normoxia_repeat 1 inner ear 861 Cardiomyopathies CNS-SCsev_InjA14d-3B-s2 Transplant Series 36 , Transplant # 3 SQ-1670-A318-5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A D_U133Plus_89_nAcc Temporal Cortex Control (AD) 9 858 Mesodermal cell 861 Brain 861 Spinal Cord Renal carcinoma 913 Ganglia, Spinal 923 14 0 Small Intestine n/a Source GEO sample is GSM177952 Last updated (according to GEO): Jun 11 2007 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184810 Last updated (according to GEO): Apr 26 2007 Exp A_2, 1mg/kg CPF Spleen 1000 /2J cingulate cortex rep2 3 27 Disease Source GEO sample is GSM176302 Last updated (according to GEO): Apr 09 2007 0 cortex 5 1000 Primary Glioblastoma 21h-Control replication 4 Keywords = preimplantation Keywords = development Source GEO sample is GSM14697 Last updated (according to GEO): May 28 2005 Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153765 Last updated (according to GEO): Jan 19 2007 3 min exposure to halothane prior to immediate perfusion with ice cold saline Keywords = Eckenhoff Keywords = anesthetics Source GEO sample is GSM11379 Last updated (according to GEO): May 28 2005 liver_1 7 0 prostate Heart failure 1000 BXD6_M7SS02042201 HCC (HBV+, SF7) 861 Brain 1000 Brain Mesenchymal Stem Cells 1000 DLBC43 on Affymetrix GeneChip Human Full Length Array HuGeneFL Mesenchymal Stem Cells 1000 861 Cardiomyopathies Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19253 Last updated (according to GEO): May 27 2005 Lymphoblastoid Cell Line for Individual 8183.4 log phase AD C+S: Alzheimer's context + shock: Alzheimer's mice were 50% C57BL/6, 50% SJL. Alzheimers animals were the double transgenic models reported by Dineley et al., (2002) J Biol Chem 277(25):22768-22780. Alzheimer's mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 2 hours after the last shock treatment. Source GEO sample is GSM4560 Last updated (according to GEO): May 27 2005 no additional Source GEO sample is GSM199383 Last updated (according to GEO): Jun 08 2007 BAL_27a_A0B0 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181168 Last updated (according to GEO): Jul 12 2007 1000 Kidney Spleen vs Interferon-beta (IFN beta) Treated B cell 120min (set1) Diversity of gene expression in adenocarcinoma of the lung. Brain 1000 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113958 Last updated (according to GEO): Jun 16 2006 hypothalamus_3 Exploiting the power of high-density gene arrays, the simultaneous expression analysis of 5600 cellular genes was executed on proliferating peripheral blood mononuclear cells (PBMCs) from three normal human donors that were infected in vitro with the T cell tropic laboratory strain of HIV-1, RF. Profiles of expressed genes were assessed at 1, 12, 24, 48, and 72 hr postinfection and compared with those of matched uninfected PBMCs. Viral infection resulted in an overall increase in the number of genes expressed with peaks of expression at 1, 12, and 48 hr postinfection. Functional clustering of genes whose expression level in infected PBMCs varied by 2-fold or greater from levels in the controls indicated that cellular activation markers, proteins associated with immune cell function and with transcription and translation, exhibited increased expression subsequent to viral infection. Gene families exhibiting a decline in gene expression were confined to the 72 hr time point and included genes associated with catabolism and a subset of genes involved with cell signaling and synthetic pathways. Self-organizing map (SOM) cluster analysis identified temporal patterns of coordinated gene expression in infected PBMCs including genes associated with the immune response, the cytoskeleton, and ribosomal subunit structural proteins required for protein synthesis.. Date GSE511 Last Updated: May 29 2005 Contributers: N L Michael L L Jagodzinski J Yalley-Ogunro M E Nau M G Lewis M T Vahey M Taubman Includes GDS171. Update date: Mar 22 2004. Dataset description GDS171: Gene expression profile of proliferating normal peripheral blood mononuclear cells (PBMC) infected with HIV type 1 RF. Assessed at 0, 12, 24, 48, and 72 hours postinfection and compared with those of matched uninfected PBMC.. Carcinoma 861 861 Blood 923 Organ of Corti 13 0 G1 optic nerve Standard Affymetrix Protocol on total RNA extracted from brain tissue Source GEO sample is GSM101414 Last updated (according to GEO): Mar 28 2006 01_0019_SepticShock_Day1_120 CNS-SC_InjB4h-2A-s2 SmaIntE165_022LAFCI_170.txt 1000 frontal lobe Anterior nares 1000 Eye 1000 861 Cartilage from liver 21 30 144 124 of bladder carcinoma 27 0 Leukemia Chronic Myelogenous Stromal Vascular Cells A on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A Rat frontal cortex RNA - VH TTX Experiment Source GEO sample is GSM92303 Last updated (according to GEO): Jan 13 2006 NCI60.22_LABEL26EXTRACT25SUB3 Source GEO sample is GSM134104 Last updated (according to GEO): Aug 06 2007 861 Cancer of Neck cin_NY20 861 Brain 12 4 of Kidney 861 Cerebral cortex CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of M?, rhM?CSF was added at 1000 U/ml on the same days. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5143 Last updated (according to GEO): Sep 08 2006 Blood Test (Blinded) Sample Source GEO sample is GSM129996 Last updated (according to GEO): Sep 18 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145530 Last updated (according to GEO): Nov 20 2006 Cerebral cortex 861 cardiac 746 752 Compare the brain transcriptomes of Gja9 (-/-) and Gja9 (+/-) mice with that of wildtype mice to detect transcriptomic alterationss induced by total or partial ablation of Gja9 Source GEO sample is GSM146902 Last updated (according to GEO): Nov 29 2006 MDA-N hgu95c M_U133Plus_122_nAcc Whole Genome array hippocampus_cocaine2 Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed 6 h to hydrostatic pressure (HP6), pressure experiment # 4 (PE4). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11392 Last updated (according to GEO): Dec 15 2006 brain 0 5 Transcriptional profiling of bipotential embryonic liver cells to identify liver progenitor cell surface markers (430A) 861 Malignant neoplasm of urinary bladder Replicate3_Voxel D2 spleen 265 270 Lung 1000 CHIPEXP_NAME: 230_2_050531tpj_20h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Vehicle_Control TREAT_TOX_MECHANISM1: Liver_Non_Toxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0 SAMPLING_TIME: 72 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197627 Last updated (according to GEO): Jun 01 2007 Liver 1000 2 hrs Post-clamp sample 4 1000 Cerebellum 69 13 from nicotinic acetylcholine receptor subunit mutant mice The nose 94 101 0 Human Cortex 11 129 2000-2 Kidney Brain 861 gene expression data from ODC mouse skin samples Source GEO sample is GSM216664 Last updated (according to GEO): Aug 09 2007 Heart failure 1000 from a primary branch 21 41 1000 Brain Gene expression data from human prostate tissue with 90 percent tumor content Source GEO sample is GSM119310 Last updated (according to GEO): Feb 23 2007 in the brain 1093 1105 mRNA expression in regenerated mdx mouse skeletal muscle DLCL-0016 Stem cells 901 249 235 their cerebella hippocampal glutamatergic CA1 pyramidal neurons Source GEO sample is GSM35803 Last updated (according to GEO): May 27 2005 days nasal epithelium 1127 1148 Lymphoblastoid Cell Line for Individual 8115.3 log phase Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211429 Last updated (according to GEO): Jul 18 2007 5 0 brain MD rep 2 1BRS02080872a_atrioventricular_node Murine_Bulk_Splenocytes_resting_4 3AJZ02022872_ fetal lung 115 cortex 121 cerebellum 552 561 119 96 in embryonic stem cells Papillary Renal Cell Carcinoma 1000 861 Brain melanoma 1000 Samp8 Retina Old Sample 2 Experimental Autoimmune Encephalomyelitis 1000 GSE3489 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132561 Last updated (according to GEO): Feb 26 2007 5 0 brain A/J periaqueductal gray rep1 (430 2.0 Array) 31 adrenal medulla 17 14 6 (amygdala 2 hours, repeat 2 0 Human Cortex 11 1000 Brain Untreated, biological rep2 1000 Hippocampus MET-303 on UMich-10k **** Source GEO sample is GSM4256 Last updated (according to GEO): May 27 2005 Utricle and 3 ampullae at E13, replicate2 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210406 Last updated (according to GEO): Jul 16 2007 1645 1642 (CJD Communicable Diseases 901 Macrophage 14smi025 Entorhinal Cortex 7 23 Spinal Cord 1000 660 mesenchymal stem cell 639 B6 day 3, biological rep 1, tech rep 2 Blood Test (Blinded) Sample Source GEO sample is GSM129934 Last updated (according to GEO): Sep 18 2007 I_U133A_80_CB 36 0 Control rat 6 ventral tegmental area Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.49 Subject: 3076 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39065 Last updated (according to GEO): May 27 2005 861 Prostate ALL-B-cell-20 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Myosin ATPase 1000 Autistic Disorder Biopsy of a colorectal adenoma from patient #16 861 Brain Control, biological rep2 CHC Con-2 65 50 Cerebellum C57BL dorsal striatum sprague 3981 whole tissue, individual animal, 10 weeks old, male Sprague Dawley dorsal striatum file:R3MH01022302 Source GEO sample is GSM15224 Last updated (according to GEO): Oct 28 2005 DBA/2J Frontal Cortex A Primary small cell lung carcinoma 1926 Source GEO sample is GSM17336 Last updated (according to GEO): May 28 2005 Control 9 Biopsy of a colorectal adenoma from patient #1 KT94_AR1 V5-P259 SN:1029150 Source GEO sample is GSM115415 Last updated (according to GEO): Jun 20 2006 Endometrium/Ovary 11 Disease Proteoglycan 1000 DMN-NF1Hippo15d-1cAv2-s2 Autistic Disorder 877 Epithelial Cells 901 36 21 from whole brain Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11221 Last updated (according to GEO): May 28 2005 M_U133A_35_AnCg human cerebellum Source GEO sample is GSM87190 Last updated (according to GEO): Feb 08 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145085 Last updated (according to GEO): Nov 20 2006 Frontal cortex 254 267 Brain 1000 PBMCs-Healthy-H126_Healthy D02 0h Media Head and neck cancer Source GEO sample is GSM155707 Last updated (according to GEO): Apr 24 2007 The changes in global gene expression in response to DNA damage may derive from either direct induction or repression by transcriptional regulation or indirectly by synchronization of cells to specific cell cycle phases, such as G1 or G2. We developed a model that successfully estimated the expression levels of >400 cell-cycle-regulated genes in normal human fibroblasts based on the proportions of cells in each phase of the cell cycle. By isolating effects on the gene expression associated with the cell cycle phase redistribution after genotoxin treatment, the direct transcriptional target genes were distinguished from genes for which expression changed secondary to cell synchronization. Application of this model to ionizing radiation (IR)-treated normal human fibroblasts identified 150 of 406 cycle-regulated genes as putative direct transcriptional targets of IR-induced DNA damage. Changes in expression of these genes after IR treatment derived from both direct transcriptional regulation and cell cycle synchronization. Last Updated (by provider): Feb 21 2007 Contributers: Yingchun Zhou Thomas Mullen Jeff Chou William Kaufmann Tong Zhou [Switched to use G4410A/B by Gemma] Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 24h after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44493 Last updated (according to GEO): May 27 2005 Kainate-hippocampus, biological rep4 13 0 Nervous System Standard Affymetrix Protocol Source GEO sample is GSM16487 Last updated (according to GEO): May 28 2005 H9RGV00110705 Primary carcinoma of the liver cells 1000 1000 Communicable Diseases 226 203 with insulin resistance Central gray substance of midbrain 861 901 Epithelial Cells CNS-SCsev_InjA28d-2A-s2 Cortex_Bulbectomized_rep4 I_U133A_33_DLPFC Brain 1000 of coronary artery disease 258 284 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210366 Last updated (according to GEO): Jul 16 2007 biopsy sample obtained from 2-year-old male individual Keywords = gene expression profile of normal human skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15823 Last updated (according to GEO): May 28 2005 CS 75h Hypothalamus of rats following subjection to hypohydration (10% loss of b. wgt, water deprivation). RNA extraction was accomplished using Tri Reagent (Molecular Research Center Inc. Ohio, USA). The probes were labeled for 1 h by the reverse transcription of total RNA (3 µg) at 42°C in a primer mix (Clontech) containing [32P]dATP (Amersham Biosciences, Buckinghamshire, UK). The reaction was terminated by adding 0.1M EDTA and 1 mg/ml glycogen (Sigma).The unincorporated 32P-labeled nucleotides were removed by Nucleo-Spin extraction columns (Clontech). Source GEO sample is GSM62950 Last updated (according to GEO): Oct 28 2005 1500 mg/kg X 12 hr Source GEO sample is GSM129879 Last updated (according to GEO): Sep 18 2007 1000 Spleen Brain 861 Tissue Source GEO sample is GSM67243 Last updated (according to GEO): Jan 19 2006 human cerebellum Source GEO sample is GSM87060 Last updated (according to GEO): Feb 08 2006 Branch 861 50 41 of cancers Sprague-Dawley Female LowSalt OuterMedulla rat702 sd_medullar_k_702r_om_070302 of the dystrophin-associated protein complex 206 249 923 Congestive heart failure Brain 1000 HC72 CN A Heart 861 1000 Prostate 7 frontal cortex 20 Subject code A44 Leukemia, Lymphocytic, Chronic 1000 Cardiac 523 530 Transcriptional profiling was done in Hoxb1 mutant E10.5 embryos in tissues primarily consisting of rhombomere 4 and surrounding branchial arches. Source GEO sample is GSM115795 Last updated (according to GEO): Aug 28 2006 861 Cerebellum Monocytes Resting 30h 1 Resting Study the transcriptomic effects of the shear stress on cultured osteoblast-like MC3T3 cells Source GEO sample is GSM201215 Last updated (according to GEO): Jun 19 2007 1000 Prostate C57BL/6 benchmark dataset: Embryonic day 12.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25157 Last updated (according to GEO): May 27 2005 865 Disorder of artery Ta gr2 tumour Source GEO sample is GSM2474 Last updated (according to GEO): May 27 2005 861 Communicable Diseases S1P2-KO-neocortex, biological rep9 (female) Tumor__Ovary_Adeno_0001c086 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 66 42 out of mouse bone marrow 567 548 the descending colon 1000 Brain gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134605 Last updated (according to GEO): Jul 09 2007 liver_2 Source GEO sample is GSM80729 Last updated (according to GEO): Mar 31 2006 liver Source GEO sample is GSM18697 Last updated (according to GEO): May 27 2005 861 medulloblastoma Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228659 Last updated (according to GEO): Sep 11 2007 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213493 Last updated (according to GEO): Jul 31 2007 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5817 Last updated (according to GEO): May 27 2005 660 mesenchymal stem cell 639 Epithelium 861 Osteoblasts 1000 1000 Coronary Arteriosclerosis 1000 Coronary Arteriosclerosis brain 0 5 prostate Source GEO sample is GSM203316 Last updated (according to GEO): Jun 21 2007 Study of in vitro granulocyte differentiation Source GEO sample is GSM137458 Last updated (according to GEO): Jun 06 2007 with some respiratory epithelium. 1039 1072 Spinal Cord 1000 861 Trachea MGJZ030207135Atestis 1000 Brain Lung 861 7 0 Pancreas bronchial epithelia 224 243 jzo016-rp1-v5-u74av2-met Brain of P10 Gja9 (-/-) C57Bl/6j mouse, replica K1 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188839 Last updated (according to GEO): Jun 06 2007 brain, cochlea: [4] Sample #4_le1 861 Blood 861 Neoplasm brain, cerebral cortex: Rat_03-43_NroLep_Lipska_e1_le1 3AMH02022201_Colorectal Adenocarc 9 0 Blood Test AD-311t1-A266-10 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113924 Last updated (according to GEO): Jun 16 2006 Cerebral cortex 1000 Lung 861 Normal Source GEO sample is GSM176245 Last updated (according to GEO): Apr 09 2007 Acetaminophen 3hr Rat 8691 blood vs. Acetaminophen 3hr Rat Pooled Control blood FormerSmoker 114 901 frontal lobe 78 66 Control blood 861 Cerebral cortex mouse left hemi-diaphragm Source GEO sample is GSM53239 Last updated (according to GEO): Jul 06 2005 metanephric mesenchyme, NGAL, 3 days, biological rep2 HNC005 091264 CAOV3(dup) on Affymetrix GeneChip Human Full Length Array HuGeneFL D2_Control_ZT 6_1 NA18508 H9RGV00111008 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hrs per day, 24 h time point Source GEO sample is GSM159765 Last updated (according to GEO): Apr 23 2007 Diaphragm 112 Day control rep 1 20 0 human caudate nucleus 861 Umbilicus 1000 Kidney Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 8030 blood Expression profiling of somatomotor cortex extracted from rats at 14d following sham surgery Source GEO sample is GSM41634 Last updated (according to GEO): May 27 2005 66 42 out of mouse bone marrow 2CdA: PK11195 intervention at 6.0h 861 Blood for morbid obesity 62 80 Gonadectomized Dahl-Iwai Female HighSalt Cortex rat4 gdahl_cortexr_k_GX_4c_051702 spinal cord 0 11 901 Parietal Lobe Cardiac-specific TNF-alpha transgenic mouse is an excellent model to study the pathologenesis of heart failure. Affytrix U74V2A was used to analyzed the gene expression profile of mice at the time point of compensated hypertrophy and dilated heart failure. Source GEO sample is GSM8991 Last updated (according to GEO): May 28 2005 Undifferentiated carcinoma 1000 CNS-SCsev_InjA14d-3C-s2 brain, cerebral cortex: Rat_02-137_TTX_Lipska_e1_le1 Male 13-week-old ddY mice (Japan SLC Co., Hamamatsu, Japan) weighing 38-43 g were used. Dose of 1.25 mg/kg olanzapine (gift from Eli Lilly and Company, Indianapolis, IN) was used in the study. The drug was dissolved in acetic anhydride and diluted with 0.9% saline, resulting in a final concentration of acetic acid of 0.5%. The drugs were injected intraperitoneally once daily for 28 consecutive days in a volume of 0.1 ml/10 g body weight. Microarray experiments were performed using an Agilent G4121A Mouse Oligo Microarray Kit as per the manufacturer?s instructions. The frontal cortex was immediately removed and the RNA was stabilized in RNAlater RNA Stabilization Reagent (Qiagen, Valencia, CA) and stored at -80°C until use. Total RNA was extracted using the RNeasy Mini Kit (Qiagen). The RNA was amplified and labeled by the Low RNA Input Fluorescent Linear Amplification Kit (Agilent). To synthesize cDNA, 200 ng total RNA was used. Vehicle-injected controls were labeled by cyanine 3 (PerkinElmer Life Sciences, Inc., Boston, MA) and drug-injected mice were labeled by cyanine 5. Hybridizations to the microarray were performed using the In situ Hybridization Kit Plus (Agilent). Doses of 750 ng cyanine 3-labeled cRNA, 750 ng cyanine 5-labeled cRNA, and control targets were mixed and fragmented in the kit?s fragmentation buffer, and then hybridized to the microarrays for 17 hours at 60°C in a hybridization rotator (Agilent) set to rotate at 4 rpm. Microarrays were washed in 6×SSC with 0.005% Triton X-102 at RT for 10 min, followed by 0.1×SSC with 0.005% Triton X-102 at 4°C for 5 min. The slides were dried, and then scanned by the Agilent G2565BA Microarray Scanner System. Data were analyzed using the Agilent Feature Extraction Software version 7.1. A rank consistency filter and LOWESS were used for dye normalization. Control mice and drug-injected mice were processed in parallel. Keywords = olanzapine Lot batch = US22502606_16011978017320 Source GEO sample is GSM25981 Last updated (according to GEO): Oct 28 2005 D2_Control_ZT 18_1 We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7. Source GEO sample is GSM200748 Last updated (according to GEO): Jul 12 2007 human frontal cortex Source GEO sample is GSM86953 Last updated (according to GEO): Feb 08 2006 052401_HF_331CB Aortic aneurysm without mention of rupture NOS 901 D_U133Plus_101_Amy Epithelium 861 none Source GEO sample is GSM246017 Last updated (according to GEO): Dec 03 2007 Muscle 1000 Normal Source GEO sample is GSM175939 Last updated (according to GEO): Apr 09 2007 2nd 4hr C-CA1 Keywords = muscle 140 157 dorsal raphe sprague2 between acute myeloid leukemia 457 486 na Source GEO sample is GSM180465 Last updated (according to GEO): Apr 04 2007 2697 The trigeminal ganglion 2675 Brain 861 17 7 hippocampi PGA-Csx_wt_7b-m4 103 85 of a past infection 36 21 from whole brain LivRegen6hr_022JAC3D_063.txt - Source GEO sample is GSM216546 Last updated (according to GEO): Aug 09 2007 861 Substantia nigra structure Spleen 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with BAFF for 30min Source GEO sample is GSM5452 Last updated (according to GEO): May 27 2005 852 842 blood flow NA Source GEO sample is GSM198908 Last updated (according to GEO): Jun 07 2007 olfactory epithelium tissue 85 111 high gestational age Source GEO sample is GSM213109 Last updated (according to GEO): Jul 25 2007 Laser capture lung cancer cells Source GEO sample is GSM191057 Last updated (according to GEO): May 25 2007 119 96 in embryonic stem cells CNS-RM_Mod24h-3C-s2 901 Caudate nucleus structure M7TW01010683 Normal Source GEO sample is GSM176024 Last updated (according to GEO): Apr 09 2007 884 Cerebral artery occlusion NOS Simple annotation: Cell-line, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3147.gif Source GEO sample is GSM79817 Last updated (according to GEO): Sep 22 2006 1000 Brain nic 3 (Experiment Neuroprotection4- Run 14985) Treatment, type=timepoint, description=primary cortical neurons were treated for 18 h with nicotine 10uM, agonist was then washed out and the cells were harvested 24h later, measurement=18.0 h Source GEO sample is GSM96727 Last updated (according to GEO): Feb 14 2006 Kidney 1000 Parkinson Disease 861 Brain 861 1000 Epithelial Cells Primary adenocarcinoma Source GEO sample is GSM16560 Last updated (according to GEO): May 28 2005 861 Adenocarcinoma of large intestine 1000 Lung osteoblast 627 637 Selective blockade of the inhibitory Fc{gamma} receptor (Fc{gamma}RIIB) in human dendritic cells and monocytes induces a type I interferon response program. Normal Source GEO sample is GSM175847 Last updated (according to GEO): Apr 09 2007 brain, cerebral cortex: Rat_02-50_VHL_Lipska_e1_le1 1000 Infection total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD40 for 30min Source GEO sample is GSM5491 Last updated (according to GEO): May 27 2005 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM119700 Last updated (according to GEO): Jul 11 2006 KPeterson-Met-26G110-s2 Ldn4 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n101 Source GEO sample is GSM2037 Last updated (according to GEO): Nov 21 2005 861 Brain EWS-C9 on NHGRI-6.5k_b STHdhQ111/Q111-C Communicable Diseases 861 with myocardial infarction 313 339 114 84 to physiologic hyperinsulinemia Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120699 Last updated (according to GEO): May 14 2007 50 41 mouse lung 921 909 of 68 tumors 861 Cerebral cortex R492P00424 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211389 Last updated (according to GEO): Jul 18 2007 Brain 1000 41 28 in mouse brain Whole blood 0 10 D_U133Plus_83_nAcc Sun187_BAV13 group 5 0 brain Brain 1000 M_U133Plus_99_nAcc 5 0 brain Large-scale analysis of the human transcriptome. Placenta Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 112.58 Stdv: 5.92 Min: 101.51 Max: 123.76 Source GEO sample is GSM2846 Last updated (according to GEO): Mar 20 2006 Spleen vs NGF (Nerve Growth Factor)Treated B cell 30min (set1) Parkinson's model voxel J4 Skin 1 Disease 0 13 861 Gland structure Hypertensive disease 1000 from SVG-A glial cells 21 43 861 Cerebellum CC11- sample 2 1000 Brain Female 21.5 yr before antibody enrichment scan 1 (U133A) 4 0 Brain Muscular Atrophy 896 iA50clone6- osteoblast 627 637 117 112 Lipids Ventral tegmental area 28 50 NCI60.43_LABEL47EXTRACT46SUB3 Source GEO sample is GSM134212 Last updated (according to GEO): Aug 06 2007 spleen 216 222 CNS-SMTC_Ctr14d-2C-s2 Assay of baseline expression in the cerebellum of an alcohol-naive Inbred Long Sleep mouse Source GEO sample is GSM67181 Last updated (according to GEO): Oct 28 2005 Brain 861 to the nose 599 609 Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181981 Last updated (according to GEO): Apr 13 2007 Brain 1000 Spleen 1000 frontal cortex wistar 3659 WGACON-99 Neoplasm 861 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19218 Last updated (according to GEO): May 27 2005 Brain 861 Exp 1 Time point 2 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:456, Count:32 Corner- Avg:31434, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:5.482294,SFGene:All Background:Avg:672.81,Stdev:8.83,Max:695.1,Min:653.5 Noise:Avg:14.89,Stdev:0.47,Max:16.2,Min:13.8 RawQ:17.21 Keywords = ALL Source GEO sample is GSM3421 Last updated (according to GEO): May 27 2005 CNS BMI-1 KO Chip C Muscle Cells 1000 M_U133A_62_HC nostrils 156 164 91 from the bone marrow 72 JMR-RatNaive-3bA-s2 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Insulin-like growth factor 1 for 240min Source GEO sample is GSM5623 Last updated (according to GEO): May 27 2005 Unsusceptible Group, Nucleus accumbens, Biological Replicate 1 131 basal ganglia 118 VDXIGRU_247401 567 548 the descending colon Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. All patients were considered sporadic cases on the basis that no clinical antecedents of familial adenomatous polyposis were reported, and those that met the clinical criteria for hereditary non-polyposis colon cancer (Amsterdam criteria) were excluded. Source GEO sample is GSM112301 Last updated (according to GEO): Jun 06 2006 Epithelial Cells 861 of the immune system 1468 1487 Penis 5 Normal Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 11 no additional Source GEO sample is GSM199297 Last updated (according to GEO): Jun 08 2007 m1-adenoma4 The induction of the heat-acclimated phenotype involves reprogramming the expression of genes encoding both constitutive and inducible proteins. In this investigation, we studied the global genomic response in the hypothalamus during heat acclimation, with and without combined hypohydration stress. Rats were acclimated for 2 days (STHA) or for 30 days (LTHA) at 34 degrees C. Hypohydration (10% decrease in body weight) was attained by water deprivation. 32P-labeled RNA samples from the hypothalamus were hybridized onto cDNA Atlas array (Clontech no. 1.2) membranes. Clustering and functional analyses of the expression profile of a battery of genes representing various central regulatory functions of body homeostasis demonstrated a biphasic acclimation profile with a transient upregulation of genes encoding ion channels, transporters, and transmitter signaling upon STHA. After LTHA, most genes returned to their preacclimation expression levels. In both STHA and LTHA, genes encoding hormones and neuropeptides, linked with metabolic rate and food intake, were downregulated. This genomic profile, demonstrating an enhanced transcription of genes linked with neuronal excitability during STHA and enhanced metabolic efficiency upon LTHA, is consistent with our previously established integrative acclimation model. The response to hypohydration was characterized by an upregulation of a large number of genes primarily associated with the regulation of ion channels, cell volume, and neuronal excitability. During STHA, the response was transiently desensitized, recovering upon LTHA. We conclude that hypohydration overrides the heat acclimatory status. It is notable that STHA and hypohydration gene profiles are analogous with the physiological profile described in the response to various types of brain injury. M7TW01013101 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225717 Last updated (according to GEO): Nov 05 2007 N2_d6 #2(16012165010081) NCI60.26_LABEL30EXTRACT29SUB3 Source GEO sample is GSM134122 Last updated (according to GEO): Aug 06 2007 861 Brain 1017 992 in traumatic brain injury 928 Endometrium ileum (pool of 4 animals)_72h monoassociation with B.thetaiotaomicron_B_5560 Source GEO sample is GSM161589 Last updated (according to GEO): Apr 23 2007 Skeletal muscle biopsy was obtained before a two-hours of hyperinsulinaemic (40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172131 Last updated (according to GEO): Feb 28 2007 0 Human Cortex 11 human frontal cortex Source GEO sample is GSM87043 Last updated (according to GEO): Feb 08 2006 Brain area 8/9_6y_RTT TNF-alpha, 02.00 hr. T-cell. 861 Colon AD-296t21-A106-03 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Liver 1000 metanephric mesenchyme, ANX, 5 days, biological rep2 Fibroblasts 38 48 of Parkinson's disease 450 471 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11453 Last updated (according to GEO): May 28 2005 Multiple Sclerosis 1000 Fibroid_2540A R686P01236 Gene expression data from human colon tumor tissue Source GEO sample is GSM173322 Last updated (according to GEO): Apr 20 2007 plasma cells 332 344 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11500 Last updated (according to GEO): May 28 2005 Disease Source GEO sample is GSM175800 Last updated (according to GEO): Apr 09 2007 for liver 26 35 Blood 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145794 Last updated (according to GEO): Nov 20 2006 ACHN hgu95e human frontal cortex Source GEO sample is GSM87001 Last updated (according to GEO): Feb 08 2006 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181103 Last updated (according to GEO): Jul 12 2007 1000 Brain 337 323 with adiposity osteoblast 627 637 SK-OV-3_CL6011_OVARIAN Brain 861 042601_HF_298FL Male 69.2 yr before antibody enrichment scan 1 (U133B) liver, PPARa-null mice, treatment with WY14643 for 5d Source GEO sample is GSM205802 Last updated (according to GEO): Jul 24 2007 Extracellular Matrix 1000 Neoplasm 861 861 Neoplasm 3 0 Lung plasma cells 50 61 1000 Mental Retardation 1000 Neoplasm Psychotic Disorders 1000 hypothalamus 0 11 Abdominal aorta structure 1000 Cerebral cortex 861 +_7369_batch1 on NHGRI-6.7k in seminoma 28 38 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188837 Last updated (according to GEO): Jun 06 2007 Adipose tissue 884 TEL-AML1-C57 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from postmorten brain regions Source GEO sample is GSM145068 Last updated (according to GEO): Nov 20 2006 aRNA probe from T7-based amplification Source GEO sample is GSM113693 Last updated (according to GEO): Jun 09 2006 brain, cerebral cortex: Rat_03-46_NroLep_Lipska_e1_le1 Occipital #2 The most common congenital cardiac abnormalities 50 97 N2_d4 #1(16012165010070) Organ 966 Skeletal bone 861 Non-defeated Control Group, Ventral tegmental area, Biological Replicate 2 129:26-3 spinal cord P12-ICHIKAWA DMSO control 24h rep2 Whole blood 0 10 91 from the bone marrow 72 I_U133A_5_AnCg Human skeletal muscle Myocardial Infarction 1000 DCN_P3_A Wild type 8 wk old male C3H/HeJ mouse pituitary gland Source GEO sample is GSM75003 Last updated (according to GEO): Feb 27 2007 Ventral Tegmental Area 5 Normal Prostate 24 Normal Parkinson Disease 861 1000 Cerebrum Coronary heart disease 913 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, air control, 6 h time point Source GEO sample is GSM159798 Last updated (according to GEO): Apr 23 2007 Epithelium 861 Human Lung Transplant - BAL Kidney OC-2B Halothane 10 exposures-2 embryonic cortical neuron treated with NMDA Source GEO sample is GSM49623 Last updated (according to GEO): May 29 2005 861 Brain Morula replication 3 Keywords = preimplantation Keywords = development Source GEO sample is GSM14689 Last updated (according to GEO): May 28 2005 15 0 skeletal muscle Brain Injuries 901 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=730600 LaserPower=4.333.79 Lot batch = LC17N093 Source GEO sample is GSM4816 Last updated (according to GEO): Nov 21 2005 Lymph Node [JunctionChip 3 of 5] Expression profiling of spinal cord section (T9) extracted from rats 12h following moderate injury Source GEO sample is GSM31528 Last updated (according to GEO): May 27 2005 Spinal Cord 1000 Spleen vs IL10 Treated B cell 120min (set1) of the postmortem brains 674 698 22-oct-2002-BrainAsubB-ab150 861 Ganglia Parkinson Disease 861 Endometrium 17 Normal Probeset expression data from NA12751 growth 3 Source GEO sample is GSM201540 Last updated (according to GEO): Aug 08 2007 Large-scale analysis of the mouse transcriptome. Umbilical cord, E18 embryos C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 325.58 Stdv: 14.55 Min: 302.16 Max: 348.55 Source GEO sample is GSM2977 Last updated (according to GEO): Mar 20 2006 Semeralul_PFC_Development_Week4_Batch1_Animal_3 Muscle Source GEO sample is GSM4294 Last updated (according to GEO): May 27 2005 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n076 Source GEO sample is GSM2086 Last updated (according to GEO): Nov 21 2005 Skin 1000 bronchial epithelia 224 243 brain, Left frontal Lobe: Extract15_le1 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments (Sample): Experiment User: jmorris Probe Array Lot: 9914791 Exp 2-17-01 Comments (Exp): Reagents: (none) Reagent Lot: (none) Algorithm: Statistical Corner+ Avg:203, Count:32 Corner- Avg:27300, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:7.478643,SFGene:All Background:Avg:422.27,Stdev:10.15,Max:448.3,Min:398.5 Noise:Avg:11.63,Stdev:0.35,Max:12.5,Min:10.4 RawQ:16.38 Keywords = ALL Source GEO sample is GSM3468 Last updated (according to GEO): May 27 2005 DBA/2J hypothalamus rep2 25 0 frontal cortex wistar 3922 Aortic Aneurysm, Abdominal 1000 861 Heart B220hi sIgM+ Mature B cells sorted out of mouse bone marrow, sort no. 9 Source GEO sample is GSM652 Last updated (according to GEO): Mar 20 2006 The overall impact of prion disease on gene expression is not well characterized. We have carried out a large-scale expression analysis of specific cell types commonly employed in studies of prion disease. Neuroblastoma cells (N2a) and hypothalamic neuronal cells (GT1) can be persistently infected with mouse-adapted scrapie prions, the latter demonstrating cytopathologic effects associated with prion neuropathology. Exploiting a mouse DNA microarray containing approximately 21,000 spotted cDNAs, we have identified several hundred differentially expressed sequences in the two cell lines when infected with prion strain RML. ScN2a and ScGT1 cells demonstrate unique changes in RNA profiles and both differ from the reported changes in human microglia and prion-infected brain studies albeit with some overlap. In addition, several of the identified changes are shared in common with other neurodegenerative diseases such as Alzheimer's disease. The results illustrate that prion infection differs in effect depending on cell type, which could be exploited for diagnostic or therapeutic intervention. 928 Hyperinsulinism Pulmonary epithelial cell line brain, hippocampus: C1-III_e1_le1 P1_KIDNEY_12 hippocampal glutamatergic CA1 pyramidal neurons Treatment, type=behavioral_stimulus Source GEO sample is GSM35846 Last updated (according to GEO): May 27 2005 Ganglia, Spinal 923 Gene expression data from postmorten brain regions Source GEO sample is GSM145116 Last updated (according to GEO): Nov 20 2006 DBA/2J ACU, Rep1 normal lung 1473 Source GEO sample is GSM17298 Last updated (according to GEO): May 28 2005 GM12892 142 138 Brain Stria 861 Expression profiling of spinal cord section (T9) extracted from rats 30m following mild injury Source GEO sample is GSM31227 Last updated (according to GEO): May 27 2005 accumbens_10 Source GEO sample is GSM80600 Last updated (according to GEO): Mar 31 2006 Heart Septal Defects, Atrial 1000 Plasma 861 nostrils 156 164 CNS-SC_InjA7d-1A-s2 Skin 861 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188836 Last updated (according to GEO): Jun 06 2007 CNS-SCsev_InjB28d-3B-s2 49 29 to pulmonary fibrosis GM18507_technical_rep_2 15 7 brainstem frontal cortex sprague 3937 whole tissue, individual animal, 10 weeks old, male Sprague Dawley frontal cortex file:p3937w Source GEO sample is GSM15174 Last updated (according to GEO): Oct 28 2005 Olfactory Epithelium 1000 with cancer 34 44 901 Mammary Neoplasms 1000 medulloblastoma Replicate1_Voxel C10 with some respiratory epithelium. 1039 1072 Large-scale analysis of the mouse transcriptome. Eye C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 272.53 Stdv: 11.06 Min: 256.80 Max: 291.32 Source GEO sample is GSM2945 Last updated (according to GEO): Mar 20 2006 Muscle Source GEO sample is GSM4288 Last updated (according to GEO): May 27 2005 Blood 1000 Spleen 1000 ALS gray matter 7 Sporadic We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201811 Last updated (according to GEO): Jun 20 2007 Nose 1000 NA Source GEO sample is GSM109464 Last updated (according to GEO): May 22 2006 Autistic Disorder 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145511 Last updated (according to GEO): Nov 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145532 Last updated (according to GEO): Nov 20 2006 1000 Spleen Gastrocnemius muscle 1 day after 100ul 10uM cardiotoxin injection Source GEO sample is GSM4271 Last updated (according to GEO): May 27 2005 861 Neoplasm 1000 Spleen Blood Test (Blinded) Sample Source GEO sample is GSM129949 Last updated (according to GEO): Sep 18 2007 875 Coronary heart disease Amygdala 9 Normal Plasma 861 Fluid induced shear stress is widely recognized as an important biophysical signal in cell-cell mechanotransduction. To identify cellular signaling pathways that are regulated by fluid shear stress, we applied the unbiased approach of transcriptional profiling. Our cDNA array analysis detected that 1165 of the 6288 sampled unigenes were significantly affected by pulsatile fluid flow. GenMapp 2.1 analysis revealed pathways of genes regulated by shear stress: angiogenesis, blood vessel morphogenesis, regulation of endothelial cell proliferation and prostaglandin biosynthesis. Individual genes significantly up-/down-regulated by shear stress included vascular endothelial growth factor A (VEGFa), cysteine rich protein 61 (CRY61), platelet derived growth factor, alpha (PDGFa), connective tissue growth factor (CTGF), Neuropilin 1 (NRP1), angiotensin II receptor, type 1a (AGTR1a) and fibroblast growth factor 1 (FGF1). Based on these findings, we hypothesize that fluid shear stress regulated VEGF most likely stimulates MC3T3-E1 cells through autocrine/paracrine release and may provide a powerful recruitment signal for osteoclasts, endothelial cells and/or stem cells during bone remodeling. Last Updated (by provider): Jun 19 2007 Contributers: Sanda Iacobas Dumitru A Iacobas David C Spray Mia M Thi Plasma 861 NG002_c human cerebellum Source GEO sample is GSM87064 Last updated (according to GEO): Feb 08 2006 It is widely assumed that genetic differences in gene expression will underpin much of the differences between individuals and many of the quantitative traits of interest to geneticists. Despite this, there has been little work on genetic variability in human gene expression and almost none in the human brain. This is because the tools for assessing this genetic variability were not available. With whole genome SNP genotyping arrays and whole transcriptome expression arrays, these experiments have now become feasible. We have carried out whole genome genotyping and expression analysis on a series of 193 neuropathologically normal human brain samples using the Affymetrix GeneChip Human Mapping 500K Array Set and Illumina HumanRefseq-8 Expression BeadChip platforms. Here we present data showing that 58% of the transcriptome is cortically expressed in at least 5% of our samples, and of these cortically expressed transcripts 21% have expression profiles that correlate with their genotype. These genetic expression effects should be useful in determining the underlying biology of associations with common diseases of the human brain and in guiding the analysis of the genomic regions involved in the control of normal gene expression. Last Updated (by provider): Nov 05 2007 Contributers: Mona Kaleem David W Craig Matthew J Huentelman Leslie Bryden Priti Nath Diane Hu-Lince Dietrich Stephan Eric M Reiman Lauren Marlowe Victoria L Zismann Christopher B Heward Doris Leung Amanda J Myers Kristen Rohrer Peter Holmans Alice Zhao Jennifer A Webster Keta Joshipura John V Pearson Keith D Coon Jesse R Gibbs John Hardy Lymphoblastoid Cell Line for Individual 8174.5 log phase Gene expression data from postmorten brain regions Source GEO sample is GSM145258 Last updated (according to GEO): Nov 20 2006 1000 Cerebral cortex AKR/J_male_hypothalamus Source GEO sample is GSM184191 Last updated (according to GEO): Apr 26 2007 Prefrontal Cortex 0 16 NCI60.31_LABEL35EXTRACT34SUB3 Source GEO sample is GSM134146 Last updated (according to GEO): Aug 06 2007 17 7 hippocampus Richard Almon-51-1133800610323 Primary tumor 19 32 444 435 infection S1P2-KO-neocortex, biological rep8 (female) intestine_wildtype_24hfasted_rep2 nic 4 (Experiment Neuroprotection4- Run 21823) Treatment, type=timepoint, description=Same sample used for Experiment Neuroprotection4-Run 14985, samples were rerun due to oven failure, measurement=0.0 h Source GEO sample is GSM96691 Last updated (according to GEO): Feb 14 2006 Bone structure of tibia 1000 24 19 (Renal Gene expression data from postmorten brain regions Source GEO sample is GSM145460 Last updated (according to GEO): Nov 20 2006 Parkinson's model voxel A4 Replicate2_Voxel B9 Spleen vs Lysophosphatidic Acid Treated B cell 120min (set1) Nasal Epithelium 865 861 Cerebral cortex 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113963 Last updated (according to GEO): Jun 16 2006 Exp B_4, 30mg/kg CPF atrial septal defects 198 218 Nasal Epithelium 865 post infection 29 42 cortex rattus_norvegicus_strain iNP animal_number 8 Brain 861 17 7 hippocampus Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26119.gif Source GEO sample is GSM81541 Last updated (according to GEO): Sep 22 2006 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225370 Last updated (according to GEO): Aug 31 2007 Tongue Main Corpus 3 Normal heart 1169 1173 Parkinson's disease sample x114 0 30 861 Prostate 41 28 in mouse brain R661P00807 9 0 Blood Test 41 minus the frontal cortex 65 41 28 in mouse brain Human retinal sphere RNA-1, chip HG-U133A from the forebrain 20 37 NeverSmoker 3 Nasal Epithelium 901 861 Immune system **** Source GEO sample is GSM4318 Last updated (according to GEO): May 27 2005 3AJZ02052302_Ovary Gene expression data from postmorten brain regions Source GEO sample is GSM145453 Last updated (according to GEO): Nov 20 2006 none Source GEO sample is GSM239909 Last updated (according to GEO): Dec 07 2007 B6 day 6, biological rep 2, tech rep 2 RNA from vastus lateralis of healthy young (21-31 year old) and older (62-77 year old) men. Signal data normalized to mean intensity of 500 over all probes sets. Analysis done with Affymetrix Microarray Suite 5.0 software.. Date GSE80 Last Updated: May 29 2005 Contributers: Charles A Thornton Stephen Welle Andrew I Brooks Includes GDS156. Update date: Apr 17 2003. Dataset description GDS156: Comparison of gene expression in vastus lateralis skeletal muscle biopsies in healthy young (21-31 year old) and older (62-77 year old) men. Sample RNAs isolated from individuals and pooled into groups of 8.. 1000 Liver Cerebral cortex 1000 RNA isolated from fetal cerebrum Keywords = trisomy Keywords = brain Keywords = Down syndrome Source GEO sample is GSM22527 Last updated (according to GEO): May 27 2005 88 FC BA9 A 1000 Brain Liver (HK2) 9 0 rat kidney Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15688 Last updated (according to GEO): May 28 2005 861 Oocytes Laser capture lung cancer cells Source GEO sample is GSM191012 Last updated (according to GEO): May 25 2007 I_U133Plus_125_AnCg Multiple Sclerosis 1000 The hypothalamic paraventricular (PVN) and supraoptic (SON) nuclei are important integrative structures that regulate co-ordinated responses to perturbations in cardiovascular homeostasis. Through descending projections from parvocellular neurons to the brainstem, the PVN acts as an autonomic 'premotor nucleus', regulating reflex changes in sympathetic nerve activity that are involved in blood pressure and blood volume regulation. Endocrine responses are mediated through axonal projections from SON and PVN magnocellular neurons (MCNs) to the capillaries of the posterior pituitary neural lobe. In response to dehydration, a massive release of the antidiuretic peptide hormone vasopressin (VP) into the circulation is accompanied by a dramatic functional remodelling of the HNS. We have used microarrays to comprehensively catalogue the genes expressed in the PVN, the SON and the neurointermediate lobe (NIL) of the pituitary gland. Further, we have identified transcripts that are regulated as a consequence of dehydration, as well as RNAs that are enriched in either the PVN or the SON. We suggest that these differentially expressed genes represent candidate regulators and effectors of HNS activity and remodelling. Last Updated (by provider): Jan 31 2006 Contributers: GEMMA BEIGHTON JULIAN PATON SONG YAO CHARLES C HINDMARCH Total RNA extracted from the forebrain of a Tg-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144385 Last updated (according to GEO): Nov 14 2006 in SVG-A glial cells 30 49 The major myeloid blood cell lineages, including erythrocytes, platelets, granulocytes and macrophages, are generated from hematopoietic stem cells (HSC) by differentiation through a series of increasingly more committed progenitor cells. Precise phenotypic identification and functional characterization of such intermediate progenitors has important consequences for understanding fundamental differentiation processes and is clinically relevant since such events become dysregulated in various disease settings, including leukemia. While previous studies have suggested a hierarchy for myeloid differentiation involving a common progenitor through which all myeloid lineages are derived, several recent studies have suggested that such a developmental intermediate might not be an absolute requirement. Here, we evaluated the functional in vitro and in vivo potentials of a range of prospectively isolated myeloid precursors with differential expression of CD150, Endoglin and CD41. Our studies reveal a complex hierarchy of myeloerythroid progenitors with distinct and developmentally restricted lineage potentials. Global gene expression signatures of these cellular subsets revealed expression patterns consistent with their functional capacities, while hierarchical clustering analysis provides details on their lineage relationships. These data challenge existing models of hematopoietic differentiation, by suggesting that progenitors of the innate and adaptive immune system in the adult separate late, and to a large extent, following the divergence of megakaryocytic/erythroid potential. Last Updated (by provider): Jul 09 2007 Contributers: Robert Månsson Charles Kwok Fai Chan Gudmundur Logi Norddahl David Bryder Mikael Sigvardsson Joanne L Attema Cornelis J Pronk Derrick J Rossi SK-MEL-2 hgu95e Coronary Arteriosclerosis 1000 91 from the bone marrow 72 cerebral cortex 7 21 7 cerebral cortex 21 -uninjured cortex 104 120 The adult mouse was injected intraperitoneal (ip) with Escherichia coli lipopolysaccharide (LPS, 0.33mg/kg body weight (BW), ~10ug/mouse; serotype O127:B8, Sigma) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use. Source GEO sample is GSM72507 Last updated (according to GEO): Sep 07 2005 the ventricular 1095 1109 Lymphoblastic Leukemia 901 Whole blood 0 10 NINDS-RNP-VTA-8aA-s2 1000 Brain Stem retina 7 12 from nose 98 106 mouse brains 187 198 PGA-MPF-BALB-bleo-24h-2bAv2-s2 Nasal Epithelium Inhalation Formaldehyde 2ppm 5d ID217 between the LAD artery 266 287 861 Eye 31 0 Conventional Descending colon 1 for blood 203 211 no additional Source GEO sample is GSM199031 Last updated (according to GEO): Jun 08 2007 1000 Cerebral cortex 707 683 defective hemidesmosomes pull-downC_8, ZT6 of somatomotor cortex 21 41 901 Autoimmune Diseases 124 FC BA9 B R456P00301 Bone Marrow 1000 PGA-E14.5_1A cerebral 0 7 Hippocampus 1000 Neoplasm 861 frontal cortex wistar 3662 whole tissue, individual animal, 10 weeks old, male Wistar frontal cortex file:p3662w Source GEO sample is GSM15120 Last updated (according to GEO): Oct 28 2005 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198632 Last updated (according to GEO): Jun 06 2007 of cultured myotubes 999 1019 brain, hippocampus: CON-CA3-19_e1_le1 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225669 Last updated (according to GEO): Nov 02 2007 Analysis of target genes induced by the Amyloid Precursor Protein Intracellular Domain Source GEO sample is GSM93713 Last updated (according to GEO): Jan 25 2006 Backskin_DN-CLIM_P6_rep1 Macrophage smi86 NMDA 10 (7/8) (Experiment NMDA1-Run 9136) Treatment, type=time_course, description=samples are treated for 10, 30 or 60 min with NMDA 1mM, the agonist is then washed out and the cells are harvested 24h later, measurement=10.0 m Source GEO sample is GSM96712 Last updated (according to GEO): Feb 14 2006 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11555 Last updated (according to GEO): May 28 2005 esophagus_3 Bone Marrow 1000 77 66 Normal Liver p53 +/+, 12 hour, replicate a Source GEO sample is GSM2556 Last updated (according to GEO): May 27 2005 Probeset expression data from NA12751 growth 1, replicate 5 Source GEO sample is GSM195207 Last updated (according to GEO): Aug 08 2007 9 0 Blood Test 861 Hypothalamic structure 861 Cardiomyopathies Date 11/30/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : embryo proper Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 0.625 mg/kg Time : 3 hrs post-injection Intervention : none Risk: subNOAEL (no increased risk of malformation) Conditional biomarker: p53 protein induction not observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 8-10 embryos pooled from same litter Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = embryo Lot batch = AI058 Source GEO sample is GSM12053 Last updated (according to GEO): May 28 2005 CNS-SMTC_Mod7d-1Cs2 Category: Lymphoma Classification Subcategory: Chronic Lymphocytic Leukemia Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n116 Source GEO sample is GSM2063 Last updated (according to GEO): Nov 21 2005 whole blood_100346 Standard Affymetrix Protocol Source GEO sample is GSM16465 Last updated (according to GEO): May 28 2005 Liver 0 4 CNS-SC_InjA30m-1B-s2 from magnocellular neuron axon terminals 652 691 1000 Cerebellum 67 40 with coronary artery disease /3T3 fibroblasts 295 310 7 0 Pancreas Neoplasm 861 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/24869.gif Source GEO sample is GSM81553 Last updated (according to GEO): Sep 22 2006 Infection 861 1000 Hippocampus 211 199 In the brain 1000 Cerebral cortex Testis 1000 of the mammalian nervous system 46 76 ileum 1000 GSE420 I_U133A_92_CB Coronary heart disease 913 334 324 The jejunum total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with BAFF for 60min Source GEO sample is GSM5455 Last updated (according to GEO): May 27 2005 CNS-SCsev_InjA4h-3C-s2 Liver 1000 SN:1006723 Source GEO sample is GSM115350 Last updated (according to GEO): Jun 20 2006 db/m 8wk 3 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CpG-oligodeoxynucleotide for 30min Source GEO sample is GSM5522 Last updated (according to GEO): May 27 2005 RIIIS-J_male_hypothalamus Epithelium 861 Adrenal Medulla 1000 56 32 out of mouse bone marrow HCC (HBV+, HK64, T6) Neuromuscular Diseases 1000 R6/2 (triple treatment) 5253 861 Brain 861 Occipital lobe 79 67 Normal Breast T47D_Untreated_0.1% hippocampal glutamatergic CA3 pyramidal neurons Source GEO sample is GSM35819 Last updated (according to GEO): May 27 2005 Microdissected CA1 region from VC mice 3 weeks off dox 1 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 18 hours after lights on. Original sample code = CM32A Source GEO sample is GSM227319 Last updated (according to GEO): Sep 10 2007 122 muscle cells 134 Olfactory Epithelium 901 M_U133A_99_DLPFC with acute measles 20 37 46 8 in docetaxel-refractory prostate cancer Expression profiling of spinal cord section (T8) extracted from rats 7d following mild injury Source GEO sample is GSM31455 Last updated (according to GEO): May 27 2005 Cortex_Control_rep6 (05SE736) 100110 1514 1487 central innate immune system Nasal Epithelium 865 Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.86 Subject: 2822 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39018 Last updated (according to GEO): May 27 2005 db/m 16 wk 3 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181116 Last updated (according to GEO): Jul 12 2007 no additional Source GEO sample is GSM199064 Last updated (according to GEO): Jun 08 2007 brain, cerebral cortex: Rat_02-36_VHL_Lipska_e1_le1 Cardiomyopathies 1000 of the atrial 647 659 5 0 Spleen Cervix 3 Normal Tissue Source GEO sample is GSM67264 Last updated (according to GEO): Jan 19 2006 with skeletal muscle atrophy 26 53 M_U133A_4_DLPFC Retina 1000 861 Hippocampus Kidney 1000 brain, hippocampus: PR-DG-11_e1_le1 Brain 861 Blood 861 Spleen 1000 7 0 prostate Brain 861 Cerebral cortex 861 861 Cerebral cortex NA12005 RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above Source GEO sample is GSM160006 Last updated (according to GEO): Feb 05 2007 Osteoblasts 1000 Neurotransmitters 861 Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. Moderate controlled cortical impact with pneumatic impactor, 6 m/s impact velocity and 1.5 mm deformation. 8h after surgery, a 4 mm diameter disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44475 Last updated (according to GEO): May 27 2005 YFPH-Amygdala-replicate2 1000 Heart failure post infection 29 42 Coronary heart disease 913 861 Cerebral cortex Retina 1000 the ventricular 1095 1109 Brain 1000 715 705 from livers 5 0 brain with Parkinson's disease 27 50 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3329 Last updated (according to GEO): Mar 21 2006 Kidney 1000 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198654 Last updated (according to GEO): Jun 06 2007 1000 Structure of trigeminal ganglion (cortex 19 25 14 days hindlimb suspended, 5 day reloaded Source GEO sample is GSM17361 Last updated (according to GEO): May 28 2005 Epithelium 861 NA12762 Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 8691 blood Control Source GEO sample is GSM176466 Last updated (according to GEO): Apr 09 2007 brain 0 5 335 325 The jejunum 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114262 Last updated (according to GEO): Jun 16 2006 Macrophage smi83 Nerve 1000 5 0 brain Heart Atrium 1000 P46 deprived visual cortex replicate 2 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211309 Last updated (according to GEO): Jul 18 2007 Neoplasm 861 GSE2178 BC305A-BE from the right forebrain 21 44 9 0 cerebellum Liver Test (Blinded) Sample Source GEO sample is GSM130064 Last updated (according to GEO): Sep 18 2007 Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. All patients were considered sporadic cases on the basis that no clinical antecedents of familial adenomatous polyposis were reported, and those that met the clinical criteria for hereditary non-polyposis colon cancer (Amsterdam criteria) were excluded. Source GEO sample is GSM112308 Last updated (according to GEO): Jun 06 2006 Brain 861 B220+c-kit+ Pre BI cells sorted out of mouse bone marrow, sort no. 10 Source GEO sample is GSM627 Last updated (according to GEO): Mar 17 2006 Fi4_1, mouse, FVB, infected, 4 days post infection_rep 1 hippocampus_9 20 0 human caudate nucleus 411_1 EOM 56 Day mdx rep 1 The nose 94 101 NCI60.32_LABEL36EXTRACT35SUB3 Source GEO sample is GSM134151 Last updated (according to GEO): Aug 06 2007 I_U133A_34_CB Adrenal medulla [JunctionChip 4 of 5] Nasal Epithelium Inhalation Formaldehyde 07ppm 8d ID145 amygdala_1 1000 Brain Mesenchymal Stem Cells 1000 accumbens rattus_norvegicus_strain iNP animal_number 10 861 Blood 80 68 Control blood Stem cells 1000 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141294 Last updated (according to GEO): Oct 26 2006 /2J periaqueductal gray rep2 3 30 Y HID D040 Spleen vs Lysophosphatidic Acid Treated B cell 60min (set1) 758 745 of trisomy 21 Blood 1000 43h-Control replication 3 Keywords = preimplantation Keywords = development Source GEO sample is GSM14703 Last updated (according to GEO): May 28 2005 Nipple Cross Section 3 Normal human cerebellum Source GEO sample is GSM87065 Last updated (according to GEO): Feb 08 2006 Nasal Epithelium Inhalation Formaldehyde 6ppm 5d ID297 Spleen 1000 Adult murine BM, Lin-Sca1lowKitlowIL7r+Flk2+ 1 NoCAD_replicate45 DCIS130 on harvard-12k Infection 861 Skeletal bone 861 17 7 hippocampus SQ-4389-A327-5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 24 7 Right Frontal Lobe Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap. 894 874 in the rat esophagus 1000 Brain P24 non-deprived visual cortex replicate 1 Normal Source GEO sample is GSM175977 Last updated (according to GEO): Apr 09 2007 20 0 atrioventricular_node A HID I D051 Parkinson Disease 1000 114 cortex 120 Nasal Epithelium 901 of U87 glioblastoma 86 104 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.86 Subject: 2822 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39014 Last updated (according to GEO): May 27 2005 GSE8240 FSCC5 on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression data from postmorten brain regions Source GEO sample is GSM145928 Last updated (according to GEO): Nov 20 2006 Psychotic Disorders 1000 Starvation 916 GBM Treatment, type=remove Source GEO sample is GSM99597 Last updated (according to GEO): Apr 21 2006 Spleen vs CD27 Treated B cell 240min (set2) 1000 frontal lobe 1000 Spleen 5 0 brain brain 0 5 1000 Spleen 861 Cerebellum CNS-SMTC_CtrT0-2A-s2 Macrophage 14smi118 Standard Affymetrix Protocol Source GEO sample is GSM16461 Last updated (according to GEO): May 28 2005 Cells captured via Arcturus LCM system, amplified (RiboAmp, 2 rounds) and labeled (Enzo) for hybridizaton to Affymetrix MG_U74Av2 arrays, using manufacturers protocols in each step. Source GEO sample is GSM6201 Last updated (according to GEO): Mar 17 2006 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2717 Source GEO sample is GSM2138 Last updated (according to GEO): Nov 21 2005 a benign tumor 37 50 WGACON-236 228 219 Hippocampi CNS-SMTC_Ctr24h-1B-s2 Wild-type-hippocampus, biological rep2 (male) Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228639 Last updated (according to GEO): Sep 11 2007 B6 day 3, biological rep 1, tech rep 1 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 24 h time point Source GEO sample is GSM159817 Last updated (according to GEO): Apr 23 2007 Parkinson Disease 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with MIP3-alpha (Macrophage inflammatory protein-3) for 120min Source GEO sample is GSM5692 Last updated (according to GEO): May 27 2005 f2#49 versus pool Mouse Brain tissue Gene expression data from postmorten brain regions Source GEO sample is GSM145164 Last updated (according to GEO): Nov 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145544 Last updated (according to GEO): Nov 20 2006 43h-AC replication 2 Keywords = preimplantation Keywords = development Source GEO sample is GSM14720 Last updated (according to GEO): May 28 2005 Mesenchymal Stem Cells 1000 Donor 3 Time point 72 hours post Infection with HIV-1, RF Source GEO sample is GSM2626 Last updated (according to GEO): May 27 2005 of Parkinson's disease 450 471 1000 ovarian neoplasm 5 0 brain PGA-HMO-NonObese-8aUA-s2 of the mouse brain 235 253 361 335 hypertrophic cardiomyopathy DLBC5 on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene Expression Comparison of First Passage vs. Primary Human and Mouse Retinal Sphere Cells - Homo sapiens Epithelial ovarian cancer 0 24 861 Ovary total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL10 for 60min Source GEO sample is GSM5636 Last updated (according to GEO): May 27 2005 Bone structure of tibia 1000 Affymetrix Mouse Genome 430 2.0 GeneChip microarrays were used to analyze murine neocortical and cerbellar astrocytes generated from postnatal (PN) day 1 wild-type (ICR) pups. Last Updated (by provider): Mar 14 2007 Contributers: Simon Loeser Ryan J Emnett Mark A Watson Jeffrey R Leonard Kenneth D Aldape David B Mansur Meredith G Albin Arie Perry Guido Reifenberger David H Gutmann Rakesh Nagarajan Mukesh K Sharma Neoplasm 861 Communicable Diseases 1000 none Source GEO sample is GSM239862 Last updated (according to GEO): Dec 07 2007 brain, hippocampus: KA24-I_e1_le1 3 0 skin 91 from the bone marrow 72 5 0 brain 118T Primary tumor 19 32 Cerebellum 1000 Substantia nigra PD rep7 adenocarcinoma 313 327 none Source GEO sample is GSM244527 Last updated (according to GEO): Nov 23 2007 Ovarian_Tumor_Endometrioid_CHTN-OE-018 D_U133A_103_DLPFC Breast 861 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11468 Last updated (according to GEO): May 28 2005 Carcinoma 861 1000 Solid tumor Prefrontal Cortex Source GEO sample is GSM105471 Last updated (according to GEO): Apr 17 2006 Medulla 861 15 0 Cerebral malaria Ganglia 861 Gene expression profiling reveals progesterone-mediated cell cycle and immunoregulatory roles of Hoxa-10 in the preimplantation uterus. by the liver 209 220 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59857.gif Developmental Stage: E8.75 Source GEO sample is GSM229831 Last updated (according to GEO): Nov 06 2007 across Peyer's patches 326 347 1000 Structure of postcentral gyrus Male 71.2 yr after antibody enrichment scan 2 (U133B) 1000 ovarian neoplasm no additional Source GEO sample is GSM199071 Last updated (according to GEO): Jun 08 2007 Platelet activating factor receptor and innate immunity: 16011868021377 DLCL-0007 || lc4b028 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13426.gif Source GEO sample is GSM79664 Last updated (according to GEO): Sep 22 2006 141 115 of parieto-occipital cortex Liver 1000 6 0 Cancers Lung 1 Normal HCC (HBV+, HK22) Gene expression data from biopsy of infected skin of subject with resolver phenotype. Source GEO sample is GSM128958 Last updated (according to GEO): Sep 13 2007 A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke. White and grey matter in the distribution on the middle cerebral artery 6 hours after administration of saline (control); third replicate; pooled mRNA from 6 brains. Source GEO sample is GSM2206 Last updated (according to GEO): May 27 2005 GSE6275 861 Cerebral cortex Richard Almon-48-1138200270883 1000 Brain HapMap CHB Male Source GEO sample is GSM159609 Last updated (according to GEO): Feb 01 2007 Kidney CR-5A Hypothalamus Source GEO sample is GSM107912 Last updated (according to GEO): Jun 06 2006 N/A Source GEO sample is GSM4331 Last updated (according to GEO): May 28 2005 1000 Brain Epithelial Cells 1000 0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point, biological rep 3 GBM Treatment, type=remove Source GEO sample is GSM99568 Last updated (according to GEO): Apr 21 2006 Cochlea 0 6 54 39 from 12 cochleas Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11222 Last updated (according to GEO): May 28 2005 METH 2 (cortex 19 25 rat model organism with depression left untreated or treated with reserpine Source GEO sample is GSM247186 Last updated (according to GEO): Dec 11 2007 brain_OFC_bipolar B_mr421 in pineal glands. 258 275 901 frontal lobe Bone Marrow 1000 861 Occipital lobe Structure of parenchyma of lung 901 Mouse model of congenital heart disease in Csx/Nkx2.5 mutant embryos. Homozygous mutant mouse at embyronic day 9.5. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2271 Last updated (according to GEO): May 27 2005 with myocardial infarction 313 339 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188779 Last updated (according to GEO): Jun 06 2007 Gene expression data from microdissected area # 1 of 2182 tumor Source GEO sample is GSM182303 Last updated (according to GEO): Apr 16 2007 Laser capture lung cancer cells Source GEO sample is GSM191043 Last updated (according to GEO): May 25 2007 5 0 brain Osteoblasts 1000 AKR/J Hippocampus B from liver 21 30 Exp A, Animal #1, control (0mg/kg) CPF Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours Source GEO sample is GSM246128 Last updated (according to GEO): Dec 03 2007 Neoplasm 861 39 21 from mammary glands Nose 1000 ovary 45 50 WGACON-130 861 Retina in the mammalian nervous system 110 141 Plasma 861 brain 0 5 911 Prostate cancer metastatic Saccule 0 6 Prostate 861 Normal Source GEO sample is GSM175789 Last updated (according to GEO): Apr 09 2007 brain, frontal cortex: pADX AM DR b_e1_le1 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11512 Last updated (according to GEO): May 28 2005 Abdominal aorta collected during autopsy within 24 hours post mortem Source GEO sample is GSM170561 Last updated (according to GEO): Jul 26 2007 Simple annotation: Reference verification, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10074.gif Source GEO sample is GSM78463 Last updated (according to GEO): Sep 22 2006 Mice sacrificed after swimming twice a day for 4 weeks. Keywords = exercise induced hypertrophy Source GEO sample is GSM2359 Last updated (according to GEO): May 27 2005 61 41 from postmortem brain Tumor__Lymphoma_Follicular_FSCC_S98_5894 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A EOM 56 Day Control rep 1 Disorder of artery 865 osteoblast 627 637 metanephric mesenchyme, control, 2 days, biological rep1 15 0 human cerebellum brain, adrenal medulla: 7A_e1_le1 861 Testis 896 Primary Neoplasm 913 Diabetes Mellitus, Non-Insulin-Dependent Heart Septal Defects 884 cerebral cortex 7 21 "8h Thy-Noc, Exp4" 18 0 In skeletal muscle 861 Blood Whole Brain 73 83 Liver (HBV+, SF32) JMR-RatInj21d-2aA-s2 861 Brain Prostate carcinoma 1000 Female 24.4 yr before antibody enrichment scan 1 (U133A) 861 Cerebral cortex S25 NLS 142Q TG2 F4/26 S25 NLS Htt exon 1 142Q Mouse 3 months Cerebellum Male Source GEO sample is GSM73204 Last updated (according to GEO): Sep 06 2005 5 0 Spleen CNS-SpinalC-conAdult-24h-2C-s2 Replicate3_Voxel F9 corticosterone_treated_rep4 (06SE460) 901 frontal lobe 284 279 Spleen Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11336 Last updated (according to GEO): May 28 2005 of human breast cancer 31 52 Macrophage 14smi047 104 79 of glioblastoma multiforme Heart 1000 673 659 by decapitation adenoma 861 CO (Experiment 4Rlong: Run 19283) Treatment, type=timepoint, measurement=0.0 m Source GEO sample is GSM96679 Last updated (according to GEO): Feb 14 2006 AKR/J Olfactory Bulb D Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3307 Last updated (according to GEO): Mar 21 2006 of somatomotor cortex 21 41 Plasma 861 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210368 Last updated (according to GEO): Jul 16 2007 PGA-lv_4h_507 2869 tumor cells 2880 urethra_2 AD-243t1x-A161-4 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Primary Neoplasm 1000 1000 Brain 6,18,30 month oculomotor nucleus and spinal cord Source GEO sample is GSM74347 Last updated (according to GEO): Sep 16 2005 PBMCs-Type 1 Diabetes-IDDM39_T1D_New cerebral_cortex_1 Lymphoblastoid Cell Line for Individual 8101.4 log phase Mental Retardation 1000 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225718 Last updated (according to GEO): Nov 05 2007 (cortex 19 25 Olfactory Epithelium 1000 1000 Spleen Adipose tissue 901 Sun197_TAV12 group Medulla 861 brain, Right Temporal Lobe: Extract77_le2 Malignant Neoplasms 1000 1000 Prostate CNS-SpinalCsev-Adult-24h-3B-s2 The insulin/IGF-IRS-PI3K-Akt pathway is highly conserved in evolution. To test whether this signaling cascade determines organ size in vertebrates, we have recently created mouse lines transgenic for constitutively active (caPI3K) and dominant-negative forms of PI3K (dnPI3K) (Shioi et al., 2000). Transgene expression is driven by the cardiac-specific a -myosin heavy chain (MHC) promoter. Both transgenic lines are characterized by moderate but highly consistent changes in heart size, despite the fact that body weight and the size of other organs are completely normal. caPI3K transgenic animals have hearts 20% larger than those of wild type littermates, whereas dnPI3K mice have hearts that are 17% smaller. The observed changes in heart size correlate with an appropriate increase or decrease in the size of transgenic cardiomyocytes. These hearts do not have cardiomyopathic changes, since the contractile function of transgenic hearts is normal, and signs of necrosis, apoptosis, or interstitial fibrosis are absent (see Physiology). These data suggest an autonomous role for PI3K in cell size regulation. Our goal is now to determine how activation of this system translates into changes in cell size by identifying the trigger and components of this signaling cascade. Heterozygous caPI3K (constitutively active PI3K) and dnPI3K (dominant-negative PI3K) transgenic female mice (5-14 months) compared with non-transgenic littermates. Transgene expression driven by the a -myosin heavy chain (a -MHC) promoter.. Date GSE558 Last Updated: Jun 15 2005 Contributers: Seigo Izumo Martina Schinke Jeffrey Brown Includes GDS446. Update date: Nov 18 2003. Dataset description GDS446: Analysis of the relationship between cardiac hypertrophy/cell size regulation with phosphoinositide 3-kinase (PI3K) signaling pathway. Constitutively active (caPI3K - hearts 20% larger) and dominant-negative (dnPI3K - hearts 17% smaller) mice examined.. brain 0 5 Gene expression data from whole brain infected mouse, day 3 Source GEO sample is GSM189650 Last updated (according to GEO): May 16 2007 T-ALL-C23 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A to psychosis 673 685 Mesenchymal Stem Cells 1000 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection). Source GEO sample is GSM36434 Last updated (according to GEO): May 27 2005 Nose 1000 Normal__Pancreas_PAN_2 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Spleen PGA-HMO-NonObese-7aUA-s2 Gene expression data from postmorten brain regions Source GEO sample is GSM144958 Last updated (according to GEO): Nov 20 2006 D_U133A_18_DLPFC Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2727 Source GEO sample is GSM2111 Last updated (according to GEO): Nov 21 2005 Spleen vs Interferon-beta (IFN beta) Treated B cell 240min (set1) Hyperdip>50-C4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Cerebral cortex 209 200 of gliomas of brain aging. 292 307 Recurrent Squamous cell carcinoma 8 0 34 Brain 1000 PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls. All samples were normalized with quantile normalization and summarized using RMA. Source GEO sample is GSM135582 Last updated (according to GEO): Dec 19 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145286 Last updated (according to GEO): Nov 20 2006 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68138 Last updated (according to GEO): Jul 07 2006 C57BL/6J hippocampus rep1 with brains 1486 1496 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs//7278.gif Source GEO sample is GSM79732 Last updated (according to GEO): Sep 22 2006 SVGR2 subclone 4-F6 GeneChip U133A 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114407 Last updated (according to GEO): Jun 16 2006 7 frontal cortex 20 hrs nasal epithelium 1126 1146 221 202 by CO2 asphyxiation Fibroblasts 824 834 amygdala wistar 3942 Epithelium 861 Lungs 153 157 NG015_c FVB/NJ periaqueductal gray rep2 861 Myopathy 901 Heart Diseases RNAtotSD_19, ZT6 Osteoblasts 1000 60 45 from 12 cochleas Olfactory Epithelium 1000 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159960 Last updated (according to GEO): Feb 01 2007 brain, cerebellum: WCb12w#1_e1_le1 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 20 hours after lights on. Original RNA code = LC15A. Source GEO sample is GSM227380 Last updated (according to GEO): Sep 10 2007 of somatomotor cortex 21 41 hippocampus: Sample #6_e1_le1 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120652 Last updated (according to GEO): May 14 2007 Heart 1000 Normal Source GEO sample is GSM176280 Last updated (according to GEO): Apr 09 2007 -_test-5_batch5 on NHGRI-6.7k PGA-MFD-MutantPD5-2aAv2-s2 11_0029_SepticShock_Day1_30 865 Disorder of artery Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108000 Last updated (according to GEO): Jun 06 2006 Bone structure of tibia 1000 901 Mammary gland olfactory epithelium 194 213 HapMap JPT Male Source GEO sample is GSM159661 Last updated (according to GEO): Feb 01 2007 PCA-404 on UMich-10k 861 Ganglia 1223 1205 from chromosome 21 MGJZ030402093Amedialolfactoryepithelium(MOE) 861 Cerebral cortex 901 Disorder of the optic nerve Chronic Lymphocytic Leukemia 19 47 frontal cortex 0 13 42 year old male 861 Cardiomyopathies Saccule at E13, replicate2 861 Cerebral cortex Head and neck cancer Source GEO sample is GSM155681 Last updated (according to GEO): Apr 24 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145100 Last updated (according to GEO): Nov 20 2006 1000 Brain cerebral cortex 7 21 Parkinson Disease 861 Gene expression data from the hippocampus of wild-type mouse Source GEO sample is GSM172954 Last updated (according to GEO): Mar 08 2007 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68240 Last updated (according to GEO): Jul 07 2006 Spinal Cord 901 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc76 Source GEO sample is GSM1900 Last updated (according to GEO): Nov 21 2005 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10407.gif Source GEO sample is GSM79912 Last updated (according to GEO): Sep 22 2006 304 280 alcoholic cardiomyopathy brain, Posterior Singulate: Sample40_e1_le1 P1.2A_KIDNEY_2 mouse cerebral cortex, cox-1 knockout, rep1 7 cerebral cortex 21 9 0 Blood Test DLCL-0010 Liver Test (Blinded) Sample Source GEO sample is GSM130166 Last updated (according to GEO): Sep 18 2007 GSE371 no additional Source GEO sample is GSM199352 Last updated (according to GEO): Jun 08 2007 Parkinson 0 8 Standard Affymetrix procedure Source GEO sample is GSM133023 Last updated (according to GEO): Aug 28 2007 Expression profiling of moderately injured raphe at 7d in rats Source GEO sample is GSM41628 Last updated (according to GEO): May 27 2005 1958 1945 out the liver The nose 94 101 1000 Hippocampus Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68305 Last updated (according to GEO): Jul 07 2006 D15 12h Media Autistic Disorder 877 long access to cocaine, septum, 6 hrs/day access to cocaine Source GEO sample is GSM93856 Last updated (according to GEO): Jan 26 2006 861 Cerebral cortex Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:277, Count:32 Corner- Avg:25496, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:5.322393,SFGene:All Background:Avg:433.71,Stdev:3.38,Max:443.8,Min:423.9 Noise:Avg:9.46,Stdev:0.28,Max:10.3,Min:8.5 RawQ:13.37 Keywords = ALL Source GEO sample is GSM3399 Last updated (according to GEO): May 27 2005 212 197 atherosclerosis at the Human Brain 726 743 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211278 Last updated (according to GEO): Jul 18 2007 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68334 Last updated (according to GEO): Jul 07 2006 Primary Neoplasm 1000 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 5 day time point Source GEO sample is GSM159726 Last updated (according to GEO): Apr 23 2007 60 42 to the X chromosome 7 cerebral cortex 21 M_U133A_35_HC Cerebral cortex 1000 Whole brain 0 10 Genetic alterations in mouse medulloblastomas and generation of tumors from cerebellar grunule neuron precursors Chronic leukemia NOS 913 accumbens_4 1000 Down Syndrome 5 0 brain Homozygous O377 mutant mouse line versus wildtype mice Source GEO sample is GSM86413 Last updated (according to GEO): Dec 08 2005 1000 Spleen Primary Carcinoma 876 7 0 prostate 901 Coronary artery Malignant neoplasm of ovary 1000 Human prostate cancer cells in different conditions Source GEO sample is GSM13081 Last updated (according to GEO): May 28 2005 Macrophage smi33 entorhinal cortex layer II stellate island cells Source GEO sample is GSM107531 Last updated (according to GEO): May 01 2006 RNA from Lymphoblastoid Cell Line from this individual Source GEO sample is GSM213299 Last updated (according to GEO): Jul 26 2007 1BJZ02051712_Testi_LeydigCell 901 Caudate nucleus structure plasma cells 332 344 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15463.gif Source GEO sample is GSM84166 Last updated (according to GEO): Sep 22 2006 Fetal cartilage selective genes identified in a genome-scale analysis Macrophage smi37 Performed by UCI Microarray Facility. Source GEO sample is GSM203234 Last updated (according to GEO): Jun 22 2007 Brain 861 901 Heart failure Hep2_37_rep2 Tumor__Leukemia_ALL-B_ALL_(9692)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A HMEC X MCF7-NCI HMEC 184 day 7 sample 1 GSE8021 Trasnsformed Lymphocytes Unaffected Twin Pair 2 (DCBD2.2)(TP8) Comparison of RNA levels in the neocortex of normal mice versus synaptically silent munc18-1 null mutants. Source GEO sample is GSM84370 Last updated (according to GEO): Aug 01 2006 Group 2 PEITC treated, EP#15 vs. reference pool from ventral prostate 21 41 Epithelium 861 Biopsy of a colorectal adenoma from patient #5 plasma cells 332 344 Cerebral cortex 901 Gene expression data of substantia nigra from postmortem brain of normal controls Source GEO sample is GSM184355 Last updated (according to GEO): May 29 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145263 Last updated (according to GEO): Nov 20 2006 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228590 Last updated (according to GEO): Sep 11 2007 913 Coronary heart disease 1000 Solid tumor HC57 FC BA4 A from the femurs 95 109 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92344 Last updated (according to GEO): Jan 13 2006 1000 Muscle in bronchial epithelia 311 332 Prosencephalon 1000 Cortex_Control_rep3 (05SE733) 861 Heart failure Five different human MPNST cell lines, mock treated or infected with G207. Source GEO sample is GSM215806 Last updated (according to GEO): Aug 07 2007 SN:1010456 Source GEO sample is GSM115397 Last updated (according to GEO): Jun 20 2006 HMEC S1 day 3 sample 2 Ovary 1000 plasma cells 332 344 861 Dislocations 5 0 Spleen CAD_replicate68 WGACON-106 5.0 mg/kg MeHg forebrain at 24.0h Head and neck cancer Source GEO sample is GSM155662 Last updated (according to GEO): Apr 24 2007 1000 Encephalitis 5 0 brain 1000 Hippocampus Wild type 8 wk old male C3H/HeJ mouse bed nucleus of the stria terminalis Source GEO sample is GSM106998 Last updated (according to GEO): Mar 05 2007 9 0 Blood Test 1000 frontal lobe Hereditary Malignant Neoplasm 876 CT18-2 GC (HKG73T) 901 Nervous system structure 1000 Heart failure Menstruation blood, HRF treatment, primary E4HRF 78 66 Control blood 132 101 from normal intestinal epithelia 861 Lung Brain 861 1000 Brain 809 777 in human mammary epithelial cells Ganglia 861 cingulate cortex 861 Laser captured visceral sensory neurons. Source GEO sample is GSM63686 Last updated (according to GEO): Dec 21 2005 for liver 26 35 To elucidate the genomics of cellular responses to cancer treatment, we analyzed the expression of over 9,600 human genes in acute lymphoblastic leukemia cells before and after in vivo treatment with methotrexate and mercaptopurine given alone or in combination. Based on changes in gene expression, we identified 124 genes that accurately discriminated among the four treatments. Discriminating genes included those involved in apoptosis, mismatch repair, cell cycle control and stress response. Only 14% of genes that changed when these medications were given as single agents also changed when they were given together. These data indicate that lymphoid leukemia cells of different molecular subtypes share common pathways of genomic response to the same treatment, that changes in gene expression are treatment-specific and that gene expression can illuminate differences in cellular response to drug combinations versus single agents.. Date GSE412 Last Updated: May 29 2005 Contributers: W Yang Ching-Hon Pui W E Evans C Cheng J R Downing M H Cheok M V Relling Includes GDS330. Update date: Apr 21 2003. Dataset description GDS330: Examination of primary acute lymphoblastic leukemia (ALL) cells before and 1 day after in vivo treatment with mercaptopurine and high/low-dose methotrexate given alone or in combination.. 84 69 by heart failure 1000 Hippocampus human cerebellum Source GEO sample is GSM87154 Last updated (according to GEO): Feb 08 2006 Aortic aneurysm without mention of rupture NOS 901 olfactory epithelium 194 213 Arteries 861 Lymphoblastoid Cell Line for Individual 8052.4 log phase Blood 1000 1000 Heart Muscle 645 650 from Brain 17 26 983 Occipital region Mature B cells 3 1000 Epilepsy the blood 393 402 36 0 Control rat 8 ventral tegmental area 5 0 Spleen 39 0 endothelial cells sprague1 whole tissue 276 270 Retinas Blood 861 of caudal 93 101 A HID U D089 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108614 Last updated (according to GEO): Aug 22 2006 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14087.gif Source GEO sample is GSM81529 Last updated (according to GEO): Sep 22 2006 Lymphoblastoid Cell Line for Individual 8161.4 log phase Structure of dentate gyrus 861 Primary tumor 19 32 Neostriatum 1000 Euploid sample 2 (cerebellum) Brain 861 WT P2 replicate 3 Lymphoblastoid Cell Line for Individual 8193.3 log phase CardiacMyocytes Source GEO sample is GSM18970 Last updated (according to GEO): Sep 25 2006 865 Disorder of artery Neostriatum 1000 91 from the bone marrow 72 Saccule 0 6 Superior_Cervical_Ganglion Source GEO sample is GSM18853 Last updated (according to GEO): Sep 25 2006 901 Stem cells NA18956 human caudate nucleus Source GEO sample is GSM86924 Last updated (according to GEO): Feb 08 2006 Ng3: Hippocampus_NT-Y_rep9 Non-inner ear tissues pooled from E11 to E15, replicate2 Liver 0 4 901 theca cell LungE165_022JAF6Y_078.txt Collagen 1000 plasma cells 332 344 adenoma 861 1000 Brain Stomach Pyloric 1 Normal Gonadectomized Dahl-Iwai Female HighSalt Cortex rat6 gdahl_cortexr_k_GX_6c_051702 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Prostaglandin E2 for 120min Source GEO sample is GSM5738 Last updated (according to GEO): May 27 2005 Mouse old heart C30-Ht-1 Parkinson's disease sample x184 Gene expression data from postmorten brain regions Source GEO sample is GSM145821 Last updated (according to GEO): Nov 20 2006 Mutant striatal cells Source GEO sample is GSM82447 Last updated (according to GEO): Jun 26 2007 frontal_lobe_5 Source GEO sample is GSM80667 Last updated (according to GEO): Mar 31 2006 13 7 cochlea 1000 Muscle PGA_PA-S_233 Expression profiling of spinal cord section (T9) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM6670 Last updated (according to GEO): May 28 2005 CNS-SpinalCmod-Adult-28d-1C-s2 Gene expression data from postmorten brain regions Source GEO sample is GSM145813 Last updated (according to GEO): Nov 20 2006 Fbx15-null ES (rep1) 1037 of transitional epithelium 1012 EOM 56 Day mdx rep 3 brain, cerebellum: Stg+/+_Crb1_e1_le1 Temporal lobe epilepsy and Alzheimer's disease Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162170 Last updated (according to GEO): Jun 12 2007 Hippocampus Treatment, type=pharmacogenomic_treatment, description=Handled (no stress) control Source GEO sample is GSM53308 Last updated (according to GEO): Jul 06 2005 12 4 of Kidney 5 0 brain Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210383 Last updated (according to GEO): Jul 16 2007 1000 Hippocampus Myocardium 861 none Source GEO sample is GSM210327 Last updated (according to GEO): Jul 16 2007 Spleen vs Lipopolysaccharide (LPS) Treated B cell 60min (set1) 1000 Rectum GRP sample 1 To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at ?80C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at ?80°C before routine processing for GeneChip analysis. Source GEO sample is GSM28668 Last updated (according to GEO): Oct 28 2005 CNS-RM_CtrT0-4C-s2 Epithelium of bronchus 983 Spleen vs Insulin-like growth factor 1 Treated B cell 30min (set3) Spleen vs Dimaprit Treated B cell 240min (set2) Parkinson Disease 1000 rat hippocampus Treatment, type=time_course, measurement=240.0 h Source GEO sample is GSM32150 Last updated (according to GEO): May 27 2005 43 0 Chorionic mesoderm-derived mesenchymal cells Gene expression data from DAOY cells stably expressing Bmi1 shRNA Source GEO sample is GSM182008 Last updated (according to GEO): Apr 23 2007 861 Cerebral cortex human frontal cortex Source GEO sample is GSM87010 Last updated (according to GEO): Feb 08 2006 brain, cerebral cortex: PC16_e1_le1 Spinal Cord 1000 Renal clear cell carcinoma 0 25 primary hepatocytes 0 19 Affymetrix RGU34A 6HA NSCLC_A549ATCC on Affymetrix GeneChip Human Full Length Array HuGeneFL 5 0 brain Whole Brain 62 72 1000 Spinal Cord WGACON-203 septum long access to cocaine replicate 2 858 Mesodermal cell fetalThyroid Source GEO sample is GSM18963 Last updated (according to GEO): Sep 25 2006 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211319 Last updated (according to GEO): Jul 18 2007 Parkinson's disease vs. controls, whole blood Microarray expression profiling of discrete microdissected mouse inner ear tissues from E9 to E15 at half-day intervals. 1000 Hippocampus brain, unknown: R2C_e1_le1 SN7d(2) brain, cortex: 7dsham4_e1_le1 brain, hippocampus: Aldh5a1-/- #3363 Hippo_e1_le1 7 0 prostate Pool of 13 cochlear tissues at E11.5 Source GEO sample is GSM182575 Last updated (according to GEO): Aug 14 2007 1000 Nervous system structure 861 Muscle Blood 1000 Bone structure of tibia 1000 UACC-62_CL10020_Melanoma on Affymetrix GeneChip Human Full Length Array HuGeneFL 12 0 ovarian tumor 861 Cerebral cortex striatum 33 41 Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92295 Last updated (according to GEO): Jan 13 2006 none Source GEO sample is GSM149605 Last updated (according to GEO): Jan 03 2007 Infection 1000 AMM_0_0_Male4_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111849 Last updated (according to GEO): Nov 21 2006 thyroid_gland_2 Source GEO sample is GSM80865 Last updated (according to GEO): Mar 31 2006 Kidney Cortex 1 Normal HCC (HBV+, SF22) PGA-MPF-C57-bleo-24h-2aAv2-s2 These experiments are designed to discover genes that are expressed selectively by synaptic nuclei in skeletal muscle with the particular goal of identifying genes that regulate motor axon growth and differentiation. We plan to isolate RNA from the dissected synaptic region of skeletal muscle and from the non-synaptic region of skeletal muscle and to identify the genes that are expressed at higher levels in the synaptic than non-synaptic region. Previously, we showed that motor axons fail to stop and differentiate in mice lacking MuSK, a receptor tyrosine kinase that is activated by motor neuron-derived Agrin. We hypothesize that MuSK activation normally leads to the production of a retrograde stop/differentiation signal that is encoded by a gene that is expressed preferentially in synaptic nuclei. In the absence of MuSK signaling, the retrograde signaling is not produced by synaptic nuclei, and consequently motor axons wander aimlessly over the muscle. We obtain 6 to 8 micrograms of total RNA from the dissected synaptic or non-synaptic region from a single P21 mouse diaphragm muscle. This is a standard procedure in the lab, and we have used these methods to analzye gene expression and to generate high-quality cDNA libraries. Because the synaptic zone is narrower in the left hemi-diaphragm, we will isolate RNA from this half of the diaphragm. In order to isolate sufficient RNA (5 micrograms from each sample), we will pool the synaptic and non-synaptic regions from two hemi-diaphragms. In order to reduce experimental variability, we wish to analzye expression in six samples: three samples of synaptic RNA and three samples of non-synaptic RNA. We will ship the isolated RNA samples to the Consortium in order to generate labeled cDNA, to screen Affymetrix mouse oligo arrays and to assist in the analysis. Several genes, including the subunits of the acetylcholine receptor, MuSK, acetylcholinesterase, and utrophin are known to be expressed preferentially in synaptic nuclei; thus, these genes serve as internal controls for the reliability and effectiveness of the screen. Most other genes, several of which we have analyzed in previous studies, including actin, GAPDH, runx1, nogoC, creatine kinase, etc. are expressed uniformly in skeletal muscle; thus, expression of these genes should be equally represented in synaptic and non-synaptic regions. Last Updated (by provider): Jun 09 2006 Contributers: S J Burden Includes GDS1838. Update date: Jun 09 2006. Dataset description GDS1838: Analysis of synaptic regions of diaphragm muscles from 16-day-old animals. Results identify genes preferentially expressed in the synaptic region of muscles. Such genes are candidates for muscle-derived retrograde signals that regulate the differentiation of motor axon terminals.. Wild type inbred mice Source GEO sample is GSM83032 Last updated (according to GEO): Nov 10 2005 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14969 Last updated (according to GEO): Oct 28 2005 Liver 1000 human frontal cortex Source GEO sample is GSM87029 Last updated (according to GEO): Feb 08 2006 AKR/J Olfactory Bulb F BALB/cByJ Basal Ganglia B MET-301 on UMich-10k 5 0 brain 1000 Cerebellum Leg 23 Day Control rep 1 Brain 1000 NA12751 growth 3, replicate 5 GM19099 1000 Brain Comparison between cell lines from 9 different cancer tissue of origin types (Breast, Central Nervous System, Colon, Leukemia, Melanoma, Non-Small Cell Lung, Ovarian, Prostate, Renal) from NCI-60 panel Last Updated (by provider): Aug 06 2007 Contributers: Ari B Kahn John N Weinstein Uma Shankavaram no additional Source GEO sample is GSM199421 Last updated (according to GEO): Jun 08 2007 1000 frontal lobe MCF7_E2_24h_rep2 Gene expression data from postmorten brain regions Source GEO sample is GSM145724 Last updated (according to GEO): Nov 20 2006 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211409 Last updated (according to GEO): Jul 18 2007 NA Source GEO sample is GSM198890 Last updated (according to GEO): Jun 07 2007 Epithelium 861 prostate Source GEO sample is GSM203340 Last updated (according to GEO): Jun 21 2007 M_U133A_17_HC Skeletal bone 861 Parkinson's disease sample x016 4 0 Brain Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188845 Last updated (according to GEO): Jun 06 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with BLC for 60min Source GEO sample is GSM5466 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM175819 Last updated (according to GEO): Apr 09 2007 CNS-RM_Mod4h-3A-s2 MOLT-4_CL7006_Leukemia on Affymetrix GeneChip Human Full Length Array HuGeneFL globus_pallidus Source GEO sample is GSM18914 Last updated (according to GEO): Sep 25 2006 pituitary_gland_6 Source GEO sample is GSM80801 Last updated (according to GEO): Mar 31 2006 brain, cerebral cortex: NMDA30 7/8_le1 Pituitary Gland 861 TEL-AML1-C7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A none Source GEO sample is GSM123184 Last updated (according to GEO): Jul 26 2006 dorsal root ganglion 0 19 1000 Heart Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16707.gif Source GEO sample is GSM91595 Last updated (according to GEO): Sep 22 2006 861 Blood pretumor.2 Olfactory Epithelium 1000 Muscle Fibers 1000 in the brain 150 162 861 Cerebral cortex CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of DC, recombinant human (rh) IL-4 and rhGMCSF were added to the culture at 50 ng/ml on days 1, 3, and 5 of culture. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5128 Last updated (according to GEO): Mar 21 2006 for liver 26 35 Replicate3_Voxel B6 Stem cells 1000 f2#224 versus pool Mouse Brain tissue total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Anti-IgM for 60min Source GEO sample is GSM5444 Last updated (according to GEO): May 27 2005 Male 25.1 yr before antibody enrichment scan 1 (U133A) 1000 Brain Liver (HBV+, HK10, S2) Wild type inbred mice Source GEO sample is GSM82911 Last updated (according to GEO): Nov 10 2005 CNS-SC_InjB14d-4A-s2 1000 Eye Expression profiling of spinal cord section (T8) extracted from rats 24h following severe injury Source GEO sample is GSM31478 Last updated (according to GEO): May 27 2005 PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls. All samples were normalized with quantile normalization and summarized using RMA. Source GEO sample is GSM135589 Last updated (according to GEO): Dec 19 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with TGF-beta (transforming growth factor-beta) for 30min Source GEO sample is GSM5793 Last updated (according to GEO): May 27 2005 Biopsy of the normal mucosa of the colon from patient #10 dorsal_root_ganglia_8 cy3:SHR control, biological rep 3g; cy5:pool of 6 WKY control rats Hep40 cells atrioventricular_node Source GEO sample is GSM18848 Last updated (according to GEO): Sep 25 2006 Epididymis [JunctionChip 5 of 5] 32 21 from retinas 70 40 without coronary artery disease Infection 1000 Stem cells 861 Gene expression data from biopsy of infected skin of subject with resolver phenotype. Source GEO sample is GSM128957 Last updated (according to GEO): Sep 13 2007 C6SPGFPslow2 Brain 861 1046 1029 in skeletal muscle HDMTX-DX-22 Expression profiling of somatomotor cortex extracted from rats at 14d following moderate injury Source GEO sample is GSM41696 Last updated (according to GEO): May 27 2005 Neural induction (N2B27 monolayer cluture) Nervous system structure 901 861 Uterus 861 Malignant Neoplasms Simple annotation: Metastatic tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12394.gif Source GEO sample is GSM79787 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145419 Last updated (according to GEO): Nov 20 2006 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19216 Last updated (according to GEO): May 27 2005 Heart 861 Heart 1000 Transplant Series 17 , Transplant # 3 1000 Brain Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11341 Last updated (according to GEO): May 28 2005 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 2 - Pair 1 - LMN Source GEO sample is GSM49870 Last updated (according to GEO): Dec 20 2005 brain, cerebral cortex: Nic4_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM145080 Last updated (according to GEO): Nov 20 2006 Replicate3_Voxel F7 kidney 37 43 olfactory epithelium SR-A mutant mouse 8 hpO Source GEO sample is GSM80204 Last updated (according to GEO): Oct 26 2005 The hypothalamoneurohypophyseal system (HNS) consists of the large peptidergic magnocellular neurons of the supraoptic hypo thalamic nucleus (SON) and the paraventricular hypothalamic nucleus (PVN), the axons of which course through the internal zone of the median eminence and terminate at blood capillaries of the posterior lobe of the pituitary gland. The HNS is a specialized brain neurosecretory apparatus responsible for the production of the antidiuretic peptide hormone vasopressin (VP). VP maintains water balance by promoting water conservation at the level of the kidney. Dehydration evokes a massive increase in the regulated release of VP from magnocellular neuron axon terminals in the posterior pituitary, which is accompanied by a plethora of changes in the morphology, electrophysiological properties, and biosynthetic and secretory activity of the HNS. We wish to understand this functional plasticity in terms of the differential expression of genes. We have therefore used microarrays to comprehensively catalog the genes expressed in the PVN, the SON and the neurointermediate lobe of the pituitary gland of control and dehydrated rats. Comparison of these gene lists has enabled us to identify transcripts that are regulated as a consequence of dehydration as well as RNAs that are enriched in the PVN or the SON. We suggest that these differentially expressed genes represent candidate regulators and effectors of HNS activity and remodeling. I_95Av2_1905_CB_1_GS Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. Source GEO sample is GSM112315 Last updated (according to GEO): Jun 06 2006 Nasal Epithelium 913 Central gray substance of midbrain 861 Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18376.gif Source GEO sample is GSM91561 Last updated (according to GEO): Sep 22 2006 861 Malaria 1037 of transitional epithelium 1012 Primary large cell carcinoma 3387 5 0 brain 1000 Retina 861 Heart mouse cerebral cortex, cox-2 heterozygous, rep2 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:364, Count:32 Corner- Avg:36544, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:15.267480,SFGene:All Background:Avg:408.40,Stdev:5.81,Max:426.0,Min:399.9 Noise:Avg:9.27,Stdev:0.43,Max:10.8,Min:8.4 RawQ:13.27 Keywords = ALL Source GEO sample is GSM3491 Last updated (according to GEO): May 28 2005 Frontal Lobe 2 Normal Hippocampus 1000 The epithelial cells 962 981 Cerebral cortex 861 Balb/c to C57/BL6 with anti CD80/86 mAb Source GEO sample is GSM8929 Last updated (according to GEO): May 28 2005 Whole Brain 62 72 706 695 in the brain 1000 Spleen cy5:WKY treated w/ angtiotensin, biological rep 1r; cy3:pool of 6 WKY control rats A39 WT1 F5/50 A39 wild type Mouse 4 months Cerebellum Female Source GEO sample is GSM73218 Last updated (according to GEO): Sep 06 2005 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184782 Last updated (according to GEO): Apr 26 2007 C Fast Rep 1 Gene expression data from whole tumor Source GEO sample is GSM182292 Last updated (according to GEO): Apr 16 2007 V5-P251 Epithelium 861 5 0 brain Cerebral cortex 861 1000 Spleen Knockout saline, biological replicate 2 150 mg/kg X 6 hr Source GEO sample is GSM129870 Last updated (according to GEO): Sep 18 2007 Adenovirus Infections 1000 9 0 Blood Test Adenovirus Infections 1000 Blood 1000 1000 Brain A HID U D019 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68132 Last updated (according to GEO): Jul 07 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145343 Last updated (according to GEO): Nov 20 2006 Lymphoblastoid Cell Line for Individual 8200.3 log phase PGA-RnSalt_h_3w_1-m5 Microarray analysis of NL and PCOS oocytes (P2) Lung; Fetal Day 18.5 Keywords = mouse gene expression database Source GEO sample is GSM29391 Last updated (according to GEO): May 27 2005 SCG explant cultured for 24 hours in vitro Source GEO sample is GSM246061 Last updated (according to GEO): Dec 03 2007 901 Germ Cells Polyamide 2 treated LNCaP cells not stimulated with DHT, biological replicate 2 Source GEO sample is GSM187381 Last updated (according to GEO): May 04 2007 OBX Day 7,# 3 1000 Tibialis anterior muscle structure 1000 Intestines, Small Hormones 861 f2#24 versus pool Mouse Brain tissue Coronary heart disease 913 high gestational age Source GEO sample is GSM213124 Last updated (according to GEO): Jul 25 2007 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120671 Last updated (according to GEO): May 14 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11541 Last updated (according to GEO): May 28 2005 GSE3412 Neoplasm 861 Gene expression data from whole brain infected mouse, day 6 Source GEO sample is GSM189659 Last updated (according to GEO): May 16 2007 Non-small cell lung cancer recurrent 1000 e14-2 normal testis 54 66 with bladder cancer 1831 1850 Normal Source GEO sample is GSM176222 Last updated (according to GEO): Apr 09 2007 Adult mouse gene expression Neoplasm 861 D_U133Plus_126_DLPFC D_U133A_12_nAcc Entorhinal Cortex 7 23 Sham 10 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107489 Last updated (according to GEO): May 01 2006 S46 NLS 142Q TG6 F4/2 S46 NLS Htt exon 1 142Q Mouse 10 months Cerebellum Female Source GEO sample is GSM73202 Last updated (according to GEO): Sep 06 2005 Mammary Gland @ Lac9, biological rep3 Sprague-Dawley Female LowSalt OuterMedulla rat701 sd_medullar_k_701r_om_070302 HepG2 + SDF 6h 3 Treated Brain 1000 human caudate nucleus Source GEO sample is GSM86897 Last updated (according to GEO): Feb 08 2006 SCG_sema3A_24h_rep1 715 702 After the eyes Fibroblasts 1000 Brn3a Wildtype DRG e13.5 430A v2.0 replicate 861 Chromosomes Gene expression data from postmorten brain regions Source GEO sample is GSM145468 Last updated (according to GEO): Nov 20 2006 14 NT C4 Treatment, type=add, description=10ng/mL Ciliary neurotrophiic factor, 4d Source GEO sample is GSM92499 Last updated (according to GEO): Jan 13 2006 HapMap JPT Female Source GEO sample is GSM159638 Last updated (according to GEO): Feb 01 2007 Spinal Cord 1000 We build a model for the molecular and cellular events underlying phenotypic discordance in glycine receptor defects (beta subunit). Some mice progress and die, while their littermates recover and get better, despite the same mutation on an inbred genetic background. We find evidence for glycine neurotransmitter toxicity and loss of glycinergic interneurons early in the disease, but some mice are able to keep things going until they can over-express homomeric alpha1 channels, whereupon they recover. In the mice progressing towards lethality, neurotransmitter toxicity too quickly extends to GABAergic interneurons and motorneurons, and they lose their window of time to upregulate the alpha1 glycine receptor, and they crash and burn. Importantly, human patients with glycine receptor defects typically show a resolution of their phenotype with age, and we propose that the same remodeling events are occuring in human patients. Source GEO sample is GSM30998 Last updated (according to GEO): May 27 2005 Leukemia, Lymphocytic, Chronic 1000 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210420 Last updated (according to GEO): Jul 16 2007 placenta-0545-uninflamed-infected-rep1 Ventral Tegmental Area 1000 Si4_2, mouse, SW, infected, 4 days post infection_rep 2 Gene expression data from postmorten brain regions Source GEO sample is GSM145163 Last updated (according to GEO): Nov 20 2006 D_U133A_13_nAcc /3T3 fibroblasts 295 310 Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181980 Last updated (according to GEO): Apr 13 2007 Cochlear nucleus structure 901 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159809 Last updated (according to GEO): Apr 23 2007 19 0 Head and neck cancer 10 0 Cord blood K562A-repro Integumentary system 1000 1000 Muscular Dystrophies 1000 Brain 8M_A31103 Wild type 8 wk old male 129S6/SvEvTac mouse hippocampus Source GEO sample is GSM74956 Last updated (according to GEO): Feb 27 2007 lateral motoneurons (LMN) 7 Standard Affymetrix procedure Source GEO sample is GSM133004 Last updated (according to GEO): Aug 28 2007 Primary Neoplasm 1000 Alveoli loss during caloric restriction time course outer medulla 31 43 NA12751 growth 3, replicate 1 Olfactory Epithelium 1000 Control gray matter 4 68 64 Lungs days nasal epithelium 1126 1147 858 Mesodermal cell 1h +TGF-beta odontoblasts 861 Blood 1000 Amygdaloid structure Gene expression data from postmorten brain regions Source GEO sample is GSM145963 Last updated (according to GEO): Nov 20 2006 Structure of entorhinal cortex 1000 PGA-MurLungRag-pbs-72h-1bA-s2 n/a Source GEO sample is GSM177973 Last updated (according to GEO): Jun 11 2007 75 44 from normal intestinal epithelia PHA, 12.00 hr. T-Cell, Repeat. Posterior root of spinal nerve 861 901 Mammary gland Penis 2 Normal Femur 1000 331 307 in central nervous system Skeletal bone 861 Small Intestine; proximal jejunum Keywords = mouse gene expression database Source GEO sample is GSM29308 Last updated (according to GEO): May 27 2005 861 Occipital lobe Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184786 Last updated (according to GEO): Apr 26 2007 Brain 861 Skin 5 Normal 2 284 279 Spleen Vector-bic-1 in seminoma 28 38 The mammalian neocortex develops layer organizations with regional differences represented by expression of multiple genes at embryonic stages. These genes could play important roles in the formation of areal cyto-architecture, yet, the number of genes identified so far is not sufficient to explain such intricate processes. Here we collected five regions--the medial, dorsal, lateral, rostral and occipital--from the dissected E16.5 mouse cerebral cortex and performed extensive gene expression analysis using the Affymetrix U74Av2 array with probes for 12,500 genes. After relative quantitative analysis, 34, 33 and 15 genes were selected as highly expressed genes in the medial, dorsal and lateral regions, respectively. The combination of GeneChip system, real-time quantitative reverse transcription polymerase chain reaction and in situ hybridization analyses allowed the successful identification of seven genes from the dorsal region (Neuropeptide Y, Wnt7b, TGF-beta RI, Nrf3, Bcl-6, MT4-MMP and Rptp kappa), three genes from the medial region (Hop-pending, HtrA and Crystallin), and three genes from the lateral region (Somatostatin, Ngef and Fxyd7). Particularly, all seven genes identified in the dorsal region demarcated the future somatosensory and auditory areas in the cortical plate with high rostrolateral-low caudomedial gradation. Their expression patterns were not uniform, but delineated either the superficial or the deep layer in the cortical plate. Furthermore, the regional expression pattern of Neuropeptide Y was shifted rostrally and the layer specificity was disorganized in the Pax6-deficient mice. Our results provide new information about a subclass of regionally expressed genes in the cortical plate at the late embryonic stage, which may help understand the molecular mechanisms of neocortical arealization. kidney 37 43 Lymphoblastic Leukemia 901 Thalamic structure 1000 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114408 Last updated (according to GEO): Jun 16 2006 M_U133Plus_36_HC 1000 Rectum 1000 Hippocampus ISR12 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9973.gif Source GEO sample is GSM79830 Last updated (according to GEO): Sep 22 2006 85 61 of chronic renal disease 304 280 alcoholic cardiomyopathy GBM: 36A35 #9 of the stria terminalis 50 72 216 Ganglia 210 Effects of SOCS3 on transcriptional response of macrophages to IL-6. Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Replicate 2 after stimulation for 400 minutes with 10 ng/ml IL-6. Source GEO sample is GSM6080 Last updated (according to GEO): Mar 17 2006 1000 Cerebrovascular accident brain, cerebral cortex: NMDA 10 3_le1 Collagen 1000 Muscle 861 brain, cerebellum: RNA#42a_le1 861 Cerebral cortex LiverE14_022QACIQ_099.txt 142 138 Brain Expression profiling of spinal cord section (T9) extracted from rats 7d following laminectomy (sham) Lot batch = Source GEO sample is GSM4484 Last updated (according to GEO): May 28 2005 RNA isolated from fetal cerebellum Keywords = trisomy Keywords = brain Keywords = Down syndrome Source GEO sample is GSM22583 Last updated (according to GEO): May 27 2005 256 235 with HIV encephalitis 91 from the bone marrow 72 1000 Malignant Neoplasms Brain 1000 MuscleRegen-con8wk-2LLAv2-s2 Leg 28 Day control rep 3 21 adrenal medulla 7 3T3-L1 Adipocytes A on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A Expression profiling of spinal cord section (T9) extracted from rats 7d following moderate injury Source GEO sample is GSM31597 Last updated (according to GEO): May 27 2005 NZB/BlNJ_female_hypothalamus Source GEO sample is GSM138570 Last updated (according to GEO): Apr 18 2007 seminoma specimen, pT1, patient age: 36y; W03 014 Fetal frontal cortex cocaine4 Cochlear nucleus structure 901 Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92278 Last updated (according to GEO): Jan 13 2006 10 weeks Source GEO sample is GSM147451 Last updated (according to GEO): Dec 01 2006 84 69 by heart failure TEL-AML1-C19 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A GBM Treatment, type=remove Source GEO sample is GSM99582 Last updated (according to GEO): Apr 21 2006 A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, glutamine, cell culture, carbon metabolism Source GEO sample is GSM5974 Last updated (according to GEO): Nov 21 2005 BREAST_MDAMB231 on Affymetrix GeneChip Human Full Length Array HuGeneFL Hormones 861 CNS-SpinalCmod-Adult-24h-1B-s2 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225677 Last updated (according to GEO): Nov 02 2007 human cerebellum Source GEO sample is GSM87187 Last updated (according to GEO): Feb 08 2006 Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A61_8 months_replicate 1 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132537 Last updated (according to GEO): Feb 26 2007 tibiae 115 120 5 0 brain Colon BD Normal 1000 Spleen Expression profiling of spinal cord section (T9) extracted from rats 24h following laminectomy (sham) Source GEO sample is GSM31250 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145957 Last updated (according to GEO): Nov 20 2006 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226156 Last updated (according to GEO): Nov 02 2007 111 of liver cells 124 Bone Marrow 1000 vehicle treatment, 24 hour time point, biological replicate 1 human frontal cortex Source GEO sample is GSM86941 Last updated (according to GEO): Feb 08 2006 nasal epithelial cells 28 49 861 HIV Infections Nucleus Accumbends, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231039 Last updated (according to GEO): Sep 26 2007 post HCMV infection 15 33 913 Coronary heart disease Gene expression data from postmorten brain regions Source GEO sample is GSM145728 Last updated (according to GEO): Nov 20 2006 Brain 861 gfp neg. sorted cells from 3 disected e14.5 cortecies Treatment, type=wait Source GEO sample is GSM135768 Last updated (according to GEO): Sep 12 2006 Unfertilized egg replication 4 Mouse model of congenital heart disease in Csx/Nkx2.5 mutant embryos. Heterozygous embyronic day 9.5 mouse. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2273 Last updated (according to GEO): May 27 2005 Starvation 916 GSE8633 PC 12Hr rat 4126 blood vs. 150mg/kg APAP 12Hr rat 4127 blood 1000 Nervous system structure Blood 1000 156 145 Their livers 14 7 amygdala 901 Nervous system structure ovary 45 50 plasma cells 50 61 Myocardial Infarction 1000 R425P00102 Fibroblasts 1000 Spleen 0 5 MGJZ030228033Aspleen WT P2 replicate 4 78 73 rectum Infected 6 weeks prior with Htt-N171-19Q-expressing recombinant lentivirus Source GEO sample is GSM34377 Last updated (according to GEO): Oct 16 2006 whole blood_100676 Primary adenocarcinoma Source GEO sample is GSM16566 Last updated (according to GEO): May 28 2005 from subcutaneous adipose tissue 25 56 Timed pregnant C57Bl6 mice were exposed to ethanol during gestational day 15 to day 18 and ethanol exposed fetuses were delivered by cessarian section on gestational day 19. Alcohol exposed fetuses were compared to control timed preg Source GEO sample is GSM116854 Last updated (according to GEO): Jul 03 2006 901 Bone Marrow 861 Brain 70 40 without coronary artery disease trauma 277 283 I_U133Plus_126_CB Neoplasm 861 total RNA extracted from one ApoE-/- mouse infected wtih a control adenovirus expressing GFP Source GEO sample is GSM157858 Last updated (according to GEO): Jan 25 2007 Liver 0 4 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202673 Last updated (according to GEO): Jun 20 2007 ventral tegmental area] 901 924 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28749 Last updated (according to GEO): May 27 2005 B2-23 on NCI-7.6k Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21758.gif Source GEO sample is GSM93118 Last updated (according to GEO): Sep 22 2006 DNA Damage 1000 1213 1208 lipid none Source GEO sample is GSM244621 Last updated (according to GEO): Nov 23 2007 Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242085 Last updated (according to GEO): Dec 04 2007 of lung high-grade neuroendocrine tumor 100 138 Heart 1000 1000 frontal lobe Epithelium 861 nico 18h + nmda 1h 8/23/02 (Experiment Neuroprotection3- Run 13276) Treatment, type=timepoint, description=primary cortical neurons were treated for 18 h with nicotine 10uM then NMDA 1mM was added and the cells were harvested 1h later, measurement=19.0 h Source GEO sample is GSM96733 Last updated (according to GEO): Feb 14 2006 Wild type 8 wk old male DBA/2J mouse periaqueductal gray Source GEO sample is GSM74994 Last updated (according to GEO): Feb 27 2007 Leg 14 Day mdx rep 1 Plasma 861 VIIIcCA1_Signal on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B Total RNA extracted from the forebrain of a Lh-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144387 Last updated (according to GEO): Nov 14 2006 Fetal occipital cortex cocaine3 92 75 of nervous system IGF1 and IGF1 receptors (IGF1R) are present in the adult heart and have been shown to be essential for myocardial performance. Insulin-like growth factor 1 (IGF1) is produced in numerous tissues particularly by the liver in response to growth hormone stimulation and is an important factor in the regulation of post-natal growth and development. We have generated and characterized transgenic mice over-expressing the IGF1R. We crossed IGF1R transgenic mice with dominant negative (dn)PI3K (p110) and with constitutively active (ca)PI3K(p110) transgenic mice. Expression profiling was performed on the ventricles of IGF1R, IGF1R-caPI3K, IGF1R-dnPI3K, caPI3K, dnPI3K transgenic female mice at 3 months of age. Non-transgenic littermates were used as controls. Keywords = insulin growth factor, IGF, cardiac, hypertrophy Source GEO sample is GSM18365 Last updated (according to GEO): May 27 2005 cDNAs were generated from 5ug of total RNA per sample by reverse transcription (RT) for two hours at 42oC using the 3DNA SubmicroTM Oligo Expression Array Detection Kit (Genisphere, Hatfield, PA) and Superscript II (Invitrogen, Carlsbad, CA). For each microarray chip two consecutive hybridizations were performed with cDNAs and the fluorescent probes following the manufacture?s specifications. Briefly, in the first hybridization reaction the solution containing the mixture of cDNAs obtained from control and treated cells was loaded onto the CAG Human 19K array and incubated overnight at 55oC in a hybridization chamber (Genemachines, San Carlos, CA). The human 19K array (www.cag.icph.org/microarray_facility.htm) contains 60-mer oligonucleotides (Compugen, San Jose, CA) representing 18,861 human genes spotted onto poly-l-lysine coated glass microscope slides. In the second hybridization reaction Cy3 (green) and Cy5 (red) fluorescent probes were used to label the cDNAs from control and PGJ2-treated cells, respectively. The second hybridization was carried out for 3 hours at 65oC in the hybridization chambers. The arrays were scanned using an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) with laser intensities adjusted to bring the brightest spot just below saturation and the data extracted with the Axon GenePix Pro software. Source GEO sample is GSM98754 Last updated (according to GEO): May 31 2006 1000 Hippocampus ovarian tumor: serous Source GEO sample is GSM139441 Last updated (according to GEO): Apr 09 2007 NH 16768A Mammary Neoplasms 861 44 in the motor cortex 62 PMN_LB_180min_Patient13 rat kidney at week 4 post birth, rep3 861 Neoplasm Abdominal aorta collected during autopsy within 24 hours post mortem Source GEO sample is GSM170560 Last updated (according to GEO): Jul 26 2007 substantia_nigra_5 Source GEO sample is GSM80847 Last updated (according to GEO): Mar 31 2006 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132544 Last updated (according to GEO): Feb 26 2007 1000 Maxilla N2_d4 #2(16012165010079) Liver Test (Blinded) Sample Source GEO sample is GSM130196 Last updated (according to GEO): Sep 18 2007 CD8+ T Lymphocytes_Healthy donor 3 HLA-matched Time 35_replicate 1 861 Hippocampus skeletal muscle sprague1 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19221 Last updated (according to GEO): May 27 2005 Frontal_Cerebrocortex_Vehicle_6hr_rep1 Replicate 1 of 3 (same genotype, same age). All replicates were individual animals. Source GEO sample is GSM138274 Last updated (according to GEO): Sep 29 2006 Adenocarcinoma 861 Gene expression data from a neocortex of saline-injected mouse Source GEO sample is GSM147399 Last updated (according to GEO): Jan 03 2007 901 frontal lobe Spleen vs IFN gamma Treated B cell GM12753 Epithelium of bronchus 983 861 Endometrium Tract 861 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114241 Last updated (according to GEO): Jun 16 2006 DCIS88 on harvard-12k 1BRS02080876a_skin 626 615 PCOS oocytes Cerebral cortex 1000 Brain 861 ovarian tumor: serous Source GEO sample is GSM139450 Last updated (according to GEO): Apr 09 2007 1000 Cerebrum bronchial epithelia 224 243 901 Caudate nucleus structure 861 Cerebral cortex Basal-like breast tumor cell line HME-CC Keywords = Agilent microarray, Expression analysis, EGFR, Breast cancer growth Source GEO sample is GSM29518 Last updated (according to GEO): Dec 13 2006 15 0 human cerebellum 752-1 660 mesenchymal stem cell 639 Bone Marrow 1000 JMR-MurNaive-2aAv2-s2 352 347 brain 39 27 the maxillary Gene expression data from postmorten brain regions Source GEO sample is GSM144865 Last updated (according to GEO): Nov 20 2006 Parkinson's disease sample x199 0 30 adenoma 861 +_test-10_batch5 on NHGRI-6.7k Gene expression data of substantia nigra from postmortem brain of PD patients Source GEO sample is GSM184367 Last updated (according to GEO): May 29 2007 V5-P481 1000 Leukemia, Myelocytic, Acute Small cell carcinoma of lung 1000 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211322 Last updated (according to GEO): Jul 18 2007 Flow cytometry sorted double negative thymocytes from wild type animal #1. Treatment, type=fractionate Source GEO sample is GSM130401 Last updated (according to GEO): Aug 24 2006 CLL-44? total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Sphingosine-1-phosphate for 60min Source GEO sample is GSM5746 Last updated (according to GEO): May 27 2005 Brain 861 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120659 Last updated (according to GEO): May 14 2007 GSE6651 Primary tumor 19 32 861 Cerebral cortex 1000 Amygdaloid structure ovarian tumor: serous Source GEO sample is GSM139468 Last updated (according to GEO): Apr 09 2007 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151973 Last updated (according to GEO): Feb 06 2007 67 40 with coronary artery disease 57 Pulmonary Hypertension 36 Category: Cell-line Subcategory: HMEC Scanning Software: ScanAlyze Software version: 2.44 Lot batch = 0097-5k Source GEO sample is GSM1931 Last updated (according to GEO): Nov 21 2005 BAL_41_A1B0 cerebellum_1 Bone Marrow 1000 with myocardial infarction 313 339 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with fMLP for 60min Source GEO sample is GSM5570 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145230 Last updated (according to GEO): Nov 20 2006 1000 Solid tumor D_U133A_63_HC D_U133A_96_Amy 20 0 human caudate nucleus plasma cells 332 344 5 0 brain Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed 6 h to hydrostatic pressure (HP6), pressure experiment # 4 (PE4) Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11393 Last updated (according to GEO): Dec 15 2006 Kidney 1000 Infection 1000 brain 0 5 7 0 Pancreas Spleen 0 5 Parkinson Disease 1000 Cultured_cortical_astrocyte_wild_type_rep2 HapMap CEU_parent Male Source GEO sample is GSM159546 Last updated (according to GEO): Feb 01 2007 SON - 3d Dehydrated Source GEO sample is GSM69843 Last updated (according to GEO): Aug 15 2005 861 Acquired Immunodeficiency Syndrome Sprague-Dawley Female LowSalt Cortex rat703 sd_cortexr_k_703c_020802 brain 0 5 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10163.gif Source GEO sample is GSM79675 Last updated (according to GEO): Sep 22 2006 f2#23 versus pool Mouse Brain tissue 861 Chromosomes Brain 1000 Structure of parenchyma of lung 901 striatum_wildtype_5S KPeterson-Met-19G110-s2 11 Bone marrow 0 Lipids 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145719 Last updated (according to GEO): Nov 20 2006 913 Coronary heart disease BAL_47b_A0B1 1000 Hippocampus f2#295 versus pool Mouse Brain tissue 1000 Bronchi 861 Blood Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 0.25 hours after lights on. Original sample code = CM19A. Source GEO sample is GSM227290 Last updated (according to GEO): Sep 10 2007 Hypoxic-ischemic (HI) injury in the developing brain is a common cause of disability in children, and there are no effective treatments at this time. Exposure to sublethal hypoxic conditions (hypoxic preconditioning) 24 hours prior to hypoxic-ischemic insult is protective in the developing rat model. We have observed protective effects on brain histopathology and on long-term sensory-motor behavioral tasks. Changes in gene expression are thought to underlie this protective effect. By comparing gene expression in rats subjected to hypoxic preconditioning or sham conditioning at several time points from 0 to 24 hrs after preconditioning, we should gain insight into the mechanisms underlying these neuroprotective effects and may identify targets for therapeutic intervention. The aim of this study is to determine the effect of hypoxic preconditioning on global gene expression, and, in littermates, to examine the effect of hypoxic preconditioning 24 h prior to hypoxic-ischemic insult on brain histopathology. We hypothesize that changes in gene expression underlie the protective effect of hypoxic preconditioning against subsequent hypoxic-ischemic insult. Gene expression will be examined in two groups, 1) preconditioned and 2) sham controls, at 4 time points. On postnatal day 6, preconditioned animals are exposed to normothermic hypoxia for 3 hrs (8.0% oxygen, 36 degrees C), and sham animals are simultaneouosly exposed to normoxia at 36 degrees C. Animals are then returned to their dams until euthanized at 4 time points (0h, 2h, 8h, and 24h later). Five brains/group/timepoint will be used, with an equal number of males and females in each group. Brains are removed and dissected on ice. Cerebral cortex is dissected from both hemispheres and rapidly frozen on dry ice. Total RNA is isolated using the QIAGEN RNeasy Protect Maxi Kit. Littermates of these animals will be exposed to hypoxic preconditioning or sham preconditioning and subjected to hypoxic-ischemic injury 24 h later. These animals are euthanized at postnatal day 14 for histopathologic evaluation of injury. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): May 01 2006 Contributers: Mary-Ann Wilson BPH142_benign prostate hyperplasia 0 33 861 Cancer of Neck Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 19 day time point Source GEO sample is GSM159776 Last updated (according to GEO): Apr 23 2007 Standard affymetrix protocol Source GEO sample is GSM119729 Last updated (according to GEO): Jul 31 2007 Coronary artery 901 The nose 94 101 1000 Prostate NMDA180 (Experiment shortNMDA: Run 19222) Treatment, type=time_course, description=primary cortical neurons were treated with 1 mM NMDA for increasing periods of time (10 to 360 min)., measurement=180.0 m Source GEO sample is GSM96769 Last updated (according to GEO): Feb 14 2006 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68337 Last updated (according to GEO): Jul 07 2006 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225699 Last updated (according to GEO): Nov 05 2007 46 8 in docetaxel-refractory prostate cancer of melanoma 67 77 Overexpression of the EGFR/FKBP12/HIF-2alpha pathway identified in childhood astrocytomas by angiogenesis gene profiling. from colonic normal mucosa 21 47 Carcinoma, Large Cell 888 861 Prosencephalon Human Hypothalamus Male 4 (technical replicate) brain, unknown: 00BD_e1_le1 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181102 Last updated (according to GEO): Jul 12 2007 Normal Source GEO sample is GSM176186 Last updated (according to GEO): Apr 09 2007 DIV14 cortical neuron, KCl 1 96 13 from fetal cerebrum Keywords = trisomy 13 Keywords = brain Keywords = Patau syndrome Epithelium of bronchus 983 brain, cerebellum: Tg+/+_Crb1_e1_le1 D_U133A_28_DLPFC 112 FC BA9 A ciliary_ganglion Source GEO sample is GSM18844 Last updated (according to GEO): Sep 25 2006 cerebral cortex 7 21 Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Expression profiling of spinal cord section (T10) extracted from rats 14d following mild injury Source GEO sample is GSM31314 Last updated (according to GEO): May 27 2005 e14-4 Replicate1_Voxel D6 bronchial epithelia 224 243 outer medulla 31 43 GM19102 Frontal cortex 254 267 1000 Amyotrophic Lateral Sclerosis Cerebral cortex 1000 Diaphram, comparison of wild type and mdx mice, 7 to 112 Days (Porter lab) p53 +/+, 0 hour, replicate a Source GEO sample is GSM2554 Last updated (according to GEO): May 27 2005 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153457 Last updated (according to GEO): Jan 11 2007 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.98 Subject: 2672 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39003 Last updated (according to GEO): May 27 2005 861 Antibodies Large-scale analysis of the human transcriptome. Prostate cancer Source: University of Virginia, see PMID 11507037 Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 127.77 Stdv: 5.58 Min: 115.47 Max: 135.25 Source GEO sample is GSM2862 Last updated (according to GEO): Mar 20 2006 Epithelium 861 68-96_Adeno This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12359 Last updated (according to GEO): May 28 2005 schizophrenia 559 572 901 Intestines, Small 1000 Intestines, Small Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132525 Last updated (according to GEO): Feb 26 2007 GSE5582 G30 neurons from somatosensory cortex Source GEO sample is GSM63027 Last updated (according to GEO): Dec 01 2005 experiment IV, hTERT, replicate 2 0 Frontal Cortex 13 144 114 from a single adult spinal cord V5-P556 Prostate 861 Gene expression data from the right forebrain of C57BL mouse received no treatment for four weeks. Source GEO sample is GSM149813 Last updated (according to GEO): Dec 12 2006 GBM: 45A9 Replicate3_Voxel E2 PriG_5%O2_Expt2_Day3_rep1 10 7 Left Myocardium 861 BACKGROUND: Myeloma cells may secrete factors that affect the function of osteoblasts, osteoclasts, or both. METHODS: We subjected purified plasma cells from the bone marrow of patients with newly diagnosed multiple myeloma and control subjects to oligonucleotide microarray profiling and biochemical and immunohistochemical analyses to identify molecular determinants of osteolytic lesions. RESULTS: We studied 45 control subjects, 36 patients with multiple myeloma in whom focal lesions of bone could not be detected by magnetic resonance imaging (MRI), and 137 patients in whom MRI detected such lesions. Different patterns of expression of 57 of approximately 10,000 genes from purified myeloma cells could be used to distinguish the two groups of patients (P<0.001). Permutation analysis, which adjusts the significance level to account for multiple comparisons in the data sets, showed that 4 of these 57 genes were significantly overexpressed by plasma cells from patients with focal lesions. One of these genes, dickkopf 1 (DKK1), and its corresponding protein (DKK1) were studied in detail because DKK1 is a secreted factor that has been linked to the function of osteoblasts. Immunohistochemical analysis of bone marrow-biopsy specimens showed that only myeloma cells contained detectable DKK1. Elevated DKK1 levels in bone marrow plasma and peripheral blood from patients with multiple myeloma correlated with the gene-expression patterns of DKK1 and were associated with the presence of focal bone lesions. Recombinant human DKK1 or bone marrow serum containing an elevated level of DKK1 inhibited the differentiation of osteoblast precursor cells in vitro. CONCLUSIONS: The production of DKK1, an inhibitor of osteoblast differentiation, by myeloma cells is associated with the presence of lytic bone lesions in patients with multiple myeloma. 1000 Cerebellum HapMap CEU_parent Male Source GEO sample is GSM159566 Last updated (according to GEO): Feb 01 2007 AD-317t1-A271-10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 901 frontal lobe skin 80 83 lateral hypothalamus 859 878 136 131 Aortae Plasma 861 DCIS112 on harvard-12k Sample43, Post Injury 24 hours Treatment, type=wait Source GEO sample is GSM53293 Last updated (according to GEO): Jul 06 2005 /HeJ mouse periaqueductal gray 27 56 Lung Neoplasms 901 Semeralul_PFC_Development_Week3_Batch1_Animal_2 AD-367t1-A110-3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A C2C12_3.0_hr 22 Normal adult mouse tissues on custom alternative transcript sensitive Affymetrix microarray used to address differeneces in tissue specific alternative splicing. Abstract: Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe expression of RNA containing at least two alternative splice junctions for about a third of the 3200 alternative events we could detect. Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues, and another 28 exons whose splicing is different in muscle. A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of protein-coding exons. By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation. Of note is a motif strikingly similar to the branchpoint consensus, but which is located downstream of the 5' splice site of exons included in muscle. Analysis of three paralogous membrane-associated guanylate kinase (MAGUK) genes reveals that each contains a paralogous tissue regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families. Last Updated (by provider): Mar 24 2006 Contributers: Charles W Sugnet Mannny Ares Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92292 Last updated (according to GEO): Jan 13 2006 nasal epithelial cells 28 49 707 696 in the brain gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134626 Last updated (according to GEO): Jul 09 2007 HeLa CD4+ cells were transfected with an epitope-tagged eTat plasmid and selected with hygromycin. Cells were treated with nocodazole and collected @3 hours. Source GEO sample is GSM8704 Last updated (according to GEO): May 27 2005 oral_mucosa_1 Source GEO sample is GSM80776 Last updated (according to GEO): Mar 31 2006 338 333 brain Gene expression data from postmorten brain regions Source GEO sample is GSM145220 Last updated (according to GEO): Nov 20 2006 CD3 + CD28 beads 06.00 hr. T-Cell HIGK cells infected with Fusobacterium nucleatum, biological rep1 Liver; Regeneration 6h Keywords = mouse gene expression database Source GEO sample is GSM29372 Last updated (according to GEO): May 27 2005 Cerebral cortex 1000 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy Keywords = pathological hypertrophy Keywords = rat Keywords = heart failure Keywords = cardiomyopathy Source GEO sample is GSM11884 Last updated (according to GEO): May 28 2005 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188692 Last updated (according to GEO): Jun 06 2007 278 255 ischemic cardiomyopathy Olfactory Epithelium 1000 861 Cerebral cortex 42 30 Control blood 861 Brain 1000 Skeletal muscle structure 861 Cartilage Acetaminophen 3hr Rat 0460 blood vs. Acetaminophen 3hr Rat Pooled Control blood 032801_HF_298MB neurological disease control sample x165 Ventral tegmental area 0 22 Congenital Abnormality 853 brain, unknown: 13786-00_e1_le1 861 Ventral Tegmental Area DLBC8 on Affymetrix GeneChip Human Full Length Array HuGeneFL cerebral cortex 7 21 1000 frontal lobe in dorsal root 38 51 861 Oocytes NMDA360 (Experiment shortNMDA: Run 19222) Treatment, type=time_course, description=primary cortical neurons were treated with 1 mM NMDA for increasing periods of time (10 to 360 min)., measurement=360.0 m Source GEO sample is GSM96770 Last updated (according to GEO): Feb 14 2006 Mucous Membrane 861 with myocardial infarction 148 173 Total RNA from brain sample of wild type mice at P0 Treatment, type=purify, measurement=0.0 years Source GEO sample is GSM113680 Last updated (according to GEO): Jun 09 2006 brain, Left frontal Lobe: Extract18_le1 1000 Astrocytoma GSE393 Gene expression profiles in skeletal muscle after gene transfer by electroporation 1000 Ectodermal Dysplasia B220+CD25+sIg- Small Pre BII cells sorted out of mouse bone marrow, sort no. 3 Source GEO sample is GSM634 Last updated (according to GEO): Mar 17 2006 1000 Spleen Central gray substance of midbrain 861 Wild type 8 wk old male C57BL/6J mouse hypothalamus Source GEO sample is GSM107022 Last updated (according to GEO): Mar 05 2007 1000 Spleen LDMTX_MP-9 Cortex 0 5 Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. Source GEO sample is GSM112311 Last updated (according to GEO): Jun 06 2006 Primary tumor 19 32 Brn3a Wildtype TG e13.5 U74Av2 1 in bronchial epithelia 311 332 Epithelium of bronchus 983 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225654 Last updated (according to GEO): Aug 31 2007 Normal Source GEO sample is GSM176110 Last updated (according to GEO): Apr 09 2007 1000 Milk 111601_HF_393FL Central gray substance of midbrain 861 Head and neck cancer Source GEO sample is GSM155714 Last updated (according to GEO): Apr 24 2007 861 Blood 1000 Spleen Substantia Nigra Control Sample4 RMA, MAS 5, dChip brain, hippocampus: PR-CA1-4_e1_le1 PNS BMI-1 KO Chip C 19 0 Head and neck cancer GM18523 Anterior nares 1000 Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203963 Last updated (according to GEO): Aug 02 2007 prostate Source GEO sample is GSM203301 Last updated (according to GEO): Jun 21 2007 36 21 from hippocampus Synapses 1000 with insulin resistance 22 44 LDLR_HF_3 retina 5 10 43 0 Chorionic mesoderm-derived mesenchymal cells total RNA from biosource CC#36 Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92466 Last updated (according to GEO): Jan 13 2006 PGA-E14.5_1 Olfactory Epithelium 901 8 week old mice that did NOT undergo swimming. Used as a control for the 10 minute, 2.5 day, 1 week, and 2 week time points. Keywords = exercised induced hypertrophy Source GEO sample is GSM2345 Last updated (according to GEO): May 27 2005 129S1/SvImJ_female_hypothalamus Source GEO sample is GSM138562 Last updated (according to GEO): Apr 18 2007 Colonic epithelium 901 Disease Source GEO sample is GSM176303 Last updated (according to GEO): Apr 09 2007 HNN023 Normal Source GEO sample is GSM176160 Last updated (according to GEO): Apr 09 2007 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184751 Last updated (according to GEO): Apr 26 2007 861 Nerve Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11609 Last updated (according to GEO): May 28 2005 2307 2289 Stress-Hippocampus Expression profiling of spinal cord section (T9) extracted from rats 48h following laminectomy (sham) Source GEO sample is GSM31267 Last updated (according to GEO): May 27 2005 cardiac 763 769 15 0 human cerebellum Primary small cell lung carcinoma 3424 0 37 I_U133A_10_DLPFC Transplant Series 42 , PrimaryTumor 154 147 in lung 861 Epithelial Cells human caudate nucleus Source GEO sample is GSM86832 Last updated (according to GEO): Feb 08 2006 4 0 Brain Nasal Epithelium 865 in vascular signaling networks 126 156 154 147 in lung 1000 ovarian neoplasm 1000 Spleen Alzheimer's Disease 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145886 Last updated (according to GEO): Nov 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145512 Last updated (according to GEO): Nov 20 2006 Brain 861 Clozapine treated 12weeks AffyGC RMA rep5 Coronary artery 901 GSE642 Gene expression data for comparing calorie restricted-fed 30-month-old to control-fed 30-month-old for investigating effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7448 Last updated (according to GEO): May 27 2005 1000 Spleen Parkinson's disease sample x176 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215069 Last updated (according to GEO): Aug 02 2007 brain, frontal cortex: Sample47_e1_le1 63 in skeletal muscle 46 brain, hippocampus: PH2_e1_le1 21 0 cerebellum wistar 3885 Lymphoblastoid Cell Line for Individual 8102.3 log phase Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 2123 left_liver_lobe Expression profiling of spinal cord section (T9) extracted from rats 30m following laminectomy (sham) Lot batch = Source GEO sample is GSM1333 Last updated (according to GEO): May 28 2005 NA18579 gene expression of 1 day LIF differentiated ESCs Source GEO sample is GSM181942 Last updated (according to GEO): Apr 12 2007 1000 Brain Ganglia, Spinal 923 Calorie restriction and aging Brain 861 for liver 26 35 21 0 Heart failure sample 5 NA12146 with Parkinson's disease 27 50 Normal Source GEO sample is GSM176011 Last updated (according to GEO): Apr 09 2007 23 18 (mtDNA 7wkB 1000 Ligaments During somitogenesis, oscillatory expression of genes in the notch and wnt signaling pathways plays a key role in regulating segmentation. These oscillations in expression levels are elements of a species-specific developmental mechanism. To date, the periodicity and components of the human clock remain unstudied. Here we show that a human mesenchymal stem/stromal cell (MSC) model can be induced to display oscillatory gene expression. We observed that the known cycling gene HES1 oscillated with a 5 hour period, consistent with available data on the rate of somitogenesis in humans. We also observed cycling of Hes1 expression in mouse C2C12 myoblasts with a period of 2 hours, consistent with previous in vitro and embryonic studies. Furthermore, we used microarray and quantitative PCR (Q-PCR) analysis to identify additional genes that display oscillatory expression both in vitro and in mouse embryos. We confirmed oscillatory expression of the notch pathway gene Maml3 and the wnt pathway gene Nkd2 by whole mount in situ hybridization analysis and Q-PCR. Expression patterns of these genes were disrupted in Wnt3atm1Amc mutants but not in Dll3pu mutants. Our results demonstrate that human and mouse in vitro models can recapitulate oscillatory expression observed in embryo and that a number of genes in multiple developmental pathways display dynamic expression in vitro. Last Updated (by provider): May 03 2007 Contributers: Biagio Saitta Dilusha A William Joshua D Gibson Stephen C Pratt Douglas M Anderson William Sewell Kenro Kusumi Eric F Rappaport Jeremy Traas Vladimir Markov Dorian M Gonzalez 861 Neoplasm cerebral cortex 7 21 BCR-ABL-#2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A NZW-LacJ_male_hypothalamus olfactory epithelium 194 213 Gene expression data from brain of adult rats Source GEO sample is GSM101049 Last updated (according to GEO): Feb 20 2007 8 hr EE repl 2 large-cell neuroendocrine carcinomas 111 146 288 of alcohol abuse 272 861 Nerve 14 NT B4 Treatment, type=add, description=10ng/mL Bonemorphogentic Protein, 4d Source GEO sample is GSM92501 Last updated (according to GEO): Jan 13 2006 n/a Source GEO sample is GSM177977 Last updated (according to GEO): Jun 11 2007 M_U133A_56_DLPFC Brain 1000 884 Structure of superior frontal gyrus 1000 Coronary Arteriosclerosis Normal Source GEO sample is GSM175943 Last updated (according to GEO): Apr 09 2007 amygdala wistar 3724 whole tissue, individual animal, 10 weeks old, male Wistar amygdala file:p3722w Source GEO sample is GSM15123 Last updated (according to GEO): Oct 28 2005 1000 Trachea prostate Source GEO sample is GSM203307 Last updated (according to GEO): Jun 21 2007 861 Cerebral cortex Array representing response at 24 h post infection of primary human foreskin fibroblasts with AD169 strain of HCMV Source GEO sample is GSM10346 Last updated (according to GEO): May 27 2005 Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Globin reduction was performed according to the Affymetrix technical note. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183404 Last updated (according to GEO): Apr 23 2007 Cochlear nuclei 0 14 Brain 861 1436 1422 into the brains CNS-SpinalC-conAdult-7d-2A-s2 3AJZ02022226_ brain, caudate nucleus Epithelium 865 ALL_3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A H13B Human Embryonic Stem cell (H13B ESC) Nrf2 +/+ mice (C57B6/SJL) were crossed with nrf2 -/- mice (C57B6/129SVJ) to generate mice heterozygous for nrf2. Interbreeding these heterozygotes generated the double-knockout mice (nrf2 -/-) as well as the corresponding littermate controls (nrf2 +/+). Mice were housed in plastic cages on a bedding of wood chips and maintained at ~22C, ~60% relative humidity, and a 12 hr light/dark cycle. The animals were fed with mouse diet 5015, which includes 30 IU/g of vitamin A and 35 IU/kg of vitamin E, (LabDiet, Richmond, IN) and drinking water ad libitum. All animal protocols were approved by the Institutional Animal Use and Care Committee at the University of Wisconsin-Madison. Total RNA was extracted from livers and spleens isolated from male and female nrf2 wildtype and knockout mice at 5 months of age (prior to the development of severe autoimmune disease). Keywords = Nrf2 Keywords = spleen Source GEO sample is GSM13472 Last updated (according to GEO): May 28 2005 PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls. All samples were normalized with quantile normalization and summarized using RMA. Source GEO sample is GSM135586 Last updated (according to GEO): Dec 19 2006 0029_1377_H95A2_KF-104_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis. Stembase Experiment ID: E189 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189 SCGP Sample ID: S238 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_196 Short description: RNA isolated from primary retinal sphere cells. Estimated purity: > 90% Num cells for RNA prep: ~600,000 Sample volume: 5.0 ul Source GEO sample is GSM87200 Last updated (according to GEO): Jan 19 2006 7 0 Synovium Spinal Cord 1000 MCF7_Untreated_10% Epithelium of bronchus 983 Wild-type-neocortex, biological rep9 (female) 9 0 Blood Test R648P01085 atrial septal defects 198 218 Liver 0 4 brain, cerebellum: KCx4w#1_e1_le1 D_U133A_98_CB 861 Fissure Sham 20 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107509 Last updated (according to GEO): May 01 2006 DMSO-control NG108 neuronal cells 8 Primary Neoplasm 1000 Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. All patients were considered sporadic cases on the basis that no clinical antecedents of familial adenomatous polyposis were reported, and those that met the clinical criteria for hereditary non-polyposis colon cancer (Amsterdam criteria) were excluded. Source GEO sample is GSM112207 Last updated (according to GEO): Jun 06 2006 861 Cerebral cortex 70 cortex 76 Ventral tegmental area, male 10.5 week old c57bl/6J mouse, NON-DEFEATED control Source GEO sample is GSM224752 Last updated (according to GEO): Aug 31 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11548 Last updated (according to GEO): May 28 2005 1BJZ02052115_Tonsil 901 Temporal Lobe 5 0 brain 9 0 Blood Test HCC (HBV+, HK49) 1000 Encephalitis 1000 Spleen 1201 1190 brain injury 12 frontal Lobe 23 Malignant neoplasm of ovary 1000 Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174504 Last updated (according to GEO): Mar 14 2007 Replicate2_Voxel G7 Macrophage 14smi072 630 612 normal fibroblasts Hippocampus 0 10 tumor 1874 1878 occipital regions 163 179 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc1077 Source GEO sample is GSM1872 Last updated (according to GEO): Nov 21 2005 Acetaminophen 24hr Rat 2431 blood vs. Acetaminophen 24hr Rat Pooled Control blood DACH1 inhibits transforming growth factor-beta signaling through binding Smad4. 5 0 brain Hepatocellular carcinoma 0 23 Mouse Liver LRD Diet 5wk 10ppb As Food Exposure, biological replicate B Brain 1000 0 Human Cortex 11 Arteries 861 of the heart 842 854 KT30_CAN 3 0 Lung Lymphoblastoid Cell Line for Individual 8168.4 log phase SW-620 hgu95c 40 21 from dorsal pancreas E2A-PBX1-#13 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A of mouse brain 9 23 in mouse hearts 40 54 1000 Liver 901 Heart failure 191 183 contusion SN:1010383 Source GEO sample is GSM115373 Last updated (according to GEO): Jun 20 2006 MuscleRegen-con8wk-2LLA-s2 1000 Brain 20 0 human caudate nucleus SpinalCo_0226AFCL_new008.txt human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155030 Last updated (according to GEO): Jun 04 2007 Pooled diaphragm RNA samples from five 8 wk old male C57BL10 mice Source GEO sample is GSM13563 Last updated (according to GEO): May 28 2005 Gene expression data from epididymal fat tissues. Source GEO sample is GSM215572 Last updated (according to GEO): Aug 07 2007 P7_cy3_1 Expression profiling of spinal cord section (T9) extracted from rats 30m following mild injury Lot batch = Source GEO sample is GSM1324 Last updated (according to GEO): May 28 2005 3AJZ02083089a_Uterus_Corpus /HeJ mouse periaqueductal gray 27 56 1285 1263 Neutralizing antibodies with Alzheimer's disease 27 50 861 Intestines none Source GEO sample is GSM149622 Last updated (according to GEO): Jan 03 2007 na Source GEO sample is GSM180468 Last updated (according to GEO): Apr 04 2007 Eye 1000 Untreated Control 12weeks AffyGC RMA rep6 858 Prostatic Neoplasms 3AJZ02040819_brainThalamus Bone Marrow 1000 861 Brain 19 0 human frontal cortex Myc oncogenic signature in Papillary type 2b Last Updated (by provider): Jun 14 2007 Contributers: Karl J Dykema Nipple Cross Section 2 Normal HC57 CN B 1000 Endometrium human caudate nucleus Source GEO sample is GSM86822 Last updated (according to GEO): Feb 08 2006 C57BL/6J hypothalamus rep1 (430 2.0 Array) 1000 Structure of trigeminal ganglion RNA isolated from post-mortem tissues Source GEO sample is GSM6827 Last updated (according to GEO): May 28 2005 36 from the facial nucleus 14 of the heart 842 854 BALB/c_PBS Replicate 3 Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1 mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Two replicates of each sample are provided. In addition, one time=0 sample is included.. Date GSE280 Last Updated: Jun 15 2005 Contributers: K C Fertuck C Gennings T R Zacharewski J E Eckel Includes GDS285. Update date: Apr 16 2003. Dataset description GDS285: Temporal examination of ethynyl estradiol (EE) in uterus of immature, ovariectomized C57BL/6. 0.1 mg/kg EE or vehicle administered and uteri harvested at 0, 2, 8, 12, or 24 hours, or three daily doses administered and uteri harvested at 72 hours.. 861 Cerebellum 1000 Descending colon Liver Test (Blinded) Sample Source GEO sample is GSM130147 Last updated (according to GEO): Sep 18 2007 Gene expression data from mouse colon Source GEO sample is GSM198112 Last updated (according to GEO): Aug 22 2007 Normal Source GEO sample is GSM176054 Last updated (according to GEO): Apr 09 2007 In postmortem Huntington's disease brains, mutant htt is present in both nuclear and cytoplasmic compartments. To dissect the impact of nuclear and extranuclear mutant htt on the initiation and progression of disease, we generated a series of transgenic mouse lines in which nuclear localization or nuclear export signal sequences have been placed N-terminal to the htt exon 1 protein carrying 144 glutamines. Our data indicate that the exon 1 mutant protein is present in the nucleus as part of an oligomeric or aggregation complex. Increasing the concentration of the mutant transprotein in the nucleus is sufficient for and dramatically accelerates the onset and progression of behavioral phenotypes. Furthermore, nuclear exon 1 mutant protein is sufficient to induce cytoplasmic neurodegeneration and transcriptional dysregulation. However, our data suggest that cytoplasmic mutant exon 1 htt, if present, contributes to disease progression. prostate Source GEO sample is GSM203366 Last updated (according to GEO): Jun 21 2007 Expression profiling of spinal cord section (T10) extracted from rats 24h following moderate injury Source GEO sample is GSM31339 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T10) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM4459 Last updated (according to GEO): May 28 2005 AML-28 on Affymetrix GeneChip Human Full Length Array HuGeneFL 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114209 Last updated (according to GEO): Jun 16 2006 Control sample 23 weeks Primary Neoplasm 1000 brain_OFC_bipolar B_mr93 10 Bone marrow 0 CD8+ T Lymphocytes_Healthy donor 3 HLA-matched Time 0_replicate 1 1000 Cerebral cortex Standard Affymetrix Protocal Keywords = microarray Keywords = muscle Source GEO sample is GSM15776 Last updated (according to GEO): May 28 2005 Parkinson Disease 1000 165 134 of diffuse large B-cell lymphoma prostate Source GEO sample is GSM203354 Last updated (according to GEO): Jun 21 2007 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n006 Source GEO sample is GSM2036 Last updated (according to GEO): Nov 21 2005 Myometrium 43 Disease with Alzheimer's disease 27 50 hrs nasal epithelium 1126 1146 13 8 Retina Spleen 1000 to the nose 599 609 with mental retardation 241 263 12 mammary gland 0 of coronary artery disease 317 342 1000 hindbrain 57 39 with endometriosis Macrophage smi120 none Source GEO sample is GSM239879 Last updated (according to GEO): Dec 07 2007 Thyroid [JunctionChip 2 of 5] Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed 48 h to hydrostatic pressure (HP48), pressure experiment # 1 (PE1). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11423 Last updated (according to GEO): Dec 15 2006 NCI60.57_LABEL61EXTRACT60SUB3 Source GEO sample is GSM134282 Last updated (according to GEO): Aug 06 2007 Normal Source GEO sample is GSM176034 Last updated (according to GEO): Apr 09 2007 mesenteric 11 20 PGA-swim_3w_s1095 67 52 descending colon 861 Blood 338 333 brain 1000 Intestines, Small 1000 Rhabdoid Tumor Seminoma 1000 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11514 Last updated (according to GEO): May 28 2005 human peripheral blood derived monocytes, 4 hour LPS stimulation, biological rep1 Source GEO sample is GSM126996 Last updated (according to GEO): Aug 15 2006 1000 Coronary Arteriosclerosis 861 Prostate NSCLC_EKVX_CL1008 on Affymetrix GeneChip Human Full Length Array HuGeneFL at the Human Brain 743 760 brain 0 5 ATCC number CRL-1502 Source GEO sample is GSM6806 Last updated (according to GEO): May 27 2005 WGACON-42 CNS-SpinalC-conAdult-T0-1A-s2 Gene expression data from whole brain of uninfected mouse Source GEO sample is GSM189629 Last updated (according to GEO): May 16 2007 M_U133A_41_DLPFC 118 86 in immune complex kidney disease Acute leukemia 913 such as Alzheimer's disease 921 948 1000 Extracellular Matrix Blood 1000 CNS-RM_Ctr7d-2C-s2 heart 1169 1173 stomach_cardiac_4 Source GEO sample is GSM80783 Last updated (according to GEO): Mar 31 2006 from colorectal adenoma 21 44 Bladder [JunctionChip 1 of 5] Spleen 1000 GC (HKG67T) GSE6514 861 Cancer of Neck Job's patient Source GEO sample is GSM211096 Last updated (according to GEO): Sep 10 2007 913 Coronary heart disease 361 335 hypertrophic cardiomyopathy Cerebral cortex 1000 Squamous epithelial cell 861 VDXRHU_5240 861 Blood NA18975 hippocampal glutamatergic CA3 pyramidal neurons Source GEO sample is GSM35816 Last updated (according to GEO): May 27 2005 Autistic Disorder 877 2534 HP24_33 with some respiratory epithelium. 1039 1072 24 0 human prostate PC3 tumors 515 504 of the liver Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162160 Last updated (according to GEO): Jun 12 2007 Wild type inbred mice Source GEO sample is GSM82965 Last updated (according to GEO): Nov 10 2005 861 Heart Diseases AMM_0_0_Female9_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111840 Last updated (according to GEO): Nov 21 2006 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225936 Last updated (according to GEO): Nov 02 2007 861 Brain n/a Source GEO sample is GSM178078 Last updated (according to GEO): Jun 11 2007 129S6/SvEvTac periaqueductal gray rep2 (430 2.0 Array) 567 548 the descending colon E10.5 craniofacial tissue, first branchial arch: WT_MXA2-2_e1_le1 small Source GEO sample is GSM67253 Last updated (according to GEO): Jan 19 2006 861 Bladder 3 0 Lung COLO-250_CL4010_Colon on Affymetrix GeneChip Human Full Length Array HuGeneFL Ganglia, Spinal 923 5 0 brain SN:Human Glioblastoma Biopsy 06723 Wild type inbred mice Source GEO sample is GSM82992 Last updated (according to GEO): Nov 10 2005 Blood 861 Spleen vs SDF1 alpha (Stromal cell derived factor-1) Treated B cell 30min (set1) H9LMS00102608 693 673 of LCCS spinal cords Gene expression data from mouse primary visual cortex Source GEO sample is GSM101710 Last updated (according to GEO): Mar 27 2006 CNS-SC_Inj14d-4Bb-s2 4 0 Brain Liver Test (Blinded) Sample Source GEO sample is GSM130146 Last updated (according to GEO): Sep 18 2007 umbilical cord_nobpd: 4F processed in batch 7 Source GEO sample is GSM90427 Last updated (according to GEO): Mar 20 2006 SR-A mutant olfactory epithelium 16 hpO replicate1 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215082 Last updated (according to GEO): Aug 02 2007 Bmi1 shRNA, biological rep3 Nasal Epithelium 865 AT1-hTERT_1.5Gy_6h_C3_21713 GSE6238 Con (0 h) B on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A 59 35 out of mouse bone marrow trachea_3 861 Epithelial Cells Category: Lymphoma Classification Subcategory: Follicular Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n010 Source GEO sample is GSM2029 Last updated (according to GEO): Nov 21 2005 AR overexpression converts antagonists to weak agonists. Date GSE846 Last Updated: May 29 2005 Contributers: Derek Welsbie Charles Sawyers Charlie Chen Includes GDS536. Update date: Mar 30 2004. Dataset description GDS536: Examination of antagonist to agonist conversion in androgen receptor-expressing hormone-sensitive LNCaP prostate cancer cells. Cells challenged with increasing doses of R1881, or bicalutamide.. 134 115 by CO2 asphyxiation oral_mucosa_2 Source GEO sample is GSM80777 Last updated (according to GEO): Mar 31 2006 Whole Brain 73 83 Neoplasm 861 Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep5 861 Malaria ALS model Source GEO sample is GSM75506 Last updated (according to GEO): Mar 06 2006 brain 0 5 Voxel H3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1441 Last updated (according to GEO): Nov 21 2005 901 Bone neoplasms 861 Blood Gene expression data from the neocortex of wild-type mouse Source GEO sample is GSM172927 Last updated (according to GEO): Mar 08 2007 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228646 Last updated (according to GEO): Sep 11 2007 19 0 human frontal cortex 277 271 Retinas 352 347 brain healthy subject Source GEO sample is GSM211075 Last updated (according to GEO): Sep 10 2007 105T GSE7476 1000 Prostate The goal of these experiments was to identify the genes that are regulated by CCAT, a novel transcription factor derived from the C-terminus of CaV1.2. Neuro2A neuroblastoma cells were transfected with the last 503 AA of CaV1.2 which is full length CCAT (CCAT FL) or with the last 280 AA of CaV1.2, a form of CCAT that lacks the transcriptional activation domain (CCAT DTA). The mRNA from either CCAT FL or CCAT DTA expressing cells was hybridized to Agilent mouse genome microarrays along with mRNA from untransfected neuro2A cells. The microarray data was subsequently analyzed with the Rossetta Luminator gene expression data analysis system. Subsequent investigation revealed that CCAT DTA can still activate transcription albeit at much lower levels than CCAT FL. Source GEO sample is GSM95634 Last updated (according to GEO): Feb 07 2006 153T 21 0 acute myeloid leukemia plasma cells 332 344 Normal__Colon_CR_1 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Expression profiling of spinal cord section (T10) extracted from rats 24h following mild injury Source GEO sample is GSM31320 Last updated (according to GEO): May 27 2005 Posterior root of spinal nerve 861 Wild type 8 wk old male A/J mouse hippocampus Source GEO sample is GSM107007 Last updated (according to GEO): Mar 05 2007 901 Status Epilepticus starved 31 37 N2_d1 #1(16012165010067) DLCL-0029 Epithelial Cells 1000 Colonic mucous membrane 913 Total RNA extracted from the forebrain of a Stg+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144388 Last updated (according to GEO): Nov 14 2006 CT58-1 Liver 1000 NZW/LacJ_female_hypothalamus 1000 Nervous system structure Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12675.gif Source GEO sample is GSM79962 Last updated (according to GEO): Sep 22 2006 M_U133A_18_HC Cochlea 0 6 7 cerebral cortex 21 Ischemia-reperfusion with AEOL 10150 #3 nasal epithelial cells 28 49 Control #2 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114446 Last updated (according to GEO): Jun 16 2006 WGACON-237 CS-B cell unirradiated replicate 1 U133B Brain_MD_16_Medulloblastoma_Desmoplastic _D on Affymetrix GeneChip Human Full Length Array HuGeneFL 20 0 atrioventricular_node M_U133A_30_HC Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp1213 Source GEO sample is GSM2170 Last updated (according to GEO): Nov 21 2005 with myocardial infarction 313 339 Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging and comparing calorie restricted-fed 30-month-old to control-fed 30-month-old to investigate effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7464 Last updated (according to GEO): May 27 2005 c_B51 olfactory epitheliumSR-A mutant mouse 0 h Source GEO sample is GSM80200 Last updated (according to GEO): Oct 26 2005 106 year old female 11 0 Hypothalamus 3AMH02082316_PB_CD14Monocytes 43h-AM replication 1 Brain 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Neuropeptide Y for 120min Source GEO sample is GSM5715 Last updated (according to GEO): May 27 2005 91 from the bone marrow 72 n/a Source GEO sample is GSM178018 Last updated (according to GEO): Jun 11 2007 Expression profiling of spinal cord section (T9) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM4477 Last updated (according to GEO): May 28 2005 1000 Brain NG007_c Nasal Epithelium 901 Gene expression data from the neocortex of wild-type mouse Source GEO sample is GSM172929 Last updated (according to GEO): Mar 08 2007 Bladder sample 441-1 Expression profiling of spinal cord section (T10) extracted from rats 7dh following severe injury Source GEO sample is GSM31389 Last updated (according to GEO): May 27 2005 To test the hypotheses that mutant huntingtin protein length and wild-type huntingtin dosage have important effects on disease-related transcriptional dysfunction, we compared the changes in mRNA in seven genetic mouse models of Huntington's disease (HD) and postmortem human HD caudate. Transgenic models expressing short N-terminal fragments of mutant huntingtin (R6/1 and R6/2 mice) exhibited the most rapid effects on gene expression, consistent with previous studies. Although changes in the brains of knock-in and full-length transgenic models of HD took longer to appear, 15- and 22-month CHL2(Q150/Q150), 18-month Hdh(Q92/Q92) and 2-year-old YAC128 animals also exhibited significant HD-like mRNA signatures. Whereas it was expected that the expression of full-length huntingtin transprotein might result in unique gene expression changes compared with those caused by the expression of an N-terminal huntingtin fragment, no discernable differences between full-length and fragment models were detected. In addition, very high correlations between the signatures of mice expressing normal levels of wild-type huntingtin and mice in which the wild-type protein is absent suggest a limited effect of the wild-type protein to change basal gene expression or to influence the qualitative disease-related effect of mutant huntingtin. The combined analysis of mouse and human HD transcriptomes provides important temporal and mechanistic insights into the process by which mutant huntingtin kills striatal neurons. In addition, the discovery that several available lines of HD mice faithfully recapitulate the gene expression signature of the human disorder provides a novel aspect of validation with respect to their use in preclinical therapeutic trials. Last Updated (by provider): Oct 19 2007 Contributers: Peggy F Shelbourne Andrew D Strand Biopsy of the normal mucosa of the colon from patient #8 201 in the frontal cortex 221 GSE4608 This is the first replicate for the SNc neurons which were captured using LCM. Source GEO sample is GSM19312 Last updated (according to GEO): May 27 2005 Parkinson Disease 861 MuscleRegen-ctx2d-1RLAv2-s2 Small Intestine; Duodenum Keywords = mouse gene expression database Source GEO sample is GSM29298 Last updated (according to GEO): May 27 2005 brain, cerebral cortex: NMDA 180 2_le1 1000 Brain Spleen 1000 861 Neoplasm Gene expression data for comparing calorie restricted-fed 30-month-old to control-fed 30-month-old for investigating effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7451 Last updated (according to GEO): May 27 2005 Brain 1000 1000 Brain 109 81 after traumatic brain injury CNS-SC_InjB7d-2A-s2 GM07348 a Keywords = colon cancer 27 52 brain 0 5 1000 Temporal Lobe the heart 987 996 CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of DC, recombinant human (rh) IL-4 and rhGMCSF were added to the culture at 50 ng/ml on days 1, 3, and 5 of culture. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5134 Last updated (according to GEO): Oct 28 2005 cingulate cortex 1000 Na+/H+ exchanger 1 deficiency alters gene expression in mouse brain. Epithelium 861 This SuperSeries is composed of the following subset Series: GSE8290: Comprehensive analysis of PPAR?-dependent regulation of hepatic lipid metabolism by expression profiling - 1 GSE8291: Comprehensive analysis of PPAR?-dependent regulation of hepatic lipid metabolism by expression profiling - 2 GSE8292: Comprehensive analysis of PPAR?-dependent regulation of hepatic lipid metabolism by expression profiling - 3 GSE8295: Comprehensive analysis of PPAR?-dependent regulation of hepatic lipid metabolism by expression profiling - 4 GSE8302: Comprehensive analysis of PPAR?-dependent regulation of hepatic lipid metabolism by expression profiling - 5 Last Updated (by provider): Contributers: Rinke Stienstra Merja Matilainen Michael Muller Philip J de Groot Maryam Rakhshandehroo Sander Kersten Linda M Sanderson Carsten Carlberg ventral striatum wistar ky 3959 gene expression data from melanoma xenografts following ILI with melphalan Source GEO sample is GSM213634 Last updated (according to GEO): Jul 27 2007 Simple annotation: Reference verification, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10075.gif Source GEO sample is GSM78464 Last updated (according to GEO): Sep 22 2006 the ventricular 1095 1109 Mice lacking p53 and one or two alleles of the cyclin D-dependent kinase inhibitor p18(Ink4c) are prone to medulloblastoma development. The tumor frequency is increased by exposing postnatal animals to ionizing radiation at a time when their cerebella are developing. In irradiated mice engineered to express a floxed p53 allele and a Nestin-Cre transgene, tumor development can be restricted to the brain. Analysis of these animals indicated that inactivation of one or both Ink4c alleles did not affect the time of medulloblastoma onset but increased tumor invasiveness. All such tumors exhibited complete loss of function of the Patched 1 (Ptc1) gene encoding the receptor for sonic hedgehog, and many exhibited other recurrent genetic alterations, including trisomy of chromosome 6, amplification of N-Myc, modest increases in copy number of the Ccnd1 gene encoding cyclin D1, and other complex chromosomal rearrangements. In contrast, medulloblastomas arising in Ptc1(+/-) mice lacking one or both Ink4c alleles retained p53 function and exhibited only limited genomic instability. Nonetheless, complete inactivation of the wild-type Ptc1 allele was a universal event, and trisomy of chromosome 6 was again frequent. The enforced expression of N-Myc or cyclin D1 in primary cerebellar granule neuron precursors isolated from Ink4c(-/-), p53(-/-) mice enabled the cells to initiate medulloblastomas when injected back into the brains of immunocompromised recipient animals. These "engineered" tumors exhibited gene expression profiles indistinguishable from those of medulloblastomas that arose spontaneously. These results underscore the functional interplay between a network of specific genes that recurrently contribute to medulloblastoma formation. Colon 1000 966 Hippocampus Retina 1000 B6:2-4 retina 39 21 from mammary glands 1000 Neoplasm T-ALL-#10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Liver 1000 B6:16-5 midbrain-thalamus CC068 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11587 Last updated (according to GEO): May 28 2005 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15754 Last updated (according to GEO): May 28 2005 Brain 861 brain, cerebellum: KCx12w#2_e1_le1 NeverSmoker 96 ventral striatum wistar 4026 20 0 human caudate nucleus Spleen vs Anti-IgM Treated B cell 30min (set2) Gene expression data from postmorten brain regions Source GEO sample is GSM144999 Last updated (according to GEO): Nov 20 2006 B2 embryonic hearts 1064 1079 17 7 hippocampus 5 0 brain 2_hypothalamus_3hrs_sleep_deprivation_#121 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16525.gif Source GEO sample is GSM91587 Last updated (according to GEO): Sep 22 2006 Analysis of target genes induced by the Amyloid Precursor Protein Intracellular Domain Source GEO sample is GSM93712 Last updated (according to GEO): Jan 25 2006 1000 Lung 861 Heart none Source GEO sample is GSM149615 Last updated (according to GEO): Jan 03 2007 adenoma 861 DRG003_b 901 Stem cells Lung metastasis genes couple breast tumor size and metastatic spread. Gene expression data from postmorten brain regions Source GEO sample is GSM145257 Last updated (according to GEO): Nov 20 2006 1000 Myeloid Leukemia, Chronic C3H 8-1 BAT testis 52 58 dorsal striatum 0 14 12 0 ovarian tumor the mouse central nervous system 335 366 DNA Damage 1000 Neoplasm 861 Spleen vs Bombesin Treated B cell 120min (set1) HT29 hgu95d with some respiratory epithelium. 1039 1072 of mouse brain 9 23 NMDA 1h 7/8 RC (Experiment NMDA1-Run 13384)) Treatment, type=time_course, description=samples are treated for 10, 30 or 60 min with NMDA 1mM, the agonist is then washed out and the cells are harvested 24h later, measurement=60.0 m Source GEO sample is GSM96763 Last updated (according to GEO): Feb 14 2006 Prostate 861 nostrils 156 164 Mucous Membrane 861 M_U133A_33_nAcc I/LnJ_male_hypothalamus Lymphoblastoid Cell Line for Individual 8115.4 log phase Expression profiling of spinal cord section (T10) extracted from rats 4h following severe injury Source GEO sample is GSM31379 Last updated (according to GEO): May 27 2005 GSE580 GIN-CingulateCortex replicate2 5 0 Spleen total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-beta (IFN beta) for 30min Source GEO sample is GSM5590 Last updated (according to GEO): May 27 2005 Unsusceptible Group, Ventral tegmental area, Biological Replicate 3 1000 Malignant Neoplasms The epithelial cells 962 981 1000 Endometriosis, site unspecified 1000 Infection Cnr1-/-/Cnr2-/- female number 2, untreated control ear (#8_Ko-C-5) Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181162 Last updated (according to GEO): Jul 12 2007 1 of 3 replicates in treatment group Source GEO sample is GSM206034 Last updated (according to GEO): Jun 29 2007 Lymphatic vessel 1000 of the colon 28 39 Cochlear structure 1000 VDXGUYU_4099 Large cell carcinoma of lung 937 no additional Source GEO sample is GSM199033 Last updated (according to GEO): Jun 08 2007 Liver 1000 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11588 Last updated (according to GEO): May 28 2005 Expression profiling of spinal cord section (T10) extracted from rats 14d following severe injury Source GEO sample is GSM31345 Last updated (according to GEO): May 27 2005 I_U133A_29_Amy Primary Neoplasm 1000 2 CN B Temporal Cortex Control (mTLE) 2 Gene expression data from postmorten brain regions Source GEO sample is GSM145281 Last updated (according to GEO): Nov 20 2006 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28761 Last updated (according to GEO): May 27 2005 Post infection 29 42 Brain 1000 Leukemia, Lymphocytic, Chronic 1000 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188852 Last updated (according to GEO): Jun 06 2007 E6, E7, hTERT, bone marrow cell 5 0 brain 1000 Retina Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM79062 Last updated (according to GEO): Oct 24 2005 67 40 with coronary artery disease Pyrethroids are neurotoxicants that disrupt nervous system function by interacting with a variety of membrane bound ion channels on neuronal plasma membranes. This study is designed to investigate the transcriptional events downstream of pyrethroid-induced disruption of nervous system excitability. Adult, male Long-Evans rats were orally dosed in vivo with a single dose of either permethrin (1, 10, or 100 mg/kg) or deltamethrin (0.3, 1, 3 mg/kg) at levels that produce only modest behaviroal effects in the whole animal (Wolansky et al. 2006). Transcriptional profiles were obtained from frontal cerebrocortical tissue 6 hours after acute exposure. The primary goals were 1) to identify dose-responsive biomarkers of effect for pyrethroids and 2) identify sensitive intracellular signaling or metabolic pathways sensitive to pyrethroid compounds. Last Updated (by provider): Sep 18 2007 Contributers: Kevin M Crofton Fred A Wright Joshua A Harrill Zhen Li the blood 393 402 5 0 brain NA19239 1000 Down Syndrome 861 Medulla from the right forebrain 21 44 tibiae 115 120 1000 Structure of locus ceruleus Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118348 Last updated (according to GEO): Jul 11 2006 1123 1114 metastasis GM10846 1000 Organ of Corti 228 219 Hippocampi AK_Control_ZT 6_2 Normal Source GEO sample is GSM176128 Last updated (according to GEO): Apr 09 2007 Hypothalamic structure 1000 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211369 Last updated (according to GEO): Jul 18 2007 none Source GEO sample is GSM123215 Last updated (according to GEO): Jul 26 2006 1000 Cerebellum 0029_1222_H95A2_KF0146_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A rat hippocampus Treatment, type=time_course, measurement=72.0 h Source GEO sample is GSM32146 Last updated (according to GEO): May 27 2005 Nervous system structure 901 E2A-PBX1-#1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Cerebral cortex EOM 112 Day Control rep 1 Gene expression data from postmorten brain regions Source GEO sample is GSM145868 Last updated (according to GEO): Nov 20 2006 of a colorectal adenoma 7 29 Epithelial Cells 1000 24 skeletal muscle 10 2.5 mg/kg 2CdA headfold at 4.5h PGA-lv_24h_515 861 Malignant Neoplasms 2500mg/kg APAP 12Hr rat 4135 blood vs. PC 12Hr rat 4126 blood Brain 861 pull-downC_13, ZT6 Liver gene expression associated with diet and lesion development in atherosclerosis-prone mice: induction of components of alternative complement pathway. Probeset expression data from NA12751 growth 3, replicate 5 Source GEO sample is GSM195217 Last updated (according to GEO): Aug 08 2007 Sample # 1682-1 Clozapine treated 12weeks AffyGC RMA rep10 660 mesenchymal stem cell 639 17 0 Trigeminal ganglia 1000 Prostate SNU475 cells knockin mouse cerebellum Treatment, type=time_course, measurement=4.0 weeks Source GEO sample is GSM53341 Last updated (according to GEO): Jul 06 2005 2 hours, repeat 1 Occipital Lobe 3 Normal Lung 861 1000 frontal lobe 861 Heart 865 Gingival epithelium Operator Name: Sample Type: Sample Description: Comments: Reagents: Reagent Lot: Algorithm: Statistical Corner+ Avg:258, Count:32 Corner- Avg:36872, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:12.314540,SFGene:All Background:Avg:749.42,Stdev:37.77,Max:891.0,Min:667.6 Noise:Avg:16.05,Stdev:3.93,Max:36.0,Min:11.9 RawQ:18.21 Keywords = ALL Source GEO sample is GSM3484 Last updated (according to GEO): May 28 2005 Wild type 8 wk old male 129S6/SvEvTac mouse amygdala Source GEO sample is GSM74912 Last updated (according to GEO): Feb 27 2007 Brain 1000 70 40 without coronary artery disease CNS-SC_InjB24h-3A-s2 861 Brain cerebellum 7 16 Colon 1000 913 frontal lobe 660 mesenchymal stem cell 639 Whole blood 0 10 n/a Source GEO sample is GSM177959 Last updated (according to GEO): Jun 11 2007 Spinal Cord 1 Normal Brain 861 gene expression data from melanoma xenografts following ILI with saline Source GEO sample is GSM213635 Last updated (according to GEO): Jul 27 2007 severe traumatic brain injury 153 181 of Parkinson's disease 450 471 861 Heart total RNA derived from a leprosy lesion Source GEO sample is GSM6766 Last updated (according to GEO): May 27 2005 Colon 1000 of the colon 28 39 Subject code A1 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 2730 left_liver_lobe 1000 Retina NINDS-RNP-SNC-7aA-s2 CNS-SCsev_InjA7d-4A-s2b Simple annotation: Drug_treatment, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/9012.gif Source GEO sample is GSM78475 Last updated (according to GEO): Sep 22 2006 861 Blood Epithelial Cells 901 RPMI-8226 hgu95e NA Source GEO sample is GSM84316 Last updated (according to GEO): Dec 01 2005 GRP sample 8 861 Blood stria terminalis 901 4R-4 2/5 (Experiment 4Rlong: Run 19283) Treatment, type=timepoint, description=Primary cortical neurons were treated for 18h with a new non competitive antagonist for nicotinic receptors (4R 2uM), the antagonist was then washed out and the cells were harvested 24h later, measurement=24.0 h Source GEO sample is GSM96742 Last updated (according to GEO): Feb 14 2006 Individual array of a bladder cancer expression experiment. Source GEO sample is GSM180996 Last updated (according to GEO): Apr 12 2007 a rare genetic defect 56 76 Nerve 1000 1000 Encephalitis 1000 Muscle To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Source GEO sample is GSM28450 Last updated (according to GEO): May 27 2005 ADH57 on harvard-12k 913 Dermatitis, Atopic from liver 21 30 3 subtypes of cortical projection neurons were purified by fluorescence-activated cell sorting at 4 different stages of development from mouse cortex. A detailed description of the data set is described in Arlotta, P et al (2005) Last Updated (by provider): May 29 2005 Contributers: Jeffrey D Macklis Bradley J Molyneaux Paola Arlotta Includes GDS1076. Update date: Mar 16 2005. Dataset description GDS1076: Analysis of corticospinal motor neurons (CSMN) of C57BL/6 at embryonic day 18 to postnatal day 14. CSMN degeneration contributes to amyotrophic lateral sclerosis. CSMN compared to callosal projection and corticotectal projection neurons. Results provide insight into CSMN development.. Rb-/- prostate epithelial cell line maintained in RPMI-1640 medium supplemented with 5% fetal bovine serum Keywords = prostate Keywords = epithelial Source GEO sample is GSM14674 Last updated (according to GEO): May 28 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with SDF1 alpha (Stromal cell derived factor-1) for 240min Source GEO sample is GSM5765 Last updated (according to GEO): May 27 2005 Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181997 Last updated (according to GEO): Apr 13 2007 no additional Source GEO sample is GSM199029 Last updated (according to GEO): Jun 08 2007 BPH-25 on NHGRI-6.5k_c cerebral cortex wistar ky 3913 HapMap CEU_parent Female Source GEO sample is GSM159563 Last updated (according to GEO): Feb 01 2007 KT87b_N CNS-SCsev_InjA4h-1C-s2 human mammary epithelial cells 314 343 of coronary artery disease 317 342 no additional Source GEO sample is GSM199344 Last updated (according to GEO): Jun 08 2007 Communicable Diseases 861 GC (HKG53T) Nasal Epithelium 865 Lymphoblastoid Cell Line for Individual 8158.3 log phase SF-295 hgu95a Primary large cell neuroendocrine carcinoma 6065 0 47 Category: Lymphoma Classification Subcategory: Hematopoetic cell lines Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b041 Source GEO sample is GSM1990 Last updated (according to GEO): Nov 21 2005 WM35, 48h treatment with 5 AzadC colon_cecum_10 Source GEO sample is GSM80632 Last updated (according to GEO): Mar 31 2006 none Source GEO sample is GSM123223 Last updated (according to GEO): Jul 26 2006 fetal lung Source GEO sample is GSM18965 Last updated (according to GEO): Sep 25 2006 NAP-102 on UMich-10k aml8-aml8_c2_ab_hu68_abms on Affymetrix GeneChip Human Full Length Array HuGeneFL Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226035 Last updated (according to GEO): Nov 02 2007 41 29 Control blood 5 0 brain 861 melanoma 26 15 endometrioid Brain 1000 Hyperdip>50-#8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A This is the fourth replicate for the SNc neurons which were captured using LCM. Source GEO sample is GSM19319 Last updated (according to GEO): May 27 2005 Tumor__Melanoma_94_I_149 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Richard Almon-36-1133800609901 5 0 brain Gene expression data from postmorten brain regions Source GEO sample is GSM145055 Last updated (according to GEO): Nov 20 2006 vestibular_nuclei_superior_10 Macrophage smi109 1000 Spleen embryonic hearts 1064 1079 ventral spinal cord 13 31 MCF7_CHX_EtOH_24h_rep4 117 cortex 123 The transcriptional program in the response of human fibroblasts to serum. Epithelium 861 Cortex from rats with cerebral cortical contusion 4 days post injury, injured cortex (ipsilateral side) -uninjured cortex (contralateral side) were hybridised onto a 6240 cDNA probe microarray. Expression ratios were calculated using injured/ un-injured cortex Source GEO sample is GSM76310 Last updated (according to GEO): Sep 29 2005 861 Cerebral cortex 238 206 to amyotrophic lateral sclerosis TAp63 alpha 24h without induction s3 Keywords = Infectious diseases 1070 1100 of viral infection 7 24 brain, Medial Temporal Gyrus: Sample34_e1_le1 Left ventricle 172 185 Expression profiles of extremely low gestational age newborns as predictors of BPD The genomic consequences of bursts of action potential firing induced by the treatment of cultured cortical neurons (9-11 DIV) with the GABAA receptor antagonist bicuculline (Bic, 50 ?M). Source GEO sample is GSM143919 Last updated (according to GEO): Nov 24 2006 Liver 0 4 normal 1361 PGA-MPF-BALB-saline-14d-1bAv2-s2 gene expression of 5 day LIF differentiated ESCs Source GEO sample is GSM181957 Last updated (according to GEO): Apr 12 2007 The nose 94 101 9 0 Blood Test Eye 1000 Expression profiling of spinal cord section (T8) extracted from rats 30m following laminectomy (sham) Source GEO sample is GSM31406 Last updated (according to GEO): May 27 2005 Medulla 861 Transitional epithelium 1000 Neoplasm 861 14 7 amygdala Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9981.gif Source GEO sample is GSM79857 Last updated (according to GEO): Sep 22 2006 Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Dye-swap. Source GEO sample is GSM15962 Last updated (according to GEO): May 28 2005 of chromosome 16 61 76 M_U133Plus_104_HC hc6 none Source GEO sample is GSM149616 Last updated (according to GEO): Jan 03 2007 1000 Liver 861 Neoplasm 861 Neoplasm Expression profiling of spinal cord section (T9) extracted from rats 7d following severe injury Lot batch = Source GEO sample is GSM7601 Last updated (according to GEO): May 28 2005 Integumentary system 1000 Nucleus Accumbends, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231028 Last updated (according to GEO): Sep 26 2007 Cultured Dendritic Cells, CD8+ subset - Expt #1 Brain 861 Stria 861 1000 Hippocampus 901 Bone Marrow 280_2 10.0 mg/kg MeHg at 3.0h 84 60 hepatocellular carcinoma Nasal Epithelium 901 of regenerating Dorsal Root Ganglia 21 55 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188749 Last updated (according to GEO): Jun 06 2007 1000 Brain Abdominal aortic aneurysm obtained from surgery to correct. Source GEO sample is GSM170555 Last updated (according to GEO): Jul 26 2007 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n097 Source GEO sample is GSM2076 Last updated (according to GEO): Nov 21 2005 9 0 Blood Test The adult mouse was injected intraperitoneal (ip) with saline (~100ul/mouse) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use. Source GEO sample is GSM73014 Last updated (according to GEO): Sep 07 2005 of ALDHhiSSClo Neural Stem Cells 16 47 with meningiomas 787 803 Mouse ileum 0 10 367 350 in the hippocampus Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132521 Last updated (according to GEO): Feb 26 2007 A control group consisting of nine C57/BL/6J mice was maintained on a normal diet consisting of Purina Rodent Chow (Harlan Teklad, catalog #5008, 6.5% fat, 49% carbohydrate, 23% protein, 3.5 kcal/ g). The experimental group consisted of nine mice grown on a specialty high-fat diet (Harlan Teklad, catalog #TD88137, 42.16% fat, 42.81% carbohydrate, 15.02% protein, 4.53 kcal/ g). Mice were maintained for ten weeks on their respective diets in a controlled environment with standard light and feeding schedule. Two days before tissue harvest, the experimental group on the high-fat diet was divided into one group of five and one group of four mice. The first group continued on the high-fat diet for the final two days, while the second group fasted. Mouse weights were recorded two days prior, and the day of tissue harvest. At the end of the fasting period liver tissue samples were harvested from each mouse. RNA was purified from the liver tissue samples. Each tissue was homogenized in 1 mL of STAT-60 (Tel-Test, Inc., Friendswood, TX) and the homogenate was mixed with 200 uL of chloroform. The aqueous phase was removed, and mixed with 500 uL of isopropanol to precipitate the RNA. The resulting RNA pellet was washed with 500 uL of 70% ethanol and allowed to air dry. The pellet was dissolved in RNase free water (Ambion, TX), quantified by UV spectroscopy, and stored at -80C. Total RNA control samples (Universal Mouse Reference RNA, catalog # 740100, Stratagene) were labeled using Cy3 dCTP (Perkin-Elmer), and liver total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). The control RNA samples were additionally mixed with 2 uL of random hexamers. The reaction mixtures were incubated at 42 C for two hours. After the reverse transcription reactions, the RNA templates were degraded by addition of 2 uL of 1 N NaOH and incubation at 65 C for 10 minutes. The alkaline conditions were neutralized by addition of 2 uL of 1 N HCl. Liver cDNA samples were then mixed with a control cDNA sample, and the mixtures were cleaned using a QIAquick Nucleotide Removal kit (Qiagen) as described by the manufacturer's instructions. The cleaned samples were concentrated in a speed vacufuge (Eppendorf) for 20 minutes at 65 C, and were dissolved in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), quantified, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 C using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), then in 1X SSC, and finally in 0.1X SSC. The arrays were dried by centrifugation and scanned using a GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and analyzed using Matlab (The MathWorks, Inc.). Microarrays were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). Arrays contained 16,847 features, printed from a synthesized oligonucleotide mouse library (Operon). The library was suspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed at approximately 50% humidity. Once printed, the probes were crosslinked using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride (Fluka AG), 239 mL 1-methyl-2-pyrrolidinone (EM Science), and 10.7 mL of 1 M boric acid (Fisher), pH 8.0. They were cleaned by rinsing twice in 250 mL of milli-Q water, followed by 250 mL of 95% ethanol (Pharmco Products). After blocking, they were dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, energy homeostasis, gene expression, microarrays Source GEO sample is GSM6596 Last updated (according to GEO): Nov 21 2005 861 Spinal Cord Parkinson Disease 861 1000 Ovary Caudal 1000 R528P00607 Prefrontal Cortex Source GEO sample is GSM105451 Last updated (according to GEO): Apr 17 2006 NA12815 Disease Source GEO sample is GSM175934 Last updated (according to GEO): Apr 09 2007 28 8 large B-cell lymphoma /3T3 fibroblasts 743 759 WGACON-34 861 Glioblastoma Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15721 Last updated (according to GEO): May 28 2005 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184682 Last updated (according to GEO): Apr 26 2007 Mouse ileum with L.monocytogenes_B_5544 Parkinson's disease sample x108 0 30 Gene expression data from postmorten brain regions Source GEO sample is GSM145044 Last updated (according to GEO): Nov 20 2006 CNS-SMTC_Mod28d-4C-s2 660 mesenchymal stem cell 639 901 Breast Carcinoma 1000 Brain mouse hippocampus, cox-2 knockout, rep2 Brain 861 Congenital Abnormality 853 brain, cerebral cortex: NMDA1H 7/8_le1 human cerebellum Source GEO sample is GSM87174 Last updated (according to GEO): Feb 08 2006 The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76951 Last updated (according to GEO): Oct 11 2005 40 21 from dorsal pancreas Semeralul_PFC_Development_Week3_Batch1_Animal_5 Skeletal bone 861 brain, hippocampus: CH1_e1_le1 928 Endometrium from the forebrain 20 37 brain 0 5 Study of in vitro granulocyte differentiation Source GEO sample is GSM137450 Last updated (according to GEO): Jun 06 2007 Bone Marrow 1000 Psychotic Disorders 1000 by brain injury 1353 1368 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181154 Last updated (according to GEO): Jul 12 2007 9 0 Blood Test in the adult heart 44 61 1037 of transitional epithelium 1012 Epithelium 865 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68176 Last updated (according to GEO): Jul 07 2006 pooled RNA of the kidney of 36 day old rats Source GEO sample is GSM86651 Last updated (according to GEO): Jun 12 2006 Primary large cell carcinoma 525 0 31 Type 1 Diabetes patient and the timepoint 4 months after diagnosis. Source GEO sample is GSM228615 Last updated (according to GEO): Sep 11 2007 low gestational age Source GEO sample is GSM213115 Last updated (according to GEO): Jul 25 2007 na Source GEO sample is GSM181288 Last updated (according to GEO): Apr 10 2007 human frontal cortex Source GEO sample is GSM87000 Last updated (according to GEO): Feb 08 2006 HOXB4ERT-LSK+ cells_ 1 hour plus TMX (continous exposure) Source GEO sample is GSM228751 Last updated (according to GEO): Sep 13 2007 Replicate1_Voxel C11 cingulate cortex 861 861 Blood Expression profiling of spinal cord section (T10) extracted from rats 24h following mild injury Source GEO sample is GSM31316 Last updated (according to GEO): May 27 2005 14 0 Uterine Fibroid Posterior root of spinal nerve 861 1000 Infection ATCC number CRL-1502 Source GEO sample is GSM6803 Last updated (according to GEO): May 27 2005 Spleen 0 5 38 12 of congenital heart disease 861 Brain JMR-RatInj4h-2bA-s2 Neoplasm 861 1000 Brain FNH (HK72) Skin; Skin postnatal Day 2-3 Keywords = mouse gene expression database Source GEO sample is GSM29434 Last updated (according to GEO): May 27 2005 7 0 Striatum Heart 1000 861 Acquired Immunodeficiency Syndrome 1000 Liver Lung [JunctionChip 1 of 5] M7TW01010681 901 frontal lobe testis Source GEO sample is GSM18823 Last updated (according to GEO): Sep 25 2006 Cerebral cortex 861 processed in batch 4 Source GEO sample is GSM90415 Last updated (according to GEO): Mar 20 2006 Gene expression data from the right forebrain of C57BL mouse received no treatment for four weeks. Source GEO sample is GSM149812 Last updated (according to GEO): Dec 12 2006 142 138 Brain infection 410 419 SON control Source GEO sample is GSM69859 Last updated (according to GEO): Dec 02 2005 HC68 CB B rat hippocampus Treatment, type=time_course, measurement=1.0 h Source GEO sample is GSM32126 Last updated (according to GEO): May 27 2005 cocaine naive, amygdala, 0 hrs/day access to cocaine Source GEO sample is GSM93825 Last updated (according to GEO): Jan 26 2006 Spinal Cord 901 Whole Brain 62 72 AD-230t1-A153-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 jejunum Liver Test (Blinded) Sample Source GEO sample is GSM130202 Last updated (according to GEO): Sep 18 2007 Colonic mucous membrane 913 adenoma 861 1000 Ciliary Body DRG_control_2h_rep1 1000 Retina f2#10 versus pool Mouse Brain tissue Brain 861 48 M arm fibroblast LS25, serum starved Mammary Gland 9 Normal H123 FC BA4 B 5 0 Spleen brain, hindbrain and spinal cord: P5WT1_e1_le1 861 Dislocations Gene expression data from whole tumor Source GEO sample is GSM182307 Last updated (according to GEO): Apr 16 2007 BXD 14_M7SS02080622 0 Human Cortex 11 1000 Hippocampus Mouse ileum 0 10 1000 Brain gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134649 Last updated (according to GEO): Jul 09 2007 Pituitary Gland 861 1000 melanoma Brain 1000 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23745.gif Source GEO sample is GSM66585 Last updated (according to GEO): Sep 22 2006 JMR-RatNaive-2cA-s2 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16594.gif Source GEO sample is GSM91559 Last updated (according to GEO): Sep 22 2006 Primary tumor 19 32 1000 Malignant neoplasm of prostate brain 0 5 I_U133A_11_AnCg Bone Marrow 1000 Head and neck cancer Source GEO sample is GSM155680 Last updated (according to GEO): Apr 24 2007 bladder 0 6 Liver (HBV+, HK26) MuscleRegen-ctx1d-3LLA-s2 Control rat 8 - substantia nigra Source GEO sample is GSM32170 Last updated (according to GEO): May 27 2005 GSE5036 33 17 tibialis anterior 347 326 from the dentate gyrus to the nose 599 609 14 0 kidney sprague1 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228631 Last updated (according to GEO): Sep 11 2007 Nasal Epithelium 901 M_U133A_99_AnCg small intestine sprague2 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. 8h after sham surgery, a 7 mm disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane and then stored at ???80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling Source GEO sample is GSM44530 Last updated (according to GEO): May 27 2005 ko mouse number 1 Source GEO sample is GSM186743 Last updated (according to GEO): Jun 11 2007 of regenerating Dorsal Root Ganglia 21 55 Levitiracetam frontal cortex 5 Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53458 Last updated (according to GEO): Jul 06 2005 R649P01087 (cortex 19 25 1000 Cerebral cortex with autism spectrum disorder 37 65 H124 CB A 1000 Liver 901 Heart failure Normal Source GEO sample is GSM176453 Last updated (according to GEO): Apr 09 2007 Lymphoblastoid Cell Line for Individual 8084.3 log phase TEL-AML1-C18 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A brain, Left Temporal Lobe: Extract44_le1 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11237 Last updated (according to GEO): May 28 2005 CNS-SC_InjB4h-1B-s2 T-ALL-C24 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A HapMap CHB Female Source GEO sample is GSM159595 Last updated (according to GEO): Feb 01 2007 PC7 Treatment, type=incubate, description=Hypoxic preconditioning Source GEO sample is GSM107481 Last updated (according to GEO): May 01 2006 3AJZ02083092b_Skeletal_Muscle_Psoas Myometrium 13 Normal WGACON-134 157 138 from the bone marrow 552 542 of adenomas 901 Caudate nucleus structure NA18871 Liver 1000 NHF3-hTERT_1.5Gy_24h_C3_21252 Blood supply aspects 1000 PGA-MAH-OuJAir-1aAv2-s1 /2J mouse pituitary gland 27 51 7 cerebral cortex 21 CNS-SMTC_Ctr3mo-2C-s2 R683P01102 atrial septal defects 198 218 We build a model for the molecular and cellular events underlying phenotypic discordance in glycine receptor defects (beta subunit). Some mice progress and die, while their littermates recover and get better, despite the same mutation on an inbred genetic background. We find evidence for glycine neurotransmitter toxicity and loss of glycinergic interneurons early in the disease, but some mice are able to keep things going until they can over-express homomeric alpha1 channels, whereupon they recover. In the mice progressing towards lethality, neurotransmitter toxicity too quickly extends to GABAergic interneurons and motorneurons, and they lose their window of time to upregulate the alpha1 glycine receptor, and they crash and burn. Importantly, human patients with glycine receptor defects typically show a resolution of their phenotype with age, and we propose that the same remodeling events are occuring in human patients. Source GEO sample is GSM30997 Last updated (according to GEO): May 27 2005 IM-3_POST none Source GEO sample is GSM244619 Last updated (according to GEO): Nov 23 2007 25 0 frontal cortex wistar 3658 nostrils 156 164 Epithelial Cells 1000 Recurrent Carcinoma 875 of Parkinson's disease 188 210 The nose 94 101 Parkinson Disease 861 in the neurological system 409 434 Colon 861 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114204 Last updated (according to GEO): Jun 16 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM146004 Last updated (according to GEO): Nov 20 2006 ALL_9 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Liver Cerebral cortex 1000 E7.25_rep1 Job's patient Source GEO sample is GSM211149 Last updated (according to GEO): Sep 10 2007 PP164_unifected_Skin biopsy via extrinsic 144 156 Epithelial ovarian cancer 1000 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the lv samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12339 Last updated (according to GEO): May 28 2005 of G protein? 285 297 Leukemia, Lymphocytic, Chronic 1000 861 Epidermis 858 Mesodermal cell a malignancy 77 88 Hippocampus 861 1000 Brain 1000 Kidney 1000 Brain Gap Junctions 1000 861 Cerebral cortex Balb/c day 6, biological rep 1, tech rep 2 861 Cerebral cortex Spleen vs SDF1 alpha (Stromal cell derived factor-1) Treated B cell 60min (set2) 1000 Hippocampus Cochlear nuclei pooled from 20 pups to generate one sample for one replicate hybridization out of 5 replicates. Cohybridized with P21_cy5_2. Source GEO sample is GSM44973 Last updated (according to GEO): Jun 08 2005 UBOC1 Exp A Day 8 (b) CNS-SC_CtrB7d-2A-s2 865 Disorder of artery freij-affy-human-91666 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:208, Count:32 Corner- Avg:35505, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:11.218446,SFGene:All Background:Avg:425.32,Stdev:14.65,Max:488.3,Min:396.6 Noise:Avg:9.75,Stdev:1.22,Max:14.7,Min:7.3 RawQ:13.05 Keywords = ALL Source GEO sample is GSM3403 Last updated (according to GEO): May 28 2005 Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 24 h to ambient pressure (CP24) and harvested with cells exposed for 24 h to hydrostatic pressure, pressure experiment # 2 (PE2). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11396 Last updated (according to GEO): Dec 15 2006 brain 0 5 DR7d(2) low dose 24h, replicate 2 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs//7250.gif Source GEO sample is GSM79917 Last updated (according to GEO): Sep 22 2006 1000 Brain Posterior root of spinal nerve 901 660 mesenchymal stem cell 639 healthy control sample x121 Muscular Dystrophy, Duchenne 913 36 21 from whole brain Epithelial Cells 901 to the nose 599 609 MELAN_UACC257 on Affymetrix GeneChip Human Full Length Array HuGeneFL DLCL-0052 none Source GEO sample is GSM244565 Last updated (according to GEO): Nov 23 2007 brain 0 5 Sporadic_s1542 on NHGRI-6.5k 861 Brain SM/J_female_hypothalamus Source GEO sample is GSM138573 Last updated (according to GEO): Apr 18 2007 Hyperdip>50-C27-N on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Nrl ko P2 replicate 3 Control Source GEO sample is GSM175970 Last updated (according to GEO): Apr 09 2007 hippocampus 7 17 hippocampus_5 Source GEO sample is GSM80668 Last updated (according to GEO): Mar 31 2006 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181229 Last updated (according to GEO): Jul 12 2007 the ventricular 1095 1109 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16596.gif Source GEO sample is GSM91568 Last updated (according to GEO): Sep 22 2006 T-ALL-C1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A C57BL/6J Hippocampus D 861 Endometrium GSE7708 KO_IL-6_400_rep1 913 Coronary heart disease Ts1Cje-2-MGU74A Large-scale analysis of the mouse transcriptome. Stomach C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 240.76 Stdv: 8.41 Min: 228.93 Max: 253.64 Source GEO sample is GSM2907 Last updated (according to GEO): Mar 20 2006 5 0 Spleen Y SIT D073 1000 Coronary Arteriosclerosis Chronic Lymphocytic Leukemia 19 47 RNA samples extracted from astrocytes cultured from wild type and Cx43 null neonatal mice were dye labeled and individually co-hybridized with a reference of labeled cDNAs pooled from a variety of tissues on eight gene arrays containing 8975 mouse DNA sequences Lot batch = 3 Source GEO sample is GSM8895 Last updated (according to GEO): May 27 2005 gfp pos. sorted cells from 3 disected e14.5 cortecies Treatment, type=wait Source GEO sample is GSM135787 Last updated (according to GEO): Sep 12 2006 Voxel C2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1391 Last updated (according to GEO): Nov 21 2005 1352 1323 of nonsensory epithelial cells Fibroblasts 861 from Rett Syndrome 113 130 R6/1 22 week transgenic_BD1Bv1 Spleen 0 5 Primary Neoplasm 1000 no additional Source GEO sample is GSM199116 Last updated (according to GEO): Jun 08 2007 bronchial epithelia 224 243 20 0 human caudate nucleus NA19140 I_U133A_52_CB 861 Cerebellum SEA/GnJ_male_hypothalamus with progressive supranuclear palsy 27 61 Lymphoblastoid Cell Line for Individual 8019.4 log phase Stem cells 901 Malignant Neoplasms 1000 anatomy 1000 with autism spectrum disorder 37 65 861 Acquired Immunodeficiency Syndrome Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP) and harvested at the beginning (0 h) of pressure experiment #3 (PE3). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11366 Last updated (according to GEO): Dec 15 2006 1000 Cardiomyopathies lymph_nodes_3 Source GEO sample is GSM80737 Last updated (according to GEO): Mar 31 2006 We used a custom Affymetrix GeneChip, the "GLYCOv2" array, to measure differences in gene expression patterns from adult and postnatal day 7 (P7) mouse cerebellum RNA. Last Updated (by provider): Mar 29 2006 Contributers: Steven R Head Timothy J Gilmartin Qiang Qu Frances I Smith HCC (HBV+, HK64, T1) 901 Mammary gland P14 cochlear nuclei 0 18 20 0 human caudate nucleus HC73 CB B CNS-SMTC_Ctr7d-1C-s2 Plasma 861 H111 FC BA4 A 25 0 Acute cognitive impairment Recurrent Squamous cell carcinoma 3 OVX/P4/6h/UTX 129 WT vs. Hoxa-10-/- Type 1 Diabetes patient and the timepoint 1 month after diagnosis. Source GEO sample is GSM228595 Last updated (according to GEO): Sep 11 2007 1000 Neoplasm Gene expression data from brain of adult rats Source GEO sample is GSM101038 Last updated (according to GEO): Feb 20 2007 913 Coronary heart disease Cerebral cortex 1000 nasal epithelial cells 28 49 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7793.gif Source GEO sample is GSM76436 Last updated (according to GEO): Sep 22 2006 Spleen vs Terbutaline Treated B cell brain 0 5 cerebellum 7 16 Spinal Cord 1000 181 170 of the brain 1000 Spleen SN:Human Glioblastoma Biopsy 12368 of heart failure 91 107 MO_control_180min_Patient3 1000 Pancreas Colon 861 Cochlear structure 1000 Bone Marrow 1000 Epithelium of bronchus 983 Normal Placenta Anterior nares 1000 861 Cerebellum tibiae 115 120 2 hrs Post-clamp sample 3 Epithelial cells 614 629 N39__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Expression profiling of spinal cord section (T9) extracted from rats 24h following moderate injury Source GEO sample is GSM31534 Last updated (according to GEO): May 27 2005 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153350 Last updated (according to GEO): Dec 27 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Leukotriene B4 (LTB4) for 30min Source GEO sample is GSM5675 Last updated (according to GEO): May 27 2005 5 0 brain f2#225 versus pool Mouse Brain tissue 1279_32d 901 Nervous system structure brain, cortex: 14dsham4_e1_le1 Blood 861 SQ-SQ5t1-A359-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A VDXRHU_5236 Subject code A24 Epithelium 861 nostrils 156 164 from cingulate cortex 57 77 temporal_lobe_5 156 145 Their livers liver, wild-type mice, control conditions Source GEO sample is GSM205815 Last updated (according to GEO): Jul 24 2007 DLBC45 on Affymetrix GeneChip Human Full Length Array HuGeneFL basal culture, 14B3, rep 2 D14 12h TLR2/1L Primary Neoplasm 1000 Heart 1000 91 from the bone marrow 72 69 50 Olfactory bulb C57BL 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113962 Last updated (according to GEO): Jun 16 2006 Untreated Control 12weeks AffyGC RMA rep10 f2#22 versus pool Mouse Brain tissue myocardial infarction 383 403 Medulla Oblongata 861 1000 Brain Heart 861 3 min exposure to halothane, immediate perfusion with ice cold saline Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5107 Last updated (according to GEO): Mar 17 2006 JMR-RatSham30m-3aA-s2 39 27 the maxillary 1000 Infection DMN-CtrHippo10d-2aAv2-s2 Epithelial Cells 901 Epithelium 861 A61 WT2 F6/21 A61 wild type Mouse 8 months Cerebellum Male Source GEO sample is GSM73228 Last updated (according to GEO): Sep 06 2005 861 Neoplasm folatedeficientAs0ppm2 Sample details: We analysed changes in gene expression in the dorsal telencephalon of forebrain-specific FGFR1 mutant mice. Gene expression was compared between the dorsal telencephalons of single E12.5 embryos of two genotypes: FGFR1 heterozygous (HET1,3,8) and homozygous mutants (HOM2,4,7) that were both heterozygous for the FoxG1 transcription factor, as Cre recombinase expression is driven off the endogenous FoxG1 locus in these animals (Hebert, J. M., Lin, M., Partanen, J., Rossant, J. and McConnell, S. K. (2003b). FGF signaling through FGFR1 is required for olfactory bulb morphogenesis. Development 130, 1101-11. & Hebert, J. M. and McConnell, S. K. (2000). Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures. Dev Biol 222, 296-306. Source GEO sample is GSM62845 Last updated (according to GEO): Aug 26 2005 901 Mammary gland Multiple Myeloma 861 119 96 in embryonic stem cells small cell lung carcinoma 4271 0 29 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118357 Last updated (according to GEO): Jul 11 2006 M7TW01013128 adACN6 ovarian tumor: serous Source GEO sample is GSM139447 Last updated (according to GEO): Apr 09 2007 1569 1549 in the wildtype brain peripheral blood-CD4TCells Source GEO sample is GSM18719 Last updated (according to GEO): Sep 25 2006 Adenoma 0 6 the blood 393 402 GSE8191 SNB-19 hgu95e 901 Cervical sympathetic ganglion 5 0 UTERUS ovary 147 151 Human Hypothalamus Male 6 (technical replicate) skeletal muscle, tibialis anterior: Innvervated Control 1_e1_le1 Prosencephalon 1000 861 Blood DRG_control_40h_rep1 Nose 1000 none Source GEO sample is GSM210322 Last updated (according to GEO): Jul 16 2007 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195341 Last updated (according to GEO): Jun 04 2007 Endothelial Cells 1000 infection 410 419 1000 Skin 1000 Brain 861 Cardiomyopathies Liver 1000 M_U133A_27_HC puroB is a clonal control(puromycin resistant) stable c17.2 neural stem cell line with similar proliferation rate as clone 42 and therefore both were matched for subsequent analysis. Source GEO sample is GSM82226 Last updated (according to GEO): Nov 07 2005 Gene expression data from microdissected area # 1of 1919 tumor Source GEO sample is GSM182297 Last updated (according to GEO): Apr 16 2007 Disorder of artery 865 129P3/J ACU, Rep1 Heart 1000 C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 4hr after experimental mice received their last shock treatment. Source GEO sample is GSM4503 Last updated (according to GEO): May 27 2005 to the nose 599 609 Serum 24 Brain 1000 861 Cerebral cortex Lymphoblastoid Cell Line for Individual 8063.4 log phase prostate Source GEO sample is GSM203281 Last updated (according to GEO): Jun 21 2007 1000 Cerebral cortex 67 40 with coronary artery disease 26 15 endometrioid 5 0 brain Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. All patients were considered sporadic cases on the basis that no clinical antecedents of familial adenomatous polyposis were reported, and those that met the clinical criteria for hereditary non-polyposis colon cancer (Amsterdam criteria) were excluded. Source GEO sample is GSM112306 Last updated (according to GEO): Jun 06 2006 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68159 Last updated (according to GEO): Jul 07 2006 Z1 biol repl 1 Cerebral cortex 861 5 0 Spleen Blood 1000 FL-9 Healthy patient. Source GEO sample is GSM228571 Last updated (according to GEO): Sep 11 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114223 Last updated (according to GEO): Jun 16 2006 1037 of transitional epithelium 1012 40 21 from dorsal pancreas GSE6093 Dominant negative cJun VZ17 - Source GEO sample is GSM216540 Last updated (according to GEO): Aug 09 2007 Epithelium 861 I_U133Plus_59_CB 3AJZ02060506_Hypothalamus gene expression data from melanoma xenografts following ILI with melphalan Source GEO sample is GSM213638 Last updated (according to GEO): Jul 27 2007 Expression profiling of laminectomized raphe at 24h in rats Source GEO sample is GSM41528 Last updated (according to GEO): May 27 2005 1037 of transitional epithelium 1012 1000 Heart failure 14 0 Small Intestine Huntington Disease 861 0 Human Cortex 11 Oocytes 1000 41 37 Lungs 1000 Coronary Arteriosclerosis C57L/J Amygdala A total RNA was extracted from liver of one ApoE-/- mouse infected with a control adenovirus expressing GFP Source GEO sample is GSM157850 Last updated (according to GEO): Jan 25 2007 Exp A, Animal #2, 50mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 50mg/kg of CPF for 96 hours Source GEO sample is GSM246142 Last updated (according to GEO): Dec 03 2007 Occipital region 983 HTI-286 in docetaxel-refractory prostate cancer (Dye Flip 1) Donor E, post G-CSF stria terminalis 901 5 0 Muscle Liver 1000 12 0 ovarian tumor Primary Neoplasm 1000 669 stem cells 660 7 cerebral cortex 21 D_U133A_47_DLPFC 31 adrenal medulla 17 1000 Heart Liver 0 4 amygdala rattus_norvegicus_strain iP animal_number 5 Adipose tissue 884 HapMap YRI_parent Male Source GEO sample is GSM159696 Last updated (according to GEO): Feb 01 2007 129 2000-2 Testes Hippocampus 1000 subsequent to viral infection 864 893 brain 0 5 Cerebral cortex 861 660 mesenchymal stem cell 639 /3T3 fibroblasts 295 310 5 0 Muscle 861 Neoplasm Pregnant females exposed to ethanol for 5 days, AF02 (Alcohol Fed) corresponds to replicate 2 Standard Affymetrix procedure Source GEO sample is GSM132991 Last updated (according to GEO): Aug 28 2007 Coronary Arteriosclerosis 1000 CNS-SCsev_InjB28d-4B-s2 128 114 in the amygdala Spleen 1000 Macrophage smi105 323 315 (midbrain "Sample 77, <5 yr survival(24 months) age 51 erp no" on vantveer-oligo Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211414 Last updated (according to GEO): Jul 18 2007 983 Structure of horn of uterus Clone 3.1 chip 1 Whole blood from a patient with multiple system atrophy Source GEO sample is GSM153409 Last updated (according to GEO): Jan 11 2007 the blood 393 402 processed in batch 7 Source GEO sample is GSM90425 Last updated (according to GEO): Mar 20 2006 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198642 Last updated (according to GEO): Jun 06 2007 861 Leukemia, Lymphocytic, Acute Site: University of California, Davis Cohort: Male/Female Control Set Diagnosis: Control pH: 6.84 Subject: 2835 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39022 Last updated (according to GEO): May 27 2005 901 Coronary artery Primary tumor 19 32 CD4+ AntiCD3+AntiCD28 1 Activated Brain 1000 ileum 0 4 acute myeloid leukemia Source GEO sample is GSM227440 Last updated (according to GEO): Sep 12 2007 GSE7880 Integumentary system 861 Medulla 861 Brain Stem 1000 adenoma 861 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11345 Last updated (according to GEO): May 28 2005 901 Prostate carcinoma To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132990 Last updated (according to GEO): Sep 12 2006 NA19102 BTBR T+ tf/J_male_hypothalamus Source GEO sample is GSM184193 Last updated (according to GEO): Apr 26 2007 Pituitary Gland 861 1000 frontal lobe 5 0 brain stomach_cardiac_3 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184755 Last updated (according to GEO): Apr 26 2007 Carcinoma, Large Cell 923 Neoplasm 861 Thyroid hormones are key regulators of metabolism that modulate transcription via nuclear receptors. Hyperthyroidism is associated with increased metabolic rate, protein breakdown, and weight loss. Although the molecular actions of thyroid hormones have been studied thoroughly, their pleiotropic effects are mediated by complex changes in expression of an unknown number of target genes. Here, we measured patterns of skeletal muscle gene expression in five healthy men treated for 14 days with 75 microg of triiodothyronine, using 24,000 cDNA element microarrays. To analyze the data, we used a new statistical method that identifies significant changes in expression and estimates the false discovery rate. The 381 up-regulated genes were involved in a wide range of cellular functions including transcriptional control, mRNA maturation, protein turnover, signal transduction, cellular trafficking, and energy metabolism. Only two genes were down-regulated. Most of the genes are novel targets of thyroid hormone. Cluster analysis of triiodothyronine-regulated gene expression among 19 different human tissues or cell lines revealed sets of coregulated genes that serve similar biologic functions. These results define molecular signatures that help to understand the physiology and pathophysiology of thyroid hormone action. 1000 Malignant Glioma T54__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Cerebellum Conjtissue1 861 Pituitary Gland spleen.1 no additional Source GEO sample is GSM199153 Last updated (according to GEO): Jun 08 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lysophosphatidic Acid for 120min Source GEO sample is GSM5657 Last updated (according to GEO): May 27 2005 from ventral prostate 21 41 1000 Malignant Glioma 861 Spinal Cord 1000 Brain Expression profiling of spinal cord section (T10) extracted from rats 30m following mild injury Source GEO sample is GSM31330 Last updated (according to GEO): May 27 2005 prostate Source GEO sample is GSM203271 Last updated (according to GEO): Jun 21 2007 1000 Primary carcinoma of the liver cells GSE459 BC708B-BE GBM Treatment, type=remove Source GEO sample is GSM99556 Last updated (according to GEO): Apr 21 2006 Neoplasm 861 5 0 brain 117 112 Lipids MAS 5.0, scaled to 500; Affymetrix Data Mining Tool 3.0; dChip was used to determine differentially expressed genes (MBEI); Statistical Analysis of microarrays(SAM) Source GEO sample is GSM107845 Last updated (according to GEO): Sep 12 2006 D_95Av2_2672_DLPFC_0_GS Hippocampus 1000 with some respiratory epithelium. 1039 1072 1000 Breast Carcinoma Nose 1000 DRG014_b We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201804 Last updated (according to GEO): Jun 20 2007 Skeletal bone 861 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=760600 LaserPower=1.971.3 Lot batch = LC17N079 Source GEO sample is GSM4807 Last updated (according to GEO): Nov 21 2005 NeverSmoker 118 660 mesenchymal stem cell 639 at the Human Brain 744 761 Differential transcriptional response to nonassociative and associative components of classical fear conditioning in the amygdala and hippocampus. Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225373 Last updated (according to GEO): Aug 31 2007 Richard Almon-21-1133800609417 861 Prostate olfactory epithelium 194 213 in the brain 150 162 1000 frontal lobe Brain 1000 1000 Mammary gland f2#320 versus pool Mouse Brain tissue Gene expression data Source GEO sample is GSM183176 Last updated (according to GEO): Jul 30 2007 Craniocerebral Trauma 861 A learning event initiates a cascade of altered gene expression leading to synaptic remodelling within the hippocampal dentate gyrus, a structure vital to memory formation. To illuminate this transcriptional program of synaptic plasticity we used microarrays to quantify mRNA from the rat dentate gyrus at increasing times following passive avoidance learning. Approximately, 500 known genes were transcriptionally regulated across the 24 h post-training period. The 0-2 h period saw up-regulation of genes involved in transcription while genes with a role in synaptic/cytoskeletal structure increased 0-6 h, consistent with structural rearrangements known to occur at these times. The most striking feature was the profound down-regulation, across all functional groups, 12 h post-training. Bioinformatics analysis identified the likely transcription factors controlling gene expression in each post-training period. The role of NF kappa B, implicated in the early post-training period was subsequently confirmed with activation and nuclear translocation seen in dentate granule neurons following training. mRNA changes for four genes, LRP3 (0 h), alpha actin (3 h), SNAP25 and NSF (6-12 h), were validated at message and/or protein level and shown to be learning specific. Thus, the memory-associated transcriptional cascade supports the cardinal periods of synaptic loosening, reorganisation and selection thought to underpin the process of long-term memory consolidation in the hippocampus. DBA-2J_male_hypothalamus Source GEO sample is GSM138581 Last updated (according to GEO): Apr 18 2007 861 Prostate carcinoma 19 0 Head and neck cancer GBM Treatment, type=remove Source GEO sample is GSM99485 Last updated (according to GEO): Apr 21 2006 granule neuron precursors, biological replicate 2; array B 1000 Urine M_U133A_50_nAcc Gene expression data from postmorten brain regions Source GEO sample is GSM145618 Last updated (according to GEO): Nov 20 2006 Fibroblasts 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL10 for 240min Source GEO sample is GSM5647 Last updated (according to GEO): May 27 2005 A VIS D096 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108622 Last updated (according to GEO): Aug 22 2006 1004 994 spinal cord Macrophage 14smi053 Type 1 Diabetes patient and the timepoint 1 month after diagnosis. Source GEO sample is GSM228632 Last updated (according to GEO): Sep 11 2007 8 CN B Epithelium of bronchus 983 Mesenchymal Stem Cells 1000 for hereditary non-polyposis colon cancer 340 380 ATCC number CRL-1502 Source GEO sample is GSM6801 Last updated (according to GEO): May 27 2005 VDXKIU_16B4 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Insulin-like growth factor 1 for 240min Source GEO sample is GSM5625 Last updated (according to GEO): May 27 2005 acetylcholine receptors 56 79 Occipital lobe 861 spleen Source GEO sample is GSM18666 Last updated (according to GEO): May 27 2005 Leg 14 Day mdx rep 3 RNA from muscle biopsy specimen Source GEO sample is GSM3715 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145798 Last updated (according to GEO): Nov 20 2006 Cerebral cortex 1000 H9LMS99102621 Leukemia 19 26 brain, brainstem: PB2_e1_le1 /3T3 fibroblasts 295 310 Brain 861 V5-P104 Gene expression data from liver Source GEO sample is GSM243389 Last updated (according to GEO): Nov 16 2007 12 frontal Lobe 23 in the mammalian nervous system 110 141 524 508 of mouse retinas PE_D_651 in dendrites 527 538 861 Cerebellum Dominant negative cJun VZ16 Spleen vs 2-Methyl-thio-ATP Treated B cell 60min (set2) HapMap JPT Female Source GEO sample is GSM159626 Last updated (according to GEO): Feb 01 2007 adACN4 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 6 hour after the last shock treatment. Source GEO sample is GSM4543 Last updated (according to GEO): May 27 2005 861 Cerebral cortex Epithelium 861 mdx5cv TA sample 2 Head and neck cancer Source GEO sample is GSM155695 Last updated (according to GEO): Apr 24 2007 865 Disorder of artery n/a Source GEO sample is GSM177989 Last updated (according to GEO): Jun 11 2007 Drug Dependence 1000 WGACON-267 CNS-SCsev_InjA24h-3B-s2 wt mouse number 1 Source GEO sample is GSM186709 Last updated (according to GEO): Jun 11 2007 1000 Brain Gene expression data from colorectal adenoma. Source GEO sample is GSM215092 Last updated (according to GEO): Aug 02 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114441 Last updated (according to GEO): Jun 16 2006 26 CB A GC (HKG1T) Brain, Cerebellum human cerebellum Source GEO sample is GSM87189 Last updated (according to GEO): Feb 08 2006 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184697 Last updated (according to GEO): Apr 26 2007 Cerebral cortex 1000 30 19 Solid tumor This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques P. Tremblay (jacques-p.tremblay@crchul.ulaval.ca; 2705 boulevard Laurier) for analysis. Stembase Experiment ID: E205 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205 SCGP Sample ID: S270 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205#SAMPLE_247 Short description: Cells from sphere were incubated in a differentiation medium. They differentiated into neurons after 7 days in culture. Analysis requested: mouse genechips RNA concentration: 0.689 ug/uL Sample volume: 15 uL total Source GEO sample is GSM93612 Last updated (according to GEO): Jan 23 2006 Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed for 6 h to hydrostatic pressure (HP6), pressure experiment # 3 (PE3). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11390 Last updated (according to GEO): Dec 15 2006 R6/2 (untreated) 5213 brain, cortex: 28dexp3_e1_le1 Standard Affymetrix procedure Source GEO sample is GSM133010 Last updated (according to GEO): Aug 28 2007 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141298 Last updated (according to GEO): Oct 26 2006 18 0 Menstruation blood RNA4 Exp1 AzaC/TSA treated cingulate cortex 1000 1444 1410 experimental demyelinating diseases 20 0 human caudate nucleus 24 12 The human eye Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15386.gif Source GEO sample is GSM84156 Last updated (according to GEO): Sep 22 2006 low dose 18h, replicate 2 small intestine wild type mice, control conditions Source GEO sample is GSM124308 Last updated (according to GEO): Jun 28 2007 in Human Hypothalamus 26 46 between the LAD artery 266 287 D_U133Plus_59_DLPFC MET-304 on UMich-10k 7109_Lung did not develop PGD 1343 skeletal muscle 1329 MO_LB_180min_Patient10 GM12813 Pool of 13 cochlear tissues at E14 Source GEO sample is GSM182585 Last updated (according to GEO): Aug 14 2007 M_U133A_74_HC Brain 861 Kidney 1000 1000 frontal lobe Brain 1000 f2#307 versus pool Mouse Brain tissue Pregnant females exposed to ethanol for 5 days, AF06 (Alcohol Fed) corresponds to replicate 6 Anterior nares 1000 861 Cardiomyopathies KHG-LG-1Av2-s2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A ANIMALS Patched heterozygous mice (Goodrich et al., 1997) were obtained from Matthew Scott?s lab at Stanford, and maintained by breeding with 129X1/SvJ mice from Jackson Laboratories. Math1-GFP transgenic mice (Lumpkin et al., 2003) were provided by Jane Johnson at UT Southwestern Medical Center. Math1-GFP/patched+/- mice were generated by crossing patched heterozygotes with Math1-GFP mice, and then backcrossing to Math1-GFP mice three times before further analysis. All mice were maintained in the Cancer Center Isolation Facility at Duke University Medical Center. ISOLATION OF CELLS Granule cell precursors (GCPs) were isolated from 7-day-old (P7) patched+/- mice; preneoplastic cells were obtained from 6 week-old patched mutants; and tumor cells were obtained from 10-25-week old patched mutants displaying physical and behavioral signs of medulloblastoma. Cells were isolated from each source using a protocol described in (Wechsler- Reya and Scott, 1999). Briefly, cerebella were digested in solution containing 10 U/ml papain Oliver et al. Pre-Neoplastic Stage of Medulloblastoma - 8 - (Worthington, Lakewood, NJ) and 250 U/ml DNase (Sigma) and triturated to obtain a cell suspension. This suspension was centrifuged through a step gradient of 35% and 65% Percoll (Amersham Biosciences, Piscataway, NJ), and cells were harvested from the 35%-65% interface. Cells were resuspended in serum-free culture medium consisting of Neurobasal containing B27 supplement, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen, Carlsbad, California) and counted on a hemacytometer. Cells used for RNA isolation were centrifuged and flash frozen in liquid nitrogen. For proliferation assays or immunostaining, cells were plated on poly-D-lysine (PDL)-coated tissue culture vessels and incubated in serum-free culture medium. MICROARRAY HYBRIDIZATION AND ANALYSIS RNA from GCPs, pre-neoplastic cells and tumor cells (isolated as described above, but not FACS-sorted) and from normal adult cerebellum (not dissociated) was converted to cDNA using the Superscript Choice cDNA kit (Invitrogen) and a T7-dT(24) primer (Genset/Proligo, Boulder, CO). cRNA was generated using a T7-transcription/labeling kit from Enzo Life Sciences and hybridized to Affymetrix U74Av2 chips (Affymetrix, Santa Clara, CA). Chips were scanned, and hybridization data were acquired using Affymetrix Suite 5.0 software. Affymetrix CEL files were normalized and quantified using Bioconductor software with the gcRMA model to quantify gene expression levels (Gentleman and Carey, 2002). Unsupervised principal components analysis (PCA) was used to identify the relationships among normal adult cerebellum, GCPs, pre-neoplastic cells and tumor cells based on expression profiles. To identify genes that were differentially expressed among GCPs, pre-neoplastic cells and tumor cells, supervised analysis was carried out. A gene-by-gene ANOVA model with three groups (GCP, pre-neoplastic, tumor) was used to fit the log2-transformed intensities. To correct for multiple comparisons, the nominal p-value was adjusted using the false discovery rate (Benjamini and Hochberg, 1995). Genes were considered to be differentially expressed if they satisfied all of the following criteria: a difference in expression greater than 1.9-fold between any two groups, a maximum absolute intensity difference larger than 32 units, and an adjusted pvalue < 0.01. There were 118 genes that met these criteria. The identities of differentially expressed genes were verified by integrating data from the Affymetrix and Unigene databases. Gene functions were determined using information from Gene Ontology, Unigene, LocusLink and PubMed databases. Clustering was performed with Cluster and Treeview (Eisen et al., 1998). All statistical analysis was performed using R-1.7 software (Dalgaard, 2002). Results were visualized with Spotfire 6.0 (Somerville, MA). Keywords = medulloblastoma Keywords = pre-neoplastic Source GEO sample is GSM45620 Last updated (according to GEO): Oct 28 2005 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181113 Last updated (according to GEO): Jul 12 2007 Pool of 12 vestibular tissues at E12 Source GEO sample is GSM182597 Last updated (according to GEO): Aug 14 2007 20 0 human caudate nucleus 901 Coronary artery 861 Occipital lobe other psychiatric disorders 1819 1846 HDMTX_MP-3 Colon 861 mouse brain ipsilateral RU486 Source GEO sample is GSM149775 Last updated (according to GEO): Mar 15 2007 NCI60.50_LABEL54EXTRACT53SUB3 Source GEO sample is GSM134244 Last updated (according to GEO): Aug 06 2007 plasma cells 332 344 H9 Human Embryonic Stem cell (H9 ESC) Transitional epithelium 1000 Lymphoblastoid Cell Line for Individual 8117.3 log phase 1000 Pancreas Cecum022QAC3E_160.txt HBL100_Untreated_10% Laser captured visceral sensory neurons. Source GEO sample is GSM63659 Last updated (according to GEO): Dec 21 2005 NG108 rat neuronal cell culture exposed to 4400 ng/ml mefloquine (treated) for two hours. 10 µg total RNA hybridized per chip. RNA STAT 60 used to extract RNA. Standard Affymetrix chip scaling factors used. No other data transformation. Source GEO sample is GSM1667 Last updated (according to GEO): Oct 28 2005 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells untreated and cultured, labeled with Cy5- time course with repeats. Date GSE402 Last Updated: May 29 2005 Contributers: Robert Hsueh Zhen Yan Sun Young Lee Sangdun Choi Mi Sook Chang Yun Anna Cao Rebecca Hart Joella Grossoehme Angela Alexander Jong-Woo Kim Includes GDS323. Update date: Nov 18 2003. Dataset description GDS323: Temporal analysis of untreated male c57BL/6 B cells. Spleen from male c57BL/6 used as reference.. 858 Prostatic Neoplasms 861 Cerebral cortex 307_1 Normal Source GEO sample is GSM176344 Last updated (according to GEO): Apr 09 2007 cerebral cortex wistar ky 3910 nasal epithelial cells 28 49 Gastrin Knockout infused with gastrin fundic RNA Source GEO sample is GSM108491 Last updated (according to GEO): May 03 2007 Non-Brain 40 48 Brain 1000 AcB55 #12262226 HCC (SF8) Nasal Epithelium Inhalation Formaldehyde 0ppm 8d ID66 1000 Kidney 1000 Prostate NINDS-RNP-SNC-1aA-s2 Basal 1000 Liver 0 4 Bone Marrow 1000 Primary tumor 19 32 5 0 Spleen Heart Atrium 1000 Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14349.gif Source GEO sample is GSM79703 Last updated (according to GEO): Sep 22 2006 GSE8065 Cell Culture Exposure (3MAC ISO1) B79 on NCI-7.6k Normal Source GEO sample is GSM176278 Last updated (according to GEO): Apr 09 2007 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour.This animal was sacrificed at 4 hours after lights on.Original sample code = CM40A Source GEO sample is GSM227326 Last updated (according to GEO): Sep 10 2007 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195295 Last updated (according to GEO): Sep 13 2007 mouse brain 478 489 Transitional epithelium 1000 Muscle 861 Exp B, Animal #3, 30mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 30mg/kg of CPF for 96 hours Source GEO sample is GSM246155 Last updated (according to GEO): Dec 03 2007 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=0 (Non-acute rejection). Source GEO sample is GSM36440 Last updated (according to GEO): May 27 2005 Microarray analysis of aortic tissue from different rat hypertensive models Brain_MD_11_Medulloblastoma_Classic_D on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression during early postnatal development of the small intestine Acetaminophen 24hr Rat 8128 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool 453 434 The descending colon Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28736 Last updated (according to GEO): May 27 2005 Blood 1000 A2780_cis_IC90_16h_3 Myocardium 861 WGACON-83 1000 Brain 1000 Mammary gland embryonic cortical neuron treated with NMDA and NitroArginine Source GEO sample is GSM49619 Last updated (according to GEO): May 29 2005 Epithelial Cells 1000 7 frontal cortex 20 Prostate 861 o Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181930 Last updated (according to GEO): Apr 13 2007 B80 on NCI-7.6k park_1148_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160718 Last updated (according to GEO): Sep 24 2007 Large-scale analysis of the human transcriptome. Kidney Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 139.26 Stdv: 7.45 Min: 125.56 Max: 152.39 Source GEO sample is GSM2871 Last updated (according to GEO): Mar 20 2006 N/A Source GEO sample is GSM6683 Last updated (according to GEO): May 28 2005 Coronary artery 901 Expression profiling of spinal cord section (T9) extracted from rats 24h following laminectomy (sham) Lot batch = Source GEO sample is GSM6672 Last updated (according to GEO): May 28 2005 USF1 haplotype comparison Acetaminophen 6hr Rat 2789 blood vs. Acetaminophen 6hr Rat Pooled Control blood Mesenchymal Stem Cells 1000 NCI60.54_LABEL58EXTRACT57SUB3 Source GEO sample is GSM134264 Last updated (according to GEO): Aug 06 2007 S1P2-KO-hippocampus, biological rep3 (male) to the central nervous system 149 178 COLO205_CL4010_COLON 861 Hippocampus N/A Source GEO sample is GSM96295 Last updated (according to GEO): Feb 13 2006 Nerve 1000 861 Oocytes P7CN2 olfactory epithelium 194 213 39 21 from mammary glands 1000 Left frontal cortex wistar ky 3926 no additional Source GEO sample is GSM199253 Last updated (according to GEO): Jun 08 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145470 Last updated (according to GEO): Nov 20 2006 Primary large cell carcinoma 525 84 69 by heart failure Ovary 9 Normal 1000 Left 1000 Cerebral cortex 26 15 endometrioid Gene expression data from postmorten brain regions Source GEO sample is GSM145139 Last updated (according to GEO): Nov 20 2006 skeletal muscle, tibialis anterior: Denervated 3-day MCK::cre 3_e1_le1 brain, hippocampus: Wt #3405 Cort_e1_le1 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 22 hours after lights on. Original RNA code = LC16A. Source GEO sample is GSM227388 Last updated (according to GEO): Sep 10 2007 361 335 hypertrophic cardiomyopathy This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195235 Last updated (according to GEO): Sep 13 2007 Anterior nares 1000 GSE1013 Female 68.4 yr after antibody enrichment scan 2 (U133A) Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188696 Last updated (according to GEO): Jun 06 2007 EKVX hgu95d Epithelium 861 17 7 hippocampus 176 166 bone marrow Primary tumor 19 32 ventral tegmental area sprague1 obtained with a 16 gauge punch from coronal brain slices from 5.0-6.3 mm posterior to bregma, pool of 5 animals, 16 weeks old, male Sprague Dawley ventral tegmental area file:R3KJF02012263 Source GEO sample is GSM15219 Last updated (according to GEO): May 28 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68320 Last updated (according to GEO): Jul 07 2006 H109 FC BA4 B 715 702 After the eyes The functional diversity of neuropeptides and/or their receptors may provide a complex means to modulate vestibular primary afferent neuronal function. The precise role of these neuropeptides in the physiology of the vestibular neuroepithelium is poorly understood. The vestibular caliceal afferent neurons when compared to the dimorphic and bouton afferent neurons have different functional properties. Immunofluorescent laser capture microdissection utilizing calretinin (calbindin 2, Calb2) antibodies allowed selective acquisition of these two primary afferent neuronal populations from the rat (Rattus norvegicus). After capturing the caliceal afferent neurons, as well as the dimorphic and bouton afferent neurons, microarray expression profiling was completed. Analysis of the resulting data revealed that there were 732 genes involved in synaptic/signaling, calcium binding/solute transport, and other. Of those genes, 52 were related to afferent modulation, including 21 genes representing neuropeptides or their receptors. The observed expression of 52 genes related to afferent modulation identified using microarray were confirmed using PCR from the Wackym-Soares normalized rat vestibular periphery cDNA library or by RT-PCR from fresh ganglia tissue. The majority of the neuropeptides and/or receptors were found to be expressed in both groups, although there were neuropeptides and/or receptors that were unique to the dimorphic and bouton afferent neuron pool. The expression of selected neuropeptides or their receptors was confirmed using immunohistochemistry in the crista ampullares. Our results suggest that the unexpected neuropeptide diversity and their differences in expression pattern could serve unique roles in the physiology of the vestibular neuroepithelium. Last Updated (by provider): Mar 13 2006 Contributers: Anne Kwitek Ricardo Cristobal Paul Popper Joseph Cioffi Tina Samuels Wolfgang Siebeneich Christy Erbe P A Wackym Carcinoma of lung 884 M_U133Plus_56_HC 091232 OVR25 on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression data from biopsy of infected skin of subject with resolver phenotype. Source GEO sample is GSM128959 Last updated (according to GEO): Sep 13 2007 721_BLymphoblasts Source GEO sample is GSM18890 Last updated (according to GEO): Sep 25 2006 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113922 Last updated (according to GEO): Jun 16 2006 1000 Hippocampus Temporal Cortex Control (mTLE) 6 Spleen 278 283 4-5 Dentate Gyrus 5 21 5 0 brain BPH138_benign prostate hyperplasia Spinal Cord 1000 Prostate 12 Disease 0 18 861 myometrium Infection 1000 Y VIS D064 17 7 hippocampus human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155057 Last updated (according to GEO): Jun 04 2007 MF-11 Gene expression regulation of transporters and phase I/II metabolic enzymes in murine small intestine during fasting Note: 6 samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: GSM124309, GSM124315, GSM124308, GSM124310, GSM124314, GSM124316, Last Updated (by provider): Jul 04 2007 Contributers: Michael Muller Meike Bunger Heleen M van den Bosch Guido J Hooiveld Jolanda van der Meijde Ganglia, Spinal 923 ER negative human primary breast tumor EA02014_41258_H133A_JA-282 Ganglia, Spinal 923 CD8+ T lymphocytes_TC RCC patient Time 0_replicate 2 comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247391 Last updated (according to GEO): Dec 11 2007 Adipocytes 861 861 Knee cerebral cortex 7 21 132 113 of the hypothalamus CNS-SpinalCsev-Adult-14d-3B-s2 control 1 week B Treatment, type=time_course, measurement=1.0 weeks Source GEO sample is GSM107851 Last updated (according to GEO): Jun 06 2006 Callosal Neurons E18 1 JMR-RatSham72h-2aA-s2 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226050 Last updated (according to GEO): Nov 02 2007 Small Intestine BD1 Normal 1000 Infection Gene expression data from postmorten brain regions Source GEO sample is GSM145376 Last updated (according to GEO): Nov 20 2006 913 Subcutaneous Tissue Skeletal bone 861 Expression profiling of spinal cord section (T9) extracted from rats 48h following laminectomy (sham) Source GEO sample is GSM31261 Last updated (according to GEO): May 27 2005 Prosencephalon 861 Epithelium 861 Breast Carcinoma 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD40 for 60min Source GEO sample is GSM5494 Last updated (according to GEO): May 27 2005 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184670 Last updated (according to GEO): Apr 26 2007 in dendrites 380 392 with myocardial infarction 313 339 7 cerebral cortex 21 1000 Heart failure 861 Hodgkin Disease Gene expression data from postmorten brain regions Source GEO sample is GSM145944 Last updated (according to GEO): Nov 20 2006 NINDS-RNP-VTA-2aA-s2 NA19207 Psychotic Disorders 1000 na Source GEO sample is GSM180474 Last updated (according to GEO): Apr 04 2007 M_U133A_17_DLPFC 901 Brain Injuries R526P00605 Normal__Peripheral_Blood_Poly_POLY1 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A CNS-SCmod_InjA4h-3A-s2 Epidermis 861 Neoplasm 861 brain, SNc and VTA: VTA6_e1_le1 1000 Brain Blood 1000 861 Lymph Transitional epithelium 1000 atrial septal defects 198 218 PGA-RnSalt_e_6w_1-3-m5 neurological disease control sample x126 of the heart 842 854 5 0 Spleen cortex rattus_norvegicus_strain iP animal_number 1 9 0 Blood Test ADH213 on harvard-12k 449 441 /- retina M_U133A_71_DLPFC S8_Muscle_Insulin_240min heart failure 583 595 Gene expression data from aneurismal tissues obtained from patients with bicuspid valves. Source GEO sample is GSM116791 Last updated (according to GEO): Jun 28 2006 of the normal mucosa 7 26 of 10 saccules 5 18 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134635 Last updated (according to GEO): Jul 09 2007 1000 Mammary gland 861 Brain 6416_Lung developed PGD WGACON-214 Nervous System; Cerebellum Keywords = mouse gene expression database Source GEO sample is GSM29413 Last updated (according to GEO): May 27 2005 GSE3075 MO_control_180min_Patient4 kidney 37 43 Brain 1000 Central gray substance of midbrain 861 Parkinson's model voxel J2 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225757 Last updated (according to GEO): Nov 02 2007 H9LMS00121802 117 112 Lipids The epithelial cells 962 981 861 Microglia Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour.This animal was sacrificed at 6 hours after lights on.Original sample code = CM5A Source GEO sample is GSM227294 Last updated (according to GEO): Sep 10 2007 from neuroepithelial stem cells 242 272 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68123 Last updated (according to GEO): Jul 07 2006 Mucous Membrane 861 HMVEC-L stimulated with LPS for 24 hours L24R3 V5-P582 S6_Muscle_Insulin_240min Bone Marrow 1000 pomeroy-embryonal 861 Neoplasm Saline control-neocortex, biological rep2 dorsal_root_ganglia_8 Source GEO sample is GSM80648 Last updated (according to GEO): Mar 31 2006 901 frontal lobe eyes 138 141 Control 3 (Experiment Neuroprotection4- Run 21823) Treatment, type=timepoint, description=Same sample used for Experiment Neuroprotection4-Run 14985, samples were rerun due to oven failure, measurement=0.0 h Source GEO sample is GSM96685 Last updated (according to GEO): Feb 14 2006 ve_NY6 Cancers; Prox.Jejunum tumor Keywords = mouse gene expression database Source GEO sample is GSM29281 Last updated (according to GEO): May 27 2005 10 weeks Source GEO sample is GSM147507 Last updated (according to GEO): Dec 01 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145923 Last updated (according to GEO): Nov 20 2006 /3T3 fibroblasts 478 493 SN:Human Glioblastoma Biopsy 07080 B10.PL mice with experimental autoimmune encephalomyelitis (MS model) were treated with either placebo or 200 ng 1,25(OH)2D3. Six hours later, the spinal cords were harvested and mRNA extracted for analysis. Naive mice served as controls. Keywords = Experimental autoimmune encephalomyelitis Keywords = multiple sclerosis Keywords = 1 Keywords = 25(OH)2D3 Source GEO sample is GSM13051 Last updated (according to GEO): May 28 2005 1000 Malignant Neoplasms Spleen [JunctionChip 3 of 5] Normal Source GEO sample is GSM176267 Last updated (according to GEO): Apr 09 2007 in Mouse Hypothalamus 26 47 7 cortex 12 in the kidney 106 119 Parkinson Disease 1000 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210364 Last updated (according to GEO): Jul 16 2007 Prosencephalon 861 /SvEvTac pituitary gland rep2 5 33 Epithelium 861 Post infection 29 42 brain, unknown: UTA_e1_le1 1000 Spleen Gene expression of stria vascularis of newborn rats_cultivation_hypoxia_repeat 2 inner ear Skeletal bone 861 01_0025_SepticShock_Day3_115 at the Human Brain 746 763 15 0 human cerebellum none Source GEO sample is GSM239929 Last updated (according to GEO): Dec 07 2007 Epithelium 861 Large-scale analysis of the mouse transcriptome. Digits C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 252.86 Stdv: 10.61 Min: 240.37 Max: 272.63 Source GEO sample is GSM2983 Last updated (according to GEO): Mar 20 2006 the liver 68 76 861 Skin 901 Bone Marrow Myopathy 875 1000 Neoplasm Female 21.5 yr after antibody enrichment scan 2 (U133A) Gene expression data from postmorten brain regions Source GEO sample is GSM144898 Last updated (according to GEO): Nov 20 2006 884 Brain 928 Endometrium Gene expression data from retinas of two young SAMP10//Ta mice Source GEO sample is GSM143737 Last updated (according to GEO): Jan 24 2007 Skeletal bone 861 M_U133A_55_nAcc 861 Malaria subthalamic_nucleus Source GEO sample is GSM18778 Last updated (according to GEO): Sep 25 2006 HPB-ALL DMSO control 24h rep2 Cerebral cortex 861 IDC148 on harvard-12k Osteoblasts 1000 861 Brain small intestine sprague2 whole tissue, individual animal, 10 weeks old, male Sprague Dawley small intestine file:R3JW02103002 Source GEO sample is GSM15202 Last updated (according to GEO): May 28 2005 M_U133A_44_nAcc cirrhotic liver tissue Source GEO sample is GSM155921 Last updated (according to GEO): Jun 21 2007 The genomic consequences of bursts of action potential firing induced by the treatment of cultured cortical neurons (9-11 DIV) with the GABAA receptor antagonist bicuculline (Bic, 50 ?M) and the potassium channel blocker 4-aminopyridine (4AP, 5 ?M). Source GEO sample is GSM144027 Last updated (according to GEO): Nov 24 2006 Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 72h. Lot batch = Source GEO sample is GSM1244 Last updated (according to GEO): May 28 2005 H137 CB B Blood 861 1000 Ischemia 04_0003_SepticShock_Day1_105 861 Muscle 021301_HF_332FL Lymphoblastoid Cell Line for Individual 8118.3 log phase no additional Source GEO sample is GSM199156 Last updated (according to GEO): Jun 08 2007 11 0 Fetal brains Carcinoma, Large Cell 867 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11228 Last updated (according to GEO): May 28 2005 no additional Source GEO sample is GSM199239 Last updated (according to GEO): Jun 08 2007 brain, cerebral cortex: Nic 4_le1 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68241 Last updated (according to GEO): Jul 07 2006 Cell phenotype 947 Carcinoma, Large Cell 1000 The most common human leukemia is B cell chronic lymphocytic leukemia (CLL), a malignancy of mature B cells with a characteristic clinical presentation but a variable clinical course. The rearranged immunoglobulin (Ig) genes of CLL cells may be either germ-line in sequence or somatically mutated. Lack of Ig mutations defined a distinctly worse prognostic group of CLL patients raising the possibility that CLL comprises two distinct diseases. Using genomic-scale gene expression profiling, we show that CLL is characterized by a common gene expression "signature," irrespective of Ig mutational status, suggesting that CLL cases share a common mechanism of transformation and/or cell of origin. Nonetheless, the expression of hundreds of other genes correlated with the Ig mutational status, including many genes that are modulated in expression during mitogenic B cell receptor signaling. These genes were used to build a CLL subtype predictor that may help in the clinical classification of patients with this disease. 1000 Brain 7 hr Hela Double Thymidine, exp2 Balb/c day 3, biological rep 3, tech rep 1 861 Malignant Neoplasms 861 Heart Unfertilized egg replication 1 Leg 14 day mdx rep 2 913 Acute leukemia Resting Source GEO sample is GSM176007 Last updated (according to GEO): Apr 09 2007 with Parkinson's disease 27 50 Expression profiling of moderately injured raphe at 14d in rats Source GEO sample is GSM41565 Last updated (according to GEO): May 27 2005 14 0 Small Intestine Gene expression data from aneurismal tissues obtained from patients with tricuspid valves. Source GEO sample is GSM116799 Last updated (according to GEO): Jun 28 2006 Macrophage 14smi082 M_U133A_26_DLPFC 861 Cerebral cortex Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 2 - Pair 4 - IML Source GEO sample is GSM49892 Last updated (according to GEO): Dec 20 2005 with myocardial infarction 313 339 10_0004_SepticShock_Day3_72 Transitional epithelium 1000 199 177 from the mouse cochlea Cerebellum 1000 BACKGROUND: The biomedical community is developing new methods of data analysis to more efficiently process the massive data sets produced by microarray experiments. Systematic and global mathematical approaches that can be readily applied to a large number of experimental designs become fundamental to correctly handle the otherwise overwhelming data sets. RESULTS: The gene selection model presented herein is based on the observation that: (1) variance of gene expression is a function of absolute expression; (2) one can model this relationship in order to set an appropriate lower fold change limit of significance; and (3) this relationship defines a function that can be used to select differentially expressed genes. The model first evaluates fold change (FC) across the entire range of absolute expression levels for any number of experimental conditions. Genes are systematically binned, and those genes within the top X% of highest FCs for each bin are evaluated both with and without the use of replicates. A function is fitted through the top X% of each bin, thereby defining a limit fold change. All genes selected by the 5% FC model lie above measurement variability using a within standard deviation (SDwithin) confidence level of 99.9%. Real time-PCR (RT-PCR) analysis demonstrated 85.7% concordance with microarray data selected by the limit function. CONCLUSION: The FC model can confidently select differentially expressed genes as corroborated by variance data and RT-PCR. The simplicity of the overall process permits selecting model limits that best describe experimental data by extracting information on gene expression patterns across the range of expression levels. Genes selected by this process can be consistently compared between experiments and enables the user to globally extract information with a high degree of confidence. M_U133A_78_DLPFC Brain trauma 9 20 7 0 Epilepsy melanoma 1000 dorsal_root_ganglia_4 Liver 1000 853 Structure of blastomere G4 cornea 26 15 endometrioid PGA-swim_4w_s903 Parkinson's disease sample x115 Mouse_E13.5_Front_Middle_Back_9 Expression profiling of spinal cord section (T10) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM6653 Last updated (according to GEO): May 28 2005 ALL_21 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A UBOC1 Exp A Day 14 (b) 1000 Malignant neoplasm of breast mouse hippocampus 0 16 CNS-SpinalCmod-Adult-72h-3A-s2 Experimental Autoimmune Encephalomyelitis 901 acute myeloid leukemia Source GEO sample is GSM227415 Last updated (according to GEO): Sep 12 2007 PHG-CtrTM-1aAv2-s2 Cell source of DN2_1, DN3_1, and DN4_1 are identical. Cell source of DN2_2, DN3_2, and DN4_2 are identical. Cell source of DN2_3, DN3_3, and DN4_3 are identical. Cell source of DN2_4, DN3_4, and DN4_4 are identical. Each cell sorce was derived from four mice. Source GEO sample is GSM188614 Last updated (according to GEO): May 16 2007 Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM Source GEO sample is GSM207686 Last updated (according to GEO): Jul 09 2007 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225723 Last updated (according to GEO): Nov 02 2007 416 389 to type 2 diabetes mellitus Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188706 Last updated (according to GEO): Jun 06 2007 Expression profiling of spinal cord section (T9) extracted from rats 48h following moderate injury Source GEO sample is GSM31560 Last updated (according to GEO): May 27 2005 Disease Source GEO sample is GSM176234 Last updated (according to GEO): Apr 09 2007 of the postmortem brains 654 678 GBM Treatment, type=remove Source GEO sample is GSM99475 Last updated (according to GEO): Apr 21 2006 BXD 28_M7SS02080624 Pre-BI cells 10b Bone Marrow 1000 Parkinson Disease 861 Epithelial Cells 1000 1000 Aorta bronchial epithelia 224 243 Gene expression data from postmorten brain regions Source GEO sample is GSM145784 Last updated (according to GEO): Nov 20 2006 Cerebral cortex 1000 The most common congenital cardiac abnormalities 50 97 Murine_NK_IL-15_24h_3 Gene expression data from mouse colon Source GEO sample is GSM198106 Last updated (according to GEO): Aug 22 2007 715 702 After the eyes Nose 1000 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P14, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3231 Last updated (according to GEO): May 28 2005 7 0 prostate R6/2 (untreated) 5197 Nose 1000 To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18422 Last updated (according to GEO): May 27 2005 15 0 skeletal muscle 51 37 without malaria gum fibroblast #2, asynchronous l Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226046 Last updated (according to GEO): Nov 02 2007 biopsy sample obtained from a 1-year-old male Duchenne Muscular Dystrophy patient Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15833 Last updated (according to GEO): Sep 08 2006 plus_720_3 brain, cerebral cortex: Rat_03-57_NroLep_Lipska_e1_le1 Ovary_PD7_Foxo3 Wt_Replica 1 901 frontal lobe CNS-RM_Mod3mo-2C-s2 861 Cerebral cortex 861 Brain Nose 1000 peripheral blood-CD4TCells Source GEO sample is GSM18878 Last updated (according to GEO): Sep 25 2006 144 135 (cirrhosis S2_Muscle_Insulin_30min 129S6/SvEvTac pituitary gland rep1 (430 2.0 Array) 861 Cardiomyopathies 1000 Heart 861 Cardiomyopathies Epithelium of bronchus 983 organs 28 33 19 0 human frontal cortex Duchenne muscular dystrophy (DMD) patient?s skeletal muscle sample 6 HCT-15 hgu95b PGA-MurLungRag-pbs-24h-1aB-s2 Lymphoblastoid Cell Line for Individual 8135.5 log phase C3H/HeJ cingulate cortex rep1 660 mesenchymal stem cell 639 AD control Treatment, type=dissect Source GEO sample is GSM119667 Last updated (according to GEO): Jul 10 2006 Tissue fiber 861 ovary 197 201 366 354 encephalitis with antibodies 400 414 Wild type 8 wk old male C3H/HeJ mouse bed nucleus of the stria terminalis Source GEO sample is GSM74935 Last updated (according to GEO): Feb 27 2007 Epithelium of bronchus 983 Macrophages, Exposed to Mycobacterium tuberculosis - Repeat #2 1000 Epithelial Cells Gene expression data from brain of adult rats Source GEO sample is GSM101045 Last updated (according to GEO): Feb 20 2007 embryonic hearts 1064 1079 AJ 1-2 BAT 11 0 spinal cord Schizophrenia 1000 of infected skin 33 48 Skeletal bone 861 1000 hindbrain Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2656.gif Source GEO sample is GSM72206 Last updated (according to GEO): Sep 22 2006 39 21 from mammary glands Gene expression data from postmorten brain regions Source GEO sample is GSM144879 Last updated (according to GEO): Nov 20 2006 913 Coronary heart disease Marfan Syndrome 861 Neuroblastoma 861 861 Cerebral cortex Exp 3 Time point 5 Gloubus Pallidum External 6 Normal Parkinson's disease sample x123 0 30 Bilateral olfactory bulbectomies were performed on male C57Bl/6 mice(6 week old) and olfactory epithelium tissue collected 7 days post-bulbectomy. Total RNA was extracted from the olfactory epithelium tissue. Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol. Keywords = olfaction Keywords = neurogenesis Keywords = apoptosis Keywords = gene silencing Keywords = microarray, transcription factor Source GEO sample is GSM45687 Last updated (according to GEO): Oct 28 2005 hip_1068_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 255 234 with HIV encephalitis Gene expression data from postmorten brain regions Source GEO sample is GSM145185 Last updated (according to GEO): Nov 20 2006 5 0 brain HapMap YRI_parent Female Source GEO sample is GSM159716 Last updated (according to GEO): Feb 01 2007 Neuraxis 1000 Localized Carcinoma 853 156 145 Their livers lung 191 195 861 Oocytes with Alzheimer's disease 27 50 54 39 from 12 cochleas Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Englow 3 552 539 in the kidney Liver samples wild type mice, control conditions Source GEO sample is GSM205748 Last updated (according to GEO): Jul 24 2007 P18 deprived visual cortex replicate 5 Replicate two: differential expression analysis of CW treatment on RBEC6 cells Source GEO sample is GSM128926 Last updated (according to GEO): Aug 16 2006 BALB-RAG_PBS Replicate 1 1000 Prostate of Parkinson's disease 450 471 Affymetrix RGU34A 24HB human cerebellum Source GEO sample is GSM87113 Last updated (according to GEO): Feb 08 2006 1000 ovarian neoplasm 19 0 Head and neck cancer dingl-affy-rat-50847 115 cortex 121 5 0 brain Experimental Autoimmune Encephalomyelitis 1000 Testes in Alzheimer's disease 1069 1090 Normal Source GEO sample is GSM176045 Last updated (according to GEO): Apr 09 2007 Ovarian_Tumor_Endometrioid_CHTN-OE-076 with bipolar disorder 146 167 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141305 Last updated (according to GEO): Oct 26 2006 129 16:4-6 Dentate Gyrus Gene expression data from liver Source GEO sample is GSM243378 Last updated (according to GEO): Nov 16 2007 861 Medulla Oblongata Medulla 861 2500 mg/kg X 24 hr Source GEO sample is GSM129852 Last updated (according to GEO): Sep 18 2007 1000 Brain SCG_control_40h_rep2 1000 Brain 1000 Epilepsy Retina 861 GBM Treatment, type=remove Source GEO sample is GSM99443 Last updated (according to GEO): Apr 21 2006 15 0 ciliary_ganglion Alzheimer's Disease 1000 SN:1010457 Source GEO sample is GSM115398 Last updated (according to GEO): Jun 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145893 Last updated (according to GEO): Nov 20 2006 Brain 861 (cortex 19 25 The supplementation of creatine (Cr) has a marked neuroprotective effect in mouse models of neurodegenerative diseases. This has been assigned to the known bioenergetic, anti-apoptotic, anti-excitotoxic, and anti-oxidant properties of Cr. As aging and neurodegeneration share pathophysiological pathways, we investigated the effect of oral Cr supplementation on aging in 162 aged C57Bl/6J mice. Outcome variables included "healthy" life span, neurobehavioral phenotyping, as well as morphology, biochemistry, and expression profiling from brain. The median healthy life span of Cr-fed mice was 9% higher than in control mice, and they performed significantly better in neurobehavioral tests. In brains of Cr-treated mice, there was a trend towards a reduction of reactive oxygen species and significantly lower accumulation of the "aging pigment" lipofuscin. Expression profiling showed an upregulation of genes implicated in neuronal growth, neuroprotection, and learning. These data show that Cr improves health and longevity in mice. Cr may be a promising food supplement to promote healthy human aging. PMN_control_360min_Patient8 Infection 1000 861 Brain Medulla 861 C57BL-6J were given saline. Lungs were harvested and frozen at 72h. Lot batch = Source GEO sample is GSM4169 Last updated (according to GEO): May 28 2005 12 0 ovarian tumor Hep2_43_rep1 normal testis 54 66 3067 CP0_42 between the LAD artery 266 287 osteoblast 627 637 1000 frontal lobe Olfactory Epithelium 1000 7 cerebral cortex 21 Integumentary system 1000 standard Affymetrix protocol, MAS 5.0 Source GEO sample is GSM9131 Last updated (according to GEO): May 28 2005 from mouse colon 21 36 brain, frontal cortex: Sample62_e1_le1 DR12h(4) 1000 Brain 1475 1457 adhesion molecules Gene expression data from postmorten brain regions Source GEO sample is GSM145268 Last updated (according to GEO): Nov 20 2006 Abdominal aorta collected during autopsy within 24 hours post mortem Source GEO sample is GSM170558 Last updated (according to GEO): Jul 26 2007 1000 Cerebral cortex GSE80 mouse hippocampus 0 17 rat cortex Treatment, type=time_course, measurement=0.1 d Source GEO sample is GSM53197 Last updated (according to GEO): Jul 06 2005 Kidney 1000 skin 48 51 AD C: Alzheimer's control. Alzheimer's mice were 50% C57BL/6, 50% SJL. Alzheimers animals were the double transgenic models reported by Dineley et al., (2002) J Biol Chem 277(25):22768-22780. Mice were handled by experimenter. No other treatment administered. RNA from control AD mice were extracted 2 hours after AD experimental mice received their last shock treatment. Source GEO sample is GSM4561 Last updated (according to GEO): May 27 2005 healthy subject Source GEO sample is GSM211047 Last updated (according to GEO): Sep 10 2007 CLL-17 861 Heart Epithelium of bronchus 983 1000 Pontine structure Primary Neoplasm 1000 FormerSmoker 27 GSE4472 1000 Pancreas Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19237 Last updated (according to GEO): May 27 2005 19 0 Head and neck cancer MF-45 M_U133A_83_DLPFC 329 306 valvular cardiomyopathy Kidney 1000 plasma cells 332 344 Heart 861 A HID B D006 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108578 Last updated (according to GEO): Aug 22 2006 5 0 brain The anterior interpositus nucleus (AIN) is the proposed site of memory formation of eyeblink conditioning. A large part of the underlying molecular events, however, remain unknown. To elucidate the molecular mechanisms, we examined transcriptional changes in the AIN of mice trained with delay eyeblink conditioning using microarray, quantitative real-time RT-PCR, and in situ hybridization techniques. Microarray analyses suggested that transcriptionally up-regulated gene sets were largely different between early (3-d training) and late (7-d) stages. Quantitative real-time RT-PCR aided by laser microdissection indicated that the expression of representative EARLY genes (Sgk, IkBa, and Plekhf1) peaked at 1-d training in both the paired and unpaired conditioning groups, and was maintained at a higher level in the paired group than in the unpaired group after 3-d training. In situ hybridization revealed increased expression of these genes in broad cerebellar areas, including the AIN, with no hemispheric preferences. In contrast, the expression of representative LATE genes (Vamp1, Camk2d, and Prkcd) was selectively increased in the AIN of the 7-d paired group, with dominance in the ipsilateral AIN. Increased Vamp1 mRNA expression was restricted to the ipsilateral dorsolateral hump, a subregion of the AIN. These expression patterns of two distinct subsets of genes fit well with the two-stage learning theory, which proposes emotional and motor learning phases, and support the notion that AIN has a crucial role in memory formation of eyeblink conditioning. JMR-MurNaive-1aAv2-s2 of the atrial 647 659 865 Disorder of artery Tissue fiber 1000 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195305 Last updated (according to GEO): Sep 13 2007 Primary tumor 19 32 cerebellum 7 16 AD-301t1-A237-8 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A long access to cocaine, lateral hypothalamus, 6 hrs/day access to cocaine Source GEO sample is GSM93846 Last updated (according to GEO): Jan 26 2006 healthy subject Source GEO sample is GSM211130 Last updated (according to GEO): Sep 10 2007 129 2000-2 Thymus 15 CN A Control H_Bchip_rep2 VP16-CREB hippocampus CA-1 region Source GEO sample is GSM88944 Last updated (according to GEO): Jan 04 2006 n/a Source GEO sample is GSM178047 Last updated (according to GEO): Jun 11 2007 9 0 Blood Test Mid secretory endometrium from patient with endometriosis Source GEO sample is GSM150214 Last updated (according to GEO): Dec 14 2006 Large-scale analysis of the human transcriptome. Pituitary gland Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 272.53 Stdv: 10.98 Min: 247.79 Max: 291.42 Source GEO sample is GSM2879 Last updated (according to GEO): Mar 20 2006 Ng4: Hippocampus_NT-Y_rep10 Mesenchymal stem cells 13 34 Brain (cerebellum) [JunctionChip 4 of 5] nasal epithelial cells 28 49 GM19142 for the G-protein 443 459 Central gray substance of midbrain 861 Doral Raphe Source GEO sample is GSM107927 Last updated (according to GEO): Jun 06 2006 Expression profiling of spinal cord section (T9) extracted from rats 48h following moderate injury Source GEO sample is GSM31548 Last updated (according to GEO): May 27 2005 430A2_1945_14_KO_neuropath_midbrain Source GEO sample is GSM242681 Last updated (according to GEO): Nov 15 2007 Hyperdip>50-C37 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 91 from the bone marrow 72 Whole Brain 73 83 GBM: 61A31 329 306 valvular cardiomyopathy Neoplasm 861 Spleen vs Tumor necrosis factor-alpha Treated B cell 120min (set2) 861 Oocytes DCIS193 on harvard-12k 1000 ovarian neoplasm Control male 1 7 cortex 12 261 259 (Ig Entorhinal Cortex 7 23 A2780_cis_IC90_6h_1 brain 0 5 858 Prostatic Neoplasms NoCAD_replicate44 19 0 human frontal cortex Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203895 Last updated (according to GEO): Aug 02 2007 Oat cell carcinoma 867 865 Ovarian Diseases Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181058 Last updated (according to GEO): Jul 12 2007 brain 0 5 28 0 frontal cortex wistar ky 3928 Contralateral 4 X-ray irradiation (2 Gy). Source GEO sample is GSM203984 Last updated (according to GEO): Jun 25 2007 Saccule at E12.5, replicate2 Primary large cell carcinoma 1531 0 32 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201778 Last updated (according to GEO): Jun 20 2007 ANIMALS Patched heterozygous mice (Goodrich et al., 1997) were obtained from Matthew Scott?s lab at Stanford, and maintained by breeding with 129X1/SvJ mice from Jackson Laboratories. Math1-GFP transgenic mice (Lumpkin et al., 2003) were provided by Jane Johnson at UT Southwestern Medical Center. Math1-GFP/patched+/- mice were generated by crossing patched heterozygotes with Math1-GFP mice, and then backcrossing to Math1-GFP mice three times before further analysis. All mice were maintained in the Cancer Center Isolation Facility at Duke University Medical Center. ISOLATION OF CELLS Granule cell precursors (GCPs) were isolated from 7-day-old (P7) patched+/- mice; preneoplastic cells were obtained from 6 week-old patched mutants; and tumor cells were obtained from 10-25-week old patched mutants displaying physical and behavioral signs of medulloblastoma. Cells were isolated from each source using a protocol described in (Wechsler- Reya and Scott, 1999). Briefly, cerebella were digested in solution containing 10 U/ml papain Oliver et al. Pre-Neoplastic Stage of Medulloblastoma - 8 - (Worthington, Lakewood, NJ) and 250 U/ml DNase (Sigma) and triturated to obtain a cell suspension. This suspension was centrifuged through a step gradient of 35% and 65% Percoll (Amersham Biosciences, Piscataway, NJ), and cells were harvested from the 35%-65% interface. Cells were resuspended in serum-free culture medium consisting of Neurobasal containing B27 supplement, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen, Carlsbad, California) and counted on a hemacytometer. Cells used for RNA isolation were centrifuged and flash frozen in liquid nitrogen. For proliferation assays or immunostaining, cells were plated on poly-D-lysine (PDL)-coated tissue culture vessels and incubated in serum-free culture medium. MICROARRAY HYBRIDIZATION AND ANALYSIS RNA from GCPs, pre-neoplastic cells and tumor cells (isolated as described above, but not FACS-sorted) and from normal adult cerebellum (not dissociated) was converted to cDNA using the Superscript Choice cDNA kit (Invitrogen) and a T7-dT(24) primer (Genset/Proligo, Boulder, CO). cRNA was generated using a T7-transcription/labeling kit from Enzo Life Sciences and hybridized to Affymetrix U74Av2 chips (Affymetrix, Santa Clara, CA). Chips were scanned, and hybridization data were acquired using Affymetrix Suite 5.0 software. Affymetrix CEL files were normalized and quantified using Bioconductor software with the gcRMA model to quantify gene expression levels (Gentleman and Carey, 2002). Unsupervised principal components analysis (PCA) was used to identify the relationships among normal adult cerebellum, GCPs, pre-neoplastic cells and tumor cells based on expression profiles. To identify genes that were differentially expressed among GCPs, pre-neoplastic cells and tumor cells, supervised analysis was carried out. A gene-by-gene ANOVA model with three groups (GCP, pre-neoplastic, tumor) was used to fit the log2-transformed intensities. To correct for multiple comparisons, the nominal p-value was adjusted using the false discovery rate (Benjamini and Hochberg, 1995). Genes were considered to be differentially expressed if they satisfied all of the following criteria: a difference in expression greater than 1.9-fold between any two groups, a maximum absolute intensity difference larger than 32 units, and an adjusted pvalue < 0.01. There were 118 genes that met these criteria. The identities of differentially expressed genes were verified by integrating data from the Affymetrix and Unigene databases. Gene functions were determined using information from Gene Ontology, Unigene, LocusLink and PubMed databases. Clustering was performed with Cluster and Treeview (Eisen et al., 1998). All statistical analysis was performed using R-1.7 software (Dalgaard, 2002). Results were visualized with Spotfire 6.0 (Somerville, MA). Keywords = cerebellar granule cell precursors (GCPs) Source GEO sample is GSM45617 Last updated (according to GEO): Oct 28 2005 Sample # 1485-1 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118337 Last updated (according to GEO): Jul 11 2006 Anterior nares 1000 Chronic Lymphocytic Leukemia 19 47 5 0 brain 861 Chondrocytes C57_HF_3 1000 adenoma Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159731 Last updated (according to GEO): Apr 23 2007 1000 Hypertrophic Cardiomyopathy Brain 861 861 Cerebellum PHG-PTM-1aAv2-s2 1000 Brain Hereditary Nonpolyposis Colorectal Neoplasms 947 Olfactory Epithelium 1000 406 395 whose hearts "Sample 65, <5 yr survival(12 months) age 42 erp no" on vantveer-oligo Exp B_2, control (0mg/kg) CPF brain, Entorhinal Cortex: 96-31 normal_e1_le1 hypothalamus_9 Source GEO sample is GSM80683 Last updated (according to GEO): Mar 31 2006 f2#141 versus pool Mouse Brain tissue 78 66 Control blood Cerebral cortex 1000 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the lv samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12331 Last updated (according to GEO): May 28 2005 Exp B_1, 5mg/kg CPF Epithelium 865 Neoplasm 861 861 Stomach of the postmortem brains 664 688 Thymus Gland 1 Normal Probeset expression data from NA12747 growth 1 Source GEO sample is GSM201532 Last updated (according to GEO): Aug 08 2007 CD8+ 1 Resting 901 Contact hypersensitivity I_U133Plus_108_Amy 1000 Cerebral cortex high gestational age Source GEO sample is GSM213106 Last updated (according to GEO): Jul 25 2007 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5829 Last updated (according to GEO): May 27 2005 1000 Left WGACON-150 Mouse Liver AIN Diet 5wk Control, biological replicate E 861 Blood GTP-Binding Proteins 1000 7 cerebral cortex 21 of coronary artery disease 317 342 I_U133A_71_CB PGA-MFD-CtrPD1-1aAv2-s2a n/a Source GEO sample is GSM178075 Last updated (according to GEO): Jun 11 2007 91 from the bone marrow 72 42 in skeletal muscle 25 PMN_control_360min_Patient16 hrs nasal epithelium 1126 1146 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24273.gif Source GEO sample is GSM66581 Last updated (according to GEO): Sep 22 2006 Trisomy 21 and TS13 19 0 Head and neck cancer S11_Muscle_Insulin_240min /3T3 fibroblasts 743 759 undigested Treatment, type=time_course, measurement=7.0 d Source GEO sample is GSM113322 Last updated (according to GEO): Jun 07 2006 C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 6hr after experimental mice received their last shock treatment. Source GEO sample is GSM4504 Last updated (according to GEO): May 27 2005 861 Hippocampus 512 501 of the liver in bronchial epithelia 311 332 M-20-76-UN on UMich-10k to the nose 599 609 none Source GEO sample is GSM210342 Last updated (according to GEO): Jul 16 2007 doxycycline, wt Source GEO sample is GSM213379 Last updated (according to GEO): Jul 26 2007 Melanoma metastatic cell line A375, biological rep1 (LeiFidler) Ganglia 1000 cerebral cortex 7 21 0 Human Cortex 11 Brain 1000 61 50 Kidney C57BL none Source GEO sample is GSM244597 Last updated (according to GEO): Nov 23 2007 284_1 CNS-SC_InjB7d-1C-s2 CD24 is expressed by myofiber synaptic nuclei and regulates synaptic transmission. na Source GEO sample is GSM180460 Last updated (according to GEO): Apr 04 2007 1000 Brain infection 278 287 Mesenchymal Stem Cells 1000 Richard Almon-11-1133800609057 Hypothalamus 1 Normal Parkinson Disease 1000 318 295 of primary brain tumors none Source GEO sample is GSM161911 Last updated (according to GEO): Feb 16 2007 Cerebellum 1000 861 Chondrocytes Liver Test (Blinded) Sample Source GEO sample is GSM130150 Last updated (according to GEO): Sep 18 2007 1000 Cerebral cortex Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181142 Last updated (according to GEO): Jul 12 2007 TONGUE Source GEO sample is GSM19017 Last updated (according to GEO): Sep 25 2006 I_U133Plus_116_CB Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188711 Last updated (according to GEO): Jun 06 2007 Hippocampus 9 Normal Plasma 861 OBJECTIVE: To analyze genome-wide changes in chondrocyte gene expression in a surgically induced model of early osteoarthritis (OA) in rats, to assess the similarity of this model to human OA, and to identify genes and mechanisms leading to OA pathogenesis. METHODS: OA was surgically induced in 5 rats by anterior cruciate ligament transection and partial medial meniscectomy. Sham surgery was performed in 5 additional animals, which were used as controls. Both groups underwent 4 weeks of forced mobilization, 3 times per week. RNA was extracted directly from articular chondrocytes in the OA (operated), contralateral, and sham-operated knees. Affymetrix GeneChip expression arrays were used to assess genome-wide changes in gene expression. Expression patterns of selected dysregulated genes, including Col2a1, Mmp13, Adamts5, Ctsc, Ptges, and Cxcr4, were validated by real-time polymerase chain reaction, immunofluorescence, or immunohistochemistry 2, 4, and 8 weeks after surgery. RESULTS: After normalization, comparison of OA and sham-operated samples showed 1,619 differentially expressed probe sets with changes in their levels of expression >/=1.5-fold, 722 with changes >/=2-fold, 135 with changes >/=4-fold, and 20 with changes of 8-fold. Dysregulated genes known to be involved in human OA included Mmp13, Adamts5, and Ptgs2, among others. Several dysregulated genes (e.g., Reln, Phex, and Ltbp2) had been identified in our earlier microarray study of hypertrophic chondrocyte differentiation. Other genes involved in cytokine and chemokine signaling, including Cxcr4 and Ccl2, were identified. Changes in gene expression were also observed in the contralateral knee, validating the sham operation as the appropriate control. CONCLUSION: Our results demonstrate that the animal model mimics gene expression changes seen in human OA, supporting the relevance of newly identified genes and pathways to early human OA. We propose new avenues for OA pathogenesis research and potential targets for novel OA treatments, including cathepsins and cytokine, chemokine, and growth factor signaling pathways, in addition to factors controlling the progression of chondrocyte differentiation. Last Updated (by provider): Jul 09 2007 Contributers: Jim Henry Vasek Pitelka Tom Appleton Frank Beier Alzheimer's Disease 861 1000 Hippocampus of somatomotor cortex 21 41 1000 Descending colon 1000 Left 15 0 human cerebellum TEL-AML1-C3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Bone Marrow 1000 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5816 Last updated (according to GEO): May 27 2005 Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200630 Last updated (according to GEO): Jun 12 2007 HapMap JPT Female Source GEO sample is GSM159657 Last updated (according to GEO): Feb 01 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with NGF (Nerve Growth Factor) for 60min Source GEO sample is GSM5700 Last updated (according to GEO): May 27 2005 1000 Spinal Cord BRCA1_s1252 on NHGRI-6.5k After 2 week acclimation to 12 hr/12 hr light/dark regimen, c57/Bl6 mice were subjected to a 36 hour period of constant darkness. Aortae were subsequently harvested at 4 hour intervals to 48 hours. Duplicate microarrays were hybridized with biotin-labeled probes derived from aorta tissue (6 pooled aortae/timepoint). Source GEO sample is GSM6094 Last updated (according to GEO): May 27 2005 SN:Human Glioblastoma Biopsy 10515 1000 Prostate 861 Cerebellum of the atrial 647 659 E6.75_rep2 adenoma 861 TEL-AML1-#14 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A SNB-75 hgu95a The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159966 Last updated (according to GEO): Feb 01 2007 7 cerebral cortex 21 cardiac 746 752 Gut 861 913 Acute leukemia N62__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Thymus Gland 1000 Substantia Nigra MML Sample4 RMA, MAS 5, dChip HC86 CN B 11 0 Normal ovary 901 Spinal Cord from brain 21 30 Primary typical carcinoid 4838 Source GEO sample is GSM17323 Last updated (according to GEO): May 28 2005 Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation. Source GEO sample is GSM228469 Last updated (according to GEO): Sep 10 2007 ovary 45 50 CNS-SpinalCmod-Adult-48h-4B-s2 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152011 Last updated (according to GEO): Feb 06 2007 I_U133A_18_Amy CNS-SpinalCmod-Adult-12h-3C-s2 nostrils 156 164 SON - Control Source GEO sample is GSM69837 Last updated (according to GEO): Aug 15 2005 1000 Brain 1000 Brain Medulla 861 Peripheral Nerves 851 1000 jejunum 1000 Epithelium 105 86 of normal myometrium GM06995_technical_rep_1 Expression profiling of spinal cord section (T8) extracted from rats 7d following severe injury Source GEO sample is GSM31500 Last updated (according to GEO): May 27 2005 Serum 08 C46 on NCI-7.6k Brain 861 Cerebral cortex 1000 B6:17-7,8,9 inferior colliculi human peripheral blood derived monocytes, 8 hour LPS stimulation, biological rep2 Gene expression data from postmorten brain regions Source GEO sample is GSM145691 Last updated (according to GEO): Nov 20 2006 1000 Liver Normal Source GEO sample is GSM176073 Last updated (according to GEO): Apr 09 2007 brain, contralateral Cortex: Trizol Extraction12_le1 osteoblast 627 637 1BMH02022809_Uterus 663 mesenchymal stem cell 642 Microarray screening of suppression subtractive hybridization-PCR cDNA libraries identifies novel RNAs regulated by dehydration in the rat supraoptic nucleus. GM11831 5 0 Spleen CNS-SC_Inj7d-2A-s2c Transitional epithelium 1000 10 0 whole brain Prosencephalon 1000 skeletal muscle sprague2 1000 DNA Damage Wild type voxel E2 vestibular_nuclei_superior_2 Ovary 1000 1000 Brain M_U133A_23_nAcc ipsi Cortex 7 17 D_U133A_76_DLPFC 072801 Time Zero Z2 T-Cell Ovarian_Tumor_Serous_CHTN-OS-089 NA12751 growth 3 plasma cells 50 61 Plasma 861 Altered gene expression in the neocortices and hippocampi of the adult S1P2-deficient and S1P3-deficient mice brain, hippocampus: Ctr-6h-P15-I_e1_le1 ISR2-WT UT2 RNA from untreated wildtype cells. The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10885 Last updated (according to GEO): May 27 2005 DBA/2J hippocampus rep2 12 Temporal Lobe 24 H113 CN A Cerebellum 861 Cerebel_2022HACI6_007.txt cerebellum wistar 3887 Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108028 Last updated (according to GEO): Jun 06 2006 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92326 Last updated (according to GEO): Jan 13 2006 5 0 brain 861 Cerebral cortex Wild type inbred mice Source GEO sample is GSM83023 Last updated (according to GEO): Nov 10 2005 25 7 Right Temporal Lobe 14 0 Small Intestine Parietal Lobe 2 Normal NMDA 10 (6/24) (Experiment NMDA1-Run 9136) Treatment, type=time_course, description=samples are treated for 10, 30 or 60 min with NMDA 1mM, the agonist is then washed out and the cells are harvested 24h later, measurement=10.0 m Source GEO sample is GSM96711 Last updated (according to GEO): Feb 14 2006 673 659 by decapitation 861 Colon 1000 Lung Mucous Membrane 861 Primary Neoplasm 1000 Secondary malignant neoplasm of lung 901 Mouse Hypothalamus Male 1 (technical replicate) OlfacCortx_0220AC37_002.txt in somatosensory cortex 26 49 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114258 Last updated (according to GEO): Jun 16 2006 Heart 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CpG-oligodeoxynucleotide for 120min Source GEO sample is GSM5527 Last updated (according to GEO): May 27 2005 between neoplastic 1385 1402 Adrenal medulla [JunctionChip 1 of 5] 1005 999 gliomas kidney_medulla_3 691 652 from magnocellular neuron axon terminals Malignant Neoplasms 861 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68231 Last updated (according to GEO): Jul 07 2006 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211368 Last updated (according to GEO): Jul 18 2007 Brain 1000 brain_OFC_control C_mr216 Small cell carcinoma of lung 867 101 CN B Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184673 Last updated (according to GEO): Apr 26 2007 84 69 by heart failure eTat - Hu3hr - 1 D_U133A_24_DLPFC 861 Cardiomyopathies Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2779 Source GEO sample is GSM2098 Last updated (according to GEO): Nov 21 2005 19 0 human frontal cortex I_95Av2_2672_DLPFC_0_GS of parieto-occipital cortex 120 146 ER negative human primary breast tumor EA02014_41288_H133A_JA-1853 Coronary artery 901 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184672 Last updated (according to GEO): Apr 26 2007 the ventricular 1095 1109 Heart failure 1000 Microarray Analysis of the G-CSF-mobilized Peripheral Blood Stem Cell Allograft GSE4076 Cockayne syndrome B (CSB) protein is a member of the SWI/SNF family and has DNA-dependent ATPase and ATP-dependent chromatin remodeling activities. The CSB protein is missing or altered in CS-B cells. CS-B cells are hypersensitive to UV light and defective in transcription-coupled DNA repair (TCR). TCR efficiently removes a variety of lesions from the transcribed strand of active genes. It has been shown that lesions specifically in the transcribed strand of active genes trigger the induction of apoptosis following UV irradiation. Several DNA damage signaling cascades, including the ATR/Chk1, p38 kinase, p53, and jun N-terminal kinase pathways are activated following UV irradiation. However, the role of TCR in cellular global transcriptional responses to UV irradiation remains to be elucidated. Using oligonucleotide microarray technology, we analyzed the time course of responses of CS-B cells (CS-B) and CS-B cells complemented with wild-type CSB cDNA (CS-B wt). Last Updated (by provider): Sep 04 2007 Contributers: Takanori T Tomura Toshiro Matsuda Seiji Takeuchi Kiyoji Tanaka Yuki Nagata frontal lobe 1000 861 Cerebellum Spleen 265 270 N/A Source GEO sample is GSM7624 Last updated (according to GEO): May 28 2005 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181206 Last updated (according to GEO): Jul 12 2007 Standard Affymetrix Protocol Source GEO sample is GSM16449 Last updated (according to GEO): May 28 2005 255 234 with HIV encephalitis brain, Right Frontal Parietal: Extract66_le1 Testes 6 Normal 1055 1047 microglia Epithelial Cells 1000 Expression profiling of spinal cord section (T9) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM1329 Last updated (according to GEO): May 28 2005 f2#223 versus pool Mouse Brain tissue spleen sprague1 whole tissue, individual animal, 10 weeks old, male Sprague Dawley spleen file:R3JW02103015 Source GEO sample is GSM15213 Last updated (according to GEO): May 28 2005 Blood 1000 3616 PC 24Hr (pool) vs. 1500mg/kg APAP 24Hr rat 3624 blood Nasal Epithelium 901 Primary Neoplasm 1000 Kr10: Hippocampus_5T-AI_rep1 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/11035.gif Source GEO sample is GSM76446 Last updated (according to GEO): Sep 22 2006 Brain 861 Spleen vs 2-Methyl-thio-ATP Treated B cell 30min (set3) Cochlea 0 6 861 Heart failure Gene expression data from mouse primary visual cortex Source GEO sample is GSM101695 Last updated (according to GEO): Mar 27 2006 A/J amygdala rep2 10 7 Left Wild type olfactory epithlium 48 hpO replicate2 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68353 Last updated (according to GEO): Jul 07 2006 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14601.gif Source GEO sample is GSM91615 Last updated (according to GEO): Sep 22 2006 An important objective in postgenomic biology is to link gene expression to function by developing physiological networks that include data from the genomic and functional levels. Here, we develop a model for the analysis of time-dependent changes in metabolites, fluxes, and gene expression in a hepatic model system. The experimental framework chosen was modulation of extracellular glutamine in confluent cultures of mouse Hepa1-6 cells. The importance of glutamine has been demonstrated previously in mammalian cell culture by precipitating metabolic shifts with glutamine depletion and repletion. Our protocol removed glutamine from the medium for 24 h and returned it for a second 24 h. Flux assays of glycolysis, the tricarboxylic acid (TCA) cycle, and lipogenesis were used at specified intervals. All of these fluxes declined in the absence of glutamine and were restored when glutamine was repleted. Isotopomer spectral analysis identified glucose and glutamine as equal sources of lipogenic carbon. Metabolite measurements of organic acids and amino acids indicated that most metabolites changed in parallel with the fluxes. Experiments with actinomycin D indicated that de novo mRNA synthesis was required for observed flux changes during the depletion/repletion of glutamine. Analysis of gene expression data from DNA microarrays revealed that many more genes were anticorrelated with the glycolytic flux and glutamine level than were correlated with these indicators. In conclusion, this model may be useful as a prototype physiological regulatory network where gene expression profiles are analyzed in concert with changes in cell function. Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11282 Last updated (according to GEO): May 28 2005 kidney 126 132 plasma cells 50 61 /Ovary 6 Disease 11 26 Parkinson's disease sample x045 0 30 Plasma 861 outer medulla 31 43 Pool of 4 non-inner ear tissue samples at E11, E11.5, E12, E15; 2 at E13, E13.5; 3 at E14, E14.5; 5 at E12.5 Source GEO sample is GSM182626 Last updated (according to GEO): Aug 14 2007 /NJ Basal Ganglia A 3 21 The epithelial cells 962 981 Arteries 861 1000 Spleen 5 0 brain CHIPEXP_NAME: 230_2_050531tpj_55h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Isoproterenol TREAT_TOX_MECHANISM1: Heart_Cardiotoxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0.5 SAMPLING_TIME: 24 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197624 Last updated (according to GEO): Jun 01 2007 Tumor__Ovary_Adeno_07-B_001B on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 5 0 brain GSE363 of the saphenous artery 43 65 638 624 that carcinomas PBMCs-Healthy-INF448_Healthy comparison of olfactory-bulbectomized and sham-operated rats with depressive-like behaviour Source GEO sample is GSM247197 Last updated (according to GEO): Dec 11 2007 Fibroblasts 1000 Osteoblasts 1000 55 31 out of mouse bone marrow 901 Temporal Lobe Diaphragm 7 Day mdx rep 3 Nasal Epithelium Inhalation Formaldehyde 6ppm 8d ID300 of Parkinson's disease 450 471 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225675 Last updated (according to GEO): Nov 02 2007 30minplus.3 from mouse colon 21 36 32h-DMSO replication 2 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195286 Last updated (according to GEO): Sep 13 2007 Mouse young heart C5-Ht-1 no additional Source GEO sample is GSM199207 Last updated (according to GEO): Jun 08 2007 Normal Source GEO sample is GSM176176 Last updated (according to GEO): Apr 09 2007 Brain 861 42 30 Control blood Hyperdip>50-C8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15716 Last updated (according to GEO): May 28 2005 Hippocampus 1000 Umbilicus 861 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9929.gif Source GEO sample is GSM79895 Last updated (according to GEO): Sep 22 2006 Cortex 0 5 1000 Cerebral cortex Lung transplantation is effective for many diseases that are unresponsive to other therapy. However, long-term survival of recipients is limited by the development of bronchiolitis obliterans syndrome. Acute rejection is a major risk factor for bronchiolitis obliterans syndrome, but noninvasive biomarkers have not been identified. To address this deficiency, gene expression microarrays were performed using bronchoalveolar lavage cells of lung transplant recipients with acute rejection (n = 7) and with no rejection (n = 27). The cell and differential counts were similar. Signal values for genes between groups were compared using t tests. One hundred thirty-five genes were upregulated in the acute-rejection group, including genes involved in acute rejection, immune response genes with an unknown role in rejection, genes not known to have a role in rejection, and genes of unknown function. Two-dimensional hierarchical clustering grouped all acute rejection samples into one cluster and the majority of the no-rejection samples into a second cluster. The acute-rejection samples showed significant changes in gene expression for seven biological pathways. Bronchoalveolar lavage cells are a reliable RNA source for microarray analysis, which is powerful in identifying acute-rejection genes. The individual genes, patterns of gene expression, or biologic pathways identified may represent novel biomarkers for acute rejection. 77 62 mesenteric C57BL in bronchial epithelia 311 332 4_hypothalamus_9hrs_sleep_#108 Gene expression data from a hippocampus from mouse injected 15 mg/kg kainate Source GEO sample is GSM147419 Last updated (according to GEO): Jan 03 2007 pfc_1061_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Coronary heart disease 913 861 Brain plasma cells 332 344 37 year old male in the brain 150 162 Brain 1000 from the viscera 132 147 V5-P364 Gene expression data from postmorten brain regions Source GEO sample is GSM144896 Last updated (according to GEO): Nov 20 2006 Richard Almon-13-1138200269789 858 Mesodermal cell of parieto-occipital cortex 222 249 901 Coronary artery Pituitary Gland 861 Cerebellum_nontransgenic control A39_10 months_replicate 1 CNS-SpinalCmod-Adult-7d-4B-s2 Head and neck cancer Source GEO sample is GSM155655 Last updated (according to GEO): Apr 24 2007 Monocytes LPS+Ifng 30h 1 Activated Lymphoblastoid Cell Line for Individual 8019.3 log phase 176 166 bone marrow Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211328 Last updated (according to GEO): Jul 18 2007 GSE6927 Spleen vs Interferon-gamma (IFN gamma) Treated B cell 30min (set2) neurological disease control sample x170 Cerebral cortex 1000 1000 Cerebral cortex 116 107 hippocampi biopsy sample obtained from 2-year-old male individual Keywords = gene expression profile of normal human skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15824 Last updated (according to GEO): May 28 2005 brain, cortex: Sample15_e1_le1 in the mammalian nervous system 110 141 1000 Milk Cerebellum 1000 Brain 1000 1000 Prostate Interatrial septum 865 with autism spectrum disorder 37 65 Arteries 861 ?Compensatory? transcriptional mechanisms: Comparison of transcriptomes of Cx43 null and knockdown astrocytes 923 Subcutaneous Fat 861 Skeletal muscle structure Epithelium 861 PGA-E16.5_1A SMCL-5937-A307-5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Structure of entorhinal cortex 1000 Coronary heart disease 913 between the LAD artery 266 287 H111 FC BA4 B human cerebellum Source GEO sample is GSM87164 Last updated (according to GEO): Feb 08 2006 861 Brain I_U133A_18_AnCg 21 0 Rat vestibular ganglia 16 7 cerebellum HS_578T_CL5006__BREAST Depolarization induced gene from primary cortical neuron Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia. 861 Muscle Leg 23 Day control rep 2 Consolidation of long-term memory (LTM) is a complex process requiring synthesis of new mRNAs and proteins. Many studies have characterized the requirement for de novo mRNA and protein synthesis; however, few studies have comprehensively identified genes regulated during LTM consolidation. We show that consolidation of long-term contextual memory in the hippocampus triggers altered expression of numerous genes encompassing many aspects of neuronal function. Like contextual memory formation, this altered gene expression required NMDA receptor activation and was specific for situations in which the animal formed an association between a physical context and a sensory stimulus. Using a bioinformatics approach, we found that regulatory elements for several transcription factors are over-represented in the upstream region of genes regulated during consolidation of LTM. Using a knock-out mouse, we found that c-rel, one of the transcription factors identified in our bioinformatics study, is necessary for hippocampus-dependent long-term memory formation. 901 Ciliary Body AD control Treatment, type=dissect Source GEO sample is GSM119632 Last updated (according to GEO): Jul 10 2006 mouse, mutant, liver, RNA B8877 Myocardium 861 Adenocarcinoma 1000 The adult mouse was injected intraperitoneal (ip) with saline (~100ul/mouse) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use. Source GEO sample is GSM73001 Last updated (according to GEO): Sep 07 2005 Myometrium 19 Normal /6J cingulate cortex rep2 5 29 Epithelial Cells 1000 HL-60_I_CL7008_Leukemia on Affymetrix GeneChip Human Full Length Array HuGeneFL 906 Adenocarcinoma, Clear Cell outer medulla 31 43 861 Muscle Spleen vs BAFF Treated B cell 120min (set2) 1000 Brain AKR/J Basal Ganglia A Primary tumor 19 32 none Source GEO sample is GSM239937 Last updated (according to GEO): Dec 07 2007 Multiple sclerosis 0 17 861 Cerebral cortex Lymph Node [JunctionChip 4 of 5] 901 Stem cells PGA-swim_2w_s1061 Cerebral cortex 1000 Uterus_Corpus Source GEO sample is GSM19015 Last updated (according to GEO): Sep 25 2006 Malignant Neoplasms 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145812 Last updated (according to GEO): Nov 20 2006 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24085.gif Source GEO sample is GSM81537 Last updated (according to GEO): Sep 22 2006 33 17 tibialis anterior of lung neuroendocrine tumors 885 913 Gene expression data from postmorten brain regions Source GEO sample is GSM145989 Last updated (according to GEO): Nov 20 2006 Liver Test (Blinded) Sample Source GEO sample is GSM130193 Last updated (according to GEO): Sep 18 2007 Plasma 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM144906 Last updated (according to GEO): Nov 20 2006 Comparison of gene expression from subjects who resolved or formed pustules to H.ducreyi. In human inoculation experiments, the cutaneous immune response to Haemophilus ducreyi consists of serum, PMN, macrophages, T cells and myeloid DC. In reinfection experiments, some subjects form pustules twice (PP group) or resolve infection twice (RR group). Although pustule formation is associated with serum resistance and phagocytic failure, there are no differences in the ability of isolated phagocytes or serum obtained from PP and RR subjects to ingest or kill H. ducreyi. To identify the basis for differential host susceptibility to H. ducreyi, we used microarrays to profile gene expression in infected and uninfected tissue and monocyte-derived DC obtained from PP and RR subjects. In infected tissue, both groups had a core response to H. ducreyi. Many additional transcripts that signify active immune function were upregulated exclusively in RR tissue, while PP tissue exclusively contained differentially regulated transcripts consistent with immune dysregulation. The core response of infected DC from both groups was typical of a DC1 response. RR DC exclusively expressed many additional transcripts indicative of DC1 function, while PP DC uniquely expressed differentially regulated transcripts characteristic of both DC1 and DCreg. The data suggest that DC from PP and RR subjects are prewired to respond differentially to H. ducreyi. Last Updated (by provider): Sep 13 2007 Contributers: Barry P Katz Xiaoman S Li Lang Li Diane M Janowicz Kate R Fortney Stanley M Spinola Howard J Edenberg David Wilkes Tricia L Humphreys Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18510.gif Source GEO sample is GSM91546 Last updated (according to GEO): Sep 22 2006 861 Encephalitis 5 0 brain 91 from the bone marrow 72 To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18450 Last updated (according to GEO): May 27 2005 N05__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Large-scale analysis of the mouse transcriptome. mammary gland from females with E18 embyros C57BL/6L, female, 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 255.59 Stdv: 10.11 Min: 238.50 Max: 271.99 Source GEO sample is GSM2975 Last updated (according to GEO): Mar 20 2006 901 Coronary artery Normal__Kidney_Norm_627NS on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Normal Source GEO sample is GSM175849 Last updated (according to GEO): Apr 09 2007 861 Cerebral cortex cy3:SHR control, biological rep 1g; cy5:pool of 6 WKY control rats 5_hypothalamus_12hrs_sleep_#114 BXD 5_M7SS02080619 1000 Parenchyma plasma cells 332 344 Microarray analysis of NL and PCOS oocytes (P6) Expression profiling of spinal cord section (T9) extracted from rats 72h following moderate injury Source GEO sample is GSM31586 Last updated (according to GEO): May 27 2005 T-47D hgu95c PriG_5%O2_Expt3_Day4_rep1 7 0 Pancreas of the atrial 647 659 7 frontal cortex 20 Blood 1000 Activated Source GEO sample is GSM176008 Last updated (according to GEO): Apr 09 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11563 Last updated (according to GEO): May 28 2005 227 223 Brain with Parkinson's disease 27 50 Parkinson Disease 1000 91 from the bone marrow 72 Mel18 shRNA, biological rep1 /3T3 fibroblasts 743 759 Blood 861 cerebellum 7 16 no additional Source GEO sample is GSM199286 Last updated (according to GEO): Jun 08 2007 Blood 861 SR-A mutant olfactory epithelium 2 hpO replicate1 Barcode: 251316210183 Source GEO sample is GSM159385 Last updated (according to GEO): Jul 17 2007 brain 0 5 with Parkinson's disease 27 50 Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153774 Last updated (according to GEO): Jan 19 2007 n/a Source GEO sample is GSM177988 Last updated (according to GEO): Jun 11 2007 Bladder sample 1327-1 GM18516_technical_rep_1 Wild type 8 wk old male A/J mouse periaqueductal gray Source GEO sample is GSM74987 Last updated (according to GEO): Feb 27 2007 5 0 Spleen Parkinson Disease 1000 1000 Maxilla nucleus raphe magnus 1000 Testis 1000 Nasal Epithelium 901 HMVEC-L stimulated with LPS for 24 hours L24R1 D2_Control_ZT 12_2 12 frontal Lobe 23 Neurites 861 41 brain cortex 52 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11178.gif Source GEO sample is GSM76441 Last updated (according to GEO): Sep 22 2006 Hippocampus_Rasgrf1KO_rep2 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3338 Last updated (according to GEO): Mar 21 2006 Olfactory Epithelium 1000 Brain 1000 bronchial epithelia 224 243 1 Retina 13 20 Disease Source GEO sample is GSM175797 Last updated (according to GEO): Apr 09 2007 of the heart 842 854 5 0 brain Meningioma Recurrent Grade 2 U133A Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108016 Last updated (according to GEO): Jun 06 2006 1000 Subcutaneous Fat SN:1012369 Source GEO sample is GSM115408 Last updated (according to GEO): Jun 20 2006 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9975.gif Source GEO sample is GSM79834 Last updated (according to GEO): Sep 22 2006 Myocardial Infarction 1000 5 0 brain Cerebral cortex 861 R646P00806 Alzheimer's Disease 1000 2CdA: PK11195 intervention at 3.0h 1000 Infection human cerebellum Source GEO sample is GSM87104 Last updated (according to GEO): Feb 08 2006 cerebral cortex sprague 3915 Morula replication 4 1000 ovarian neoplasm 1000 Cerebral cortex with acute measles 20 37 861 Malignant Neoplasms GM12004 Day 3_M_-LIF_Bchip Tissue fiber 861 7 0 prostate Amyotrophic Lateral Sclerosis 1000 Cardiac 523 530 Squamous cell carcinoma 6 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:364, Count:32 Corner- Avg:36544, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:15.267480,SFGene:All Background:Avg:408.40,Stdev:5.81,Max:426.0,Min:399.9 Noise:Avg:9.27,Stdev:0.43,Max:10.8,Min:8.4 RawQ:13.27 Keywords = ALL Source GEO sample is GSM3474 Last updated (according to GEO): May 28 2005 Neostriatum 1000 of Parkinson's disease 450 471 R726P01003 100302 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11482 Last updated (according to GEO): May 28 2005 onto a collagen 71 85 39 21 from mammary glands from epididymal fat tissues 21 48 Wild type inbred mice Source GEO sample is GSM83034 Last updated (according to GEO): Nov 10 2005 MDA Mb231 6h + 75 nM Cxcl12 1 Treated Ovarian_Tumor_ClearCell_CHTN-OC-012 brain, SNc and VTA: SNc1_e1_le1 90 81 in stroke 10 7 Left Standard affymetrix protocol Source GEO sample is GSM119493 Last updated (according to GEO): Jul 31 2007 901 Skeletal muscle structure G42 neurons from lateral geniculate nucleus (LGN) Source GEO sample is GSM63031 Last updated (according to GEO): Dec 01 2005 Parkinson's disease sample x178 Skeletal muscle structure 1000 Hereditary Nonpolyposis Colorectal Neoplasms 947 liver, PPARa-null mice, treatment with WY14643 for 5 days Source GEO sample is GSM205764 Last updated (according to GEO): Jul 24 2007 CAF 2585 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A brain, cerebral cortex: Rat_03-60_NroLep_Lipska_e1_le1 Balb/c day 0, biological rep 1, tech rep 1 Gene expression data from skeletal muscle following 30 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230439 Last updated (according to GEO): Sep 19 2007 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19211.gif Source GEO sample is GSM91581 Last updated (according to GEO): Sep 22 2006 mdx5cv quadriceps sample 2 Exp C, Animal #2, 5mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 5mg/kg of CPF for 96 hours Source GEO sample is GSM246165 Last updated (according to GEO): Dec 03 2007 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.12 Subject: 3108 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39071 Last updated (according to GEO): May 27 2005 5 0 Muscle Laser captured visceral sensory neurons. Source GEO sample is GSM63688 Last updated (according to GEO): Dec 21 2005 Cerebral cortex 861 brain, Left frontal Lobe: Extract26_le2 human caudate nucleus Source GEO sample is GSM86894 Last updated (according to GEO): Feb 08 2006 from SVGR2 glial cells 21 43 3068 CP0_43 Brain 1000 Brain 861 Prosencephalon 861 Primary Neoplasm 1000 Simple annotation: Leukemia/Lymphoma Cell Lines, Prolymphocytic Leukemia (PLL) Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2874.gif Source GEO sample is GSM72211 Last updated (according to GEO): Sep 22 2006 861 Colon 923 Congestive heart failure Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs//27677.gif Source GEO sample is GSM66564 Last updated (according to GEO): Sep 22 2006 subsequent to viral infection 865 894 KT12_CAN/AR3 high gestational age Source GEO sample is GSM213072 Last updated (according to GEO): Jul 25 2007 Animals were sacrificed and organs were rapidly frozen in liquid nitrogen, and subsequently stored at <ETH>80oC. Tissues were mechanically homogenized with a polytron and total cellular RNA was extracted using a commercially available reagent (TMTRIzol; Invitrogen). The poly-(A)+ fraction of the RNA was isolated by chromatography with oligo d(T) cellulose beads. For cDNA labeling, either 25 mg of total RNA or 2.5 mg of poly-(A) RNA was converted into cDNA using reverse transcriptase (RT; Super Script II, Invitrogen) and alternatively Cy5 or Cy3-labeled dCTP (1mM, Perkin Elmer-Cetus/NEN, Boston) in a reaction mixture containing 1.5 mL oligo (dT) (100pmol/ mL), 3 mL dNTP-dCTP (6.67mM each), 1 mL dCTP (2mM), 4 mL DTT (100mM), 8 mL 5 X RT Buffer (Invitrogen, California). The reactions were carried out at 42¼C for 3 hrs, after which the RNA was degraded by the addition of 0.5 mL RNase A (1 mg/mL) and 1.5 mL RNaseH 5 units/mL). Labeled cDNA was separated from unincorporated nucleotides (Qiagen column) and further concentrated by evaporation under vacuum. The arrays were pre-hybridized for 1-2hrs with DIGEasy hybridization buffer (Roche) containing 10ug/ml denatured salmon sperm DNA, and 10ug/ml yeast tRNA. The Cy5 and Cy3 labelled cDNAs were combined and hybridized in the same medium and incubated with the arrays for 16-18hrs at 37Co. Finally, the arrays were washed 3 x 10 mins in 0.1 x SSC (20 X SSC is 3M sodium chloride, 0.3 M sodium citrate, pH 7.0), 0.1%SDS at 50Co, and 4 x 3min in 0.1 x SSC at room temperature, and dried by centrifugation. Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray fluorescent scanner and image intensity data were extracted and analyzed with QuantArray 3.0 analysis software. Quantification data was imported in GeneSpring (Silicon Genetics). The import format was modified to maintain information relevant to user-contributed flagging as well as QC parameter furnished by the array manufacturer. Dye swap and Intensity-based normalization (Lowess) were performed using the default settings. Keywords = spleen Keywords = malaria Source GEO sample is GSM11010 Last updated (according to GEO): Oct 28 2005 614 601 resident glia Neoplasm 861 of the normal mucosa 7 26 OVCAR-3 hgu95e Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10165.gif Source GEO sample is GSM79678 Last updated (according to GEO): Sep 22 2006 1000 Coronary Arteriosclerosis Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11474 Last updated (according to GEO): May 28 2005 1000 Brain 421 412 infection Sample24, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53275 Last updated (according to GEO): Jul 06 2005 PGA-RnSalt_e_6w_2-m5 Myometrium 28 Disease Ovarian Granulosa Cell Tumor 5 32 Brain 1000 Brain 861 1000 Heart failure NCI60.55_LABEL59EXTRACT58SUB3 Source GEO sample is GSM134273 Last updated (according to GEO): Aug 06 2007 ER negative human primary breast tumor EA02014_41273_H133A_JA-1535 150 mg/kg X 6 hr Source GEO sample is GSM129859 Last updated (according to GEO): Sep 18 2007 Gene expression data from brain of adult rats Source GEO sample is GSM101029 Last updated (according to GEO): Feb 20 2007 861 Brain rat hippocampus Treatment, type=time_course, measurement=1.0 h Source GEO sample is GSM32127 Last updated (according to GEO): May 27 2005 Parkinson's disease sample x149 Nose 1000 CVB3_V-3h Whole brain 0 10 of parieto-occipital cortex 120 146 861 Communicable Diseases Simple annotation: Adenoma, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10029.gif Source GEO sample is GSM79871 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM144959 Last updated (according to GEO): Nov 20 2006 with some respiratory epithelium. 1039 1072 Stem cells persist throughout life by self-renewing in numerous tissues including the central and peripheral nervous systems. This raises the issue of whether there is a conserved mechanism to effect self-renewing divisions. Deficiency in the polycomb family transcriptional repressor Bmi-1 leads to progressive postnatal growth retardation and neurological defects. Here we show that Bmi-1 is required for the self-renewal of stem cells in the peripheral and central nervous systems but not for their survival or differentiation. The reduced self-renewal of Bmi-1-deficient neural stem cells leads to their postnatal depletion. In the absence of Bmi-1, the cyclin-dependent kinase inhibitor gene p16Ink4a is upregulated in neural stem cells, reducing the rate of proliferation. p16Ink4a deficiency partially reverses the self-renewal defect in Bmi-1-/- neural stem cells. This conserved requirement for Bmi-1 to promote self-renewal and to repress p16Ink4a expression suggests that a common mechanism regulates the self-renewal and postnatal persistence of diverse types of stem cell. Restricted neural progenitors from the gut and forebrain proliferate normally in the absence of Bmi-1. Thus, Bmi-1 dependence distinguishes stem cell self-renewal from restricted progenitor proliferation in these tissues. 16 6 (transverse Plasma 861 Squamous cell carcinoma 875 Normal__Bladder_BL_6 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A /NJ periaqueductal gray rep1 3 30 Fibroblasts 38 48 Neurites 861 1000 frontal lobe 0 Human Cortex 11 ExpressionLevel:GXN-00532 on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A Epithelium 861 The most common congenital cardiac abnormalities 50 97 901 Caudate nucleus structure Malignant neoplasm of lung 1000 I_U133A_3_DLPFC 1000 Cytokeratin Transcriptional response of rat cerebrocortical tissue following acute exposure to permethrin or deltamethrin. mouse brain 478 489 I_U133A_28_CB 60 45 of the Pituitary Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3277 Last updated (according to GEO): Mar 17 2006 of the tumors 337 349 Interatrial septum 865 n/a Source GEO sample is GSM178068 Last updated (according to GEO): Jun 11 2007 861 Cerebral cortex mouse brains 187 198 Control Source GEO sample is GSM176472 Last updated (according to GEO): Apr 09 2007 91 from the bone marrow 72 1000 Brain ILS/ISS_cerebellum_naive_479 Brain 861 861 Heart Stem cells 1000 Cerebral cortex 861 AMM_0_0_Female3_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111853 Last updated (according to GEO): Nov 21 2006 Hypothalamic structure 1000 Hair; Awn Hair (back) catagen Keywords = mouse gene expression database Source GEO sample is GSM29337 Last updated (according to GEO): May 27 2005 861 Cerebral cortex with autism spectrum disorder 37 65 Cerebral cortex 1000 GM12003 Immune_Peripheral Blood Mononuclear Cells (ficoll)_2 Keywords = mouse gene expression database Source GEO sample is GSM29446 Last updated (according to GEO): May 27 2005 Gene expression data from rat metanephric mesenchymes cultured for 7 days in the presence of the ANX fraction Source GEO sample is GSM126228 Last updated (according to GEO): Dec 08 2006 Untreated versus treated (bortezomib) breast cancer cells. Source GEO sample is GSM120353 Last updated (according to GEO): Jul 20 2006 Amygdala Source GEO sample is GSM107960 Last updated (according to GEO): Jun 06 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145471 Last updated (according to GEO): Nov 20 2006 SN:1010404 Source GEO sample is GSM115387 Last updated (according to GEO): Jun 20 2006 UBOC1 Exp A Day 4 (b) The left hippocampus was dissected out of a male, 12 month-old mouse overexpressing amyloid precursor protein with the Swedish mutation (Tg2576; APPSw). Total RNA was extracted and the data were analyzed with MAS 5.0 and scaled to 2500. Source GEO sample is GSM26709 Last updated (according to GEO): May 27 2005 M_U133A_41_nAcc 144 114 from a single adult spinal cord Liver 1000 Amygdala Source GEO sample is GSM107914 Last updated (according to GEO): Jun 06 2006 Ts1Cje-4-MGU74B 3AJZ02031306_brainThalamus 4-cell embryo replication 4 Keywords = preimplantation Keywords = development Source GEO sample is GSM14682 Last updated (according to GEO): May 28 2005 Cerebral Cortex 4 Normal Gene expression data from mouse brain infected with GNPs infected with retroviruses that express N-myc Source GEO sample is GSM148581 Last updated (according to GEO): Mar 14 2007 2530 CP24_32 29 0 cerebral cortex wistar ky 3911 77 66 Normal Ovary Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=720630 LaserPower=4.323.79 Lot batch = LC17N092 Source GEO sample is GSM4815 Last updated (according to GEO): Nov 21 2005 Leukemia, Lymphocytic, Acute 901 M-5-5-BO on UMich-10k Osteoblasts 1000 1000 Brain 0.5 mg/kg/ml Isoproterenol treatment, 1 hour time point, biological rep 1 Skeletal bone 861 40 21 from the hippocampus of acute myocardial infarction 93 122 rad001 48h, biological rep5 from the olfactory epithelium tissue 172 208 Stria 861 861 Neoplasm 1000 Brain Gloubus Pallidum External 1 Disease Brain 1000 Brain 50 55 The nose 94 101 Gene expression data from mouse primary visual cortex Source GEO sample is GSM101693 Last updated (according to GEO): Mar 27 2006 Lung tissue from C57BL/6 mice calorie restricted by 2/3 and sacrificed 96hrs after the onset of calorie restriction. Lot batch = Source GEO sample is GSM4033 Last updated (according to GEO): May 28 2005 861 Myopathy Liver 1000 PGA_PA-N_325 198-96_Adeno 861 Heart 1000 Brain Scheck-3U24NS043571-01S1-2 1000 Brain 21 adrenal medulla 7 Coxsackievirus Infections 861 Arteries 861 861 Alzheimer's Disease Testes 2 Normal HTI-286 in docetaxel-refractory prostate cancer Source GEO sample is GSM206168 Last updated (according to GEO): Jun 29 2007 Colonic mucous membrane 913 Neoplasm 861 Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for four weeks.. Source GEO sample is GSM149805 Last updated (according to GEO): Dec 12 2006 R584P01064 Lymphoma (Burkitts Raji) [JunctionChip 3 of 5] Aorta 861 Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed for 24 h to hydrostatic pressure (HP24), pressure experiment # 3 (PE3). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11415 Last updated (according to GEO): Dec 15 2006 Neoplasm 861 spinal cord 0 10 1000 Cardiomyopathy, Alcoholic 46 8 in docetaxel-refractory prostate cancer adenocarcinoma 3447 0 18 Hep2_43_rep3 1000 Fibroblasts KIDNEY Source GEO sample is GSM18797 Last updated (according to GEO): Sep 25 2006 bronchial epithelia 224 243 Epithelium of bronchus 983 Bone Marrow 1000 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7583.gif Source GEO sample is GSM79843 Last updated (according to GEO): Sep 22 2006 HUVEC Cell Line 1 Normal nasal epithelial cells 28 49 HSC_21Months_A of heart failure 1348 1364 Nicotine-hippocampus, biological rep6 Adipose tissue 884 1000 Uterus 861 Neoplasm Mesenchymal Stem Cells 1000 Brain 861 Spleen 257 262 Wild-type-neocortex, biological rep2 (male) Brain 861 of parieto-occipital cortex 122 148 861 medulloblastoma ovarian tumor: serous Source GEO sample is GSM139452 Last updated (according to GEO): Apr 09 2007 1000 Retina Hypertension, Pulmonary 1000 861 Branch Expression profiling of moderately injured raphe at 4h in rats Source GEO sample is GSM41618 Last updated (according to GEO): May 27 2005 Primary adenocarcinoma 0 21 Duoden022KAF6T_066.txt Parkinson Disease 1000 349 317 for early embryonic cell division of brain neurospheres 39 59 RNA samples extracted from astrocytes cultured from wild type and Cx43 null neonatal mice were dye labeled and individually co-hybridized with a reference of labeled cDNAs pooled from a variety of tissues on eight gene arrays containing 8975 mouse DNA sequences Lot batch = 2 Source GEO sample is GSM8894 Last updated (according to GEO): May 27 2005 none Source GEO sample is GSM244577 Last updated (according to GEO): Nov 23 2007 DCN_P7_A Heart 1000 /Ovary 8 Disease 11 26 901 Hepatocyte 5 0 brain Female 65.9 yr after antibody enrichment scan 2 (U133A) Time point at 18h post HCMV infection 1000 Rectum 129 2000-2 Heart Study of in vitro granulocyte differentiation Source GEO sample is GSM137447 Last updated (according to GEO): Jun 06 2007 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3509.gif Source GEO sample is GSM76432 Last updated (according to GEO): Sep 22 2006 CNS-SC_InjB30m-3bA-s2 Wild type olfactory epithlium 0 h replicate2 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120665 Last updated (according to GEO): May 14 2007 1000 Structure of entorhinal cortex Pituitary Gland 861 E2A-PBX1-C1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 0 Lung tissue 10 I_U133A_42_AnCg of infection 673 684 Gene expression data from brain of adult rats Source GEO sample is GSM101007 Last updated (according to GEO): Feb 20 2007 M_U133A_41_HC none Source GEO sample is GSM244643 Last updated (according to GEO): Nov 23 2007 901 Epithelial Cells MDA Mb231 6h 5 Control /3T3 fibroblasts 478 493 CNS-SpinalCmod-Adult-12h-2A-s2 Bladder sample 669-7 Primary Carcinoma 876 Sample details: We analysed changes in gene expression in the dorsal telencephalon of forebrain-specific FGFR1 mutant mice. Gene expression was compared between the dorsal telencephalons of single E12.5 embryos of two genotypes: FGFR1 heterozygous (HET1,3,8) and homozygous mutants (HOM2,4,7) that were both heterozygous for the FoxG1 transcription factor, as Cre recombinase expression is driven off the endogenous FoxG1 locus in these animals (Hebert, J. M., Lin, M., Partanen, J., Rossant, J. and McConnell, S. K. (2003b). FGF signaling through FGFR1 is required for olfactory bulb morphogenesis. Development 130, 1101-11. & Hebert, J. M. and McConnell, S. K. (2000). Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures. Dev Biol 222, 296-306. Source GEO sample is GSM62847 Last updated (according to GEO): Aug 26 2005 Squamous cell carcinoma 10 0 25 PGA-Band_1h_15-m5 Nasal Epithelium 865 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16867.gif Source GEO sample is GSM91508 Last updated (according to GEO): Sep 22 2006 901 Caudate nucleus structure of lung neuroendocrine tumors 2223 2252 CNS-RM_Ctr7d-1A-s2 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11492 Last updated (according to GEO): May 28 2005 Five different human MPNST cell lines, mock treated or infected with G207. Source GEO sample is GSM215808 Last updated (according to GEO): Aug 07 2007 Malignant neoplasm of lung 1000 540 518 of human breast tumours Neoplasm 861 Nose 1000 mouse cerebral cortex 0 21 84 69 by heart failure brain, brainstem: CB3_e1_le1 BPH-40 on UMich-10k Gene expression data from postmorten brain regions Source GEO sample is GSM145689 Last updated (according to GEO): Nov 20 2006 Bone Marrow 1000 1BJZ02053112_PrefrontalCortex Gene expression data from whole brain of uninfected mouse Source GEO sample is GSM189630 Last updated (according to GEO): May 16 2007 858 Prostatic Neoplasms 861 Neoplasm Macrophage 14smi042 WGACON-47 NCI60.57_LABEL61EXTRACT60SUB3 Source GEO sample is GSM134280 Last updated (according to GEO): Aug 06 2007 42 30 Control blood Brain_Ncer_2_Normal cerebellum on Affymetrix GeneChip Human Full Length Array HuGeneFL 5 0 Spleen ES Gene expression data from rat metanephric mesenchymes cultured for 7 days in the presence of LIF Source GEO sample is GSM126204 Last updated (according to GEO): Dec 08 2006 A2780_cis_IC25_16h_1 88 68 with bicuspid valves Biopsy of the normal mucosa of the colon from patient #16 Infection 1176 1185 Sample is skeletal muscle from nonobese patient undergoing elective abdominal surgery Source GEO sample is GSM3989 Last updated (according to GEO): May 28 2005 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201231 Last updated (according to GEO): Jun 14 2007 midbrain_3 with mental retardation 241 263 Probeset expression data from NA12750 growth 3, replicate 1 Source GEO sample is GSM195200 Last updated (according to GEO): Aug 08 2007 Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 1286 blood 861 Cerebral cortex Large-scale analysis of the mouse transcriptome. Cortex frontal C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 317.49 Stdv: 10.43 Min: 295.14 Max: 331.45 Source GEO sample is GSM2914 Last updated (according to GEO): Sep 27 2006 brain, hippocampus: CON-DG-3_e1_le1 hindbrain 7 15 Richard Almon-17-1133800609276 Bone Marrow 1000 747 715 primitive neuroectodermal tumours Brain 1000 5 0 brain After 2 week acclimation to 12 hr/12 hr light/dark regimen, c57/Bl6 mice were subjected to a 36 hour period of constant darkness. Aortae were subsequently harvested at 4 hour intervals to 48 hours. Duplicate microarrays were hybridized with biotin-labeled probes derived from aorta tissue (6 pooled aortae/timepoint). Source GEO sample is GSM6100 Last updated (according to GEO): May 27 2005 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188843 Last updated (according to GEO): Jun 06 2007 human melanoma metastatic cell line A375 Source GEO sample is GSM195328 Last updated (according to GEO): Jun 04 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CpG-oligodeoxynucleotide for 120min Source GEO sample is GSM5526 Last updated (according to GEO): May 27 2005 A39 WT2 F5/53 A39 wild type Mouse 4 months Cerebellum Female Source GEO sample is GSM73221 Last updated (according to GEO): Sep 06 2005 Semeralul_PFC_Development_Week10_Batch1_Animal_8 22 0 Normal epithelial cells Osteoblasts 1000 22-3 olfactory bulbs 4 23 Neoplasm 861 Cerebral cortex 861 10 0 Cord blood Kidney 861 short access to cocaine, nucleus accumbens, 1 hr/day access to cocaine Source GEO sample is GSM93817 Last updated (according to GEO): Jan 26 2006 CNS-SC_InjA7d-3C-s2 PC 12Hr rat 4126 blood vs. 1500mg/kg APAP 12Hr rat 4132 blood Ta gr2 tumour Source GEO sample is GSM2487 Last updated (according to GEO): May 27 2005 1000 Retina Brain 1000 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15744 Last updated (according to GEO): May 28 2005 Transcription profiling involves H3 methyltransferase G9a-deleted MEFs reconstituted with empty vector (delta), wild type FLAG-G9a (WT), FLAG-G9a K165A (K165A) or FLAG-G9a H1093K catalytic mutant (H1093K). Source GEO sample is GSM197813 Last updated (according to GEO): Jul 16 2007 of 2182 tumor 50 62 1000 Spleen SR-A mutant olfactory epithelium 8 hpO replicate1 5 0 brain Gene expression data from postmorten brain regions Source GEO sample is GSM145482 Last updated (according to GEO): Nov 20 2006 Nasal Epithelium 901 nucleus raphe magnus 1000 Heart 861 male C57BL6, double amplification Source GEO sample is GSM5419 Last updated (according to GEO): Mar 17 2006 GBM Treatment, type=remove Source GEO sample is GSM99552 Last updated (according to GEO): Apr 21 2006 Brain (corpus callosum) [JunctionChip 4 of 5] tTA +Doxy 7486 Communicable Diseases 1000 Liver 1000 1106 1088 adhesion molecules 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201269 Last updated (according to GEO): Jun 14 2007 SEA/GnJ_male_hypothalamus Source GEO sample is GSM184217 Last updated (according to GEO): Apr 26 2007 17 0 Trigeminal ganglia Cerebral cortical contusion in rat, 1dpi, #1 DR48h(2) Neoplasm 861 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68296 Last updated (according to GEO): Jul 07 2006 embryo day 8.5 Source GEO sample is GSM18634 Last updated (according to GEO): May 27 2005 1000 Brain 1000 Brain Stem Female 65.1 yr after antibody enrichment scan 2 (U133A) plasma cells 332 344 M_U133A_21_nAcc MLL-R2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A duodenum 17 24 Femur 1000 M_U133A_71_AnCg 1000 Eye BTBR T+ tf/tf Frontal Cortex A UBOC1 Exp A Day 5 (b) Infected 6 weeks prior with Htt-N171-82Q-expressing recombinant lentivirus Source GEO sample is GSM34380 Last updated (according to GEO): Oct 16 2006 brain 0 5 3915 3900 locus coeruleus Bone marrow cell, primary H4-1 5 0 brain nucleus accumbens, whole wistar2 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM209847 Last updated (according to GEO): Aug 31 2007 Neoplasm 861 Macrophages treated with LPS, 20 min, Replicate 1 Source GEO sample is GSM241134 Last updated (according to GEO): Nov 02 2007 Cells captured via Arcturus LCM system, amplified (RiboAmp, 2 rounds) and labeled (Enzo) for hybridizaton to Affymetrix MG_U74Av2 arrays, using manufacturers protocols in each step. Source GEO sample is GSM6199 Last updated (according to GEO): May 27 2005 NMDA 1H (5/7) (Experiment NMDA1-Run 9136) Treatment, type=time_course, description=samples are treated for 10, 30 or 60 min with NMDA 1mM, the agonist is then washed out and the cells are harvested 24h later, measurement=60.0 m Source GEO sample is GSM96757 Last updated (according to GEO): Feb 14 2006 Exp 3 Time point 8 ileum 0 4 The epithelial cells 962 981 CNS-SpinalCmod-Adult-12h-3A-s2 Con (32 h) A on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132496 Last updated (according to GEO): Feb 26 2007 1000 Aorta 861 Cancer of Neck Epithelial Cells 901 osteoblast 630 640 To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132996 Last updated (according to GEO): Sep 12 2006 Testis 861 NA12872 Retina 861 Astrocyte reactivity (i.e., activation) and associated neuroinflammation are increasingly thought to contribute to neurodegenerative disease. However, the mechanisms that trigger astrocyte activation are poorly understood. Here, we studied the Ca2+-dependent phosphatase calcineurin, which regulates inflammatory signaling pathways in immune cells, for a role in astrogliosis and brain neuroinflammation. Adenoviral transfer of activated calcineurin to primary rat hippocampal cultures resulted in pronounced thickening of astrocyte somata and processes compared with uninfected or virus control cultures, closely mimicking the activated hypertrophic phenotype. This effect was blocked by the calcineurin inhibitor cyclosporin A. Parallel microarray studies, validated by extensive statistical analyses, showed that calcineurin overexpression also induced genes and cellular pathways representing most major markers associated with astrocyte activation and recapitulated numerous changes in gene expression found previously in the hippocampus of normally aging rats or in Alzheimer's disease (AD). No genomic or morphologic evidence of apoptosis or damage to neurons was seen, indicating that the calcineurin effect was mediated by direct actions on astrocytes. Moreover, immunocytochemical studies of the hippocampus/neocortex in normal aging and AD model mice revealed intense calcineurin immunostaining that was highly selective for activated astrocytes. Together, these studies show that calcineurin overexpression is sufficient to trigger essentially the full genomic and phenotypic profiles associated with astrocyte activation and that hypertrophic astrocytes in aging and AD models exhibit dramatic upregulation of calcineurin. Thus, the data identify calcineurin upregulation in astrocytes as a novel candidate for an intracellular trigger of astrogliosis, particularly in aging and AD brain. Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 8918 left_liver_lobe of the colon 28 39 Parkinson Disease 861 Simple annotation: Cell-line, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2866.gif Source GEO sample is GSM79862 Last updated (according to GEO): Sep 22 2006 the blood 393 402 H9LMS00102612 nostrils 156 164 Category: Lymphoma Classification Subcategory: Chronic Lymphocytic Leukemia Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n115 Source GEO sample is GSM2080 Last updated (according to GEO): Nov 21 2005 brain, hippocampus: ADX PM Hip_e1_le1 NCI-H460 hgu95e Medulla 861 Normal Source GEO sample is GSM176269 Last updated (according to GEO): Apr 09 2007 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213489 Last updated (according to GEO): Jul 31 2007 Spleen vs TGF-beta (transforming growth factor-beta) Treated B cell 64 50 Umbilical cord with experimental autoimmune encephalomyelitis 12 57 1000 Epidermis T170 Brain 50 55 Heart Atrium 1000 Cerebral cortex 1000 AMM_0_0_Female8_Olfact_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111838 Last updated (according to GEO): Nov 21 2006 DBA/2J Olfactory Bulb A Spleen 1000 Cerebral cortex 861 Thalamus 9 Normal 861 HIV Infections 1000 ovarian neoplasm CNS-RM_Ctr14d-1A-s2 Cerebral cortex 966 861 Cerebral cortex 65 24 from umbilical subcutaneous adipose tissue Control 8 4 0 Colon C57L/J Amygdala C Cochlea 0 6 Nrl ko 2 mon replicate 2 Lymphoblastoid Cell Line for Individual 8135.3 log phase the spinal cords 144 159 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b034 Source GEO sample is GSM1972 Last updated (according to GEO): Nov 21 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68167 Last updated (according to GEO): Jul 07 2006 707 660 (cytoskeletal-cell membrane-extracellular matrix Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11290 Last updated (according to GEO): May 28 2005 Epithelium 861 861 Brain Liver 0 4 PC 6Hr rat 3586 blood vs. 150mg/kg APAP 6Hr rat 3587 blood eTat - Noco0hr - 2 "Sample 32,>5 yr survival(145 months) age 54 erp yes" on vantveer-oligo Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 19 day time point Source GEO sample is GSM159773 Last updated (according to GEO): Apr 23 2007 861 Fissure nostrils 156 164 MDA-MB-231 transfected with EGRE3-VgRXR and pIND-DACH1, selected by Zeocin and G418. Induced DACH1 expression was confirmed by western blot. Source GEO sample is GSM11373 Last updated (according to GEO): May 28 2005 40 25 in breast cancer Osteoblasts 1000 32 21 from retinas GSE1139 Cells were either prestimulated (1_X) or not (0_X) for 18h with 100 ng/ml LPS. Media was exchanged and after 2h rest, cells either restimulated (X_1) or not (X_0) with again 100 ng/ml LPS. This resulted in 4 experimental conditions: 0_0, 0_1, 1_0 and 1_1. There were 3 biological replicates done, resulting in 12 arrays altogether. Source GEO sample is GSM213696 Last updated (according to GEO): Aug 01 2007 brain, hippocampus: Hippocampus 2_le1 C3H/HeJ hippocampus rep1 (430 2.0 Array) 31 0 Familial combined hyperlipidemia Spleen vs Untreated B cell Time 0 (set22) 5 0 brain 337 323 with adiposity post HCMV infection 18 36 HapMap CHB Female Source GEO sample is GSM159583 Last updated (according to GEO): Feb 01 2007 B6:17-7,8,9 amygdala GSE6971 NMDA 1h 7/8 RC (Experiment NMDA1-Run 9136) Treatment, type=time_course, description=samples are treated for 10, 30 or 60 min with NMDA 1mM, the agonist is then washed out and the cells are harvested 24h later, measurement=60.0 m Source GEO sample is GSM96760 Last updated (according to GEO): Feb 14 2006 Normal Source GEO sample is GSM176147 Last updated (according to GEO): Apr 09 2007 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 h time point Source GEO sample is GSM159760 Last updated (according to GEO): Apr 23 2007 FBX15-iPS MEF4-7 (rep1) 901 frontal lobe Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7430.gif Source GEO sample is GSM79825 Last updated (according to GEO): Sep 22 2006 GSE8441 Primary small cell lung carcinoma 2243 Source GEO sample is GSM17339 Last updated (according to GEO): May 28 2005 Measles 1000 20 0 human caudate nucleus Tacrine 2.7mg/kg/day from 5 weeks Moclobemide 10mg/kg/day Creatine 1%w/v added to wet mash Lot batch = 5227 Source GEO sample is GSM13362 Last updated (according to GEO): May 28 2005 1000 Brain 28 0 Adult frontal cortex cocaine5 Cerebellum 4 Normal liver 184 189 121 103 somatic cell nuclei This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques P. Tremblay (jacques-p.tremblay@crchul.ulaval.ca; 2705 boulevard Laurier) for analysis. Stembase Experiment ID: E205 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205 SCGP Sample ID: S270 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205#SAMPLE_247 Short description: Cells from sphere were incubated in a differentiation medium. They differentiated into neurons after 7 days in culture. Analysis requested: mouse genechips RNA concentration: 0.689 ug/uL Sample volume: 15 uL total Source GEO sample is GSM93610 Last updated (according to GEO): Jan 23 2006 from adenomas 67 80 1000 Descending colon Cerebral cortex 861 plasma cells 332 344 861 Liver ProstateCancer-10 on NHGRI-6.5k_c Whole Brain 62 72 734 721 of the tumours Cerebral cortex 861 Brain 1000 AK_SleepDep_ZT 0_3 861 Cancer of Neck osteoblast 627 637 from aorta 152 162 "21 hr Hela Double Thymidine, exp3" 861 Colon CNS-SpinalC-conAdult-48h-1B-s2 1500 mg/kg X 6 hr Source GEO sample is GSM129838 Last updated (according to GEO): Sep 18 2007 for encephalopathy 224 241 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 30 minutes following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10956 Last updated (according to GEO): May 27 2005 Nasal Epithelium 865 DMN-CtrHippo28d-1bAv2-s2 B6:21-1 spinal cord GSE590 Spleen vs BAFF Treated B cell 120min (set1) Integumentary system 1000 Epithelium of bronchus 983 1000 Hippocampus Acetaminophen 6hr Rat 8918 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool Brain 861 AD-327t1-A276-10 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Colorectal Adenocarcinoma (SW480) [JunctionChip 2 of 5] 875 Subcutaneous Tissue Coronary Arteriosclerosis 1000 40 21 from skeletal muscle heart failure 583 595 B300 on Affymetrix GeneChip Human Full Length Array HuGeneFL 468 459 the rectum 14 7 amygdala 861 Epithelial Cells Wild type 8 wk old male 129S6/SvEvTac mouse pituitary gland Source GEO sample is GSM74997 Last updated (according to GEO): Feb 27 2007 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184724 Last updated (according to GEO): Apr 26 2007 Spinal Cord 1000 Occipital lobe 861 in muscle 678 687 29 14 from spinal cord Bone Marrow 1000 7 0 Midbrain CS-B wt-rescued cell UVC-irradiated (2hour) replicate 2 U133A 902 Immune System Diseases PGA_MI_ilv_4h_389 Cerebral cortex 861 NeverSmoker 60 AT1-hTERT_1.5Gy_24h_C3_21394 103 FC BA9 B Age-related defects in stem cells can limit proper tissue maintenance and hence contribute to a shortened life-span. Using highly purified hematopoietic stem cells from mice aged 2 to 21 months, we demonstrate a deficit in function yet an increase in stem cell number with advancing age. Expression analysis of more than 14,000 genes identified 1500 that were age-induced and 1600 that were age-repressed. Genes associated with the stress response, inflammation, and protein aggregation dominated the upregulated expression profile, while the downregulated profile was marked by genes involved in the preservation of genomic integrity and chromatin remodeling. Many chromosomal regions showed coordinate loss of transcriptional regulation, and an overall increase in transcriptional activity with aged, and inappropriate expression genes normally regulated by epigenetic mechanisms was observed. Hematopoietic stem cells from early-aging mice expressing a mutant p53 allele reveal that aging of stem cells can be uncoupled from aging at an organismal level. These studies show that HSC are not protected from aging. Instead, loss of epigenetic regulation at the chromatin level may drive both functional attenuation of cells, as well as other manifestations of aging, including the increased propensity for neoplastic transformation. Last Updated (by provider): Apr 27 2007 nasal epithelial cells 28 49 BXD40_M7SS02042215 1000 Integumentary system Fibroblasts 861 Standard Affymetrix Protocal Keywords = microarray Keywords = muscle Source GEO sample is GSM15775 Last updated (according to GEO): May 28 2005 Gene expression data from dorsal pancreas at e12.5, MG-U74C version2 Source GEO sample is GSM199464 Last updated (according to GEO): Jun 08 2007 M_U133A_30_DLPFC NoCAD_replicate31 cerebral cortex 7 21 Leg 28 Day control rep 2 Skeletal bone 1000 861 Blood Normal__Lung_LU_7 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A The magnocellular neurons (MCNs) of the supraoptic nucleus (SON) and paraventricular nucleus (PVN) of the hypothalamus are the principal site of biosynthesis of prepropeptide precursor of the antidiuretic hormone vasopressin (VP). This precursor is processed during anterograde axonal transportation to terminals in the posterior pituitary gland, where biologically active VP is stored until release into the general circulation in response to physiological activation of the SON by osmotic cues. By binding to V2-type receptors located in the kidney, VP decreases the amount of water lost in urine. Osmotic activation of the SON is accompanied by a dramatic morphological and functional remodeling. We have sought to understand the mechanistic basis of this plasticity in terms of the differential expression of genes. To identify such genes, we adopted an unbiased global approach based on suppressive subtractive hybridization-polymerase chain reaction (SSH-PCR) Using this method, we generated libraries of clones putatively differentially expressed in control vs. dehydrated SON. To rapidly screen these libraries, 1,152 clones were subjected to microarray analysis, resulting in the identification of 459 differentially expressed transcripts. cDNA clones corresponding to 56 of these RNAs were sequenced, revealing many of them to be novel expressed sequence tags (ESTs). Four transcripts were shown by in situ hybridization (ISH) to be significantly up- or downregulated in the SON after dehydration. These genes may represent novel effectors or mediators of SON physiological remodeling. I_95Av2_1905_DLPFC_1_GS total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Dimaprit for 60min Source GEO sample is GSM5536 Last updated (according to GEO): May 27 2005 Infection 861 Replicate one: differential expression analysis of CW treatment on RBEC6 cells Source GEO sample is GSM128921 Last updated (according to GEO): Aug 16 2006 Semeralul_PFC_Development_Week2_Batch1_Animal_3 bone marrow-CD71EarlyErythroid Source GEO sample is GSM18749 Last updated (according to GEO): Sep 25 2006 PGA-swim_10min_n997 Carcinoma, Large Cell 867 5 0 brain 4 0 Brain 1000 Pituitary Gland Voxel F3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1425 Last updated (according to GEO): Nov 21 2005 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:239, Count:32 Corner- Avg:38822, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:7.316926,SFGene:All Background:Avg:371.14,Stdev:5.69,Max:385.0,Min:359.1 Noise:Avg:10.15,Stdev:0.33,Max:11.2,Min:9.4 RawQ:12.76 Keywords = ALL Source GEO sample is GSM3496 Last updated (according to GEO): May 28 2005 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15703 Last updated (according to GEO): May 28 2005 no additional Source GEO sample is GSM199375 Last updated (according to GEO): Jun 08 2007 40 21 from skeletal muscle 861 Blood 334 320 Keywords = HIV Osteoblasts 1000 861 Neoplasm coronary_artery_4 ALLB-cell69 on Affymetrix GeneChip Human Full Length Array HuGeneFL 102 93 Carcinomas 861 Cardiomyopathies 861 Brain Cerebellum 861 of the normal mucosa 7 26 SN:Human Glioblastoma Biopsy 10383 of trauma 603 612 HDMTX_MP-10 1000 Brain Tolerizing allografts 7 days No.1 We have combined large-scale mRNA expression and gene mapping methods to identify genes and loci that control hematopoietic stem cell (HSC) functioning. mRNA expression levels were measured in purified HSC isolated from a panel of densely genotyped recombinant inbred mouse strains. Quantitative trait loci (QTLs) associated with variation in expression of thousands of transcripts were mapped. Comparison of the physical transcript position with the location of the controlling QTL identified polymorphic cis-acting stem cell genes. In addition, multiple trans-acting control loci were highlighted that modify expression of large numbers of genes. These groups of co-regulated transcripts identify pathways that specify variation in stem cells. We illustrate this concept with the identification of strong candidate genes involved with HSC turnover. We compared expression QTLs in HSC and brain from the same animals, and document both shared and tissue-specific QTLs. Our data are accessible through WebQTL, a web-based interface that allows custom genetic linkage analysis and identification of co-regulated transcripts.. Date GSE2031 Last Updated: Jun 29 2005 Contributers: Bert Dontje Kenneth F Manly Sue Sutton Michael Cooke Rudi Alberts Gerald de Haan Jintao Wang Edo Vellenga Ellen Weersing Elissa Chesler Leonid Bystrykh Andrew I Su Tim Wiltshire Mathew T Pletcher Robert W Williams Ritsert C Jansen Lu Lu Includes GDS1077. Update date: Mar 16 2005. Dataset description GDS1077: Expression profiling of Lin- Sca-1+ c-kit+ hematopoietic stem cells (HSC) from 22 different BXD recombinant inbred (RI) strains. Each RI strain is homozygous for alleles at about 98% of loci. Results combined with QTL mapping to identify candidate genes for the control of HSC function.. 966 Organ Spleen 259 264 human caudate nucleus Source GEO sample is GSM86814 Last updated (according to GEO): Feb 08 2006 50 43 jejunum Healthy patient. Source GEO sample is GSM228580 Last updated (according to GEO): Sep 11 2007 Hippocampus 1985 15 month Old WT 1 14 7 amygdala brain, hippocampus: CON-CA3-A5_e1_le1 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with TGF-beta (transforming growth factor-beta) for 60min Source GEO sample is GSM5794 Last updated (according to GEO): May 27 2005 17 7 hippocampus 38 12 of congenital heart disease 13 6 Awn Hair in the adult heart 44 61 Type 2 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228677 Last updated (according to GEO): Sep 11 2007 78 66 Control blood The nose 94 101 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Neuropeptide Y for 240min Source GEO sample is GSM5719 Last updated (according to GEO): May 27 2005 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD6 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD6 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36674 Last updated (according to GEO): May 27 2005 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=760600 LaserPower=4.333.89 Lot batch = LC17N005 Source GEO sample is GSM4810 Last updated (according to GEO): Nov 21 2005 bone_marrow_1 Whole Brain 62 72 human frontal cortex Source GEO sample is GSM86988 Last updated (according to GEO): Feb 08 2006 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181185 Last updated (according to GEO): Jul 12 2007 1000 Cerebellum ScGT1_4 Superficial 1000 Spleen vs Terbutaline Treated B cell 120min (set3) Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2719 Source GEO sample is GSM2140 Last updated (according to GEO): Nov 21 2005 G5 nasal retina 1000 Skeletal muscle structure AK_Control_ZT 0_2 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 7763 left_liver_lobe of mouse brain 9 23 Global analyses of gene expression in early experimental osteoarthritis. f2#61 versus pool Mouse Brain tissue Muscle 861 Gastrointestinal Stromal Tumors 966 nostrils 156 164 /3T3 fibroblasts 307 322 Tumor__Leukemia_AML_AML_(5,PK)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Liver Test (Blinded) Sample Source GEO sample is GSM130140 Last updated (according to GEO): Sep 18 2007 liver 186 191 Infection 1000 VDXKIU_1246 Creatine-treated, biological rep2 1000 Kidney 1000 Brain 861 Heart 430A2_2045_85_control_sham_medulla Source GEO sample is GSM242708 Last updated (according to GEO): Nov 15 2007 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225952 Last updated (according to GEO): Nov 02 2007 1000 Brain 865 Disorder of artery brain, frontal cortex: LabeledExtract3 901 Stem cells C41 on NCI-7.6k Subject code A6EB Liver 1000 of a colorectal adenoma 7 29 Control Source GEO sample is GSM176478 Last updated (according to GEO): Apr 09 2007 Richard Almon-10-1133800609010 1000 Spleen Replicate1_Voxel D5 AJ 12-1 Thymus HCC (HBV+, HK38) 901 Temporal Lobe embryonic hearts 1064 1079 983 Anatomical compartment processed in batch 1 Source GEO sample is GSM90450 Last updated (according to GEO): Mar 20 2006 Prefrontal Cortex 0 16 high dose 24h, replicate 2 Brain Amygdala Source GEO sample is GSM18928 Last updated (according to GEO): Sep 25 2006 Lymphoblastoid Cell Line for Individual 8137.4 log phase 861 Duodenum Blood 861 SK-MEL-5 hgu95c 861 Muscle Cockayne syndrome B wt-rescued cell Source GEO sample is GSM226617 Last updated (according to GEO): Sep 04 2007 SmoothMuscle Source GEO sample is GSM18971 Last updated (according to GEO): Sep 25 2006 1000 Rectum Cerebral cortex 1000 SN:1012386 Source GEO sample is GSM115414 Last updated (according to GEO): Jun 20 2006 in blood 16 23 Lymphoblastoid Cell Line for Individual 8146.4 log phase MGMH030228084Aembryoday6.5 1000 Neuraxis Epithelium of bronchus 983 BALB/cJ strain, brain hemisphere, biological rep2 the central nervous system 2156 2181 901 Malignant neoplasm of prostate Expression profiling of moderately injured raphe at 7d in rats Lot batch = Source GEO sample is GSM42000 Last updated (according to GEO): May 27 2005 5 0 brain hrs nasal epithelium 1126 1146 Simple annotation: Chronic Lymphocytic Leukemia, Fludarabine chemotherapy Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/3087.gif Source GEO sample is GSM72182 Last updated (according to GEO): Sep 22 2006 Spleen vs Insulin-like growth factor 1 Treated B cell 30min (set1) A HID B D088 peripheral blood-CD8TCells Source GEO sample is GSM18879 Last updated (according to GEO): Sep 25 2006 N/A Source GEO sample is GSM96298 Last updated (according to GEO): Feb 13 2006 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n128 Source GEO sample is GSM2057 Last updated (according to GEO): Nov 21 2005 none Source GEO sample is GSM244615 Last updated (according to GEO): Nov 23 2007 Primary tumor 19 32 BTBR T+ tf/tf Hippocampus A C6SPGFPfast2 Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM Source GEO sample is GSM207678 Last updated (according to GEO): Jul 09 2007 Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. such as neuroblastoma 922 942 331 307 in central nervous system 5 0 brain Dendritic Cells, Exposed to Leishmania donovani - Repeat #2 4 0 Brain 861 Cerebellum Lb19: Hippocampus_5T-AU_rep4 CNS-SpinalCmod-Adult-48h-1B-s2 V5-P079 Gene expression data from mouse colon Source GEO sample is GSM198102 Last updated (according to GEO): Aug 22 2007 Semeralul_PFC_Development_Week2_Batch1_Animal_6 I_U133A_1_CB Accumbens 3 Normal 858 Mesodermal cell Gene expression data from postmorten brain regions Source GEO sample is GSM144920 Last updated (according to GEO): Nov 20 2006 of the fibers 544 556 in spinal cords 1033 1047 Spleen [JunctionChip 2 of 5] PGA-HMO-MObese-8aUA-s2 Expression profiling of moderately injured raphe at 24h in rats Source GEO sample is GSM41582 Last updated (according to GEO): May 27 2005 CLL-60 || lc4b069 Lung 861 Brain 1000 Cerebral cortex 861 Whole Brain 62 72 1000 Brain TGFbeta added. Source GEO sample is GSM203987 Last updated (according to GEO): Jun 25 2007 M_U133A_34_HC Cerebellum 1000 Olfactory Epithelium 1000 Brain 861 4 0 Brain 3ARS02080777b_subthalamic_nucleus NA Source GEO sample is GSM84317 Last updated (according to GEO): Dec 01 2005 1012 1008 basal cocaine naive, amygdala, 0 hrs/day access to cocaine Source GEO sample is GSM93826 Last updated (according to GEO): Jan 26 2006 9 0 Blood Test gene expression of 1 day LIF differentiated ESCs Source GEO sample is GSM181947 Last updated (according to GEO): Apr 12 2007 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153460 Last updated (according to GEO): Jan 11 2007 Spleen 0 5 Leg 56 Day mdx rep 1 VDXGUYU_4044 I_U133A_10_AnCg Liver 0 4 Myocardial Infarction 1000 rat cortex Treatment, type=time_course, measurement=7.0 d Source GEO sample is GSM53217 Last updated (according to GEO): Jul 06 2005 Medulla Oblongata 861 Expression profiling of spinal cord section (T10) extracted from rats 14d following mild injury Source GEO sample is GSM31305 Last updated (according to GEO): May 27 2005 901 Connective Tissue G2 Inf. Retina (rep) Female 68.4 yr before antibody enrichment scan 1 (U133B) Gene expression data from postmorten brain regions Source GEO sample is GSM145515 Last updated (according to GEO): Nov 20 2006 RNA isolated from post-mortem tissues Source GEO sample is GSM6828 Last updated (according to GEO): May 28 2005 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11478 Last updated (according to GEO): May 28 2005 accumbens_9 Source GEO sample is GSM80599 Last updated (according to GEO): Mar 31 2006 BUB/BnJmale_hypothalamus Source GEO sample is GSM184194 Last updated (according to GEO): Apr 26 2007 in hippocampus 18 32 Heart Atrium 2 Normal 861 Blood Ganglia, Spinal 1000 from colorectal adenoma 21 44 (cortex 19 25 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 1 hour after the last shock treatment. Source GEO sample is GSM4539 Last updated (according to GEO): May 27 2005 274 progenitor cells 289 M_U133A_47_AnCg 176 166 bone marrow Ovary 1000 Standard Affymetrix procedure Source GEO sample is GSM133017 Last updated (according to GEO): Aug 28 2007 M_95A_1871_CB_0_GS Expression profiling of spinal cord section (T9) extracted from rats 28d following severe injury Source GEO sample is GSM31603 Last updated (according to GEO): May 27 2005 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210374 Last updated (according to GEO): Jul 16 2007 Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. Source GEO sample is GSM112312 Last updated (according to GEO): Jun 06 2006 plasma cells 332 344 D_U133A_100_CB 1000 Neoplasm human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195336 Last updated (according to GEO): Jun 04 2007 Chronic leukemia NOS 913 the blood 393 402 Mesenchymal Stem Cells 1000 19 0 human frontal cortex Liver Test (Blinded) Sample Source GEO sample is GSM130112 Last updated (according to GEO): Sep 18 2007 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47528 Last updated (according to GEO): May 29 2005 Plasma 861 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3303 Last updated (according to GEO): Mar 21 2006 PMN_LB_180min_Patient1 Blood Test (Blinded) Sample Source GEO sample is GSM129969 Last updated (according to GEO): Sep 18 2007 brain 0 5 Day 1_H_-LIF_Achip_rep2 Frontal Lobe 10 Normal Cerebral cortex 1000 human frontal cortex Source GEO sample is GSM87036 Last updated (according to GEO): Feb 08 2006 Total RNA extracted from mouse brain Source GEO sample is GSM103425 Last updated (according to GEO): Sep 21 2006 Liver (HCV+, SF29, S2) Brain 1000 The Inbred Long Sleep (ILS) and Inbred Short Sleep (ISS) mouse strains have a 16-fold difference in duration of loss of the righting response (LORR) following administration of a sedative dose of ethanol. Four quantitative trait loci (QTLs) have been mapped in these strains for this trait. Underlying each of these QTLs must be one or more genetic differences (polymorphisms in either gene coding or regulatory regions) influencing ethanol sensitivity. Because prior studies have tended to focus on differences in coding regions, genome-wide expression profiling in cerebellum was used here to identify candidate genes for regulatory region differences in these two strains. Fifteen differentially expressed genes were found that map to the QTL regions and polymorphisms were identified in the promoter regions of four of these genes by direct sequencing of ILS and ISS genomic DNA. Polymorphisms in the promoters of three of these genes, Slc22a4, Rassf2, and Tax1bp3, disrupt putative transcription factor binding sites. Slc22a4 and another candidate, Xrcc5, have human orthologs that map to genomic regions associated with human ethanol sensitivity in genetic linkage studies. These genes represent novel candidates for the LORR phenotype and provide new targets for future studies into the neuronal processes underlying ethanol sensitivity. 1000 Down Syndrome 0 Human Cortex 11 low gestational age Source GEO sample is GSM213107 Last updated (according to GEO): Jul 25 2007 days nasal epithelium 1126 1147 brain, contralateral HC: Trizol Extraction25_le1 Cerebral cortex 861 A detailed description of this cell lines and the infection with prions, can be found in Schätzl et al., 1997. By single cell cloning consecutive subclones of ScGT1 cells were prepared. RNA was isolated from control and infected cell lines by the Trizol method. 20µg total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 30µl hybridisation buffer (6x SSC, 0,5% SDS 5 fold Denhardt's solution and 50% formamide) and mixed with 30µl of reference cDNA solution labelled with the second dye. This hybridisation mixture was placed on a pre hybriddised microarray, covered with cover slip, placed into a hybridisation chamber (Genomatix) and immersed in a thermostatic bath at 42°C for at least 16 hours. Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Maen intensities with substracted background were normalised so that the median of their rations has became 1 Keywords = prion Keywords = hypothalamus Keywords = GT1 Source GEO sample is GSM31111 Last updated (according to GEO): Oct 28 2005 Whole brain 0 10 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14943 Last updated (according to GEO): Oct 28 2005 1037 of transitional epithelium 1012 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2715 Source GEO sample is GSM2135 Last updated (according to GEO): Nov 21 2005 human caudate nucleus Source GEO sample is GSM86895 Last updated (according to GEO): Feb 08 2006 The epithelial cells 962 981 21 7 adrenal medulla f2#123 versus pool Mouse Brain tissue aa_NY82 Gene expression data from postmorten brain regions Source GEO sample is GSM146005 Last updated (according to GEO): Nov 20 2006 M_U133A_104_DLPFC 1000 Impaired cognition Skeletal bone 861 5 0 brain Bone Marrow 1000 Pancr_022AAFD2_060w.txt 1000 Brain Epithelium 861 RIIIS/J_female_hypothalamus from brain 21 30 Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP) and harvested at the beginning (0 h) of pressure experiment # 1 (PE1). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11351 Last updated (according to GEO): Dec 15 2006 D08 0h Media 861 Infection 861 Cerebral cortex low gestational age Source GEO sample is GSM213120 Last updated (according to GEO): Jul 25 2007 Malignant Neoplasms 861 H9RGV00111403 361 335 hypertrophic cardiomyopathy with progressive supranuclear palsy 27 61 Replicate1_Voxel A9 TEL-AML1-C11 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A cy3:WKY treated w/ angtiotensin, biological rep 1g; cy5:pool of 6 WKY control rats Trauma 1000 na Source GEO sample is GSM181285 Last updated (according to GEO): Apr 10 2007 861 Occipital lobe total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5830 Last updated (according to GEO): May 27 2005 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225367 Last updated (according to GEO): Aug 31 2007 outer medulla 31 43 Epithelium of bronchus 983 BXD33_M7SS02042211 Nose 1000 8067_Lung did not develop PGD Gene expression data from postmorten brain regions Source GEO sample is GSM144947 Last updated (according to GEO): Nov 20 2006 Mesenchymal Stem Cells 1000 heart 1169 1173 1000 Cerebellum Gene expression data from postmorten brain regions Source GEO sample is GSM145327 Last updated (according to GEO): Nov 20 2006 1000 Trauma Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=720670 LaserPower=1.951.31 Lot batch = LC17N104 Source GEO sample is GSM4825 Last updated (according to GEO): Nov 21 2005 26T_Infect_1 19 0 human frontal cortex Sample details: Three pools of rostral (R1-3), three pools of middle (M1-3), and three pools of caudal (C1-3) E13.5 MF1 neocortex were collected from 4 embryos. All possible 18 comparisons were carried out. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. Source GEO sample is GSM62824 Last updated (according to GEO): Aug 26 2005 1000 Pituitary Gland processed in batch 4 Source GEO sample is GSM90423 Last updated (according to GEO): Mar 20 2006 1000 Spleen 884 Cervix carcinoma against breast cancer 1376 1396 with Parkinson's disease 27 50 897 Endothelium standard Affymetrix protocol, MAS 5.0 Source GEO sample is GSM9129 Last updated (according to GEO): May 28 2005 CS 109h forebrain 7 15 Blood 1000 none Source GEO sample is GSM161876 Last updated (according to GEO): Feb 16 2007 1000 Hemorrhage 816 794 in the maxillary branch Insulin Resistance 1000 912 904 of tumors D_U133A_76_CB B6_SleepDep_ZT 0_3 129/SvImJ Cingulate Cortex C none Source GEO sample is GSM244535 Last updated (according to GEO): Nov 23 2007 brain, hippocampus: Hippocampus 10_le1 221 202 by CO2 asphyxiation Expression profiling of spinal cord section (T9) extracted from rats 24h following severe injury Lot batch = Source GEO sample is GSM7575 Last updated (according to GEO): May 28 2005 5 0 Spleen 5 0 Testes 1000 Maxilla B2-24 on NCI-7.6k N44__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A mouse brain ipsilateral control, biological rep3 ALS gray matter 3 Sporadic MO_LB_180min_Patient3 1000 Cerebral cortex 277 271 Retinas Heart 1000 90 81 in stroke 287 260 at the longitudinal fissure none Source GEO sample is GSM239835 Last updated (according to GEO): Dec 07 2007 of the heart 842 854 861 Colon 123 FC BA9 A Adenocarcinoma 7 Fibroblasts 861 5 0 brain 32 21 from retinas Gene expression data from postmorten brain regions Source GEO sample is GSM145987 Last updated (according to GEO): Nov 20 2006 Spleen vs Interferon-gamma (IFN gamma) Treated B cell 240min (set3) Peripheral Nervous System 1000 AML_2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A IRTGFBd8_21 LCCS sample 20 weeks Menstrual phase - Follicular Source GEO sample is GSM175775 Last updated (according to GEO): Apr 09 2007 928 Endometrium 861 Cerebellum D_U133A_60_Amy Lymphatic Metastasis 877 Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242045 Last updated (according to GEO): Dec 04 2007 5 0 brain of meningiomas 490 503 Seminoma 1000 total RNA from biosource CC#40 Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92481 Last updated (according to GEO): Jan 13 2006 Muscle_inadequate protein_female_rep2 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11295 Last updated (according to GEO): May 28 2005 Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 2222 blood Brain 1000 between the LAD artery 266 287 Ovarian_Tumor_Endometrioid_CHTN-OE-080 Chronic leukemia NOS 913 of somatomotor cortex 21 41 Mouse_E13.5_Front_Middle_Back_13 Gene expression in the rat dentate gyrus following passive avoidance training. Last Updated (by provider): May 10 2007 Contributers: Keith J Murphy Niamh C O'Sullivan Ciaran M Regan Includes GDS2711. Update date: Aug 22 2007. Dataset description GDS2711: Analysis of hippocampal dentate gyri of animals at various time points up to 24 hours following passive avoidance training. The hippocampal dentate gyrus is a structure vital to memory formation. Results provide insight into the molecular basis of memory consolidation in the hippocampus.. Nothing in line. Source GEO sample is GSM154216 Last updated (according to GEO): Jul 05 2007 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P7, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3185 Last updated (according to GEO): May 28 2005 0029_1353_H95A2_KF-176_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Cerebral cortex 1000 3AJZ02021913_ UTERUS 1000 Lung CNS-SpinalCmod-Adult-21d-1A-s2 ileum 0 4 39 21 from mammary glands 21 0 Mammary Gland @ Lac1 Cochlear nuclei pooled from 20 pups to generate one sample for one replicate hybridization out of 5 replicates. Cohybridized with P21_cy5_1. Source GEO sample is GSM44972 Last updated (according to GEO): Jun 08 2005 Control (5/7) (Experiment NMDA1-Run 9136)) Treatment, type=time_course, measurement=0.0 m Source GEO sample is GSM96661 Last updated (according to GEO): Feb 14 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM144936 Last updated (according to GEO): Nov 20 2006 Gene expression data from brain of adult rats Source GEO sample is GSM101008 Last updated (according to GEO): Feb 20 2007 8074_Lung developed PGD Performed by UCI Microarray Facility. Source GEO sample is GSM203418 Last updated (according to GEO): Jun 22 2007 brain 0 5 Mice on a mixed 129/SvJ and C57BL6/J background were sacrificed and livers frozen. RNA was isolated using RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol. Data were normalized by AffyMetrix MAS5.0 using defaults. Keywords = liver cholesterol abc Source GEO sample is GSM9284 Last updated (according to GEO): May 27 2005 N-6_PRE Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 13 hours after lights on. Original sample code = CM29A Source GEO sample is GSM227321 Last updated (according to GEO): Sep 10 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145514 Last updated (according to GEO): Nov 20 2006 Brain_Rhab_5_AT/RT (Extra Renal) on Affymetrix GeneChip Human Full Length Array HuGeneFL 15 0 human cerebellum none Source GEO sample is GSM123198 Last updated (according to GEO): Jul 26 2006 epidermis; dorsal skin without fur Source GEO sample is GSM18640 Last updated (according to GEO): May 27 2005 Nasal; Olfactory Epithelium Keywords = mouse gene expression database Source GEO sample is GSM29408 Last updated (according to GEO): May 27 2005 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11296 Last updated (according to GEO): May 28 2005 C3H/HeJ hypothalamus rep1 (430 2.0 Array) Adult murine BM, Lin-Sca1-Kit+Itga2b+Slamf1+ 1 in bronchial epithelia 311 332 1000 Malignant Neoplasms 61 41 from postmortem brain CNS-SpinalCmod-Adult-7d-3B-s2 863 836 of severe autoimmune disease Leukemia, Myelocytic, Acute 861 17 6 (hippocampus 37 15 of the heart myocardium 861 Kidney subthalamic_nucleus Source GEO sample is GSM18779 Last updated (according to GEO): Sep 25 2006 Brain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM144875 Last updated (according to GEO): Nov 20 2006 861 Blood CAD_replicate75 Spinal Cord 1000 70 40 without coronary artery disease 1000 Brain 1000 Spinal Cord Injuries Normal Source GEO sample is GSM176182 Last updated (according to GEO): Apr 09 2007 IM-7_POST Plasma 861 N-8_POST V5-P250 gene expression of 5 day LIF differentiated ESCs Source GEO sample is GSM181959 Last updated (according to GEO): Apr 12 2007 Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174528 Last updated (according to GEO): Mar 14 2007 1000 Glioma D_U133Plus_122_nAcc 262 diabetes 254 Control rat 6 substantia nigra Source GEO sample is GSM32167 Last updated (according to GEO): May 27 2005 none Source GEO sample is GSM210339 Last updated (according to GEO): Jul 16 2007 ER-/LN+/Marks217 on Affymetrix GeneChip Human Full Length Array HuGeneFL no additional Source GEO sample is GSM199203 Last updated (according to GEO): Jun 08 2007 861 Cerebral cortex n/a Source GEO sample is GSM177938 Last updated (according to GEO): Jun 11 2007 Genetic basis of sensitivity to pulmonary fibrosis 901 Temporal Lobe Heart 1000 Spleen 1000 861 Malignant Neoplasms 225636DE_4 19 0 human frontal cortex Embryonal tumours of the central nervous system (CNS) represent a heterogeneous group of tumours about which little is known biologically, and whose diagnosis, on the basis of morphologic appearance alone, is controversial. Medulloblastomas, for example, are the most common malignant brain tumour of childhood, but their pathogenesis is unknown, their relationship to other embryonal CNS tumours is debated, and patients' response to therapy is difficult to predict. We approached these problems by developing a classification system based on DNA microarray gene expression data derived from 99 patient samples. Here we demonstrate that medulloblastomas are molecularly distinct from other brain tumours including primitive neuroectodermal tumours (PNETs), atypical teratoid/rhabdoid tumours (AT/RTs) and malignant gliomas. Previously unrecognized evidence supporting the derivation of medulloblastomas from cerebellar granule cells through activation of the Sonic Hedgehog (SHH) pathway was also revealed. We show further that the clinical outcome of children with medulloblastomas is highly predictable on the basis of the gene expression profiles of their tumours at diagnosis. with Parkinson's disease 27 50 861 Longitudinal Ovary 1000 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs//7274.gif Source GEO sample is GSM79724 Last updated (according to GEO): Sep 22 2006 Blood 861 Y HID D080 1000 Prostate 1521 1500 of the failing hearts SCN2.2 Sample 15 (Exp#2-18 hr) GSE5140 573 556 of atherosclerosis Collagen 1000 brain 0 5 Liver 1000 Rett Syndrome 861 Expression profiling of somatomotor cortex extracted from rats at T0 naive Source GEO sample is GSM41682 Last updated (according to GEO): May 27 2005 of breast cancer 1007 1023 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:493, Count:32 Corner- Avg:38326, Count:32 BF:testadult.CHP Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:5.589355,SFGene:All Background:Avg:441.73,Stdev:7.77,Max:458.3,Min:425.9 Noise:Avg:10.12,Stdev:0.29,Max:11.1,Min:9.4 RawQ:14.32 Keywords = ALL Source GEO sample is GSM3473 Last updated (according to GEO): May 27 2005 26 0 frontal cortex sprague 3932 Brain 861 1000 Cerebral cortex Nodose Nucleus 5 Normal Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181121 Last updated (according to GEO): Jul 12 2007 Primary tumor 19 32 The adult mouse was injected intraperitoneal (ip) with saline (~100ul/mouse) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use. Source GEO sample is GSM73015 Last updated (according to GEO): Sep 07 2005 H9RGV00111003 M_U133Plus_110_nAcc 1000 Brain 59 35 out of mouse bone marrow Intestines, Small 1000 Brain 1000 I_U133A_5_Amy 1000 Brain Gastrointestinal Neoplasms 896 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195343 Last updated (according to GEO): Jun 04 2007 Gene expression data from epididymal fat tissues. Source GEO sample is GSM215585 Last updated (according to GEO): Aug 07 2007 Mesenchymal Stem Cells 1000 Expression profiling of spinal cord section (T9) extracted from rats 48h following moderate injury Source GEO sample is GSM31553 Last updated (according to GEO): May 27 2005 from a primary branch 21 41 Autistic Disorder 877 Examination of host genome-wide changes upon encounters with pathogens provides insight into the pathogenesis of infection and disease. When performed comparatively, it may shed light on the mechanisms underlying host susceptibility. In this study, gene expression in the mouse colon was investigated in two cognate lines of mice that differ in their response to Citrobacter rodentium infection; susceptible inbred FVB/N (FVB) and resistant outbred Swiss Webster (SW) mice. Gene expression in the distal colon was investigated prior to infection and at 4 and 9 days post-inoculation using a whole mouse genome Affymetrix array. Computational analysis identified 462 (1%) probe sets differentially expressed by more than 2-fold between uninoculated SW and FVB mice. In response to C. rodentium infection, 5,123 probe sets (11.4%) were significantly modulated in one or both lines of mice. Microarray data were validated by quantitative real time RT-PCR on 35 selected genes (r = 0.87, p < 0.001) and were found to have a 94% concordance. Transcripts represented by 1,547 probe sets (3.4%), were differentially expressed between FVB and SW mice regardless of infection status (host effect). Genes associated with transport were over-represented to a greater extent than immune response-related genes (25% vs. 11% of enrichment, respectively). Electrolyte analysis revealed hypochloremia and hyponatremia in susceptible animals. The results support the hypothesis that mortality in C. rodentium-infected FVB mice is associated with impaired ion transport and development of fatal hypovolemia. These studies contribute to our understanding of the pathogenesis of C. rodentium and suggest novel strategies for the prevention and treatment of diarrhea associated with bacterial infections of the intestinal tract. Last Updated (by provider): Aug 22 2007 Contributers: James G Fox Diana Borenshtein Vincent J Carey David B Schauer Prashant R Nambiar Rebecca C Fry Elizabeth B Groff 1000 Spleen AR-Veh-2 /3T3 fibroblasts 295 310 41 36 spleen All the array experiments published in "Gene expression patterns in human liver cancers" by Chen X, et al. Hepatocellular carcinoma (HCC) is a leading cause of death worldwide. Using cDNA microarrays to characterize patterns of gene expression in HCC, we found consistent differences between the expression patterns in HCC compared with those seen in nontumor liver tissues. The expression patterns in HCC were also readily distinguished from those associated with tumors metastatic to liver. The global gene expression patterns intrinsic to each tumor were sufficiently distinctive that multiple tumor nodules from the same patient could usually be recognized and distinguished from all the others in the large sample set on the basis of their gene expression patterns alone. The distinctive gene expression patterns are characteristic of the tumors and not the patient; the expression programs seen in clonally independent tumor nodules in the same patient were no more similar than those in tumors from different patients. Moreover, clonally related tumor masses that showed distinct expression profiles were also distinguished by genotypic differences. Some features of the gene expression patterns were associated with specific phenotypic and genotypic characteristics of the tumors, including growth rate, vascular invasion, and p53 overexpression. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Last Updated (by provider): Dec 27 2005 Contributers: Xin Chen [Switched to use SH-HL by Gemma] Brain of P10 Gja9 (-/-) C57Bl/6j mouse, replica K3 Primary tumor 19 32 861 Acquired Immunodeficiency Syndrome tibiae 115 120 /tf Cerebellum A 10 25 NFIA P16KO2 15 0 human cerebellum ER-/LN+/Nevins8 on Affymetrix GeneChip Human Full Length Array HuGeneFL Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24276.gif Source GEO sample is GSM66582 Last updated (according to GEO): Sep 22 2006 Spleen 0 5 Gene expression data from male mice. Source GEO sample is GSM115534 Last updated (according to GEO): Jun 13 2007 experiment I, passage 9, replicate 1 126T R626P01184 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225762 Last updated (according to GEO): Nov 02 2007 V5-P599 Epithelium 861 AML 53 0 5 1000 Cerebral cortex MLL_10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A adrenal_gland_cortex_1 Melanoma metastatic cell line A375, biological rep7 (LeiFidler) Brain 1000 1000 Bronchioles 256 235 dilated heart failure DMN-CtrHippo15d-1aAv2-s2 The genomic influcence of the combination of three reagents on cultured cortical neurons (9-11 DIV). Bursts of action potential firing were induced by the treatment of cultured cortical neurons with 50 ?M bicuculline (Bic) and 5 ?M 4-aminopyridine (4AP), which were abolished by the addition of the sodium channel blocker TTX (1 ?M). Source GEO sample is GSM144058 Last updated (according to GEO): Nov 24 2006 1000 Mammary gland 41 30 PCOS oocytes 219-97_SCC Blood 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145172 Last updated (according to GEO): Nov 20 2006 0 Down syndrome 12 Blood 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11338 Last updated (according to GEO): May 28 2005 278 255 ischemic cardiomyopathy GSE8030 861 Bladder Spleen vs TGF-beta Treated B cell 120min (set3) Disorder of artery 865 dorsal_root_ganglia_4 Source GEO sample is GSM80614 Last updated (according to GEO): Mar 31 2006 861 Cerebral cortex 2 hr EE repl 1 381 363 of childhood asthma 901 Caudate nucleus structure B6 day 3, biological rep 2, tech rep 2 901 Coronary artery Spinal Cord 901 20 0 human caudate nucleus wtPrE serum 3 Intestines, Small 1000 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 24 h time point Source GEO sample is GSM159819 Last updated (according to GEO): Apr 23 2007 in seminoma 28 38 Pre-BI cells 1b Prefrontal Cortex Source GEO sample is GSM105458 Last updated (according to GEO): Apr 17 2006 Gene expression data from the right forebrain of C57BL mouse received no treatment for twelve weeks. Source GEO sample is GSM148681 Last updated (according to GEO): Dec 12 2006 Retina 861 Diet induced changes in mouse liver mRNA profiles. One of 3 replicates of C57BL/6 mice maintained for 12 weeks on low fat diet. Keywords = LDL receptor deficiency, high fat diet, atherosclerosis, liver Source GEO sample is GSM5408 Last updated (according to GEO): May 27 2005 Liver 1000 A SIT D100 tibiae 115 120 7 cerebral cortex 21 0 Human Cortex 11 Backskin_WT_P6_rep1 M7TW00122040 Dahl Salt Sensitive Rat Lung- Hypoxia with SU-5416 rep1b C Fed Rep 1 6 0 Leprosy 12 0 ovarian tumor CAD_replicate96 Synovium; normal Keywords = mouse gene expression database Source GEO sample is GSM29441 Last updated (according to GEO): May 27 2005 M_U133A_15_DLPFC lymphnode; mesenteric Source GEO sample is GSM18617 Last updated (according to GEO): May 27 2005 1000 Spleen 861 Amygdaloid structure High-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we have generated and analyzed gene expression from a set of samples spanning a broad range of biological conditions. Specifically, we profiled gene expression from 91 human and mouse samples across a diverse array of tissues, organs, and cell lines. Because these samples predominantly come from the normal physiological state in the human and mouse, this dataset represents a preliminary, but substantial, description of the normal mammalian transcriptome. We have used this dataset to illustrate methods of mining these data, and to reveal insights into molecular and physiological gene function, mechanisms of transcriptional regulation, disease etiology, and comparative genomics. Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website (http://expression.gnf.org) that integrates data visualization and curation of current gene annotations. Last Updated (by provider): May 29 2005 Contributers: A Moqrich R G Vega P G Schultz M P Cooke A I Su T Wiltshire A P Orth K A Ching L M Sapinoso J B Hogenesch J R Walker Y Hakak A Patapoutian G M Hampton Includes GDS181. Update date: May 13 2004. Dataset description GDS181: Gene expression profiles from a diverse array of tissues, organs, and cell lines, from the normal physiological state. Represents a preliminary description of the normal mammalian transcriptome.. Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153330 Last updated (according to GEO): Dec 27 2006 G42 neurons from lateral geniculate nucleus (LGN) Source GEO sample is GSM63030 Last updated (according to GEO): Dec 01 2005 1000 Spleen Brain 861 Bladder sample 880-1 051801_HF_331FL 230 205 of inclusion body myositis atrial septal defects 198 218 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19229 Last updated (according to GEO): May 27 2005 Infection 1000 Macrophage smi93 n/a Source GEO sample is GSM177940 Last updated (according to GEO): Jun 11 2007 peripheral blood-CD56NKCells Source GEO sample is GSM18876 Last updated (according to GEO): Sep 25 2006 Molecular portraits of human breast tumors 995 of stem cells 1007 SN:1012384 Source GEO sample is GSM115413 Last updated (according to GEO): Jun 20 2006 Primary tumor 19 32 of peripheral nervous system 73 100 Alzheimer's Disease 861 Recurrent tumor 913 Gene expression data from postmorten brain regions Source GEO sample is GSM145446 Last updated (according to GEO): Nov 20 2006 "Sample 12,>5 yr survival(94 months) age 46 erp no" on vantveer-oligo 89 70 isolated theca cells human melanoma metastatic cell line A375 Source GEO sample is GSM155031 Last updated (according to GEO): Jun 04 2007 NHF1-hTERT_sham_6h_C5_20077 P1.2A_KIDNEY_4 osteoblast 627 637 Brain 1000 mild cognitive impairment - superior frontal gyrus 2 HNC3046 Glioblastoma multiforme (GBM) is the most common form of malignant glioma and is characterized by marked genetic instability, extensive intra-tumoral histopathological variability, and unpredictable variation in its clinical behavior. We investigated global gene expression in surgical samples of primary brain tumors. Gene expression profiling revealed large differences between normal brain samples and tumor tissues and between GBMs and lower grade oligodendroglial tumors. Extensive differences in gene expression were found among GBMs, particularly in genes involved in angiogenesis, immune cell infiltration, and extracellular matrix re-modeling. Significantly, we found that the global gene expression patterns in paired specimens from the same GBM invariably were more closely related to each other than to any other tumor, even when the paired specimens had strikingly divergent histologies. Survival analyses revealed a set of approximately 70 genes that were more highly expressed in rapidly progressing tumors and which stratified GBMs into two groups that differed by more than four-fold in median duration of survival. We further investigated one gene from the group, FABP7, and confirmed its association with survival in two unrelated cohorts totaling 105 patients. Expression of FABP7 enhanced the motility of glioma-derived cells in vitro. Our analyses thus provide a series of prognostic markers and suggest that their expression may enhance the invasive potential of tumor cells. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Last Updated (by provider): Jan 18 2006 Contributers: Max Diehn [Switched to use SH-24k by Gemma] of a colorectal adenoma 7 29 Expression profiling of spinal cord section (T10) extracted from rats 0h following laminectomy (naïve) Source GEO sample is GSM31306 Last updated (according to GEO): Oct 28 2005 1000 Lymphoma liver, wild type mice, control conditions Source GEO sample is GSM205768 Last updated (according to GEO): Jul 24 2007 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153342 Last updated (according to GEO): Dec 27 2006 V5-P131 Spleen vs Dimaprit Treated B cell 120min (set1) of somatomotor cortex 21 41 Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. 8h after sham surgery, a 4 mm diameter disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44514 Last updated (according to GEO): May 27 2005 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184733 Last updated (according to GEO): Apr 26 2007 19 0 human frontal cortex 36 21 from whole brain of a colorectal adenoma 7 29 1000 Brain (cortex 19 25 13 0 Nervous System 216 200 of neural retinas Brain 861 C57BL/6J pituitary gland rep2 1000 Colon 677 652 of adhesion molecule BP180 7 cerebral cortex 21 none Source GEO sample is GSM239911 Last updated (according to GEO): Dec 07 2007 1000 Colon no additional Source GEO sample is GSM199268 Last updated (according to GEO): Jun 08 2007 Primary tumor 19 32 05_0010_SepticShock_Day3_94 Expression profiling of spinal cord section (T9) extracted from rats 12h following moderate injury Source GEO sample is GSM31521 Last updated (according to GEO): May 27 2005 Starvation 916 lymph_nodes_2 1718 Cerebral cortex 1732 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114231 Last updated (according to GEO): Jun 16 2006 hrs nasal epithelium 1126 1146 44 21 during placental malaria The effect of human cytomegalovirus infection on cellular mRNA accumulation was analyzed by gene chip technology over a 48h time course. Date GSE675 Last Updated: May 29 2005 Contributers: Thomas Shenk Edward P Browne Bret Wing David Coleman Includes GDS476. Update date: Nov 25 2003. Dataset description GDS476: Expression profiles of foreskin fibroblasts at 12 time points beginning 30 minutes after infection by human cytomegalovirus (HCMV) and continuing until 48 hours after infection.. 1000 Cerebral cortex Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181225 Last updated (according to GEO): Jul 12 2007 of coronary artery disease 258 284 of the postmortem brains 654 678 Skeletal bone 861 with Parkinson's disease 27 50 80 68 Control blood WGACON-30 D2_Control_ZT 12_3 Primary tumor 19 32 I_U133A_35_CB Pressure-overload induced hypertrophy model. Mouse was sacrificed 48 hours after aortic banding. Keywords = Cardiac hypertrophy Source GEO sample is GSM2241 Last updated (according to GEO): May 27 2005 PGA-MurLungRag-pbs-24h-1bC-s2 NCI-H23 hgu95b I_U133A_96_AnCg Neoplasm 861 olfactory epithelium 194 213 43 0 Chorionic mesoderm-derived mesenchymal cells 1000 frontal lobe 5 0 brain brain, forebrain: Total RNA_le1 430A2_1945_65_control_sham_medulla Source GEO sample is GSM242692 Last updated (according to GEO): Nov 15 2007 rad001 6d, biological rep1 SF-295 hgu95b the ventricular 1095 1109 Parkinson's disease sample x188 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16952.gif Source GEO sample is GSM91569 Last updated (according to GEO): Sep 22 2006 85 year old male Mouse model of congenital heart disease in Csx/Nkx2.5 mutant embryos. Homozygous mutant mouse at embyronic day 9.5. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2272 Last updated (according to GEO): May 27 2005 5 0 brain 1000 Hippocampus 901 Coronary artery 1000 Axon to the nose 599 609 168T M_U133Plus_113_nAcc Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160724 Last updated (according to GEO): Sep 24 2007 901 Coronary artery 861 Retina Adenovirus Infections 1000 H120 CB B 901 Caudate nucleus structure Whole Brain Source GEO sample is GSM18921 Last updated (according to GEO): Sep 25 2006 The nose 94 101 Gene expression data from postmorten brain regions Source GEO sample is GSM145006 Last updated (according to GEO): Nov 20 2006 LymphNodeImm_022ZAFAW_094.txt Gene expression data from rat metanephric mesenchymes cultured for 1 day in the presence of NGAL Source GEO sample is GSM126206 Last updated (according to GEO): Dec 08 2006 27 year old female welsh-ovarian 861 Esophagus Mouse Liver Female 1 (technical replicate) Untreated, biological rep3 Synovial Membrane 3 Normal T1 gr3 tumour Source GEO sample is GSM2519 Last updated (according to GEO): May 27 2005 (No additional Information) Source GEO sample is GSM114394 Last updated (according to GEO): Jun 19 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145398 Last updated (according to GEO): Nov 20 2006 Nrl ko samples were compared to wt at postnatal 10. Source GEO sample is GSM227458 Last updated (according to GEO): Sep 07 2007 0029_1241_H95A2_KF0142_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A hypothalamus Source GEO sample is GSM18590 Last updated (according to GEO): May 27 2005 Category: Lymphoma Classification Subcategory: Hematopoetic cell lines Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n075 Source GEO sample is GSM2020 Last updated (according to GEO): Nov 21 2005 1000 frontal lobe 901 frontal lobe 32 10 from cultured modiolus Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198649 Last updated (according to GEO): Jun 06 2007 SW872 SCN2.2 Sample 1 (Exp#1-0 hr b) of parieto-occipital cortex 222 249 Microarray Analysis of the Developing Murine Prefrontal Cortex of neuroblastoma 2657 2673 CHIPEXP_NAME: 230_2_050531tpj_53h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Isoproterenol TREAT_TOX_MECHANISM1: Heart_Cardiotoxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0.5 SAMPLING_TIME: 24 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197622 Last updated (according to GEO): Jun 01 2007 Brain 1000 144 114 from a single adult spinal cord Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7550.gif Source GEO sample is GSM79946 Last updated (according to GEO): Sep 22 2006 CNS-SC_InjA4h-2B-s2 Expression profiling of the developing and mature Nrl -/- mouse retina (Yoshida et al. 2004, HMG) Prostate 861 1000 Spleen MDA-MB-435 hgu95c 24 0 human prostate PC3 tumors AT3-hTERT_1.5Gy_24h_C3_27020 861 Cerebellum 48 M arm fibroblast LS25, asynchronous GBM Treatment, type=remove Source GEO sample is GSM99470 Last updated (according to GEO): Apr 21 2006 MGJZ030207054Aheart infection 433 442 Brain 861 meningioma 1000 The epithelial cells 962 981 NCI60.59_LABEL123EXTRACT61SUB3 Source GEO sample is GSM134290 Last updated (according to GEO): Aug 06 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145408 Last updated (according to GEO): Nov 20 2006 Affymetrix protocol Source GEO sample is GSM213820 Last updated (according to GEO): Aug 02 2007 Mesenchymal Stem Cells 1000 22 0 cerebellum sprague 3900 ileum 0 4 MuscleRegen-ctx11d-2LLAv2-s2 NCI60.58_LABEL62EXTRACT61SUB3 Source GEO sample is GSM134285 Last updated (according to GEO): Aug 06 2007 Osteoblasts 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145346 Last updated (according to GEO): Nov 20 2006 Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68043.gif Source GEO sample is GSM137407 Last updated (according to GEO): Sep 26 2006 Heart Ventricle 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withSLC (Secondary lymphoid-organ chemokine) for 240min Source GEO sample is GSM5776 Last updated (according to GEO): May 27 2005 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11557 Last updated (according to GEO): May 28 2005 DLCL-0051 || lc4b057 ci_NY8 820 DNA damage 811 Cerebral cortex 1000 seminoma specimen, pT1, patient age: 31y; W98 100 kidney 176 182 CD3 + CD28 beads + FK506 02.00 hr. T-cell Subject code A5 days nasal epithelium 1126 1147 into the heart 1259 1272 861 Cancer of Neck Expression data from Cerebral Cortex or Hippocampus of COX-1 or COX-2 null mice Post Natally excised Control 7 mouse brain ipsilateral RU486 Source GEO sample is GSM149778 Last updated (according to GEO): Mar 15 2007 cerebral cortex 7 21 913 Coronary heart disease Pressure-overload induced hypertrophy model. Mouse was sacrificed 8 weeks after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2264 Last updated (according to GEO): May 27 2005 brain, frontal cortex: Sham PM S b_e1_le1 1000 Pancreas RENAL_SN12C on Affymetrix GeneChip Human Full Length Array HuGeneFL Macrophage smi52 1000 Encephalitis Brain 861 "26 hr Hela Double Thymidine, exp3" 331 307 in central nervous system R588P01069 958 Autonomic nerve structure Expression profiling of somatomotor cortex extracted from rats at 3 months following moderate injury Source GEO sample is GSM41732 Last updated (according to GEO): May 27 2005 olfactory epithelium 194 213 GBM Treatment, type=remove Source GEO sample is GSM99526 Last updated (according to GEO): Apr 21 2006 Control total RNA was pooled from the kidney of five normal BALB/c mice. Total RNA was extracted from the kidney of BALB/c mice injected with anti-GBM antibody for 16 day. Source GEO sample is GSM15082 Last updated (according to GEO): May 28 2005 from mouse colon 21 36 O377 homozygotes versus wt Performed by UCI Microarray Facility. Source GEO sample is GSM203505 Last updated (according to GEO): Jun 22 2007 Spleen 0 5 M_U133A_5_nAcc Placenta [JunctionChip 5 of 5] Retina 1000 Female 68.4 yr before antibody enrichment scan 1 (U133A) This is replicate 2 of the 3 hour sample from passive avoidance trained rats. Source GEO sample is GSM18234 Last updated (according to GEO): Aug 22 2007 SVG-A subclone 4-G5 GeneChip U133B 861 Mammary gland Whole blood 0 10 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. 72h after sham surgery, a 7 mm disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44483 Last updated (according to GEO): May 27 2005 P1_KIDNEY_2 114T 1037 of transitional epithelium 1012 1000 Brain Plasma 861 PC 6Hr rat 3586 blood vs. 2500mg/kg APAP 6Hr rat 3597 blood Phenytoin brainstem 5 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53416 Last updated (according to GEO): Jul 06 2005 Cerebral cortex 1000 MCF7 treated with E2 for 24h Source GEO sample is GSM213326 Last updated (according to GEO): Jul 26 2007 Mammary Gland @ Invo2, biological rep1 Parkinson Disease 861 Colon 861 297 285 by the liver CNS-SpinalC-conAdult-30m-1B-s2 Nasal Epithelium 865 no additional Source GEO sample is GSM199204 Last updated (according to GEO): Jun 08 2007 testis 52 58 129:24-6 cortex Blood 1000 MSE_D_97A Flow cytometry sorted double negative thymocytes from wild type animal #2. Treatment, type=fractionate Source GEO sample is GSM130402 Last updated (according to GEO): Aug 24 2006 Kidney_6wk_FVB_Female Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hour time point Source GEO sample is GSM159739 Last updated (according to GEO): Apr 23 2007 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162164 Last updated (according to GEO): Jun 12 2007 VDXRHU_5226 Epithelium 861 Communicable Diseases 1000 861 Mammary gland Voxel F4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1427 Last updated (according to GEO): Nov 21 2005 865 Disorder of artery Stria 861 1000 Brain Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174506 Last updated (according to GEO): Mar 14 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145316 Last updated (according to GEO): Nov 20 2006 1 hr Hela Double Thymidine, exp2 Expression profiling of spinal cord section (T9) extracted from rats 4h following severe injury Lot batch = Source GEO sample is GSM7579 Last updated (according to GEO): May 28 2005 liver, wild type mice, treatment with WY14643 for 5d Source GEO sample is GSM205785 Last updated (according to GEO): Jul 24 2007 Osteoblasts 1000 myocardial infarction 383 403 Leukemia, Lymphocytic, Chronic 1000 Sample represents the supraoptic nucleus from 5 dehydrated animals (3 Days) Source GEO sample is GSM69457 Last updated (according to GEO): Dec 15 2005 Whole Brain 73 83 861 Blood Simple annotation: Chronic Lymphocytic Leukemia, ARA-G in vivo chemotherapy Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2765.gif Source GEO sample is GSM72210 Last updated (according to GEO): Sep 22 2006 Whole ganglioneuroblastoma intermixed tumor_1134 Lung tissue from C57BL/6 mice that were always fed by 2/3 and sacrificed. Lot batch = Source GEO sample is GSM4034 Last updated (according to GEO): May 28 2005 Lymphoblastoid Cell Line for Individual 8162.4 log phase Basal 861 GM18522_technical_rep_1 Small cell carcinoma of lung 888 granulosa cell tumor 923 901 Mammary gland Gene expression data from a placenta without malaria Source GEO sample is GSM183606 Last updated (according to GEO): Apr 23 2007 32 10 from cultured modiolus from mouse brain 20 35 in the brain 150 162 44 minus the frontal cortex 68 PMN_control_360min_Patient18 the blood 393 402 PGA-E13.5_1 Mammary Gland 10 Normal LPS, 30 min, Rep_2 human frontal cortex Source GEO sample is GSM87018 Last updated (according to GEO): Feb 08 2006 901 Myeloid Leukemia Rats 240h after injection with dose kainate. Treatment, type=time_course, description=KA animals are treated with kainate., measurement=240.0 h Source GEO sample is GSM32094 Last updated (according to GEO): May 27 2005 Ovary 1 Normal 2 with some respiratory epithelium. 1039 1072 mouse hippocampus, cox-2 WT, rep1 Ovarian_Tumor_Serous_CU-OS-04 GSE479 901 frontal lobe 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113948 Last updated (according to GEO): Jun 16 2006 Pancreas at e13.5, Chip A, rep 1 Mammary Gland @ Lac2, biological rep2 Gene expression data from postmorten brain regions Source GEO sample is GSM145303 Last updated (according to GEO): Nov 20 2006 865 Disorder of artery Primary Neoplasm 983 1000 frontal lobe 367 in Turner syndrome 384 12 frontal Lobe 23 CerebellumPeduncles Source GEO sample is GSM18915 Last updated (according to GEO): Sep 25 2006 Melanoma xenograft, MEC2_Lung_B (LeiFidler) high dose 6h, replicate 2 Neuroblastoma 861 Pool of total RNA from 3 euploid cerebella at P15 postnatal stage Keywords = Down syndrome Keywords = Chromosome 21 Keywords = Transcriptome Keywords = Microarray Keywords = Brain Keywords = Cerebellum Keywords = Development Source GEO sample is GSM27474 Last updated (according to GEO): May 27 2005 D_U133A_74_DLPFC Transplant Series 25 Left, Transplant # 1 no doxycycline, no AAT Source GEO sample is GSM213375 Last updated (according to GEO): Jul 26 2007 brain, cerebral cortex: Rat_03-30_NroLep_Lipska_e1_le1 A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism Source GEO sample is GSM5993 Last updated (according to GEO): Nov 21 2005 335 325 The jejunum Schizophrenia 1000 Endometrium 0 10 Inflammatory myopathy specimen GEIM20 Lymphoblastoid Cell Line for Individual 8017.4 log phase 346 338 in brains PAX sample 2 M_U133A_88_AnCg mouse cerebral cortex from COX-2 heterozygous Source GEO sample is GSM121433 Last updated (according to GEO): Jan 31 2007 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195276 Last updated (according to GEO): Sep 13 2007 to the nose 599 609 BC115A-AF none Source GEO sample is GSM246000 Last updated (according to GEO): Dec 03 2007 406 395 whose hearts Gene expression data from postmorten brain regions Source GEO sample is GSM145090 Last updated (according to GEO): Nov 20 2006 pooled RNA of the kidney of 36 day old rats Source GEO sample is GSM86660 Last updated (according to GEO): Jun 12 2006 neurological disease control sample x172 1000 Carcinoma, Embryonal 43h-Control replication 1 Keywords = preimplantation Keywords = development Source GEO sample is GSM14701 Last updated (according to GEO): May 28 2005 c_M101 Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 2330 left_liver_lobe n/a Source GEO sample is GSM177927 Last updated (according to GEO): Jun 11 2007 D_U133Plus_110_DLPFC 1354 1317 of the peripheral innate immune system A YOKE D025 Brain_PNET_4_PNET on Affymetrix GeneChip Human Full Length Array HuGeneFL Parkinson Disease 861 V5-P495 Starvation 916 1000 Heart failure To determine if there exists a consistent gene signature associated with vascular hypertrophy among different rat hypertensive models: treated and untreated Wistar Kyoto (WKY) rats and treated and untreated Spontaneous Hypertensive Rat (SHR) rats. Last Updated (by provider): Apr 10 2007 Contributers: Denis deBlois Evelyne Marchand Lynn M Amon Xi Wang Hangjun Duan David Pritchard Stephen M Schwartz Larry Adams Cultured_cortical_astrocyte_Cx43_siRNA_rep3 901 Coronary artery CVB3_VU-9h-4 Amyotrophic Lateral Sclerosis 923 Gene expression data from postmorten brain regions Source GEO sample is GSM145447 Last updated (according to GEO): Nov 20 2006 Hippocampus Treatment, type=pharmacogenomic_treatment, description=Chronic Immobilization Stress Source GEO sample is GSM53304 Last updated (according to GEO): Jul 06 2005 Normal__Kidney_KT_4 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 0 Many neurodegenerative disorders 31 Cerebral cortex 861 9 hr Hela Double Thymidine, exp2 1000 Learning Disorders Fbx15 is specifically espressed in ES cells, but Fbx15-null ES cells do not show obvious phenotypes. Source GEO sample is GSM190223 Last updated (according to GEO): May 18 2007 brain, cerebral cortex: PC9_e1_le1 2N-1-MGU74A of the stria terminalis 49 71 1000 Spleen n/a Source GEO sample is GSM177963 Last updated (according to GEO): Jun 11 2007 cerebellum Source GEO sample is GSM18917 Last updated (according to GEO): Sep 25 2006 plasma cells 332 344 1000 Spinal Cord 1000 Mammary gland brain_OFC_control C_mr170 1000 frontal lobe 17 0 McLean Hippocampus whole blood_101584 of the atrial 647 659 of the same brain 1054 1071 Lymphoblastoid Cell Line for Individual 8012.4 log phase V5-P053 1000 Retina Cerebral cortex 861 901 Hepatocyte 1000 jejunum brain_control_sampleid_mr523 Altered gene expression in the sphingosine 1-phosphate receptor 2 (S1P2)-deficient or sphingosine 1-phosphate receptor 3 (S1P3)-deficient brain. Last Updated (by provider): Mar 08 2007 Contributers: Noriyuki Akahoshi Isao Ishii Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:552, Count:32 Corner- Avg:39747, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:6.128169,SFGene:All Background:Avg:544.60,Stdev:3.21,Max:553.7,Min:534.1 Noise:Avg:11.73,Stdev:0.39,Max:12.7,Min:10.2 RawQ:15.46 Keywords = ALL Source GEO sample is GSM3420 Last updated (according to GEO): May 28 2005 C57_LF_3 EOM 14 Day Control rep 2 Bone structure of tibia 1000 Liver (HBV+, SF17) Myocardial Infarction 1000 brain, Posterior Singulate: Sample46_e1_le1 1000 Chromatin Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9923.gif Source GEO sample is GSM79888 Last updated (according to GEO): Sep 22 2006 Pressure-overload induced hypertrophy model. Mouse was sacrificed 48 hours after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2257 Last updated (according to GEO): May 27 2005 913 Coronary heart disease Amygdala Treatment, type=pharmacogenomic_treatment, description=Handled (no stress) control Source GEO sample is GSM53305 Last updated (according to GEO): Jul 06 2005 NCI-H23 hgu95e Parkinson Disease 861 1000 Coronary Arteriosclerosis HapMap JPT Female Source GEO sample is GSM159634 Last updated (according to GEO): Feb 01 2007 Head and neck cancer Source GEO sample is GSM155708 Last updated (according to GEO): Apr 24 2007 Viral infection 435 449 thalamus_10 CNS-SCsev_InjB7d-4B-s2 Comparison of RNA levels in the neocortex of normal mice versus synaptically silent munc18-1 null mutants. Source GEO sample is GSM84369 Last updated (according to GEO): Aug 01 2006 P21 cochlear nuclei pooled from 5 pups for one replicate hybridization out of 3 replicates. Source GEO sample is GSM44856 Last updated (according to GEO): Jun 08 2005 C6slow1 SN12C_CL9008_Renal on Affymetrix GeneChip Human Full Length Array HuGeneFL 3ARS0207263HB_PLACENTA NG008_c -_test-1_batch5 on NHGRI-6.7k Brain 1000 Papillary thyroid carcinoma (PTC) is clinically heterogeneous. Apart from an association with ionizing radiation, the etiology and molecular biology of PTC is poorly understood. We used oligo-based DNA arrays to study the expression profiles of eight matched pairs of normal thyroid and PTC tissues. Additional PTC tumors and other tissues were studied by reverse transcriptase-PCR and immunohistochemistry. The PTCs showed concordant expression of many genes and distinct clustered profiles. Genes with increased expression in PTC included many encoding adhesion and extracellular matrix proteins. Expression was increased in 8/8 tumors for 24 genes and in 7/8 tumors for 22 genes. Among these genes were several previously known to be overexpressed in PTC, such as MET, LGALS3, KRT19, DPP4, MDK, TIMP1, and FN1. The numerous additional genes include CITED1, CHI3L1, ODZ1, N33, SFTPB, and SCEL. Reverse transcriptase-PCR showed high expression of CITED1, CHI3L1, ODZ1, and SCEL in 6/6 additional PTCs. Immunohistochemical analysis detected CITED1 and SFTPB in 49/52 and 39/52 PTCs, respectively, but not in follicular thyroid carcinoma and normal thyroid tissue. Genes underexpressed in PTC included tumor suppressors, thyroid function-related proteins, and fatty acid binding proteins. Expression was decreased in 7/8 tumors for eight genes and decreased in 6/8 tumors for 19 genes. We conclude that, despite its clinical heterogeneity, PTC is characterized by consistent and specific molecular changes. These findings reveal clues to the molecular pathways involved in PTC and may provide biomarkers for clinical use. Gene expression data from liver Source GEO sample is GSM243386 Last updated (according to GEO): Nov 16 2007 412_2 C123 on NCI-7.6k CNS-SpinalCsev-Adult-24h-2A-s2 Synovial Membrane 1 Normal RNA of Kidney was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 biological replicates were analyzed. Keywords = db/m mice Keywords = kidney Source GEO sample is GSM9925 Last updated (according to GEO): May 27 2005 Ovarian_Tumor_ClearCell_CHTN-OC-004 663 mesenchymal stem cell 642 901 Coronary artery 69 55 /- mouse retina 89 72 Normal hippocampus of the postmortem brains 655 679 Donor 2 Time point 72 hours Autologous control (uninfected) Source GEO sample is GSM2615 Last updated (according to GEO): May 27 2005 brain, Left frontal Lobe: Extract18_le2 Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16255.gif Source GEO sample is GSM91521 Last updated (according to GEO): Sep 22 2006 prefrontal cortex sprague1 whole tissue, pool of 5 animals, 20 weeks old, male Sprague Dawley prefrontal cortex file:R3MH02052401 Source GEO sample is GSM15229 Last updated (according to GEO): May 28 2005 Total RNA from cultured organ of Corti, pool from 12 cochleas. Source GEO sample is GSM124843 Last updated (according to GEO): Aug 04 2006 Gene expression data from liver Source GEO sample is GSM243398 Last updated (according to GEO): Nov 16 2007 Viral infection 434 448 cardiac 763 769 1000 Neoplasm Metastasis Adenovirus Infections 1000 1037 of transitional epithelium 1012 1000 Atherosclerosis in brain 2053 2060 861 Cardiomyopathies liver_wildtype_control_5d_rep2 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11335 Last updated (according to GEO): May 28 2005 liver 165 170 M_U133A_12_HC Cerebral cortex 861 8182 Fvbn control T-ALL-#3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 091231 OVR24 on Affymetrix GeneChip Human Full Length Array HuGeneFL CNS-RM_Mod7d-4C-s2 passive avoidance trained rats 4-6 Dentate Gyrus 7 23 1232 1219 in the spleens OVCAR-3 hgu95c Parkinson's disease sample x193 0 30 Gene expression data from rat metanephric mesenchymes cultured for 3 days in the presence of NGAL Source GEO sample is GSM126210 Last updated (according to GEO): Dec 08 2006 96 13 from fetal cerebrum Keywords = trisomy 13 Keywords = brain Keywords = Patau syndrome Liver 1000 This is replicate 1 of the 6 hour sample from passive avoidance trained rats. Source GEO sample is GSM17401 Last updated (according to GEO): Aug 22 2007 Expression profiling of spinal cord section (T8) extracted from rats 7d following laminectomy (sham) Lot batch = Source GEO sample is GSM6628 Last updated (according to GEO): May 28 2005 days nasal epithelium 1126 1147 GBM Treatment, type=remove Source GEO sample is GSM99536 Last updated (according to GEO): Apr 21 2006 Interatrial septum 865 Collagen 1000 S9_2, mouse, SW, control (non-infected), 9 day time matched control_rep 2 kidney Source GEO sample is GSM18689 Last updated (according to GEO): May 27 2005 Healthy patient. Source GEO sample is GSM228572 Last updated (according to GEO): Sep 11 2007 B226 immature DCs treated with isotype control antibody COID-COID5t1-A342-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Heart failure s1 24 0 human prostate PC3 tumors 257 245 odontoblasts brain, Right Frontal Lobe: Extract54_le2 1000 Hippocampus 1000 Malignant Neoplasms Aim: To gain insight into the pathways by which GABABR activation may influence long-term changes in synaptic plasticity and neuronal growth and morphology we investigated changes in gene expression in cultured hippocampal neurones evoked by the GABABR agonist baclofen. We used cDNA microarray gene expression profiling to identify candidate genes that are differentially expressed in the hippocampal neurones following GABABR activation. Experimental design: The cDNA microarray used in the present study is the NIA Neuroarray containing 1152 genes relevant to neurobiology. NIA Neuroarray probes were hybridised in triplicate with targets derived from control and baclofen-treated neurones. Conclusion: Our novel data on down-stream, late phase consequences of GABABR signalling provide a basis for future studies to investigate these changes in gene expression at the protein, cell biology and functional levels. Furthermore, the changes in gene expression identified will shed light on the multiple roles of GABABRs. Last Updated (by provider): May 29 2005 Contributers: Kevin G Becker Jeremy M Henley Mohamed T Ghorbel Lymphoma Burkitt 50 65 Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160713 Last updated (according to GEO): Sep 24 2007 Lymphoblastoid Cell Line for Individual 8182.4 log phase Macrophage 14smi070 Brain 861 nasal epithelial cells 28 49 861 Alzheimer's Disease 5 0 Muscle Timed pregnant C57Bl6 mice were exposed to ethanol during gestational day 15 to day 18 and ethanol exposed fetuses were delivered by cessarian section on gestational day 19. Alcohol exposed fetuses were compared to control timed preg Source GEO sample is GSM116857 Last updated (according to GEO): Jul 03 2006 9 of prefrontal cortex 28 13 0 Nervous System GM06991 FC 55h Primary Neoplasm 1000 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181046 Last updated (according to GEO): Jul 12 2007 brain, forebrain: WCx4w#1_e1_le1 Study the transcriptomic effects of the shear stress on cultured osteoblast-like MC3T3 cells Source GEO sample is GSM201203 Last updated (according to GEO): Jun 19 2007 HCC (HBV+, HK63, T2) in the striatum 1046 1060 Immune system 901 human frontal cortex Source GEO sample is GSM86929 Last updated (according to GEO): Feb 08 2006 Euploid sample 3 (cerebrum_TS13) 1000 Brain Stem Fat Pair-Fed Repl2 Blood 1000 156 120 of the substantia nigra pars compacta 21 adrenal medulla 7 Normal Source GEO sample is GSM175949 Last updated (according to GEO): Apr 09 2007 Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 3046 blood M7TW01013106 67 40 with coronary artery disease Epithelial Cells 901 Blood B cells;anti-IgM+CD40L+IL-4 6h Nose 1000 861 Eminence high gestational age Source GEO sample is GSM213110 Last updated (according to GEO): Jul 25 2007 PGA-MurLungRag-pbs-24h-1aC-s2 placebo 15d, biological rep2 nerve 0 5 brain, Left frontal Lobe: Extract25_le2 brain, hippocampus: Sample22_e1_le1 c_NY102 AT3-hTERT_sham_6h_C5_27043 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc115 Source GEO sample is GSM1892 Last updated (according to GEO): Nov 21 2005 Cerebellum 1000 Alzheimer's Disease 861 HCC (HBV+, HK4) frontal_lobe_3 Source GEO sample is GSM80661 Last updated (according to GEO): Mar 31 2006 Bone Marrow 1000 from liver 21 30 1000 Left Leukemia, Lymphocytic, Chronic 1000 861 Brain Brain 1000 brain, Left frontal Lobe: Extract16_le2 Pancreas at e15.5, Chip C, rep 2 Skeletal bone 861 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188744 Last updated (according to GEO): Jun 06 2007 with autism spectrum disorder 37 65 To identify genes dysregulated in bipolar disorder (BD1), we carried out global gene expression profiling using whole-genome microarrays. To minimize genetic variation in gene expression levels between cases and controls, we compared expression profiles in lymphoblastoid cell lines from monozygotic twin pairs discordant for the disease. We identified 82 genes that were differentially expressed by >/=1.3-fold in three BD1 cases compared to their co-twins, and which were statistically (P</=0.05) differentially expressed between the groups of BD1 cases and controls. Using quantitative reverse transcriptase-polymerase chain reaction, we confirmed the differential expression of some of these genes, including: KCNK1, MAL, PFN2, TCF7, PGK1 and PI4KCB, in at least two of the twin pairs. In contrast to the findings of a previous study by Kakiuchi and colleagues with similar discordant BD1 twin design, our data do not support the dysregulation of XBP1 and HSPA5. From pathway and gene ontology analysis, we identified upregulation of the WNT signalling pathway and the biological process of apoptosis. The differentially regulated genes and pathways identified in this study may provide insights into the biology of BD1.Molecular Psychiatry (2007) 12, 815-825; doi:10.1038/sj.mp.4001998; published online 17 April 2007. SN:Human Glioblastoma Biopsy 07086 Primary carcinoma of the liver cells 1000 Bone Marrow 1000 BACKGROUND: Previous genomic studies with human tissues have compared differential gene expression between 2 conditions (ie, normal versus diseased) to identify altered gene expression in a binary manner; however, a potentially more informative approach is to correlate the levels of gene expression with quantitative physiological parameters. METHODS AND RESULTS: In this study, we have used this approach to examine genes whose expression correlates with arterial stiffness in human aortic specimens. Our data identify 2 distinct groups of genes, those associated with cell signaling and those associated with the mechanical regulation of vascular structure (cytoskeletal-cell membrane-extracellular matrix). Although previous studies have concentrated on the contribution of the latter group toward arterial stiffness, our data suggest that changes in expression of signaling molecules play an equally important role. Alterations in the profiles of signaling molecules could be involved in the regulation of cell cytoskeletal organization, cell-matrix interactions, or the contractile state of the cell. CONCLUSIONS: Although the influence of smooth muscle contraction/relaxation on arterial stiffness could be controversial, our provocative data would suggest that further studies on this subject are indicated.. Date GSE420 Last Updated: May 29 2005 Contributers: Richard Pratt Stephane Laurent Includes GDS461. Update date: Nov 20 2003. Dataset description GDS461: Examination of molecular basis of aortic stiffness which predicts pulse pressure, coronary disease, stroke and cardiovascular mortality. Biopsies from patients with increased aortic stiffness compared with patients with distensible aorta.. 913 frontal lobe eTat - Hu0hr - 1 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225737 Last updated (according to GEO): Nov 02 2007 f2#48 versus pool Mouse Brain tissue Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141314 Last updated (according to GEO): Oct 26 2006 861 Cerebral cortex Myocardium 861 SR-A mutant olfactory epithelium 0 h replicate1 Spinal Cord 1000 15 0 human cerebellum 1000 Uterus 3x24 hr EE repl 2 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225950 Last updated (according to GEO): Nov 02 2007 spinal cord 0 11 Wild type inbred mice Source GEO sample is GSM82960 Last updated (according to GEO): Nov 10 2005 Bicalutamide_1 Spleen vs IL10 Treated B cell 240min (set3) hippocampal glutamatergic CA1 pyramidal neurons Source GEO sample is GSM35809 Last updated (according to GEO): May 27 2005 olfactory epithelium SR-A mutant mouse 2 hpO Source GEO sample is GSM80203 Last updated (according to GEO): Oct 26 2005 266 257 infection HTI-286 in docetaxel-refractory prostate cancer Source GEO sample is GSM206359 Last updated (according to GEO): Jun 29 2007 Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3880 Last updated (according to GEO): May 27 2005 LNCaP B on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Fibroblasts 861 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92381 Last updated (according to GEO): Jan 13 2006 65 24 from umbilical subcutaneous adipose tissue Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11552 Last updated (according to GEO): May 28 2005 02_0001_SepticShock_Day1_108 Islets0228AC33_060.txt 913 Coronary heart disease Cockayne syndrome B wt-rescued cell Source GEO sample is GSM226628 Last updated (according to GEO): Sep 04 2007 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P18, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3234 Last updated (according to GEO): May 28 2005 1000 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145421 Last updated (according to GEO): Nov 20 2006 CNS-RM_Ctr4h-2A-s2 "Sample 91, BRCA1 mutation(3 months) age 45 erp no" on vantveer-oligo PC8 Treatment, type=incubate, description=Hypoxic preconditioning Source GEO sample is GSM107482 Last updated (according to GEO): May 01 2006 M_U133A_112_nAcc putamen_9 Source GEO sample is GSM80595 Last updated (according to GEO): Mar 31 2006 Human prostate cancer cells in different conditions Source GEO sample is GSM13083 Last updated (according to GEO): May 28 2005 Nervous system structure 901 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141329 Last updated (according to GEO): Oct 26 2006 M7TW00121820 E10.5 craniofacial tissue, first branchial arch: 5_6_MNA-1_e1_le1 prefrontal cortex sprague1 5 0 brain Whole Brain 62 72 102 91 in the liver Type 2 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228678 Last updated (according to GEO): Sep 11 2007 1000 Hippocampus Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9984.gif Source GEO sample is GSM79864 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM144988 Last updated (according to GEO): Nov 20 2006 Biopsy of the normal mucosa of the colon from patient #20 5 0 brain 4535 4527 hepatoma 861 Medulla Oblongata DLCL-0009 || lc4b027 Cockayne syndrome B cell Source GEO sample is GSM226287 Last updated (according to GEO): Sep 04 2007 CNS-SpinalC-conAdult-14d-1A-s2 mouse brains 187 198 HMEC X NB1 Skin 10 Normal Lymphoblastoid Cell Line for Individual 8193.6 log phase 522 504 of prostate cancer brain 0 5 cerebral cortex sprague 3918 228 219 Hippocampi olfactory epithelium 194 213 Testis 1000 Epithelium of bronchus 983 Parkinson Disease 861 Brain 861 NA12739 growth 3 in the brain 150 162 Testis 861 Oat cell carcinoma 867 Mesenchymal Stem Cells 1000 Stomach Fundus 3 Normal Epithelial Cells 901 high gestational age Source GEO sample is GSM213101 Last updated (according to GEO): Jul 25 2007 Parkinson Disease 1000 20 0 human caudate nucleus Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211421 Last updated (according to GEO): Jul 18 2007 1000 Kidney medial motoneurons (MMN) 3 78 66 Control blood P1_KIDNEY_7 3AJZ02021911_ PROSTATE Sporadic_s1320 on NHGRI-6.5k Gene expression data from colorectal adenoma. Source GEO sample is GSM215111 Last updated (according to GEO): Aug 02 2007 Heart Ventricle 1000 pfc_1042_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 861 Blood Kidney BD Normal 1000 Spinal Cord to drug addiction 1478 1495 Average value of duplicate experiments of gut neurospheres (neurospheres of peripheral nervous system) of BMI-1 knockout mice (postnatal day 0). The cRNAs for hybridization were generated by two round RNA amplifications. Source GEO sample is GSM9251 Last updated (according to GEO): May 27 2005 D_U133A_80_HC Normal Source GEO sample is GSM175853 Last updated (according to GEO): Apr 09 2007 1000 Coronary Arteriosclerosis DRG_control_24h_rep2 B60 on NCI-7.6k Mesenchymal Stem Cells 1000 Olfactory Epithelium 1000 Cerebral cortex 966 Bladder sample 928-1 Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 7558 blood f2#40 versus pool Mouse Brain tissue Dahl Salt Sensitive Rat Lung- Hypoxia alone rep2 cerebral_cortex_9 Spleen 0 5 NA Source GEO sample is GSM198907 Last updated (according to GEO): Jun 07 2007 Ischemia-reperfusion #3 Hippocampus VC mice 2 week off dox 2 Prosencephalon 1000 Tumor__Pancreas_Adeno_Pan_2T on Affymetrix GeneChip Human 35K SubA Array Hu35k-A liver_2 Heart Atrium 1000 1000 Brain 440_1 The genomic consequences of bursts of action potential firing induced by the treatment of cultured cortical neurons (9-11 DIV) with the GABAA receptor antagonist bicuculline (Bic, 50 ?M) and the potassium channel blocker 4-aminopyridine (4AP, 5 ?M). Source GEO sample is GSM144048 Last updated (according to GEO): Nov 24 2006 1000 leukemia Spleen vs Leukotriene B4 (LTB4)Treated B cell 60min (set1) Neonatal (P0) whole brain mRNA from 40,XX females In(X)/C3H x C57BL/6J Source GEO sample is GSM27455 Last updated (according to GEO): May 27 2005 786-0_CL9018_Renal on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Liver 32h-Control replication 1 Keywords = preimplantation Keywords = development Source GEO sample is GSM14698 Last updated (according to GEO): May 28 2005 f2#288 versus pool Mouse Brain tissue 1000 Neuraxis Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226147 Last updated (according to GEO): Nov 02 2007 NA18502 The study was designed in order to identify genes differentially expressed when glucocorticoid signaling is blocked by a glucocorticoid-receptor antagonist (RU486 ? mifepristone) in the context of brain inflammation induced by bacterial lipopolysaccharide (LPS). LPS is only able to cause murine brain damage in our experimental conditions upon RU486 pre-treatment. Hence, the study may reveal potential candidate genes to mediate neuroprotection or neurotoxicity. Due to the factorial design of the experiment, RU486 main-effect could be dissociated from the effects resultant of RU486/inflammation interaction. In addition, brain dissection was conducted to verify the effects in the brain side ipsilateral or contralateral to the site of intracerebral LPS infusion. Last Updated (by provider): Mar 15 2007 Contributers: Serge Rivest Ariel Chernomoretz Isaias Glezer Epithelium 861 861 Blood of the stria terminalis rep2 19 46 Wild type inbred mice Source GEO sample is GSM83030 Last updated (according to GEO): Nov 10 2005 HOXB4ERT_w/o TMX, 1hour, biological rep1 D_U133A_15_DLPFC 1037 of transitional epithelium 1012 during measles 743 757 - Source GEO sample is GSM216545 Last updated (according to GEO): Aug 09 2007 861 Cerebral cortex osteoblast 627 637 PGA-MurLungRag-rwp-72h-1bCv2-s2 Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM107990 Last updated (according to GEO): Jun 06 2006 COID-COID7t1-A344-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A pharyngeal_mucosa_1 plasma cells 50 61 of the colon 28 39 Brain 1000 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15270.gif Source GEO sample is GSM91513 Last updated (according to GEO): Sep 22 2006 MuscleRegen-ctx2d-5RLA-s2 FVB/NJ cingulate cortex rep2 wild-type mouse 1 Spleen 1000 Backskin_WT_P14_rep3 Gene expression from Dendritic cells from human subject with resolver phenotype uninfected. Source GEO sample is GSM128968 Last updated (according to GEO): Sep 13 2007 GRP sample 7 Parkinson Disease 861 Primary Neoplasm 1000 38 21 from a hippocampus Nervous system structure 901 3 min exposure to halothane, immediate perfusion with ice cold saline Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5106 Last updated (according to GEO): Mar 17 2006 5 0 brain CNS-SpinalCsev-Adult-24h-2C-s2 comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247390 Last updated (according to GEO): Dec 11 2007 Heart failure 1000 Spinal Cord 1000 1000 Spleen of parieto-occipital cortex 226 253 Serotonin 1000 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211325 Last updated (according to GEO): Jul 18 2007 Liver samples PPARa-null mice, control conditions Source GEO sample is GSM205751 Last updated (according to GEO): Jul 24 2007 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211354 Last updated (according to GEO): Jul 18 2007 Kg15: Hippocampus_21PT-AU_rep2 255 235 dilated heart failure Chronic Lymphocytic Leukemia 19 47 Brain 861 with some respiratory epithelium. 1039 1072 20 0 human caudate nucleus Medulla 861 Cerebral cortex 1000 Nasal Epithelium Inhalation Formaldehyde 2ppm 6h ID209 Heart 861 skeletal_muscle_2 Source GEO sample is GSM80790 Last updated (according to GEO): Mar 31 2006 Cerebellum Control (AD) 2 to the nose 599 609 Saccule 0 6 PGA-E10.5_3 brain, cortex: 3dexp3_e1_le1 234 227 Epilepsy 91 from the bone marrow 72 ABSTRACT: BACKGROUND: Expression quantitative trait locus (eQTL) mapping is used to find loci responsible for the transcriptional activity of a particular gene. In recent eQTL studies, expression profiles were derived from either homogenized whole brain or collections of large brain regions. However, the brain is a very heterogeneous organ and expression profiles of different brain regions vary significantly. Because of the importance and potential power of eQTL studies to identify regulatory networks, we analyzed gene expression patterns in different brain regions from multiple inbred mouse strains and investigated the implications for the design and analysis of eQTL studies. RESULTS: Gene expression profiles of five brain regions in six inbred mouse strains were studied. Few genes showed a significant strain-specific expression pattern, while a large number of genes showed brain region-specific patterns. We constructed phylogenetic trees based on the expression relationships between the strains and compared them to a DNA-level relationship tree. The trees based on the expression of strain-specific genes were constant across brain regions and mirrored DNA-level variation. However, the trees based on region-specific genes showed a different set of strain relationships depending on the brain region. An eQTL analysis showed an enrichment of cis-acting regulators among strain-specific genes, while brain region-specific genes seem mainly regulated by trans-acting elements. CONCLUSIONS: Our results suggest that many regulatory networks are highly brain region-specific and indicate the importance of conducting eQTL mapping studies using data from brain regions or tissues that are physiologically and phenotypically relevant to the trait of interest. The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169492 Last updated (according to GEO): Feb 21 2007 Nervous system structure 901 between the LAD artery 266 287 cervix_9 corpus_callosum_9 1000 Brain 1000 Cerebrovascular accident MPTP 3 6 0 Cancers Nasal Epithelium 865 striatum 32 40 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188731 Last updated (according to GEO): Jun 06 2007 Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM Source GEO sample is GSM207683 Last updated (according to GEO): Jul 09 2007 Treated Source GEO sample is GSM176463 Last updated (according to GEO): Apr 09 2007 Primary small cell lung carcinoma 2425 0 37 Female8, Olfactory RNA_Nasal olfactory epithelium_Tissue was preserved in RNA later and collected from nose NA07000 coronary_artery_5 Locus Coeruleus Source GEO sample is GSM107977 Last updated (according to GEO): Jun 06 2006 25 0 The gastrointestinal tract 1000 Spleen Rett Syndrome 861 Gene expression data from rat metanephric mesenchymes freshly dissected Source GEO sample is GSM126187 Last updated (according to GEO): Dec 08 2006 Communicable Diseases 901 Epithelium 861 Cerebral cortex 861 Pathways and genes differentially expressed in the motor cortex of patients with sporadic amyotrophic lateral sclerosis. 861 Ovary Pool of total RNA from 3 euploid cerebella at P0 postnatal stage Keywords = Down syndrome Keywords = Chromosome 21 Keywords = Transcriptome Keywords = Microarray Keywords = Brain Keywords = Cerebellum Keywords = Development Source GEO sample is GSM27472 Last updated (according to GEO): May 27 2005 861 Neoplasm BC114A-BE 460_1 The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76941 Last updated (according to GEO): Oct 11 2005 Neoplasm 861 1000 Malignant neoplasm of urinary bladder Fertilized egg replication 4 0 27 IDC193 on harvard-12k brain 0 5 Mesenchymal stem cells 3895 3917 B6 day 0, biological rep 1, tech rep 1 1000 Lipids 1000 Coronary Arteriosclerosis Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Dye-swap. Source GEO sample is GSM15956 Last updated (according to GEO): May 28 2005 Gene expression profile of the cell line UB/OC-1 grown for 6 days under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1539 Last updated (according to GEO): May 27 2005 Kidney 1000 VDXOXFU_1328 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50640.gif Developmental Stage: E7.5 Source GEO sample is GSM229808 Last updated (according to GEO): Nov 06 2007 38/OVX/P4/6h/UTX 129 Hoxa-10-/- Primary Carcinoma 875 Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22580 Last updated (according to GEO): Sep 14 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145373 Last updated (according to GEO): Nov 20 2006 CC225 Lung 861 1000 Brain 715 702 After the eyes 1000 Lipids 1000 Liver 0 cortex 5 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184700 Last updated (according to GEO): Apr 26 2007 00290952H95A2-T01407v2p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Fetal fibroblast, primary GSE1075 Brain (thalamus) [JunctionChip 5 of 5] CNS-SC_Inj14d-3A-s2x Day 2_M_+RA_Bchip Investigation into murine dermal burn wound. Mouse thermal injury induced, and skin excised at different times post-injury. Source GEO sample is GSM7488 Last updated (according to GEO): May 27 2005 Lymphoblastoid Cell Line for Individual 8041.4 log phase 164 136 of the middle cerebral artery Pancreas at e13.5, Chip C, rep 2 Myocardium 861 untreated A Treatment, type=time_course, measurement=1.0 weeks Source GEO sample is GSM107847 Last updated (according to GEO): Jun 06 2006 2869 tumor cells 2880 A HID B D021 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108582 Last updated (according to GEO): Aug 22 2006 1000 Malaria 17 7 hippocampus 406 391 by brain injury CVB3 infection 289 303 1000 Structure of superior frontal gyrus Communicable Diseases 901 12 0 ovarian tumor cerebellum_4 Source GEO sample is GSM80619 Last updated (according to GEO): Mar 31 2006 12 4 of Kidney 129 21-2 WAT cortex from B6 mice at ZT21 rep3 Source GEO sample is GSM160463 Last updated (according to GEO): Feb 05 2007 brain, Left frontal Lobe: Extract29_le2 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11328 Last updated (according to GEO): May 28 2005 Osteoblasts 1000 Bone Marrow 1000 Liver 1000 26 0 Bone marrow [JunctionChip 2 110 94 of heart failure Tumor__Ovary_Adeno_07-B_014G on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Cochlea_D257A_9mo_1 1000 Brain of the atrial 647 659 Cerebral cortex 1000 1000 Infection Integumentary system 1000 17 7 hippocampus 861 hair 7 cerebral cortex 21 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc101 Source GEO sample is GSM1888 Last updated (according to GEO): Nov 21 2005 87 77 to adenomas Wild-type 5 months old, female Source GEO sample is GSM154350 Last updated (according to GEO): Jan 09 2007 spinal cord 37 47 10 7 Left on brains 21 29 bronchial epithelia 224 243 TS21 sample 2 (heart) 20 0 Primary glioblastomas 1000 Bone Marrow 983 Malignant neoplasm of breast HOXB4 mediates expansion of adult and embryo-derived hematopoietic stem cells (HSCs) when expressed ectopically. To define the underlying molecular mechanisms, we performed gene expression profiling in combination with subsequent functional analysis using enriched adult HSCs expressing inducible HOXB4. A substantial number of the identified HOXB4 target genes are involved in signaling pathways important for controlling self-renewal, maintenance and differentiation of stem cells. Functional assays performed on selected pathways confirmed the biological coherence of the array results. HOXB4 activity protected adult HSCs from the detrimental effects mediated by the proinflammatory cytokine TNF-alpha. Furthermore, we demonstrate that HOXB4 activity and FGF-signaling are intertwined. HOXB4-mediated expansion of adult HSCs was enhanced by specific and complete inhibition of FGF-receptors. Based on our results we propose that HOXB4 governs pivotal cell-intrinsic pathways involved in the regulation of cell cycle, differentiation and apoptosis. Our results strongly suggest that HOXB4 modulates the response of HSCs to multiple extrinsic signals in a concerted manner, thereby shifting the balance towards stem cell self-renewal. Last Updated (by provider): Sep 11 2007 Contributers: Moises Mallo H Klump W Ostertag H Auer C Baum K Kornacker B Schiedlmeier Brain 861 Uterine Fibroid and Normal Myometrial Expression Profiles- U133 Arrays The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76938 Last updated (according to GEO): Oct 11 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM146037 Last updated (according to GEO): Nov 20 2006 mouse brain ipsilateral control Source GEO sample is GSM149767 Last updated (according to GEO): Mar 15 2007 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211433 Last updated (according to GEO): Jul 18 2007 5 0 brain Neuroblastoma 1000 rat hippocampus Treatment, type=time_course, measurement=72.0 h Source GEO sample is GSM32143 Last updated (according to GEO): May 27 2005 E2A-PBX1-#9 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A CNS-RM_Mod28d-1B-s2 Lymphoblastoid Cell Line for Individual 8105.4 log phase 861 Encephalitis GSE986 of cortex 1764 1772 1000 Brain 14 0 Small Intestine 17 7 hippocampus mouse hippocampus from COX-1 Knockout Source GEO sample is GSM121440 Last updated (according to GEO): Jan 31 2007 1000 Basal Ganglia 36 21 from whole brain 286 255 to the leukocyte immunoglobulin- SCG explant cultured for 5 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246039 Last updated (according to GEO): Dec 03 2007 I_U133A_63_Amy UT rep 1 Tumor__Melanoma_93_I_262 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A no additional Source GEO sample is GSM199190 Last updated (according to GEO): Jun 08 2007 66 CB B 5 0 brain NA19160 Control male 3 861 Cardiomyopathies The Dlx homeodomain transcription factors are implicated in regulating the function of inhibitory neurons; therefore understanding their functions will provide insights into disorders such as epilepsy, mental retardation, autism and cerebral palsy. Identify genes that are dysregulated in the telencephalon of Dlx1/2 mutants. I am sending separate samples of the Basal Ganglia (BG) and cortex (Ctx). Comparing gene expression in the embryonic basal ganglia and cortex in wild type and dlx1/2 mutant mice will provide information regarding the types of genes that are downstream of Dlx1/2 function. Perform gene array analyses in duplicate or triplicate; compare expression profile of total RNA from wild type and dlx1/2 telencephalons. I am sending separate samples of the Basal Ganglia (BG) and cortex. I want to perform gene expression comparison between: 1) wild type and dlx1/2 basal ganglia (BG) 2) wild typee and dlx1/2 cortex (ctx) Age of all mice has been indicated as 14 days to satisfy system requirements, however all mice are embryonic day 14.5.. Date GSE2161 Last Updated: May 29 2005 Contributers: John L Rubenstein Includes GDS1084. Update date: May 08 2005. Dataset description GDS1084: Expression profiling of cortex and basal ganglia from embryonic telencephalon of homozygous and heterozygous Dlx1/2 mutants. Mutants examined at embryonic day 14.5. Dlx homeobox transcription factors are implicated in regulating the function of inhibitory neurons.. Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging and comparing calorie restricted-fed 30-month-old to control-fed 30-month-old to investigate effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7462 Last updated (according to GEO): May 27 2005 Gene expression data from aneurismal tissues obtained from patients with tricuspid valves. Source GEO sample is GSM116804 Last updated (according to GEO): Jun 28 2006 PGA-lv2_1h_514 brain, frontal cortex: Sample57_e1_le1 with myocardial infarction 313 339 Brain 861 Communicable Diseases 1000 BC111B-BE Kidney; Fetal Day 18.5 Keywords = mouse gene expression database Source GEO sample is GSM29362 Last updated (according to GEO): May 27 2005 Heart 861 1000 Brain Wild type 8 wk old male A/J mouse hippocampus Source GEO sample is GSM74957 Last updated (according to GEO): Feb 27 2007 Menstruation blood, primary Hippocampus 861 5 0 Spleen no additional Source GEO sample is GSM199042 Last updated (according to GEO): Jun 08 2007 Lung; Day 12 postnatal Keywords = mouse gene expression database Source GEO sample is GSM29381 Last updated (according to GEO): May 27 2005 brain 0 5 none Source GEO sample is GSM123232 Last updated (according to GEO): Jul 26 2006 PMN_control_180min_Patient3 1000 Brain 1000 Basal Ganglia Normal Source GEO sample is GSM176115 Last updated (according to GEO): Apr 09 2007 1000 Brain 16 7 cerebellum I_U133A_74_Amy Whole Brain 73 83 Epilepsy 861 Mesenchymal Stem Cells 1000 SCG_sema3A_2h_rep2 cerebellum 7 16 RNA of Kidney was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 biological replicates were analyzed. Keywords = db/m mice Keywords = kidney Source GEO sample is GSM9931 Last updated (according to GEO): May 27 2005 Lymphoblastoid Cell Line for Individual 8108.3 log phase NCI60.49_LABEL53EXTRACT52SUB3 Source GEO sample is GSM134242 Last updated (according to GEO): Aug 06 2007 normal testis 54 66 M_U133Plus_73_DLPFC HMEC 184 day 7 sample 2 amygdala rattus_norvegicus_strain iP animal_number 4 GM12145 LivRegen24hr022CAC3C_180.txt Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159749 Last updated (according to GEO): Apr 23 2007 913 Coronary heart disease Ovarian Diseases 877 Head and neck cancer Source GEO sample is GSM155675 Last updated (according to GEO): Apr 24 2007 Neostriatum 1000 CNS-RM_Mod14d-2A-s2 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188792 Last updated (according to GEO): Jun 06 2007 114 101 brains quickly Cerebral cortex 861 Spinal Cord 1000 901 Heart Ventricle I_U133Plus_124_AnCg Cerebral cortex 861 Identification of temporal patterns of gene expression in the uteri of immature, ovariectomized mice following exposure to ethynylestradiol. Gene expression data from postmorten brain regions Source GEO sample is GSM145574 Last updated (according to GEO): Nov 20 2006 861 Neoplasm Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226047 Last updated (according to GEO): Nov 02 2007 CLL-10 of somatomotor cortex 21 41 CingulateCortex Source GEO sample is GSM18781 Last updated (according to GEO): Sep 25 2006 Molecular determinants of resistance to antiandrogen therapy. none Source GEO sample is GSM244628 Last updated (according to GEO): Nov 23 2007 ovarian tumor: endometrioid Source GEO sample is GSM139411 Last updated (according to GEO): Apr 09 2007 Myometrium 40 Disease 1000 Brain 51 32 of Placental Malaria GSE376 434 414 in the nervous system 12 hr vehicle repl 1 CurrentSmoker 67 CHIPEXP_NAME: 230_2_050531tpj_34h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Isoproterenol TREAT_TOX_MECHANISM1: Heart_Cardiotoxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0.5 SAMPLING_TIME: 1 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197608 Last updated (according to GEO): Jun 01 2007 Testis_6wk_FVB Wt 901 Gastrocnemius muscle structure V5-P340 Richard Almon-5-1138200269524 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188702 Last updated (according to GEO): Jun 06 2007 adenoma 861 Menstrual phase - Luteal Source GEO sample is GSM175769 Last updated (according to GEO): Apr 09 2007 Primary Neoplasm 1000 UACC-257 hgu95c 913 Coronary heart disease 1000 Congestive heart failure Stem cells 901 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68212 Last updated (according to GEO): Jul 07 2006 Brown Fat 1000 tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44860 Last updated (according to GEO): May 27 2005 5 0 brain 09_0002_SepticShock_Day3_75 1000 Ovary brain, hippocampus: Aldh5a1-/- #3389 Cereb_e1_le1 4-cell embryo replication 3 accumbens rattus_norvegicus_strain iP animal_number 2 901 Coronary artery Malignant neoplasm of breast 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145372 Last updated (according to GEO): Nov 20 2006 from ventral prostate 21 41 H14A Human Embryonic Stem cell (H14A ESC) high dose 24h, replicate 1 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132520 Last updated (according to GEO): Feb 26 2007 Spleen vs Interferon-beta (IFN beta) Treated B cell 60min (set2) Liver 49 54 Gene expression data from human colon tumor tissue Source GEO sample is GSM173333 Last updated (according to GEO): Apr 20 2007 86 48 in the mammalian central nervous system in the cerebellum 212 229 861 Cerebellum RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above Source GEO sample is GSM160010 Last updated (according to GEO): Feb 05 2007 Hereditary Nonpolyposis Colorectal Neoplasms 947 502 483 congenital myopathy 1000 Left Ventral tegmental area, male 10.5 week old c57bl/6J mouse, SUSCEPTIBLE group Source GEO sample is GSM224747 Last updated (according to GEO): Aug 31 2007 Prosencephalon 1000 Whole Brain 73 83 Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183409 Last updated (according to GEO): Apr 23 2007 Revealing targeted therapy for human cancer by gene module maps A major goal of cancer research is to match specific therapies to molecular targets in cancer. Genome-scale expression profiling has identified new subtypes of cancer based on consistent patterns of variation in gene expression, leading to improved prognostic predictions. However, how these new genetic subtypes of cancers should be treated is unknown. Here we show that a gene module map can guide the prospective identification of targeted therapies for genetic subtypes of cancer. By visualizing genome-scale gene expression in cancer as combinations of activated and deactivated functional modules, gene module maps can reveal specific functional pathways associated with each subtype that might be susceptible to targeted therapies. We show that in human breast cancers, activation of a poor prognosis ?wound signature? is strongly associated with induction of a proteasome gene module. Inhibition of proteasome activity by bortezomib, a drug approved for human use in multiple myeloma, abrogated wound signature expression and selectively killed breast cells expressing the wound signature. Thus, gene module maps may enable rapid translation of complex genomic signatures in human disease to targeted therapeutic strategies. Last Updated (by provider): Jul 20 2006 Contributers: David Wong Meihong Lin Dimitry S Nuyten Howard Y Chang Eran Segal Marc J Van de Vijver Gene expression regulated by DACH1-7 861 Brain Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13152.gif Source GEO sample is GSM79718 Last updated (according to GEO): Sep 22 2006 1000 frontal lobe Wild type inbred mice Source GEO sample is GSM82932 Last updated (according to GEO): Nov 10 2005 75 44 from Normal Intestinal Epithelia Gene expression data from whole brain of uninfected mouse Source GEO sample is GSM189634 Last updated (according to GEO): May 16 2007 1000 Heart of hepatocellular carcinoma 1486 1512 Pituitary Gland 861 D_U133A_20_DLPFC human caudate nucleus Source GEO sample is GSM86831 Last updated (according to GEO): Feb 08 2006 DLBC18 on Affymetrix GeneChip Human Full Length Array HuGeneFL in bronchial epithelia 311 332 B2-25 on NCI-7.6k 12 frontal Lobe 23 1BJZ02083092b_Skeletal_Muscle_Psoas Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181193 Last updated (according to GEO): Jul 12 2007 Communicable Diseases 1000 AcB61 #12250554 brain, hippocampus: P5 FAE 2_e1_le1 infection 255 264 ventral tegmental area short access to cocaine replicate 3 Hypothalamus Source GEO sample is GSM107954 Last updated (according to GEO): Jun 06 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145082 Last updated (according to GEO): Nov 20 2006 Pool of 7 saccules at E13.5 Source GEO sample is GSM182615 Last updated (according to GEO): Aug 14 2007 cingulate cortex 861 HDMTX-4 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153371 Last updated (according to GEO): Dec 27 2006 Blood 1000 for nicotinic receptors 158 180 Interatrial septum 865 D03 3h TLR2/1L Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 19 day time point Source GEO sample is GSM159774 Last updated (according to GEO): Apr 23 2007 2046 2018 of adhering connective tissue contralateral Cortex 7 27 na Source GEO sample is GSM181257 Last updated (according to GEO): Apr 10 2007 NA Source GEO sample is GSM198903 Last updated (according to GEO): Jun 07 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145103 Last updated (according to GEO): Nov 20 2006 LEUKEMIA 15 22 fibronectin 937 947 ER-/LN-/Marks222 on Affymetrix GeneChip Human Full Length Array HuGeneFL 51 47 Lungs PGA-MurLungRag-rwp-24h-1bCv2-s2 I_U133A_50_AnCg Bipolar Disorder 1000 7 0 prostate 1000 adenoma HNCB1 861 Spinal Cord Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184817 Last updated (according to GEO): Apr 26 2007 5 0 brain 861 Neoplasm human frontal cortex Source GEO sample is GSM87012 Last updated (according to GEO): Feb 08 2006 Plasma 861 tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44880 Last updated (according to GEO): May 27 2005 CNS-SCsev_InjA4h-4C-s2 861 Epithelium Brain 861 BRCA2_s1486 on NHGRI-6.5k 24 0 human prostate PC3 tumors B214 on Affymetrix GeneChip Human Full Length Array HuGeneFL Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Source GEO sample is GSM15950 Last updated (according to GEO): May 28 2005 osteosarcoma-C-TEST-3 on NHGRI-6.5k_b 40 21 from skeletal muscle 1000 Malignant Neoplasms Normal Source GEO sample is GSM175810 Last updated (according to GEO): Apr 09 2007 Coronary heart disease 913 to the nose 599 609 1037 of transitional epithelium 1012 5 0 brain Chronic Lymphocytic Leukemia 19 47 Hippocampus 861 1000 Left of the auditory organ 199 219 None Source GEO sample is GSM214246 Last updated (according to GEO): Aug 01 2007 WT P10 replicate 4 Testis 1000 Accumbens P10 Normal 1000 Hippocampus 1000 Rectum Mouse_FGFR1_E12.5_hets_vs_hom_8 Heart 1000 A39 WT3 F7/3 A39 wild type Mouse 4 months Cerebellum Male Source GEO sample is GSM73231 Last updated (according to GEO): Sep 06 2005 -_6247_batch2 on NHGRI-6.7k 1000 Brain CC507 150 mg/kg X 6 hr Source GEO sample is GSM129868 Last updated (according to GEO): Sep 18 2007 Mice sacrificed at 12 weeks of age. Can be used as a control for the 3 and 4 week swim mice. Keywords = exercise induced hypertrophy Source GEO sample is GSM2362 Last updated (according to GEO): May 27 2005 Type 1 Diabetes patient and the timepoint 4 months after diagnosis. Source GEO sample is GSM228624 Last updated (according to GEO): Sep 11 2007 infection 64 72 Anterior interpositus nucleus-centered deep cerebellar nuclei were sampled using syringe needles. Source GEO sample is GSM84977 Last updated (according to GEO): Mar 29 2006 Normal Source GEO sample is GSM176364 Last updated (according to GEO): Apr 09 2007 1000 frontal lobe brain 0 5 Disease Source GEO sample is GSM176442 Last updated (according to GEO): Apr 09 2007 Gene expression data from whole brain infected mouse, day 6 Source GEO sample is GSM189653 Last updated (according to GEO): May 16 2007 861 Hormones Normal Source GEO sample is GSM175834 Last updated (according to GEO): Apr 09 2007 Spleen vs Neuropeptide Y Treated B cell 60min (set3) Y VIS D029 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211230 Last updated (according to GEO): Jul 18 2007 861 Leukemia, Myelocytic, Acute 3rd 1hr C+S-CA1 144 114 from a single adult spinal cord 1645 in bipolar disorder 1663 Ovary 1000 Cerebral cortex 861 comparing tumor 773 787 Donor D, prior to G-CSF Source GEO sample is GSM178552 Last updated (according to GEO): Aug 09 2007 1000 Spleen progressive supranuclear palsy 743 772 osteoblast 627 637 GBM Treatment, type=remove Source GEO sample is GSM99555 Last updated (according to GEO): Apr 21 2006 861 Brain CVB3_V-0.5h-2 Nasal Epithelium 901 RMS-C10 on NHGRI-6.5k_b M_U133A_26_HC 6 0 Mammary Nervous System; Spinal Cord Keywords = mouse gene expression database Source GEO sample is GSM29427 Last updated (according to GEO): May 27 2005 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10129.gif Source GEO sample is GSM79671 Last updated (according to GEO): Sep 22 2006 Branch 861 Gene expression data from the hippocampus of S1P2-knockout mouse Source GEO sample is GSM172969 Last updated (according to GEO): Mar 08 2007 54h-AM replication 1 Keywords = preimplantation Keywords = development Source GEO sample is GSM14713 Last updated (according to GEO): May 28 2005 Arteries 861 Blood 861 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201254 Last updated (according to GEO): Jun 14 2007 Liver Test (Blinded) Sample Source GEO sample is GSM130077 Last updated (according to GEO): Sep 18 2007 262 257 Spleen Brucella requires a functional Type IV secretion system to elicit innate immune responses in mice. Spinal Cord 1000 68 64 Lungs 861 Mammary gland Control (for PS cDKO) 6 months Liver Test (Blinded) Sample Source GEO sample is GSM130183 Last updated (according to GEO): Sep 18 2007 adult nNOS Knockout mouse (c57bl) brain cortex Source GEO sample is GSM49562 Last updated (according to GEO): May 29 2005 90minplus.3 304 280 alcoholic cardiomyopathy TNF TG-13w-m-3 GBM Treatment, type=remove Source GEO sample is GSM99545 Last updated (according to GEO): Apr 21 2006 HeLa CD4+ cells were transfected with an epitope-tagged eTat plasmid and selected with hygromycin. Cells were treated with nocodazole and collected @3 hours. Source GEO sample is GSM8705 Last updated (according to GEO): May 27 2005 Unusual intron conservation near tissue-regulated exons found by splicing microarrays. ColonTumor022KAFBT_cta.txt GSE414 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114238 Last updated (according to GEO): Jun 16 2006 Kidney 861 on chromosomes 9 1025 1040 0 Frontal Cortex 13 hedenfalk-familial 1BJZ02022644_kidney This study was conducted using affymetrix microarrays. We were interested in determining the effects of tTA expression in the hearts of FVBN mice. We compared expression to wild type mice Keywords = tTA FVBN alpha MHC promoter Source GEO sample is GSM15056 Last updated (according to GEO): May 28 2005 U87 glioblastoma cell, clone 3.1 (neo-resistant negative control) Keywords = bioinformatics Keywords = gene expression Keywords = cancer Keywords = platelet-derived growth factor Keywords = sterol regulatory element binding protein Keywords = glioblastoma multiformae Keywords = microarray Source GEO sample is GSM34581 Last updated (according to GEO): May 27 2005 Myocardial Infarction 1000 f2#354 versus pool Mouse Brain tissue B265 on Affymetrix GeneChip Human Full Length Array HuGeneFL Spleen vs CGS Treated B cell 60min (set2) V5-P061 136 with bipolar disorder 157 seminoma specimen, pT1, patient age: 37y; W03 023 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3291 Last updated (according to GEO): Mar 21 2006 HCC (HBV+, SF21) Pool of 17 vestibular tissues at E11 Source GEO sample is GSM182593 Last updated (according to GEO): Aug 14 2007 Striatal gene expression data from 12 months-old Hdh4/Q80 mice and control mice. 865 Alcohol-Related Disorders intestine_wildtype_control_rep1 Osteoblasts 1000 1000 Spleen Muscular Dystrophy, Duchenne 913 1000 Descending colon PGA-MFD-CtrPD1-2aCv2-s2 D5 aggregate culture, 9A1, rep 2 FSCC7 on Affymetrix GeneChip Human Full Length Array HuGeneFL 245-97_node Acetaminophen 3hr Rat 7763 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool CAD_replicate30 Pre-BI cells 9 Fibroblasts 861 Day 3_H_-LIF_Achip Stem cells 1000 Fibroblasts 1000 V5-P117 Leukemic fractions of ID32 AML patient have been hybridized. Source GEO sample is GSM103103 Last updated (according to GEO): Feb 26 2007 mouse brain ipsilateral LPS.Dmso, biological rep5 HTI-286 in docetaxel-refractory prostate cancer Biological Replicate 2 rat cortex Treatment, type=time_course, measurement=28.0 d Source GEO sample is GSM53230 Last updated (according to GEO): Jul 06 2005 865 Disorder of artery 91 from the bone marrow 72 93 58 in laminin-rich extracellular matrix Mesenchymal Stem Cells 1000 Cerebral cortex 901 male C57/BL6, double amplification Source GEO sample is GSM5416 Last updated (according to GEO): Mar 17 2006 Macrophage 14smi012 1000 Descending colon brain, cerebellum: Lh+/+_Crb3_e1_le1 nmd treated 2 Cerebellum 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM144878 Last updated (according to GEO): Nov 20 2006 5 0 Spleen 663 mesenchymal stem cell 642 no additional Source GEO sample is GSM199188 Last updated (according to GEO): Jun 08 2007 total RNA from biosource CC#5S Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92472 Last updated (according to GEO): Jan 13 2006 Voxel J2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1456 Last updated (according to GEO): Nov 21 2005 Day 1_L_-LIF_Bchip of Parkinson's disease 450 471 Mouse Liver AIN Diet 8hr 1mg/kg As Injection, biological replicate D Replicate3_Voxel E3 Heart 1000 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184762 Last updated (according to GEO): Apr 26 2007 7 cortex 12 corpus callosum agenesis 249 273 1000 Bone Marrow CNS-SpinalCsev-Adult-7d-2A-s2 Testis 1000 Nasal Epithelium 865 how the liver 649 661 861 Cerebral cortex Neoplasm 861 1000 Heart Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14352.gif Source GEO sample is GSM79621 Last updated (according to GEO): Sep 22 2006 V5-P368 3 CN A Gene expression data from postmorten brain regions Source GEO sample is GSM146082 Last updated (according to GEO): Nov 20 2006 MSS-Ctr12moM-1aAv2-s2 Ventral Tegmental Area 884 40 21 from skeletal muscle 2500 mg/kg X 6 hr Source GEO sample is GSM129865 Last updated (according to GEO): Sep 18 2007 901 Temporal Lobe DRG_sema3A_5h_rep1 358 353 tumors Brain 861 nostrils 156 164 Coronary heart disease 913 MSE_N_659 Branch 861 in glucose-6-phosphate dehydrogenase 384 419 contralateral Cortex 7 27 JMR-MurSham24h-1cAv2-s2 575 567 Melanomas of mouse brain 9 23 972 Structure of middle temporal gyrus C57BL/6 benchmark dataset: Embryonic day 13.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25166 Last updated (according to GEO): May 27 2005 Liver Test (Blinded) Sample Source GEO sample is GSM130144 Last updated (according to GEO): Sep 18 2007 1000 Brain O377 homozygotes brains 8 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28819 Last updated (according to GEO): May 27 2005 Spinal Cord 1000 1000 Malignant Neoplasms AD-169t2-A211-8 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Malignant Neoplasms The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159951 Last updated (according to GEO): Feb 01 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11550 Last updated (according to GEO): May 28 2005 Gene expression data from a placenta without malaria, but with histological evidence of a past infection and inflammatory cells Source GEO sample is GSM183623 Last updated (according to GEO): Apr 23 2007 142 116 of parieto-occipital cortex Keywords = Heart 505 521 861 Neoplasm 1037 of transitional epithelium 1012 NA12716 GSE383 Myocardium 861 Kidney 1000 Bone Marrow 1000 KPeterson-Met-3box2-1G110-s2 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210394 Last updated (according to GEO): Jul 16 2007 Heart 1000 2522 CP0_31 Cerebral cortex 861 861 Cerebral cortex Plasma 861 hypothalamus sprague1 Cardiac 523 530 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.98 Subject: 2672 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39007 Last updated (according to GEO): May 27 2005 861 Trachea Connexin43 null neonatal mouse brain4 (K43-4) Expression profiling of moderately injured raphe at 3 months in rats Source GEO sample is GSM41599 Last updated (according to GEO): May 27 2005 Brain 1000 from brain 21 30 ISR20 966 Amygdaloid structure Multiple Myeloma 1000 Spleen vs IL4 Treated B cell 30min (set3) Osteoblasts 1000 BACKGROUND: Down syndrome, caused by trisomic chromosome 21, is the leading genetic cause of mental retardation. Recent studies demonstrated that dosage-dependent increases in chromosome 21 gene expression occur in trisomy 21. However, it is unclear whether the entire transcriptome is disrupted, or whether there is a more restricted increase in the expression of those genes assigned to chromosome 21. Also, the statistical significance of differentially expressed genes in human Down syndrome tissues has not been reported. RESULTS: We measured levels of transcripts in human fetal cerebellum and heart tissues using DNA microarrays and demonstrated a dosage-dependent increase in transcription across different tissue/cell types as a result of trisomy 21. Moreover, by having a larger sample size, combining the data from four different tissue and cell types, and using an ANOVA approach, we identified individual genes with significantly altered expression in trisomy 21, some of which showed this dysregulation in a tissue-specific manner. We validated our microarray data by over 5,600 quantitative real-time PCRs on 28 genes assigned to chromosome 21 and other chromosomes. Gene expression values from chromosome 21, but not from other chromosomes, accurately classified trisomy 21 from euploid samples. Our data also indicated functional groups that might be perturbed in trisomy 21. CONCLUSIONS: In Down syndrome, there is a primary transcriptional effect of disruption of chromosome 21 gene expression, without a pervasive secondary effect on the remaining transcriptome. The identification of dysregulated genes and pathways suggests molecular changes that may underlie the Down syndrome phenotypes. 3x24 hr vehicle repl 1 GSE6254 06_0003_SepticShock_Day1_89 embryonic hearts 1064 1079 Tonsil (Hu. Ton. 5.29.98) SN:1007080 Source GEO sample is GSM115361 Last updated (according to GEO): Jun 20 2006 Epithelium 861 Expression profiling of laminectomized raphe at 7d in rats Source GEO sample is GSM41548 Last updated (according to GEO): May 27 2005 n/a Source GEO sample is GSM177903 Last updated (according to GEO): Jun 11 2007 innervated tibialis anterior muscles from runx1f/-; MCK::cre mice Treatment, type=remove, description=MCK::cre; runx1f/- Source GEO sample is GSM99425 Last updated (according to GEO): Mar 08 2006 861 Brain Nose 1000 Duodenum [JunctionChip 2 of 5] 861 Colon Category: Cell-line Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.31 Lot batch = svcc72 Source GEO sample is GSM1919 Last updated (according to GEO): Nov 21 2005 Prostate 15 Disease 430A2_2045_39_KO_neuropath_medulla Source GEO sample is GSM242696 Last updated (according to GEO): Nov 15 2007 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD6 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD6 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36673 Last updated (according to GEO): May 27 2005 brain, cerebral cortex: Rat_02-52_VHL_Lipska_e1_le1 Spleen 0 5 8-cell embryo replication 2 Ptdsr-/- fibroblast_rep5 861 Occipital lobe SCG_sema3A_5h_rep2 144 114 from a single adult spinal cord 861 Pancreas The most common congenital cardiac abnormalities 50 97 HeLa CD4+ cells were transfected with an epitope-tagged eTat plasmid and selected with hygromycin. Cells were treated with hydroxyurea and collected @9 hours. Source GEO sample is GSM8701 Last updated (according to GEO): May 27 2005 Brain 1000 5 0 Spleen 861 HIV Infections Whole Brain 62 72 olfactory epithelium 194 213 Lymphoblastic Leukemia 901 GM19173 Small cell carcinoma of lung 888 Male 23.4 yr after antibody enrichment scan 2 (U133B) 1000 Brain Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:215, Count:32 Corner- Avg:34690, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:20.939404,SFGene:All Background:Avg:370.42,Stdev:5.24,Max:379.7,Min:353.7 Noise:Avg:7.00,Stdev:0.17,Max:7.5,Min:6.1 RawQ:11.93 Keywords = ALL Source GEO sample is GSM3415 Last updated (according to GEO): May 27 2005 25 7 Right Temporal Lobe olfactory epithelium 194 213 Keywords = kidney 236 253 Date 2/5/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : headfold Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 2.5 mg/kg Time : 4.5 hrs post-injection Intervention : none Risk: benchmark dose modeled for 5% increased risk of microphthalmia Conditional biomarker: post-injection interval at the time of p53 protein induction Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 16-20 headfolds pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = embryo Keywords = microphthalmia Lot batch = AM035 Source GEO sample is GSM12073 Last updated (according to GEO): May 28 2005 7 cortex 12 Lymphoblastic Leukemia 901 Nasal Epithelium 865 861 Blood 1000 Spleen 19 0 primary hepatocytes -_6756_batch1 on NHGRI-6.7k GSE5817 Cerebral cortex 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11249 Last updated (according to GEO): May 28 2005 Wild type 8 wk old male C57BL/6J mouse periaqueductal gray Source GEO sample is GSM107034 Last updated (according to GEO): Mar 05 2007 of lung adenocarcinoma 413 435 A YOKE D095 NA11995 jzo020-rp1-v5-u74av2-met.TXT 901 Caudate nucleus structure 31 20 Whole thymus Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11540 Last updated (according to GEO): May 28 2005 H9LMS99081101 Spleen vs MIP3-alpha Treated B cell 60min (set1) Epithelium 861 Nicotine-hippocampus, biological rep4 Gene expression data from postmorten brain regions Source GEO sample is GSM145363 Last updated (according to GEO): Nov 20 2006 B6:17-4,5,6 inferior colliculi 7 cerebral cortex 21 Dahl-Iwai Female LowSalt Cortex rat104 dahl_cortexr_k_104c_072001 1026 1009 that glioblastomas iron biological rep3 VDXKIU_15H4 1000 Bone Marrow 630 597 The neuronal ceroid lipofuscinoses total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CGS for 120min Source GEO sample is GSM5516 Last updated (according to GEO): May 27 2005 Nose 1000 Expression profiling of spinal cord section (T10) extracted from rats 0h following laminectomy (naïve) Source GEO sample is GSM31300 Last updated (according to GEO): Oct 28 2005 1000 Descending colon E2A-PBX1-C2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Y YOKE D023 for liver 26 35 at heart failure 1567 1583 1000 jejunum Nasal Epithelium 865 HapMap CEU_parent Female Source GEO sample is GSM159551 Last updated (according to GEO): Feb 01 2007 913 Coronary heart disease Type 1 Diabetes patient and the timepoint 1 month after diagnosis. Source GEO sample is GSM228617 Last updated (according to GEO): Sep 11 2007 cerebellum 133 143 Parkinson 0 8 CCAT regulated gene expression 43 0 Chorionic mesoderm-derived mesenchymal cells high gestational age Source GEO sample is GSM213105 Last updated (according to GEO): Jul 25 2007 Ovarian_Tumor_Serous_CHTN-OS-010 Brain 1000 Cerebral cortex 861 Primary tumor 19 32 human caudate nucleus Source GEO sample is GSM86859 Last updated (according to GEO): Feb 08 2006 Melanoma (G361) [JunctionChip 5 of 5] Neoplasm 861 25 7 Right Temporal Lobe 1291 1283 in liver 1000 Modiolus anguli oris Occipital lobe 983 22 0 Mammary Gland @ Preg19 plasma cells 332 344 1000 medulloblastoma T36__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A none Source GEO sample is GSM239845 Last updated (according to GEO): Dec 07 2007 liver 0 5 1000 Muscle Cells Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141277 Last updated (according to GEO): Oct 26 2006 DLBC17 on Affymetrix GeneChip Human Full Length Array HuGeneFL DBA 1-1-1 BAT Plasma 861 Large cell carcinoma of lung 901 Cerebral cortex 861 e_M43B 1000 Amygdaloid structure brain, cerebellum: 3 hrs A LK_e1_le1 none Source GEO sample is GSM149613 Last updated (according to GEO): Jan 03 2007 ovarian tumor: serous Source GEO sample is GSM139472 Last updated (according to GEO): Apr 09 2007 Prefrontal Cortex 0 16 Gene expression data from colorectal adenoma. Source GEO sample is GSM215083 Last updated (according to GEO): Aug 02 2007 CAD_replicate43 DBA 1-1-1 Liver Parkinson Disease 1000 1000 Descending colon 5.0 mg/kg MeHg forebrain at 12.0h Expression data from mouse SCN after 30-min light pulse Cerebral cortex 1000 mild cognitive impairment - hippocampus 5 Posterior root of spinal nerve 901 16 0 Medulla_Oblongata Motor Neuron Disease 1000 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225758 Last updated (according to GEO): Nov 02 2007 732 720 in the brain f2#346 versus pool Mouse Brain tissue Brain 1000 frontal_lobe_8 Human Hypothalamus Female 2 (technical replicate) Site: University of California, Davis Cohort: Male/Female Control Set Diagnosis: Control pH: 6.43 Subject: 2846 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39031 Last updated (according to GEO): May 27 2005 PGA_MI_ilv_1h_394 901 Coronary artery Array representing response of human foreskin fibroblasts at 10h post HCMV infection Source GEO sample is GSM10347 Last updated (according to GEO): May 27 2005 Endometrium 12 Normal Bone Marrow 1000 MP-DX-12 156 145 Their livers C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 4 hour after the last shock treatment. Source GEO sample is GSM4542 Last updated (according to GEO): May 27 2005 861 Cerebral cortex 901 Coronary artery 5 0 brain Expression profiling of spinal cord section (T8) extracted from rats 30m following mild injury Source GEO sample is GSM31446 Last updated (according to GEO): May 27 2005 brain 0 5 brain, amygdala: ADX AM A b_e1_le1 MO_control_180min_Patient2 Leg 112 Day mdx rep 1 12 0 ovarian tumor The hippocampus 0 14 Replicate1_Voxel G3 7 0 Pancreas 67 40 with coronary artery disease Affymetrix protocol Source GEO sample is GSM213812 Last updated (according to GEO): Aug 02 2007 10 Bone marrow 0 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:201, Count:32 Corner- Avg:37367, Count:32 BF:testadult.CHP Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:8.311234,SFGene:All Background:Avg:442.52,Stdev:8.47,Max:475.3,Min:427.8 Noise:Avg:10.13,Stdev:0.36,Max:11.2,Min:9.2 RawQ:13.41 Keywords = ALL Source GEO sample is GSM3471 Last updated (according to GEO): May 28 2005 SCG_control_5h_rep2 861 Mesentery total RNA derived from a leprosy lesion Source GEO sample is GSM6767 Last updated (according to GEO): May 27 2005 Pituitary Gland 861 21 6 (caudate nucleus Standard Affymetrix procedure Source GEO sample is GSM132964 Last updated (according to GEO): Aug 28 2007 pituitary_gland_9 hip_1017_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Voxel I2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1447 Last updated (according to GEO): Nov 21 2005 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181133 Last updated (according to GEO): Jul 12 2007 169 pituitary gland 155 Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 2483 left_liver_lobe 19 0 Bladder tumour 934-1 1000 frontal lobe left 35 38 Neoplasm 861 22-oct-2002-liverA1-Mu11KsubBsc Normal Source GEO sample is GSM176016 Last updated (according to GEO): Apr 09 2007 92 38 of nicotinic acetylcholine receptor subunit mutant mice Nervous system structure 901 Caudal 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145131 Last updated (according to GEO): Nov 20 2006 0 Frontal Cortex 13 Gene expression data from skeletal muscle following 240 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230431 Last updated (according to GEO): Sep 19 2007 Sample 3 at Time 3 Source GEO sample is GSM113091 Last updated (according to GEO): Jun 06 2006 brain 0 5 Bone Marrow 1000 799 784 Hyperinsulinemia Brain 861 27 0 H1 Human Embryonic Stem cell 17 7 hippocampus Liver Test (Blinded) Sample Source GEO sample is GSM130172 Last updated (according to GEO): Sep 18 2007 90 81 in stroke Sample details: Three pools of rostral (R1-3), three pools of middle (M1-3), and three pools of caudal (C1-3) E13.5 MF1 neocortex were collected from 4 embryos. All possible 18 comparisons were carried out. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. Source GEO sample is GSM62828 Last updated (according to GEO): Aug 26 2005 AD control Treatment, type=dissect Source GEO sample is GSM119643 Last updated (according to GEO): Jul 10 2006 Female; Uterus - pregnant day4.5 Keywords = mouse gene expression database Source GEO sample is GSM29329 Last updated (according to GEO): May 27 2005 Heart Septal Defects, Atrial 1000 Striatal sample from a 12-month-old Hdh4/Q80 mouse. Source GEO sample is GSM238692 Last updated (according to GEO): Oct 19 2007 1000 Lens, Crystalline 0029_1469_H95A2_T94-71_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Heart Macrophage smi59 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48015.gif Developmental Stage: E8.5 Source GEO sample is GSM229821 Last updated (according to GEO): Nov 06 2007 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14947 Last updated (according to GEO): Oct 28 2005 H9LMS00111501 1000 Brain 1000 Solid tumor Tumor__Prostate_Adeno_P_0030 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Healthy patient. Source GEO sample is GSM228569 Last updated (according to GEO): Sep 11 2007 T-ALL-C11 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 0 Human Cortex 11 Gene expression data from whole brain infected mouse, day 3 Source GEO sample is GSM189615 Last updated (according to GEO): May 16 2007 Hippocampus wild type 2 CNS-SMTC_Mod4h-3B-s2 Gene expression data from postmorten brain regions Source GEO sample is GSM145839 Last updated (according to GEO): Nov 20 2006 Gene expression evidence for remodeling of lateral hypothalamic circuitry in cocaine addiction. Gene expression data from colorectal adenoma. Source GEO sample is GSM215098 Last updated (according to GEO): Aug 02 2007 304 280 alcoholic cardiomyopathy Gene expression data from whole brain infected mouse, day 1 Source GEO sample is GSM189643 Last updated (according to GEO): May 16 2007 38 12 of congenital heart disease 1000 Spinal Cord Kidney (fetal) [JunctionChip 2 of 5] Role of cocaine- and amphetamine-regulated transcript in estradiol-mediated neuroprotection. 1000 Liver from progenitor cells 68 88 M_U133A_33_HC Hypertensive disease 861 923 Carcinoma in Situ To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132998 Last updated (according to GEO): Sep 12 2006 16 6 (transverse extracellular matrix 1497 1517 mouse hippocampus 0 16 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68234 Last updated (according to GEO): Jul 07 2006 Female 22.5 yr after antibody enrichment scan 2 (U133A) 3AJZ02041226_salivarygland Liver Test (Blinded) Sample Source GEO sample is GSM130070 Last updated (according to GEO): Sep 18 2007 901 Coronary artery Heart 1000 nucleus accumbens short access to cocaine replicate 2 from mouse brain 20 35 metanephric mesenchyme, NGAL, 1 day, biological rep2 M_U133Plus_59_DLPFC Hep2_37_rep3 43h-DMSO replication 2 12 frontal Lobe 23 7 0 prostate starved 30 36 ovary 199 203 19 0 Head and neck cancer Brn3a Knockout TG e13.5 U74Bv2 2 no additional Source GEO sample is GSM199386 Last updated (according to GEO): Jun 08 2007 Primary Neoplasm 1000 1000 hindbrain clone 48 is a clonal Nurr1 stable c17.2 neural stem cell line with similar proliferation rate as puroD and therefore both were matched for subsequent analysis. Source GEO sample is GSM82225 Last updated (according to GEO): Nov 07 2005 861 Cerebral cortex testis 52 58 human cerebellum Source GEO sample is GSM87137 Last updated (according to GEO): Feb 08 2006 CNS-SC_InjB30m-3bB-s2 Integumentary system 1000 Diaphragm 112 Day mdx rep 2 Wild type inbred mice Source GEO sample is GSM83026 Last updated (according to GEO): Nov 10 2005 nerve, HumanSuralNerve: Human Schwann cell RNA extracts 330 Passage 3_le1 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114445 Last updated (according to GEO): Jun 16 2006 861 Heart Neoplasm 861 36 21 from whole brain 1000 frontal lobe 1000 Kidney 14 6 (amygdala 12 frontal Lobe 23 8 0 leukemia total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Sphingosine-1-phosphate for 120min Source GEO sample is GSM5749 Last updated (according to GEO): May 27 2005 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211424 Last updated (according to GEO): Jul 18 2007 Expression profiling of spinal cord section (T9) extracted from rats 48h following moderate injury Source GEO sample is GSM31557 Last updated (according to GEO): May 27 2005 861 Brain Basal 1000 R701P01101 Blood 1000 HA96-37B glial fibrillary acidic protein 1398 1428 1BJZ02052107_TestiGermCell Natural variation in human gene expression assessed in lymphoblastoid cells adenocarcinoma 3368 0 18 Liver (HCV+, SF28, 1) Obesity 861 brain, cerebral cortex: Rat_03-53_NroLep_Lipska_e1_le1 IDC43 on harvard-12k 66 56 femur C57BL no additional Source GEO sample is GSM199215 Last updated (according to GEO): Jun 08 2007 Intestines, Small 1000 10 hr Hela Double Thymidine Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:494, Count:32 Corner- Avg:27549, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:7.694901,SFGene:All Background:Avg:402.38,Stdev:3.13,Max:414.0,Min:396.1 Noise:Avg:8.80,Stdev:0.24,Max:9.4,Min:8.1 RawQ:12.70 Keywords = ALL Source GEO sample is GSM3440 Last updated (according to GEO): May 27 2005 Approximately 10 pairs of the most anterior dorsal root ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until sufficient tissue was harvested to be pooled by genotype. Ganglia from 5 embryos were pooled for a single analysis and RNA extracted using the RNeasy system (Qiagen). Source GEO sample is GSM132430 Last updated (according to GEO): Aug 30 2006 861 Brain Epithelial Cells 1000 Expression profiling of spinal cord section (T10) extracted from rats 28d following severe injury Source GEO sample is GSM31366 Last updated (according to GEO): May 27 2005 901 Heart Diseases 166 156 of retinal 228 219 Hippocampi 6419_Lung developed PGD cerebral cortex 7 21 861 Blood Ovary 1000 166 135 of surrounding carcinoma in situ 1282 CP48_12 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28789 Last updated (according to GEO): May 27 2005 1000 Brain Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184808 Last updated (according to GEO): Apr 26 2007 rad001 6d, biological rep2 f2#273 versus pool Mouse Brain tissue IleumSham_022SAF6P_176.txt Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2720 Source GEO sample is GSM2141 Last updated (according to GEO): Nov 21 2005 O377 homozygotes brains 9 T3 treatment for ind I TEL-AML1-C41 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A cervix_8 Source GEO sample is GSM80633 Last updated (according to GEO): Mar 31 2006 Ovarian_Tumor_ClearCell_KU-OC-003 Cerebral cortex 1000 901 Caudate nucleus structure Abdomen 861 GM19092 91 from the bone marrow 72 FormerSmoker 95 1935 1922 out the liver Gene expression data of substantia nigra from postmortem brain of PD patients Source GEO sample is GSM184369 Last updated (according to GEO): May 29 2007 the blood 393 402 1000 Hippocampus SCG_sema3A_24h_rep2 1000 Spinal Cord Central gray substance of midbrain 861 Infection 1112 1121 embryonic hearts 1064 1079 278 255 ischemic cardiomyopathy HapMap YRI_parent Male Source GEO sample is GSM159675 Last updated (according to GEO): Feb 01 2007 Liver 0 4 Prostate Gland 1 Normal 861 Mammary gland TAp63 alpha 24h induction s2 15 0 Hindlimb muscle the superficial 1417 1431 Lung carcinoma (A549) [JunctionChip 5 of 5] septum short access to cocaine replicate 2 Parkinson's disease sample x190 11 0 Hypothalamus Pooled EDL RNA samples from five 8 wk old male mdx5cv mice Source GEO sample is GSM13667 Last updated (according to GEO): May 28 2005 Seminoma 1000 Pool of 10 cochlear tissues at E13 Source GEO sample is GSM182580 Last updated (according to GEO): Aug 14 2007 CNS-RM_Ctr3mo-2B-s2 1000 Hippocampus CNS-RM_Mod28d-4A-s2 5 0 thymus brain, cerebral cortex: NMDA 5_le1 10 0 Hippocampus 1000 Cerebral cortex Hyperdip>50-C10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Brain brain, cerebral cortex: Rat_03-02_NroLep_Lipska_e1_le1 Plasma 861 1000 Communicable Diseases total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with TGF-beta (transforming growth factor-beta) for 120min Source GEO sample is GSM5796 Last updated (according to GEO): May 27 2005 in the postnatal mouse cochlear nucleus 45 83 Transcriptome fingerprints distinguish hallucinogenic and nonhallucinogenic 5-hydroxytryptamine 2A receptor agonist effects in mouse somatosensory cortex. Spindle Cell Neoplasm 983 146 138 in aorta Lymphoblastoid Cell Line for Individual 8150.3 log phase brain 0 5 Spleen 0 5 Gene expression profiles of human breast cancer progression. Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10166.gif Source GEO sample is GSM79679 Last updated (according to GEO): Sep 22 2006 osteoblast 627 637 m1-WT4 1000 Glaucoma brain_DLPFC_bipolar B_mr427 129S6/SvEvTac amygdala rep2 PGA-Csx_het_3a-m4 Primary tumor 19 32 Backskin_WT_P14_rep1 Heart 861 of the heart 842 854 Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. Moderate controlled cortical impact with pneumatic impactor, 6 m/s impact velocity and 1.5 mm deformation. 4h after surgery, a 4 mm diameter disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44502 Last updated (according to GEO): May 27 2005 for liver 26 35 n/a Source GEO sample is GSM177922 Last updated (according to GEO): Jun 11 2007 1000 Rectum Category: Lymphoma Classification Subcategory: Hematopoetic cell lines Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b043 Source GEO sample is GSM1989 Last updated (according to GEO): Nov 21 2005 65 41 in murine small intestine Study of in vitro granulocyte differentiation Source GEO sample is GSM137467 Last updated (according to GEO): Jun 06 2007 Spleen 1000 Control Abdominal Aorta 1-F Bone Marrow 1000 1000 Spleen Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:273, Count:32 Corner- Avg:33301, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:8.009797,SFGene:All Background:Avg:488.49,Stdev:12.51,Max:512.3,Min:457.4 Noise:Avg:11.13,Stdev:0.38,Max:12.7,Min:9.9 RawQ:14.77 Keywords = ALL Source GEO sample is GSM3405 Last updated (according to GEO): May 27 2005 Lung cancer 0 10 of fibroblasts 107 120 1000 Brain Stem Expression profiling of spinal cord section (T10) extracted from rats 7d following laminectomy (sham) Lot batch = Source GEO sample is GSM4439 Last updated (according to GEO): May 28 2005 25 7 Right Temporal Lobe 15 of the cerebral cortex 36 Left ventricular structure 865 1115 1102 cardiomyopathy Affymetrix RGU34A 0H B 861 Brain 1000 Aorta TGFBd8_22 14 0 Small Intestine 1000 Brain Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188828 Last updated (according to GEO): Jun 06 2007 brain, cortex: 3dsham2_e1_le1 NCI60.39_LABEL43EXTRACT42SUB3 Source GEO sample is GSM134188 Last updated (according to GEO): Aug 06 2007 19 0 bone marrow sprague2 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with ELC for 60min Source GEO sample is GSM5549 Last updated (according to GEO): May 27 2005 OAC:_92A2 Amygdala 5 Normal 906 Blood Cells Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp1215 Source GEO sample is GSM2172 Last updated (according to GEO): Nov 21 2005 Total RNA from fresh prepared stria vascularis, pool from 12 cochleas (=6 animals); used as control Source GEO sample is GSM124574 Last updated (according to GEO): Aug 04 2006 Brain_Aged_Salineip_4hr_mouse3(OP3_#63) HCC-2998_CL4002_Colon on Affymetrix GeneChip Human Full Length Array HuGeneFL Normal Source GEO sample is GSM176093 Last updated (according to GEO): Apr 09 2007 12 0 Blood T cells N2_d3 #2(16012165010078) To investigate the gene program activated by serotonergic hallucinogens in mouse somatosensory cortex, the effects of the 5-HT2A agonist (±)2,5-dimethoxy 4-iodoamphetamine (DOI) on gene expression was studied. The 5-HT2A serotonin receptor is a member of the 5-HT2 receptor subfamily of G protein?coupled receptors. The 5-HT2A receptor is thought to modulate processes related to cognition, appetite, mood, anxiety, sleep, and sexual behavior. Abnormal function of this receptor has been implicated in neuropsychiatric disorders such as major depression and schizophrenia. In particular, the 5-HT2A receptor has been implicated in the modulation of the mechanisms related to psychosis. We compared gene response patterns in the somatosensory cortical brain area, which has a high density of 5-HT2A receptors and has been implicated in the action of hallucinogenic drugs. Mice (strain 129Sv) were injected with DOI (2 mg/kg or 10 mg/kg) or vehicle, animals were sacrificed after 1 h, and somatosensory cortex samples dissected on ice for RNA extraction. Seven independent microarray hybridizations from seven different DOI- or vehicle-treated mouse pairs were performed. In this particular hybridization, 15 µg of RNA was used. Keywords = somatosensory cortex 5-HT2A receptor DOI Source GEO sample is GSM3378 Last updated (according to GEO): Oct 28 2005 259 246 from 6 brains P1_KIDNEY_6 human frontal cortex Source GEO sample is GSM86964 Last updated (according to GEO): Feb 08 2006 DLCL-0027 Tumor__Pancreas_Adeno_Pan_17T on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Modiolus anguli oris Striat_022MAC35_004.txt 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113959 Last updated (according to GEO): Jun 16 2006 91 from the bone marrow 72 Primary Neoplasm 1000 14 NT C4 Treatment, type=add, description=10ng/mL Ciliary neurotrophiic factor, 4d Source GEO sample is GSM92505 Last updated (according to GEO): Jan 13 2006 UBOC1 Exp B Day 0 (b) Levitiracetam brainstem 4 Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53429 Last updated (according to GEO): Jul 06 2005 Arteries 861 Nasal; Upper Repiratory Mucosa Keywords = mouse gene expression database Source GEO sample is GSM29410 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153439 Last updated (according to GEO): Jan 11 2007 Spleen vs Tumor necrosis factor-alpha Treated B cell 30min (set1) Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181181 Last updated (according to GEO): Jul 12 2007 142 116 of parieto-occipital cortex Study of in vitro granulocyte differentiation Source GEO sample is GSM137433 Last updated (according to GEO): Jun 06 2007 26 0 Spinal cord [JunctionChip 3 256 235 dilated heart failure Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 8089 left_liver_lobe 861 Acquired Immunodeficiency Syndrome Mammary Neoplasms 901 1000 Seizures Leukemia Lymphoblastic (MOLT-4) [JunctionChip 3 of 5] Foreskin Microarray data set (Sample 4) Gene expression data from whole tumor Source GEO sample is GSM182287 Last updated (according to GEO): Apr 16 2007 861 Cerebral cortex Putamen P8 Normal lg_NY51 861 Brain Gene expression data from liver Source GEO sample is GSM243404 Last updated (according to GEO): Nov 16 2007 I_U133A_107_Amy Blood 1000 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15116.gif Source GEO sample is GSM91608 Last updated (according to GEO): Sep 22 2006 Gene expression data from rat metanephric mesenchymes cultured for 5 days in the presence of the ANX fraction Source GEO sample is GSM126225 Last updated (according to GEO): Dec 08 2006 HOP-62 hgu95c outer medulla 31 43 1000 Brain 22-oct-2002-liverA2-Mu11KsubAsc Lymphoblastoid Cell Line for Individual 8112.3 log phase 255 234 with HIV encephalitis kidney 37 43 Blood 1000 DLCL-0019 Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Source GEO sample is GSM15954 Last updated (according to GEO): May 28 2005 5 0 brain DBA/2J CHR, Rep3 GSE7475 Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108007 Last updated (according to GEO): Jun 06 2006 5 0 brain Performed by UCI Microarray Facility. Source GEO sample is GSM203501 Last updated (according to GEO): Jun 22 2007 Muscle 1000 26 15 endometrioid To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18481 Last updated (according to GEO): May 27 2005 Breast 861 Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2666.gif Source GEO sample is GSM72137 Last updated (according to GEO): Sep 22 2006 901 Coronary artery 861 DNA Damage 5 0 brain brain, Right Frontal Lobe: Extract55_le2 7 frontal cortex 20 0029_1464_H95A2_T92-58_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A osteoblast 627 637 Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231048 Last updated (according to GEO): Sep 26 2007 204 194 of retinal 1189 for epithelial cells 1208 Gene expression training data set from rat blood samples exposed to either 150, 1500 or 2500 mg/kg of APAP for 6, 12 or 24 hours. Last Updated (by provider): Sep 18 2007 Contributers: Richard S Paules Alexandra N Heinloth Pierre R Bushel B304 immature Dcs IFN alpha treatment R582P01062 Hippocampus 1986 15 month Old 1000 Prostate HDMTX-8 Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181999 Last updated (according to GEO): Apr 13 2007 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153351 Last updated (according to GEO): Dec 27 2006 pituitary Source GEO sample is GSM18612 Last updated (according to GEO): May 27 2005 2500 mg/kg X 6 hr Source GEO sample is GSM129844 Last updated (according to GEO): Sep 18 2007 Myocardial Infarction 1000 Lung (fetal) [JunctionChip 2 of 5] H123 CN B mouse hippocampus 0 16 Infection 1000 MDA Mb231 Treated 3 Treated Voxel A2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1127 Last updated (according to GEO): Nov 21 2005 NFIA P16WT3 Sample is skeletal muscle from obese patient undergoing elective abdominal surgery Source GEO sample is GSM4002 Last updated (according to GEO): May 28 2005 GC (HKG82T) in bronchial epithelia 311 332 NB-C1 on NHGRI-6.5k_b Semeralul_PFC_Development_Week3_Batch1_Animal_6 Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108013 Last updated (according to GEO): Jun 06 2006 Trauma 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-gamma (IFN gamma) for 60min Source GEO sample is GSM5605 Last updated (according to GEO): May 27 2005 CNS-SMTC_CtrT0-3B-s2 Primary Neoplasm 1000 ND018 Whole Brain 73 83 Timepoint10r no additional Source GEO sample is GSM199026 Last updated (according to GEO): Jun 08 2007 Testis 861 Spleen 1000 E7.0_rep1 Nose 1000 CNS-RM_Mod3mo-2A-s2 from rat lungs 21 34 1000 Hippocampus in brain 1123 1130 246 219 of parieto-occipital cortex n/a Source GEO sample is GSM177941 Last updated (according to GEO): Jun 11 2007 no additional Source GEO sample is GSM199080 Last updated (according to GEO): Jun 08 2007 kidney 178 184 VDXIGRU_246821 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226157 Last updated (according to GEO): Nov 02 2007 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection). Source GEO sample is GSM36426 Last updated (according to GEO): May 27 2005 1000 Kidney Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:364, Count:32 Corner- Avg:36544, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:15.267480,SFGene:All Background:Avg:408.40,Stdev:5.81,Max:426.0,Min:399.9 Noise:Avg:9.27,Stdev:0.43,Max:10.8,Min:8.4 RawQ:13.27 Keywords = ALL Source GEO sample is GSM3495 Last updated (according to GEO): May 28 2005 901 Stem cells PGA-MurLungRag-pbs-24h-1bB-s2 brain, unknown: Sample56_e1_le1 Heart 1000 30 19 Solid tumor 129:23-4,5,6 amygdala human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155041 Last updated (according to GEO): Jun 04 2007 KPeterson-NonMet-24G110-s2 brain 0 5 OccipitalLobe Source GEO sample is GSM18932 Last updated (according to GEO): Sep 25 2006 Osteoblasts 1000 10 week control spinal cord rep 1 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19251 Last updated (according to GEO): May 27 2005 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 5 day time point Source GEO sample is GSM159794 Last updated (according to GEO): Apr 23 2007 kidney 37 43 CNS-SC_InjA7d-1C-s2 54h-Control replication 1 Keywords = preimplantation Keywords = development Source GEO sample is GSM14704 Last updated (according to GEO): May 28 2005 Fibroblasts 38 48 brain, Right Frontal Temporal: Extract69_le1 A genome-scale map of expression for a mouse brain section obtained using voxelation. PMN_control_180min_Patient14 861 Brain Brain 1000 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD9 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD9 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36699 Last updated (according to GEO): May 27 2005 Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22578 Last updated (according to GEO): May 27 2005 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153424 Last updated (according to GEO): Jan 11 2007 PMN_LB_180min_Patient12 Mesenchymal Stem Cells 1000 of human breast cancer 31 52 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188713 Last updated (according to GEO): Jun 06 2007 Category: Cell-line Subcategory: HMEC Scanning Software: unknown Software version: unknown Lot batch = 0130-5k Source GEO sample is GSM1943 Last updated (according to GEO): Nov 21 2005 from a primary branch 21 41 brain, cerebral cortex: 14999_e2_le1 41 28 in mouse brain GBM Treatment, type=remove Source GEO sample is GSM99487 Last updated (according to GEO): Apr 21 2006 Expression profiling of spinal cord section (T10) extracted from rats 30m following mild injury Source GEO sample is GSM31331 Last updated (according to GEO): May 27 2005 201 184 uterine leiomyomas with Alzheimer's disease 27 50 D_U133Plus_19_DLPFC_R LDMTX_MP-DX-2 Endometrial Stromal Sarcoma (SF26) no additional Source GEO sample is GSM199373 Last updated (according to GEO): Jun 08 2007 Male 21.5 yr after antibody enrichment scan 2 (U133A) GSE6959 1000 Integumentary system Squamous cell carcinoma 875 - Source GEO sample is GSM216544 Last updated (according to GEO): Aug 09 2007 NINDS-RNP-SNC-5aA-s2 healthy control sample x191 Cochlea 0 6 nodose_nucleus_4 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68146 Last updated (according to GEO): Jul 07 2006 110 94 of heart failure 23 6 (postcentral gyrus 1000 Left 1000 Lipids 861 Occipital lobe 278 255 ischemic cardiomyopathy 17 7 hippocampus HC74 CB B 109 FC BA9 B Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47520 Last updated (according to GEO): May 29 2005 Expression data after reversal of DNA methylation Source GEO sample is GSM230908 Last updated (according to GEO): Sep 20 2007 9 0 Blood Test 861 Arteries prostate Source GEO sample is GSM203298 Last updated (according to GEO): Jun 21 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145517 Last updated (according to GEO): Nov 20 2006 BL-C1 on NHGRI-6.5k_b 1000 ovarian neoplasm "Sample 90, BRCA1 mutation(1 months) age 29 erp no" on vantveer-oligo Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184793 Last updated (according to GEO): Apr 26 2007 MGMH030212058Bspinalcordupper GM18504 Lymphoblastoid Cell Line for Individual 8183.3 log phase 861 Blood Keywords = Heart 505 521 of a colorectal adenoma 7 29 Gonadectomized Dahl-Iwai Male LowSalt Cortex rat9 gdahl_cortexr_k_GX_9c_051702 M_U133Plus_111_HC Gene expression of organ of Corti of newborn rats_cultivation_hypoxia_repeat 2 inner ear Brain 861 brain, cerebral cortex: Rat_02-55_VHL_Lipska_e1_le1 Liver Test (Blinded) Sample Source GEO sample is GSM130152 Last updated (according to GEO): Sep 18 2007 ovarian neoplasm 902 Brain 1000 from colonic normal mucosa 21 47 MAS 5.0, scaled to 500; Affymetrix Data Mining Tool 3.0; dChip was used to determine differentially expressed genes (MBEI); Statisticaly Analysis of Microarrays (SAM), as described in Miller et al. 2004. Source GEO sample is GSM108080 Last updated (according to GEO): Sep 12 2006 GM18863 M_U133A_101_DLPFC_R Hippocampus 1000 36 0 Within the vertebrate nervous system Control replicate 1 1000 Atherosclerosis 861 Heart Sample represents the supraoptic nucleus from 5 control animals Source GEO sample is GSM69465 Last updated (according to GEO): Dec 15 2005 Type 1 Diabetes patient and the timepoint 4 months after diagnosis. Source GEO sample is GSM228638 Last updated (according to GEO): Sep 11 2007 Disorder of artery 865 Coronary Arteriosclerosis 1000 861 Adenocarcinoma CNS-RM_Ctr24h-2B-s2 Parkinson Disease 1000 858 Mesodermal cell Cerebral Cortex 9 Normal human cerebellum Source GEO sample is GSM87162 Last updated (according to GEO): Feb 08 2006 Epithelial Cells 901 1st 1hr C-CA1 Measles 861 Mutations in the adenomatous polyposis coli (APC) gene that result in excessive beta-catenin-induced cell signaling are implicated in the risk of colon cancer. Although the mechanism of APC-mediated tumorigenesis is known, the pathways that translate beta-catenin signaling into tumor growth in vivo are undefined. To address this, gene expression profiles of normal intestinal epithelial cells were compared with those from adenomas and carcinomas from APC(Min/+) mice, a model of APC-related colorectal cancer. The gene expression profiles of adenomas and carcinomas were very similar, which is consistent with the theory that carcinomas progress from adenomas in this model system. Tumors had altered transcript abundance for members of several pathways that influence cell growth and proliferation including growth factors/receptors, molecules involved in apoptosis, and protein processing and catabolism enzymes. Comparison of gene expression between adenomas and carcinomas revealed nine differentially expressed transcripts. These included members of three growth-regulating pathways, and the results are consistent with the increased growth potential of carcinomas. SRY-box containing gene 17 (Sox 17), a negative regulator of beta-catenin signaling, and calbindin-D9K, a factor that enhances calcium transport, were more highly expressed in adenomas than carcinomas (approximately 4-fold and 15- to 22-fold, respectively). Transcript abundance for insulin-like growth factor binding protein 5, which mediates insulin-like growth factor function, was 2.6-fold greater in carcinomas. Because the changes in gene expression observed in this study are directly associated with a deficiency in APC, the data provide new insights into how loss of this important tumor suppressor translates into benign and malignant tumor growth. Anterior nares 1000 WT 2 mon replicate 4 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28764 Last updated (according to GEO): May 27 2005 H9LMS00102605 1000 Brain Primary Neoplasm 1000 Exp C, Animal #1, 1mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours Source GEO sample is GSM246160 Last updated (according to GEO): Dec 03 2007 Gene expression data from rat metanephric mesenchymes cultured for 4 days in the presence of LIF Source GEO sample is GSM126199 Last updated (according to GEO): Dec 08 2006 Lymphoblastoid Cell Line for Individual 8104.3 log phase 1000 Brain gene expression of 5 day LIF differentiated ESCs Source GEO sample is GSM181955 Last updated (according to GEO): Apr 12 2007 Brain 1000 24 0 human prostate PC3 tumors Heart failure 1000 Nasal Epithelium 901 Brain_MD_8_Medulloblastoma_Classic_D on Affymetrix GeneChip Human Full Length Array HuGeneFL 15 0 human cerebellum Cerebral cortex 861 dorsal striatum wistar 3966 whole tissue, individual animal, 10 weeks old, male Wistar dorsal striatum file:p3981w Source GEO sample is GSM15190 Last updated (according to GEO): Oct 28 2005 Medulla Oblongata 861 GSE4058 5 0 brain Carcinoma, Large Cell 888 Primary small cell lung carcinoma 2942 0 37 Collagen 1000 Traumatic brain injury 0 21 ALL_10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit. Source GEO sample is GSM200596 Last updated (according to GEO): Jul 09 2007 1000 Infection none Source GEO sample is GSM123213 Last updated (according to GEO): Jul 26 2006 1000 ovarian neoplasm 1000 Spleen PGA-MLS-RA-1bAv2-s1 intestine_PPARa_kockout_24hfasted_rep3 901 Coronary artery 78 73 rectum 1000 Prostate Nervous system structure 901 0 hours, repeat 3 1000 Brain 24 0 human prostate PC3 tumors N/A Source GEO sample is GSM6688 Last updated (according to GEO): May 28 2005 normal testis 54 66 NA12750 growth 1, replicate 3 447 438 infection 1000 Left MO_control_0min_Patient9 Trasnsformed Lymphocytes Bipolar Disorder Affected Twin Pair 3 (DCBD3.1)(TP9) Large Pre-BII cells 1b Liver 1000 rat cortex Treatment, type=time_course, measurement=7.0 d Source GEO sample is GSM53214 Last updated (according to GEO): Jul 06 2005 Branch 861 1000 melanoma control 2 weeks A Treatment, type=time_course, measurement=2.0 weeks Source GEO sample is GSM107856 Last updated (according to GEO): Jun 06 2006 Parkinson Disease 861 This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis. Stembase Experiment ID: E189 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189 SCGP Sample ID: S240 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_198 Short description: RNA isolated from primary retinal sphere cells. Estimated purity: > 90% RNA concentration: > 0.7 ug/ul Num cells for RNA prep: ~600,000 Sample volume: 5.0 ul Source GEO sample is GSM87201 Last updated (according to GEO): Jan 19 2006 lateral hypothalamus 860 879 14 7 amygdala Morula replication 1 Keywords = preimplantation Keywords = development Source GEO sample is GSM14687 Last updated (according to GEO): May 28 2005 Richard Almon-19-1138200270008 41 29 Control blood NA Source GEO sample is GSM84323 Last updated (according to GEO): Dec 01 2005 17 7 hippocampus brain 0 5 vestibular_nuclei_superior_2 Source GEO sample is GSM80879 Last updated (according to GEO): Mar 31 2006 abdominal aortic aneurysm 45 69 Whole Brain 62 72 CNS-SpinalCmod-Adult-4h-2C-s2 /NJ mouse pituitary gland 27 51 vestibular_nuclei_superior_4 days nasal epithelium 1126 1147 plasma cells 50 61 8070_Lung did not develop PGD 861 Degenerative polyarthritis NSCLC_NCIH226 on Affymetrix GeneChip Human Full Length Array HuGeneFL non-branched in vitro-formed UBs and MM, rep2 330 324 uterus Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181231 Last updated (according to GEO): Jul 12 2007 18 0 Trigeminal_Ganglion Primary Neoplasm 1000 Neuraxis 923 the heart 987 996 Autistic Disorder 877 Brain 861 Elucidation of the phenotypic, functional and molecular topography of a myeloerythroid progenitor cell hierarchy Gene expression data from postmorten brain regions Source GEO sample is GSM145710 Last updated (according to GEO): Nov 20 2006 CNS-SpinalCmod-Adult-4h-2A-s2 1000 Prostate Subject code A20 607 597 the rectum due to prostate carcinoma 59 84 901 Bone Marrow lh brain 1722 1730 f2#82 versus pool Mouse Brain tissue Blood 861 Gene expression data from postmorten brain regions Source GEO sample is GSM144966 Last updated (according to GEO): Nov 20 2006 Flow cytometry sorted double negative thymocytes from Egr1/Egr3 double knockout animal #2. Treatment, type=fractionate Source GEO sample is GSM130405 Last updated (according to GEO): Aug 24 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145241 Last updated (according to GEO): Nov 20 2006 Pituitary Gland, Posterior 1000 1000 Impaired cognition C87 on NCI-7.6k 1037 of transitional epithelium 1012 1000 Heart /3T3 fibroblasts 743 759 Expression profiling of spinal cord section (T8) extracted from rats 24h following mild injury Source GEO sample is GSM31433 Last updated (according to GEO): May 27 2005 Cerebellum 1000 1037 of transitional epithelium 1012 ovary 45 50 Disease Source GEO sample is GSM176356 Last updated (according to GEO): Apr 09 2007 trigeminal_ganglia_8 Source GEO sample is GSM80905 Last updated (according to GEO): Mar 31 2006 115 86 of subcutaneous adipose tissue 865 Disorder of artery Plasma 861 Cockayne syndrome B cell Source GEO sample is GSM226611 Last updated (according to GEO): Sep 04 2007 Hippocampus 1 Normal D_U133A_33_nAcc C3H/HeJ Olfactory Bulb F from aorta 150 160 N/A Source GEO sample is GSM96299 Last updated (according to GEO): Feb 13 2006 Epithelium 861 from whole tumor 21 36 brain, frontal cortex: Sample56_e1_le1 Vector-veh-1 5 0 brain acute myeloid leukemia Source GEO sample is GSM227426 Last updated (according to GEO): Sep 12 2007 91 from the bone marrow 72 Gene expression data from postmorten brain regions Source GEO sample is GSM145434 Last updated (according to GEO): Nov 20 2006 Fibroblasts 861 901 Bone Marrow 1000 Hypothalamic structure Blood 1000 Muscle 861 257 247 /m kidneys 3AJZ02082987B_TONGUE 901 Temporal Lobe Disorder of artery 865 Liver 0 4 Recurrent Adenocarcinoma 9 Brain Stem 1000 5 0 brain Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed for 24 h to hydrostatic pressure (HP24), pressure experiment # 3 (PE3). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11411 Last updated (according to GEO): Dec 15 2006 from ventral prostate 21 41 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11493 Last updated (according to GEO): May 28 2005 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 1 hours after lights on. Original RNA code = LC20A. Source GEO sample is GSM227405 Last updated (according to GEO): Sep 10 2007 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181064 Last updated (according to GEO): Jul 12 2007 from liver 21 30 861 Neoplasm 1000 Neuraxis Expression profiling of moderately injured raphe at 4h in rats Source GEO sample is GSM41615 Last updated (according to GEO): May 27 2005 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188818 Last updated (according to GEO): Jun 06 2007 Expression profiling of somatomotor cortex extracted from rats at 28d following moderate injury Source GEO sample is GSM41711 Last updated (according to GEO): May 27 2005 1000 Neoplasm pfc_1054_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A of schizophrenia 651 666 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18935.gif Source GEO sample is GSM84138 Last updated (according to GEO): Sep 22 2006 Acetaminophen 24hr Rat 1987 blood vs. Acetaminophen 24hr Rat Pooled Control blood Recurrent Squamous cell carcinoma 3 0 34 hippocampus 7 17 901 Caudate nucleus structure with prostate cancer increasingly 56 88 49 40 from liver brain_DLPFC_bipolar C_mr523 Expression profiling of somatomotor cortex extracted from rats at 14d following moderate injury Source GEO sample is GSM41688 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T8) extracted from rats 4h following severe injury Source GEO sample is GSM31506 Last updated (according to GEO): May 27 2005 Frontal Cortex Source GEO sample is GSM107939 Last updated (according to GEO): Jun 06 2006 Primary Neoplasm 1000 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc83 Source GEO sample is GSM1844 Last updated (according to GEO): Nov 21 2005 /NJ mouse periaqueductal gray 27 55 ANIMALS Patched heterozygous mice (Goodrich et al., 1997) were obtained from Matthew Scott?s lab at Stanford, and maintained by breeding with 129X1/SvJ mice from Jackson Laboratories. Math1-GFP transgenic mice (Lumpkin et al., 2003) were provided by Jane Johnson at UT Southwestern Medical Center. Math1-GFP/patched+/- mice were generated by crossing patched heterozygotes with Math1-GFP mice, and then backcrossing to Math1-GFP mice three times before further analysis. All mice were maintained in the Cancer Center Isolation Facility at Duke University Medical Center. ISOLATION OF CELLS Granule cell precursors (GCPs) were isolated from 7-day-old (P7) patched+/- mice; preneoplastic cells were obtained from 6 week-old patched mutants; and tumor cells were obtained from 10-25-week old patched mutants displaying physical and behavioral signs of medulloblastoma. Cells were isolated from each source using a protocol described in (Wechsler- Reya and Scott, 1999). Briefly, cerebella were digested in solution containing 10 U/ml papain Oliver et al. Pre-Neoplastic Stage of Medulloblastoma - 8 - (Worthington, Lakewood, NJ) and 250 U/ml DNase (Sigma) and triturated to obtain a cell suspension. This suspension was centrifuged through a step gradient of 35% and 65% Percoll (Amersham Biosciences, Piscataway, NJ), and cells were harvested from the 35%-65% interface. Cells were resuspended in serum-free culture medium consisting of Neurobasal containing B27 supplement, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen, Carlsbad, California) and counted on a hemacytometer. Cells used for RNA isolation were centrifuged and flash frozen in liquid nitrogen. For proliferation assays or immunostaining, cells were plated on poly-D-lysine (PDL)-coated tissue culture vessels and incubated in serum-free culture medium. MICROARRAY HYBRIDIZATION AND ANALYSIS RNA from GCPs, pre-neoplastic cells and tumor cells (isolated as described above, but not FACS-sorted) and from normal adult cerebellum (not dissociated) was converted to cDNA using the Superscript Choice cDNA kit (Invitrogen) and a T7-dT(24) primer (Genset/Proligo, Boulder, CO). cRNA was generated using a T7-transcription/labeling kit from Enzo Life Sciences and hybridized to Affymetrix U74Av2 chips (Affymetrix, Santa Clara, CA). Chips were scanned, and hybridization data were acquired using Affymetrix Suite 5.0 software. Affymetrix CEL files were normalized and quantified using Bioconductor software with the gcRMA model to quantify gene expression levels (Gentleman and Carey, 2002). Unsupervised principal components analysis (PCA) was used to identify the relationships among normal adult cerebellum, GCPs, pre-neoplastic cells and tumor cells based on expression profiles. To identify genes that were differentially expressed among GCPs, pre-neoplastic cells and tumor cells, supervised analysis was carried out. A gene-by-gene ANOVA model with three groups (GCP, pre-neoplastic, tumor) was used to fit the log2-transformed intensities. To correct for multiple comparisons, the nominal p-value was adjusted using the false discovery rate (Benjamini and Hochberg, 1995). Genes were considered to be differentially expressed if they satisfied all of the following criteria: a difference in expression greater than 1.9-fold between any two groups, a maximum absolute intensity difference larger than 32 units, and an adjusted pvalue < 0.01. There were 118 genes that met these criteria. The identities of differentially expressed genes were verified by integrating data from the Affymetrix and Unigene databases. Gene functions were determined using information from Gene Ontology, Unigene, LocusLink and PubMed databases. Clustering was performed with Cluster and Treeview (Eisen et al., 1998). All statistical analysis was performed using R-1.7 software (Dalgaard, 2002). Results were visualized with Spotfire 6.0 (Somerville, MA). Keywords = medulloblastoma Keywords = pre-neoplastic Source GEO sample is GSM45618 Last updated (according to GEO): Oct 28 2005 Adenocarcinoma 861 Liver 1000 17 7 hippocampus HNC008 1000 Obesity seminoma specimen, pT1, patient age: 38y; W97 082 Gene expression data from postmorten brain regions Source GEO sample is GSM145975 Last updated (according to GEO): Nov 20 2006 HapMap JPT Female Source GEO sample is GSM159630 Last updated (according to GEO): Feb 01 2007 1000 Muscular Atrophy Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181104 Last updated (according to GEO): Jul 12 2007 923 Subcutaneous Fat plasma cells 50 61 Brain 1000 901 Bone Marrow Gene expression data from postmorten brain regions Source GEO sample is GSM145927 Last updated (according to GEO): Nov 20 2006 Normal__Breast_BR_2 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Blood Test (Blinded) Sample Source GEO sample is GSM130006 Last updated (according to GEO): Sep 18 2007 G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol receptor ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage.. Date GSE628 Last Updated: May 29 2005 Contributers: Mitchell J Weiss John J Welch Lewis A Chodosh Includes GDS568. Update date: Nov 10 2005. Dataset description GDS568: Analysis of erythroid differentiation using G1E ER4 clone cells. Estradiol addition induces Gata-1 triggering synchronous differentiation. 30 hour time course corresponds to late burst-forming unit-erythroid stage through orthochromatic erythroblast stage.. osteoblast 627 637 106 88 of P15 hippocampus ovarian tumor: serous Source GEO sample is GSM139459 Last updated (according to GEO): Apr 09 2007 HMEC X BC1369 861 Brain 22 0 cerebellum sprague 3901 Skeletal bone 861 1000 Amygdaloid structure cortex 7 12 Stress Disorders, Post-Traumatic 937 R530P00643 Gene expression data from postmorten brain regions Source GEO sample is GSM145865 Last updated (according to GEO): Nov 20 2006 D07 12h Media AML cDNA hybridization-ID28-L PGA-RnSalt_h_6w_1-2-m5 **** Source GEO sample is GSM4310 Last updated (according to GEO): May 27 2005 of caudal 93 101 Cerebral cortex 1000 3AJZ02060417_IsletCell Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181212 Last updated (according to GEO): Jul 12 2007 mdx diaphragm sample 2 861 Cardiomyopathies meningiomas 1421 1431 DLCL-0034 Two 90 minute exposures (3 hr recovery in between) to 1.0% isoflurane every day for 2.5 days, for a total of 5 exposures Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5117 Last updated (according to GEO): Mar 17 2006 To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132974 Last updated (according to GEO): Sep 12 2006 endometrium_8 Transitional epithelium 1000 in cancer 594 602 MDA-MB-435 hgu95a Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13149.gif Source GEO sample is GSM79693 Last updated (according to GEO): Sep 22 2006 none Source GEO sample is GSM244634 Last updated (according to GEO): Nov 23 2007 human cerebellum Source GEO sample is GSM87146 Last updated (according to GEO): Feb 08 2006 AA Treatment, type=remove Source GEO sample is GSM99502 Last updated (according to GEO): Apr 21 2006 Expression profiling of spinal cord section (T9) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31256 Last updated (according to GEO): May 27 2005 C57L/J Cerebellum B mouse cerebral cortex 0 21 Diet Induced Obese rat C8 Macrophage smi39 Genomic profiling of the human heart before and after mechanical support with a ventricular assist device reveals alterations in vascular signaling networks. GC (HKG3T) gene expression of 5 day LIF differentiated ESCs Source GEO sample is GSM181960 Last updated (according to GEO): Apr 12 2007 Primary Neoplasm 1000 13_360plus1 hrs nasal epithelium 1126 1146 Primary Carcinoma 876 NINDS-RNP-VTA-5aA-s2 Nasal Epithelium 901 3AJZ02022760_kidney Gene expression data from the hippocampus of wild-type mouse Source GEO sample is GSM172953 Last updated (according to GEO): Mar 08 2007 861 Cerebral cortex 861 Cerebral cortex Pool of 13 saccules at E14 Source GEO sample is GSM182617 Last updated (according to GEO): Aug 14 2007 Macrophages, Exposed to Brugia malayi (5) - Repeat #2 I_U133A_62_Amy total RNA extracted from one ApoE-/- mouse infected wtih an adenovirus expressing dominant negative cJun Source GEO sample is GSM157863 Last updated (according to GEO): Jan 25 2007 NCI60.21_LABEL25EXTRACT24SUB3 Source GEO sample is GSM134096 Last updated (according to GEO): Aug 06 2007 bronchial epithelia 224 243 1000 Brain ANIMALS Patched heterozygous mice (Goodrich et al., 1997) were obtained from Matthew Scott?s lab at Stanford, and maintained by breeding with 129X1/SvJ mice from Jackson Laboratories. Math1-GFP transgenic mice (Lumpkin et al., 2003) were provided by Jane Johnson at UT Southwestern Medical Center. Math1-GFP/patched+/- mice were generated by crossing patched heterozygotes with Math1-GFP mice, and then backcrossing to Math1-GFP mice three times before further analysis. All mice were maintained in the Cancer Center Isolation Facility at Duke University Medical Center. ISOLATION OF CELLS Granule cell precursors (GCPs) were isolated from 7-day-old (P7) patched+/- mice; preneoplastic cells were obtained from 6 week-old patched mutants; and tumor cells were obtained from 10-25-week old patched mutants displaying physical and behavioral signs of medulloblastoma. Cells were isolated from each source using a protocol described in (Wechsler- Reya and Scott, 1999). Briefly, cerebella were digested in solution containing 10 U/ml papain Oliver et al. Pre-Neoplastic Stage of Medulloblastoma - 8 - (Worthington, Lakewood, NJ) and 250 U/ml DNase (Sigma) and triturated to obtain a cell suspension. This suspension was centrifuged through a step gradient of 35% and 65% Percoll (Amersham Biosciences, Piscataway, NJ), and cells were harvested from the 35%-65% interface. Cells were resuspended in serum-free culture medium consisting of Neurobasal containing B27 supplement, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen, Carlsbad, California) and counted on a hemacytometer. Cells used for RNA isolation were centrifuged and flash frozen in liquid nitrogen. For proliferation assays or immunostaining, cells were plated on poly-D-lysine (PDL)-coated tissue culture vessels and incubated in serum-free culture medium. MICROARRAY HYBRIDIZATION AND ANALYSIS RNA from GCPs, pre-neoplastic cells and tumor cells (isolated as described above, but not FACS-sorted) and from normal adult cerebellum (not dissociated) was converted to cDNA using the Superscript Choice cDNA kit (Invitrogen) and a T7-dT(24) primer (Genset/Proligo, Boulder, CO). cRNA was generated using a T7-transcription/labeling kit from Enzo Life Sciences and hybridized to Affymetrix U74Av2 chips (Affymetrix, Santa Clara, CA). Chips were scanned, and hybridization data were acquired using Affymetrix Suite 5.0 software. Affymetrix CEL files were normalized and quantified using Bioconductor software with the gcRMA model to quantify gene expression levels (Gentleman and Carey, 2002). Unsupervised principal components analysis (PCA) was used to identify the relationships among normal adult cerebellum, GCPs, pre-neoplastic cells and tumor cells based on expression profiles. To identify genes that were differentially expressed among GCPs, pre-neoplastic cells and tumor cells, supervised analysis was carried out. A gene-by-gene ANOVA model with three groups (GCP, pre-neoplastic, tumor) was used to fit the log2-transformed intensities. To correct for multiple comparisons, the nominal p-value was adjusted using the false discovery rate (Benjamini and Hochberg, 1995). Genes were considered to be differentially expressed if they satisfied all of the following criteria: a difference in expression greater than 1.9-fold between any two groups, a maximum absolute intensity difference larger than 32 units, and an adjusted pvalue < 0.01. There were 118 genes that met these criteria. The identities of differentially expressed genes were verified by integrating data from the Affymetrix and Unigene databases. Gene functions were determined using information from Gene Ontology, Unigene, LocusLink and PubMed databases. Clustering was performed with Cluster and Treeview (Eisen et al., 1998). All statistical analysis was performed using R-1.7 software (Dalgaard, 2002). Results were visualized with Spotfire 6.0 (Somerville, MA). CORRESPONDING AUTHOR Robert J. Wechsler-Reya* Dept. of Pharmacology & Cancer Biology, Duke University Medical Center Box 3813, Durham, NC 27710 Phone: 919-613-8754. Fax: 919-668-3556. Email: rw.reya@duke.edu Keywords = medulloblastoma Keywords = brain tumor Source GEO sample is GSM45623 Last updated (according to GEO): Oct 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM144873 Last updated (according to GEO): Nov 20 2006 from the femurs 95 109 whole blood_101446 Heart 1000 1000 Coronary Arteriosclerosis Hypothalamus of rats before and during subjection to short (2 days) term heat acclimation. RNA extraction was accomplished using Tri Reagent (Molecular Research Center Inc. Ohio, USA). The probes were labeled for 1 h by the reverse transcription of total RNA (3 µg) at 42°C in a primer mix (Clontech) containing [32P]dATP (Amersham Biosciences, Buckinghamshire, UK). The reaction was terminated by adding 0.1M EDTA and 1 mg/ml glycogen (Sigma).The unincorporated 32P-labeled nucleotides were removed by Nucleo-Spin extraction columns (Clontech). Source GEO sample is GSM62948 Last updated (according to GEO): Oct 28 2005 Whole blood 0 10 39 21 from mammary glands Gene expression data from human colon tumor tissue Source GEO sample is GSM173335 Last updated (according to GEO): Apr 20 2007 m1-carcinoma3 Nasal Epithelium 901 small.intestine.2 861 Ganglia total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD40 for 60min Source GEO sample is GSM5495 Last updated (according to GEO): May 27 2005 U87 glioblastoma cell, clone 8.1 (expresses PDGF-A dominant-negative) Keywords = bioinformatics Keywords = gene expression Keywords = cancer Keywords = platelet-derived growth factor Keywords = sterol regulatory element binding protein Keywords = glioblastoma multiformae Keywords = microarray Source GEO sample is GSM34587 Last updated (according to GEO): May 27 2005 1000 Maxilla Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184824 Last updated (according to GEO): Apr 26 2007 861 Colon OVCAR-4_CL6002_Ovarian on Affymetrix GeneChip Human Full Length Array HuGeneFL Brain 1000 Lymphoblastoid Cell Line for Individual 8175.5 log phase Background: Colorectal cancers are believed to arise predominantly from adenomas. Although these precancerous lesions have been subjected to extensive clinical, pathological, and molecular analyses, little is currently known about the global gene expression changes accompanying their formation. Results: To characterize the molecular processes underlying the transformation of normal colonic epithelium, we compared the transcriptomes of 32 prospectively collected adenomas with those of normal mucosa from the same individuals. Important differences emerged not only between the expression profiles of normal and adenomatous tissues, but also between those of small and large adenomas. A key feature of the transformation process was the remodeling of the Wnt pathway reflected in patent over- and underexpression of 78 known components of this signaling cascade. Conclusions: Our transcriptomic profiles of normal colonic mucosa and colorectal adenomas shed new light on the early stages of colorectal tumorigenesis. Last Updated (by provider): Aug 02 2007 Contributers: Hubert Rehrauer Giancarlo Marra Jacob Sabates 7 year !Sample_source_name_ch1 = Post Natally excised Human lung tissue Source GEO sample is GSM107835 Last updated (according to GEO): May 04 2006 Plasma 861 MuscleRegen-ctx14d-1RLAv2-s2 ALL-B-cell-12 on Affymetrix GeneChip Human Full Length Array HuGeneFL H9SGK99092001 901 Lateral Sclerosis 407 psychiatric disorders 427 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11561 Last updated (according to GEO): May 28 2005 Brain 861 1000 Hippocampus GSE5446 AD control Treatment, type=dissect Source GEO sample is GSM119651 Last updated (according to GEO): Jul 10 2006 176 157 Analyzed spinal cord GSE9594 Cerebral cortex 861 of amyotrophic lateral sclerosis 151 182 Hippocampus 3 Normal 875 Refractory Carcinoma Two 90 minute exposures (3 hr recovery in between) to 1.0% isoflurane every day for 5 days, for a total of 10 exposures Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5114 Last updated (according to GEO): Mar 17 2006 Primary tumor 19 32 5 0 brain 0 cortex 5 small intestine 0 14 Brain 861 1000 Cerebral cortex 1500mg/kg APAP 24Hr rat 3625 blood vs. 3616 PC 24Hr (pool) 861 Breast Cerebral cortex 861 Lung 1000 Cerebral cortex Mk13: Hippocampus_21PT-AI_rep1 /J Frontal Cortex A 4 22 XX2_Paf HCC-2998 hgu95d GM19144 M_U133Plus_113_DLPFC 28 0 Adult frontal cortex cocaine3 2_cerebral_cortex_12hrs_sleep_#20 Pancreas at e13.5, Chip A, rep 2 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27029 Last updated (according to GEO): May 27 2005 CAD_replicate74 Bone Marrow 1000 901 Coronary artery 1000 Cerebral cortex hypothalamus sprague2 whole tissue, pool of 5 animals, 16 weeks old, male Sprague Dawley hypothalamus file:R3MH02061201 Source GEO sample is GSM15234 Last updated (according to GEO): May 28 2005 6 0 trachea Normal__Colon_CR_10 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Replicate2_Voxel E1 1000 Ischemia Lymphoblastoid Cell Line for Individual 8122.3 log phase Wild type 8 wk old male DBA/2J mouse pituitary gland Source GEO sample is GSM75006 Last updated (according to GEO): Feb 27 2007 901 Caudate nucleus structure AD 2hr C+S-DG 228 219 Hippocampi brain, hippocampus: CON-DG-22_e1_le1 Glial Fibrillary Acidic Protein 1000 CNS-SMTC_Mod4h-4C-s2 Tumor__Melanoma_MGH_8907 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Brain 1355 1318 of the peripheral innate immune system 21 0 Mammary Gland @ Lac9 Whole blood from a patient with corticobasal degeneration Source GEO sample is GSM153431 Last updated (according to GEO): Jan 11 2007 HC62 CN A Autistic Disorder 1000 like breast tumors frequently 537 565 f2#342 versus pool Mouse Brain tissue 239 233 Retinas Normal Bone Marrow processed in batch 4 Source GEO sample is GSM90422 Last updated (according to GEO): Mar 20 2006 plasma cells 50 61 28 7 Superior Frontal Gyrus CT6-CingulateCortex-replicate2 1000 Malignant neoplasm of breast metanephric mesenchyme, LIF, 4 days, biological rep2 Cell Culture Exposure (1MAC Halo2) C57BL10 TA sample 2 Epithelium 861 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15772.gif Source GEO sample is GSM91501 Last updated (according to GEO): Sep 22 2006 Plasma 861 Blood 1000 the blood 393 402 1000 Muscle snout epidermis; vibrissa epidermal region Source GEO sample is GSM18644 Last updated (according to GEO): May 27 2005 100307 brain, cerebral cortex: 14996_e2_le1 with myocardial infarction 313 339 Wild type 8 wk old male A/J mouse bed nucleus of the stria terminalis Source GEO sample is GSM106994 Last updated (according to GEO): Mar 05 2007 GBM Treatment, type=remove Source GEO sample is GSM99465 Last updated (according to GEO): Apr 21 2006 861 Cancer of Neck with autism spectrum disorder 37 65 MGMH030311036Bthymus pull-downSD_10, ZT6 660 mesenchymal stem cell 639 Wild type 8 wk old male A/J mouse pituitary gland Source GEO sample is GSM75000 Last updated (according to GEO): Feb 27 2007 Cochlear structure 1000 1255 1233 of tenascin-C null mice NMDA 10 (7/8) (Experiment NMDA1-Run 13384) Treatment, type=time_course, description=samples are treated for 10, 30 or 60 min with NMDA 1mM, the agonist is then washed out and the cells are harvested 24h later, measurement=10.0 m Source GEO sample is GSM96709 Last updated (according to GEO): Feb 14 2006 112 98 from the kidney Gene expression data from postmorten brain regions Source GEO sample is GSM145598 Last updated (according to GEO): Nov 20 2006 Plasma 861 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/9636.gif Source GEO sample is GSM79886 Last updated (according to GEO): Sep 22 2006 GSE1004 Tissue Source GEO sample is GSM67224 Last updated (according to GEO): Jan 19 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with MIP3-alpha (Macrophage inflammatory protein-3) for 30min Source GEO sample is GSM5686 Last updated (according to GEO): May 27 2005 Nucleus accumbens, male 10.5 week old c57bl/6J mouse, NON-DEFEATED control Source GEO sample is GSM224749 Last updated (according to GEO): Aug 31 2007 861 Oocytes Brain 861 substantia_nigra_1 Source GEO sample is GSM80830 Last updated (according to GEO): Mar 31 2006 HDMTX-DX-6 AML62 on Affymetrix GeneChip Human Full Length Array HuGeneFL db/m 16 wk 2 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114220 Last updated (according to GEO): Jun 16 2006 NA18540 Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep3 Pituitary Gland 861 Liver damage 1000 autism 100 105 DBA/2J Cingulate Cortex B Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11241 Last updated (according to GEO): May 28 2005 Endometrium/Ovary 5 Disease Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15718 Last updated (according to GEO): May 28 2005 Blood 1000 1000 Heart failure Parkinson's disease 0 18 Female 23.5 yr after antibody enrichment scan 2 (U133B) Spleen vs Platelet activating factor Treated B cell 240min (set2) 05_0008_SepticShock_Day1_97 861 Heart 0 Parkinson's disease 18 The sample is a part of a series describing gene expression changes during postnatal development of the small intestine Source GEO sample is GSM198880 Last updated (according to GEO): Jun 11 2007 861 Descending colon 5 0 brain WGACON-91 Heart 861 5 0 brain osteoclasts 87 98 Gap Junctions 1000 AM Treatment, type=remove Source GEO sample is GSM99509 Last updated (according to GEO): Apr 21 2006 Examination of molecular basis of malaria resistance. Spleens from malaria resistant AcB55 and AcB61strains compared with A/J mice. Animals were sacrificed and spleens were rapidly frozen in liquid nitrogen, and subsequently stored at 80oC. Tissues were mechanically homogenized with a polytron and total cellular RNA was extracted using a commercially available reagent (TMTRIzol; Invitrogen). The poly-(A)+ fraction of the RNA was isolated by chromatography with oligo d(T) cellulose beads. For cDNA labeling, either 25 mg of total RNA or 2.5 mg of poly-(A) RNA was converted into cDNA using reverse transcriptase (RT; Super Script II, Invitrogen) and alternatively Cy5 or Cy3-labeled dCTP (1mM, Perkin Elmer-Cetus/NEN, Boston) in a reaction mixture containing 1.5 mL oligo (dT) (100pmol/ mL), 3 mL dNTP-dCTP (6.67mM each), 1 mL dCTP (2mM), 4 mL DTT (100mM), 8 mL 5 X RT Buffer (Invitrogen, California). The reactions were carried out at 42¼C for 3 hrs, after which the RNA was degraded by the addition of 0.5 mL RNase A (1 mg/mL) and 1.5 mL RNaseH 5 units/mL). Labeled cDNA was separated from unincorporated nucleotides (Qiagen column) and further concentrated by evaporation under vacuum. The arrays were pre-hybridized for 1-2hrs with DIGEasy hybridization buffer (Roche) containing 10ug/ml denatured salmon sperm DNA, and 10ug/ml yeast tRNA. The Cy5 and Cy3 labelled cDNAs were combined and hybridized in the same medium and incubated with the arrays for 16-18hrs at 37Co. Finally, the arrays were washed 3 x 10 mins in 0.1 x SSC (20 X SSC is 3M sodium chloride, 0.3 M sodium citrate, pH 7.0), 0.1%SDS at 50Co, and 4 x 3min in 0.1 x SSC at room temperature, and dried by centrifugation. Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray fluorescent scanner and image intensity data were extracted and analyzed with QuantArray 3.0 analysis software. Quantification data was imported in GeneSpring (Silicon Genetics). The import format was modified to maintain information relevant to user-contributed flagging as well as QC parameter furnished by the array manufacturer. Dye swap and Intensity-based normalization (Lowess) were performed using the default settings.. Date GSE709 Last Updated: Oct 28 2005 Contributers: Anny Fortin Gundula Min-Oo Andre Nantel Philippe Gros Mi-Fong Tang Mary M Stevenson Includes GDS471. Update date: Nov 20 2003. Dataset description GDS471: Examination of molecular basis of malaria resistance. Spleens from malaria resistant recombinant congenic strains AcB55 and AcB61 compared with malaria susceptible A/J mice.. 1000 Rectum Normal Source GEO sample is GSM176036 Last updated (according to GEO): Apr 09 2007 brain, cerebral cortex: Co 6/24_le1 861 Malaria CNS-SMTC_Ctr3mo-1A-s2 673 659 by decapitation A HID U D049 healthy control sample x058 Leukemia Lymphoblastic (MOLT-4) [JunctionChip 1 of 5] Leukemic fractions of ID73 AML patient have been hybridized. Source GEO sample is GSM154057 Last updated (according to GEO): Feb 26 2007 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15767.gif Source GEO sample is GSM91605 Last updated (according to GEO): Sep 22 2006 Parkinson Disease 1000 Starvation 916 brain, hippocampus: Sham PM Hip b_e1_le1 Intestines 861 Fibroblasts 861 Anxiety Disorders 901 High-density progenitors Source GEO sample is GSM47544 Last updated (according to GEO): Jun 10 2005 719 693 in the posterior pituitary Cerebral cortex 861 SQ-2557-A320-5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 9 0 Cerebellum lymphnode Source GEO sample is GSM18744 Last updated (according to GEO): Sep 25 2006 Heart; Atrium Keywords = mouse gene expression database Source GEO sample is GSM29340 Last updated (according to GEO): May 27 2005 1BJZ02031305_fetallung in mouse hearts 40 54 D_U133A_32_DLPFC 254 238 of neural retinas Neostriatum 1000 Blood 1000 Stom Mucos Keywords = mouse gene expression database Source GEO sample is GSM39101 Last updated (according to GEO): May 27 2005 Gene expression data from PD1 Foxo3 Null ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203844 Last updated (according to GEO): Aug 02 2007 861 Neoplasm 1000 Brain Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153489 Last updated (according to GEO): Jan 11 2007 Nose 1000 Heart Atrium 1000 7 frontal cortex 20 Renal Cell Carcinoma 1000 1000 Retina starved 30 36 Gene expression data from postmorten brain regions Source GEO sample is GSM145671 Last updated (according to GEO): Nov 20 2006 901 Caudate nucleus structure of muscles 223 233 9 0 Blood Test Prostate 861 861 Cerebral cortex This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195297 Last updated (according to GEO): Sep 13 2007 Spleen 1000 HMEC X Matrigel Cortex Source GEO sample is GSM53372 Last updated (according to GEO): Jul 06 2005 Midbrain 10 Normal Ganglia 1000 Coronary Arteriosclerosis 1000 NA19007 Liver Test (Blinded) Sample Source GEO sample is GSM130083 Last updated (according to GEO): Sep 18 2007 719 in the posterior pituitary 693 Cerebral cortex 861 NHF10-hTERT_S_C5_26585 861 Cerebral cortex mammary_gland_8 CVB3_V-3h-1 M_U133A_49_DLPFC in the mammalian nervous system 110 141 Nose 1000 healthy subject Source GEO sample is GSM211018 Last updated (according to GEO): Sep 10 2007 896 Myomatous neoplasm Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11586 Last updated (according to GEO): May 28 2005 1000 Uterus mouse left hemi-diaphragm Source GEO sample is GSM53238 Last updated (according to GEO): Jul 06 2005 SN:1007091 Source GEO sample is GSM115369 Last updated (according to GEO): Jun 20 2006 901 Optic Nerve Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs//7252.gif Source GEO sample is GSM79919 Last updated (according to GEO): Sep 22 2006 Wild type voxel D3 Septum Source GEO sample is GSM107904 Last updated (according to GEO): Jun 06 2006 SN:1010454 Source GEO sample is GSM115395 Last updated (according to GEO): Jun 20 2006 Spleen 1000 neurological disease control sample x128 199 185 of hippocampus Blood 1000 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153337 Last updated (according to GEO): Dec 27 2006 CVB3_S-9h-2 T-47D hgu95d Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11593 Last updated (according to GEO): May 28 2005 BAL_17_A0B0 1000 Infection P1_KIDNEY_11 110 94 of heart failure C57BL-6J were given intratracheal bleomycin (1.5U per kg) and sacrificed at 24hrs. Lot batch = Source GEO sample is GSM4161 Last updated (according to GEO): May 28 2005 Clone 8.1 no PDGF Presynaptic Terminals 861 320 306 Keywords = HIV /3T3 fibroblasts 295 310 14 0 G5 ciliary body Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11266 Last updated (according to GEO): May 28 2005 Mouse old heart w/ a- & g-tocopherol agT-Ht-4 onto a collagen 72 86 1000 Brain Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68128 Last updated (according to GEO): Jul 07 2006 eye 0 3 36 0 Control rat 2 ventral tegmental area 660 mesenchymal stem cell 639 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 23.75 hours after lights on.Original sample code = CM54A Source GEO sample is GSM227314 Last updated (according to GEO): Sep 10 2007 50 Adipose tissue 64 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs//27680.gif Source GEO sample is GSM66570 Last updated (according to GEO): Sep 22 2006 Tissue transferred into RNAlater within 30 minutes of removal, and frozen at -20C Source GEO sample is GSM9102 Last updated (according to GEO): May 28 2005 Brain 1000 to the nose 599 609 scalp fibroblast (1.1F) asynch NA Source GEO sample is GSM198888 Last updated (according to GEO): Jun 07 2007 Whole brain 0 10 Cochlear nucleus structure 1000 brain, cerebral cortex: Rat_03-10_NroLep_Lipska_e1_le1 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151978 Last updated (according to GEO): Feb 06 2007 Spleen 2 Normal PGA-swim_2.5d_s1003 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24087.gif Source GEO sample is GSM81543 Last updated (according to GEO): Sep 22 2006 Epithelial Cells 1000 0 Human Cortex 11 S9_Muscle_Baseline_0min Myocardial Infarction 1000 WGACON-57 plasma cells 332 344 rat model organism with depression left untreated or treated with reserpine Source GEO sample is GSM247177 Last updated (according to GEO): Dec 11 2007 /HeJ mouse pituitary gland 27 52 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withSLC (Secondary lymphoid-organ chemokine) for 60min Source GEO sample is GSM5772 Last updated (according to GEO): May 27 2005 1000 Lung f2#267 versus pool Mouse Brain tissue Whole Brain 73 83 901 frontal lobe Normal Source GEO sample is GSM176346 Last updated (according to GEO): Apr 09 2007 1000 Brain 901 Temporal Lobe TEL-AML1-C54 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from whole brain infected mouse, day 3 Source GEO sample is GSM189613 Last updated (according to GEO): May 16 2007 1 of 3 replicates in treatment group Source GEO sample is GSM206038 Last updated (according to GEO): Jun 29 2007 Cerebral cortex 1000 normal liver tissue Source GEO sample is GSM155948 Last updated (according to GEO): Jun 21 2007 861 Hormones Gene expression data of substantia nigra from postmortem brain of normal controls Source GEO sample is GSM184358 Last updated (according to GEO): May 29 2007 (cortex 19 25 B220+c-kit+ Pre BI cells sorted out of mouse bone marrow, sort no. 9 Source GEO sample is GSM631 Last updated (according to GEO): Mar 17 2006 brain, cerebellum: Lh-/-_Crb3_e1_le1 17 0 Trigeminal ganglia D_U133A_1_HC Acetaminophen 24hr Rat 9388 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool Basal- 0 5 Lymphoblastoid Cell Line for Individual 8023.4 log phase Keywords = muscle 124 141 **** Source GEO sample is GSM4257 Last updated (according to GEO): May 27 2005 D_U133Plus_33_DLPFC_R 374 330 by the cardiac-specific a -myosin heavy chain 861 Asthma 923 Organ of Corti Cerebral cortex 1000 Gene expression data from DAOY cells stably expressing Alk shRNA Source GEO sample is GSM182017 Last updated (according to GEO): Apr 23 2007 brain, Right Frontal Lobe: Extract62_le1 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198625 Last updated (according to GEO): Jun 06 2007 875 Refractory Carcinoma R469P00501 Medulla Oblongata 861 in seminoma 28 38 SCG_control_5h_rep1 12 0 ovarian tumor Olfactory Epithelium 1000 861 Cerebellum Wild type inbred mice Source GEO sample is GSM82950 Last updated (according to GEO): Nov 10 2005 HapMap CEU_parent Female Source GEO sample is GSM159567 Last updated (according to GEO): Feb 01 2007 Vagina 10 Normal 3657 3643 The trunk blood 315-99_normal Liver Test (Blinded) Sample Source GEO sample is GSM130067 Last updated (according to GEO): Sep 18 2007 The sample is a part of a series describing gene expression changes during postnatal development of the small intestine Source GEO sample is GSM198832 Last updated (according to GEO): Jun 11 2007 MD rep 1 WGACON-268 100 from prefrontal cortex 121 none Source GEO sample is GSM244602 Last updated (according to GEO): Nov 23 2007 Recent findings support a model for neocortical area formation in which neocortical progenitor cells become patterned by extracellular signals to generate a protomap of progenitor cell areas that in turn generate area-specific neurons. The protomap is thought to be underpinned by spatial differences in progenitor cell identity that are reflected at the transcriptional level. We systematically investigated the nature and composition of the protomap by genomic analyses of spatial and temporal neocortical progenitor cell gene expression. We did not find gene expression evidence for progenitor cell organisation into domains or compartments, instead finding rostrocaudal gradients of gene expression across the entire neocortex. Given the role of Fgf signalling in rostrocaudal neocortical patterning, we carried out an in vivo global analysis of cortical gene expression in Fgfr1 mutant mice, identifying consistent alterations in the expression of candidate protomap elements. One such gene, Mest, was predicted by those studies to be a direct target of Fgf8 signalling and to be involved in setting up, rather than implementing, the progenitor cell protomap. In support of this, we confirmed Mest as a direct transcriptional target of Fgf8-regulated signalling in vitro. Functional studies demonstrated that this gene has a role in establishing patterned gene expression in the developing neocortex, potentially by acting as a negative regulator of the Fgf8-controlled patterning system. WGACON-36 1000 Retina 1041 1018 luminal epithelial cells 12 0 ovarian tumor This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12353 Last updated (according to GEO): May 28 2005 10 7 Left 7 0 prostate stria terminalis 1000 AKR/J Frontal Cortex F 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114235 Last updated (according to GEO): Jun 16 2006 Whole Brain 73 83 40 21 from skeletal muscle 1000 Hypothalamic structure 68 64 Lungs C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 6hr after experimental mice received their last shock treatment. Source GEO sample is GSM4513 Last updated (according to GEO): May 27 2005 R6/2 (untreated) 5270 74 CB A WGACON-86 Mild cognitive impairment - neuronal expression (6 regions) Lymphoblastoid Cell Line for Individual 8148.3 log phase Medulla Oblongata 861 normal human skeletal muscle sample 5 osteoblast 627 637 of the lung currently 260 280 Expression profiling of spinal cord section (T8) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31403 Last updated (according to GEO): May 27 2005 Abdominal aortic aneurysm obtained from surgery to correct. Source GEO sample is GSM170552 Last updated (according to GEO): Jul 26 2007 15 7 brainstem Colonic mucous membrane 913 Molecular profiling of murine sensory neurons in the nodose and dorsal root ganglia labeled from the peritoneal cavity. 4 0 Brain CC034A PMN_LB_360min_Patient12 CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of DC, recombinant human (rh) IL-4 and rhGMCSF were added to the culture at 50 ng/ml on days 1, 3, and 5 of culture. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5140 Last updated (according to GEO): Mar 21 2006 Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160714 Last updated (according to GEO): Sep 24 2007 1268 1260 Carcinoma 586 576 such tumors Neostriatum 1000 H124 CN B none Source GEO sample is GSM123261 Last updated (according to GEO): Jul 26 2006 Melanoma xenograft, MC1_Sub_B (LeiATCC) 861 Pancreas n/a Source GEO sample is GSM178009 Last updated (according to GEO): Jun 11 2007 N/A Source GEO sample is GSM4330 Last updated (according to GEO): May 28 2005 1000 Brain Stem Heart 1000 Gene expression data of substantia nigra from postmortem brain of PD patients Source GEO sample is GSM184364 Last updated (according to GEO): May 29 2007 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the lv samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12335 Last updated (according to GEO): May 28 2005 GRP sample 5 3AMH02082111_PB_BDCA4DentriticCells 861 Cerebellum SF-268 hgu95a GSE614 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132531 Last updated (according to GEO): Feb 26 2007 901 Hepatocyte 901 frontal lobe infection 255 264 High-density progenitors Source GEO sample is GSM47545 Last updated (according to GEO): Jun 10 2005 amygdala wistar 3720 whole tissue, individual animal, 10 weeks old, male Wistar amygdala file:p3950w Source GEO sample is GSM15177 Last updated (according to GEO): Oct 28 2005 striatum_wt_18m_12 Skeletal bone 861 Liver Test (Blinded) Sample Source GEO sample is GSM130103 Last updated (according to GEO): Sep 18 2007 na Source GEO sample is GSM181280 Last updated (according to GEO): Apr 10 2007 GM19203 Skin 1000 1000 Nervous system structure Plasma 861 brain, amygdala: Control-Amygdala_e1_le1 861 Malignant Neoplasms SVG-A subclone 3-D6 GeneChip U133A Brain 1000 Testi_LeydigCell Source GEO sample is GSM18983 Last updated (according to GEO): Sep 25 2006 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184740 Last updated (according to GEO): Apr 26 2007 Wild type voxel B4 NCI60.53_LABEL57EXTRACT56SUB3 Source GEO sample is GSM134261 Last updated (according to GEO): Aug 06 2007 The most common congenital cardiac abnormalities 50 97 Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.71 Subject: 3023 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39055 Last updated (according to GEO): May 27 2005 Brain 861 A549/ATCC hgu95d of the postmortem brains 675 699 Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID322 Nasal Epithelium Inhalation Formaldehyde 6ppm 19d ID310 spleen 36 41 Pool of 7 cochlear tissues at E14.5 Source GEO sample is GSM182586 Last updated (according to GEO): Aug 14 2007 Macrophage smi72 861 Asphyxia CNS-SCsev_InjB24h-1C-s2 1000 Spleen Hepatocyte 913 Anterior nares 1000 Nose 1000 A2780_cis_IC10_16h_1 none Source GEO sample is GSM239850 Last updated (according to GEO): Dec 07 2007 none Source GEO sample is GSM210350 Last updated (according to GEO): Jul 16 2007 5 0 brain Adipocytes from WAT B on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A 861 Bone Marrow striatum 22 30 Standard Affymetrix Protocol Source GEO sample is GSM16480 Last updated (according to GEO): May 28 2005 NCI60.54_LABEL58EXTRACT57SUB3 Source GEO sample is GSM134266 Last updated (according to GEO): Aug 06 2007 Gene expression data from colorectal adenoma. Source GEO sample is GSM215093 Last updated (according to GEO): Aug 02 2007 R491P00345 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153464 Last updated (according to GEO): Jan 11 2007 HC81 FC BA4 B Blood Test (Blinded) Sample Source GEO sample is GSM129935 Last updated (according to GEO): Sep 18 2007 5 0 brain 861 Cerebral cortex BCR-ABL-Hyperdip-#10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Primary large cell neuroendocrine carcinoma 5020 109 105 iris 1000 Structure of middle cerebral artery M_U133Plus_36_AnCg D_U133A_21_DLPFC 1000 Brain Fibroblasts 1000 901 Mammary gland SCG_control_24h_rep1 aml-aml8_645_ab_hu68_abms on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153367 Last updated (according to GEO): Dec 27 2006 Spleen vs IL10 Treated B cell 60min (set2) Category: Cell-line Subcategory: Reproducibility This experiment was an out file converted from rana. The original files were not provided to load this experiment in Oracle. Category and Subcategories were made by curators. Scanning Software: unknown Software version: unknown Lot batch = dtp3679 Source GEO sample is GSM2153 Last updated (according to GEO): Nov 21 2005 861 Brain 10 0 whole brain Normal Source GEO sample is GSM176385 Last updated (according to GEO): Apr 09 2007 thyroid_gland_4 Source GEO sample is GSM80867 Last updated (according to GEO): Mar 31 2006 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7439.gif Source GEO sample is GSM79839 Last updated (according to GEO): Sep 22 2006 Pregnant females exposed to ethanol for 5 days, AF07 (Alcohol Fed) corresponds to replicate 7 After 2 week acclimation to 12 hr/12 hr light/dark regimen, c57/Bl6 mice were subjected to a 36 hour period of constant darkness. Aortae were subsequently harvested at 4 hour intervals to 48 hours. Duplicate microarrays were hybridized with biotin-labeled probes derived from aorta tissue (6 pooled aortae/timepoint). Source GEO sample is GSM6095 Last updated (according to GEO): May 27 2005 B6Midbrain(2)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B 1000 Cerebellum with autism spectrum disorder 37 65 PGA-MAH-OuJO3-1bAv2-s1 NA Source GEO sample is GSM109468 Last updated (according to GEO): May 22 2006 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198638 Last updated (according to GEO): Jun 06 2007 Expression profiling of spinal cord section (T8) extracted from rats 24h following laminectomy (sham) Lot batch = Source GEO sample is GSM4427 Last updated (according to GEO): May 28 2005 from brains 17 27 brain, cortex: 14dexp3_e1_le1 V5-P596 Abdominal aorta collected during autopsy within 24 hours post mortem Source GEO sample is GSM170559 Last updated (according to GEO): Jul 26 2007 control for Abca1 +/- ES, RNA 78 none Source GEO sample is GSM239848 Last updated (according to GEO): Dec 07 2007 861 Tract 19 0 human frontal cortex A HID I D048 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108595 Last updated (according to GEO): Aug 22 2006 0 Human Cortex 11 Cardiac 523 530 1000 Turner's Syndrome Lymphoblastoid Cell Line for Individual 8063.3 log phase brain 0 5 Cerebral cortex 861 884 Cerebral artery occlusion NOS 1000 Prostate human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195350 Last updated (according to GEO): Jun 04 2007 Measles 114 120 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11438 Last updated (according to GEO): May 28 2005 Fibroblasts 1000 Anterior nares 1000 23 11 of the kidney Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2817 Source GEO sample is GSM2127 Last updated (according to GEO): Nov 21 2005 between the LAD artery 266 287 brain 0 5 mdx quadriceps sample 1 1000 Endometriosis, site unspecified 1000 Bipolar Disorder 5 0 Spleen Gene expression data from liver Source GEO sample is GSM243394 Last updated (according to GEO): Nov 16 2007 3AJZ02053107_CardiacMyocytes the heart 987 996 Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 48 h to ambient pressure (CP48) and harvested with cells exposed for 48 h to hydrostatic pressure, pressure experiment # 2 (PE2). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11418 Last updated (according to GEO): Dec 15 2006 Stria 861 Mammary Gland @ Preg3, biological rep2 knockin mouse cerebellum Treatment, type=time_course, measurement=4.0 weeks Source GEO sample is GSM53349 Last updated (according to GEO): Jul 06 2005 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 0 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM11029 Last updated (according to GEO): May 28 2005 MCF7 human breast cancer cells treated with 100 nM of dioxin to quantify RNA differences in a 2 platform, three replicate experiment Source GEO sample is GSM188022 Last updated (according to GEO): May 11 2007 858 Prostatic Neoplasms Exp A_2, 50mg/kg CPF 663 mesenchymal stem cell 642 Primary Neoplasm 1000 of somatomotor cortex 21 41 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68347 Last updated (according to GEO): Jul 07 2006 1000 Spleen Myocardial Infarction 1000 Infection 861 The most common congenital cardiac abnormalities 50 97 Wild type voxel D4 AKR/J Amygdala E 1000 Down Syndrome spinal cord 0 11 901 Epithelial Cells 15 0 human cerebellum olfactory epithelium 194 213 processed in batch 2 Source GEO sample is GSM90433 Last updated (according to GEO): Mar 20 2006 1000 Spleen Total RNA extracted from the cerebellum of a stg+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144398 Last updated (according to GEO): Nov 14 2006 418 401 folate deficiency Gene expression data from postmorten brain regions Source GEO sample is GSM146030 Last updated (according to GEO): Nov 20 2006 n/a Source GEO sample is GSM177892 Last updated (according to GEO): Jun 11 2007 bc-ZT21-3 Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 2507 blood This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195270 Last updated (according to GEO): Sep 13 2007 5 0 brain Brain 1000 DCIS43 on harvard-12k YFP labeled neurons in amygdala. Source GEO sample is GSM63046 Last updated (according to GEO): Dec 01 2005 HTI-286 in docetaxel-refractory prostate cancer Source GEO sample is GSM206166 Last updated (according to GEO): Jun 29 2007 Abdomen 861 5 0 Muscle 2 CN A D_U133A_80_DLPFC Posterior root of spinal nerve 861 Cortex_Control_rep4 (05SE1758) Lymphoblastoid Cell Line for Individual 8197.3 log phase Heart Septal Defects 884 901 Caudate nucleus structure Gene expression data from postmorten brain regions Source GEO sample is GSM144868 Last updated (according to GEO): Nov 20 2006 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169487 Last updated (according to GEO): Feb 21 2007 Prediction of central nervous system embryonal tumour outcome based on gene expression. 861 Neoplasm D2_TP-0_I plasma cells 332 344 0 Human Cortex 11 Primary Neoplasm 1000 861 Cerebral cortex healthy subject Source GEO sample is GSM211014 Last updated (according to GEO): Sep 10 2007 Epithelium of bronchus 983 Hindbrain Voxel F1 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1422 Last updated (according to GEO): Nov 21 2005 Mouse neuroblastoma 0 18 Seminoma 1000 M7TW01013105 Post Natally excised CCAM 1 DMN-NF1Hippo20d-1bAv2-s2 17 7 hippocampus Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120697 Last updated (according to GEO): May 14 2007 1000 Cerebral cortex CNS-SpinalCmod-Adult-7d-1B-s2 Coronary heart disease 913 1000 Brain cy5:WKY treated w/ angtiotensin, biological rep 2r; cy3:pool of 6 WKY control rats 278 255 ischemic cardiomyopathy 5 0 brain GM19139 861 Brain 284 264 ectodermal dysplasia skeletal_muscle_3 Source GEO sample is GSM80791 Last updated (according to GEO): Mar 31 2006 EWS-T-TEST-12 on NHGRI-6.5k_b 8078_Lung did not develop PGD This is the second replicate for the VTA neurons which were captured using LCM. Source GEO sample is GSM19331 Last updated (according to GEO): May 27 2005 BXD 9_M7SS02080607 CAD_replicate71 peripheral blood-CD19BCells Source GEO sample is GSM18722 Last updated (according to GEO): Sep 25 2006 Saccule structure 1000 HapMap CEU_parent Male Source GEO sample is GSM159518 Last updated (according to GEO): Feb 01 2007 Fibroblasts 861 104T Expression profiling of spinal cord section (T8) extracted from rats 30m following mild injury Source GEO sample is GSM31438 Last updated (according to GEO): May 27 2005 7 cerebral cortex 21 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs//9154.gif Source GEO sample is GSM93129 Last updated (according to GEO): Sep 22 2006 PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls. All samples were normalized with quantile normalization and summarized using RMA. Source GEO sample is GSM135585 Last updated (according to GEO): Dec 19 2006 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27034 Last updated (according to GEO): May 27 2005 38 12 of congenital heart disease no additional Source GEO sample is GSM199213 Last updated (according to GEO): Jun 08 2007 1000 Structure of postcentral gyrus 7 0 prostate parietal_lobe_9 Source GEO sample is GSM80762 Last updated (according to GEO): Mar 31 2006 Primary Neoplasm 1000 Primary tumor 19 32 in the brain 150 162 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159782 Last updated (according to GEO): Apr 23 2007 brain, hippocampus: Ctr-1h-P15-II_e1_le1 Normal Source GEO sample is GSM176150 Last updated (according to GEO): Apr 09 2007 Probeset expression data from NA12750 growth 2, replicate 3 Source GEO sample is GSM195197 Last updated (according to GEO): Aug 08 2007 nostrils 156 164 comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247395 Last updated (according to GEO): Dec 11 2007 Wild type 8 wk old male C3H/HeJ mouse pituitary gland Source GEO sample is GSM75004 Last updated (according to GEO): Feb 27 2007 Nodose Nucleus 3 Normal "Sample 57, <5 yr survival(28 months) age 28 erp no" on vantveer-oligo GIN-Homogenate-CingulateCortex replicate3 7 cerebral cortex 21 861 Neoplasm Macrophage smi90 Left 1000 861 Brain of coronary artery disease 258 284 Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92280 Last updated (according to GEO): Jan 13 2006 Coronary heart disease 913 starved 32 38 Oncolytic herpes simplex viruses 81 112 Gene expression data from postmorten brain regions Source GEO sample is GSM145899 Last updated (according to GEO): Nov 20 2006 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15749 Last updated (according to GEO): May 28 2005 Exp 3 Time point 1 Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles. PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity. Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence. To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips. Source GEO sample is GSM136560 Last updated (according to GEO): Jun 05 2007 cerebral cortex wistar 3904 1000 Retina KT26b_CAN Brain 1000 Endometrium/Ovary-Disease 10 I_U133A_23_DLPFC 901 Bone Marrow GM12878 granule neuron precursors, biological replicate 3; array A 1000 Temporal Lobe normal lung 3370 Source GEO sample is GSM17305 Last updated (according to GEO): May 28 2005 of uterine horns 289 304 Olfactory Epithelium 1000 858 Prostatic Neoplasms NA11994 21 7 adrenal medulla 861 Colon Plasma 861 Disorder of artery 865 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11312 Last updated (according to GEO): May 28 2005 43 29 from the kidney 7 cerebral cortex 21 Anterior nares 1000 861 Blood CNS-RM_Mod14d-3B-s2 Amygdaloid structure 1000 5 0 brain /J Amygdala A 4 16 Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14340.gif Source GEO sample is GSM79691 Last updated (according to GEO): Sep 22 2006 0 Human Cortex 11 Gene expressions affected by TNF alpha Source GEO sample is GSM189810 Last updated (according to GEO): May 21 2007 nasal epithelial cells 28 49 Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit. Source GEO sample is GSM200590 Last updated (according to GEO): Jul 09 2007 of the atrial 647 659 30 19 Solid tumor CNS-RM_CtrT0-1A-s2 Gene expression data from postmorten brain regions Source GEO sample is GSM145677 Last updated (according to GEO): Nov 20 2006 kidney 37 43 Aortic Aneurysm 901 Prosencephalon 1000 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b031 Source GEO sample is GSM1975 Last updated (according to GEO): Nov 21 2005 11 0 Hypothalamus Disease Source GEO sample is GSM176238 Last updated (according to GEO): Apr 09 2007 of the hippocampus 337 354 861 Myositis 1000 Heart failure Brain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145025 Last updated (according to GEO): Nov 20 2006 BTBR T+ tf/tf Amygdala C Job's patient Source GEO sample is GSM211140 Last updated (according to GEO): Sep 10 2007 Communicable Diseases 1000 1000 frontal lobe HA96-112B short access to cocaine, ventral tegmental area, 1 hr/day access to cocaine Source GEO sample is GSM93863 Last updated (according to GEO): Jan 26 2006 amygdala wistar 3942 whole tissue, individual animal, 10 weeks old, male Wistar amygdala file:p3723w Source GEO sample is GSM15124 Last updated (according to GEO): Oct 28 2005 Pituitary Gland 861 Ovarian_Tumor_Serous_CHTN-OS-098 Epithelium 861 BC807A-BE The murine pulmonary response is strain specific. Susceptible strains such as C57BL6/J experience an inflammatory response followed by progressive lung disease. Resistant strains such as Balb/c do not experience significant degrees of inflammation or fibrosis. This study aims to determine the genetic basis of sensitivity differences between strains. Date GSE485 Last Updated: Jul 27 2006 Contributers: David Moller Y W Chen Includes GDS251. Update date: Jun 27 2003. Dataset description GDS251: Determination of genetic basis of sensitivity to pulmonary fibrosis induced by bleomycin by comparing susceptible (C57BL6/J) and resistant (Balb/c) strains. C57BL6/J experience inflammatory response then progressive lung disease, Balb/c do not.. MCF10A_Untreated_#4 3608 3584 layer III pyramidal cells total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with TGF-beta (transforming growth factor-beta) labeled with Cy5- time course with repeats. Date GSE400 Last Updated: May 29 2005 Contributers: Zhen Yan Joella Grossoehme Angela Alexander Jong-Woo Kim Mi Sook Chang Robert Hsueh Yun Anna Cao Rebecca Hart Sangdun Choi Sun Young Lee Includes GDS321. Update date: Nov 18 2003. Dataset description GDS321: Temporal analysis of effects induced by 0.4 nM transforming growth factor-beta in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. Skeletal bone 861 RNA samples extracted from astrocytes cultured from wild type and Cx43 null neonatal mice were dye labeled and individually co-hybridized with a reference of labeled cDNAs pooled from a variety of tissues on eight gene arrays containing 8975 mouse DNA sequences. Lot batch = 2 Source GEO sample is GSM8890 Last updated (according to GEO): May 27 2005 Amygdaloid structure 1000 Fetal brains were obtained from 3 pregnant rats at pregnant day 17. Primary cortical neurons were isolated and pooled separately from each mother and plated onto 100mm ´ dishes, for a total of 4 plates from each pregnant rat. At Day in Vitro (DIV) 16, 3 of the 4 platesfrom the same mother, were exposed to either 1 or 3 MAC halothane (about 1% or 3%) or 3 MAC isoflurane (about 4%) in a gas tight chamber inside the culture incubator for 6 hr. The 4th plate from each mother treated with air were used (inside the same incubator, but outside the chamber) as controls. Isoflurane at 1 MAC was not conducted because of the complete lack of transcriptional response in the animals exposed to 1 MAC of isoflurane. The cells were recovered for an additional 6 hr, harvested, frozen by liquid nitrogen, and stored at ?80oC. Source GEO sample is GSM61797 Last updated (according to GEO): Oct 28 2005 Gene expression data from skeletal muscle at baseline Source GEO sample is GSM230432 Last updated (according to GEO): Sep 19 2007 fertilized egg Source GEO sample is GSM18698 Last updated (according to GEO): May 27 2005 245 218 of parieto-occipital cortex healthy subject Source GEO sample is GSM211108 Last updated (according to GEO): Sep 10 2007 17 7 hippocampus Starvation 916 Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 1 Prostate Gland 4 Normal GSE1501 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7553.gif Source GEO sample is GSM79950 Last updated (according to GEO): Sep 22 2006 Saccule 0 6 Expression profile of genes in mouse brain Source GEO sample is GSM21059 Last updated (according to GEO): May 27 2005 67 40 with coronary artery disease Endometrium/Ovary 9 Disease pull-downSD_7, ZT6 B6:2M-3 retina 1000 Brain The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27022 Last updated (according to GEO): May 27 2005 Gene expression data from male mice. Source GEO sample is GSM115535 Last updated (according to GEO): Jun 13 2007 861 Lymphoblastic Leukemia 861 Alzheimer's Disease OlfactoryBulb Source GEO sample is GSM19019 Last updated (according to GEO): Sep 25 2006 Chronic leukemia NOS 913 none Source GEO sample is GSM123202 Last updated (according to GEO): Jul 26 2006 NA07055 Cerebral cortex 1000 of ventricles 92 104 Rats 72h after injection with dose kainate. Treatment, type=time_course, description=KA animals are treated with kainate., measurement=72.0 h Source GEO sample is GSM32087 Last updated (according to GEO): May 27 2005 Exp A, Animal #2, 1mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours Source GEO sample is GSM246133 Last updated (according to GEO): Dec 03 2007 Pancreas Source GEO sample is GSM18978 Last updated (according to GEO): Sep 25 2006 Brain 861 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lysophosphatidic Acid for 240min Source GEO sample is GSM5658 Last updated (according to GEO): May 27 2005 #16 (isolate 22 low serum media VEGF-A 24hours) Menstrual phase - Luteal Source GEO sample is GSM175768 Last updated (according to GEO): Apr 09 2007 901 Spinal Cord We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201734 Last updated (according to GEO): Jun 20 2007 Nose 1000 5 0 brain 19 0 Head and neck cancer Pituitary Gland 861 24 0 Colorectal Adenocarcinoma PGA-RnSalt_h_6w_2-m5 of Parkinson's disease 450 471 None Source GEO sample is GSM198099 Last updated (according to GEO): Jul 16 2007 AD-127T1-A14-1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181159 Last updated (according to GEO): Jul 12 2007 861 Skeletal system Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184754 Last updated (according to GEO): Apr 26 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28730 Last updated (according to GEO): May 27 2005 SAMR1 Hippocampus Young Sample 1 GSE5035 361 335 hypertrophic cardiomyopathy of the hippocampus. 218 237 n/a Source GEO sample is GSM177979 Last updated (according to GEO): Jun 11 2007 rat hippocampus Treatment, type=time_course, measurement=6.0 h Source GEO sample is GSM32132 Last updated (according to GEO): May 27 2005 heart 169 174 861 Brain Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 5545 blood Wild type 8 wk old male C57BL/6J mouse periaqueductal gray Source GEO sample is GSM74990 Last updated (according to GEO): Feb 27 2007 132-95_Adeno CNS-SC_CtrA30m-1C-s2 prostate Source GEO sample is GSM203309 Last updated (according to GEO): Jun 21 2007 JMR-RatInj24hf-1aA-s2 GSE377 normal lung 1302 1312 28 13 from fetal heart Myocardium 861 CF knockout HFCF CHN308 30 19 Solid tumor 901 Epithelial Cells Knockout cocaine, biological replicate 5 olfactory epithelium SR-A mutant mouse 0 h Source GEO sample is GSM80198 Last updated (according to GEO): Oct 26 2005 Spinal cord tissue from wildtype mice Treatment, type=linear_amplification, description=T7-based RNA amplification Source GEO sample is GSM113696 Last updated (according to GEO): Nov 22 2006 5 0 brain 861 Longitudinal Expression profiling of spinal cord section (T8) extracted from rats 24h following severe injury Source GEO sample is GSM31479 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 Cerebral cortex 1000 901 Nervous system structure Breast 4 Disease Posterior root of spinal nerve 901 Neonatal (P0) whole brain mRNA from 39,Xp (XpO) In(X)/C3H x C57BL/6J Source GEO sample is GSM27449 Last updated (according to GEO): May 27 2005 861 Neoplasm 861 Cerebellum Whole Brain 73 83 Blood Test (Blinded) Sample Source GEO sample is GSM130005 Last updated (according to GEO): Sep 18 2007 861 Cerebral cortex that CLL 501 508 Spinal cord 1152 1162 BRCA2_s1787 on NHGRI-6.5k Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181144 Last updated (according to GEO): Jul 12 2007 901 Bone Marrow 21 6 (caudate nucleus Nonmalignant human mammary epithelial cells (HMEC) seeded in laminin-rich extracellular matrix (lrECM) form polarized acini and, in doing so, transit from a disorganized proliferating state to an organized growth-arrested state. We hypothesized that the gene expression pattern of organized and growth-arrested HMECs would share similarities with breast tumors with good prognoses. Using Affymetrix HG-U133A microarrays, we analyzed the expression of 22,283 gene transcripts in 184 (finite life span) and HMT3522 S1 (immortal nonmalignant) HMECs on successive days after seeding in a lrECM assay. Both HMECs underwent growth arrest in G0-G1 and differentiated into polarized acini between days 5 and 7. We identified gene expression changes with the same temporal pattern in both lines and examined the expression of these genes in a previously published panel of microarray data for 295 breast cancer samples. We show that genes that are significantly lower in the organized, growth-arrested HMEC than in their proliferating counterparts can be used to classify breast cancer patients into poor and good prognosis groups with high accuracy. This study represents a novel unsupervised approach to identifying breast cancer markers that may be of use clinically. Diet induced changes in mouse liver mRNA profiles. One of 3 replicates of LDL receptor deficient mice maintained for 12 weeks on low fat diet. Keywords = LDL receptor deficiency, high fat diet, atherosclerosis, liver Source GEO sample is GSM5414 Last updated (according to GEO): May 27 2005 187-96_Adeno 1000 Structure of ciliary ganglion 1079 1075 brain Spinal Cord 861 5 0 brain Plasma 861 72 CB A Control 4 (Experiment Neuroprotection4- Run 14985) Treatment, type=timepoint, measurement=0.0 h Source GEO sample is GSM96672 Last updated (according to GEO): Feb 14 2006 AD-AD19T1-A393-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Blood 861 P18 deprived visual cortex replicate 3 861 Breast 5 0 Spleen Myocardium 861 Anterior nares 1000 17 7 hippocampi 1000 Adrenal Medulla Neoplasm 861 plasma cells 332 344 AD control Treatment, type=dissect Source GEO sample is GSM119668 Last updated (according to GEO): Jul 10 2006 gum fibroblast, asynchronous l Gene expression data from postmorten brain regions Source GEO sample is GSM145289 Last updated (according to GEO): Nov 20 2006 Saccule structure 861 leukemia 861 cerebral cortex 7 21 Gene expression data from microdissected area # 2 of 1589 tumor Source GEO sample is GSM182291 Last updated (according to GEO): Apr 16 2007 Liver 0 4 5 0 brain Mouse Liver LRD Diet 5wk 100ppb Drinking Water Exposure, biological replicate D The epithelial cells 962 981 Frontal_Cerebrocortex_Vehicle_6hr_rep6 Wild type olfactory epithelium 8 hpO replicate1 liver.1 17 7 hippocampus 156 145 Their livers 1BJZ02053104_HBEC Brain 1000 IDC178 on harvard-12k Spinal Cord 1000 Cochlea at E13, replicate1 5 0 Spleen KT95b_AR2/DT/IN Anterior nares 1000 1000 Brain 861 Ventral Tegmental Area in bronchial epithelia 311 332 occipital regions 163 179 Communicable Diseases 901 of the postmortem brains 673 697 Whole Brain 73 83 Neoplasm 861 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181201 Last updated (according to GEO): Jul 12 2007 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211400 Last updated (according to GEO): Jul 18 2007 39 CB B total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with SDF1 alpha (Stromal cell derived factor-1) for 120min Source GEO sample is GSM5763 Last updated (according to GEO): May 27 2005 KO_sham_mid_4 no additional Source GEO sample is GSM199214 Last updated (according to GEO): Jun 08 2007 SON - 1d Dehydrated Source GEO sample is GSM69842 Last updated (according to GEO): Aug 15 2005 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM80007 Last updated (according to GEO): Oct 26 2005 Head and neck cancer Source GEO sample is GSM155690 Last updated (according to GEO): Apr 24 2007 Lv3: Hippocampus_21PT-Y_rep8 Neoplasm 1000 CCRF-CEM hgu95d MCF10A_Untreated_#6 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156697 Last updated (according to GEO): Jan 22 2007 Mesenchymal Stem Cells 1000 Sample represents the Neurointermediate lobe of the Pituitary from 5 control animals Source GEO sample is GSM69790 Last updated (according to GEO): Dec 15 2005 1000 Temporal Lobe 20 0 3AJZ02022226_ brain Me1: Hippocampus_NT-Y_rep2 KHG-LG-4Av2-s2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 5 0 brain cingulate cortex 1000 primary cortical neurons sprague2 Testis 861 Heart failure 1000 Sporadic_s1649 on NHGRI-6.5k total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with BLC for 120min Source GEO sample is GSM5470 Last updated (according to GEO): May 27 2005 Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Meningioma Primary Grade 2. Source GEO sample is GSM108035 Last updated (according to GEO): Jun 06 2006 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9881.gif Source GEO sample is GSM79979 Last updated (according to GEO): Sep 22 2006 Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 5924 left_liver_lobe 861 Amygdaloid structure 9 0 Blood Test 7 cerebral cortex 21 Adrenal Medulla 1000 temporal_lobe_9 Source GEO sample is GSM80851 Last updated (according to GEO): Mar 31 2006 HapMap YRI_parent Female Source GEO sample is GSM159689 Last updated (according to GEO): Feb 01 2007 Wild type inbred mice Source GEO sample is GSM83000 Last updated (according to GEO): Nov 10 2005 91 from the bone marrow 72 Arteries 861 1000 Hippocampus 6423_Lung developed PGD Occipital lobe 983 Expression profiling of spinal cord section (T9) extracted from rats 24h following laminectomy (sham) Lot batch = Source GEO sample is GSM6673 Last updated (according to GEO): May 28 2005 (cortex 19 25 CD8+ T lymphocytes_TC RCC patient Time 0_replicate 1 Five different human MPNST cell lines, mock treated or infected with G207. Source GEO sample is GSM215800 Last updated (according to GEO): Aug 07 2007 861 Pancreas Neoplasm 861 testis 52 58 brain, cerebral cortex: Rat_02-38_VHL_Lipska_e1_le1 Fibroblasts 1000 747 tumor cells 757 Amygdala 2 Normal Peripheral Nerve Sheath Neoplasm 884 Parkinson Disease 1000 Medulla Oblongata 861 861 Fibroblasts Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 19 day time point Source GEO sample is GSM159741 Last updated (according to GEO): Apr 23 2007 Spleen 1000 1000 Brain 7 cerebral cortex 21 M_U133A_79_DLPFC Spinal Cord 1000 1000 Endometrium nucleus accumbens long access to cocaine replicate 1 nodose_nucleus_4 Source GEO sample is GSM80771 Last updated (according to GEO): Mar 31 2006 Spleen vs Platelet activating factor Treated B cell 30min (set3) Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9982.gif Source GEO sample is GSM79859 Last updated (according to GEO): Sep 22 2006 Recurrent Adenocarcinoma 4 Seminoma 1000 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68161 Last updated (according to GEO): Jul 07 2006 MLL_15 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 197 176 with coxsackievirus B3 prostate Source GEO sample is GSM203404 Last updated (according to GEO): Jun 21 2007 BALB-RAG_OVA Replicate 2 23 0 mammary epithelial cells NHE1 null mutation cerebellum-3 Whole Brain 62 72 1000 Hippocampus quetiapine-treated mouse brain Simple annotation: Metastatic tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5190.gif Source GEO sample is GSM79853 Last updated (according to GEO): Sep 22 2006 blood 0 5 1726 1721 brains CO_NP_med_4 SOCS3 negatively regulates IL-6 signaling in vivo. 1000 Solid tumor park_1024_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Dimaprit for 30min Source GEO sample is GSM5533 Last updated (according to GEO): May 27 2005 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13143.gif Source GEO sample is GSM79683 Last updated (according to GEO): Sep 22 2006 861 Pancreas 861 Carcinoma Ganglia, Spinal 923 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD31 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD31 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36682 Last updated (according to GEO): May 27 2005 no additional Source GEO sample is GSM199115 Last updated (according to GEO): Jun 08 2007 in the mouse cerebral cortex 108 136 Expression profiling of spinal cord section (T9) extracted from rats 4h following moderate injury Source GEO sample is GSM31572 Last updated (according to GEO): May 27 2005 V5-P371 CNS-SCsev_InjA4h-4A-s2 GSE7866 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13115.gif Source GEO sample is GSM79978 Last updated (according to GEO): Sep 22 2006 Normal__Prostate_PR_7 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A S46 WT2 F5/8 S46 wild type Mouse 3.5 months Cerebellum Female Source GEO sample is GSM73224 Last updated (according to GEO): Sep 06 2005 144 114 from a single adult spinal cord B. abortus 2308 ADH4.2 replicate 1 897 Skeletal tissue 861 Cerebral cortex Infected 6 weeks prior with GFP-expressing recombinant lentivirus Source GEO sample is GSM34390 Last updated (according to GEO): Oct 16 2006 Nasal Epithelium 901 n/a Source GEO sample is GSM177999 Last updated (according to GEO): Jun 11 2007 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228656 Last updated (according to GEO): Sep 11 2007 GSE571 mouse cerebral cortex 0 21 Acetaminophen 24hr Rat 8658 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153410 Last updated (according to GEO): Jan 11 2007 plasma cells 332 344 PGA-Band_1w_3-m5 Colorectal cancers 12 29 rat hippocampus Treatment, type=time_course, measurement=6.0 h Source GEO sample is GSM32133 Last updated (according to GEO): May 27 2005 CurrentSmoker 68 Neostriatum 1000 A2780_control_16h_4 3AJZ02031411_thymus CNS-SC_InjA14d-2C-s2 Exp A, Animal #2, control (0mg/kg) CPF Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours Source GEO sample is GSM246129 Last updated (according to GEO): Dec 03 2007 875 Cerebellar Diseases Anterior nares 1000 Hippocampus 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145045 Last updated (according to GEO): Nov 20 2006 1000 Brain 20 0 human caudate nucleus 1000 frontal lobe 861 Blood Cerebral cortex 861 to the nose 599 609 Gene expression data from postmorten brain regions Source GEO sample is GSM145123 Last updated (according to GEO): Nov 20 2006 with multiple myeloma 1383 1403 Spleen vs CD40 Treated B cell 60min (set1) ventral striatum wistar 4028 288 253 of anti-glomerular basement membrane Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228604 Last updated (according to GEO): Sep 11 2007 5 0 brain 861 Patau's syndrome NOS Hypothalamus Source GEO sample is GSM18775 Last updated (according to GEO): Sep 25 2006 406 395 whose hearts Carcinoma, Large Cell 867 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11527 Last updated (according to GEO): May 28 2005 89 68 with tricuspid valves We will separately dissect the maxillary and mandibular branches of the E10.5 first branchial arch from wild type, dlx2, dlx1/2 and Dlx5/6 mutants. The tissues wil be flash frozen within 1 min of removal.We have not performed the dissections yet so we dont know how much RNA will be get from each sample, but previous experience suggests that we will need ~10 branchial arches/experiment. Treatment, type=nucleic_acid_extraction, description=We anticipate using this method as it was recommended by TGEN for small amounts of tissue. Source GEO sample is GSM107880 Last updated (according to GEO): Jun 06 2006 901 Caudate nucleus structure spinal cord, spinal cord: G1F_le1 901 Kidney Diseases Carcinoma, Large Cell 884 Frontal_Cerebrocortex_Vehicle_6hr_rep4 Feeder-independent ES cell line was grown using standard culture conditions. RNA was isolated using RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol. Data were normalized by AffyMetrix MAS5.0 using defaults. Keywords = embryonic stem cholesterol transport Source GEO sample is GSM9275 Last updated (according to GEO): May 27 2005 0 Human Cortex 11 Primary tumor 19 32 none Source GEO sample is GSM210353 Last updated (according to GEO): Jul 16 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114261 Last updated (according to GEO): Jun 16 2006 5 0 Spleen Macrophage smi85 Heart Septal Defects, Atrial 1000 40 21 from skeletal muscle Hypertensive disease 1000 1037 of transitional epithelium 1012 D2_Control_ZT 0_2 A/J bed nucleus of the stria terminalis rep2 (430 2.0 Array) Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13154.gif Source GEO sample is GSM79721 Last updated (according to GEO): Sep 22 2006 Gene expression profiles of 75 tissue samples were analyzed representing the stepwise carcinogenic process from pre-neoplastic lesions (cirrhosis and dysplasia) to HCC, including four neoplastic stages (very early HCC to metastatic tumors) from patients with HCV infection. Gene signatures that accurately reflect the pathological progression of disease at each stage were identified and potential molecular markers for early diagnosis uncovered. Pathway analysis revealed dysregulation of the Notch and Toll-like receptor pathways in cirrhosis, followed by deregulation of several components of the Jak/STAT pathway in early carcinogenesis, then up-regulation of genes involved in DNA replication and repair and cell cycle in late cancerous stages. Last Updated (by provider): Jun 21 2007 Contributers: Ying-bei Chen Elisa Wurmbach Jordi Bruix Sassan Roayaie Weijia Zhang Greg Khitrov Scott Friedman Swan Thung Samuel Waxman Isabel Fiel Josep M Llovet Myron Schwartz Vincenzo Mazzaferro Erwin Bottinger 6-00_LCLC Blood 7 11 Tissue Source GEO sample is GSM67214 Last updated (according to GEO): Jan 19 2006 Cerebral cortex 1000 861 Cerebral cortex 7 0 prostate Richard Almon-8-1138200269617 Gene expression data from postmorten brain regions Source GEO sample is GSM145366 Last updated (according to GEO): Nov 20 2006 Olfactory Epithelium 1000 861 Fibroblasts 1000 Prostate Heart 1000 Gland structure 861 1000 Spleen 15 0 human cerebellum 861 Cerebral cortex Collagen 1000 of the postmortem brains 674 698 none Source GEO sample is GSM246009 Last updated (according to GEO): Dec 03 2007 89 70 isolated theca cells ISR9 60 50 Heart C57BL Expression profiling of spinal cord section (T10) extracted from rats 4h following severe injury Source GEO sample is GSM31384 Last updated (according to GEO): May 27 2005 Myocardium 861 Liver 1000 D_U133A_74_Amy Normal Source GEO sample is GSM175835 Last updated (according to GEO): Apr 09 2007 626 615 PCOS oocytes RNA samples extracted from astrocytes cultured from wild type and Cx43 null neonatal mice were dye labeled and individually co-hybridized with a reference of labeled cDNAs pooled from a variety of tissues on eight gene arrays containing 8975 mouse DNA sequences Lot batch = 3 Source GEO sample is GSM8891 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145474 Last updated (according to GEO): Nov 20 2006 A39 WT6 F2/11 A39 wild type Mouse 10 months Cerebellum Male Source GEO sample is GSM73189 Last updated (according to GEO): Sep 06 2005 tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44870 Last updated (according to GEO): May 27 2005 Identification of genes regulated by transcription factor KLF7 in differentiating olfactory sensory neurons. Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:215, Count:32 Corner- Avg:29814, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:5.679840,SFGene:All Background:Avg:701.58,Stdev:18.01,Max:727.4,Min:653.6 Noise:Avg:12.10,Stdev:0.29,Max:13.6,Min:11.3 RawQ:17.41 Keywords = ALL Source GEO sample is GSM3401 Last updated (according to GEO): May 27 2005 Several recent reports show that the cerebral cortex in humans and animals with altered expressions of Wnt/cadherin network-associate molecules display cytoarchitectural abnormalities reminiscent of cortical dysplasias seen in some (mouse-, rat-, and monkey-based) animal models of prenatal cocaine exposure. Therefore, we employed oligo microarrays followed by real-time RT-PCR to compare expressions of genes involved in Wnt and cadherin systems in the cerebral wall of 18-day-old (E18) fetuses from cocaine-treated (20 mg/kg cocaine, s.c., b.i.d., E8-18) and drug-naive (saline, s.c.) mice. The pregnant mice chronically treated with cocaine in the above-described manner represent one of the animal models producing offspring with widespread cortical dysplasias. Out of more than 150 relevant genes in the arrays, 32 were upregulated and 9 were downregulated in cocaine-exposed fetuses. The majority of these genes (30 out of 41) were similarly affected in the frontal and occipital regions of the cerebral wall. We also used Western immunoblotting to examine the ability of cocaine to regulate the protein levels of beta-catenin, the key functional component of both Wnt and cadherin systems. While the total cell levels of beta-catenin were increased throughout the cerebral wall of cocaine-exposed fetuses, its nuclear (gene-transcription driving) levels remained unaltered. This suggests a transcription-unrelated role for cocaine-induced upregulation of this protein. Overall, our findings point to an intriguing possibility that that cerebral cortical dysplasias observed in several animal models of prenatal cocaine exposure may be at least in part related to alterations in the Wnt/cadherin molecular network. It has been demonstrated that exposure to cocaine increases cell death in the fetal CNS. To examine the molecular mechanisms of this effect, we employed mouse oligo microarrays followed by real-time reverse transcriptase-polymerase chain reaction (real-time RT-PCR) to compare expressions of apoptosis-related genes in the cerebral wall of 18-day-old (E18) fetuses from cocaine-treated (20 mg/kg cocaine, s.c., b.i.d., E8th-E18th) and drug-naive (saline, s.c.) mice. Out of approximately 400 relevant genes in the arrays, 53 showed alterations in expression in cocaine-exposed fetuses. Upregulation was observed in 35 proapoptotic and 8 antiapoptotic genes; 4 proapoptotic and 6 antiapoptotic genes were down-regulated. The affected genes encode a wide range of apoptosis-related proteins, including death receptors (NTF-R1, NTF-R2, DR3, DR5, LTbeta-R, GITR, P57 TR-1) and their adaptor and regulatory proteins (MASGE-D1, TRAF-2, SIVA, MET, FLIP, FAIM, IAP1, ATFA), members of transcription regulatory pathways (JNK, NF-kappaB, P53), members of BCL-2 family of proteins (BID, BAD, BAX, BIK, NIP21, NIP3, NIX, BCL-2), DNA damage sensor (PARP-1), caspases and their substrates and regulatory proteins (caspases 8, 4, 9, and 3, ACINUS, CIDE-A, CIDE-B, GAS2), mitochondrially released factors (cytochrome c, AIF, PRG3), specific endoplasmic reticulum- and oxidative stress-associated factors (BACH2, ABL1, ALG2, CHOP), members of cell survival AKT and HSP70 pathways (PIK3GA, PTEN, HSP70, BAG1, BAG2), and others. This suggests that cocaine affects survival of developing cerebral cells via multiple apoptosis-regulating mechanisms. Last Updated (by provider): Jan 17 2007 Contributers: Michael S Lidow Irina Badan Svetlana I Novikova Jie Bai Irina A Lidow Fang He 1100 1087 heart failure Stem cells 913 Plasma 861 Timepoint10 Muscle_adequate protein_female_rep1 Epithelial Cells 1000 Bone Marrow 1000 Liver Test (Blinded) Sample Source GEO sample is GSM130155 Last updated (according to GEO): Sep 18 2007 Sample # 1154-1 Neural tube, treated, GD9:12, T215586 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11560 Last updated (according to GEO): May 28 2005 Cerebral cortex 1000 69 50 Olfactory bulb C57BL processed in batch 1 Source GEO sample is GSM90445 Last updated (according to GEO): Mar 20 2006 Lung 861 Cultured_osteoblast-like_shear-stressed_MC3T3-E1_cells_rep4 Normal Source GEO sample is GSM176321 Last updated (according to GEO): Apr 09 2007 Gene expression data from PD14 Foxo3 wild-type ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203831 Last updated (according to GEO): Aug 02 2007 861 Huntington Disease no additional Source GEO sample is GSM199353 Last updated (according to GEO): Jun 08 2007 V5-P301 Transplant Series 34 , Transplant # 1 Blood 861 CLL-51 || lc8n119 Spleen 1000 Muscle 861 Endometrium 0 10 with some respiratory epithelium. 1039 1072 Testis 1000 Brain 1000 Brain 861 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=690620 LaserPower=4.323.79 Lot batch = LC17N090 Source GEO sample is GSM4813 Last updated (according to GEO): Nov 21 2005 Hereditary Nonpolyposis Colorectal Neoplasms 947 Stem cells 861 Macrophages, Exposed to Brugia malayi (5) - Repeat #1 Phenytoin frontal cortex 5 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53465 Last updated (according to GEO): Jul 06 2005 CC028 7 0 Amygdala 406 395 whose hearts GSE9676 Myometrium 15 Normal Nd14: Hippocampus_21PT-AU_rep6 brain_DLPFC_bipolar B_mr953 Plasma 861 EP-48HRS Bone Marrow 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145654 Last updated (according to GEO): Nov 20 2006 Neoplasm 861 53 39 in spinal cords eye 0 3 Cerebral cortex 861 Standard Affymetrix Protocol Source GEO sample is GSM15857 Last updated (according to GEO): May 28 2005 dorsal striatum wistar ky 3970 Hypothalamus 8 Normal 197 176 with coxsackievirus B3 McLean Parkinson's brain, Right Temporal Lobe: Extract79_le2 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184679 Last updated (according to GEO): Apr 26 2007 of Parkinson's disease 450 471 CNS-RM_CtrT0-2C-s2 Whole Brain 62 72 861 Acquired Immunodeficiency Syndrome Cochlea_WT_9mo_2 1000 Testis Blood Test (Blinded) Sample Source GEO sample is GSM130020 Last updated (according to GEO): Sep 18 2007 278 241 for bronchiolitis obliterans syndrome Rat vestibular ganglia_calretinin_positive_rep2 129Hippocampus(2)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B Spleen vs Prostaglandin E2 Treated B cell This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12377 Last updated (according to GEO): May 28 2005 14 0 Small Intestine 1000 Spleen 673 659 by decapitation Gene expression data from postmorten brain regions Source GEO sample is GSM145537 Last updated (according to GEO): Nov 20 2006 Neonatal (P0) whole brain mRNA from 39,Xm (XmO) C57BL/6J x C3H/Paf Source GEO sample is GSM27445 Last updated (according to GEO): May 27 2005 Primary large cell lung carcinoma 1531 0 37 1000 Hippocampus 1000 ovarian neoplasm SN12h(1) 913 Hereditary Malignant Neoplasm Mental Retardation 1000 238 232 Retinas Nrf2 +/+ mice (C57B6/SJL) were crossed with nrf2 -/- mice (C57B6/129SVJ) to generate mice heterozygous for nrf2. Interbreeding these heterozygotes generated the double-knockout mice (nrf2 -/-) as well as the corresponding littermate controls (nrf2 +/+). Mice were housed in plastic cages on a bedding of wood chips and maintained at ~22C, ~60% relative humidity, and a 12 hr light/dark cycle. The animals were fed with mouse diet 5015, which includes 30 IU/g of vitamin A and 35 IU/kg of vitamin E, (LabDiet, Richmond, IN) and drinking water ad libitum. All animal protocols were approved by the Institutional Animal Use and Care Committee at the University of Wisconsin-Madison. Total RNA was extracted from livers and spleens isolated from male and female nrf2 wildtype and knockout mice at 5 months of age (prior to the development of severe autoimmune disease). Keywords = Nrf2 Keywords = spleen Source GEO sample is GSM13467 Last updated (according to GEO): May 28 2005 GSE2437 I-7_PRE C3H/HeJ Cerebellum F Category: Cell-line Subcategory: Breast Scanning Software: unknown Software version: unknown Lot batch = svcc40 Source GEO sample is GSM1926 Last updated (according to GEO): Nov 21 2005 ExpressionLevel:GXN-00533 on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A none Source GEO sample is GSM244586 Last updated (according to GEO): Nov 23 2007 Human prostate cancer and benign prostatic hyperplasia: molecular dissection by gene expression profiling. Stem cells 901 17 7 hippocampus Bone Marrow BD Normal Epithelium of bronchus 983 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152015 Last updated (according to GEO): Feb 06 2007 Spleen vs CD27 Treated B cell 30min (set2) 5 0 brain CNS-RM_Mod14d-3C-s2 Amplified RNA from lungs of ovalbumen sensitized and challenged C3H 5 mouse vs. pool of amplified RNA from lungs of control C3H mice. Source GEO sample is GSM6742 Last updated (according to GEO): Nov 21 2005 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart Keywords = Cardiac Keywords = Assist Device Keywords = LVAD Keywords = GATA-4 Keywords = Sprouty1 Keywords = microarray Keywords = heart failure Source GEO sample is GSM14952 Last updated (according to GEO): Oct 28 2005 1000 Hyperlipidemia, Familial Combined no additional Source GEO sample is GSM199416 Last updated (according to GEO): Jun 08 2007 Neoplasm Metastasis 1000 none Source GEO sample is GSM210309 Last updated (according to GEO): Jul 16 2007 Malignant Neoplasms 861 1000 Intestines, Small mouse brain 478 489 dorsal_root_ganglia_3 Source GEO sample is GSM80613 Last updated (according to GEO): Mar 31 2006 Anterior nares 1000 Bladder sample 524-1 Spleen 0 5 Performed by UCI Microarray Facility. Source GEO sample is GSM203199 Last updated (according to GEO): Jun 22 2007 64 CN B TEL-AML1-C4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Lymphoblastoid Cell Line for Individual 8180.4 log phase osteoblast 627 637 Mammary Gland @ Preg12, biological rep2 plasma cells 332 344 Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Meningioma Primary Grade 2. Source GEO sample is GSM108011 Last updated (according to GEO): Jun 06 2006 bronchial epithelia 224 243 5 0 brain 1000 Kidney O377 homozygotes brains 6 RMS-C3 on NHGRI-6.5k_b Colonic mucous membrane 913 1000 Brain This data series describes expression data for eight paired, control and treated cell cultures obtained on independent occasions. NG108 rat neuronal cell cultures were exposed to either 0.25% DMSO (control) or 4400 ng/ml mefloquine (treated) for two hours. Validation: Modulation of the following transcripts by mefloquine was confirmed by semi-quantitative RT-PCR: U30186, X63594cds_g_at, X63594cds_at, X17163cds_s_at, rc_AI175959 and rc_AA945867 (unpaired, unequal variance, one tailed t-test, p < 0.05). Last Updated (by provider): May 29 2005 Contributers: Geoffrey S Dow Includes GDS199. Update date: Apr 09 2003. Dataset description GDS199: Neuroblastoma cells NG108 exposed to a physiological dose (4400 ng/ml) of antimalarial mefloquine (Lariam), or 0.25% DMSO (control), for 2 hours. Mefloquine appears to disrupt neuronal function through disrupted calcium homeostasis and ER stress.. CNS-SMTC_Mod14d-4C-s2 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11234 Last updated (according to GEO): May 28 2005 10 0 Hippocampus 27 Alzheimer's disease 45 Blood 861 0 Lung tissue 10 18 month oculomotor nucleus rep 2 1000 Brain Primary Neoplasm 1000 1000 Coronary Arteriosclerosis Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=680640 LaserPower=1.981.32 Lot batch = LC17N025 Source GEO sample is GSM4777 Last updated (according to GEO): Nov 21 2005 Normal epithelial cells were removed by dissection and digestion from bronchi of donor long tissue from normal subject. Source GEO sample is GSM3920 Last updated (according to GEO): May 27 2005 NA Source GEO sample is GSM198936 Last updated (according to GEO): Jun 07 2007 of regenerating Dorsal Root Ganglia 21 55 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc97 Source GEO sample is GSM1903 Last updated (according to GEO): Nov 21 2005 9 0 Blood Test In this time course pregnant CD-1 (outbred) dams were exposed to MeHg as monomethylmercuric chloride intraperitoneally on 9 d.p.c. The test dose of 5.0 mg/kg MeHg was selected as a dose with an estimated 20% increased risk for encephalopathy in term fetuses, with no evidence of maternal toxicosis. Exposed embryos were co-treated with PK11195, a nontoxic ligand of the mitochondrial peripheral-type benzodiazepine receptor (Bzrp) that effectively suppresses developmental toxicity induced with MeHg. The anticipated remediation with 5.0 mg/kg and 4.0 mg/kg PK11195 is <10% malformations. Sampling intervals ranged from 3.0h to 6.0h post-exposure. All measurements were on RNA from the embryonic forebrain (prosencephalon).. Date GSE1077 Last Updated: May 29 2005 Contributers: Amar V Singh Kimberly R Nemeth Thomas B Knudsen Jeffrey H Charlap Includes GDS637. Update date: Jul 14 2004. Dataset description GDS637: Temporal analysis of methylmercury (MeHg) exposure, and PK11195 intervention. Pregnant 9 days post coitum CD-1 dams injected with 5.0 mg/kg MeHg. Embryonic forebrain examined at 3, 4.5 and 6 hours. MeHg induces symptoms of fetal minamata disease (FMD).. 278 255 ischemic cardiomyopathy 861 Lateral Sclerosis Primary tumor 19 32 MLL-R3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Endometrium-Normal 2 1000 Bronchi HMEC S1 day 3 sample 1 36 21 from whole brain Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153766 Last updated (according to GEO): Jan 19 2007 742 737 heart Gene expression data of substantia nigra from postmortem brain of PD patients Source GEO sample is GSM184368 Last updated (according to GEO): May 29 2007 3867 3859 amygdala 1000 Primary carcinoma of the liver cells Gut 1000 Mice were sacrificed at 13 weeks of age. They can be used as controls for the 4 week swim 1 week rest mice. Keywords = exercise induced hypertrophy Source GEO sample is GSM2369 Last updated (according to GEO): May 27 2005 Metastatic tumor 19 35 Brain_MD_46_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL Spleen vs Anti-IgM Treated B cell 120min (set1) of a colorectal adenoma 7 29 meningioma 1000 Colon 1000 861 Hippocampus 15 0 human cerebellum medulla_3 1000 Blood Vessels Examining the effects of tTA expression in mouse hearts Cerebral cortex 861 CNS-SpinalC-24hAdult-4C-s2b Hyperdip>50-2M#2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Mice sacrificed after swimming twice a day for 2 weeks. Keywords = exercise induced hypertrophy Source GEO sample is GSM2353 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM176421 Last updated (according to GEO): Apr 09 2007 Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3873 Last updated (according to GEO): May 27 2005 Kidney CR-1A 112 77 Keywords = congenital heart disease 325 321 lung 861 Cerebral cortex 1BJZ02052313_HUMANCULTUREDADIPOCYTE PGA-MCR-CR-2h-1bAv2-s1 3ARS02080776a_skin Disorder of artery 865 Small cell carcinoma of lung 901 Mouse Liver LRD Diet 5wk 100ppb Drinking Water Exposure, biological replicate E 660 mesenchymal stem cell 639 15 0 human cerebellum Cerebral cortex 861 Skeletal bone 861 30 year old female Liver 1000 1000 Pancreas 1000 Brain Transplant Series 19 , Transplant # 2 Epithelium 861 S25 WT1 F4/27 S25 wild type Mouse 3 months Cerebellum Male Source GEO sample is GSM73205 Last updated (according to GEO): Sep 06 2005 Normal Source GEO sample is GSM175993 Last updated (according to GEO): Apr 09 2007 861 Cerebral cortex Cerebral cortex 1000 C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P10 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25119 Last updated (according to GEO): May 27 2005 Parkinson Disease 861 1000 Amygdaloid structure with autism spectrum disorder 37 65 NoCAD_replicate28 Cerebral cortex 861 to the nose 599 609 PGA-MurLungRag-pbs-72h-1aB-s2 0 Human Cortex 11 Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92300 Last updated (according to GEO): Jan 13 2006 Brain 1000 5 0 brain heart 169 174 Brain 1000 C57BL/6J Basal Ganglia E Liver (HBV+, HK6) Blood Test (Blinded) Sample Source GEO sample is GSM129986 Last updated (according to GEO): Sep 18 2007 40 21 from skeletal muscle Bone Marrow 1000 none Source GEO sample is GSM239833 Last updated (according to GEO): Dec 07 2007 Skeletal bone 861 jzo015-rp1-v5-u74av2-met 861 Cerebral cortex 861 Intestines 1000 Cerebral cortex Osteoblasts 1000 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:334, Count:32 Corner- Avg:38033, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:4.198062,SFGene:All Background:Avg:363.07,Stdev:3.48,Max:373.7,Min:355.4 Noise:Avg:7.99,Stdev:0.29,Max:8.7,Min:7.1 RawQ:11.86 Keywords = ALL Source GEO sample is GSM3443 Last updated (according to GEO): May 27 2005 861 Cerebral cortex Cerebral cortex 1000 14 0 Small Intestine 983 Malignant neoplasm of cervix uteri Brain 861 Prosencephalon 1000 Large cell neuroendocrine carcinoma 1000 Structure of dentate gyrus 861 PE_D_26A 5 0 Spleen Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:239, Count:32 Corner- Avg:38822, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:7.316926,SFGene:All Background:Avg:371.14,Stdev:5.69,Max:385.0,Min:359.1 Noise:Avg:10.15,Stdev:0.33,Max:11.2,Min:9.4 RawQ:12.76 Keywords = ALL Source GEO sample is GSM3504 Last updated (according to GEO): May 28 2005 Gastrin Knockout infused with saline fundic RNA Source GEO sample is GSM108486 Last updated (according to GEO): May 03 2007 901 Ciliary Body Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD31 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD31 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36681 Last updated (according to GEO): May 27 2005 Control hippocampus 5 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53451 Last updated (according to GEO): Jul 06 2005 with autism spectrum disorder 37 65 Mid secretory endometrium from patient with endometriosis Source GEO sample is GSM150218 Last updated (according to GEO): Dec 14 2006 0.5 mg/kg/ml Isoproterenol treatment, 24 hour time point, biological rep 4 short access to cocaine, amygdala, 1 hr/day access to cocaine Source GEO sample is GSM93831 Last updated (according to GEO): Jan 26 2006 1000 Amygdaloid structure Epithelium 861 1000 Neoplasm none Source GEO sample is GSM239866 Last updated (according to GEO): Dec 07 2007 182 in skeletal muscles 163 Category: Cell-line Subcategory: Breast Hs578T obtained as part of the NCI60 cell line set Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc110 Source GEO sample is GSM1869 Last updated (according to GEO): Nov 21 2005 Mouse model of congenital heart disease. Wild-type embyronic day 9.5 mouse. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2266 Last updated (according to GEO): May 27 2005 1000 Heart none Source GEO sample is GSM239924 Last updated (according to GEO): Dec 07 2007 Gene expression data from retinas of two old SAMP8/Ta mice Source GEO sample is GSM143738 Last updated (according to GEO): Jan 24 2007 in blood 16 23 AK_Control_ZT 18_2 plasma cells 50 61 Autistic Disorder 877 Lymphoblastoid Cell Line for Individual 8034.3 log phase wildtype neonatal mouse brain4 (W-4) 91 from the bone marrow 72 of coronary artery disease 258 284 Epithelial Cells 1000 Job's patient Source GEO sample is GSM211117 Last updated (according to GEO): Sep 10 2007 FVB/NJ_male_hypothalamus Source GEO sample is GSM184204 Last updated (according to GEO): Apr 26 2007 12 frontal Lobe 23 Deltoid Muscle 5 Normal 221 185 in the developing trigeminal ganglion 5 0 brain 861 Cerebral cortex 1000 Breast Carcinoma 1000 Atherosclerosis none Source GEO sample is GSM239925 Last updated (according to GEO): Dec 07 2007 861 Fibroid Tumor Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11596 Last updated (according to GEO): May 28 2005 Liver 1000 231 222 Hippocampi NA19206 861 Muscle brain, hippocampus: Sample20_e1_le1 in the brain 150 162 with mental retardation 241 263 human frontal cortex Source GEO sample is GSM86981 Last updated (according to GEO): Feb 08 2006 1000 Hypertrophic Cardiomyopathy mild cognitive impairment - entorhinal cortex 2 Heart 1000 Chronic leukemia NOS 853 eye, retina: Pineal at CT 12_e1_le1 Neostriatum 1000 I_95Av2_2846_AnCg_1_GS HCC (HBV+, HK58) 129/SvImJ Frontal Cortex A CN018 Brain 861 Cocaine-induced changes in the gene expression in the mammalian nervous system 110 141 Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 2864 blood Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 24h. Lot batch = Source GEO sample is GSM1238 Last updated (according to GEO): May 28 2005 966 Hippocampus stomach_pyloric_4 Large-scale analysis of the human transcriptome. Spinal cord Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 188.45 Stdv: 7.54 Min: 172.74 Max: 197.83 Source GEO sample is GSM2855 Last updated (according to GEO): Mar 20 2006 brain, cerebral cortex: Rat_03-11_NroLep_Lipska_e1_le1 1000 Epidermis Gene expression data from postmorten brain regions Source GEO sample is GSM145260 Last updated (according to GEO): Nov 20 2006 Transitional epithelium 1000 861 Adipose tissue Gene expression data from postmorten brain regions Source GEO sample is GSM145324 Last updated (according to GEO): Nov 20 2006 Liver Test (Blinded) Sample Source GEO sample is GSM130163 Last updated (according to GEO): Sep 18 2007 in the cerebral cortex 207 228 V5-P474 R6/1 18 week wildtype_F272 Liver Test (Blinded) Sample Source GEO sample is GSM130102 Last updated (according to GEO): Sep 18 2007 M7TW00121852 1000 Spleen 7 0 prostate M_U133A_48_HC Prostate 861 dorsal root ganglion fisher2 whole tissue, pool of 5 animals, 16 weeks old, male Fisher dorsal root ganglion file:p3972w Source GEO sample is GSM15188 Last updated (according to GEO): May 28 2005 15 0 Bone marrow cell brain, cerebellum: 6hrs B LK_e1_le1 GSE9101 Fertilized egg replication 4 Keywords = preimplantation Keywords = development Source GEO sample is GSM14666 Last updated (according to GEO): May 28 2005 Transitional epithelium 1000 cerebral.hemisphere.3 none Source GEO sample is GSM123193 Last updated (according to GEO): Jul 26 2006 Kidney 1000 CNS-SC_InjB4h-2C-s2 5 0 Spleen Cockayne syndrome B wt-rescued cell Source GEO sample is GSM226629 Last updated (according to GEO): Sep 04 2007 Untreated, biological rep5 Tumor__Prostate_Adeno_P_0036 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A ADH210 on harvard-12k 1000 Brain Large Intestine; Distal Colon Keywords = mouse gene expression database Source GEO sample is GSM29289 Last updated (according to GEO): May 27 2005 3734 3725 The brains with Alzheimer's disease 27 50 SmaliE165_022EAFCH_170.txt Parkinson Disease 1000 Brain 861 NB-T-TEST-25 on NHGRI-6.5k_b 901 Bone Marrow 1000 Amygdaloid structure in the cortex 1631 1643 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226038 Last updated (according to GEO): Nov 02 2007 Parkinson Disease 1000 brain, hippocampus: PH1_e1_le1 901 Autoimmune Diseases Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225354 Last updated (according to GEO): Aug 31 2007 1000 Brain 84 69 by heart failure preoptic Source GEO sample is GSM18593 Last updated (according to GEO): May 27 2005 GSE974 nasal epithelial cells 28 49 901 frontal lobe Gene expression data from rat lungs exposed to FiO2 of ~9.5%, SU5416, and Sorafenib (hypoxia-SU5416-Sorafenib). Source GEO sample is GSM201492 Last updated (according to GEO): Jun 14 2007 861 Coxsackievirus Infections PGA-MPF-C57-saline-72h-1aAv2-s2 Mammary Gland @ Preg19, biological rep4 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc116 Source GEO sample is GSM1901 Last updated (according to GEO): Nov 21 2005 861 Cerebellum M_U133A_60_AnCg in blood 16 23 no additional Source GEO sample is GSM199154 Last updated (according to GEO): Jun 08 2007 Epithelial Cells 1000 AD-115T1-A12-1 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A #5 (isolate C rich media control) 1000 Brain Feeder-independent ES cell line was grown using standard culture conditions. RNA was isolated using RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol. Data were normalized by AffyMetrix MAS5.0 using defaults. Keywords = embryonic stem cholesterol transport Source GEO sample is GSM9277 Last updated (according to GEO): May 27 2005 0 Human Cortex 11 E7.0_rep2 997 983 to hypertension with experimental autoimmune encephalomyelitis 12 57 olfactory epithelium SR-A mutant mouse 8 hpO Source GEO sample is GSM80205 Last updated (according to GEO): Oct 26 2005 1000 Hippocampus Ovarian_Tumor_Serous_CHTN-OS-048 1000 Brain B6 2000-1 Thymus Colorectal cancer patient SC7_vs_Pool gene expression data from melanoma xenografts following ILI with saline Source GEO sample is GSM213626 Last updated (according to GEO): Jul 27 2007 ILS/ISS_cerebellum_naive_474 BALB/cByJ Cerebellum B 2404 in cortex 2412 Mesenchymal Stem Cells 1000 BALB/cByJ Hippocampus A Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118556 Last updated (according to GEO): Jul 11 2006 mouse brain ipsilateral LPS.RU486 Source GEO sample is GSM149781 Last updated (according to GEO): Mar 15 2007 Pancr_022HAFD3_060w.txt 861 Epidermis nidogen 1 1176 1184 901 Nervous system structure Mouse ileum 0 10 64 28 the most common malignant brain tumor parietal_lobe_5 of the atrial 647 659 leukemia 1000 901 Bone Marrow 24 0 Substantia nigra PD rep15 N/A Source GEO sample is GSM4325 Last updated (according to GEO): May 28 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68244 Last updated (according to GEO): Jul 07 2006 Expression profiling of somatomotor cortex extracted from rats at 28d following moderate injury Source GEO sample is GSM41716 Last updated (according to GEO): May 27 2005 Replicate2_Voxel E5 Hyperdip>50-C40 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Susceptible Group, Nucleus accumbens, Biological Replicate 1 Sham 8 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107487 Last updated (according to GEO): May 01 2006 1000 Cerebral cortex N61__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Heart Atrium 1000 Hippocampus Source GEO sample is GSM107919 Last updated (according to GEO): Jun 06 2006 To dissect the impact of nuclear and extranuclear mutant htt on the initiation and progression of disease, we generated a series of transgenic mouse lines in which nuclear localization (NLS) or nuclear export sequences (NES) have been placed N-terminal to the htt exon 1 protein carrying 144 glutamines. Our data indicate that the exon 1 mutant protein is present in the nucleus as part of an oligomeric or aggregation complex. Increasing the concentration of the mutant transprotein in the nucleus is sufficient for, and dramatically accelerates the onset and progression of behavioral phenotypes. Furthermore, nuclear exon 1 mutant protein is sufficient to induce cytoplasmic neurodegeneration and transcriptional dysregulation. However, our data suggests that cytoplasmic mutant exon 1 htt, if present, contributes to disease progression. Last Updated (by provider): Dec 21 2005 Contributers: Caroline L Benn Andrew D Strand Ben Woodman James M Olson Gillian P Bates Includes GDS2169. Update date: Aug 28 2006. Dataset description GDS2169: Analysis of cerebella of transgenics expressing mutant huntingtin (htt) exon 1 protein in nucleus only or in both nucleus and cytoplasm. The polyglutamine (polyQ) expansion in htt results in Huntington's disease (HD). Results provide insight into the impact of subcellular location of polyQ in HD.. Olfactory Epithelium 1000 Replicate1_Voxel D3 Replicate2_Voxel A6 embryonic hearts 1064 1079 1695 1668 with inflammatory myopathies MuscleRegen-ctx13d-1RLAv2-s2 253 237 of neural retinas Heart Ventricle 861 foreskin fibroblast #4, serum starved' heart_atrium_2 Source GEO sample is GSM80654 Last updated (according to GEO): Mar 31 2006 Spleen 0 5 87 71 Normal Cerebellum Communicable Diseases 861 accumbens_2 Pituitary Gland 861 amygdala rattus_norvegicus_strain iNP animal_number 11 Comprehensive analysis of PPARa-dependent regulation of hepatic lipid metabolism by expression profiling - Homo sapiens Caudal 1000 Plasma 861 5 0 brain Heart Ventricle 1000 Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM107991 Last updated (according to GEO): Jun 06 2006 5 0 Muscle kidney 37 43 Ganglia 861 Disease Source GEO sample is GSM175931 Last updated (according to GEO): Apr 09 2007 Osteoblasts 1000 Brain 1000 1000 Brain Colorectal Adenocarc Source GEO sample is GSM18865 Last updated (according to GEO): Sep 25 2006 1BJZ02081483b_Trigeminal_Ganglion Brain 861 17 7 hippocampus T31__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A The discovery of quantitative trait loci (QTL) in model organisms has relied heavily on the ability to perform controlled breeding to generate genotypic and phenotypic diversity. Recently, we and others have demonstrated the use of an existing set of diverse inbred mice (referred to here as the mouse diversity panel, MDP) as a QTL mapping population. The use of the MDP population has many advantages relative to traditional F(2) mapping populations, including increased phenotypic diversity, a higher recombination frequency, and the ability to collect genotype and phenotype data in community databases. However, these methods are complicated by population structure inherent in the MDP and the lack of an analytical framework to assess statistical power. To address these issues, we measured gene expression levels in hypothalamus across the MDP. We then mapped these phenotypes as quantitative traits with our association algorithm, resulting in a large set of expression QTL (eQTL). We utilized these eQTL, and specifically cis-eQTL, to develop a novel nonparametric method for association analysis in structured populations like the MDP. These eQTL data confirmed that the MDP is a suitable mapping population for QTL discovery and that eQTL results can serve as a gold standard for relative measures of statistical power. LCM 800 biological rep5 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n051 Source GEO sample is GSM2084 Last updated (according to GEO): Nov 21 2005 Homozygous O377 mutant mouse line versus wildtype mice Source GEO sample is GSM86419 Last updated (according to GEO): Dec 08 2005 34 30 Lungs Gene expression data from postmorten brain regions Source GEO sample is GSM145437 Last updated (according to GEO): Nov 20 2006 Gene expression data from liver Source GEO sample is GSM243397 Last updated (according to GEO): Nov 16 2007 nodose_nucleus_8 Control rats 24h after injection with PBS Treatment, type=time_course, description=Control animals are treated with PBS, measurement=24.0 h Source GEO sample is GSM32084 Last updated (according to GEO): May 27 2005 67 40 with coronary artery disease 861 Malignant neoplasm of prostate 1000 Spleen Osteoblasts 1000 12 0 ovarian tumor Brain 1000 CurrentSmoker 10 Primary large cell neuroendocrine carcinoma 5020 0 47 Bipolar Disorder 1000 IDC79 on harvard-12k Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226055 Last updated (according to GEO): Nov 02 2007 in the tumors 941 953 in bronchial epithelia 311 332 Parkinson's disease sample x023 861 Heart 810 802 blisters Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n083 Source GEO sample is GSM2083 Last updated (according to GEO): Nov 21 2005 341 330 odontoblasts Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=1 (Non-acute rejection). One of three samples from the same patient, different visits. Source GEO sample is GSM36456 Last updated (according to GEO): May 27 2005 913 Coronary heart disease 5 0 Muscle Gene expression data from postmorten brain regions Source GEO sample is GSM145213 Last updated (according to GEO): Nov 20 2006 from the right forebrain 21 44 Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles. PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity. Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence. To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips. Source GEO sample is GSM136561 Last updated (according to GEO): Jun 05 2007 brain, adrenal medulla: Sample#B4(Ctrl Pt4)_e1_le1 D_U133A_10_nAcc 901 frontal lobe for liver 26 35 14 days hindlimb suspended RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis. Source GEO sample is GSM10053 Last updated (according to GEO): May 28 2005 pull-downC_9, ZT6 Liver 1000 with autism spectrum disorder 37 65 Medulla Oblongata 861 CNS-SMTC_Ctr24h-1C-s2 Brain (postcentral gyrus) [JunctionChip 3 of 5] AJ 3-1 Adrenal WGACON-20 Mental Retardation 1000 Determination of gene expression changes in extraocular muscle of mdx (dystrophin-deficient) mice at postnatal ages 7, 14, 23, 28, 56, and 112 days. 3 independent replicates/age/strain. Data form part of publication: Human Molecular Genetics 13:257-269, 2004.. Date GSE1026 Last Updated: May 29 2005 Contributers: John D Porter Includes GDS638. Update date: Jul 14 2004. Dataset description GDS638: Temporal analysis of diaphram muscle from dystrophin-deficient mdx mice, a Duchenne muscular dystrophy (DMD) model. Postnatal ages 7 to 112 days examined. Results provide insight into mechanisms of muscular dystrophy pathogenesis.. Exp B_3, 0.5mg/kg CPF 22 19 left NCI60.37_LABEL41EXTRACT40SUB3 Source GEO sample is GSM134179 Last updated (according to GEO): Aug 06 2007 ALLB-cell56 on Affymetrix GeneChip Human Full Length Array HuGeneFL C3H/HeJ Cingulate Cortex D Gene expression in papillary thyroid carcinoma reveals highly consistent profiles. 861 Amygdaloid structure RNA isolated from fetal cerebellum Keywords = trisomy Keywords = brain Keywords = Down syndrome Source GEO sample is GSM22584 Last updated (according to GEO): May 27 2005 22-oct-2002-liverA2-Mu11KsubBsc from vastus lateralis 4 24 35 0 Chronic contusion spinal cord injury brain, cortex: Sample4_e1_le1 GSE8700 253 237 of neural retinas 928 Synapses amygdala no access to cocaine replicate 4 Embryonal carcinoma, NCR-G3, adherent kidney 37 43 1000 Endometriosis, site unspecified Parkinson Disease 1000 none Source GEO sample is GSM246012 Last updated (according to GEO): Dec 03 2007 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 19 day time point Source GEO sample is GSM159799 Last updated (according to GEO): Apr 23 2007 Standard Affymetrix Protocol Source GEO sample is GSM15863 Last updated (according to GEO): May 28 2005 861 Ganglia Day 5_M_-LIF_Bchip atrial septal defects 198 218 1000 Spleen (cortex 19 25 7 0 prostate 861 Blood 901 Cell Adhesion Molecules Gene expression data from postmorten brain regions Source GEO sample is GSM146040 Last updated (according to GEO): Nov 20 2006 Nose 1000 welsh-prostate 0 13 MDA-MB-231 transfected with EGRE3-VgRXR and pIND-DACH1, selected by Zeocin and G418. Induced DACH1 expression was confirmed by western blot. Source GEO sample is GSM11370 Last updated (according to GEO): May 28 2005 whole brain from wild-type littermate of nicotinic acetylcholine receptor subunit mutant mice Source GEO sample is GSM120577 Last updated (according to GEO): Sep 22 2006 NA19204 264 242 gastrointestinal tract 1000 Brain from liver 21 30 1000 Brain Stem Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181205 Last updated (according to GEO): Jul 12 2007 Type 1 Diabetes patient and the timepoint 4 months after diagnosis. Source GEO sample is GSM228630 Last updated (according to GEO): Sep 11 2007 Liver (HBV+, SF22) Gene expression data from postmorten brain regions Source GEO sample is GSM145943 Last updated (according to GEO): Nov 20 2006 B6:16-4 midbrain-thalamus 0 Human Cortex 11 17 7 hippocampus 10 7 Left Circadian Time Treatment, type=time_course, measurement=6.0 h Source GEO sample is GSM53332 Last updated (according to GEO): Jul 06 2005 brain, amygdala: Amygdala 2_le1 Hydrocephalus 1000 109T 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114250 Last updated (according to GEO): Jun 16 2006 salivary_gland_1 54 29 in anatomical compartments Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151976 Last updated (according to GEO): Feb 06 2007 Spleen 0 5 Gene expression data from liver Source GEO sample is GSM243364 Last updated (according to GEO): Nov 16 2007 Cerebral cortex 901 Examining the effects of tTA expression in mouse hearts Source GEO sample is GSM15064 Last updated (according to GEO): May 28 2005 Laser capture lung cancer cells Source GEO sample is GSM191014 Last updated (according to GEO): May 25 2007 660 mesenchymal stem cell 639 Normal Source GEO sample is GSM176126 Last updated (according to GEO): Apr 09 2007 /2 brain 1467 1475 Ovarian_Tumor_Endometrioid_CHTN-OE-053 UO-31 hgu95a KT1002a_DT 861 Neoplasm 513 491 murine small intestine prostate Source GEO sample is GSM203388 Last updated (according to GEO): Jun 21 2007 Primary Carcinoma 876 Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP), exposed 6 h more to ambient pressure (CP6) and harvested with cells exposed for 6 h to hydrostatic pressure, pressure experiment # 3 (PE3). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11386 Last updated (according to GEO): Dec 15 2006 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184813 Last updated (according to GEO): Apr 26 2007 1000 Intestines, Small testes_2 brain, hippocampus: Sample15_e1_le1 olfactory epithelium wild type mouse 48 hpO Source GEO sample is GSM80196 Last updated (according to GEO): Oct 26 2005 Parkinson Disease 1000 146 131 descending colon Muscle Fibers 1000 cerebral cortex 7 21 hippocampus 709 719 Lymphoblastoid Cell Line for Individual 8210.4 log phase 5 0 brain Parkinson 0 8 of hepatic progenitor cells 1652 1679 22 0 Mammary Gland @ Preg17 SK-OV-3_CL6011_Leukemia on Affymetrix GeneChip Human Full Length Array HuGeneFL GBM Treatment, type=remove Source GEO sample is GSM99459 Last updated (according to GEO): Apr 21 2006 CO (Experiment shortNMDA: Run 19222) Treatment, type=time_course, measurement=0.0 m Source GEO sample is GSM96674 Last updated (according to GEO): Feb 14 2006 Male 71.2 yr after antibody enrichment scan 2 (U133A) no additional Source GEO sample is GSM199068 Last updated (according to GEO): Jun 08 2007 MLL-C1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Occipital lobe total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5827 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145919 Last updated (according to GEO): Nov 20 2006 GM11881 Parkinson 0 8 Wild type inbred mice Source GEO sample is GSM82953 Last updated (according to GEO): Nov 10 2005 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells cultured for 240min Source GEO sample is GSM5848 Last updated (according to GEO): May 27 2005 Malignant neoplasm of breast 1000 279 267 of the tumors PGA-MFD-MutantPD1-1aAv2-s2b Epithelium 861 20 0 human caudate nucleus MGMH030228086Aembryoday8.5 861 Muscle in the mammalian nervous system 110 141 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213481 Last updated (according to GEO): Jul 31 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114450 Last updated (according to GEO): Jun 16 2006 CD28 beads 00.00 hr. T-Cell Control frontal cortex 7 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53473 Last updated (according to GEO): Jul 06 2005 421 412 infection NCI60.20_LABEL24EXTRACT23SUB3 Source GEO sample is GSM134091 Last updated (according to GEO): Aug 06 2007 WGACON-125 39 21 from mammary glands 24 0 human prostate PC3 tumors Coronary Arteriosclerosis 1000 1000 Spleen in mouse hearts 40 54 67 40 with coronary artery disease 861 Breast Malignant neoplasm of breast 901 Microdissected area # 1 of 1761 tumor with some respiratory epithelium. 1039 1072 Control rats 240h after injection with PBS Treatment, type=time_course, description=Control animals are treated with PBS, measurement=240.0 h Source GEO sample is GSM32093 Last updated (according to GEO): May 27 2005 cortex 27 33 from aorta 150 160 861 Malignant neoplasm of brain 70 40 without coronary artery disease 3rd 4hr C+S-CA1 Gene expression data from PD1 Foxo3 wild-type ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203841 Last updated (according to GEO): Aug 02 2007 NoCAD_replicate7 C3H/HeJ Amygdala D Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47526 Last updated (according to GEO): May 29 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68163 Last updated (according to GEO): Jul 07 2006 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184777 Last updated (according to GEO): Apr 26 2007 Survey of gene expression in ten common inbred strains of laboratory mouse. Seven brain regions examined: amygdala, basal ganglia, cerebellum, frontal cortex, hippocampus, cingulate cortex, olfactory bulb. Last Updated (by provider): Oct 31 2006 Contributers: Hanwen Huang Fei Zou Fred A Wright Jessica J Nadler Terry R Magnuson 1000 Coronary Arteriosclerosis from the somatosensory cortex 510 539 5 0 brain Squamous cell carcinoma 884 Tumor__CNS_Medulloblastoma_M06_D92 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A V5-P503 Presynaptic Terminals 861 a malignancy 77 88 Normal Source GEO sample is GSM176119 Last updated (according to GEO): Apr 09 2007 Neoplasm 861 FormerSmoker 18 Novel endothelial cell markers in hepatocellular carcinoma. 19 0 Head and neck cancer GM19130 Gene expression data from epididymal fat tissues. Source GEO sample is GSM215575 Last updated (according to GEO): Aug 07 2007 Vestibular organ at E12, replicate1 Richard Almon-2-1133800608760 Gene expression data from liver Source GEO sample is GSM243401 Last updated (according to GEO): Nov 16 2007 Whole Brain 73 83 of the nephron 46 59 91 from the bone marrow 72 861 Cardiomyopathies 1000 Colon Carcinoma PGA-MLS-RA-Dex-1bAv2-s1 865 Disorder of artery 861 Endometrium 861 Cardiomyopathies from intraabdominal 227 245 (No additional Information) Source GEO sample is GSM114431 Last updated (according to GEO): Jun 19 2006 The nose 94 101 SN:1006729 Source GEO sample is GSM115354 Last updated (according to GEO): Jun 20 2006 80 68 Control blood 24 0 human prostate PC3 tumors PGA-HMO-Obese-4bUA-s2 total RNA from biosource CC#8S Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92485 Last updated (according to GEO): Jan 13 2006 406 395 whose hearts infection 255 264 Expression profiling of spinal cord section (T8) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM4442 Last updated (according to GEO): May 28 2005 LiverP14_022XACIR_062.txt Kidney 1000 1000 Blind Vision Wild type 8 wk old male A/J mouse pituitary gland Source GEO sample is GSM107044 Last updated (according to GEO): Mar 05 2007 /SvEvTac pituitary gland rep2 5 33 Brain 861 Neoplasm 861 Epithelium 861 Category: Lymphoma Classification Subcategory: Chronic Lymphocytic Leukemia Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b070 Source GEO sample is GSM2018 Last updated (according to GEO): Nov 21 2005 CNS-SC_InjA30m-3C-s2 Blood Test (Blinded) Sample Source GEO sample is GSM129950 Last updated (according to GEO): Sep 18 2007 861 Cardiomyopathies Expression profiling of moderately injured raphe at 24h in rats Source GEO sample is GSM41584 Last updated (according to GEO): May 27 2005 brain 0 5 Blood Test (Blinded) Sample Source GEO sample is GSM130019 Last updated (according to GEO): Sep 18 2007 Blood supply aspects 983 51 CN B CNS-SpinalC-conAdult-4h-2A-s2 983 Cor pulmonale Parkinson Disease 1000 5 0 brain 1000 frontal lobe none Source GEO sample is GSM149559 Last updated (according to GEO): Jan 03 2007 Bone Marrow 1000 Testis 861 no additional Source GEO sample is GSM199330 Last updated (according to GEO): Jun 08 2007 from SVGR2 glial cells 21 43 between tumor 261 273 leukemia, promyelocytic-HL-60 Source GEO sample is GSM18893 Last updated (according to GEO): Sep 25 2006 no additional Source GEO sample is GSM199424 Last updated (according to GEO): Jun 08 2007 22 14 (cerebrum to the nose 599 609 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68299 Last updated (according to GEO): Jul 07 2006 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211334 Last updated (according to GEO): Jul 18 2007 Primary Neoplasm 1000 1000 Pituitary Gland Mental Retardation 1000 Biopsy of the normal mucosa of the colon from patient #21 Thyroid carcinoma 901 MuscleRegen-ctx12h-2LLA-s2 Recurrent Adenocarcinoma 8 metanephric mesenchyme, LIF, 7 days, biological rep1 days nasal epithelium 1126 1147 adrenal_gland_cortex_3 Source GEO sample is GSM80607 Last updated (according to GEO): Mar 31 2006 GSE1656 We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7. Source GEO sample is GSM200742 Last updated (according to GEO): Jul 12 2007 Wildtype cocaine, technical replicate 1 none Source GEO sample is GSM123229 Last updated (according to GEO): Jul 26 2006 from nose 96 104 5 0 brain 1000 Turner's Syndrome 861 Heart small intestine; duodenum Source GEO sample is GSM18691 Last updated (according to GEO): May 27 2005 Spinal Cord 1000 in the brain 150 162 Endometrium/Ovary 8 Disease 1983 1969 adhering blood 1000 Kidney Leukemia Chronic Myelogenous (K562) [JunctionChip 2 of 5] Primary Neoplasm 1000 ExpressionLevel:GXN-00540 on Affymetrix GeneChip Mouse Expression Array 430A and Mouse Genome 430A 2.0 Array Olfactory Epithelium 1000 Donor 2 Time point 12 hours Autologous control (uninfected) Source GEO sample is GSM2609 Last updated (according to GEO): May 27 2005 Large-scale analysis of the mouse transcriptome. Bone marrow, flushed from femur C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 285.45 Stdv: 7.90 Min: 273.18 Max: 300.08 Source GEO sample is GSM2969 Last updated (according to GEO): Mar 20 2006 of mouse brain 9 23 7 0 prostate Muscle Source GEO sample is GSM4284 Last updated (according to GEO): May 27 2005 Liver 1000 901 Temporal Lobe 1000 Cardiomyopathy, Alcoholic 1000 Cerebellum 7 cerebral cortex 21 Prostate 10 Disease of the postmortem brains 675 699 Macrophage 14smi015 Olfactory Epithelium 1000 1000 Brain Endometrial Stromal Sarcoma 901 Abdominal aorta 0 14 1000 Liver 1345 1323 by cervical dislocation HeartHDmekt_022KAFIN_123t.txt GSE281 1000 Retina 5 0 brain Normal Source GEO sample is GSM176219 Last updated (according to GEO): Apr 09 2007 Male4, Olfactory RNA_Nasal olfactory epithleium_Tissue was preserved in RNA later and collected from nose from cingulate cortex 18 38 Hippocampus 1000 skeletal muscle Source GEO sample is GSM18680 Last updated (according to GEO): May 27 2005 comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247386 Last updated (according to GEO): Dec 11 2007 Activated Source GEO sample is GSM176284 Last updated (according to GEO): Apr 09 2007 Seminoma 1000 923 Congestive heart failure Kidney OC-4A Small cell carcinoma of lung 901 1000 Spleen plasma cells 332 344 dopamine receptors 1386 1405 7 cerebral cortex 21 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Prostaglandin E2 for 30min Source GEO sample is GSM5731 Last updated (according to GEO): May 27 2005 Liver 0 4 1000 Structure of entorhinal cortex BALB/cJ strain, brain hemisphere, biological rep1 We have used microarrays to investigate the changes in gene expression at various times after stroke. Our findings reported that gene expression screening can detect known and unknown transcriptional features of stroke. Last Updated (by provider): Oct 29 2007 Contributers: Pat Kumar Mark Slevin Nick Mitsios John Gaffney Shant Kumar Jurek Krupinski 660 mesenchymal stem cell 639 in prostate epithelial cells 165 192 861 Bladder 326 291 of muscular dystrophy pathogenesis. of coronary artery disease 317 342 1000 Left 901 Caudate nucleus structure 913 Myeloid Leukemia peripheral blood-CD56NKCells Source GEO sample is GSM18717 Last updated (according to GEO): Sep 25 2006 43 0 Chorionic mesoderm-derived mesenchymal cells normal testis 54 66 Squamous cell carcinoma 875 Tumor__Leukemia_ALL-B_ALL_(17281)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 352 340 encephalitis Adipose tissue 901 CNS-SMTC_Ctr14d-2A-s2 in seminoma 28 38 Abdomen 861 28 0 frontal cortex wistar ky 3927 913 Coronary heart disease of coronary artery disease 258 284 Cerebral cortex 861 HCC (HBV+, HK24) Osteoblasts 1000 Oat cell carcinoma 867 brain 0 5 89 68 with tricuspid valves Pooled Total Prefrontal cortex RNA from 4 female mice overexpressing the human synaptic AChE. Source GEO sample is GSM14622 Last updated (according to GEO): May 28 2005 nic + nmda3 (Experiment Neuroprotection4- Run 21823) Treatment, type=timepoint, description=Same sample used for Experiment Neuroprotection4-Run 14985, samples were rerun due to oven failure, measurement=0.0 h Source GEO sample is GSM96700 Last updated (according to GEO): Feb 14 2006 Healthy patient. Source GEO sample is GSM228579 Last updated (according to GEO): Sep 11 2007 from somatosensory cortex 12 36 S1P2-KO-neocortex, biological rep2 (male) gene expression of 5 day LIF differentiated ESCs Source GEO sample is GSM181956 Last updated (according to GEO): Apr 12 2007 Experimental asthma was induced in BALB/c mice by sensitization and challenge with the allergen ovalbumin. Control groups received PBS. To investigate the innate immune component of experimental asthma, we also analyzed recombinase activating gene (RAG) deficient mice following exposure to ovalbumin and control PBS Last Updated (by provider): Apr 23 2007 Contributers: Xin Lu Patricia W Finn Vipul V Jain David L Perkins Fetal Liver BD Normal 608 569 of the posterior pituitary neural lobe 1000 ovarian neoplasm 5 0 brain CLL-41 Thalamus Subthalamic Nucleus 1 Disease 0 37 09_0001_SepticShock_Day1_78 26 15 endometrioid CON(SN)(3) Lung tissue from C57BL/6 mice that were always fed by 2/3 and sacrificed 4hrs after the onset of calorie-restriction in calorie-restricted mice. Lot batch = Source GEO sample is GSM4042 Last updated (according to GEO): May 28 2005 Plasma 861 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188797 Last updated (according to GEO): Jun 06 2007 24 19 (Renal Blood 1000 421 412 infection 61 41 from postmortem brain Nose 1000 2_cerebral_cortex_12hrs_sleep_deprivation_#10 4089 4084 liver Hippocampus 1000 79 75 Lungs Posterior root of spinal nerve 861 retina 0 5 Human prostate cancer cells in different conditions Source GEO sample is GSM13080 Last updated (according to GEO): May 28 2005 frontal cortex sprague 3937 Brain 861 Liver Test (Blinded) Sample Source GEO sample is GSM130116 Last updated (according to GEO): Sep 18 2007 Medulla Oblongata 861 schizophrenia 559 572 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9960.gif Source GEO sample is GSM79799 Last updated (according to GEO): Sep 22 2006 gene expression data from ODC mouse skin samples Source GEO sample is GSM216673 Last updated (according to GEO): Aug 09 2007 C57BL/6J female number 1, DNFB-treated allergic ear (#4_Wt-Tr-3) 37 32 stroke HUVEC A on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A ISR22 Coronary Arteriosclerosis 1000 BALB/cByJ Frontal Cortex B Cerebral cortex 901 spinal cord, spinal cord: G2B_le1 Cerebral cortex 1000 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201272 Last updated (according to GEO): Jun 14 2007 starved 143 149 vagina_10 To investigate the gene program activated by serotonergic hallucinogens in mouse somatosensory cortex, the effects of the 5-HT2A agonist (±)2,5-dimethoxy 4-iodoamphetamine (DOI) on gene expression was studied. The 5-HT2A serotonin receptor is a member of the 5-HT2 receptor subfamily of G protein?coupled receptors. The 5-HT2A receptor is thought to modulate processes related to cognition, appetite, mood, anxiety, sleep, and sexual behavior. Abnormal function of this receptor has been implicated in neuropsychiatric disorders such as major depression and schizophrenia. In particular, the 5-HT2A receptor has been implicated in the modulation of the mechanisms related to psychosis. We compared gene response patterns in the somatosensory cortical brain area, which has a high density of 5-HT2A receptors and has been implicated in the action of hallucinogenic drugs. Mice (strain 129Sv) were injected with DOI (2 mg/kg or 10 mg/kg) or vehicle, animals were sacrificed after 1 h, and somatosensory cortex samples dissected on ice for RNA extraction. Seven independent microarray hybridizations from seven different DOI- or vehicle-treated mouse pairs were performed. In this particular hybridization, 15 µg of RNA was used. Keywords = somatosensory cortex 5-HT2A receptor DOI Source GEO sample is GSM3381 Last updated (according to GEO): Oct 28 2005 1089 into hair cells 1104 KHG-HG-6Av2-s2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Expression profiling of spinal cord section (T10) extracted from rats 24h following severe injury Source GEO sample is GSM31362 Last updated (according to GEO): May 27 2005 1000 Brain nostrils 156 164 Blood 861 Prostate 861 Head and neck cancer Source GEO sample is GSM155679 Last updated (according to GEO): Apr 24 2007 from liver 21 30 of Parkinson's disease 450 471 CD3 beads 01.00 hr. T-Cell, Repeat. Brain 1000 processed in batch 6 Source GEO sample is GSM90432 Last updated (according to GEO): Mar 20 2006 DLBC10 on Affymetrix GeneChip Human Full Length Array HuGeneFL 74 59 stria vascularis 1000 Modiolus anguli oris Epithelial Cells 901 1000 Heart failure Circadian Time Treatment, type=time_course, measurement=12.0 h Source GEO sample is GSM53339 Last updated (according to GEO): Jul 06 2005 1000 Amygdaloid structure nasal epithelial cells 28 49 Spleen 0 5 VDXKIU_284C63 Epithelium 861 861 Liver Normal Ovary 1000 ovarian neoplasm brain, cochlea: [2] Sample #2_le1 no additional Source GEO sample is GSM199166 Last updated (according to GEO): Jun 08 2007 0 Human Cortex 11 Gene expression profiling predicts clinical outcome of breast cancer. Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11466 Last updated (according to GEO): May 28 2005 18 0 3AJZ02021915_ LIVER 7 cerebral cortex 21 no additional Source GEO sample is GSM199097 Last updated (according to GEO): Jun 08 2007 Nose 1000 Primary typical carcinoid 4423 stria terminalis 1000 747 tumor cells 757 Epithelial Cells 901 5 0 brain Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181059 Last updated (according to GEO): Jul 12 2007 1000 Spleen /Ovary 16 Disease 11 27 Lymphoblastoid Cell Line for Individual 8093.3 log phase Normal Source GEO sample is GSM176106 Last updated (according to GEO): Apr 09 2007 AD control Treatment, type=dissect Source GEO sample is GSM119652 Last updated (according to GEO): Jul 10 2006 sal-PVH_1 Breast Carcinoma 1000 in human brain 151 164 901 frontal lobe tongue epidermis 0 15 AK_SleepDep_ZT 6_2 Putamen 9 Normal JVM-HH 42 31 to infection Liver Test (Blinded) Sample Source GEO sample is GSM130090 Last updated (according to GEO): Sep 18 2007 Epithelium of bronchus 983 Muscular Dystrophy, Duchenne 1000 DBA/2J Hippocampus A of agranulocytosis 170 188 CNS-SC_Inj7d-3A-s2b Control H_Achip_rep2 I_U133A_64_CB CT42-1 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Sphingosine-1-phosphate for 60min Source GEO sample is GSM5748 Last updated (according to GEO): May 27 2005 MCF10A_Untreated_#5 Voxel E4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1420 Last updated (according to GEO): Nov 21 2005 Spleen 0 5 Gene expression data from postmorten brain regions Source GEO sample is GSM144892 Last updated (according to GEO): Nov 20 2006 no additional Source GEO sample is GSM199183 Last updated (according to GEO): Jun 08 2007 Epithelial Cells 1000 663 mesenchymal stem cell 642 ALDHhiSSClo stem cells 354 375 brain, frontal cortex: ADX AM DR_e1_le1 Trachea [JunctionChip 5 of 5] 179 169 of diabetes (No additional Information) Source GEO sample is GSM114427 Last updated (according to GEO): Jun 19 2006 144 114 from a single adult spinal cord 1000 Cerebellum of AML 1167 1172 325 314 to infection L_D2_SleepDep_ZT 6_3 164 157 by milk Spleen vs Dimaprit Treated B cell testis 52 58 from epididymal fat tissues 21 48 861 Liver 12 0 Nervous Sysem 861 Blood 1000 Spinal Cord 1000 Brain Transitional epithelium 1000 n/a Source GEO sample is GSM177962 Last updated (according to GEO): Jun 11 2007 U251 hgu95a 11_0009_Control_Day1_51 cerebellum 7 16 Diffuse large B-cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is curable in less than 50% of patients. Prognostic models based on pre-treatment characteristics, such as the International Prognostic Index (IPI), are currently used to predict outcome in DLBCL. However, clinical outcome models identify neither the molecular basis of clinical heterogeneity, nor specific therapeutic targets. We analyzed the expression of 6,817 genes in diagnostic tumor specimens from DLBCL patients who received cyclophosphamide, adriamycin, vincristine and prednisone (CHOP)-based chemotherapy, and applied a supervised learning prediction method to identify cured versus fatal or refractory disease. The algorithm classified two categories of patients with very different five-year overall survival rates (70% versus 12%). The model also effectively delineated patients within specific IPI risk categories who were likely to be cured or to die of their disease. Genes implicated in DLBCL outcome included some that regulate responses to B-cell-receptor signaling, critical serine/threonine phosphorylation pathways and apoptosis. Our data indicate that supervised learning classification techniques can predict outcome in DLBCL and identify rational targets for intervention. Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 23.75 hours after lights on. Original sample code = CM36A Source GEO sample is GSM227340 Last updated (according to GEO): Sep 10 2007 hippocampus rattus_norvegicus_strain iNP animal_number 11 9 0 Lymph Node total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lipopolysaccharide (LPS) for 30min Source GEO sample is GSM5663 Last updated (according to GEO): May 27 2005 brain, hippocampus: Wt #3406 Cereb_e1_le1 5 0 brain plasma cells 50 61 Isoflurane 10 exposures-1 mod098_100nM-3 Blood 861 Cortex Treatment, type=pharmacogenomic_treatment, description=Handled (no stress) control Source GEO sample is GSM53316 Last updated (according to GEO): Jul 06 2005 12M_120502 Lymphoblastoid Cell Line for Individual 8177.3 log phase of the stria terminalis rep1 26 53 901 Epithelial Cells none Source GEO sample is GSM149606 Last updated (according to GEO): Jan 03 2007 901 Prostatic hypertrophy 1000 Cerebral cortex blood, adrenal medulla: Ctx -/- replicate 2_e1_le1 32 16 of organ of Corti AT2-hTERT_sham_6h_C5_26743 19 0 human frontal cortex brain, cerebral cortex: Co 5/7_le1 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9977.gif Source GEO sample is GSM79836 Last updated (according to GEO): Sep 22 2006 88 68 with bicuspid valves rat cortex Treatment, type=time_course, measurement=14.0 d Source GEO sample is GSM53225 Last updated (according to GEO): Jul 06 2005 Cerebral cortex 861 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection). Source GEO sample is GSM36445 Last updated (according to GEO): May 27 2005 281 (orbitofrontal cortex 301 5 0 Spleen 110 94 of heart failure Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 24 h to ambient pressure (CP24) and harvested with cells exposed for 24 h to hydrostatic pressure, pressure experiment # 3 (PE3). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11401 Last updated (according to GEO): Dec 15 2006 Epithelial Cells 901 this sample is from a 16-week-old male mdx mice gastrocnemius muscle Source GEO sample is GSM4378 Last updated (according to GEO): May 28 2005 NCI-H322_CL1017_NSCLC 5 0 brain (ALS 184 187 GSE2888 human caudate nucleus Source GEO sample is GSM86792 Last updated (according to GEO): Feb 08 2006 GBM Treatment, type=remove Source GEO sample is GSM99490 Last updated (according to GEO): Apr 21 2006 Whole brain 0 10 Liver 1000 1000 Hippocampus Expression profile of genes in mouse brain Source GEO sample is GSM21052 Last updated (according to GEO): May 27 2005 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14088.gif Source GEO sample is GSM81533 Last updated (according to GEO): Sep 22 2006 The nose 94 101 Sample details: Three pools of rostral (R1-3), three pools of middle (M1-3), and three pools of caudal (C1-3) E13.5 MF1 neocortex were collected from 4 embryos. All possible 18 comparisons were carried out. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. Source GEO sample is GSM62825 Last updated (according to GEO): Aug 26 2005 Neoplasm 861 1000 Brain 861 Cardiomyopathies Supranuclear Palsy, Progressive 1000 Brain 861 n/a Source GEO sample is GSM177897 Last updated (according to GEO): Jun 11 2007 I_U133Plus_123_CB Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242044 Last updated (according to GEO): Dec 04 2007 67 40 with coronary artery disease Fibroblasts 1000 olfactory epithelium 194 213 Gene expression data from mammary glands of involuting mice Source GEO sample is GSM202703 Last updated (according to GEO): Jun 20 2007 in the brain 150 162 C57L/J Olfactory Bulb B 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114256 Last updated (according to GEO): Jun 16 2006 total RNA extracted from one ApoE-/- mouse infected wtih a control adenovirus expressing GFP Source GEO sample is GSM157860 Last updated (according to GEO): Jan 25 2007 1000 Alzheimer's Disease 5 0 Spleen Expression profiling of spinal cord section (T9) extracted from rats 48h following moderate injury Source GEO sample is GSM31564 Last updated (according to GEO): May 27 2005 in the brain 150 162 Epithelium 861 GSE8425 1000 Brain DBA/2J Acute morphine treated, striatum, biological replicate 3 Source GEO sample is GSM187988 Last updated (according to GEO): Jun 14 2007 Blood 861 of the postmortem brains 674 698 placebo 15d, biological rep9 Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16866.gif Source GEO sample is GSM91505 Last updated (according to GEO): Sep 22 2006 SK-MEL-28_CL10008_MELANOMA Heart 861 Nose 1000 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153454 Last updated (according to GEO): Jan 11 2007 db/db 8wk 2 /6J mouse periaqueductal gray 29 57 In situ synthesized oligo arrays, U74Av2, from Affymetrix were used to measure differential gene expression in RNA samples generated from the liver (GSE864) and spleen (GSE865) of Nrf2 knockout and wildtype mice at 5 months of age. This SuperSeries is composed of the following subset Series: GSE864: Nrf2 Knockout vs. Wildtype mice, liver sample GSE865: Nrf2 Knockout vs. Wildtype mice, spleen sample Last Updated (by provider): Apr 25 2006 Contributers: Jeffrey A Johnson Thor D Stein Jiang Li Includes GDS514. Update date: Mar 19 2004. Dataset description GDS514: Analysis of spleen and liver tissue of 5 month old male and female transcription factor nuclear factor E2-related factor 2 (Nrf2) double knockouts. Nrf2-deficient female mice develop lupus-like autoimmune nephritis.. Standard affymetrix protocol Source GEO sample is GSM119726 Last updated (according to GEO): Jul 31 2007 of fibroblasts 107 120 Conventional Rectum 2 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16257.gif Source GEO sample is GSM91525 Last updated (according to GEO): Sep 22 2006 O377 homozygotes brains 12 Ventral Tegmental Area 3 Normal Epithelium 861 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15726 Last updated (according to GEO): May 28 2005 M_U133A_6_HC 1000 Infection 22 CN B 25 7 Right Parietal Lobe Liver Test (Blinded) Sample Source GEO sample is GSM130081 Last updated (according to GEO): Sep 18 2007 Intraabdominal stromo vascular fraction, rep2 Fetal occipital cortex cocaine5 Spleen vs SDF1 alpha Treated B cell 240min (set3) NCI60.32_LABEL36EXTRACT35SUB3 Source GEO sample is GSM134153 Last updated (according to GEO): Aug 06 2007 913 Coronary heart disease GIN (Gad1 inhibitory ref. (pubmed id:10777798) ) neurons from hippocampus Source GEO sample is GSM63016 Last updated (according to GEO): Dec 01 2005 1000 jejunum 489 470 of bladder carcinoma 39 27 the maxillary 19 0 Head and neck cancer Plasma 861 O377 homozygotes brains_2 brain, frontal cortex: pADX AM LC_e1_le1 27 0 H7 Human Embryonic Stem cell D_U133Plus_34_DLPFC C114 on NCI-7.6k in the mdx muscle 610 626 861 leukemia Mesenchymal Stem Cells 1000 Cerebellum 1000 Replicate2_Voxel B8 PGA-RnSalt_c_3w_1-m5 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114207 Last updated (according to GEO): Jun 16 2006 1000 Kidney TGFBd8_23 CO_NP_mid_3 1000 medulloblastoma 861 Neoplasm Osteoblasts 1000 Estrogen response after stroke in blood 16 23 Skeletal bone 861 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141301 Last updated (according to GEO): Oct 26 2006 Prefrontal Cortex Source GEO sample is GSM105468 Last updated (according to GEO): Apr 17 2006 C111 on NCI-7.6k Coronary heart disease 913 Normal hippocampus MPL13E_untreated_10% brain, frontal cortex: Sample44_e1_le1 Spleen 0 5 Gene expression data from older female during 1 week of adequate protein intake Source GEO sample is GSM209829 Last updated (according to GEO): Jul 11 2007 heart.2 239 233 Retinas "43 hr Hela Double Thymidine, exp3" Primary Carcinoma 876 861 Kidney /testicles 202 212 865 Disorder of artery rat hippocampus Treatment, type=time_course, measurement=24.0 h Source GEO sample is GSM32137 Last updated (according to GEO): May 27 2005 1000 Brain 875 Cerebellar Diseases 861 Cerebral cortex 9 of prefrontal cortex 28 861 Extracellular Matrix 1000 Brain Voxel A3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1386 Last updated (according to GEO): Nov 21 2005 1000 frontal lobe with autism spectrum disorder 37 65 861 Cerebral cortex starved 143 149 Category: Lymphoma Classification Subcategory: Hematopoetic cell lines Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b040 Source GEO sample is GSM1962 Last updated (according to GEO): Nov 21 2005 Diet Induced Obese rat C1 BXD32_M7SS02042219 cy5:SHR treated w/ nifedipine, biological rep 4r; cy3:pool of 6 WKY control rats liver_PPARa-knockout_WY14643_6h_rep4 Large-scale analysis of the human transcriptome. Ovary, pooled Source: CHTN, see PMID 11158614 Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 281.10 Stdv: 26.00 Min: 240.25 Max: 341.39 Source GEO sample is GSM2851 Last updated (according to GEO): Mar 20 2006 Expression profiling of somatomotor cortex extracted from rats at 4h following moderate injury Source GEO sample is GSM41734 Last updated (according to GEO): May 27 2005 D_U133Plus_112_Amy 118 FC BA9 A The central nervous system 0 25 cortex 7 12 Anterior nares 1000 861 Cardiomyopathies I_U133A_30_CB by muscle atrophy 247 264 7 0 prostate of the atrial 647 659 Primary Neoplasm 1000 Mouse Liver LRD Diet 5wk 100ppb Drinking Water Exposure, biological replicate F 861 Cerebellum PGA-E16.5_2A mouse cerebral cortex 0 21 SN:1007085 Source GEO sample is GSM115366 Last updated (according to GEO): Jun 20 2006 Dahl-Iwai Female LowSalt OuterMedulla rat103 dahl_medullar_103_1_OM_053001 DRG acutely dissected from embryos Source GEO sample is GSM246071 Last updated (according to GEO): Dec 03 2007 31 0 Cerebellum Alzheimer's disease 6 Mouse old brain w/ a-tocopherol aT-Br-2 skeletal Source GEO sample is GSM67248 Last updated (according to GEO): Jan 19 2006 MDA-MB-231/ATCC hgu95e To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18479 Last updated (according to GEO): May 27 2005 melanoma 861 very advanced HCC Source GEO sample is GSM155949 Last updated (according to GEO): Jun 21 2007 Liver Test (Blinded) Sample Source GEO sample is GSM130126 Last updated (according to GEO): Sep 18 2007 19 0 human frontal cortex 901 Muscular Dystrophies 861 Liver 861 Brain 1000 Carcinoma 1000 Structure of parenchyma of lung mouse cerebral cortex from COX-2 WT Source GEO sample is GSM121427 Last updated (according to GEO): Jan 31 2007 50 10 of pediatric acute lymphoblastic leukemia ALL_2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Neoplasm 861 Recurrent tumor grade 3 164 187 Gene expression data from postmorten brain regions Source GEO sample is GSM145575 Last updated (according to GEO): Nov 20 2006 861 Longitudinal Neuroglia 901 Semeralul_PFC_Development_Week2_Batch1_Animal_5 1000 Cochlear structure Cerebral cortex 1000 1000 Endothelial Cells 1000 Brain 1000 Cerebellum Brain 861 fetal lung fibroblast #1, asynchronous Donor 1 time point 0 Infected with HIV-1, RF Source GEO sample is GSM2595 Last updated (according to GEO): May 27 2005 Neoplasm 861 1000 Cardiomyopathies 197 169 a Duchenne muscular dystrophy 1000 Cardiomyopathy, Alcoholic of Parkinson's disease 450 471 Expression profiling of spinal cord section (T10) extracted from rats 7d following mild injury Source GEO sample is GSM31335 Last updated (according to GEO): May 27 2005 liver 0 5 M_U133Plus_106_HC spinal cord 13 23 of somatomotor cortex 21 41 Synovium; chronic arthritis Keywords = mouse gene expression database Source GEO sample is GSM29439 Last updated (according to GEO): May 27 2005 singh-prostate 0 13 Gene expression data from the hippocampus of S1P2-knockout mouse Source GEO sample is GSM172964 Last updated (according to GEO): Mar 08 2007 Disease Source GEO sample is GSM176311 Last updated (according to GEO): Apr 09 2007 Plasma 861 cy3:WKY control, biological rep 5g; cy5:pool of 6 WKY control rats Lymphoma (Burkitts Raji) [JunctionChip 4 of 5] Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21465.gif Source GEO sample is GSM91485 Last updated (according to GEO): Sep 22 2006 NB-C11 on NHGRI-6.5k_b NCI60.45_LABEL49EXTRACT48SUB3 Source GEO sample is GSM134220 Last updated (according to GEO): Aug 06 2007 /NJ Olfactory Bulb A 3 22 876 Lymphoma, Diffuse CT8 5 0 brain Parkinson's disease sample x174 0 30 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155051 Last updated (according to GEO): Jun 04 2007 4_hypothalamus_9hrs_sleep_deprivation_#100 Ovum 861 861 Cardiomyopathies Stria 861 861 Nerve 861 Cerebral cortex 861 Brain ventral tegmental area short access to cocaine replicate 2 Craniocerebral Trauma 861 Brain 861 1000 Antibodies Sample 114 on vantveer-oligo Spinal Cord 1000 91 from the bone marrow 72 Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep1 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15697 Last updated (according to GEO): May 28 2005 human cerebellum Source GEO sample is GSM87134 Last updated (according to GEO): Feb 08 2006 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10136.gif Source GEO sample is GSM79707 Last updated (according to GEO): Sep 22 2006 Epithelium of bronchus 983 Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002. Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily. Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France). Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h. After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hepatic gene expression analysis. From these 5 mice, livers were dissected according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancourt, France), which consisted of carefully dissecting out the liver, rinsing with 70% EtOH to remove adhering blood, trimming of adhering connective tissue with scissors, cutting into 100-150 mg subsections, freezing in liquid N2, and storing at -80°C until gene expression and lipid analysis. Hepatic lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5). Liver tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hepatic RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips. Source GEO sample is GSM2565 Last updated (according to GEO): Oct 28 2005 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47540 Last updated (according to GEO): May 29 2005 D_U133Plus_119_DLPFC from hippocampus 57 72 1BJZ02061205_fetalThyroid 913 Acute leukemia Large-scale analysis of the mouse transcriptome. Kidney C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 307.61 Stdv: 20.38 Min: 273.80 Max: 348.81 Source GEO sample is GSM2949 Last updated (according to GEO): Mar 20 2006 Spinal Cord 901 rat_hepatocytes_WY24h_pooled Colon 861 NL-4353-A334-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 901 Bone Marrow 2737 tumor cells 2747 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225686 Last updated (according to GEO): Nov 05 2007 mouse brain 478 489 PGA-Csx_null_8a-m4 of the stria terminalis 50 72 U87 glioblastoma cell, clone 8.1 (expresses PDGF-A dominant-negative) Keywords = bioinformatics Keywords = gene expression Keywords = cancer Keywords = platelet-derived growth factor Keywords = sterol regulatory element binding protein Keywords = glioblastoma multiformae Keywords = microarray Source GEO sample is GSM34586 Last updated (according to GEO): May 27 2005 Myopathy 875 Mouse Kidney Male 1 V5-P054 Mesenchymal Stem Cells 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM146053 Last updated (according to GEO): Nov 20 2006 Expression profile of genes in mouse brain Source GEO sample is GSM21045 Last updated (according to GEO): May 27 2005 Prosencephalon 861 Germ free Descending colon 1 Brain 1000 Endometrium/Ovary 6 Disease Brain 861 Spleen 1000 861 Alzheimer's Disease GSE5918 1000 Heart of the normal mucosa 7 26 15401 on TGRI-6.5k ovarian tumor: serous Source GEO sample is GSM139475 Last updated (according to GEO): Apr 09 2007 CNS-SC_InjB14d-1B-s2 cardiac 763 769 86 70 Fetal liver cells Caudal 1000 Prostate carcinoma 901 none Source GEO sample is GSM239908 Last updated (according to GEO): Dec 07 2007 Insulin-like growth factor 1 (IGF1) heart study Melanoma xenograft, MC2_Sub_C (LeiATCC) Mammary Gland @ Preg7, biological rep4 Infection 1112 1121 1000 frontal lobe UBOC1 Exp B Day 4 (a) Temporal neocortex mTLE 3 HC74 CB A hypothalamus control euhydration 1278 1271 jejunum nasal epithelial cells 28 49 Healthy patient. Source GEO sample is GSM228570 Last updated (according to GEO): Sep 11 2007 861 Neoplasm none Source GEO sample is GSM123199 Last updated (according to GEO): Jul 26 2006 Penis 1 Normal HCC (HK2) PBMCs-Type 1 Diabetes-IDDM27_T1D_1MO Expression profiling of spinal cord section (T8) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM4446 Last updated (according to GEO): May 28 2005 p53 -/-, 12 hour, replicate a Source GEO sample is GSM2548 Last updated (according to GEO): May 27 2005 17 7 hippocampus 3AMH02022603_LymphomaRaji 90 81 in stroke Heart 1000 Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.86 Subject: 2822 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39016 Last updated (according to GEO): May 27 2005 starved 32 38 Posterior root of spinal nerve 861 5 0 brain NA18945 861 Mammary gland E7, hTERT, bone marrow cell UET13 5 0 brain cytoskeletal proteins 992 1012 pharyngeal_mucosa_2 of cancers 40 50 Olfactory Epithelium 1000 5 0 brain We analyzed the lumbar spinal cord tract of transplanted nmd mice (n=3), untransplanted nmd mice (n=3) and wild-type mice (n=3) (all mice are of male gender). The latter groups underwent surgical procedure with vehicle. The surgical procedure and spinal cord-derived neural stem cell transplantation (intratechal injection) were done at P1 and the animals were sacrificed at 6 weeks of age. Frozen tissue was stored at -80°C. Total RNA was purified from tissue, using the EUROZol Kit (EuroClone Ltd., United Kingdom) following the manufacturer?s instructions. Total RNA (5 ug) was reverse-transcribed with a cDNA synthesis kit in the presence of SuperScript II RT (Invitrogen-Life Technologies, Inc.) and an oligo dT-T7 primer (Affymetrix Inc., Santa Clara, CA). After phenol/chloroform extraction and ethanol precipitation, the cDNA pellet was air-dried and re-suspended in 12 uL of diethyl pyrocarbonate-treated water and quantified by spectrophotometer measurement. An aliquot of each sample was conserved for gel electrophoresis and for inspection of RNA quality (i.e., 28S:18S RNA ratio). 10 ul was used for the IVT (In Vitro Transcription) amplification reaction, in the presence of biotinylated nucleotides (Enzo Biochem Inc.). Labeled cRNA (15 ug) was fragmented by incubation at 94°C for 35 minutes in fragmentation buffer (GeneChip Sample Cleanup, Qiagen) and the fragmented cRNA was then hybridized competitively against the Affymetrix 430 2.0 Array oligonucleotide array. Hybridization occurred at 47°C overnight. The arrays were scanned using a GeneArray 2500 Scanner (Affymetrix) and analyzed using MicroArray Suite 5.0 (Affymetrix). All experiments were validated after direct measures of cRNA quality: 5':3' ratios for beta-actin and for GAPDH (determined from Affymetrix chip hybridization analysis) are indirect indicators of overall RNA preservation. The default parameters were used for the statistical algorithm and for probe set scaling. The target intensity was set to 1,000 to normalize expression levels across all samples. Source GEO sample is GSM67530 Last updated (according to GEO): Dec 21 2005 Kg12: Hippocampus_21PT-AU_rep1 HL-60_II_CL7008_Leukemia on Affymetrix GeneChip Human Full Length Array HuGeneFL Brain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145285 Last updated (according to GEO): Nov 20 2006 519 510 (cirrhosis Primary tumor 19 32 with some respiratory epithelium. 1039 1072 To gain insight into the molecular changes of sleep need, this study addresses gene expression changes in a subpopulation of neurons selectively activated by sleep deprivation. Whole brain expression analyses after 6h sleep deprivation clearly indicate that Homer1a is the best index of sleep need, consistently in all mouse strains analyzed. Transgenic mice expressing a FLAG-tagged poly(A)-binding protein (PABP) under the control of Homer1a promoter were generated. Because PABP binds the poly(A) tails of mRNA, affinity purification of FLAG-tagged PABP proteins from whole brain lysates, is expected to co-precipitate all mRNAs from neurons expressing Homer1a. Three other activity-induced genes (Ptgs2, Jph3, and Nptx2) were identified by this technique to be over-expressed after sleep loss. All four genes play a role in recovery from glutamate-induced neuronal hyperactivity. The consistent activation of Homer1a suggests a role for sleep in intracellular calcium homeostasis for protecting and recovering from the neuronal activation imposed by wakefulness. Last Updated (by provider): Dec 07 2007 Contributers: Paul Franken Stéphanie Maret Mehdi Tafti Alexandra Paillusson Otto Hagenbuchle Laure Gurcel Sylvain Pradervand Synovium; acute arthritis Keywords = mouse gene expression database Source GEO sample is GSM29438 Last updated (according to GEO): May 27 2005 981 vascular cells 995 PC 6Hr rat 3586 blood vs. 1500mg/kg APAP 6Hr rat 3593 blood brain 0 5 for liver 26 35 Muscular Dystrophy, Duchenne 1000 Mucous Membrane 861 bronchial epithelia 224 243 no additional Source GEO sample is GSM199134 Last updated (according to GEO): Jun 08 2007 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.49 Subject: 3076 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39062 Last updated (according to GEO): May 27 2005 Trigeminal Ganglion Source GEO sample is GSM53321 Last updated (according to GEO): Jul 06 2005 78 66 Control blood lymph_nodes_1 The epithelial cells 962 981 normal testis 54 66 Heart 1000 220 215 trauma AD-285t2c-A263-10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 48M_122002 CNS-SpinalC-conAdult-7d-1C-s2b 861 Presynaptic Terminals accumbens rattus_norvegicus_strain iP animal_number 4 1000 Hypothalamic structure 20 0 Nicotine-hippocampus human caudate nucleus Source GEO sample is GSM86889 Last updated (according to GEO): Feb 08 2006 928 Endometrium Whole Brain 62 72 Identification of genes that are dysregulated in the telencephalon of Dlx1/2 mutants. Rubenstein-2R01MH049428-11 1000 frontal lobe 15 0 skeletal muscle 19 0 Head and neck cancer 36 21 from whole brain Neoplasm 861 DRG acutely dissected from embryos Source GEO sample is GSM246045 Last updated (according to GEO): Dec 03 2007 GBM Treatment, type=remove Source GEO sample is GSM99588 Last updated (according to GEO): Apr 21 2006 dorsal root ganglia 135 153 5 0 Spleen DRG_0225AFCQ_new018.txt Gene expression data from NICM NYHA III-IV CHF patients Source GEO sample is GSM231009 Last updated (according to GEO): Sep 21 2007 861 Muscle Neoplasm 861 3 0 Skin 1000 Spleen LPS_pre_no_restimulation_rep_C Blood Test (Blinded) Sample Source GEO sample is GSM129909 Last updated (according to GEO): Sep 18 2007 81 66 mesenteric C57BL PBMCs-Type 1 Diabetes-IDDM50_T1D_New I_95Av2_2846_DLPFC_1_GS plasma cells 332 344 H104 CB B Standard Affymetrix Protocol Source GEO sample is GSM16504 Last updated (according to GEO): May 28 2005 none Source GEO sample is GSM210303 Last updated (according to GEO): Jul 16 2007 PBMCs-Type 1 Diabetes-IDDM30_T1D_1MO Normal Source GEO sample is GSM176158 Last updated (according to GEO): Apr 09 2007 Plasma 861 OVAR_OVCAR3 on Affymetrix GeneChip Human Full Length Array HuGeneFL Richard Almon-33-1138200270461 with autism spectrum disorder 37 65 Tumor__Bladder_TCC_B_0007 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Lymphoblastoid Cell Line for Individual 8150.4 log phase brain, cerebral cortex: Nico 9/06_le1 1000 Infection Lung [JunctionChip 2 of 5] Individual LCL vs Pooled control LCLs Source GEO sample is GSM3275 Last updated (according to GEO): Mar 15 2006 prosc-affy-rat-185420 Wild type inbred mice Source GEO sample is GSM82924 Last updated (according to GEO): Nov 10 2005 organs 28 33 9 0 Blood Test C3H/HeJ bed nucleus of the stria terminalis rep2 frontal lobe 1000 brain, cerebral cortex: Nic 3_le1 long access to cocaine, lateral hypothalamus, 6 hrs/day access to cocaine Source GEO sample is GSM93847 Last updated (according to GEO): Jan 26 2006 in amygdala 20 31 NCI60.39_LABEL43EXTRACT42SUB3 Source GEO sample is GSM134189 Last updated (according to GEO): Aug 06 2007 PGA-Pi3k_dn_1449v2 Normal Source GEO sample is GSM176023 Last updated (according to GEO): Apr 09 2007 216 200 of neural retinas Fibroblasts 38 48 Disease Source GEO sample is GSM176259 Last updated (according to GEO): Apr 09 2007 EWS-T13 on NHGRI-6.5k_b Normal Source GEO sample is GSM176313 Last updated (according to GEO): Apr 09 2007 Nose 1000 5 0 brain 1BJZ02052201_AdrenalCortex tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44878 Last updated (according to GEO): May 27 2005 cerebral cortex 7 21 contralateral Cortex 7 27 1000 Glioma Prostate 861 Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 6173 blood Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5455.gif Source GEO sample is GSM93148 Last updated (according to GEO): Sep 22 2006 DR24h(2) Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18899.gif Source GEO sample is GSM84130 Last updated (according to GEO): Sep 22 2006 Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis. 660 mesenchymal stem cell 639 88 68 with bicuspid valves 19 0 human frontal cortex M_U133A_12_DLPFC_R Endometrium 22 Normal MET-306 on UMich-10k Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID53 2N-3-MGU74A NHF1-hTERT_1.5Gy_2h_C5_20081 Medulla Oblongata 861 GSE1705 901 Pyramidal Cells Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:179, Count:32 Corner- Avg:32377, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:10.951877,SFGene:All Background:Avg:533.85,Stdev:14.67,Max:561.2,Min:501.0 Noise:Avg:9.33,Stdev:0.31,Max:10.1,Min:8.3 RawQ:14.88 Keywords = ALL Source GEO sample is GSM3424 Last updated (according to GEO): May 28 2005 Exp C, Animal #1, control (0mg/kg) CPF, 1st repeat Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours Source GEO sample is GSM246157 Last updated (according to GEO): Dec 03 2007 AML cDNA hybridization-ID06-L Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11600 Last updated (according to GEO): May 28 2005 umbilical cord_bpd: 5B of regenerating Dorsal Root Ganglia 21 55 Kidney 1000 90 FC BA9 B gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134651 Last updated (according to GEO): Jul 09 2007 Nasal Epithelium 865 865 Disorder of artery HMVEC-L stimulated with LPS for 8 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114559 Last updated (according to GEO): Sep 20 2006 Epithelial Cells 1000 Expression profiling of the developing and mature Nrl-/- mouse retina: identification of retinal disease candidates and transcriptional regulatory targets of Nrl. PBMCs-Healthy-H124_Healthy Spleen vs CD40 Treated B cell 240min (set2) Whole blood 0 10 Adenocarcinoma 1000 Neoplasm 861 Adenocarcinoma 861 53 42 in the brain of somatomotor cortex 21 41 Infection 1000 1000 frontal lobe (No additional Information) Source GEO sample is GSM114430 Last updated (according to GEO): Jun 19 2006 Skeletal bone 861 spinal cord 37 47 Effect of insulin infusion on human skeletal muscle 861 Heart CNS-RM_Ctr4h-2C-s2 /testicles 152 162 liver 0 5 5 0 brain 12 0 ovarian tumor AJ 12-2-1 Muscle CC029 901 frontal lobe FVB/NJ Basal Ganglia A 607 597 the rectum Wild type inbred mice Source GEO sample is GSM83036 Last updated (according to GEO): Nov 10 2005 Sample33, Post Injury 24 hours Treatment, type=wait Source GEO sample is GSM53284 Last updated (according to GEO): Jul 06 2005 Prostate 13 Disease 0 18 of the postmortem brains 676 700 1000 Endometrium Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213497 Last updated (according to GEO): Jul 31 2007 saccule 906 912 1000 Memory Disorders ventral striatum sprague 3962 freehand block dissections, removed only cortex, individual animal, 10 weeks old, male Sprague Dawley ventral striatum file:p3962w Source GEO sample is GSM15184 Last updated (according to GEO): Oct 28 2005 G6 lens Cortex_Control_rep1 (06SE453) Gene expression data from postmorten brain regions Source GEO sample is GSM145563 Last updated (according to GEO): Nov 20 2006 brain 0 5 Primary Neoplasm 1000 Malignant Neoplasms 861 10 7 Left BRCA2_s1616 on NHGRI-6.5k Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132541 Last updated (according to GEO): Feb 26 2007 4 0 Nasal Brain 861 in the brains 491 503 5 0 Spleen DRG_sema3A_12h_rep2 1000 Communicable Diseases 1000 Diaphragm 1000 Brain Mouse model of congenital heart disease. Wild-type embyronic day 9.5 mouse. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2283 Last updated (according to GEO): May 27 2005 Cerebral cortex 1000 Bipolar affective disorder 0 25 Skeletal bone 861 from mouse brain 20 35 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215080 Last updated (according to GEO): Aug 02 2007 T147 of a colorectal adenoma 7 29 Kidney 1000 Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe differential expression of RNA containing at least two alternative splice junctions for about 40% of the 6,216 alternative events we could detect. Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues and another 28 exons whose splicing is different in muscle. A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of protein-coding exons. By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation. Of note is a motif that is strikingly similar to the branchpoint consensus but is located downstream of the 5' splice site of exons included in muscle. Analysis of three paralogous membrane-associated guanylate kinase genes reveals that each contains a paralogous tissue-regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families. Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188795 Last updated (according to GEO): Jun 06 2007 Whole Brain 62 72 of the colon 28 39 Spleen vs Terbutaline Treated B cell 240min (set3) HNCS2 CNS-RM_Ctr30m-1A-s2 3AJZ02053105_SmoothMuscle Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153471 Last updated (according to GEO): Jan 11 2007 861 Lung TestiIntersitial Source GEO sample is GSM18829 Last updated (according to GEO): Sep 25 2006 (cortex 19 25 901 frontal lobe 33 CB B 928 Endometrium The most common congenital cardiac abnormalities 50 97 Uterus 861 1000 Brain Recurrent Squamous cell carcinoma 2 Aortic banding is an excellent model system to evaluate the process of development of left ventricular hypertrophy in response to hemodynamic stress. The Affymetrix GeneChip MgU74Av1 was used to analyze expression profiles of mice at different time points after surgical intervention for pressure-overload induced hypertrophy. More information about this model may be obtained at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/band_home.html. Date GSE76 Last Updated: May 29 2005 Contributers: Martina Schinke Seigo Izumo Lauren E Riggi Iuan Chen Includes GDS41. Update date: Apr 17 2003. Dataset description GDS41: Expression profiles at various time points after surgical intervention for pressure-overload induced hypertrophy. Provides information on the initial adaptation process and the transition from compensated hypertrophy to failure.. Gene expression data from postmorten brain regions Source GEO sample is GSM145097 Last updated (according to GEO): Nov 20 2006 Blood 1000 1000 Infection Male8, Respiratory RNA_Nasal respiratory epithelium_Tissue was preserved in RNA Later and collected from nose none Source GEO sample is GSM244617 Last updated (according to GEO): Nov 23 2007 Expression profiling of spinal cord section (T9) extracted from rats 30m following mild injury Source GEO sample is GSM31224 Last updated (according to GEO): May 27 2005 Leukemia, Lymphocytic, Acute 901 20 0 Human prostate cancer Nasal Epithelium Instilation Formaldehyde 0mM 6h ID354 GSE4412 none Source GEO sample is GSM246006 Last updated (according to GEO): Dec 03 2007 Epithelium 861 NA12874 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132513 Last updated (according to GEO): Feb 26 2007 106 FC BA9 B Skeletal bone 1000 18 0 Menstruation blood none Source GEO sample is GSM123272 Last updated (according to GEO): Jul 27 2006 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159957 Last updated (according to GEO): Feb 01 2007 Plasma 861 M_U133A_20_AnCg Expression profiling of spinal cord section (T8) extracted from rats 14d following mild injury Source GEO sample is GSM31429 Last updated (according to GEO): May 27 2005 from the forebrain 20 37 Bone Marrow 1000 9 0 Blood Test 1000 Spleen Olfactory Epithelium 1000 1000 Left 1000 Down Syndrome embryonic hearts 1064 1079 901 frontal lobe Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3290 Last updated (according to GEO): Mar 21 2006 Stem cells 861 Spinal cord [JunctionChip 4 of 5] 345 313 in the posterior pituitary gland Cerebral cortex 1000 Wild type 8 wk old male DBA/2J mouse periaqueductal gray Source GEO sample is GSM74993 Last updated (according to GEO): Feb 27 2007 Spleen 1000 LPS plus IL-10, 20 min, Rep_2 1000 Hippocampus nostrils 156 164 Time point at 12h post HCMV infection Cervix carcinoma 901 Skeletal bone 861 93 86 of brain Primary Neoplasm 1000 01_0030_SepticShock_Day3_109 1000 Prostate 901 Basal Ganglia Liver Test (Blinded) Sample Source GEO sample is GSM130149 Last updated (according to GEO): Sep 18 2007 19 0 Embryonal carcinoma 861 Brain Germ free Corpus 2 Nasal Epithelium Inhalation Formaldehyde 15ppm 6h ID337 861 Heart mammary gland ; females with E18 embryos Source GEO sample is GSM18684 Last updated (according to GEO): May 27 2005 901 frontal lobe Replicate1_Voxel A4 spinal_cord_5 Sample details: We analysed changes in gene expression in the dorsal telencephalon of forebrain-specific FGFR1 mutant mice. Gene expression was compared between the dorsal telencephalons of single E12.5 embryos of two genotypes: FGFR1 heterozygous (HET1,3,8) and homozygous mutants (HOM2,4,7) that were both heterozygous for the FoxG1 transcription factor, as Cre recombinase expression is driven off the endogenous FoxG1 locus in these animals (Hebert, J. M., Lin, M., Partanen, J., Rossant, J. and McConnell, S. K. (2003b). FGF signaling through FGFR1 is required for olfactory bulb morphogenesis. Development 130, 1101-11. & Hebert, J. M. and McConnell, S. K. (2000). Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures. Dev Biol 222, 296-306. Source GEO sample is GSM62844 Last updated (according to GEO): Aug 26 2005 0 Human Cortex 11 /3T3 fibroblasts 743 759 of the heart 842 854 Inflammatory myopathy specimen GEIM27 human frontal cortex Source GEO sample is GSM87055 Last updated (according to GEO): Feb 08 2006 LiverE14_0223ACI4_099.txt Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188854 Last updated (according to GEO): Jun 06 2007 5 0 Kidney Olfactory Epithelium 1000 36 0 Control rat 5 ventral tegmental area PGA-swim_4w1w_s1127 olfactory epithelium 194 213 Spleen vs MIP3-alpha Treated B cell 120min (set1) from spinal cord 2013 2029 cerebellum 7 16 1000 Primary carcinoma of the liver cells 286_2 NA18858 164 136 of the middle cerebral artery Cerebellum_nontransgenic control S46_3.5 months_replicate 1 GSE700 Effect of NHE1 null mutation on gene expression in different brain regions Last Updated (by provider): May 29 2005 Contributers: Orit Gavrialov Jin Xue Gabriel G Haddad Dan Zhou Osteoblasts 1000 Laser captured visceral sensory neurons. Source GEO sample is GSM63674 Last updated (according to GEO): Dec 21 2005 Nasal Epithelium 901 1000 Rectum C_C7 heart failure 583 595 in bronchial epithelia 311 332 Brain 861 Blood 1000 Hyperdip>50-R1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 2 Retina 13 20 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211235 Last updated (according to GEO): Jul 18 2007 T32__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Muscle Source GEO sample is GSM4259 Last updated (according to GEO): May 27 2005 none Source GEO sample is GSM149542 Last updated (according to GEO): Jan 03 2007 5 0 brain AD-347t1a-A125-3 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Communicable Diseases 1000 Whole blood 0 10 Carcinoma, Large Cell 884 901 Nervous system structure 243 224 Left heart ventricle 129:22-3 olfactory bulbs To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Source GEO sample is GSM28447 Last updated (according to GEO): May 27 2005 Simple annotation: Chronic Lymphocytic Leukemia, ARA-G in vivo chemotherapy Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2701.gif Source GEO sample is GSM72156 Last updated (according to GEO): Sep 22 2006 G1E_7_B Blood Test (Blinded) Sample Source GEO sample is GSM129915 Last updated (according to GEO): Sep 18 2007 RNA isolated from spinal cord of human fetus suffering from Lethal Congenital Contracture Syndrome Source GEO sample is GSM25310 Last updated (according to GEO): May 27 2005 mouse brain 478 489 Gene expression data from postmorten brain regions Source GEO sample is GSM145291 Last updated (according to GEO): Nov 20 2006 Heart Ventricle 1 Normal PGA_PA-S_464 1373 1359 than carcinomas N/A Source GEO sample is GSM4326 Last updated (according to GEO): May 28 2005 Brain 861 Expression profiling of somatomotor cortex extracted from rats at 28d following moderate injury Source GEO sample is GSM41719 Last updated (according to GEO): May 27 2005 Infection 1000 PGA-MurLungRag-pbs-72h-1bBv2-s2 Colonic mucous membrane 913 1000 Brain 1000 Thalamic structure Brain 861 HCC (HBV+, SF17) 1000 Cerebral cortex 241 224 for encephalopathy SCN2.2 Sample 5 (Exp#1-12 hr b) Platelet activating factor receptor and innate immunity: 251186821691 Gene expression signature in organized and growth-arrested mammary acini predicts good outcome in breast cancer. Malignant neoplasm of breast 983 Affymetrix protocol Source GEO sample is GSM213806 Last updated (according to GEO): Aug 02 2007 Nervous system structure 901 Hypertensive disease 1000 JMR-MurInj4h-1aAv2-s2 Jejunum [JunctionChip 4 of 5] Dendrites 1000 D2_TP-24_I 861 Brain 101043 861 Retinal macula 1000 Structure of parenchyma of lung 283 271 These cancers Brain 861 NHF10-hTERT_G1_C3_26583 1000 Hypertrophic Cardiomyopathy mammary epithelial cells transduced with BABE empty vector Source GEO sample is GSM5171 Last updated (according to GEO): May 27 2005 brain_DLPFC_bipolar C_mr407 Cerebral cortex 861 HA99-96A 660 mesenchymal stem cell 639 GSE7036 of chromosome 16 61 76 Male C57Bl/6 mice (6 week old) were sham-operated and olfactory epithelium tissue collected 5 days post-operation. Total RNA was extracted from the olfactory epithelium tissue. Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol. Keywords = olfaction Keywords = neurogenesis Keywords = apoptosis Keywords = gene silencing Keywords = microarray, transcription factor Source GEO sample is GSM45680 Last updated (according to GEO): Oct 28 2005 Lymphoblastoid Cell Line for Individual 8173.4 log phase for spinal muscular atrophy 206 232 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11502 Last updated (according to GEO): May 28 2005 NCI60.46_LABEL50EXTRACT49SUB3 Source GEO sample is GSM134226 Last updated (according to GEO): Aug 06 2007 Lung 3 Normal 1000 Prostate Exp 3 Time point 6 NA12154 4 0 Brain during neurite outgrowth 1257 1281 Infection 1000 NCI60.57_LABEL61EXTRACT60SUB3 Source GEO sample is GSM134281 Last updated (according to GEO): Aug 06 2007 NHF1-hTERT_G1_C3_16136 Parietal Lobe 10 Normal Hippocampus 1000 hippocampal glutamatergic CA3 pyramidal neurons Source GEO sample is GSM35837 Last updated (according to GEO): May 27 2005 Blood 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM144874 Last updated (according to GEO): Nov 20 2006 Expression profiling of laminectomized raphe at 24h in rats Source GEO sample is GSM41526 Last updated (according to GEO): May 27 2005 133 128 Spleen Gene expression data from postmorten brain regions Source GEO sample is GSM144876 Last updated (according to GEO): Nov 20 2006 Adipose tissue 901 Neuroglia 901 Spleen 1000 R706P01301 osteoblast 627 637 Ganglia, Spinal 923 1000 Spleen Bone Marrow 1000 AD-269t1-A94-3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A GSE58 adenocarcinoma 3863 0 18 Sample # 1124-1 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=770610 LaserPower=4.323.79 Lot batch = LC17N091 Source GEO sample is GSM4814 Last updated (according to GEO): Nov 21 2005 none Source GEO sample is GSM149637 Last updated (according to GEO): Jan 03 2007 LPS, 10 min, Rep_2 Lungs from ovalbumen sensitized and challenged C3H mice BC123A-AF D_U133A_20_HC Gene expression correlates of clinical prostate cancer behavior. Ovarian_Tumor_Serous_UM-OS-10 863 836 of severe autoimmune disease Heart 1000 D_U133A_14_DLPFC 861 Neoplasm 072801 100% CD28 beads 01.00 hr. T-Cell Brain 1000 1_cerebral_cortex_12hrs_sleep_#16 Ganglia, Spinal 1000 430A2_2045_74_control_neuropath_midbrain Source GEO sample is GSM242703 Last updated (according to GEO): Nov 15 2007 Phenytoin frontal cortex 3 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53463 Last updated (according to GEO): Jul 06 2005 40 21 from dorsal pancreas Liver 1000 of hippocampal dentate gyri 86 112 861 Retinal macula NA12155 cerebellum 7 16 Brain 1000 no additional Source GEO sample is GSM199397 Last updated (according to GEO): Jun 08 2007 Lymphoblastoid Cell Line for Individual 8045.4 log phase of underlying brain 171 190 Liver 1000 1000 frontal lobe Carcinoma, Large Cell 867 brain, adrenal medulla: Sample#B1(Ctrl Pt1)_e1_le1 lymph nodes 944 outer medulla 31 43 Lung 1000 Acetaminophen 24hr Rat 2342 blood vs. Acetaminophen 24hr Rat Pooled Control blood 20 0 human caudate nucleus Anterior nares 1000 Occipital lobe 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145349 Last updated (according to GEO): Nov 20 2006 Gene expression data from UET-13 cells Source GEO sample is GSM213317 Last updated (according to GEO): Jul 26 2007 Primary Neoplasm 1000 Cerebral cortex 861 HTI-286 in docetaxel-refractory prostate cancer_docet (Biological Replicate3) M_95A_1871_Cg_0_GS 24 0 human prostate PC3 tumors The loss of the retinoblastoma tumor suppressor gene (RB) is common in many human cancers, including prostate. We previously reported that engineered deletion of RB in prostate epithelial cells results in sustained cell growth in serum-free media, a predisposition to develop hyperplasia and dysplasia in prostate tissue recombinant grafts, and sensitization to hormonal carcinogenesis. Examining the molecular consequence of RB loss in this system, we show that cyclooxygenase-2 (COX-2) is significantly up-regulated following RB deletion in prostate tissue recombinants. To study the effect of RB deletion on COX-2 regulation, we generated wild-type (PrE) and Rb-/- (Rb-/-PrE) prostate epithelial cell lines rescued by tissue recombination. We show elevated COX-2 mRNA and protein expression in Rb-/-PrE cell lines with increased prostaglandin synthesis. We also find that loss of Rb leads to deregulated E2F activity, with increased expression of E2F target genes, and that exogenous expression of E2F1 results in elevated COX-2 mRNA and protein levels. COX-2 promoter studies reveal that E2F1 transcriptionally activates COX-2, which is dependent on the transactivation and DNA-binding domains of E2F1. Further analysis revealed that the E2F1 target gene, c-myb, is elevated in Rb-/-PrE cells and E2F1-overexpressing cells, whereas ectopic overexpression of c-myb activates the COX-2 promoter in prostate epithelial cells. Additionally, cotransfection with E2F1 and a dominant-negative c-myb inhibited E2F1 activation of the COX-2 promoter. Taken together, these results suggest activation of a transcriptional cascade by which E2F1 regulates COX-2 expression through the c-myb oncogene. This study reports a novel finding describing that deregulation of the Rb/E2F complex results in increased COX-2 expression and activity. Extensive studies are currently being performed to associate disease susceptibility with one form of genetic variation, namely single nucleotide polymorphisms (SNPs). In recent years another type of common genetic variation has been characterised, namely structural variation, including copy number variations (CNVs). To determine the overall contribution of CNVs to complex phenotypes we have performed association analyses of expression levels of 14,925 transcripts with SNPs and CNVs in individuals who are part of the International HapMap project. SNPs and CNVs captured 83.6% and 17.7% of the total detected genetic variation in gene expression, respectively, but the signals from the two types of variation had little overlap. Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans. Last Updated (by provider): Feb 01 2007 Contributers: Chris Tyler-Smith Simon Tavare Stephen W Scherer Anna de Grassi Nigel Carter Barbara E Stranger Matthew S Forrest Natalie Thorne Christine P Bird Panagiotis Deloukas Emmanouil T Dermitzakis Charles Lee Matthew E Hurles Richard Redon Mark Dunning Catherine E Ingle Claude Beazley 861 Cerebral cortex P104 non-deprived visual cortex replicate 1 uterus 0 5 0 Human Cortex 11 1000 Spinal Cord 437_2 VDXOXFU_1210 20 hr Hela Double Thymidine PGA-RnSalt_c_6w_3-m5 Balb/c day 6, biological rep 4, tech rep 2 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9872.gif Source GEO sample is GSM79940 Last updated (according to GEO): Sep 22 2006 Cockayne syndrome B wt-rescued cell Source GEO sample is GSM226627 Last updated (according to GEO): Sep 04 2007 Richard Almon-50-1138200270930 human cerebellum Source GEO sample is GSM87110 Last updated (according to GEO): Feb 08 2006 875 Refractory Carcinoma with experimental autoimmune encephalomyelitis 12 57 HC103 CN B E10.5 craniofacial tissue, first branchial arch: WT_MXA-2_e1_le1 GM18862 CNS-SMTC_Mod7d-2C-s2 Brain 861 Tract 861 Pyramidal neurons in hippocampus. Source GEO sample is GSM63044 Last updated (according to GEO): Dec 01 2005 210 195 atherosclerosis 1000 Heart Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210421 Last updated (according to GEO): Jul 16 2007 KT38_CAN Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13150.gif Source GEO sample is GSM79716 Last updated (according to GEO): Sep 22 2006 Whole ganglioneuroma tumor_2782 861 Heart Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28713 Last updated (according to GEO): May 27 2005 GI_canc, Duodenal Tumor Keywords = mouse gene expression database Source GEO sample is GSM29270 Last updated (according to GEO): May 27 2005 1000 Parkinson Disease Whole Brain 62 72 Expression profiling of spinal cord section (T9) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31258 Last updated (according to GEO): May 27 2005 1000 Intestines, Small Neoplasm 861 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211272 Last updated (according to GEO): Jul 18 2007 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226145 Last updated (according to GEO): Nov 02 2007 Pool of 16 otic vesicles at E10 Source GEO sample is GSM182569 Last updated (according to GEO): Aug 14 2007 67 40 with coronary artery disease Mammary gland 1000 1000 Brain GC (HKG57T) Epithelium 861 Lung tissue from C57BL/6 mice calorie restricted by 2/3 and sacrificed 4hrs after the onset of calorie restriction. Lot batch = Source GEO sample is GSM4029 Last updated (according to GEO): May 28 2005 SQ-SQ6t1-A360-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A BAL_20a_A1B1 Tumor__CNS_Glioblastoma_GlioB_7 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A I + P T-Cell 02.00 hr. Brain 861 1000 Brain 21 Pulmonary hypertension 0 NG108 rat neuronal cell culture exposed to 4400 ng/ml mefloquine (treated) for two hours. 10 µg total RNA hybridized per chip. RNA STAT 60 used to extract RNA. Standard Affymetrix chip scaling factors used. No other data transformation. Source GEO sample is GSM1668 Last updated (according to GEO): Oct 28 2005 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114395 Last updated (according to GEO): Jun 16 2006 61 year old female Normal Source GEO sample is GSM176013 Last updated (according to GEO): Apr 09 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145350 Last updated (according to GEO): Nov 20 2006 20 0 human caudate nucleus Expression profiling of spinal cord section (T8) extracted from rats 30m following mild injury Source GEO sample is GSM31442 Last updated (according to GEO): May 27 2005 Macrophage 14smi097 small intestine PPARa knockout mice, fasted for 24 hours Source GEO sample is GSM154799 Last updated (according to GEO): Jul 04 2007 ER negative human primary breast tumor EA02014_41253_H133A_JA-755 0 cortex 5 Bone Marrow 1000 1000 Brain Jejunum [JunctionChip 3 of 5] 468 459 the rectum Motor neurons obtained from a SOD1 mutant mouse by laser capture microdissection. Source GEO sample is GSM113721 Last updated (according to GEO): Jun 09 2006 brain 0 5 Integumentary system 1000 1000 Coronary Arteriosclerosis Chronic leukemia NOS 913 78 73 rectum of heart 128 135 0 Human Cortex 11 Brain 1000 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7718.gif Source GEO sample is GSM79815 Last updated (according to GEO): Sep 22 2006 720 709 mouse brains Aortic Aneurysm 901 brain 0 5 from liver 21 30 126 122 /neck heart_ventricle_3 Brain 861 352 340 encephalitis Mature B cells 8 Gene expression data from postmorten brain regions Source GEO sample is GSM146027 Last updated (according to GEO): Nov 20 2006 68 CB A S4_Muscle_Insulin_240min 1000 Skeletal muscle structure The ageing of the human brain is a cause of cognitive decline in the elderly and the major risk factor for Alzheimer's disease. The time in life when brain ageing begins is undefined. Here we show that transcriptional profiling of the human frontal cortex from individuals ranging from 26 to 106 years of age defines a set of genes with reduced expression after age 40. These genes play central roles in synaptic plasticity, vesicular transport and mitochondrial function. This is followed by induction of stress response, antioxidant and DNA repair genes. DNA damage is markedly increased in the promoters of genes with reduced expression in the aged cortex. Moreover, these gene promoters are selectively damaged by oxidative stress in cultured human neurons, and show reduced base-excision DNA repair. Thus, DNA damage may reduce the expression of selectively vulnerable genes involved in learning, memory and neuronal survival, initiating a programme of brain ageing that starts early in adult life. 3 hrs Post-clamp sample 6 129S6/SvEvTac periaqueductal gray rep1 (430 2.0 Array) Epithelium 861 from the olfactory epithelium tissue 172 208 of somatomotor cortex 21 41 5 0 brain organs 28 33 Liver 1000 1000 Leukemia, Myelocytic, Acute Ovum 861 Wild type P18 mouse visual cortex ipsilateral to monocular enucleation Source GEO sample is GSM97195 Last updated (according to GEO): Feb 17 2006 GSE5038 Mortal human skin fibroblasts ATCC number CRL-1502 Source GEO sample is GSM6798 Last updated (according to GEO): May 27 2005 TUMOR 22 0 7 Gene expression data from postmorten brain regions Source GEO sample is GSM145165 Last updated (according to GEO): Nov 20 2006 Category: Serum-response Subcategory: Fibroblasts Scanning Software: unknown Software version: unknown Lot batch = 416 Source GEO sample is GSM2165 Last updated (according to GEO): Nov 21 2005 Normal human tissue:Normal Stomach Keywords = Human, Normal Tissue, Normal Stomach Source GEO sample is GSM44703 Last updated (according to GEO): May 27 2005 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc108 Source GEO sample is GSM1877 Last updated (according to GEO): Nov 21 2005 VDXRHU_329 A2780_control_0h mouse brain contralateral LPS.Dmso, biological rep5 Heart failure 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11314 Last updated (according to GEO): May 28 2005 Ewing, ETV4, Cancer Heart failure 1000 none Source GEO sample is GSM246015 Last updated (according to GEO): Dec 03 2007 on neuronal plasma membranes 129 157 9 0 Blood Test NCI60.36_LABEL40EXTRACT39SUB3 Source GEO sample is GSM134174 Last updated (according to GEO): Aug 06 2007 901 Coronary artery Colon 1000 BPH142_benign prostate hyperplasia 861 Neoplasm 5 0 brain Neuroglia 1000 from brains 17 27 Spleen 0 5 141 137 Brain 20 0 human caudate nucleus CN543 Endometrium/Ovary-Disease 6 Structure of dentate gyrus 901 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28786 Last updated (according to GEO): May 27 2005 5 0 Spleen with the control muscles 1517 1541 Spleen vs Bombesin Treated B cell 30min (set3) mouse hippocampus 0 17 Murine Spastic Spinal Cord Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Globin reduction was performed according to the Affymetrix technical note. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183401 Last updated (according to GEO): Apr 23 2007 1000 Muscle NO_KIDNEY_11 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11504 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145791 Last updated (according to GEO): Nov 20 2006 G3 Ciliary Body Gene expression data from postmorten brain regions Source GEO sample is GSM145717 Last updated (according to GEO): Nov 20 2006 Large-scale analysis of the mouse transcriptome Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184781 Last updated (according to GEO): Apr 26 2007 30 0 Adrenal medulla [JunctionChip 3 1000 ovarian neoplasm Gene expression data from postmorten brain regions Source GEO sample is GSM145639 Last updated (according to GEO): Nov 20 2006 none Source GEO sample is GSM149563 Last updated (according to GEO): Jan 03 2007 108 91 in the mouse brain Job's patient Source GEO sample is GSM211088 Last updated (according to GEO): Sep 10 2007 from brain 21 30 no additional Source GEO sample is GSM199173 Last updated (according to GEO): Jun 08 2007 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc104 Source GEO sample is GSM1882 Last updated (according to GEO): Nov 21 2005 zhao-hippocampus 0 15 Malignant neoplasm of cervix uteri 1000 The epithelial cells 962 981 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with TGF-beta (transforming growth factor-beta) for 240min Source GEO sample is GSM5798 Last updated (according to GEO): May 27 2005 1000 Brain acute myeloid leukemia Source GEO sample is GSM227421 Last updated (according to GEO): Sep 12 2007 HC55 CN A Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225939 Last updated (according to GEO): Nov 02 2007 Cerebral cortex 861 D_U133Plus_93_nAcc 861 Asphyxia Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68153 Last updated (according to GEO): Jul 07 2006 Kidney 1000 ovarian tumor: mucinous Source GEO sample is GSM139426 Last updated (according to GEO): Apr 09 2007 Seminoma 1000 PGA_PA-S_342 1000 Pancreas #32 (isolate 9 rich media untreated) 1000 Skeletal muscle structure D_U133Plus_70_HC the heart 987 996 3AJZ02062605_OccipitalLobe This SuperSeries is composed of the following subset Series: GSE1831: Temporal analysis of P15 hippocampus in kainate-induced seizures. Koh-2K08NS002068-04 GSE1834: Temporal analysis of hippocampus in kainate-induced seizures. Koh-7K08NS002068-05-3. Date GSE4236 Last Updated: Feb 14 2006 Includes GDS1642. Update date: Aug 22 2006. Dataset description GDS1642: Analysis of hippocampi of immature animals up to 10 days following kainite (KA) induced status epilepticus (SE). Unlike adults, KA-induced SE in immature animals causes neither cell death nor recurrent spontaneous seizures. Results provide insight into the molecular basis of this difference.. Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3888 Last updated (according to GEO): May 27 2005 B6 day 1, biological rep 1, tech rep 1 901 Bone Marrow no_pre_LPS_restimulation_rep_B solid tumors 1376 1388 CNS-SC_InjB24h-1A-s2 comparison of olfactory-bulbectomized and sham-operated rats with depressive-like behaviour Source GEO sample is GSM247199 Last updated (according to GEO): Dec 11 2007 913 Coronary heart disease no additional Source GEO sample is GSM199095 Last updated (according to GEO): Jun 08 2007 DCN_P7_C Gonadectomized Dahl-Iwai Female HighSalt Cortex rat5 gdahl_cortexr_k_GX_5c_051702 G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Source GEO sample is GSM9638 Last updated (according to GEO): May 28 2005 stria terminalis 901 19 0 human frontal cortex 861 Cerebellum 2500mg/kg APAP 12Hr rat 4137 blood vs. PC 12Hr rat 4126 blood of malaria 237 246 Large-scale analysis of the human transcriptome. Uterus Source: Research Genetics, http://www.resgen.com/products/DLmRNA.php3 Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 223.30 Stdv: 9.40 Min: 195.15 Max: 234.28 Source GEO sample is GSM2853 Last updated (according to GEO): Mar 20 2006 Kainate-neocortex, biological rep2 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, air control, 6 h time point Source GEO sample is GSM159796 Last updated (according to GEO): Apr 23 2007 Cerebral cortex 1000 Gene expression data for comparing calorie restricted-fed 30-month-old to control-fed 30-month-old for investigating effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7454 Last updated (according to GEO): May 27 2005 "Sample 64, <5 yr survival(17 months) age 33 erp no" on vantveer-oligo NL-3681-A332-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 308 290 murine brain damage Standard Affymetrix Protocol Keywords = microarray Keywords = muscle Source GEO sample is GSM15845 Last updated (according to GEO): May 28 2005 052401_HF_323CB Mouse Liver AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate A WT P10 replicate 1 10 week control spinal cord rep 2 frontal lobe 1000 1000 frontal lobe Spinal cord tissue from SOD1 mutant mice Treatment, type=linear_amplification, description=T7-based RNA amplification Source GEO sample is GSM113700 Last updated (according to GEO): Jun 09 2006 (cortex 19 25 Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203996 Last updated (according to GEO): Aug 02 2007 861 Dislocations Gene expression data from colonic normal mucosa. Source GEO sample is GSM215059 Last updated (according to GEO): Aug 02 2007 861 Cerebral cortex hippocampal glutamatergic CA1 pyramidal neurons Source GEO sample is GSM35838 Last updated (according to GEO): May 27 2005 Blood 1000 1000 Blood f2#323 versus pool Mouse Brain tissue Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002. Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Part of the medium chain triacylglycerol oil in control diet was replaced with: 1.1% fungal oil (providing 0.5 dietary wt% AA and 1.0en%). Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily. Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France). Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h. After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hepatic gene expression analysis. From these 5 mice, livers were dissected according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancourt, France), which consisted of carefully dissecting out the liver, rinsing with 70% EtOH to remove adhering blood, trimming of adhering connective tissue with scissors, cutting into 100-150 mg subsections, freezing in liquid N2, and storing at -80°C until gene expression and lipid analysis. Hepatic lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5). Liver tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hepatic RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips. Source GEO sample is GSM2569 Last updated (according to GEO): Oct 28 2005 1000 Skeletal muscle structure Expression profiling of spinal cord section (T9) extracted from rats 72h following moderate injury Source GEO sample is GSM31579 Last updated (according to GEO): May 27 2005 91 from the bone marrow 72 prostate Source GEO sample is GSM203338 Last updated (according to GEO): Jun 21 2007 MDA-MB-231/ATCC hgu95a Brain 861 S46 NLS 142Q TG1 F5/2 S46 NLS Htt exon 1 142Q Mouse 3.5 months Cerebellum Male Source GEO sample is GSM73215 Last updated (according to GEO): Sep 06 2005 Epithelium 861 Communicable Diseases 1000 Cerebral cortex 1000 MAS 5.0, scaled to 500; Affymetrix data Mining Tool 3.0; dChip was used to determine differentially expressed genes (MBEI); Statistical Analysis of Microarrays(SAM), as described in Miller et al. 2004. Source GEO sample is GSM108086 Last updated (according to GEO): Sep 12 2006 C2C12_3.5_hr GSE8989 Ovarian_Tumor_Endometrioid_CHTN-OE-046 PGA-swim_4w1w_s1126 1000 Malaria 9 0 Blood Test Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. 24h after sham surgery, a 4 mm diameter disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44468 Last updated (according to GEO): May 27 2005 Parkinson's disease sample x012 0 30 67 40 with coronary artery disease 12 occipital regions 28 Olfactory Epithelium 1000 Wild type 8 wk old male C57BL/6J mouse bed nucleus of the stria terminalis Source GEO sample is GSM106996 Last updated (according to GEO): Mar 05 2007 861 Medulla none Source GEO sample is GSM149543 Last updated (according to GEO): Jan 03 2007 Spleen vs SDF1 alpha Treated B cell 120min (set2) 40 26 from the kidney Tumor__Lymphoma_Follicular_FSCC_S93_23356 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A from mouse colon 21 36 Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 24 h to ambient pressure (CP24) and harvested with cells exposed for 24 h to hydrostatic pressure, pressure experiment # 3 (PE3). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11399 Last updated (according to GEO): Dec 15 2006 352 347 brain 1000 Mammary gland Phenytoin frontal cortex 1 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53461 Last updated (according to GEO): Jul 06 2005 1000 ovarian neoplasm Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=1 (Non-acute rejection). Source GEO sample is GSM36441 Last updated (according to GEO): May 27 2005 NA18504 Male; Epididymis-head Keywords = mouse gene expression database Source GEO sample is GSM29392 Last updated (according to GEO): May 27 2005 digits Source GEO sample is GSM18643 Last updated (according to GEO): May 27 2005 dorsal root ganglia 64 82 861 Brain 320 306 Keywords = HIV for liver 26 35 861 Cerebellum Gene expression data from rat lungs exposed to FiO2 of ~9.5% and SU-5416 (hypoxia-SU-5416). Source GEO sample is GSM201488 Last updated (according to GEO): Jun 14 2007 T41__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Date 9/22/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : embryo proper Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 1.25 mg/kg Time : 3 hrs post-injection Intervention : none Risk: NOAEL (no increased risk of malformation) Conditional biomarker: p53 protein induction not observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 8-10 embryos pooled from same litter Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = embryo Lot batch = AG626 Source GEO sample is GSM12054 Last updated (according to GEO): May 28 2005 Systemic lupus erythematosus (SLE) is an autoimmune disorder with immune-complex deposition that affects multiple organs. Previous studies have suggested the involvement of oxidative stress and apoptosis in SLE, but no clear link to etiology has been established. Here we show that mice deficient in a transcription factor responsible for controlling the expression of numerous detoxification and antioxidant genes develop an autoimmune disease with multiple organ pathologies that closely resembles human SLE. Aged female mice with a knockout of nuclear factor, erythroid-derived 2, like 2 (nrf2) are prone to develop antibodies against double-stranded DNA and the Smith antigen as well as IgG, IgM, and C3 deposition in kidney, liver, heart, and brain. Prior to the development of autoimmune antibodies and organ pathology, oxidative damage occurs in the liver and kidney as indicated by the increased levels of the DNA oxidation marker 8-hydroxydeoxyguanosine and the later increase in the lipid peroxidation product malondialdehyde. Gene expression profiles demonstrate an early decrease in numerous antioxidant and detoxification genes in the livers and altered levels of cytokines and T and B cell-specific genes in the spleens of nrf2 knockout mice. These data strongly suggest that a deficiency in detoxification and increased oxidative stress can result in the development of a systemic autoimmune disease. 19 0 Head and neck cancer WGACON-80 Brain 861 brain 0 5 of the postmortem brains 654 678 A HID B D011 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108605 Last updated (according to GEO): Aug 22 2006 278 255 ischemic cardiomyopathy 1037 of transitional epithelium 1012 Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 24h. Lot batch = Source GEO sample is GSM1237 Last updated (according to GEO): May 28 2005 Gene expression data of substantia nigra from postmortem brain of normal controls Source GEO sample is GSM184360 Last updated (according to GEO): May 29 2007 352 347 brain Prostatic Diseases 913 Blood 7 11 Nasal Epithelium 865 C57_LF_2 Coronary heart disease 913 jzo013-rp1-v5-u74av2-met liver 0 5 406 395 whose hearts human melanoma metastatic cell line A375 Source GEO sample is GSM195320 Last updated (according to GEO): Jun 04 2007 in seminoma 28 38 jzo023-rp1-v5-u74av2-met Fibroblasts 861 brain, hippocampus: Wt #3396 Cereb_e1_le1 T-ALL-#7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 24 h to ambient pressure (CP24) and harvested with cells exposed for 24 h to hydrostatic pressure, pressure experiment # 2 (PE2). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11398 Last updated (according to GEO): Dec 15 2006 Spleen vs CD27 Treated B cell 240min (set3) Melanoma xenograft, MED1_Sub_B (LeiFidler) 10 Bone marrow 0 prostate Source GEO sample is GSM203400 Last updated (according to GEO): Jun 21 2007 D_U133A_58_DLPFC CNS-SCsev_InjB24h-1A-s2 334 320 Keywords = HIV AD-AD31-A289-10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A We used microarrays to detail the global program of gene expression underlying Parkinson's disease Last Updated (by provider): May 29 2007 Contributers: Jarlath M Ffrench-Mullen HCC (HBV+, SF23) 39 12 of congenital heart disease 171 139 of glaucomatous optic neuropathy 633 616 in the aged brain FSCC8 on Affymetrix GeneChip Human Full Length Array HuGeneFL PGA_PA-D_85 rat cortex Treatment, type=time_course, measurement=7.0 d Source GEO sample is GSM53216 Last updated (according to GEO): Jul 06 2005 Pre Natal CCAM 2 313 292 dilated heart failure 7 frontal cortex 20 none Source GEO sample is GSM244581 Last updated (according to GEO): Nov 23 2007 24hr time point after 3 Gy of IR exposure Source GEO sample is GSM10971 Last updated (according to GEO): May 28 2005 Spinal Cord 1000 Melanoma metastatic cell line A375, biological rep4 (LeiFidler) Monocular deprivation right cortex, biological rep3 Fetal Brain BD Normal Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210404 Last updated (according to GEO): Jul 16 2007 46 18 of the central nervous system 17 7 hippocampus Hereditary Nonpolyposis Colorectal Neoplasms 947 4-cell embryo replication 1 Keywords = preimplantation Keywords = development Source GEO sample is GSM14679 Last updated (according to GEO): May 28 2005 Plasma 861 861 Cerebral cortex Gene expression data from skeletal muscle following 30 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230448 Last updated (according to GEO): Sep 19 2007 Acetaminophen 6hr Rat 2927 blood vs. Acetaminophen 6hr Rat Pooled Control blood Pulmonary alveoli are complex architectural units thought to undergo endogenous or pharmacologically induced programs of regeneration and degeneration. To study the molecular mechanism of alveoli loss mice were calorie restricted at different timepoints. Lungs were harvested and processed for RNA extraction.. Date GSE478 Last Updated: Jul 14 2006 Contributers: Donald Massaro Gloria D Massaro Includes GDS241. Update date: Jun 27 2003. Dataset description GDS241: Temporal study of lung alveoli destruction induced by caloric restriction. Alveoli number and surface area are linked to oxygen consumption, and calorie restriction lowers oxygen consumption.. Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118335 Last updated (according to GEO): Jul 11 2006 Thymic T cells;Fetal CD4+ I+P Stimulated 31 21 spinal cord 70 40 without coronary artery disease 901 Coronary artery Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9979.gif Source GEO sample is GSM79838 Last updated (according to GEO): Sep 22 2006 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114208 Last updated (according to GEO): Jun 16 2006 HSC_12Months_p53m_B M_U133Plus_126_nAcc 15 0 human cerebellum Duchenne muscular dystrophy (DMD) patient?s skeletal muscle sample 1 1000 Lipids preoptic Source GEO sample is GSM18592 Last updated (according to GEO): May 27 2005 1000 Hippocampus Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14351.gif Source GEO sample is GSM79620 Last updated (according to GEO): Sep 22 2006 Gene expressions affected by TNF alpha Source GEO sample is GSM189813 Last updated (according to GEO): May 21 2007 861 pars compacta Nasal Epithelium Inhalation Formaldehyde 6ppm 6h ID286 We used microarrays to identify genes implicated in breast cancer progression Last Updated (by provider): Oct 26 2006 Contributers: Faisal M Merchant James D Iglehart Xin Lu Penelope L Miron Maren M Chan from colonic normal mucosa 21 47 Primary Neoplasm 1000 Total RNA from cultured organ of Corti, pool from 12 cochleas. Source GEO sample is GSM124844 Last updated (according to GEO): Aug 04 2006 Biopsy of the normal mucosa of the colon from patient #12 testis 0 5 1000 Muscle RNA isolated from spinal cord of human fetus suffering from Lethal Congenital Contracture Syndrome Source GEO sample is GSM25309 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T10) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM6656 Last updated (according to GEO): May 28 2005 Cerebral cortex 861 B6 4-2 Adrenal 120 cortex 126 high-grade dysplastic liver tissue Source GEO sample is GSM155929 Last updated (according to GEO): Jun 21 2007 Mesenchymal Stem Cells 1000 ileum 0 4 in blood 16 23 acute myeloid leukemia Source GEO sample is GSM227419 Last updated (according to GEO): Sep 12 2007 7 cerebral cortex 21 There are critical periods in development when sensory experience directs the maturation of synapses and circuits within neocortex. We report that the critical period in mouse visual cortex has a specific molecular logic of gene regulation. Four days of visual deprivation regulated one set of genes during the critical period, and different sets before or after. Dark rearing perturbed the regulation of these age-specific gene sets. In addition, a 'common gene set', comprised of target genes belonging to a mitogen-activated protein (MAP) kinase signaling pathway, was regulated by vision at all ages but was impervious to prior history of sensory experience. Together, our results demonstrate that vision has dual effects on gene regulation in visual cortex and that sensory experience is needed for the sequential acquisition of age-specific, but not common, gene sets. Thus, a dynamic interplay between experience and gene expression drives activity-dependent circuit maturation. 14 7 amygdala Epithelium 861 SN:1012378 Source GEO sample is GSM115410 Last updated (according to GEO): Jun 20 2006 1000 Coronary Arteriosclerosis Ganglia, Spinal 923 Whole Brain 62 72 none Source GEO sample is GSM149634 Last updated (according to GEO): Jan 03 2007 Total RNA from fresh prepared organ of Corti, pool from 12 cochleas (=6 animals); used as control Source GEO sample is GSM124564 Last updated (according to GEO): Aug 04 2006 7 cerebral cortex 21 Mesenchymal Stem Cells 1000 70 40 without coronary artery disease tibiae 115 120 14 0 Large Intestine Timed pregnant C57Bl6 mice were exposed to ethanol during gestational day 15 to day 18 and ethanol exposed fetuses were delivered by cessarian section on gestational day 19. Alcohol exposed fetuses were compared to control timed preg Source GEO sample is GSM116859 Last updated (according to GEO): Jul 03 2006 D1_TP-72_C Primary Neoplasm 1000 901 Nervous system structure 1000 Cell Transformation, Neoplastic NFIA E18WT3 Gene expression data from a hippocampus from mouse injected 15 mg/kg kainate Source GEO sample is GSM147422 Last updated (according to GEO): Jan 03 2007 7 cerebral cortex 21 Gene expression data from postmorten brain regions Source GEO sample is GSM146029 Last updated (according to GEO): Nov 20 2006 Central gray substance of midbrain 861 umbilical cord_nobpd: 9D 7 0 prostate 861 Heart mammary epithelial cells transduced with empty LXSN vector Source GEO sample is GSM5161 Last updated (according to GEO): May 27 2005 Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM182000 Last updated (according to GEO): Apr 13 2007 91 from the bone marrow 72 dentate granule cells Source GEO sample is GSM35831 Last updated (according to GEO): May 27 2005 Neoplasm 861 Expression profiling of spinal cord section (T10) extracted from rats 24h following severe injury Source GEO sample is GSM31359 Last updated (according to GEO): May 27 2005 1000 Brain prostate Source GEO sample is GSM203319 Last updated (according to GEO): Jun 21 2007 B220+CD25+sIg- Small Pre BII cells sorted out of mouse bone marrow, sort no. 9 Source GEO sample is GSM636 Last updated (according to GEO): May 27 2005 Whole Brain 73 83 1000 Polymyositis f2#55 versus pool Mouse Brain tissue 1000 Pancreas Spleen 0 5 -_7732_batch1 on NHGRI-6.7k Saccule structure 1000 1000 Solid tumor brain, contralateral Cortex: Trizol Extraction11_le1 Bone Marrow 1000 plasma cells 332 344 Parkinson Disease 861 EWS-T2 on NHGRI-6.5k_b E6, E7, hTERT, dedifferentiated chondrocyte f2#229 versus pool Mouse Brain tissue 5 0 brain 901 Cerebral cortex A39 NES 142Q TG1 F5/51 A39 NES Htt exon 1 142Q Mouse 4 months Cerebellum Female Source GEO sample is GSM73219 Last updated (according to GEO): Sep 06 2005 Liver Test (Blinded) Sample Source GEO sample is GSM130151 Last updated (according to GEO): Sep 18 2007 GSE4088 7 frontal cortex 20 107T Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68323 Last updated (according to GEO): Jul 07 2006 30 19 Solid tumor 5 0 Spleen Large cell neuroendocrine carcinoma 901 Amygdaloid structure 1000 7 cerebral cortex 21 Brain 1000 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15445.gif Source GEO sample is GSM84126 Last updated (according to GEO): Sep 22 2006 861 Communicable Diseases Spleen vs Anti-IgM Treated B cell 30min (set3) Macrophage 14smi029 1000 Brain Stem that lymphoblastic leukemias 400 427 Large-scale analysis of the mouse transcriptome. Trachea C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 313.87 Stdv: 11.93 Min: 285.27 Max: 332.14 Source GEO sample is GSM2990 Last updated (according to GEO): Mar 20 2006 Sex Specific Transciption in Mouse Hypothalamus, Liver, Kidney, Ovary and Testis. For each somatic tissue there are 3 biological samples from different pools comprised of 10 animals for each sex each with a technical replicate. For each of the reproductive tissues there are 3 biological samples from different pools comprised of 10 animals with a technical replicate for each. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): May 29 2005 Contributers: Petur Petersen Michael P Snyder Weimin Zhong Ian J Laurenzi Kaiyong Zon Mark Gerstein John L Rinn Joel S Rozowsky Includes GDS565. Update date: Apr 21 2004. Dataset description GDS565: Analysis of sex specific transcription in somatic and reproductive tissues. Hypothalamus, liver, kidney, ovary, and testis tissues pooled from 10 different animals examined.. 1000 Eye I_U133A_21_AnCg 12 frontal Lobe 23 Expression profiling of somatomotor cortex extracted from rats at T0 naive Source GEO sample is GSM41676 Last updated (according to GEO): May 27 2005 861 Cancer of Neck sandberg-mousebrain Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120684 Last updated (according to GEO): May 14 2007 1000 frontal lobe 861 Brain Trigeminal Ganglia 8 Normal Expression profiling of spinal cord section (T9) extracted from rats 28d following severe injury Source GEO sample is GSM31601 Last updated (according to GEO): May 27 2005 Wild type 8 wk old male FVB/NJ mouse bed nucleus of the stria terminalis Source GEO sample is GSM107003 Last updated (according to GEO): Mar 05 2007 923 Subcutaneous Fat Gene expression data from 9A1 BMEL cells cultured under Matrigel conditions. Source GEO sample is GSM160079 Last updated (according to GEO): Jul 11 2007 Cerebellum 1000 861 Neoplasm Collagen 1000 Molecular profiling of tumor progression in NSCLC Heart 861 1000 ovarian neoplasm 24 0 human prostate PC3 tumors Heart Atrium 1000 During somitogenesis, oscillatory expression of genes in the notch and wnt signaling pathways plays a key role in regulating segmentation. These oscillations in expression levels are elements of a species-specific developmental mechanism. To date, the periodicity and components of the human clock remain unstudied. Here we show that a human mesenchymal stem/stromal cell (MSC) model can be induced to display oscillatory gene expression. We observed that the known cycling gene HES1 oscillated with a 5 h period consistent with available data on the rate of somitogenesis in humans. We also observed cycling of Hes1 expression in mouse C2C12 myoblasts with a period of 2 h, consistent with previous in vitro and embryonic studies. Furthermore, we used microarray and quantitative PCR (Q-PCR) analysis to identify additional genes that display oscillatory expression both in vitro and in mouse embryos. We confirmed oscillatory expression of the notch pathway gene Maml3 and the wnt pathway gene Nkd2 by whole mount in situ hybridization analysis and Q-PCR. Expression patterns of these genes were disrupted in Wnt3a(tm1Amc) mutants but not in Dll3(pu) mutants. Our results demonstrate that human and mouse in vitro models can recapitulate oscillatory expression observed in embryo and that a number of genes in multiple developmental pathways display dynamic expression in vitro. BCR-ABL-Hyperdip-R5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Brain 1000 Parkinson's model voxel B3 7 cerebral cortex 21 M_U133Plus_59_CB Organ 861 Heart 1000 normal liver tissue Source GEO sample is GSM155927 Last updated (according to GEO): Jun 21 2007 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195288 Last updated (according to GEO): Sep 13 2007 Transitional epithelium 1000 Primary tumor 19 32 onto a collagen 70 84 Simple annotation: Metastatic tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12395.gif Source GEO sample is GSM79788 Last updated (according to GEO): Sep 22 2006 healthy subject Source GEO sample is GSM211040 Last updated (according to GEO): Sep 10 2007 Coronary heart disease 913 Exp B_3, 30mg/kg CPF Skeletal bone 861 861 Brain Utricle 0 6 Acetaminophen 6hr Rat 9676 blood vs. Acetaminophen 6hr Rat Pooled Control blood Skeletal muscle structure 1000 Diaphragm 56 Day mdx rep 1 861 Kidney total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Platelet activating factor for 240min Source GEO sample is GSM5730 Last updated (according to GEO): May 27 2005 913 Neurodegenerative Disorders 861 Coxsackievirus Infections bone marrow sprague1 whole tissue, pool of 5 animals, 10 weeks old, male Sprague Dawley bone marrow file:R3JW02103005 Source GEO sample is GSM15205 Last updated (according to GEO): May 28 2005 Dystrophin 1000 1BMH02082911_PB_BDCA4DendriticCells Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15706 Last updated (according to GEO): May 28 2005 HUVEC isolate V low serum media PlGF 24hours cf. #27 Source GEO sample is GSM12920 Last updated (according to GEO): May 28 2005 237-97_Adeno Chronic Lymphocytic Leukemia 19 47 1000 Kidney +_5955_batch1 on NHGRI-6.7k Melanoma xenograft, MEC1_Lung_A (LeiFidler) cirrhotic liver tissue Source GEO sample is GSM155966 Last updated (according to GEO): Jun 21 2007 39 21 from mammary glands peripheral blood-BDCA4DendriticCells Source GEO sample is GSM18715 Last updated (according to GEO): Sep 25 2006 SN48h(1) The epithelial cells 962 981 60 50 Liver C57BL Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc117 Source GEO sample is GSM1898 Last updated (according to GEO): Nov 21 2005 Axon 1000 none Source GEO sample is GSM123212 Last updated (according to GEO): Jul 26 2006 30 19 Solid tumor subthalamic_nucleus_2 861 Brain Fibroblasts 861 Total RNA extracted from the forebrain of a Stg+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144407 Last updated (according to GEO): Nov 14 2006 Brain 861 Brain 1000 9 0 Blood Test Spleen vs Untreated B cell 60min (set4) Control VZ14 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12670.gif Source GEO sample is GSM79953 Last updated (according to GEO): Sep 22 2006 experiment I hTERT replicate 2 /cByJ Basal Ganglia A 4 24 Subject code A5EB 13 7 cochlea of Parkinson's disease 450 471 Expression profiling of spinal cord section (T8) extracted from rats 28d following severe injury Source GEO sample is GSM31480 Last updated (according to GEO): May 27 2005 PBMCs-Healthy-H98_Healthy D_U133Plus_104_nAcc GSE6955 Liver 0 4 LDMTX_MP-DX-6 52 28 of newborn rats inner ear oculomotor nuclei 899 915 male MhmBN chip 26 Affymetrix RGU34A 3HA of the atrial 647 659 Sample 5 at Time 5 Source GEO sample is GSM113097 Last updated (according to GEO): Jun 06 2006 Bone Marrow 1000 861 Malignant Neoplasms Heart 1000 1BJZ02060414_OlfactoryBulb 59 35 out of mouse bone marrow 7 0 PROSTATE 5.0 mg/kg MeHg forebrain at 1.5h Prostate cancer gene expression profiles were studied in this project. A total RNA from 148 prostate sample with various amount of different cell types were hybridized to Affymetrix U133A arrays. The percentage of different cell types vary considerably among samples and were determined by pathologist. Cell type specific genes can be determined by linear regression using the methods of Stuart et al, PNAS, 2004. Last Updated (by provider): Jun 25 2007 Contributers: Yipeng Wang Normal Pituitary Gland from colonic normal mucosa 21 47 334 320 Keywords = HIV 57 53 Lungs 928 Endometrium Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11476 Last updated (according to GEO): May 28 2005 Primary Neoplasm 1000 901 Bone Marrow 228 219 Hippocampi 1000 Spleen N20__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Cerebral cortex WGACON-75 CHIPEXP_NAME: 230_2_050531tpj_18h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Vehicle_Control TREAT_TOX_MECHANISM1: Liver_Non_Toxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0 SAMPLING_TIME: 24 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197621 Last updated (according to GEO): Jun 01 2007 plasma cells 50 61 36 21 from hippocampus "Sample 36,>5 yr survival(121 months) age 52 erp yes" on vantveer-oligo 1000 Cerebellum Organotypic hippocampal slice cultures of male, postnatal day 15 mice (C57B6/SJL) were maintained in culture for 13 days and treated with 1 nM sAPPalpha (sAPPalpha) for an additional 24 h. Cultures were maintained on filter inserts in Neurobasal media with B-27 supplement (Invitrogen) and 1 mM glutamine. The sample consists of 9 slices from 4 mice. Data were analyzed with MAS 5.0 and scaled to 2500. Keywords = Alzheimer?s disease Keywords = neuroprotection Keywords = sAPPalpha Source GEO sample is GSM26704 Last updated (according to GEO): Oct 28 2005 AD control Treatment, type=dissect Source GEO sample is GSM119630 Last updated (according to GEO): Jul 10 2006 156T 861 Neoplasm Spleen 1000 19 0 amygdala wistar 3724 Large-scale analysis of the mouse transcriptome. Brown fat, interscapular depression C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 254.58 Stdv: 7.52 Min: 242.45 Max: 266.08 Source GEO sample is GSM2921 Last updated (according to GEO): Mar 20 2006 972 Structure of middle temporal gyrus HapMap YRI_parent Male Source GEO sample is GSM159708 Last updated (according to GEO): Feb 01 2007 cingulate cortex 1000 Acetaminophen 3hr Rat 5339 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool 1000 Cartilage Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162149 Last updated (according to GEO): Jun 12 2007 Hippocampus 861 Spleen vs Lysophosphatidic Acid Treated B cell 240min (set3) hip_1008_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A WT-Nrf2-Male-1 Performed by UCI Microarray Facility. Source GEO sample is GSM203479 Last updated (according to GEO): Jun 22 2007 Replicate3_Voxel D9 D_U133Plus_55_CB Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211289 Last updated (according to GEO): Jul 18 2007 standard Affymetrix protocol, MAS 5.0 Source GEO sample is GSM9133 Last updated (according to GEO): May 28 2005 Laser capture lung cancer cells Source GEO sample is GSM191045 Last updated (according to GEO): May 25 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD27 for 60min Source GEO sample is GSM5489 Last updated (according to GEO): May 27 2005 Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153771 Last updated (according to GEO): Jan 19 2007 B6_SleepDep_ZT 0_1 Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7467 Last updated (according to GEO): May 27 2005 from colorectal adenoma 21 44 Gene expression data from whole brain of uninfected mouse Source GEO sample is GSM189598 Last updated (according to GEO): May 16 2007 Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP), exposed 6 h more to ambient pressure (CP6) and harvested with cells exposed for 6 h to hydrostatic pressure, pressure experiment # 1 (PE1). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11384 Last updated (according to GEO): Dec 15 2006 C3H-HeOuJ mice exposed to filterd air for 72hrs- lungs were removed-frozen in liquid nitrogen-RNA extraction. Lot batch = Source GEO sample is GSM4016 Last updated (according to GEO): May 28 2005 861 Brain Blood Cells 853 SN:Human Glioblastoma Biopsy 06726 Neuroblastoma 861 no additional Source GEO sample is GSM199366 Last updated (according to GEO): Jun 08 2007 healthy subject Source GEO sample is GSM211107 Last updated (according to GEO): Sep 10 2007 8 0 amygdala (cortex 19 25 to chromosome 8q24 888 906 Left 1000 I_U133A_104_Amy 19 0 Head and neck cancer 12 0 ovarian tumor Liver 1000 Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. All patients were considered sporadic cases on the basis that no clinical antecedents of familial adenomatous polyposis were reported, and those that met the clinical criteria for hereditary non-polyposis colon cancer (Amsterdam criteria) were excluded. Source GEO sample is GSM112208 Last updated (according to GEO): Jun 06 2006 IGF1 and IGF1 receptors (IGF1R) are present in the adult heart and have been shown to be essential for myocardial performance. Insulin-like growth factor 1 (IGF1) is produced in numerous tissues particularly by the liver in response to growth hormone stimulation and is an important factor in the regulation of post-natal growth and development. We have generated and characterized transgenic mice over-expressing the IGF1R. We crossed IGF1R transgenic mice with dominant negative (dn)PI3K (p110) and with constitutively active (ca)PI3K(p110) transgenic mice. Expression profiling was performed on the ventricles of IGF1R, IGF1R-caPI3K, IGF1R-dnPI3K, caPI3K, dnPI3K transgenic female mice at 3 months of age. Non-transgenic littermates were used as controls.. Date GSE1143 Last Updated: May 29 2005 Contributers: Seigo Izumo Peter M Kang Sekwon Kong Megan C Sherwood Tetsuo Shioi Julie McMullen Oleg Tarnavski Egbert Bisping Weei-Yuarn Huang Jeffrey Brown Lauren E Riggi Li Zhang Martina Schinke Includes GDS648. Update date: Aug 02 2004. Dataset description GDS648: Characterization of ventricles from transgenics with an overexpressed IGF1R, and from double transgenics with an overexpressed IGF1R and either a constitutively active phosphatidylinositol-3-kinase (PI3K) or a dominan. Affymetrix RGU34A 3HB NCI60.19_LABEL23EXTRACT22SUB3 Source GEO sample is GSM134087 Last updated (according to GEO): Aug 06 2007 1000 Brain 861 Cerebral cortex CNS-SCsev_InjA4h-1A-s2 A VIS D031 Trigeminal_Ganglion Source GEO sample is GSM18846 Last updated (according to GEO): Sep 25 2006 D_U133Plus_115_DLPFC 1000 Prostate Lymphoblastoid Cell Line for Individual 8097.3 log phase Myocardial Infarction 1000 NA Source GEO sample is GSM84318 Last updated (according to GEO): Dec 01 2005 1000 Brain Transforming growth factor beta 1 (TGF-?1) is the most extensively studied growth factor in dentin-pulp complex, with pleiotropic effects on pulp response and healing. Our main objective was to analyze the expression profile of pulp tissue and odontoblasts, and the effects of TGF-?1 on these profiles in cultured human pulp and odontoblasts with a specific interest in the anti- and pro-inflammatory cytokines. Last Updated (by provider): Aug 09 2007 Contributers: Leo Tjäderhane Virve Pääkkönen Tuula Salo Jussi T Vuoristo 161 143 of the hypothalamus 861 Cerebral cortex 129:24-4 cortex Leg 7 Day mdx rep 3 1000 Brain 1000 Brain CNS-SMTC_Mod28d-4B-s2 3072 HP6_41 from mouse colon 21 36 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195330 Last updated (according to GEO): Jun 04 2007 VDXRHU_535 brain, amygdala: Control-Amygdala_e1_le2 Expression profiling of spinal cord section (T8) extracted from rats 24h following severe injury Source GEO sample is GSM31467 Last updated (according to GEO): May 27 2005 1000 Liver Epithelium 861 203 193 of retinal Expression profiling of spinal cord section (T8) extracted from rats 14d following severe injury Source GEO sample is GSM31462 Last updated (according to GEO): May 27 2005 RNA isolated from fetal cerebrum Keywords = trisomy Keywords = brain Keywords = Down syndrome Source GEO sample is GSM22526 Last updated (according to GEO): May 27 2005 Leg 23 Day mdx rep 2 Bone Marrow 1000 80 67 duodenum C57BL Epithelial Cells 1000 f2#146 versus pool Mouse Brain tissue 1000 Cardiomyopathies GSE36 Primary Neoplasm 1000 861 Adrenal Medulla 19 6 after ischemia Myometrium 32 Disease 5 0 brain GBM Treatment, type=remove Source GEO sample is GSM99548 Last updated (according to GEO): Apr 21 2006 Gene expression data from experimental treatment D-UT = 48h after PMA induced differentiated SH-SY5Y cells. Source GEO sample is GSM102876 Last updated (according to GEO): May 11 2006 Vestibular Nuclei Superior 4 Normal n/a Source GEO sample is GSM178081 Last updated (according to GEO): Jun 11 2007 861 Oocytes prostate Source GEO sample is GSM203384 Last updated (according to GEO): Jun 21 2007 Cerebral Cortex 5 Normal of underlying brain 171 190 Plasma 861 with myocardial infarction 313 339 Fetal brains were obtained from 3 pregnant rats at pregnant day 17. Primary cortical neurons were isolated and pooled separately from each mother and plated onto 100mm ´ dishes, for a total of 4 plates from each pregnant rat. At Day in Vitro (DIV) 16, 3 of the 4 platesfrom the same mother, were exposed to either 1 or 3 MAC halothane (about 1% or 3%) or 3 MAC isoflurane (about 4%) in a gas tight chamber inside the culture incubator for 6 hr. The 4th plate from each mother treated with air were used (inside the same incubator, but outside the chamber) as controls. Isoflurane at 1 MAC was not conducted because of the complete lack of transcriptional response in the animals exposed to 1 MAC of isoflurane. The cells were recovered for an additional 6 hr, harvested, frozen by liquid nitrogen, and stored at ?80oC. Source GEO sample is GSM61802 Last updated (according to GEO): Oct 28 2005 Various human cell types Colonic mucous membrane 913 Autistic Disorder 877 Brain 1000 Effects of SOCS3 on transcriptional response of macrophages to IL-6. Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Replicate 1 after stimulation for 100 minutes with 10 ng/ml IL-6. Source GEO sample is GSM6073 Last updated (according to GEO): Mar 17 2006 1000 Brain MSS-Ctr9moF-1aAv2-s2 GSE4757 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120663 Last updated (according to GEO): May 14 2007 1000 Structure of trigeminal ganglion DCIS198 on harvard-12k 861 Cancer of Neck 1000 Transverse of the postmortem brains 664 688 901 Myeloid Leukemia Frontal Lobe 7 Normal Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132500 Last updated (according to GEO): Feb 26 2007 HCC (HBV+, HK66, T4) Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 0426 blood in the brain 25 36 adenoma 861 Blood Test (Blinded) Sample Source GEO sample is GSM129990 Last updated (according to GEO): Sep 18 2007 wtPrE serum 1 901 Mammary gland ventral spinal cord 13 31 in fibroblasts 1222 1236 Labyrinth 1000 M7TW01010699 9 0 Blood Test CNS-SpinalCmod-Adult-7d-2A-s2 Matrigel culture, 9A1, rep 1 f2#95 versus pool Mouse Brain tissue days nasal epithelium 1126 1147 CNS-SMTC_Mod14d-2B-s2 Diabetes Mellitus 1000 Malignant Neoplasms 861 ColonTum_022HAFC9_cta.txt 861 Brain nostrils 156 164 861 Encephalitis Normal Source GEO sample is GSM176156 Last updated (according to GEO): Apr 09 2007 913 Acute leukemia Transitional epithelium 1000 53 30 (interventricular septum 231 227 liver Gene expression data from postmorten brain regions Source GEO sample is GSM145521 Last updated (according to GEO): Nov 20 2006 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11442 Last updated (according to GEO): May 28 2005 experiment I, passage 13, replicate 1 1000 Heart 1206 1184 by cervical dislocation 7 cerebral cortex 21 no additional Source GEO sample is GSM199336 Last updated (according to GEO): Jun 08 2007 mouse brains 187 198 12 Temporal Lobe 24 Donor 1 time point 12 hours Post infection with HIV-1, RF Source GEO sample is GSM2599 Last updated (according to GEO): May 27 2005 Mental Retardation 1000 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12965.gif Source GEO sample is GSM79975 Last updated (according to GEO): Sep 22 2006 1000 Liver Normal human fetal cartilage from 18-22 weeks. Source GEO sample is GSM149645 Last updated (according to GEO): Jul 06 2007 TNFTG-40w-f-1 182 170 HCV infection Brain_Melanotransferrin Knockout_affs275-1101 Lymphoblastoid Cell Line for Individual 8179.3 log phase from liver 21 30 111 95 in breast cancer an autoimmune inflammatory disease 51 84 1BMH02022807_Whole Brain Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11533 Last updated (according to GEO): May 28 2005 Mammary Gland @ Lac2, biological rep1 1000 Parkinson Disease 444 429 of primary tumor PGA-MLS-Dil-1aAv2-s1 Nucleus accumbens, male 10.5 week old c57bl/6J mouse, SUSCEPTIBLE group Source GEO sample is GSM224750 Last updated (according to GEO): Aug 31 2007 normal testis 54 66 1000 Cerebellum Mucous Membrane 861 VDXIGRU_256734 Nidogen 861 Meningioma Primary Grade 3 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Meningioma Primary Grade 2. Source GEO sample is GSM108041 Last updated (according to GEO): Jun 06 2006 CO_NP_med_1 Hyperdip>50-#10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Spleen vs Interferon-beta (IFN beta) Treated B cell 240min (set3) 901 frontal lobe 5 0 brain 0029_1357_H95A2_KF-187_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs//7300.gif Source GEO sample is GSM79706 Last updated (according to GEO): Sep 22 2006 none Source GEO sample is GSM149523 Last updated (according to GEO): Jan 03 2007 5 0 brain Neoplasm 1000 V5-P048 MO_CTC_SON_NCBI brain, cerebral cortex: NMDA 8/23_le1 NZW-LacJ_male_hypothalamus Source GEO sample is GSM138583 Last updated (according to GEO): Apr 18 2007 Neostriatum 1000 Exp 3 Time point 7 Spleen 0 5 human caudate nucleus Source GEO sample is GSM86828 Last updated (according to GEO): Feb 08 2006 H118 CN B Spinal Cord 1000 putamen_7 Source GEO sample is GSM80601 Last updated (according to GEO): Mar 31 2006 Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002. Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Part of the medium chain triacylglycerol oil in control diet was replaced with: 1.1% fungal oil (providing 0.5 dietary wt% AA and 1.0en%). Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily. Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France). Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h. After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hepatic gene expression analysis. From these 5 mice, livers were dissected according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancourt, France), which consisted of carefully dissecting out the liver, rinsing with 70% EtOH to remove adhering blood, trimming of adhering connective tissue with scissors, cutting into 100-150 mg subsections, freezing in liquid N2, and storing at -80°C until gene expression and lipid analysis. Hepatic lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5). Liver tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hepatic RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips. Source GEO sample is GSM2570 Last updated (according to GEO): Oct 28 2005 osteoblast 627 637 901 Coronary artery KM12 hgu95d 1000 Brain Liver 1000 to the nose 599 609 pituitary_gland_3 861 Cochlear structure 747 tumor cells 757 RNA of Kidney was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 biological replicates were analyzed. Keywords = db/m mice Keywords = kidney Source GEO sample is GSM9923 Last updated (according to GEO): May 27 2005 tumor.5 Intestines 861 of infected skin 33 48 CNS-RM_Ctr4h-2B-s2 Osteoblasts 1000 Communicable Diseases 1000 Heart 861 frontal cortex wistar 3660 whole tissue, individual animal, 10 weeks old, male Wistar frontal cortex file:p3660w Source GEO sample is GSM15119 Last updated (according to GEO): Oct 28 2005 HairAnag_0223ACIX_038.txt 39 12 of congenital heart disease Whole Brain 73 83 Dahl-Iwai Female LowSalt OuterMedulla rat104 dahl_medullar_104_1_OM_053001 human frontal cortex Source GEO sample is GSM86937 Last updated (according to GEO): Feb 08 2006 9 0 Blood Test Parkinson 0 8 Sph 1, chip MOE430A C57BL/6J Saline treated, striatum, biological replicate 1 Source GEO sample is GSM187974 Last updated (according to GEO): Jun 14 2007 218 214 liver Brain 861 SCG_sema3A_65h_rep1 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188850 Last updated (according to GEO): Jun 06 2007 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198623 Last updated (according to GEO): Jun 06 2007 PMN_control_180min_Patient8 3ARS02080772b_atrioventricular_node 33 17 tibialis anterior Balb/c day 3, biological rep 1, tech rep 2 169 143 in mammary epithelial cells 1000 Coronary Arteriosclerosis Gene expression data from older female during 1 week of adequate protein intake Source GEO sample is GSM209831 Last updated (according to GEO): Jul 11 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with SDF1 alpha (Stromal cell derived factor-1) for 60min Source GEO sample is GSM5759 Last updated (according to GEO): May 27 2005 human caudate nucleus Source GEO sample is GSM86826 Last updated (according to GEO): Feb 08 2006 Expression profiling of somatomotor cortex extracted from rats at 30 min following sham surgery Source GEO sample is GSM41651 Last updated (according to GEO): May 27 2005 1000 Amygdaloid structure Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188838 Last updated (according to GEO): Jun 06 2007 jzo007-rp1-v5-u74av2-met embryo day 10.5 Source GEO sample is GSM18630 Last updated (according to GEO): May 27 2005 Richard Almon-46-1138200270821 Brain 861 Replicate3_Voxel C11 CNS-SpinalCmod-Adult-72h-3B-s2 spinal cord, spinal cord: G1C_le1 Exp C_3, 1mg/kg CPF Heart (NL051) DCN_U7_A Bone structure of tibia 1000 V5-P066 861 Heart f2#196 versus pool Mouse Brain tissue 28 13 from fetal heart 7 0 Melanoma CNS BMI-1 KO ChipB 5 0 brain Plasma 861 7 0 prostate Vagal afferent neurons are thought to convey primarily physiological information, whereas spinal afferents transmit noxious signals from the viscera to the central nervous system. In order to elucidate molecular identities for these different properties, we compared gene expression profiles of neurons located in nodose ganglia (NG) and dorsal root ganglia (DRG) in mice. Intraperitoneal administration of Alexa Fluor-488 conjugated Cholera toxin B allowed identification of neurons projecting to the viscera. Fluorescent neurons in DRG (from T10 to T13) and NG were isolated using laser capture microdissection. Gene expression profiles of visceral afferent neurons, obtained by microarray hybridization, were analysed using multivariate spectral map analysis, SAM algorithm (Significance Analysis of Microarray data) and fold-difference filtering. A total of 1996 genes were found to be differentially expressed in DRG versus NG, including 41 G-protein coupled receptors and 60 ion channels. Expression profiles obtained on laser-captured neurons were contrasted to those obtained on whole ganglia demonstrating striking differences and the need for microdissection when studying visceral sensory neurons because of dilution of the signal by somatic sensory neurons. Furthermore, a detailed catalogue of all adrenergic and cholinergic, GABA, glutamate, serotonin and dopamine receptors, voltage-gated potassium, sodium and calcium channels and transient receptor potential cation channels present in visceral afferents is provided. Our genome-wide expression profiling data provide novel insight into molecular signatures that underlie both functional differences and similarities between NG and DRG visceral sensory neurons. Moreover, these findings will offer novel insight into mode of action of pharmacologic agents modulating visceral sensation. Last Updated (by provider): Dec 21 2005 Contributers: Hinrich W. Göhlmann Pieter J. Peeters David Grundy Ronald H. Stead Jeroen Aerssens Bernard Coulie Ann Meulemans Ronald de Hoogt Andrzej Stanisz Kirk Hillsley Includes GDS1634. Update date: Aug 29 2006. Dataset description GDS1634: Comparison of whole nodose ganglia (NG) and dorsal root ganglia (DRG) vs. the population of laser-captured visceral sensory neurons. Results identify striking differences and the need for microdissection when studying visceral sensory neurons because of dilution of signal by somatic sensory neurons.. Includes GDS1635. Update date: Aug 29 2006. Dataset description GDS1635: Analysis of laser-captured neurons of the nodose (NG) and dorsal root ganglia (DRG). Vagal afferents arise from NG and convey mostly physiological information, while spinal afferents arise from DRG and transmit noxious signals. Results elucidate molecular identities for these different properties.. Expression profiling of spinal cord section (T8) extracted from rats 14d following severe injury Source GEO sample is GSM31463 Last updated (according to GEO): May 27 2005 24 skeletal muscle 10 861 Encephalitis 861 Cochlear structure 406 395 whose hearts 1579 1561 in small intestine gut neurospheres 243 258 Muscular Dystrophies 901 human frontal cortex Source GEO sample is GSM86994 Last updated (according to GEO): Feb 08 2006 Parkinson's disease sample x153 DR24h(3) 861 Lateral Sclerosis Head and neck cancer Source GEO sample is GSM155658 Last updated (according to GEO): Apr 24 2007 brain, cortex: norm2_e1_le2 Gene expression data from brain of adult rats Source GEO sample is GSM101033 Last updated (according to GEO): Feb 20 2007 Postnatal day 3 callosal projection neurons purified by fluorescence-activated cell sorting. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription. Source GEO sample is GSM37084 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 Ovary 1000 Expression profiling of spinal cord section (T8) extracted from rats 30m following mild injury Source GEO sample is GSM31441 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM176099 Last updated (according to GEO): Apr 09 2007 406 395 whose hearts 1000 Iris /3T3 fibroblasts 743 759 standard Affymetrix protocol, MAS 5.0 Source GEO sample is GSM9130 Last updated (according to GEO): May 28 2005 Spleen 0 5 We combined large-scale mRNA expression analysis and gene mapping to identify genes and loci that control hematopoietic stem cell (HSC) function. We measured mRNA expression levels in purified HSCs isolated from a panel of densely genotyped recombinant inbred mouse strains. We mapped quantitative trait loci (QTLs) associated with variation in expression of thousands of transcripts. By comparing the physical transcript position with the location of the controlling QTL, we identified polymorphic cis-acting stem cell genes. We also identified multiple trans-acting control loci that modify expression of large numbers of genes. These groups of coregulated transcripts identify pathways that specify variation in stem cells. We illustrate this concept with the identification of candidate genes involved with HSC turnover. We compared expression QTLs in HSCs and brain from the same mice and identified both shared and tissue-specific QTLs. Our data are accessible through WebQTL, a web-based interface that allows custom genetic linkage analysis and identification of coregulated transcripts. AD C: Alzheimer's control. Alzheimer's mice were 50% C57BL/6, 50% SJL. Alzheimers animals were the double transgenic models reported by Dineley et al., (2002) J Biol Chem 277(25):22768-22780. Mice were handled by experimenter. No other treatment administered. RNA from control AD mice were extracted 2 hours after AD experimental mice received their last shock treatment. Source GEO sample is GSM4558 Last updated (according to GEO): May 27 2005 1000 Structure of entorhinal cortex IRTGFBd8_11 Large-scale analysis of the mouse transcriptome. Epidermis, dorsal skin without fur C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 362.52 Stdv: 21.48 Min: 334.00 Max: 406.09 Source GEO sample is GSM2965 Last updated (according to GEO): May 27 2005 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184713 Last updated (according to GEO): Apr 26 2007 387 cortex 392 861 Modiolus anguli oris healthy subject Source GEO sample is GSM211062 Last updated (according to GEO): Sep 10 2007 9 0 Blood Test 1000 jejunum 24 0 3AJZ02022115_ lymph node 1000 Tricuspid valve structure Monocular deprivation right cortex, biological rep1 plasma cells 50 61 of parieto-occipital cortex 121 147 Muscle 1000 mild cognitive impairment - posterior cingulate cortex 3 Normal Source GEO sample is GSM175792 Last updated (according to GEO): Apr 09 2007 The functional relationships and properties of different subtypes of dendritic cells (DC) remain largely undefined. To better characterize these cells, we used global gene analysis to determine gene expression patterns among murine CD11c(high) DC subsets. CD4(+), CD8alpha(+), and CD8alpha(-) CD4(-) (double negative (DN)) DC were purified from spleens of normal C57/BL6 mice and analyzed using Affymetrix microarrays. The CD4(+) and CD8alpha(+) DC subsets showed distinct basal expression profiles differing by >200 individual genes. These included known DC subset markers as well as previously unrecognized, differentially expressed CD Ags such as CD1d, CD5, CD22, and CD72. Flow cytometric analysis confirmed differential expression in nine of nine cases, thereby validating the microarray analysis. Interestingly, the microarray expression profiles for DN cells strongly resembled those of CD4(+) DC, differing from them by <25 genes. This suggests that CD4(+) and DN DC are closely related phylogenetically, whereas CD8alpha(+) DC represent a more distant lineage, supporting the historical distinction between CD8alpha(+) and CD8alpha(-) DC. However, staining patterns revealed that in contrast to CD4(+) DC, the DN subset is heterogeneous and comprises at least two subpopulations. Gene Ontology and literature mining analyses of genes expressed differentially among DC subsets indicated strong associations with immune response parameters as well as cell differentiation and signaling. Such associations offer clues to possible unique functions of the CD11c(high) DC subsets that to date have been difficult to define as rigid distinctions. Kidney 861 Diaphragm 56 Day control rep 3 5 0 brain Heart Atrium 1000 FVB/NJ Amygdala A 1000 Kidney SCG_control_40h_rep1 Heart 861 HCC (HBV+, HK27) brain 0 5 CH2114 Male; Testes Keywords = mouse gene expression database Source GEO sample is GSM29396 Last updated (according to GEO): May 27 2005 335 325 The jejunum 1000 Lung Prostatic Diseases 913 Seminoma 861 1000 Blood Vessels The nose 94 101 5 0 brain This is a wildtype littermate at postnatal day 5 pool of 5 animals Lot batch = Source GEO sample is GSM4059 Last updated (according to GEO): May 28 2005 CNS-SCsev_InjA24h-1B-s2 no additional Source GEO sample is GSM199106 Last updated (according to GEO): Jun 08 2007 Melanoma metastatic cell line A375, biological rep1 (LeiATCC) cingulate cortex 1000 Plasma 861 EGFR inhibitors block basal-like breast cancer growth Colon 1000 12 0 ovarian tumor Spleen vs Leukotriene B4 (LTB4)Treated B cell 30min (set1) of atrophic soleus muscle 1493 1517 H129 FC BA4 A mouse brain 478 489 7 0 prostate brain 0 5 bhattacharjee-lung stomach_fundus_1 GC (HKG59T) Breast cancer 0 12 103 85 of a past infection 115T Microdissected area # 1 of 1919 tumor ovarian tumor: serous Source GEO sample is GSM139436 Last updated (according to GEO): Apr 09 2007 Group 2 PEITC treated, pool #EP13 vs. reference pool heart 1169 1173 normal testis 54 66 1000 Malignant neoplasm of urinary bladder kidney 126 132 nic 4 (Experiment Neuroprotection4- Run 14985) Treatment, type=timepoint, description=primary cortical neurons were treated for 18 h with nicotine 10uM, agonist was then washed out and the cells were harvested 24h later, measurement=18.0 h Source GEO sample is GSM96728 Last updated (according to GEO): Feb 14 2006 Primary tumor 19 32 916 Starvation Liver Test (Blinded) Sample Source GEO sample is GSM130189 Last updated (according to GEO): Sep 18 2007 Chronic Lymphocytic Leukemia 19 47 adipose_tissue_omental_1 Source GEO sample is GSM80561 Last updated (according to GEO): Mar 31 2006 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2788 Source GEO sample is GSM2104 Last updated (according to GEO): Nov 21 2005 861 Liver NB-T-TEST-16 on NHGRI-6.5k_b plasma cells 50 61 Large-scale analysis of the human transcriptome. Promyelocytic leukemia Source: ATCC Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 122.84 Stdv: 2.81 Min: 118.81 Max: 129.03 Source GEO sample is GSM2877 Last updated (according to GEO): May 27 2005 Primary Neoplasm 1000 gene expression of 1 day RA differentiated ESCs Source GEO sample is GSM181965 Last updated (according to GEO): Apr 12 2007 861 Blood 3AJZ02061902_CerebellumPeduncles 865 Disorder of artery from brain 21 30 1000 Cerebral cortex 861 Prostate carcinoma of parieto-occipital cortex 117 143 The molecular mechanisms underlying the changes in the nigrostriatal pathway in Parkinson?s disease (PD) are not completely understood. Here we use microarrays and mass spectrometry to study the transcriptomic and proteomic changes in the striatum of two mouse models of PD induced by distinct neurotoxins, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and methamphetamine (METH). Transcripts and proteins were found with similar abundance changes in both models which may be involved in the pathophysiology of PD. GFAP transcript and protein levels were significantly up-regulated by both neurotoxins, confirming the known astrocytic response to these drugs. Other genes and proteins were idiosyncratic in their responses to the two toxins, suggesting specific toxicological responses. Comparing transcript and protein levels revealed that efficiently translated genes used more commonly occurring codons than inefficiently translated genes. Additionally, a potential role was found for miRNAs in translational control in the striatum. The results constitute one of the largest datasets integrating transcript and protein changes for these two neurotoxin models with many similar endpoint phenotypes but distinct pathologies. Using multiple toxins while examining proteins and transcripts can be an effective method of delineating the molecular pathology of neurodegenerative diseases. Last Updated (by provider): Jul 16 2007 Contributers: Desmond J Smith David G Camp II Wei-Jun Qian Haixing Wang Daniel M Sforza Joshua S Bloom Mark H Chin Diana J Bigelow Arshad H Khan Dahai Liu Vladislav A Petyuk William P Melega Richard D Smith Goran Lacan Rita M Cantor Colon 1000 Healthy patient. Source GEO sample is GSM228563 Last updated (according to GEO): Sep 11 2007 278 255 ischemic cardiomyopathy Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9972.gif Source GEO sample is GSM79826 Last updated (according to GEO): Sep 22 2006 1000 Brain 306-99_normal /3T3 fibroblasts 295 310 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68237 Last updated (according to GEO): Jul 07 2006 cerebellum 7 16 none Source GEO sample is GSM244640 Last updated (according to GEO): Nov 23 2007 1000 Coronary Arteriosclerosis Lymphoblastic Leukemia 901 none Source GEO sample is GSM149547 Last updated (according to GEO): Jan 03 2007 to the brainstem 251 267 H9LMS00111005 Hippocampus Treatment, type=pharmacogenomic_treatment, description=Chronic Immobilization Stress Source GEO sample is GSM53302 Last updated (according to GEO): Jul 06 2005 Bipolar Disorder 1000 Nose 1000 1000 Heart failure 1000 Anatomical location Normal Source GEO sample is GSM176407 Last updated (according to GEO): Apr 09 2007 5 0 brain Lymphoblastoid Cell Line for Individual 8127.3 log phase adenocarcinoma 1282 1296 Gene expression data from postmorten brain regions Source GEO sample is GSM145464 Last updated (according to GEO): Nov 20 2006 brain 0 5 30 19 Solid tumor mouse brain 478 489 Ovary 1000 Cerebral cortex 1000 861 Brain Standard Affymetrix Protocol Source GEO sample is GSM16506 Last updated (according to GEO): May 28 2005 Brain 861 0 Human Cortex 11 healthy subject Source GEO sample is GSM211078 Last updated (according to GEO): Sep 10 2007 Expression data from Human MPNST cancer cells infected with G207 and oncolytic HSV AD control Treatment, type=dissect Source GEO sample is GSM119675 Last updated (according to GEO): Jul 10 2006 ALS model Source GEO sample is GSM75464 Last updated (according to GEO): Mar 06 2006 1000 Left mouse brain ipsilateral LPS.Dmso, biological rep3 896 Primary Neoplasm mouse brain 478 489 CAD_replicate41 M_U133Plus_108_AnCg 133 98 Keywords = Congestive heart failure ci_NY3 Animals were sacrificed and organs were rapidly frozen in liquid nitrogen, and subsequently stored at <ETH>80oC. Tissues were mechanically homogenized with a polytron and total cellular RNA was extracted using a commercially available reagent (TMTRIzol; Invitrogen). The poly-(A)+ fraction of the RNA was isolated by chromatography with oligo d(T) cellulose beads. For cDNA labeling, either 25 mg of total RNA or 2.5 mg of poly-(A) RNA was converted into cDNA using reverse transcriptase (RT; Super Script II, Invitrogen) and alternatively Cy5 or Cy3-labeled dCTP (1mM, Perkin Elmer-Cetus/NEN, Boston) in a reaction mixture containing 1.5 mL oligo (dT) (100pmol/ mL), 3 mL dNTP-dCTP (6.67mM each), 1 mL dCTP (2mM), 4 mL DTT (100mM), 8 mL 5 X RT Buffer (Invitrogen, California). The reactions were carried out at 42¼C for 3 hrs, after which the RNA was degraded by the addition of 0.5 mL RNase A (1 mg/mL) and 1.5 mL RNaseH 5 units/mL). Labeled cDNA was separated from unincorporated nucleotides (Qiagen column) and further concentrated by evaporation under vacuum. The arrays were pre-hybridized for 1-2hrs with DIGEasy hybridization buffer (Roche) containing 10ug/ml denatured salmon sperm DNA, and 10ug/ml yeast tRNA. The Cy5 and Cy3 labelled cDNAs were combined and hybridized in the same medium and incubated with the arrays for 16-18hrs at 37Co. Finally, the arrays were washed 3 x 10 mins in 0.1 x SSC (20 X SSC is 3M sodium chloride, 0.3 M sodium citrate, pH 7.0), 0.1%SDS at 50Co, and 4 x 3min in 0.1 x SSC at room temperature, and dried by centrifugation. Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray fluorescent scanner and image intensity data were extracted and analyzed with QuantArray 3.0 analysis software. Quantification data was imported in GeneSpring (Silicon Genetics). The import format was modified to maintain information relevant to user-contributed flagging as well as QC parameter furnished by the array manufacturer. Dye swap and Intensity-based normalization (Lowess) were performed using the default settings. Keywords = spleen Keywords = malaria Source GEO sample is GSM11002 Last updated (according to GEO): Oct 28 2005 Primary tumor 19 32 Brain Injuries 1000 901 Caudate nucleus structure mouse left hemi-diaphragm Source GEO sample is GSM53237 Last updated (according to GEO): Jul 06 2005 Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles. PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity. Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence. To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips. Source GEO sample is GSM136562 Last updated (according to GEO): Jun 05 2007 Melanoma xenograft, MA2_Lung_B (LeiATCC) Pool Ts1Cje_P15_hyb1 Male Sprague-Dawley albino rats (Charles River) initially weighting approximately 200 grams were randomly assigned to one of the following: 1) olanzapine (2 mg/kg/day, I.P.) (N=20) or 2) Saline (N=20) and administered olanzapine or saline for 21 days. Frontal cortex (N=4/group) was dissected and homogenized for microarray, QPCR and western blotting following previous methods (Fatemi et al. 2003; Brooks et al. 2003). RNA isolation, cDNA preparation, microarray hybridization and QPCR followed previous methods (Brooks et al. 2003). Keywords = olanzapine Keywords = frontal cortex Source GEO sample is GSM48579 Last updated (according to GEO): Apr 10 2006 brain, left frontal temporal lobe: Extract42_le1 from subcutaeous adipose tissue 20 50 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113947 Last updated (according to GEO): Jun 16 2006 8 0 Cartilage Endometrium 0 10 NCI60.48_LABEL52EXTRACT51SUB3 Source GEO sample is GSM134235 Last updated (according to GEO): Aug 06 2007 bronchial epithelia 224 243 Coronary artery 901 1000 Cerebral cortex 5 0 Spleen 329 306 valvular cardiomyopathy 39 21 from mammary glands 2533 HP24_32 D_U133A_65_DLPFC heart_atrium_3 bronchial epithelia 224 243 Skeletal bone 861 Standard Affymetrix procedure Source GEO sample is GSM133020 Last updated (according to GEO): Aug 28 2007 1BJZ02051613_ParietalLobe collagen 302 310 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11245 Last updated (according to GEO): May 28 2005 Replicate2_Voxel B6 CAD_replicate99 118 110 of asthma Muscle 263 268 We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7. Source GEO sample is GSM200749 Last updated (according to GEO): Jul 12 2007 24 hr Hela Double Thymidine, exp2 Brain 861 anterior cingulate cortex 521 546 The epithelial cells 962 981 D_U133A_11_HC Liver 0 4 Ovarian_Tumor_Mucinous_KU-OM-006 Huntington Disease 1000 V5-P239 Brain 1000 Normal Source GEO sample is GSM176067 Last updated (according to GEO): Apr 09 2007 B10.PL mice with experimental autoimmune encephalomyelitis (MS model) were treated with either placebo or 200 ng 1,25(OH)2D3. Six hours later, the spinal cords were harvested and mRNA extracted for analysis. Naive mice served as controls. Keywords = Experimental autoimmune encephalomyelitis Keywords = multiple sclerosis Keywords = 1 Keywords = 25(OH)2D3 Source GEO sample is GSM13050 Last updated (according to GEO): May 28 2005 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50643.gif Developmental Stage: E8.5 Source GEO sample is GSM229812 Last updated (according to GEO): Nov 06 2007 GM19145 rat hippocampus Treatment, type=time_course, measurement=72.0 h Source GEO sample is GSM32145 Last updated (according to GEO): May 27 2005 Organ 966 Spleen vs IFN beta Treated B cell Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228601 Last updated (according to GEO): Sep 11 2007 913 Coronary heart disease 861 Bladder 1000 Hypothalamic structure COID-COID8t1-A345-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 14 days hindlimb suspended, 5 day reloaded RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis. Source GEO sample is GSM17357 Last updated (according to GEO): May 28 2005 Expression profiling of moderately injured raphe at 14d in rats Source GEO sample is GSM41571 Last updated (according to GEO): May 27 2005 in the mammalian nervous system 110 141 The amyloid precursor protein (APP) plays a central role in the pathogenesis of Alzheimer?s disease (AD). Processing of APP by ?- and ?-secretase activities results in the production of ß-amyloid (Aß), the main constituent of Alzheimer plaques, but also in the generation of the APP intracellular domain (AICD). Recently, it has been demonstrated that AICD has transactivation potential, however, the targets of AICD dependent gene regulation and hence the physiological role of AICD remain largely unknown. In this work we analysed transcriptome changes during AICD dependent gene regulation using a human neural cell culture system inducible for expression of AICD, its co-activator Fe65, or the combination of both. Induction of AICD was associated with increased expression of genes with known function in the organization and dynamics of the actin cytoskeleton as well as genes involved in the regulation of apoptosis. Last Updated (by provider): Jan 25 2006 Contributers: Rupert Egensperger Donat Kögel Jochen Prehn Caoimhin Concannon Thorsten Müller Manus Ward Includes GDS1979. Update date: Jun 14 2006. Dataset description GDS1979: Analysis of neural cells induced to express amyloid precursor protein (APP) intracellular domain (AICD) or the combination of AICD and its co-activator Fe65. Secretase processing of APP produces beta-amyloid, the main constituent of Alzheimer plaques, and AICD. Results identify target genes of AICD.. DLCL-0025 Eye_6wk_FVB_Male Gene expression data from postmorten brain regions Source GEO sample is GSM145911 Last updated (according to GEO): Nov 20 2006 heart 1169 1173 901 nervous system disorder blastocysts Source GEO sample is GSM18687 Last updated (according to GEO): May 27 2005 Job's Syndrome 911 Mesenchymal Stem Cells 1000 Barcode: 251316210195 Source GEO sample is GSM159390 Last updated (according to GEO): Jul 17 2007 Spleen vs BAFF Treated B cell 30min (set1) Endometrium 0 10 Myocardial Infarction 1000 Spinal Cord 1000 352 340 encephalitis 861 Intestines Nervous system structure 901 none Source GEO sample is GSM123253 Last updated (according to GEO): Jul 26 2006 days nasal epithelium 1126 1147 Gene expression data from postmorten brain regions Source GEO sample is GSM145807 Last updated (according to GEO): Nov 20 2006 Mesenchymal Stem Cells 1000 brain, hippocampus: KA-240h-P15-I_e1_le1 rat cortex Treatment, type=time_course, measurement=7.0 d Source GEO sample is GSM53218 Last updated (according to GEO): Jul 06 2005 1000 Amygdaloid structure HC82 CB A Expression profiling of spinal cord section (T9) extracted from rats 7d following moderate injury Source GEO sample is GSM31581 Last updated (according to GEO): May 27 2005 861 Mammary gland Exp C, Animal #4, 1mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours Source GEO sample is GSM246163 Last updated (according to GEO): Dec 03 2007 861 Heart failure cerebellum 7 16 861 Hypothalamic structure HMEC X BC14 : 0096-5k ovary 199 203 1115 1102 cardiomyopathy Gene expression data from postmorten brain regions Source GEO sample is GSM145662 Last updated (according to GEO): Nov 20 2006 607 597 the rectum 861 Brain Gene expression data from whole brain infected mouse, day 3 Source GEO sample is GSM189619 Last updated (according to GEO): May 16 2007 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181132 Last updated (according to GEO): Jul 12 2007 NA18507 1000 Encephalitis 1000 Cerebral cortex Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188705 Last updated (according to GEO): Jun 06 2007 35 CB A cerebellum 7 16 Y VIS D065 The aim of this study was to characterize the basal expression of OC, MOD and SV of newborn rats (3-5 day old) and its changes by short?term cultivation (24 hrs) and mild hypoxia (5 hrs). Three varieties of tissue samples were analyzed (i) Freshly prepared tissue, used as control; (ii) cultures held under normoxic conditions and (iii) cultures exposed during cultivation to 5 h hypoxia. The gene expression was analyzed using the Affymetrix GeneChip RN-U34. The functional specificity of the cochlea regions are well reflected by the gene expression pattern. For example, the basal expression of Organ of Corti is characterized by genes involved in potassium and calcium homeostasis. The MOD is characterized by genes involved in regulation of maturation of neuronal cells. The SV is characterized by genes involved in ion homeostasis and blood flow. Cultivation dramatically changes the gene expression. In contrast, mild hypoxia showed only small changes. The changes are interpreted as stress response. We used this analysis as screening approach to detect significant changes in gene expression and used the RT-PCR analyses of independent sister cultures for confirmation. Correlation analysis showed close relations of the expression levels when aliquots of the biological material were compared. However, comparisons of the expression levels received by microarray and by RT-PCR analysis of independent sister samples resulted in 70-90 % in similar predictions. This data indicate that possible discrepancies has its basis in biological sampling rather than factors of methodical errors on the level of RT-PCR. Last Updated (by provider): Aug 03 2006 Contributers: Johann Gross Heidemarie Haupt Ute Ungethüm Astrid Machulik Ralf-Jürgen Kuban Nyamaa Amarjargal Frank-Uwe Fuchs Birgit Mazurek pancreas Source GEO sample is GSM18702 Last updated (according to GEO): May 27 2005 brain, cerebral cortex: Co1_le1 Lungs 153 157 Mesenchymal Stem Cells 1000 861 Cerebral cortex HapMap JPT Female Source GEO sample is GSM159650 Last updated (according to GEO): Feb 01 2007 in blood 16 23 adipose tissue; mesenteric Source GEO sample is GSM18624 Last updated (according to GEO): May 27 2005 17 7 hippocampus Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153369 Last updated (according to GEO): Dec 27 2006 D3_TP-48_C 4_hypothalamus_time_0_#129 mouse brains 187 198 Expression profiling of spinal cord section (T10) extracted from rats 7d following laminectomy (sham) Source GEO sample is GSM31286 Last updated (according to GEO): May 27 2005 201 181 Ilea epithelial cells Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153491 Last updated (according to GEO): Jan 11 2007 Gene expression data from human colon tumor tissue Source GEO sample is GSM173374 Last updated (according to GEO): Apr 20 2007 GSE8512 P2B_KIDNEY_4 4525 4520 liver 3rd 2hr C+S-CA1 1781 CP24_21 861 Asphyxia Skeletal bone 861 Epithelium transition profile 5 0 brain rat cortex Treatment, type=time_course, measurement=7.0 d Source GEO sample is GSM53212 Last updated (according to GEO): Jul 06 2005 of mouse brain 9 23 Neostriatum 1000 of epithelial markers E-cadherin 782 814 1 Retina 13 20 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198645 Last updated (according to GEO): Jun 06 2007 Myocardium 861 ER+/LN-/Marks204 on Affymetrix GeneChip Human Full Length Array HuGeneFL Spinal Cord 1000 MCF7_CHX_EtOH_24h_rep1 Bone Marrow 1000 WGACON-97 1000 Brain Heart 861 901 Heart failure of caudal 93 101 0 Human Cortex 11 861 Cerebral cortex CVB3_V-3h-3 AcB61 #12250573 liver 0 5 Mouse neuroblastoma 0 18 amygdala, central nucleus sprague1 861 Adipose tissue Simple annotation: Chronic Lymphocytic Leukemia, Fludarabine chemotherapy Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2842.gif Source GEO sample is GSM72134 Last updated (according to GEO): Sep 22 2006 HCC (HBV+, SF34, 2) Gene expression data from aneurismal tissues obtained from patients with bicuspid valves. Source GEO sample is GSM116788 Last updated (according to GEO): Jun 28 2006 861 Neoplasm HCC (HBV+, HK42) brain, cerebral cortex: Rat_03-03_NroLep_Lipska_e1_le1 the blood 393 402 Gene expression data from SVG-A glial cells. Source GEO sample is GSM189716 Last updated (according to GEO): May 16 2007 608 589 of proximal jejunum 861 Blood Ovary 1000 Heart Ventricle 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11231 Last updated (according to GEO): May 28 2005 1640 1615 Creutzfeldt-Jacobs disease Neostriatum 1000 1000 Kidney Osteoblasts 1000 A control group consisting of nine C57/BL/6J mice was maintained on a normal diet consisting of Purina Rodent Chow (Harlan Teklad, catalog #5008, 6.5% fat, 49% carbohydrate, 23% protein, 3.5 kcal/ g). The experimental group consisted of nine mice grown on a specialty high-fat diet (Harlan Teklad, catalog #TD88137, 42.16% fat, 42.81% carbohydrate, 15.02% protein, 4.53 kcal/ g). Mice were maintained for ten weeks on their respective diets in a controlled environment with standard light and feeding schedule. Two days before tissue harvest, the experimental group on the high-fat diet was divided into one group of five and one group of four mice. The first group continued on the high-fat diet for the final two days, while the second group fasted. Mouse weights were recorded two days prior, and the day of tissue harvest. At the end of the fasting period liver tissue samples were harvested from each mouse. RNA was purified from the liver tissue samples. Each tissue was homogenized in 1 mL of STAT-60 (Tel-Test, Inc., Friendswood, TX) and the homogenate was mixed with 200 uL of chloroform. The aqueous phase was removed, and mixed with 500 uL of isopropanol to precipitate the RNA. The resulting RNA pellet was washed with 500 uL of 70% ethanol and allowed to air dry. The pellet was dissolved in RNase free water (Ambion, TX), quantified by UV spectroscopy, and stored at -80C. Total RNA control samples (Universal Mouse Reference RNA, catalog # 740100, Stratagene) were labeled using Cy3 dCTP (Perkin-Elmer), and liver total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). The control RNA samples were additionally mixed with 2 uL of random hexamers. The reaction mixtures were incubated at 42 C for two hours. After the reverse transcription reactions, the RNA templates were degraded by addition of 2 uL of 1 N NaOH and incubation at 65 C for 10 minutes. The alkaline conditions were neutralized by addition of 2 uL of 1 N HCl. Liver cDNA samples were then mixed with a control cDNA sample, and the mixtures were cleaned using a QIAquick Nucleotide Removal kit (Qiagen) as described by the manufacturer's instructions. The cleaned samples were concentrated in a speed vacufuge (Eppendorf) for 20 minutes at 65 C, and were dissolved in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), quantified, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 C using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), then in 1X SSC, and finally in 0.1X SSC. The arrays were dried by centrifugation and scanned using a GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and analyzed using Matlab (The MathWorks, Inc.). Microarrays were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). Arrays contained 16,847 features, printed from a synthesized oligonucleotide mouse library (Operon). The library was suspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed at approximately 50% humidity. Once printed, the probes were crosslinked using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride (Fluka AG), 239 mL 1-methyl-2-pyrrolidinone (EM Science), and 10.7 mL of 1 M boric acid (Fisher), pH 8.0. They were cleaned by rinsing twice in 250 mL of milli-Q water, followed by 250 mL of 95% ethanol (Pharmco Products). After blocking, they were dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, energy homeostasis, gene expression, microarrays Source GEO sample is GSM6594 Last updated (according to GEO): Nov 21 2005 1000 Left CAST/EiJ_male_hypothalamus Source GEO sample is GSM184200 Last updated (according to GEO): Apr 26 2007 onto a collagen 71 85 V5-P051 Cerebral cortex 861 Nrl ko samples were compared to wt at postnatal 2. Source GEO sample is GSM227449 Last updated (according to GEO): Sep 07 2007 Blood 861 Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242087 Last updated (according to GEO): Dec 04 2007 0 Human Cortex 11 brain, hippocampus: ADX AM Hip b_e1_le1 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Tumor necrosis factor-alpha for 240min Source GEO sample is GSM5810 Last updated (according to GEO): May 27 2005 none Source GEO sample is GSM244630 Last updated (according to GEO): Nov 23 2007 placebo 48h, biological rep3 1000 Brain Liver 0 4 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9857.gif Source GEO sample is GSM79896 Last updated (according to GEO): Sep 22 2006 (cortex 19 25 901 Bone Marrow Osteoblasts 1000 1000 Heart None Source GEO sample is GSM198094 Last updated (according to GEO): Jul 16 2007 Gene expression data from DAOY cells stably expressing Bmi1 and Mel18 shRNA Source GEO sample is GSM182012 Last updated (according to GEO): Apr 23 2007 Gene expression data from aneurismal tissues obtained from patients with tricuspid valves. Source GEO sample is GSM116796 Last updated (according to GEO): Jun 28 2006 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156595 Last updated (according to GEO): Jan 22 2007 PAX sample 3 P104 deprived visual cortex replicate 2 none Source GEO sample is GSM123234 Last updated (according to GEO): Jul 26 2006 D_95Av2_3076_CB_1_GS BXD42_M7SS02042218 Brain 861 healthy subject Source GEO sample is GSM211048 Last updated (according to GEO): Sep 10 2007 AD control Treatment, type=dissect Source GEO sample is GSM119644 Last updated (according to GEO): Jul 10 2006 216 212 liver Hippocampus 1000 Heart 1000 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19230 Last updated (according to GEO): May 27 2005 Sample represents the supraoptic nucleus from 5 control animals Source GEO sample is GSM69464 Last updated (according to GEO): Dec 15 2005 PMN_control_360min_Patient3 1000 Left Temporal Lobe 1 Normal 861 Neoplasm brain, cerebral cortex: Co 3 (4/28)_le1 Gene expression data from whole brain of uninfected mouse Source GEO sample is GSM189600 Last updated (according to GEO): May 16 2007 brain, frontal cortex: Sham AM S b_e1_le1 1000 frontal lobe Lymphoblastoid Cell Line for Individual 8040.4 log phase Parkinson's disease sample x076 0 30 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211280 Last updated (according to GEO): Jul 18 2007 FL-10 Expression data from ovarian cancer cells with time-course and concentration-profiles 861 Cerebral cortex Blood Test (Blinded) Sample Source GEO sample is GSM130033 Last updated (according to GEO): Sep 18 2007 IDC14 on harvard-12k /SvEvTac mouse pituitary gland 29 58 1000 Spleen Primary tumor 19 32 V5-P399 HMVEC-L stimulated without LPS for 24 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114572 Last updated (according to GEO): Sep 20 2006 Posterior root of spinal nerve 861 1037 of transitional epithelium 1012 858 Prostatic Neoplasms 983 Epiphysial cartilage Cochlear nuclei 0 14 Gene expression data from brain of adult rats Source GEO sample is GSM101032 Last updated (according to GEO): Feb 20 2007 1500 mg/kg X 24 hr Source GEO sample is GSM129891 Last updated (according to GEO): Sep 18 2007 1000 Palatine Tonsil 861 Colorectal Cancer human frontal cortex Source GEO sample is GSM87047 Last updated (according to GEO): Feb 08 2006 NCI60.49_LABEL53EXTRACT52SUB3 Source GEO sample is GSM134241 Last updated (according to GEO): Aug 06 2007 hypothalamussa Mouse old heart C30-Ht-2 901 Myeloid Leukemia the retina 856 865 Leukopheresis (Post-ficoll) 600 592 in urine none Source GEO sample is GSM210352 Last updated (according to GEO): Jul 16 2007 861 Heart 1000 Nervous system structure brain_DLPFC_bipolar B_mr409 in blood 16 23 Expression profiling of somatomotor cortex extracted from rats at 14d following moderate injury Source GEO sample is GSM41689 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145060 Last updated (according to GEO): Nov 20 2006 41 29 Control blood 861 Blood CNS-SC_InjB4h-4bB-s2 3066 CP0_41 Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. 861 Brain human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155034 Last updated (according to GEO): Jun 04 2007 1000 Left Gene expression data Source GEO sample is GSM230351 Last updated (according to GEO): Sep 19 2007 Cerebral cortex 1000 Cochlea at E13, replicate2 1000 Endometriosis, site unspecified Wild-type-neocortex, biological rep1 (male) 8 0 leukemia KO-Nrf2-Male-1 jzo034-rp1-v5_u74av2-met 1000 frontal lobe 1000 Neuraxis outer medulla 31 43 Plasma 861 Structure of entorhinal cortex 1000 68 53 from 12 cochleas Control Abdominal Aorta Male Pool I Brain 861 Investigation into murine dermal burn wound. Mouse thermal injury induced, and skin excised at different times post-injury. Source GEO sample is GSM7486 Last updated (according to GEO): May 27 2005 4535 4527 hepatoma Pituitary Gland 861 I_U133A_64_AnCg DBA/2J amygdala rep2 spinal cord, spinal cord: G5F_le1 616 606 DNA damage Five different human MPNST cell lines, mock treated or infected with G207. Source GEO sample is GSM215809 Last updated (according to GEO): Aug 07 2007 thymocytes_DN4_2 mouse brains 187 198 2635 2621 muscle spindles Cerebral cortex 1000 Probeset expression data from NA12750 growth 1, replicate 5 Source GEO sample is GSM195195 Last updated (according to GEO): Aug 08 2007 865 Ovarian Diseases at the Human Brain 736 753 1037 of transitional epithelium 1012 of the postmortem brains 673 697 Transplant Series 17 , Transplant # 1 Neoplasm 1000 forebrain 7 15 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n110 Source GEO sample is GSM2073 Last updated (according to GEO): Nov 21 2005 Ny7: Hippocampus_21PT-AU_rep10 Infection 1000 na Source GEO sample is GSM180483 Last updated (according to GEO): Apr 04 2007 0 Human Cortex 11 Tumor__Mesothelioma_169_T7 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Chronic leukemia NOS 913 Plasma 861 2h mitotic selection I_U133A_9_Amy Whole Brain 62 72 DBA 1-1-4 Kidney of the postmortem brains 656 680 Y SIT D076 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108645 Last updated (according to GEO): Aug 22 2006 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.71 Subject: 3023 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39052 Last updated (according to GEO): May 27 2005 no additional Source GEO sample is GSM199261 Last updated (according to GEO): Jun 08 2007 Brain 1000 5 0 brain Heart 1000 G1E_30_A GSE5786 B6 day 6, biological rep 4, tech rep 2 861 HIV Infections Wild type 8 wk old male A/J mouse amygdala Source GEO sample is GSM74915 Last updated (according to GEO): Feb 27 2007 Neural tube, treated, GD9:00, T215580 MSS-Spa2-2moF-1aAv2-s2 in the mammalian nervous system 110 141 Cortex_reserpine_treated_rep1 Parkinson's disease sample x001 861 Blood 124 FC BA9 A 70 40 without coronary artery disease Brain 1000 NL-6084-A335-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Malignant Neoplasms AT2-hTERT_1.5Gy_24h_C5_26771 Macrophage 14smi117 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19224 Last updated (according to GEO): May 27 2005 NA18566 Exaggerated neuroinflammation and sickness behavior in aged mice following activation of the peripheral innate immune system. Pharyngeal Mucosa 4 Normal Subject code A10 276 270 Retinas 1000 Myocardium ISR15 This is a 8-week-old mouse untreated gastrocnemius muscle Source GEO sample is GSM4249 Last updated (according to GEO): May 27 2005 983 Occipital region Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120682 Last updated (according to GEO): May 14 2007 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28469 Last updated (according to GEO): May 27 2005 plasma cells 50 61 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc118 Source GEO sample is GSM1873 Last updated (according to GEO): Nov 21 2005 111601_HF_393VC hippocampus 1067 1078 Integumentary system 1000 Bone Marrow 1000 122 113 hippocampi Brain 861 Small cell carcinoma of lung 867 Liver Test (Blinded) Sample Source GEO sample is GSM130120 Last updated (according to GEO): Sep 18 2007 Myocardium 861 nasal epithelial cells 28 49 I_U133A_55_Amy f2#43 versus pool Mouse Brain tissue Liver 1000 901 Caudate nucleus structure Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM Source GEO sample is GSM207677 Last updated (according to GEO): Jul 09 2007 Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231054 Last updated (according to GEO): Sep 26 2007 intestinal disease 126 143 5 0 brain 1000 Cardiomyopathy, Alcoholic Mouse primary retinal sphere, chip MOE430A 366 354 encephalitis Gene expression data from postmorten brain regions Source GEO sample is GSM145862 Last updated (according to GEO): Nov 20 2006 6,18,30 month oculomotor nucleus and spinal cord Source GEO sample is GSM74337 Last updated (according to GEO): Sep 16 2005 of the colon 28 39 The primary cause of Duchenne muscular dystrophy (DMD) is a mutation in the dystrophin gene leading to the absence of the corresponding RNA transcript and protein. Absence of dystrophin leads to disruption of the dystrophin-associated protein complex and substantial changes in skeletal muscle pathology. Although the histological pathology of dystrophic tissue has been well documented, the underlying molecular pathways remain poorly understood. To examine the pathogenic pathways and identify new or modifying factors involved in muscular dystrophy, expression microarrays were used to compare individual gene expression profiles of skeletal muscle biopsies from 12 DMD patients and 12 unaffected control patients. Two separate statistical analysis methods were used to interpret the resulting data: t test analysis to determine the statistical significance of differential expression and geometric fold change analysis to determine the extent of differential expression. These analyses identified 105 genes that differ significantly in expression level between unaffected and DMD muscle. Many of the differentially expressed genes reflect changes in histological pathology. For instance, immune response signals and extracellular matrix genes are overexpressed in DMD muscle, an indication of the infiltration of inflammatory cells and connective tissue. Significantly more genes are overexpressed than are underexpressed in dystrophic muscle, with dystrophin underexpressed, whereas other genes encoding muscle structure and regeneration processes are overexpressed, reflecting the regenerative nature of the disease. The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27016 Last updated (according to GEO): May 27 2005 1000 Muscle Proliferative endometrium from normal patient Source GEO sample is GSM150199 Last updated (according to GEO): Dec 14 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145587 Last updated (according to GEO): Nov 20 2006 GC (HKG29T) 1037 of transitional epithelium 1012 Parkinson's disease sample x204 0 30 Primary adenocarcinoma 0 21 896 Primary Neoplasm Mesenchymal Stem Cells 1000 H132 FC BA4 B Primary tumor 19 32 Sex Specific Transciption in Human Hypothalamus 428 408 Keywords = Alzheimer? Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14357.gif Source GEO sample is GSM79626 Last updated (according to GEO): Sep 22 2006 Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35371 Last updated (according to GEO): May 27 2005 1000 Heart failure 861 Kidney Gene expression data from brain hemispheres of experimentally naive male mice Source GEO sample is GSM172397 Last updated (according to GEO): Jun 27 2007 906 893 a human organ human cerebellum Source GEO sample is GSM87124 Last updated (according to GEO): Feb 08 2006 1000 Neostriatum hippocampus rattus_norvegicus_strain iP animal_number 4 Brain 1000 0 Human Cortex 11 Neural tube, treated, GD8:15, T216811 1000 Communicable Diseases 5 0 brain 111 89 by ectodermal dysplasia Macrophage 14smi018 Neostriatum 1000 81 year old female Male 69.6 yr after antibody enrichment scan 2 (U133B) 1000 Cerebral cortex Normal Source GEO sample is GSM176279 Last updated (according to GEO): Apr 09 2007 884 Cell Adhesion Molecules VDXRHU_1315 257 242 of uterine horns 1000 frontal lobe Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 4623 left_liver_lobe Parkinson Disease 1000 entorhinal cortex layer II stellate island cells Source GEO sample is GSM107529 Last updated (according to GEO): May 01 2006 HNN053 Average value of duplicate experiments of brain neurospheres of BMI-1 knockout mice (postnatal day 0). The cRNAs for hybridization were generated by one round RNA amplification. Source GEO sample is GSM9247 Last updated (according to GEO): May 27 2005 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n106 Source GEO sample is GSM2052 Last updated (according to GEO): Nov 21 2005 Unfertilized egg replication 4 Keywords = preimplantation Keywords = development Source GEO sample is GSM14662 Last updated (according to GEO): May 28 2005 Primary tumor 19 32 Gloubus Pallidum Internal 5 Normal I_U133A_27_DLPFC Pancreas at e16.5, Chip B, rep 1 Neostriatum 1000 HCC (HBV+, HK65, T1) R6/1 transgenic, brain hemisphere Source GEO sample is GSM83867 Last updated (according to GEO): Apr 20 2007 Malignant Neoplasms 861 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11571.gif Source GEO sample is GSM76442 Last updated (according to GEO): Sep 22 2006 913 Coronary heart disease PGA-lv_1h_511 267 262 Spleen Lymphoblastoid Cell Line for Individual 8184.5 log phase ovary.1 myometrium_9 861 Brain 607 597 the rectum Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell 60min (set2) Expression profiling of laminectomized raphe at 3min in rats Source GEO sample is GSM41535 Last updated (according to GEO): May 27 2005 D_U133Plus_111_HC Expression data from monocytes of individuals with different collateral flow index CFI Whole neuroblastoma tumor_2056 Nervous system structure 901 We analyzed the lumbar spinal cord tract of transplanted nmd mice (n=3), untransplanted nmd mice (n=3) and wild-type mice (n=3) (all mice are of male gender). The latter groups underwent surgical procedure with vehicle. The surgical procedure and spinal cord-derived neural stem cell transplantation (intratechal injection) were done at P1 and the animals were sacrificed at 6 weeks of age. Frozen tissue was stored at -80°C. Total RNA was purified from tissue, using the EUROZol Kit (EuroClone Ltd., United Kingdom) following the manufacturer?s instructions. Total RNA (5 ug) was reverse-transcribed with a cDNA synthesis kit in the presence of SuperScript II RT (Invitrogen-Life Technologies, Inc.) and an oligo dT-T7 primer (Affymetrix Inc., Santa Clara, CA). After phenol/chloroform extraction and ethanol precipitation, the cDNA pellet was air-dried and re-suspended in 12 uL of diethyl pyrocarbonate-treated water and quantified by spectrophotometer measurement. An aliquot of each sample was conserved for gel electrophoresis and for inspection of RNA quality (i.e., 28S:18S RNA ratio). 10 ul was used for the IVT (In Vitro Transcription) amplification reaction, in the presence of biotinylated nucleotides (Enzo Biochem Inc.). Labeled cRNA (15 ug) was fragmented by incubation at 94°C for 35 minutes in fragmentation buffer (GeneChip Sample Cleanup, Qiagen) and the fragmented cRNA was then hybridized competitively against the Affymetrix 430 2.0 Array oligonucleotide array. Hybridization occurred at 47°C overnight. The arrays were scanned using a GeneArray 2500 Scanner (Affymetrix) and analyzed using MicroArray Suite 5.0 (Affymetrix). All experiments were validated after direct measures of cRNA quality: 5':3' ratios for beta-actin and for GAPDH (determined from Affymetrix chip hybridization analysis) are indirect indicators of overall RNA preservation. The default parameters were used for the statistical algorithm and for probe set scaling. The target intensity was set to 1,000 to normalize expression levels across all samples. Source GEO sample is GSM67529 Last updated (according to GEO): Dec 21 2005 Expression profiling reveals multiple myelin alterations in murine succinate semialdehyde dehydrogenase deficiency. 1000 Brain Measles 861 7 0 prostate VDXIGRU_272823 liver_wildtype_WY14643_5d_pooled Gene expression data from skeletal muscle following 240 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230461 Last updated (according to GEO): Sep 19 2007 195 180 atherosclerosis Communicable Diseases 861 Mouse old heart w/ a- & g-tocopherol agT-Ht-2 biopsy sample obtained from 5-year-old female individual Keywords = gene expression profile of normal human skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15829 Last updated (according to GEO): May 28 2005 Brain 1000 23 11 of the kidney 9 on NHGRI-13.8k in synaptic 557 567 Disease Source GEO sample is GSM176090 Last updated (according to GEO): Apr 09 2007 plasma cells 332 344 5 0 brain Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225664 Last updated (according to GEO): Nov 02 2007 Creatine improves health and survival of mice. frontal cortex sprague 3935 whole tissue, individual animal, 10 weeks old, male Sprague Dawley frontal cortex file:p3935w Source GEO sample is GSM15172 Last updated (according to GEO): Oct 28 2005 861 Brain hind Source GEO sample is GSM67221 Last updated (according to GEO): Jan 19 2006 875 Cerebellar Diseases 78 66 Control blood at the Human Brain 744 761 from progenitor satellite cells 36 66 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114202 Last updated (according to GEO): Jun 16 2006 Optimal activation of T cells requires effective occupancy of both the antigen-specific T cell receptor and a second coreceptor such as CD28. We used cDNA microarrays to characterize the genomic expression program in human peripheral T cells responding to stimulation of these receptors. We found that CD28 agonists alone elicited few, but reproducible, changes in gene expression, whereas CD3 agonists elicited a multifaceted temporally choreographed gene expression program. The principal effect of simultaneous engagement of CD28 was to increase the amplitude of the CD3 transcriptional response. The induced genes whose expression was most enhanced by costimulation were significantly enriched for known targets of nuclear factor of activated T cells (NFAT) transcription factors. This enhancement was nearly abolished by blocking the nuclear translocation of NFATc by using the calcineurin inhibitor FK506. CD28 signaling promoted phosphorylation, and thus inactivation, of the NFAT nuclear export kinase glycogen synthase kinase-3 (GSK3), coincident with enhanced dephosphorylation of NFATc proteins. These results provide a detailed picture of the transcriptional program of T cell activation and suggest that enhancement of transcriptional activation by NFAT, through inhibition of its nuclear export, plays a key role in mediating the CD28 costimulatory signal. Spleen 1000 nostrils 156 164 onto a collagen 72 86 BUB-BnJ_male_hypothalamus 25 20 (Brain GSE5389 STHdhQ111/Q111-B 4 0 Colon 176 166 bone marrow umbilical cord_nobpd: 2E Whole blood 0 10 Salivary Gland 3 Normal of neuroblastic tumors 815 836 Standard affymetrix protocol Source GEO sample is GSM119721 Last updated (according to GEO): Jul 31 2007 Parkinson Disease 1000 of mouse brain 9 23 H104 CN B CS-B wt-rescued cell UVC-irradiated (12hour) replicate 3 U133B CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of M?, rhM?CSF was added at 1000 U/ml on the same days. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5145 Last updated (according to GEO): Sep 08 2006 Primary Carcinoma 876 M_U133A_63_DLPFC Tumor__Bladder_TCC_B_0002 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A MuscleRegen-ctx12d-1LLAv2-s2 80 68 Control blood Gene expression data from postmorten brain regions Source GEO sample is GSM144979 Last updated (according to GEO): Nov 20 2006 from cingulate cortex 18 38 Hippocampus 2004 2 month Old 1000 jejunum 727 721 spleens Total RNA was extracted from olfactory epithelium tissue from male C57Bl/6 mice (6 week old). Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol. Keywords = olfaction Keywords = neurogenesis Keywords = apoptosis Keywords = gene silencing Keywords = microarray, transcription factor Source GEO sample is GSM45676 Last updated (according to GEO): Oct 28 2005 Ld4 KM12 hgu95e AKR/J Hippocampus C Bicalutamide_3 brainstem 7 15 PAX sample 7 Wildtype saline, biological replicate 1 Richard Almon-28-1138200270321 Communicable Diseases 861 midbrain_1 heart failure 583 595 PriG_5%O2_Expt2_Day17_rep1 Normal Source GEO sample is GSM176046 Last updated (according to GEO): Apr 09 2007 H121 CN B Malignant Neoplasms 1000 861 Cerebral cortex Fibroblasts 38 48 Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM199480 Last updated (according to GEO): Jun 12 2007 Mesenchymal stem cells 13 34 31 20 Whole thymus Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68154 Last updated (according to GEO): Jul 07 2006 861 Occipital lobe Corpus Callosum 8 Normal 861 Cerebral cortex 3448 3430 entorhinal cortex 2 Neoplasm 861 1000 Endometrium H121 CB A Treated Source GEO sample is GSM176467 Last updated (according to GEO): Apr 09 2007 Keywords = Infectious diseases 1133 1163 from epididymal fat tissues 21 48 none Source GEO sample is GSM239935 Last updated (according to GEO): Dec 07 2007 861 Parkinsonian Disorders 10 7 Left "Sample 63, <5 yr survival(55 months) age 37 erp yes" on vantveer-oligo Macrophage smi110 the cytoskeleton 1283 1299 PP243_uninfected_DC 9 of prefrontal cortex 28 1000 Cardiomyopathies mouse brain 1049 1060 eye, retina: 2 Retina at ZT 12_e1_le1 2 hr vehicle repl 2 901 Prostatic hypertrophy 913 Acute leukemia Germ free Corpus 3 Plasma 861 Gene expression data from postmorten brain regions Source GEO sample is GSM144893 Last updated (according to GEO): Nov 20 2006 MOLF/EiJ_male_hypothalamus Infection 1113 1122 5 0 brain To screen for specific circadian outputs that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared to that found in the rat SCN in vivo and SCN2.2 cells in vitro. Similar to the scope of circadian gene expression in SCN2.2 cells and the rat SCN, NIH/3T3 fibroblasts exhibited circadian fluctuations in the expression of the core clock genes, Per2, Bmal1 (Mop3), and Cry1 and 323 functionally diverse transcripts (2.6%), many of which were involved in cell communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among cellular pathways mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase, the enzyme responsible for the production of nitric oxide, in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that this gaseous neurotransmitter may play a key role in SCN pacemaker function. Thus, this comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective identification of circadian signals involved in the coupling of SCN oscillators and the regulation of rhythmicity in downstream cells or tissues. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Sep 12 2006 Contributers: Nichole Neuendorff Gus J Menger David J Earnest Gregg C Allen Terry Thomas Sang Nahm Vincent M Cassone Kim Lu 861 Cerebral cortex 626 615 PCOS oocytes HCT-15_CL4015_Colon on Affymetrix GeneChip Human Full Length Array HuGeneFL Absence epilepsy 179 194 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3525.gif Source GEO sample is GSM93137 Last updated (according to GEO): Sep 22 2006 861 Muscle Replicate2_Voxel C3 Alternative pre-mRNA splicing increases proteomic diversity and provides a potential mechanism underlying both phenotypic diversity and susceptibility to genetic disorders in human populations. To investigate the variation in splicing among humans on a genomewide scale, we use a comprehensive exon-targeted microarray to examine alternative splicing in lymphoblasts derived from the CEPH HapMap population. We show the identification of transcripts containing annotated and novel sequence verified exon skipping, intron retention, and cryptic splice site usage that are specific between individuals. Using family-based linkage analysis, we demonstrate Mendelian inheritance and segregation of specific splice isoforms with regulatory haplotypes for three genes. Allelic association was further used to identify individual SNPs or regulatory haplotype blocks linked to the alternative splicing event, taking advantage of the high-resolution genotype information from the CEPH HapMap population. Last Updated (by provider): Aug 08 2007 Contributers: Jacek Majewski Tony Kwan This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195299 Last updated (according to GEO): Sep 13 2007 none Source GEO sample is GSM239894 Last updated (according to GEO): Dec 07 2007 Ovarian Diseases 877 1000 Heart failure Pool of 16 cochlear tissues at E11 Source GEO sample is GSM182573 Last updated (according to GEO): Aug 14 2007 Gene expression profile changes are commonly modulated across models and species after traumatic brain injury. Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3527.gif Source GEO sample is GSM93139 Last updated (according to GEO): Sep 22 2006 We studied the global genomic response in the hypothalamus during heat acclimation, with and without combined hypohydration stress. Rats were acclimated for 2 days or for 30 days at 34°C. Hypohydration (10% decrease in body weight) was attained by water deprivation. Functional analyses demonstrated a bi-phasic acclimatory profile with a transient upregulation of genes encoding ion channels, transporters, and transmitter signaling upon 2 days acclimation, suggesting enhanced neuronal excitability at that acclimation phase. Following long acclimation most genes returned to their pre-acclimation expression levels. In both acclimation phases, genes encoding hormones and neuropeptides, linked with metabolic rate and food intake, were downregulated. The response to hypohydration was characterized by an upregulation of a large number of genes primarily associated with the regulation of ion channels and cell-volume and neuronal excitability. During 2 days acclimation, the response was transiently desensitized, recovering upon LTHA. The results suggest that hypohydration overrides the heat acclimatory status. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Feb 28 2006 Contributers: Michal Horowitz Hagit Schwimmer Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 1871 left_liver_lobe Prediction of central nervous system embryonal tumour outcome based on gene expression. M_U133A_68_nAcc 430 414 cervical cancers NA Source GEO sample is GSM84325 Last updated (according to GEO): Dec 01 2005 Control Mouse 3 Accumbens P5 Normal 1000 Cerebral cortex Gene expression data from a placenta without malaria, but with histological evidence of a past infection Source GEO sample is GSM183622 Last updated (according to GEO): Apr 23 2007 leukemias correctly 701 719 1000 Spinal Cord Brain 1000 1000 Nervous system structure spinal cord 1530 1541 Spleen vs Leukotriene B4 (LTB4) Treated B cell We have used Affymetrix high-density gene arrays to generate a temporal profile of gene expression during differentiation of UB/OC-1, a conditionally immortal cell line derived from the mouse cochlea. Gene expression was assessed daily for 14 days under differentiating conditions. The experiment was replicated in two separate populations of cells. Profiles for selected genes were correlated with those obtained by RT-PCR, TaqMan analysis, immunoblotting, and immunofluorescence. The results suggest that UB/OC-1 is derived from a population of nonsensory epithelial cells in the greater epithelial ridge that have the potential to differentiate into a hair-cell-like phenotype, without the intervention of Math1. Elements of the Notch signaling cascade were identified, including the receptor Notch3, with a transient up-regulation that suggests a role in hair cell differentiation. Several genes showed a profile similar to Notch3, including the transcriptional co-repressor Groucho1. UB/OC-1 also expressed Me1, a putative partner of Math1 that may confer competence to differentiate into hair cells. Cluster analysis revealed expression profiles for neural guidance genes associated with Gata3. The temporal dimension of this analysis provides a powerful tool to study genetic mechanisms that underlie the conversion of nonsensory epithelial cells into hair cells. C57BL/6J Frontal Cortex B NHF10-hTERT_sham_6h_C3_21705 1000 Transverse adenoma 861 673 659 by decapitation Ptdsr-/- fibroblast_rep11 Nasal Epithelium 901 DRG006_b Nervous system structure 901 GBM Treatment, type=remove Source GEO sample is GSM99530 Last updated (according to GEO): Apr 21 2006 100336 272 254 with HCV infection JMR-RatInj30m-5aA-s2 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with 2-Methyl-thio-ATP for 30min Source GEO sample is GSM5422 Last updated (according to GEO): May 27 2005 Endometrium/Ovary 7 Disease CNS-SMTC_Ctr28d-1Cs2 back fibroblast 4 18 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132533 Last updated (according to GEO): Feb 26 2007 for bipolar disorder 53 72 V5-P522 of coronary artery disease 317 342 Craniocerebral Trauma 861 70 40 without coronary artery disease Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68332 Last updated (according to GEO): Jul 07 2006 Brain 861 brain 0 5 I_U133A_54_CB 5 0 brain 4 0 Colon Brain 861 Prostate 7 Disease none Source GEO sample is GSM244642 Last updated (according to GEO): Nov 23 2007 nasal epithelial cells 28 49 NCI60.34_LABEL38EXTRACT37SUB3 Source GEO sample is GSM134163 Last updated (according to GEO): Aug 06 2007 mouse brain 478 489 Blood 1000 Cerebral cortex 861 Stromal Neoplasm 901 1000 HIV Infections Macrophage smi78 Spleen vs Tumor necrosis factor-alpha Treated B cell 901 Kidney Diseases Examining the effects of tTA expression in mouse hearts Source GEO sample is GSM15069 Last updated (according to GEO): May 28 2005 1500mg/kg APAP 12Hr rat 4133 blood vs. PC 12Hr rat 4126 blood Carcinoma, Large Cell 884 0 Human Cortex 11 NA12750 growth 1, replicate 1 Gene Expression data from the suprachiasmatic nucleus of an animal euthanized 1.5 hours after lights off. Source GEO sample is GSM159293 Last updated (according to GEO): Oct 31 2007 Craniocerebral Trauma 861 Fibroblasts 1000 Normal Source GEO sample is GSM176349 Last updated (according to GEO): Apr 09 2007 Stomach [JunctionChip 5 of 5] HC55 CN B 953 939 in the amygdala Expression profiling of spinal cord section (T8) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31397 Last updated (according to GEO): May 27 2005 1000 Brain to certain neurodegenerative disorders 466 504 853 Refractory Carcinoma TEL-AML1-C50 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A CCRF-CEM hgu95c 861 Neoplasm To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18432 Last updated (according to GEO): May 27 2005 GSE837 Gene expression data from liver Source GEO sample is GSM243365 Last updated (according to GEO): Nov 16 2007 865 Disorder of artery 861 Cerebral cortex 660 mesenchymal stem cell 639 10 7 left Brain 861 testis 0 5 Liver 1000 5 0 brain 1000 Cerebral cortex AML cDNA hybridization-ID44-L processed in batch 5 Source GEO sample is GSM90409 Last updated (according to GEO): Mar 20 2006 Epithelium 865 vagina_3 of regenerating Dorsal Root Ganglia 21 55 CLL-71 brain 0 5 neurological disease control sample x053a Epithelium 861 NCI60.7_LABEL10EXTRACT9SUB3 Source GEO sample is GSM134025 Last updated (according to GEO): Aug 06 2007 plasma cells 332 344 of the intestinal tract 1784 1807 150 mg/kg X 24 hr Source GEO sample is GSM129860 Last updated (according to GEO): Sep 18 2007 861 HIV Infections Brain 861 Expression profiling of spinal cord section (T10) extracted from rats 28d following severe injury Source GEO sample is GSM31369 Last updated (according to GEO): May 27 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withTerbutaline for 60min Source GEO sample is GSM5782 Last updated (according to GEO): May 27 2005 (prosencephalon 707 721 22-oct-2002-liverF-Mu11KsubBsc 1000 Retina adenoma 861 Gap Junctions 1000 660 mesenchymal stem cell 639 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n039 Source GEO sample is GSM2021 Last updated (according to GEO): Nov 21 2005 NA12751 growth 3, replicate 2 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 9 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10958 Last updated (according to GEO): May 27 2005 Neoplasm 861 Sprague-Dawley Female HighSalt Cortex rat706 sd_cortexr_k_706c_020802 1000 Descending colon Liver (HBV+, HK13) Epithelium 861 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16603.gif Source GEO sample is GSM91489 Last updated (according to GEO): Sep 22 2006 Whole Brain 62 72 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226034 Last updated (according to GEO): Nov 02 2007 ISR14-Fv2E-PERK UT2, RNA from an Fv2E-PERK expressing mouse fibroblast cell line in an eIF2 alpha SS (wildtype), PERK-/- background. The PERK-/- background was used in order to obtain a cell line that expressed high levels of the Fv2E-PERK transgene. (We were unable to obtain clones with high levels of expression in wildtype cells.) The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10897 Last updated (according to GEO): May 28 2005 Plasma 861 P21 cochlear nuclei pooled from 5 pups for one replicate hybridization out of 2 replicates. Source GEO sample is GSM44855 Last updated (according to GEO): Jun 08 2005 Gene expression data from liver Source GEO sample is GSM243357 Last updated (according to GEO): Nov 16 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145577 Last updated (according to GEO): Nov 20 2006 Brain 861 861 Bladder Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92322 Last updated (according to GEO): Jan 13 2006 1000 Glioblastoma Parkinson Disease 1000 Liver Test (Blinded) Sample Source GEO sample is GSM130158 Last updated (according to GEO): Sep 18 2007 Normal Source GEO sample is GSM176409 Last updated (according to GEO): Apr 09 2007 Sample 116 on vantveer-oligo none Source GEO sample is GSM149552 Last updated (according to GEO): Jan 03 2007 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202668 Last updated (according to GEO): Jun 20 2007 "10h Thy-Noc, Exp4" temporal_lobe_2 Drug Dependence 1000 tourt-affy-human-131547 7 cerebral cortex 21 1000 Neuroblastoma Epithelium of bronchus 983 B6 16-2 WAT Infection 1000 Gene expression data from UET-13TR-EWS/FLI1 cells incubated in the presence of tetracycline for 24 hours Source GEO sample is GSM214921 Last updated (according to GEO): Aug 02 2007 5 0 brain /J mouse cingulate cortex 25 49 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153331 Last updated (according to GEO): Dec 27 2006 none Source GEO sample is GSM123235 Last updated (according to GEO): Jul 26 2006 none Source GEO sample is GSM149551 Last updated (according to GEO): Jan 03 2007 861 Brain heart 0 4 GSE9134 861 Stomach 861 Oocytes brain, Right Temporal Lobe: Extract78_le2 Gene expression data from skeletal muscle at baseline Source GEO sample is GSM230435 Last updated (according to GEO): Sep 19 2007 272 of the median eminence 251 Fibroblasts 861 with multiple myeloma 445 465 Infected 6 weeks prior with Htt-N171-82Q-expressing recombinant lentivirus Source GEO sample is GSM34382 Last updated (according to GEO): Oct 16 2006 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184687 Last updated (according to GEO): Apr 26 2007 Gene expression data from brain of adult rats Source GEO sample is GSM101003 Last updated (according to GEO): Feb 20 2007 CNS-SCsev_InjA4h-2A-s2 pfc_1052_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 1000 Integumentary system NB-C-TEST-1 on NHGRI-6.5k_b 913 Coronary heart disease Resting murine bulk splenocytes were lysed in Trizol and assessed for gene expression on Affy MOE430_2 microarray Source GEO sample is GSM188007 Last updated (according to GEO): May 09 2007 861 Blood 7 0 prostate CNS-SMTC_Mod14d-1A-s2 Serum 04 Tumor__Lung_Adeno_93_I_226 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A wild-type mouse forebrain Treatment, type=time_course, measurement=4.0 weeks Source GEO sample is GSM53352 Last updated (according to GEO): Jul 06 2005 1000 Mammary gland Gene expression data from postmorten brain regions Source GEO sample is GSM145837 Last updated (according to GEO): Nov 20 2006 Replicate2_Voxel C7 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153334 Last updated (according to GEO): Dec 27 2006 861 Blood V5-P249 db/db 8 wk 1 Plasma 861 Normal Source GEO sample is GSM176300 Last updated (according to GEO): Apr 09 2007 Sample 4 at Time 4 Source GEO sample is GSM113094 Last updated (according to GEO): Jun 06 2006 0 cortex 5 RNA1 Exp1 untreated This mouse is transgenic for dominant-negative forms of PI3k. dnPI3K transgenic animals have hearts that are 17% smaller than those of wild type littermates. These arrays were scanned at a PMT of 10%. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/pi3k_home.html Keywords = cardiac, pi3k, hypertrophy Source GEO sample is GSM8522 Last updated (according to GEO): May 27 2005 861 Asphyxia 861 Coxsackievirus Infections Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184800 Last updated (according to GEO): Apr 26 2007 Lymphoblastoid Cell Line for Individual 8136.3 log phase whole blood_101669 pituitary_gland_8 Source GEO sample is GSM80802 Last updated (according to GEO): Mar 31 2006 Parkinson's disease sample x015 0 30 with autism spectrum disorder 37 65 080301_HF_392Fl 41 minus the frontal cortex 65 Simple annotation: aging, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17369.gif Source GEO sample is GSM81568 Last updated (according to GEO): Sep 22 2006 901 Mammary gland Parkinson 0 8 The most common congenital cardiac abnormalities 50 97 mouse brain contralateral control, biological rep4 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15705 Last updated (according to GEO): May 28 2005 S1P3-KO-neocortex, biological rep3 (female) Epithelium 861 Wnt (48 h) A on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A Gene expression data from UET-13TR-EWS/FLI1 cells incubated in the presence of tetracycline for 72 hours Source GEO sample is GSM214923 Last updated (according to GEO): Aug 02 2007 4R 3 (Experiment 4R18h: Run 19869) Treatment, type=timepoint, description=Primary cortical neurons were treated for 18h with a new non competitive antagonist for nicotinic receptors (4R 2uM), and then the cells were harvested, measurement=18.0 h Source GEO sample is GSM96732 Last updated (according to GEO): Feb 14 2006 Cerebral cortex 901 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132509 Last updated (according to GEO): Feb 26 2007 PBMCs-Type 1 Diabetes-IDDM1_T1D_New no additional Source GEO sample is GSM199170 Last updated (according to GEO): Jun 08 2007 in amygdala 20 31 861 Cochlear structure BUB-BnJ_male_hypothalamus Source GEO sample is GSM138579 Last updated (according to GEO): Apr 18 2007 1000 Tonsil D_U133A_10_DLPFC Epithelium 861 plasma cells 332 344 Wild type inbred mice Source GEO sample is GSM82974 Last updated (according to GEO): Nov 10 2005 861 Retinitis gene expression of 1 day LIF differentiated ESCs Source GEO sample is GSM181944 Last updated (according to GEO): Apr 12 2007 accumbens rattus_norvegicus_strain iP animal_number 6 Epithelium 861 Pooled gastroc RNA samples from five 8 wk old male mdx5cv mice Source GEO sample is GSM13683 Last updated (according to GEO): May 28 2005 165 155 of retinal 1000 Liver damage 1000 Obesity from brain 21 30 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225937 Last updated (according to GEO): Nov 02 2007 67 52 descending colon Transitional epithelium 1000 194 164 from pancreas progenitor cells C57BL/6J Frontal Cortex D ventral spinal cord 13 31 Balb/c day 1, biological rep 1, tech rep 2 brain, hindbrain and spinal cord: N0 cDNA hrs nasal epithelium 1126 1146 280 269 to epilepsy Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211420 Last updated (according to GEO): Jul 18 2007 861 Muscle ko mouse number 1 Source GEO sample is GSM187136 Last updated (according to GEO): Jun 11 2007 stomach.3 722 708 from hippocampi human melanoma metastatic cell line A375 Source GEO sample is GSM155033 Last updated (according to GEO): Jun 04 2007 in bronchial epithelia 311 332 high-grade dysplastic liver tissue Source GEO sample is GSM155970 Last updated (according to GEO): Jun 21 2007 5 0 brain Lung Diseases, Obstructive 905 ipsi Cortex 7 17 861 Brain Metabotropic receptor 859 adult wild-type mouse littermate (c57bl) brain cortex Source GEO sample is GSM49563 Last updated (according to GEO): May 29 2005 Wildtype saline, biological replicate 3 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28759 Last updated (according to GEO): May 27 2005 Control total RNA was pooled from the kidney of five normal BALB/c mice. Total RNA was extracted from the kidney of BALB/c mice injected with anti-GBM antibody for 1 day. Source GEO sample is GSM15083 Last updated (according to GEO): May 28 2005 1000 frontal lobe Replicate1_Voxel B11 nic 5 (Experiment Neuroprotection4- Run 14985) Treatment, type=timepoint, description=primary cortical neurons were treated for 18 h with nicotine 10uM, agonist was then washed out and the cells were harvested 24h later, measurement=18.0 h Source GEO sample is GSM96729 Last updated (according to GEO): Feb 14 2006 Rosenfeld-5R01NS034934-14 2921 2913 28S rRNA of somatomotor cortex 21 41 DBA/2J SAL, Rep1 7 cortex 12 Nose 1000 Pancreas at e16.5, Chip A, rep 1 788 771 in the hippocampus N32__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Intense angiogenesis proliferation, a histopathological hallmark distinguishing malignant from benign astrocytoma, is vital for tumor progression. Thus, identifying and targeting specific pathways that promote malignant astrocytoma-induced angiogenesis could have substantial therapeutic benefit. Expression profiling of 13 childhood astrocytomas to determine the expression pattern of 133 angiogenesis-related genes revealed that 44 (33%) genes were differentially expressed (17 were overexpressed, and 27 were underexpressed) between malignant high-grade astrocytomas (HGAs) and benign low-grade astrocytomas. Hierarchical clustering and principal components analysis using only the 133 angiogenesis-related genes distinguished HGA from low-grade astrocytoma in 100% of the samples analyzed, as did unsupervised analyses using the entire set of 9198 expressed genes represented on the array, indicating that the angiogenesis-related genes were reliable markers of pathological grade. A striking new finding was significant overexpression of hypoxia-inducible transcription factor (HIF)-2alpha as well as high-level expression of FK506-binding protein (FKBP) 12 by HGA. Furthermore, 9 of 21 (43%) genes overexpressed by HGA were HIF/FKBP-associated genes. This group included the epidermal growth factor receptor (EGFR), which promotes HIF synthesis, as well as insulin-like growth factor-binding protein 2 (IGFBP2), a target gene of HIF activity. Differential protein expression of HIF-2alpha was validated in an independent group of 16 astrocytomas (P = 0.02). We conclude that the EGFR/FKBP12/HIF-2alpha pathway is important in childhood HGA and represents a potential new therapeutic target. BCR-ABL-#9 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Utricle structure 861 1000 Infection Hyperdip>50-C24 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A for liver 26 35 Uterus_Corpus Source GEO sample is GSM18857 Last updated (according to GEO): Sep 25 2006 brain 0 5 D_U133Plus_121_Amy 1000 Coronary Arteriosclerosis Whole blood from a healthy control Source GEO sample is GSM153423 Last updated (according to GEO): Jan 11 2007 f2#60 versus pool Mouse Brain tissue brain, hippocampus: CON-CA1-A8_e1_le1 136 131 Aortae human caudate nucleus Source GEO sample is GSM86853 Last updated (according to GEO): Feb 08 2006 S1P2-KO-hippocampus, biological rep7 (female) Heart Ventricle 1000 861 Brain Epithelium 861 none Source GEO sample is GSM123249 Last updated (according to GEO): Jul 26 2006 Mesenchymal Stem Cells 1000 Breast Carcinoma 1000 low-grade dysplastic liver tissue Source GEO sample is GSM155973 Last updated (according to GEO): Jun 21 2007 Neuron susceptibility to seizure-induced injury. Dingledine-5R01NS031373-10-2 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181214 Last updated (according to GEO): Jul 12 2007 liver_3 embryonic hearts 1064 1079 1636 1612 with systemic infections f2#197 versus pool Mouse Brain tissue Expression profiling of somatomotor cortex extracted from rats at 24h following moderate injury Source GEO sample is GSM41709 Last updated (according to GEO): May 27 2005 5 0 brain control wild-type prostate epithelial cell line maintained in RPMI-1640 medium supplemented with 5% fetal bovine serum Keywords = prostate Keywords = epithelial Source GEO sample is GSM14659 Last updated (according to GEO): May 28 2005 in seminoma 28 38 861 Cardiomyopathies the blood 393 402 Brain 1000 V5-P037 669 stem cells 660 amplified by Nugen kit Source GEO sample is GSM113692 Last updated (according to GEO): Jun 09 2006 16 0 Rats hypothalamus Gene expression data from postmorten brain regions Source GEO sample is GSM145485 Last updated (according to GEO): Nov 20 2006 861 HIV Infections Whole brain 0 10 DBA/2J periaqueductal gray rep2 (430 2.0 Array) of regenerating Dorsal Root Ganglia 21 55 R705P01282 Cochlear structure 1000 GSE8134 91 from the bone marrow 72 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28710 Last updated (according to GEO): May 27 2005 Patient4E O377 homozygotes brains Plasma 861 361 335 hypertrophic cardiomyopathy 1000 Mammary gland H9RGV00111004 1000 Encephalitis Fetal brains were obtained from 3 pregnant rats at pregnant day 17. Primary cortical neurons were isolated and pooled separately from each mother and plated onto 100mm ´ dishes, for a total of 4 plates from each pregnant rat. At Day in Vitro (DIV) 16, 3 of the 4 platesfrom the same mother, were exposed to either 1 or 3 MAC halothane (about 1% or 3%) or 3 MAC isoflurane (about 4%) in a gas tight chamber inside the culture incubator for 6 hr. The 4th plate from each mother treated with air were used (inside the same incubator, but outside the chamber) as controls. Isoflurane at 1 MAC was not conducted because of the complete lack of transcriptional response in the animals exposed to 1 MAC of isoflurane. The cells were recovered for an additional 6 hr, harvested, frozen by liquid nitrogen, and stored at ?80oC. Source GEO sample is GSM61806 Last updated (according to GEO): Oct 28 2005 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153435 Last updated (according to GEO): Jan 11 2007 Parkinson Disease 861 Expression profiling of spinal cord section (T9) extracted from rats 72h following laminectomy (sham) Source GEO sample is GSM31509 Last updated (according to GEO): May 27 2005 861 Cerebral cortex Disease Source GEO sample is GSM175806 Last updated (according to GEO): Apr 09 2007 5.0 mg/kg MeHg at 3.0h Y VIS D066 dorsal root ganglion Source GEO sample is GSM18611 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM176015 Last updated (according to GEO): Apr 09 2007 Pituitary Gland 861 1000 Retina 2N-5-MGU74A 150mg/kg APAP 12Hr rat 4128 blood vs. PC 12Hr rat 4126 blood 1000 Brain the brain 302 310 brain, forebrain: Sample8_e1_le1 Aortic Aneurysm, Abdominal 1000 Heart Septal Defects 884 Cell membrane 1000 The goal of these experiments was to identify the genes that are regulated by CCAT, a novel transcription factor derived from the C-terminus of CaV1.2. Neuro2A neuroblastoma cells were transfected with the last 503 AA of CaV1.2 which is full length CCAT (CCAT FL) or with the last 280 AA of CaV1.2, a form of CCAT that lacks the transcriptional activation domain (CCAT DTA). The mRNA from either CCAT FL or CCAT DTA expressing cells was hybridized to Agilent mouse genome microarrays along with mRNA from untransfected neuro2A cells. The microarray data was subsequently analyzed with the Rossetta Luminator gene expression data analysis system. Subsequent investigation revealed that CCAT DTA can still activate transcription albeit at much lower levels than CCAT FL. Source GEO sample is GSM95643 Last updated (according to GEO): Feb 07 2006 Expression profiling of somatomotor cortex extracted from rats at T0 naive Source GEO sample is GSM41675 Last updated (according to GEO): May 27 2005 853 Structure of blastomere 15 0 human cerebellum RNA characterization of tissue from the injury location (~T8) in an uninjured animal. From the Christopher Reeve Paralysis Foundation Research Consortium microarray study (www.crpf.org/microarray) Source GEO sample is GSM49938 Last updated (according to GEO): May 27 2005 Bladder sample 709-1 Squamous cell carcinoma 923 Prefrontal Cortex Source GEO sample is GSM105460 Last updated (according to GEO): Apr 17 2006 216 212 liver 1000 Brain Large-scale analysis of the mouse transcriptome. Cortex C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 257.91 Stdv: 8.90 Min: 241.50 Max: 274.99 Source GEO sample is GSM2967 Last updated (according to GEO): Mar 20 2006 Infection 1000 Male 75.1 yr after antibody enrichment scan 2 (U133A) Pool of 10 cochlear tissues at E13 Source GEO sample is GSM182581 Last updated (according to GEO): Aug 14 2007 861 Heart to psychosis 673 685 brain, hippocampus: P5 FAE 1_e1_le1 Normal__Cerebellum_Brain_Ncer_NCB1 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Liver 1000 Coronary Artery 5 Normal 1000 Brain To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18448 Last updated (according to GEO): May 27 2005 Suprachiasmatic Nucleus after 30-min Light pulse rep2 1000 Brain 901 frontal lobe Gene expression data from UET-13TR-EWS/FLI1 cells incubated in the absence of tetracycline for 24 hours Source GEO sample is GSM214918 Last updated (according to GEO): Aug 02 2007 Day 3 Mouse #33 - 3rd replicate Abnormal development 0 19 Brain_Wild-type_MiceNoLT346 983 Epithelial ovarian cancer Alzheimer's Disease 861 Mesenchymal Stem Cells 1000 none Source GEO sample is GSM244547 Last updated (according to GEO): Nov 23 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145646 Last updated (according to GEO): Nov 20 2006 Mel18 shRNA, biological rep3 1000 Cerebellum 901 Spinal Cord Gene expression data from embryos at day 1.5. Source GEO sample is GSM176483 Last updated (according to GEO): Mar 19 2007 901 Bone Marrow Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell 120min (set3) Voxel A2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1384 Last updated (according to GEO): Nov 21 2005 ALL B-cell44 on Affymetrix GeneChip Human Full Length Array HuGeneFL corticosterone_treated_rep8 (06SE465) Sensitized on days 0 and 3 with ragweed pollen protein and alum, challenged intratrecheally on days 10 and 17 with ragweed pollen protein and sacrificed after 24h. Lot batch = Source GEO sample is GSM1267 Last updated (according to GEO): May 28 2005 the blood 393 402 BC124B-AF 52 37 without malaria M-22-61-LI on UMich-10k wild type placebo 15d, biological rep1 no additional Source GEO sample is GSM199049 Last updated (according to GEO): Jun 08 2007 V5-P501 from progenitor satellite cells 36 66 42 30 Control blood Sample is skeletal muscle from a morbidly obese patient undergoing elective abdominal surgery Source GEO sample is GSM3982 Last updated (according to GEO): May 28 2005 none Source GEO sample is GSM239846 Last updated (according to GEO): Dec 07 2007 striatum 32 40 Hepatocyte 861 wild type placebo 48h, biological rep2 Stroke_short-term 911 posterior cingulate gyrus Spinal Cord Injuries 884 0 Human Cortex 11 Gene expression data from postmorten brain regions Source GEO sample is GSM145432 Last updated (according to GEO): Nov 20 2006 Skeletal bone 861 of regenerating Dorsal Root Ganglia 21 55 Amygdaloid structure 1000 AML57 on Affymetrix GeneChip Human Full Length Array HuGeneFL Transforming growth factor beta-1 (TGFbeta) is a tumor suppressor during the initial stage of tumorigenesis, but it can switch to a tumor promoter during neoplastic progression. Ionizing radiation (IR), both a carcinogen and a therapeutic agent, induces TGFbeta activation in vivo. We now show that IR sensitizes human mammary epithelial cells (HMEC) to undergo TGFbeta-mediated epithelial to mesenchymal transition (EMT). Non-malignant HMEC (MCF10A, HMT3522 S1 and 184v) were irradiated with 2 Gy shortly after attachment in monolayer culture, or treated with a low concentration of TGFbeta (0.4 ng/ml), or double-treated. All double-treated (IR+TGFbeta) HMEC underwent a morphological shift from cuboidal to spindle-shaped. This phenotype was accompanied by decreased expression of epithelial markers E-cadherin, beta-catenin and ZO-1, remodeling of the actin cytoskeleton, and increased expression of mesenchymal markers N-cadherin, fibronectin and vimentin. Furthermore, double-treatment increased cell motility, promoted invasion and disrupted acinar morphogenesis of cells subsequently plated in Matrigel. Neither radiation nor TGFbeta alone elicited EMT, even though IR increased chronic TGFbeta signaling and activity. Gene expression profiling revealed that double treated cells exhibit a specific 10-gene signature associated with Erk/MAPK signaling. We hypothesized that IR-induced MAPK activation primes non-malignant HMEC to undergo TGFbeta-mediated EMT. Consistent with this, Erk phosphorylation were transiently induced by irradiation, persisted in irradiated cells treated with TGFbeta, and treatment with U0126, a Mek inhibitor, blocked the EMT phenotype. Together, these data demonstrate that the interactions between radiation-induced signaling pathways elicit heritable phenotypes that could contribute to neoplastic progression. Last Updated (by provider): Jun 25 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Bombesin for 30min Source GEO sample is GSM5474 Last updated (according to GEO): May 27 2005 Primary Neoplasm 1000 Spleen vs BLC Treated B cell 1000 Spleen Primary large cell lung carcinoma 525 Source GEO sample is GSM18306 Last updated (according to GEO): May 27 2005 Brain 861 S7_Muscle_Baseline_0min Medulla 861 CAD_replicate11 Autistic Disorder 877 3x3 pooling strategy. See Nadler et al, 2006 Source GEO sample is GSM114537 Last updated (according to GEO): Jun 16 2006 brain, frontal cortex: Sham AM LC b_e1_le1 HS 578T hgu95a gut neurospheres 243 258 Gene expression data from postmorten brain regions Source GEO sample is GSM145634 Last updated (according to GEO): Nov 20 2006 processed in batch 3 Source GEO sample is GSM90436 Last updated (according to GEO): Mar 20 2006 Untreated versus treated (bortezomib), untranformed MCF10A and Transformed (see Adler et al, Nature Gen. 2006) Source GEO sample is GSM120222 Last updated (according to GEO): Jul 20 2006 1000 Heart failure 792 785 amygdala 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201288 Last updated (according to GEO): Jun 14 2007 none Source GEO sample is GSM244614 Last updated (according to GEO): Nov 23 2007 Untreated LNCaP cells not stimulated with DHT, biological replicate 2 Source GEO sample is GSM187370 Last updated (according to GEO): May 04 2007 KT89_AR2 861 Cerebral cortex Lymphoblastoid Cell Line for Individual 8207.4 log phase f2#21 versus pool Mouse Brain tissue VDXKIU_15E2 Multiple Sclerosis 1000 Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 5999 left_liver_lobe 913 Coronary heart disease NA12744 growth 1 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153455 Last updated (according to GEO): Jan 11 2007 no additional Source GEO sample is GSM199360 Last updated (according to GEO): Jun 08 2007 C3H/HeJ hippocampus rep1 in the mammalian nervous system 110 141 E8.0b_rep2 MGJZ030212025Bprostate brain 0 5 1278 endothelial cells 1294 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195339 Last updated (according to GEO): Jun 04 2007 adenoma 861 Brain 861 5 0 Spleen 5 0 brain CNS-SCsev_InjB28d-2A-s2 NCI60.5_LABEL8EXTRACT7SUB3 Source GEO sample is GSM134017 Last updated (according to GEO): Aug 06 2007 Gene expression data from epididymal fat tissues. Source GEO sample is GSM215578 Last updated (according to GEO): Aug 07 2007 Spleen vs fMLP Treated B cell 30min (set2) Brain 1000 335 329 medulla Nasal Epithelium Inhalation Formaldehyde 2ppm 5d ID216 rad001 9d, biological rep1 901 Coronary artery Wild type olfactory epithelium 2 hpO replicate1 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 2 - Pair 5 - LMN Source GEO sample is GSM49894 Last updated (according to GEO): Dec 20 2005 from SVGR2 glial cells 21 43 Activity-dependent changes in synapses rely on functional changes in resident proteins and on gene expression. We addressed the relationship between synapse activity and the expression of synaptic genes by comparing RNA levels in the neocortex of normal mice versus synaptically silent munc18-1 null mutants, using microarray expression analysis, quantitative PCR and Northern blotting. We hypothesized that genes under control of synaptic activity are differentially expressed between mutants and controls and found that few synaptic signaling genes were differentially expressed. However, all neuropeptide genes with detectable expression on the microarray were differentially expressed, being 3-20 fold higher in control cortex. Genes encoding their receptors and most other synaptic components were not differentially expressed. Differential expression of the neuropeptide genes was confirmed by qPCR analysis. In situ hybridization indicated that the difference in neuropeptide expression was uniform and not due to the loss of specific cells in the mutant. In primary sensory neurons, which do not depend on synaptic activity for their input, the differential expression of neuropeptides was not observed. These data reveal no simple relation between activity of synapses and expression of their resident proteins, but instead identified a unique feature of neuropeptide gene expression, which appears to depend on synaptic activity. Last Updated (by provider): Aug 01 2006 Contributers: Betty Wächtler Bauke Ylstra Sabine Spijker Matthijs Verhage Desirée Schut Jildau Bouwman August B Smit GSE5658 Tonsil GC Centroblasts Primary tumor 19 32 CNS-RM_CtrT0-2A-s2 Prostate 861 Brain 1000 1000 Coronary Arteriosclerosis Brown Fat 1000 Gene expression data from liver Source GEO sample is GSM243383 Last updated (according to GEO): Nov 16 2007 NA18949 HC72 CB A Absence Epilepsy 1000 7 0 prostate brain, forebrain: Sample6_e1_le1 Expression profiling of moderately injured raphe at 14d in rats Source GEO sample is GSM41566 Last updated (according to GEO): May 27 2005 1000 Kidney Epithelial Cells 901 in seminoma 28 38 719 708 with gliomas Normal Source GEO sample is GSM176080 Last updated (according to GEO): Apr 09 2007 Gene expression from Dendritic cells from human subject with resolver phenotype infected with H. ducreyi. Source GEO sample is GSM128970 Last updated (according to GEO): Sep 13 2007 861 Cerebral cortex Cochlea_D257A_9mo_4 RST-PVH3_1 Coronary heart disease 913 Cerebellum_nontransgenic control S46_3.5 months_replicate 3 Seminoma 1000 placenta-0540-inflamed-past-rep1 in urine 476 484 liver, PPARa-null mice, treatment with WY14643 for 5d Source GEO sample is GSM205789 Last updated (according to GEO): Jul 24 2007 M_U133Plus_119_DLPFC none Source GEO sample is GSM149548 Last updated (according to GEO): Jan 03 2007 93 58 in laminin-rich extracellular matrix Cerebral cortex 1000 tumor.4 1000 Prostate f2#31 versus pool Mouse Brain tissue 1000 Lens, Crystalline WGACON-58 Fibroblasts 861 Epithelial Cells 1000 Heart Atrium 1000 Blood 1000 Collagen 1000 901 Heart Diseases osteoblast 627 637 This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques P. Tremblay (jacques-p.tremblay@crchul.ulaval.ca; 2705 boulevard Laurier) for analysis. Stembase Experiment ID: E205 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205 SCGP Sample ID: S269 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205#SAMPLE_246 Short description: Adult mouse muscle was enzymatically dissociated. Muscle derived stem cells proliferate unattached, in spheres, in the proliferation medium. Analysis requested: mouse genechips RNA concentration: 0.336ug/uL Sample volume: 14uL total Source GEO sample is GSM93604 Last updated (according to GEO): Jan 23 2006 Gene expression data Source GEO sample is GSM230357 Last updated (according to GEO): Sep 19 2007 seminoma specimen, pT2, patient age: 40y; W03 025 Tumor__Lung_Adeno_LT14 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A DRG002_c Brain 1000 BTBR T+ tf/tf Cerebellum C 84 FC BA9 A 7 0 Pancreas Gene expression data from postmorten brain regions Source GEO sample is GSM145458 Last updated (according to GEO): Nov 20 2006 40 21 from skeletal muscle 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14950 Last updated (according to GEO): Oct 28 2005 1500 mg/kg X 24 hr Source GEO sample is GSM129864 Last updated (according to GEO): Sep 18 2007 from ventral prostate 21 41 M_U133A_97_nAcc MGJZ030212072Bsubstantianigra 861 Colon Whole Brain 73 83 VIIIcSC_Signal on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B Primary Neoplasm 1000 Transplant Series 32 , Transplant # 3 GSE8507 ventral_tegmental_area_5 Source GEO sample is GSM80892 Last updated (according to GEO): Mar 31 2006 BCR-ABL-#3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 27 0 cerebral cortex sprague 3916 1000 Pancreas CNS-SpinalCsev-Adult-4h-1A-s2 861 Heart Expression profiling of laminectomized raphe at 4h in rats Source GEO sample is GSM41542 Last updated (according to GEO): May 27 2005 40 21 from skeletal muscle pfc_1040_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181066 Last updated (according to GEO): Jul 12 2007 Skeletal bone 861 stomach.1 1000 Brain VDXKIU_2743 of somatomotor cortex 21 41 Gene expression data from postmorten brain regions Source GEO sample is GSM145072 Last updated (according to GEO): Nov 20 2006 1000 Brain Normal Source GEO sample is GSM176037 Last updated (according to GEO): Apr 09 2007 adLacZ6 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P10, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3187 Last updated (according to GEO): May 28 2005 NA Source GEO sample is GSM7621 Last updated (according to GEO): May 28 2005 Expression profile of genes in mouse brain Source GEO sample is GSM21043 Last updated (according to GEO): May 27 2005 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15393.gif Source GEO sample is GSM84171 Last updated (according to GEO): Sep 22 2006 myocardial infarction 383 403 1000 medulloblastoma 901 frontal lobe osteoblast 630 640 858 Prostatic Neoplasms Heart 861 9 0 Blood Test A/OVX/P4/3h/UTX 129/SvImJ WT normal liver tissue Source GEO sample is GSM155964 Last updated (according to GEO): Jun 21 2007 Parkinson Disease 1000 3 hrs Pre-clamp sample 5 Starvation 916 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68297 Last updated (according to GEO): Jul 07 2006 V5-P385 Cerebral cortex 861 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134609 Last updated (according to GEO): Jul 09 2007 of the developing cortex 20 44 Blood 1000 1000 Left CAD_replicate80 Mesenchymal Stem Cells 1000 NCI/ADR-RES hgu95c 901 Caudate nucleus structure 660 mesenchymal stem cell 639 Lymphatic Metastasis 877 861 Patau's syndrome NOS of somatomotor cortex 21 41 17 7 hippocampus C57BL/6J Chronic morphine treated, striatum, biological replicate 3 Source GEO sample is GSM187982 Last updated (according to GEO): Jun 14 2007 SK-MEL-2_CL10005_Melanoma on Affymetrix GeneChip Human Full Length Array HuGeneFL 5 0 brain 861 Brain DLBC30 on Affymetrix GeneChip Human Full Length Array HuGeneFL Liver 1000 to the nose 599 609 1000 jejunum Transcriptome analysis of Ts1Cje (mouse model of Down syndrome) and euploids murine cerebellum during postnatal development. Date GSE1611 Last Updated: Mar 27 2006 Contributers: Randal Moldrich Isabelle Rivals Pierre-Marie Sinet Stylianos E Antonarakis Robert Lyle Geoffroy Golfier Luce Dauphinot Laurence Ettwiller Kiyoko Toyama Charles J Epstein Léon Personnaz Maire-Claude Potier Minh Tran Dang Jean Rossier Includes GDS994. Update date: Jan 11 2005. Dataset description GDS994: Expression profiling of brain cerebella from Ts1Cje males at postnatal days 0, 15, and 30. RNA pooled from 3 males at each developmental stage. Results provide insight into the molecular changes contributing to the pathogenesis of Down syndrome.. Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11231.gif Source GEO sample is GSM76413 Last updated (according to GEO): Sep 22 2006 Parkinson's model voxel B4 from a primary branch 21 41 Aortic Aneurysm 901 Morula replication 2 in the mammalian nervous system 110 141 B6Cerebellum(2)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B 1000 Cerebral cortex Gene expression data from older male during 1 week of inadequate protein intake Source GEO sample is GSM209812 Last updated (according to GEO): Jul 11 2007 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201267 Last updated (according to GEO): Jun 14 2007 Testis 1000 Parkinson Disease 1000 5 0 brain Brain 1000 cirrhotic liver tissue Source GEO sample is GSM155967 Last updated (according to GEO): Jun 21 2007 117 112 Lipids 1000 Colon ER+/LN+/Marks205 on Affymetrix GeneChip Human Full Length Array HuGeneFL total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL10 for 120min Source GEO sample is GSM5645 Last updated (according to GEO): May 27 2005 Cerebral cortex 1000 cecum 17 21 607 597 the rectum MuscleRegen-ctx4.5d-2RLAv2-s2 861 Neoplasm Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 14 hours after lights on. Original RNA code = LC30A. Source GEO sample is GSM227374 Last updated (according to GEO): Sep 10 2007 5 0 brain Parkinson's disease sample x020a The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160203 Last updated (according to GEO): Feb 08 2007 Plasma 861 0 Human Cortex 11 high-grade dysplastic liver tissue Source GEO sample is GSM155930 Last updated (according to GEO): Jun 21 2007 AML 50 0 5 Nasal Epithelium 901 Left 1000 1500 mg/kg X 24 hr Source GEO sample is GSM129848 Last updated (according to GEO): Sep 18 2007 G9a-delta 48 44 Lungs Coronary heart disease 913 Malignant Neoplasms 861 1000 Tibialis anterior muscle structure MCF7 human breast cancer cells treated with DMSO and used as a control in a 2 platform, three replicate experiment Source GEO sample is GSM188012 Last updated (according to GEO): May 11 2007 Date : 3/29/2002 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 4.5 hrs post-injection Intervention : 4.0 mg/kg PK11195 co-administered Risk: anticipated remediation to <10% malformations Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots Keywords = methylmercury Keywords = PK11195 Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = SC862 Source GEO sample is GSM12262 Last updated (according to GEO): May 28 2005 Cx43 KO cortical astrocytes 4 GBM Treatment, type=remove Source GEO sample is GSM99576 Last updated (according to GEO): Apr 21 2006 Lymphoblastoid Cell Line for Individual 8096.4 log phase from intraabdominal adipose tissue 25 58 osteoblast 627 637 1000 Skeletal muscle structure Gene expression data from mouse primary visual cortex Source GEO sample is GSM101719 Last updated (according to GEO): Jun 15 2006 Liver 1000 Dorsal Root Ganglia 3 Normal CNS-SCsev_InjA4h-3B-s2 117 112 Lipids 863 836 of severe autoimmune disease The sample is a part of a series describing gene expression changes during postnatal development of the small intestine Source GEO sample is GSM198939 Last updated (according to GEO): Jun 11 2007 NucAccumbs_0226AFBR_005.txt 67 40 with coronary artery disease Expression data from mouse primary visual cortex under different deprivation conditions Mammary gland 861 861 Fibroblasts Blood Test (Blinded) Sample Source GEO sample is GSM130003 Last updated (according to GEO): Sep 18 2007 NA Source GEO sample is GSM109471 Last updated (according to GEO): May 22 2006 SN12h(3) onto a collagen 72 86 901 Temporal Lobe of cerebellum 86 98 intermediolateral column motoneurons (IML) 5 S462_Infect_1 Kidney OC-3B The epithelial cells 962 981 786 767 of the Basal Ganglia Neuraxis 1000 Gene expression data from the neocortex of wild-type mouse Source GEO sample is GSM172930 Last updated (according to GEO): Mar 08 2007 Gene expression data from whole brain infected mouse, day 1 Source GEO sample is GSM189642 Last updated (according to GEO): May 16 2007 861 Eye mouse brain 478 489 861 Adipose tissue Macrophage 14smi016 Blood 861 HapMap YRI_parent Male Source GEO sample is GSM159690 Last updated (according to GEO): Feb 01 2007 PBMCs-Healthy-H166_Healthy 5 0 brain Communicable Diseases 901 Gene expression data from brain of adult rats Source GEO sample is GSM101000 Last updated (according to GEO): Feb 20 2007 of regenerating Dorsal Root Ganglia 21 55 Disease Source GEO sample is GSM176105 Last updated (according to GEO): Apr 09 2007 Key stages in mammary gland development. 21 6 (corpus callosum 2500 mg/kg X 12 hr Source GEO sample is GSM129883 Last updated (according to GEO): Sep 18 2007 Endoplasmic Reticulum 1000 I_U133A_32_Amy Epithelial Cells 1000 M7TW00121465 Wild-type-hippocampus, biological rep3 (male) PBMCs-Healthy-H28_Healthy 78 66 Control blood 91 from the bone marrow 72 C57BL-6J were given intratracheal bleomycin (1.5U per kg). Lungs were harvested and frozen at 14d. Lot batch = Source GEO sample is GSM4159 Last updated (according to GEO): May 28 2005 Brain_MD_51_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL Lymphoblastoid Cell Line for Individual 8005.4 log phase Transitional epithelium 1000 within a complex organ 963 984 small intestine PPARa knockout mice, fasted for 24 hours Source GEO sample is GSM154798 Last updated (according to GEO): Jul 04 2007 7 0 prostate Glial Fibrillary Acidic Protein 1000 Brain 861 Gene expression data from aldosterone-producing adenoma Source GEO sample is GSM211457 Last updated (according to GEO): Jul 18 2007 Brain 861 Myocardium 861 heart 1169 1173 62 50 Trachea C57BL Brain 1000 901 Coronary artery Smooth Muscle Tissue 1000 Colon 1000 15 0 human cerebellum 861 Ataxia 861 Colon 1000 Pilocytic Astrocytoma NA19159 Wild type P104 mouse visual cortex contralateral to monocular enucleation Source GEO sample is GSM97224 Last updated (according to GEO): Feb 17 2006 ADH131 on harvard-12k of parieto-occipital cortex 120 146 RNA6 Exp2 AzaC treated Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5715.gif Source GEO sample is GSM76416 Last updated (according to GEO): Sep 22 2006 parietal_lobe_5 Source GEO sample is GSM80752 Last updated (according to GEO): Mar 31 2006 117T 1000 Cerebral cortex Lymphoblastoid Cell Line for Individual 8159.3 log phase Gene expression data from brain of adult rats Source GEO sample is GSM101027 Last updated (according to GEO): Feb 20 2007 Mental Retardation 1000 spinal cord 0 11 19 0 Kainate-hippocampus Endometrium 1000 Heart 861 Olfactory Epithelium 1000 Brain 1000 901 frontal lobe brain, caudate nucleus Source GEO sample is GSM18919 Last updated (according to GEO): Sep 25 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145129 Last updated (according to GEO): Nov 20 2006 861 Adipose tissue the ventricular 1095 1109 hTERT, bone marrow cell cy3:SHR treated w/ nifedipine, biological rep 1g; cy5:pool of 6 WKY control rats 12 4 of Kidney GSE1392 861 Neuroepithelium 861 Myopathy 408_1 stria terminalis 901 Lymphoblastoid Cell Line for Individual 8066.3 log phase I_U133A_26_CB hindbrain 7 15 Colonic mucous membrane 913 brain_DLPFC_bipolar B_mr420 Prefrontal Cortex Source GEO sample is GSM105463 Last updated (according to GEO): Apr 17 2006 1000 frontal lobe Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160723 Last updated (according to GEO): Sep 24 2007 with some respiratory epithelium. 1039 1072 212 191 with coxsackievirus B3 Utricle structure 861 0 prefrontal cortex 16 stria terminalis 901 from brain 21 30 Expression profiling of K14-DN-Clim mouse backskin 861 Glioma ES cell control, RNA 298 at the Human Brain 724 741 High Freezing Source GEO sample is GSM92430 Last updated (according to GEO): Jan 13 2006 0029_1435_H95A2_T97-0075_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 13 0 Brain Amygdala CAD_replicate58 with autism spectrum disorder 37 65 starved 143 149 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151991 Last updated (according to GEO): Feb 06 2007 21 0 3AJZ02021911_ PROSTATE Changes in mouse liver mRNA profiles following intraperitoneal cytokine injection. One of 2 replicates of albumin-cre(-) Socs3(w/fl) mice, injected with interleukin-6, and killed after 4h. Source GEO sample is GSM5959 Last updated (according to GEO): May 27 2005 Standard affymetrix protocol Source GEO sample is GSM119499 Last updated (according to GEO): Jul 31 2007 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162188 Last updated (according to GEO): Jun 12 2007 Kidney 1000 placenta-0475-uninflamed-past-rep1 16 7 cerebellum from nose 100 108 Brain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145555 Last updated (according to GEO): Nov 20 2006 The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76945 Last updated (according to GEO): Oct 11 2005 Cerebral cortex 1000 1000 Lung 79 CB B Epithelium 861 D_U133Plus_77_nAcc Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection). Source GEO sample is GSM36431 Last updated (according to GEO): May 27 2005 Affymetrix RGU34A 12HA Gene expression data from postmorten brain regions Source GEO sample is GSM146051 Last updated (according to GEO): Nov 20 2006 Anterior nares 1000 747 tumor cells 757 Job's patient Source GEO sample is GSM211022 Last updated (according to GEO): Sep 10 2007 1000 Cerebellum FormerSmoker 107 861 Eminence Cytoprotection by pre-emptive conditional phosphorylation of translation initiation factor 2. of somatomotor cortex 21 41 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc85 Source GEO sample is GSM1847 Last updated (according to GEO): Nov 21 2005 Brain Amygdala Source GEO sample is GSM18768 Last updated (according to GEO): Sep 25 2006 861 Cardiomyopathies DCIS44 on harvard-12k Diaphragm-skeletal muscle, left hemi-diaphragm: synaptic region_e1_le1 2888 2871 lipid peroxidation such as the cochlea 874 893 This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis. Stembase Experiment ID: E189 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189 SCGP Sample ID: S232 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_190 Short description: RNA isolated from first passage retinal sphere cells. Estimated purity: > 90% RNA concentration: > 0.15ug/ul Num cells for RNA prep: ~1.7x10e6 Sample volume: 10.0 ul Source GEO sample is GSM87198 Last updated (according to GEO): Jan 19 2006 Primary tumor 19 32 adenoma 861 from the right forebrain 21 44 45 year old male Nasal Epithelium 901 Extraocular muscle, comparison of wild type and mdx mice, 14 to 112 Days (Porter lab) Parkinson Disease 861 Acetaminophen 3hr Rat 7558 blood vs. Acetaminophen 3hr Rat Pooled Control blood Nodose Nucleus 4 Normal 90 81 in stroke of regenerating Dorsal Root Ganglia 21 55 Gene expression data from male mice. Source GEO sample is GSM115531 Last updated (according to GEO): Jun 13 2007 M7TW00121466 861 Blood 2500 mg/kg X 24 hr Source GEO sample is GSM129857 Last updated (according to GEO): Sep 18 2007 from axons 1298 1308 19 0 Head and neck cancer Pituitary Gland 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145027 Last updated (according to GEO): Nov 20 2006 Gene expression data from brain of adult rats Source GEO sample is GSM101019 Last updated (according to GEO): Feb 20 2007 brain, Left Parietal Lobe: Extract39_le1 Fibroblasts 1000 Nasal Epithelium 901 1000 Kidney We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201777 Last updated (according to GEO): Jun 20 2007 660 mesenchymal stem cell 639 D2_Control_ZT 0_3 Parkinson's disease sample x015 0 Human Cortex 11 32h-Control replication 1 M_95Av2_3076_DLPFC_1_GS Medulla Oblongata 861 20 0 human caudate nucleus Macrophage smi125 Investigation into murine dermal burn wound. Mouse thermal injury induced, and skin excised at different times post-injury. Source GEO sample is GSM7480 Last updated (according to GEO): May 27 2005 861 anatomic valve Osteoblasts 1000 Parkinson Disease 1000 NA07357 Tacrine 2.7mg/kg/day from 5 weeks Moclobemide 10mg/kg/day Creatine 1%w/v added to wet mash Lot batch = 5270 Source GEO sample is GSM13364 Last updated (according to GEO): May 28 2005 1000 Brain Epithelial Cells 1000 ovary_9 AJ 1-2-1 Testes SPRET/EiJ_male_hypothalamus To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132975 Last updated (according to GEO): Sep 12 2006 brain, cerebral cortex: Rat_03-49_NroLep_Lipska_e1_le1 01_0026_SepticShock_Day3_113 Leg 7 Day Control rep 3 To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18444 Last updated (according to GEO): May 27 2005 The epithelial cells 962 981 Normal Source GEO sample is GSM176424 Last updated (according to GEO): Apr 09 2007 TUMOR 6 0 6 1000 Left Brain 1000 Tissue Source GEO sample is GSM67227 Last updated (according to GEO): Jan 19 2006 Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Source GEO sample is GSM15960 Last updated (according to GEO): May 28 2005 Plasma 861 CerebellumPeduncles Source GEO sample is GSM18756 Last updated (according to GEO): Sep 25 2006 10 Bone marrow 0 from the femurs 95 109 ipsi Cortex 7 17 7 cortex 12 284 272 of the tumor 120 FC BA9 B none Source GEO sample is GSM244536 Last updated (according to GEO): Nov 23 2007 Liver 0 4 f2#219 versus pool Mouse Brain tissue Follicular thyroid carcinoma 1000 Osteoblasts 1000 Cerebral cortex 1000 Thyroid [JunctionChip 5 of 5] 861 Occipital lobe 861 Cerebellum no additional Source GEO sample is GSM199282 Last updated (according to GEO): Jun 08 2007 333 323 hippocampus cerebellum_7 Source GEO sample is GSM80636 Last updated (according to GEO): Mar 31 2006 Myocardial Infarction 1000 Cerebellum 1830 1839 Fluid-percussion head injury 83 110 total RNA from biosource CC#1 Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92461 Last updated (according to GEO): Jan 13 2006 mammary epithelial cells transduced with BABE empty vector Source GEO sample is GSM5173 Last updated (according to GEO): May 27 2005 Blood Test (Blinded) Sample Source GEO sample is GSM129960 Last updated (according to GEO): Sep 18 2007 1000 Brain C57BL-6J were given intratracheal bleomycin (1.5U per kg). Lungs were harvested and frozen at 72h. Lot batch = Source GEO sample is GSM4164 Last updated (according to GEO): May 28 2005 1000 Brain hippocampus rattus_norvegicus_strain iNP animal_number 8 901 Coronary artery ScN2a_4 Plasma 861 148 137 optic nerve Arteries 861 AD-336t1-A223-8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Bladder sample 747-7 Cell Culture: Hippocampal cells from E18 rat embryos were plated at a density of 500,000 cells per 60 mm poly-L-lysine (1mg/ml; Sigma) coated dish. Cultures were maintained at 37 C in 5% CO2 humidified incubator and used for experiments at 21 day in vitro (DIV). Control and experimental group cultures were incubated with 10 micro M TTX for 15 min followed by addition of 100 micro M baclofen or vehicle. Total RNA preparation: Each experimental group was compared as replicates of three. For each replicate cultured hippocampal neurones were harvested after 2 hours incubation +/- baclofen and total RNA was isolated using RNeasy Mini kit (Qiagen, UK) according to the manufacturer's protocol. Microarray Target Labelling and Hybridisation: Targets for cDNA microarrays were generated using 5 micro g of total RNA in a standard reverse transcription (RT) reaction. RNA was annealed, in 16 micro l water, with 1 micro g of 24-mer poly(dT) primer (Invitrogen, UK), by heating at 65oC for 10 min and cooling on ice for 2 min. The RT reaction was performed by adding 8 micro l of 5X first strand RT buffer (Life technologies, MD), 4 micro l of 20mM dNTPs minus dCTP (Pharmacia, UK), 4 micro l of 0.1M DTT, 40U of RNAse OUT (Life Technologies, MD), 6 micro l of 3000 Ci/mmol 33P-dCTP (ICN Biomedicals, UK) to the RNA/primer mixture to a final volume of 40 micro l. Two micro l (400 U) of Superscript II reverse transcriptase (Life Technologies, MD) was then added and the sample incubated for 30 min at 42oC followed by additional 2 micro l of Superscript II reverse transcriptase and another 30 min incubation. The reaction was stopped by addition of 5 micro l 0.5 M EDTA. Samples were incubated at 65oC for 30 min after addition of 10 micro l of 0.1M NaOH to hydrolyse and remove RNA. Samples were pH neutralized with 45 micro l 0.5M Tris, pH 8.0 and purified using Bio-Rad 6 purification columns (BioRad, UK). The NIA NeuroArray consists of 1152 cDNAs printed on nylon membrane in duplicate. The arrays were hybridised with alpha-33P-dCTP labelled cDNA probes overnight at 50oC in 4ml of hybridisation solution. Hybridised arrays were rinsed in 50ml of 2XSSC and 1%SDS twice at 55oC followed by two washes in 2X SSC and 1% SDS at 55oC for 15 min each. The microarrays were exposed to phosphorimager screens for 1-3 days. The screens were then scanned with Molecular Dynamics STORM PhosphorImager (Sunnyvale, CA) at 25 micro m resolution. Source GEO sample is GSM28446 Last updated (according to GEO): May 27 2005 Skeletal bone 861 The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76961 Last updated (according to GEO): Oct 11 2005 none Source GEO sample is GSM244604 Last updated (according to GEO): Nov 23 2007 1037 of transitional epithelium 1012 corpus_callosum_1 Source GEO sample is GSM80620 Last updated (according to GEO): Mar 31 2006 17 7 hippocampus DCIS45 on harvard-12k 1000 Kidney Adenocarcinoma 861 V5-P588 Cerebral cortex 1000 HC65 CB A Expression profiling of spinal cord section (T9) extracted from rats 14d following mild injury Source GEO sample is GSM31196 Last updated (according to GEO): May 27 2005 in the mammalian nervous system 110 141 pooled RNA of the kidney of 36 day old rats Source GEO sample is GSM86654 Last updated (according to GEO): Jun 12 2006 Carcinoma, Large Cell 888 CNS-SpinalCmod-Adult-7d-3A-s2 Oral Mucosa 3 Normal 861 Cerebral cortex NCR-EW3 861 Lens, Crystalline cerebellum 7 16 Chronic Lymphocytic Leukemia 19 47 Primary tumor 19 32 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-gamma (IFN gamma) for 120min Source GEO sample is GSM5610 Last updated (according to GEO): May 27 2005 1366 1355 in melanomas total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells cultured for 60min Source GEO sample is GSM5844 Last updated (according to GEO): May 27 2005 Nervous system structure 901 Liver 1000 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15707 Last updated (according to GEO): May 28 2005 Gene expression data from the right forebrain of C57BL mouse received Haloperidol oral treatment for four weeks. Source GEO sample is GSM149809 Last updated (according to GEO): Dec 12 2006 in the mouse heart 91 108 1000 Bone Marrow MOLF/EiJ_male_hypothalamus Source GEO sample is GSM184208 Last updated (according to GEO): Apr 26 2007 Day 1_M_-LIF_Bchip NCI60.57_LABEL61EXTRACT60SUB3 Source GEO sample is GSM134283 Last updated (according to GEO): Aug 06 2007 1000 Structure of entorhinal cortex low gestational age Source GEO sample is GSM213100 Last updated (according to GEO): Jul 25 2007 Collagen 1000 tibiae 115 120 M_U133A_2_HC by the liver 210 221 Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP), exposed 6 h more to ambient pressure (CP6) and harvested with cells exposed for 6 h to hydrostatic pressure, pressure experiment # 1 (PE1). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11382 Last updated (according to GEO): Dec 15 2006 Molecular profiles of dystophin-deficient patients and normal human skeletal muscles on Affymetrix HG-U95A arrays Last Updated (by provider): May 29 2005 Contributers: Steven A Greenberg Alvin T Kho Despina Sanoudou Alan H Beggs Louis M Kunkel Isaac S Kohane Richard R Bennett Judith N Haslett Includes GDS563. Update date: Jul 08 2004. Dataset description GDS563: Search for modifying factors and pathogenic pathways involved in Duchenne muscular dystrophy (DMD). Quadricep skeletal muscle biopsies from 12 DMD patients and 12 unaffected control patients examined.. comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247394 Last updated (according to GEO): Dec 11 2007 Gene expression data from whole brain infected mouse, day 1 Source GEO sample is GSM189610 Last updated (according to GEO): May 16 2007 Heart 1000 testis with regular spermatogenesis from orchiectomy cases due to prostate carcinoma, patient age: 58y; W03 003 "Sample 88, BRCA1 mutation(8 months) age 33 erp no" on vantveer-oligo 1000 Hippocampus YFPH-Hippocampus-replicate2 Fibroblasts 861 HapMap CEU_parent Male Source GEO sample is GSM159523 Last updated (according to GEO): Feb 01 2007 PBMCs-Type 1 Diabetes-IDDM34_T1D_4MO 858 Prostatic Neoplasms 14 0 Locus Coeruleus Diaphragm 23 Day control rep 3 CNS-SpinalCmod-Adult-72h-4C-s2 A2780_cis_IC25_16h_2 3_hypothalamus_3hrs_sleep_deprivation_#124 H9RGV00102608 Primary Neoplasm 1000 Gene expression data from hippocampus of one young SAMP10//Ta mouse Source GEO sample is GSM143749 Last updated (according to GEO): Jan 24 2007 10 weeks Source GEO sample is GSM147511 Last updated (according to GEO): Dec 01 2006 Voxel J4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1459 Last updated (according to GEO): Nov 21 2005 Extracellular Matrix 1000 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68124 Last updated (according to GEO): Jul 07 2006 Succinic semialdehyde dehydrogenase (SSADH) deficiency, a rare genetic defect of GABA degradation recently modelled in mice (SSADH(-/-) mice), manifests early absence seizures that evolve into generalized convulsive seizures and lethal status epilepticus in gene-ablated mice. Disrupted GABA homeostasis, in conjunction with the epileptic phenotype and increased gamma-hydroxybutyric acid (GHB), suggested that expression profiling with the U74Av2 Affymetrix system would reveal dysregulation of receptor genes associated with GABAergic and glutamatergic neurotransmission. Unexpectedly, we found significant downregulation for genes associated with myelin biogenesis and compaction, predominantly in hippocampus and cortex. These results were confirmed by: (1) myelin basic protein (MBP) immunohistochemistry; (2) western blotting of myelin-associated glycoprotein (MAG) and MBP; (3) qRT-PCR analyses of myelin-associated oligodendrocytic basic protein (MOBP), MAG, MBP and proteolipid protein (PLP) in hippocampus, cortex and spinal cord; (4) quantitation of ethanolamine and choline plasmalogens, all core myelin components; (5) evaluation of myelin content in brain sections employing toluidine blue staining; and (6) ultrastructural evaluation of myelin sheath thickness via electron microscopy. We speculate that increased GABA/GHB, acting through GABAergic systems, results in decreased levels of the neurosteroids progesterone and allopregnanolone [Gupta et al (2003) Ann Neurol 54(Supplement 6): S81-S90] and phosphorylation of mitogen-activated protein (MAP) kinase, with resulting myelin protein abnormalities primarily in the cortex of SSADH(-/-) mice. Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242058 Last updated (according to GEO): Dec 04 2007 SynovAcAr_022HACJ0_151.txt Blood Test (Blinded) Sample Source GEO sample is GSM129970 Last updated (according to GEO): Sep 18 2007 from mouse colon 21 36 Neuroendocrine Tumors 901 Expression profiling of spinal cord section (T9) extracted from rats 7d following severe injury Lot batch = Source GEO sample is GSM7592 Last updated (according to GEO): May 28 2005 Fibroblasts 861 Spinal cord [JunctionChip 3 of 5] LPS, 20 min, Rep_3 41 29 Control blood Breast Carcinoma 1000 156 145 Their livers 928 Endometrium Pooled quad RNA samples from five 8 wk old male mdx mice Source GEO sample is GSM13723 Last updated (according to GEO): May 28 2005 Ovarian_Tumor_Serous_KU-OS-003 Si4_1, mouse, SW, infected, 4 days post infection_rep 1 Age-related transcriptional changes and the effect of dietary supplementation of vitamin E in the mouse brain in the brain 614 625 Voxel E3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1417 Last updated (according to GEO): Nov 21 2005 Expression profiling of spinal cord section (T8) extracted from rats 4h following laminectomy (sham) Lot batch = Source GEO sample is GSM6626 Last updated (according to GEO): May 28 2005 660 mesenchymal stem cell 639 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68203 Last updated (according to GEO): Jul 07 2006 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225954 Last updated (according to GEO): Nov 02 2007 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132546 Last updated (according to GEO): Feb 26 2007 cardiomyopathy 190 203 None Source GEO sample is GSM198096 Last updated (according to GEO): Jul 16 2007 HC105 CB A Mental Retardation 1000 Gene expression data from aneurismal tissues obtained from patients with bicuspid valves. Source GEO sample is GSM116783 Last updated (according to GEO): Jun 28 2006 Recommended Affymetrix protocols were followed. Source GEO sample is GSM148470 Last updated (according to GEO): May 01 2007 1000 Brain long access to cocaine, septum, 6 hrs/day access to cocaine Source GEO sample is GSM93855 Last updated (according to GEO): Jan 26 2006 Deltoid Muscle 6 Normal Coronary artery 901 19 0 Head and neck cancer 112 77 Keywords = congenital heart disease 20 0 human caudate nucleus 1000 Solid tumor with antibodies 492 506 substantia_nigra_9 Source GEO sample is GSM80859 Last updated (according to GEO): Mar 31 2006 1000 Cardiomyopathies Expression profiling of spinal cord section (T10) extracted from rats 14d following mild injury Source GEO sample is GSM31312 Last updated (according to GEO): May 27 2005 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b063 Source GEO sample is GSM1976 Last updated (according to GEO): Nov 21 2005 Gene expression data from dorsal pancreas at e15.5, MG-U74A version2 Source GEO sample is GSM199450 Last updated (according to GEO): Jun 08 2007 Molecular taxonomy of major neuronal classes in the adult mouse forebrain. 1000 ovarian neoplasm 10 Bone marrow 0 GC (HKG38L) Primary Neoplasm 1000 1000 Cerebral cortex Melanoma metastatic cell line A375, biological rep9 (LeiATCC) Simple annotation: Cell-cycle, Mitotic selection Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16446.gif Source GEO sample is GSM79676 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145003 Last updated (according to GEO): Nov 20 2006 Sample36, Post Injury 24 hours Treatment, type=wait Source GEO sample is GSM53287 Last updated (according to GEO): Jul 06 2005 DMSO-control NG108 neuronal cells 3 Whole Brain 62 72 Heart 1000 164 136 of the middle cerebral artery Cerebellum_nontransgenic control S25_3 months_replicate 2 f2#11 versus pool Mouse Brain tissue Wild type 8 wk old male C3H/HeJ mouse hippocampus Source GEO sample is GSM107011 Last updated (according to GEO): Mar 05 2007 Prefrontal Cortex 0 16 BAL_13_A0B0 in prostate epithelial cells 1397 1425 4 0 Brain Infection 1113 1122 Heart 861 Parkinson Disease 861 NCI60.3_LABEL6EXTRACT5SUB3 Source GEO sample is GSM134009 Last updated (according to GEO): Aug 06 2007 from cingulate cortex 12 32 Gene expression data from postmorten brain regions Source GEO sample is GSM145276 Last updated (according to GEO): Nov 20 2006 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195278 Last updated (according to GEO): Sep 13 2007 384 368 of the epithelium Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225741 Last updated (according to GEO): Nov 02 2007 PC 12Hr rat 4126 blood vs. 2500mg/kg APAP 12Hr rat 4137 blood 59 50 Lung C57BL C57BL/6J cingulate cortex rep2 Standard Affymetrix procedure, RNA from frozen tissue. Date GSE595 Last Updated: Jun 15 2005 Contributers: Mei Han Peter B Kang Despina Sanoudou Alan H Beggs Judith N Haslett Louis M Kunkel Includes GDS511. Update date: Mar 18 2004. Dataset description GDS511: Transcriptional profile of normal skeletal muscle collected at autopsy compared to surgical specimens.. 1000 Adrenal Medulla 252 240 to 85 gliomas tTA 7311 OVCAR-4 hgu95c Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep5 from the right forebrain 21 44 NHF10-hTERT_Basal_C5_53958 Kidney 1000 none Source GEO sample is GSM244641 Last updated (according to GEO): Nov 23 2007 Leukemia, Myelocytic, Acute 1000 skin Source GEO sample is GSM19002 Last updated (according to GEO): Sep 25 2006 Neoplasm Metastasis 861 brain, Left frontal Lobe: Extract34_le2 no additional Source GEO sample is GSM199362 Last updated (according to GEO): Jun 08 2007 from the abdominal aorta 16 39 1000 Brain Keywords = Heart 505 521 Expression profiling of spinal cord section (T10) extracted from rats 4h following severe injury Source GEO sample is GSM31385 Last updated (according to GEO): May 27 2005 +_9030_batch1 on NHGRI-6.7k Gene expression data from postmorten brain regions Source GEO sample is GSM145606 Last updated (according to GEO): Nov 20 2006 mRNA was isolated after 8 hours of incubation from IMR-90 cells seeded onto a collagen/chondroitin sulfate tissue engineering scaffold mesh material. Cells were seeded at a density of 1 x 10^6 cells/ mesh, and this chip represents a pooling of cells from 4 meshes. Keywords = tissue engineering mesh, collagen, chondroitin sulfate, biomaterials design Source GEO sample is GSM6065 Last updated (according to GEO): May 27 2005 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hour time point Source GEO sample is GSM159729 Last updated (according to GEO): Apr 23 2007 Spinal Cord 1000 19 0 Head and neck cancer 861 Brain 1000 Spleen 901 Lateral Sclerosis 25 7 Right Temporal Lobe WGACON-234 Liver Test (Blinded) Sample Source GEO sample is GSM130194 Last updated (according to GEO): Sep 18 2007 iFA50clone8- Gene expression data from skeletal muscle at baseline Source GEO sample is GSM230462 Last updated (according to GEO): Sep 19 2007 Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3875 Last updated (according to GEO): May 27 2005 928 Endometrium Liver 1000 Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep1 Expression profile of genes in mouse brain Source GEO sample is GSM21061 Last updated (according to GEO): May 27 2005 Bone structure of tibia 1000 of peripheral nervous system 73 100 Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35381 Last updated (according to GEO): May 27 2005 NCI60.51_LABEL55EXTRACT54SUB3 Source GEO sample is GSM134253 Last updated (according to GEO): Aug 06 2007 1000 Spleen Posterior root of spinal nerve 861 Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160712 Last updated (according to GEO): Sep 24 2007 stria terminalis 901 Prosencephalon 1000 Nose 1000 specific phobias 205 220 /testicles 204 214 m1-adenoma1 Sample 112 on vantveer-oligo cy5:WKY control, biological rep 3r; cy3:pool of 6 WKY control rats -_8111_batch1 on NHGRI-6.7k with mental retardation 241 263 1000 Endometriosis, site unspecified lymphomaburkittsDaudi Source GEO sample is GSM18736 Last updated (according to GEO): Sep 25 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145753 Last updated (according to GEO): Nov 20 2006 861 frontal lobe Testis 1000 5 0 brain HMEC X BC24 Myocardial Infarction 1000 5 0 brain 861 Thymus Gland The rod photoreceptor-specific neural retina leucine zipper protein Nrl is essential for rod differentiation and plays a critical role in regulating gene expression. In the mouse retina, rods account for 97% of the photoreceptors; however, in the absence of Nrl (Nrl-/-), no rods are present and a concomitant increase in cones is observed. Using mouse GeneChips (Affymetrix), we have generated expression profiles of the wild-type and Nrl-/- retina at three time-points representing distinct stages of photoreceptor differentiation. Last Updated (by provider): Sep 07 2007 Contributers: Rafal Farjo Alfred O Hero Anand Swaroop Edwin Oh James S Friedman Yuezhou Jing Shirley He Alan J Mears Gilles Fleury Shigeo Yoshida Todd Carter Carrolee Barlow Control Mouse 2 Gene expression data from postmorten brain regions Source GEO sample is GSM145824 Last updated (according to GEO): Nov 20 2006 Neoplasm 861 T-47D__CL5014__BREAST from liver 21 30 Cerebellum_nontransgenic control A39_4 months_replicate 4 GSE8998 D_95Av2_2846_CB_1_GS 861 Communicable Diseases PC-3 hgu95c brain, Right Temporal Lobe: Extract80_le1 comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247380 Last updated (according to GEO): Dec 11 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145001 Last updated (according to GEO): Nov 20 2006 C57BL/6J amygdala rep2 A61 NES 142Q TG3 F6/23 A61 NES Htt exon 1 142Q Mouse 8 months Cerebellum Male Source GEO sample is GSM73230 Last updated (according to GEO): Sep 06 2005 Gene expression data from whole brain infected mouse, day 6 Source GEO sample is GSM189623 Last updated (according to GEO): May 16 2007 1000 Uterus This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12362 Last updated (according to GEO): May 28 2005 67 40 with coronary artery disease outer medulla 31 43 1BJZ02052109_TestiIntersitial 1000 Brain Spleen 0 5 861 Cerebral cortex D_U133Plus_56_nAcc C84 on NCI-7.6k 861 Colon 43 0 Chorionic mesoderm-derived mesenchymal cells Liver Test (Blinded) Sample Source GEO sample is GSM130101 Last updated (according to GEO): Sep 18 2007 Heart failure 1000 1000 Spinal Cord /6J mouse pituitary gland 29 53 Nasal Epithelium 901 144 109 Keywords = congenital heart disease Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11251 Last updated (according to GEO): May 28 2005 The sample is a part of a series describing gene expression changes during postnatal development of the small intestine Source GEO sample is GSM198887 Last updated (according to GEO): Jun 11 2007 Heart Atrium 1000 Brain 1000 Adenocarcinoma 2 0 15 WGACON-60 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2728 Source GEO sample is GSM2112 Last updated (according to GEO): Nov 21 2005 Bone Marrow 1000 1632 1616 neurite outgrowth 1000 Spinal Cord Animals were sacrificed and organs were rapidly frozen in liquid nitrogen, and subsequently stored at <ETH>80oC. Tissues were mechanically homogenized with a polytron and total cellular RNA was extracted using a commercially available reagent (TMTRIzol; Invitrogen). The poly-(A)+ fraction of the RNA was isolated by chromatography with oligo d(T) cellulose beads. For cDNA labeling, either 25 mg of total RNA or 2.5 mg of poly-(A) RNA was converted into cDNA using reverse transcriptase (RT; Super Script II, Invitrogen) and alternatively Cy5 or Cy3-labeled dCTP (1mM, Perkin Elmer-Cetus/NEN, Boston) in a reaction mixture containing 1.5 mL oligo (dT) (100pmol/ mL), 3 mL dNTP-dCTP (6.67mM each), 1 mL dCTP (2mM), 4 mL DTT (100mM), 8 mL 5 X RT Buffer (Invitrogen, California). The reactions were carried out at 42¼C for 3 hrs, after which the RNA was degraded by the addition of 0.5 mL RNase A (1 mg/mL) and 1.5 mL RNaseH 5 units/mL). Labeled cDNA was separated from unincorporated nucleotides (Qiagen column) and further concentrated by evaporation under vacuum. The arrays were pre-hybridized for 1-2hrs with DIGEasy hybridization buffer (Roche) containing 10ug/ml denatured salmon sperm DNA, and 10ug/ml yeast tRNA. The Cy5 and Cy3 labelled cDNAs were combined and hybridized in the same medium and incubated with the arrays for 16-18hrs at 37Co. Finally, the arrays were washed 3 x 10 mins in 0.1 x SSC (20 X SSC is 3M sodium chloride, 0.3 M sodium citrate, pH 7.0), 0.1%SDS at 50Co, and 4 x 3min in 0.1 x SSC at room temperature, and dried by centrifugation. Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray fluorescent scanner and image intensity data were extracted and analyzed with QuantArray 3.0 analysis software. Quantification data was imported in GeneSpring (Silicon Genetics). The import format was modified to maintain information relevant to user-contributed flagging as well as QC parameter furnished by the array manufacturer. Dye swap and Intensity-based normalization (Lowess) were performed using the default settings. Keywords = spleen Keywords = malaria Source GEO sample is GSM10999 Last updated (according to GEO): Oct 28 2005 Brain 861 861 Blood processed in batch 1 Source GEO sample is GSM90448 Last updated (according to GEO): Mar 20 2006 1000 Brain V5-P278 of caudal 93 101 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188790 Last updated (according to GEO): Jun 06 2007 thymus 0 5 Normal Source GEO sample is GSM176057 Last updated (according to GEO): Apr 09 2007 Muscle 861 Skeletal muscle structure 1000 14 7 amygdala HC57 CN A Gene expression data from whole brain infected mouse, day 1 Source GEO sample is GSM189605 Last updated (according to GEO): May 16 2007 Coronary Arteriosclerosis 1000 817 with cell proliferative, cytoskeletal, extracellular matrix 758 Primary small cell lung carcinoma 2760 0 37 Hippocampal expression analyses reveal selective association of immediate-early, neuroenergetic, and myelinogenic pathways with cognitive impairment in aged rats. E8.5a_rep2 GSE8423 Group 1 Control Untreated, pool #EP2 vs. reference pool GM12057 1000 Heart glucocorticoid hypertension 237 264 Spleen 1000 NMDA10 (Experiment shortNMDA: Run 19222) Treatment, type=time_course, description=primary cortical neurons were treated with 1 mM NMDA for increasing periods of time (10 to 360 min)., measurement=10.0 m Source GEO sample is GSM96718 Last updated (according to GEO): Feb 14 2006 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160208 Last updated (according to GEO): Feb 08 2007 BALB-RAG_OVA Replicate 3 Telomerase modulates expression of growth-controlling genes and enhances cell proliferation. Lymphoblastic Leukemia 901 G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Source GEO sample is GSM9636 Last updated (according to GEO): May 28 2005 1000 Coronary Arteriosclerosis R539P00546 114 101 brains quickly Affymetrix GeneChip® Mouse Genome 430 2.0 Array Source GEO sample is GSM197119 Last updated (according to GEO): May 31 2007 bronchial epithelia 224 243 C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P20 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25139 Last updated (according to GEO): May 27 2005 Sun204_TAV12 group Cardiac 523 530 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:288, Count:32 Corner- Avg:31510, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:5.414648,SFGene:All Background:Avg:457.38,Stdev:5.50,Max:474.0,Min:445.1 Noise:Avg:9.32,Stdev:0.18,Max:9.8,Min:8.8 RawQ:13.50 Keywords = ALL Source GEO sample is GSM3432 Last updated (according to GEO): May 27 2005 L_AK_SleepDep_ZT 6_2 1037 of transitional epithelium 1012 861 Neoplasm 19 0 human frontal cortex 346 309 Cerebellum Alzheimer's Disease GSE6778 Neurites 861 Parkinson Disease 861 Lung diseases 861 Gene expression data from controls Source GEO sample is GSM231005 Last updated (according to GEO): Sep 21 2007 Category: Tissue Rejection Subcategory: Kidney UTI/Pyelonephritis also Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=760670 LaserPower=2.21.29 Lot batch = LC17N052 Source GEO sample is GSM4797 Last updated (according to GEO): Nov 21 2005 Malignant neoplasm of liver 901 861 Pancreas 913 Coronary heart disease 265 260 Aortae Epithelium 865 29 0 Salivary Gland [JunctionChip 5 /6J pituitary gland rep1 5 28 **** Source GEO sample is GSM4293 Last updated (according to GEO): May 27 2005 Whole blood 0 10 Saccule 0 6 1037 of transitional epithelium 1012 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/24868.gif Source GEO sample is GSM81552 Last updated (according to GEO): Sep 22 2006 Amygdala 8 Normal RPMI-8226_CL7010__LEUKEMIA HCC (HBV+, CH3) for liver 26 35 Liver 0 4 Nose 1000 Gene expression data from a NB cell line Source GEO sample is GSM213315 Last updated (according to GEO): Jul 26 2007 861 Brain Spleen 1000 B432 on Affymetrix GeneChip Human Full Length Array HuGeneFL Treated Source GEO sample is GSM176468 Last updated (according to GEO): Apr 09 2007 The sequencing of the human genome has resulted in greater attention to genetic variation among individuals, and variation at the DNA sequence level is now being extensively studied. At the same time, it has become possible to study variation at the level of gene expression by various methods. At present, it is largely unknown how widespread this variation in transcript levels is over the entire genome and to what extent individual differences in expression level are genetically determined. In the present study, we used lymphoblastoid cells to examine variation in gene expression and identified genes whose transcript levels differed greatly among unrelated individuals. We also found evidence for familial aggregation of expression phenotype by comparing variation among unrelated individuals, among siblings within families and between monozygotic twins. These observations suggest that there is a genetic contribution to polymorphic variation in the level of gene expression. nic 2 (Experiment Neuroprotection4- Run 21823) Treatment, type=timepoint, description=Same sample used for Experiment Neuroprotection4-Run 14985, samples were rerun due to oven failure, measurement=0.0 h Source GEO sample is GSM96689 Last updated (according to GEO): Feb 14 2006 2737 tumor cells 2747 Ovarian Diseases 877 Ovary_PD7_Foxo3 Null_Replica 1 913 Coronary heart disease M_U133A_32_DLPFC 2006 1992 adhering blood 861 Malignant Neoplasms Large Intestine 1000 embryonic hearts 1064 1079 1037 of transitional epithelium 1012 adenoma 861 Posterior root of spinal nerve 861 neurological disease control sample x180 Wild type inbred mice Source GEO sample is GSM82900 Last updated (according to GEO): Nov 10 2005 Total RNA extracted from mouse brain Source GEO sample is GSM103426 Last updated (according to GEO): Sep 21 2006 21 6 (caudate nucleus Brain 861 Localized Malignant Neoplasm 853 Primary small cell lung carcinoma 2243 861 Neoplasm the mouse central nervous system 334 365 with autism spectrum disorder 37 65 brain, hippocampus: Aldh5a1-/- #3403 Hippo_e1_le1 from the lung 309 322 AD-259t1-A171-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Trigeminal ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until enough tissue was harvested to be pooled by genotype. Approximately 10-12 ganglia were pooled for a single analysis, which was extracted using the RNeasy system (Qiagen). Source GEO sample is GSM89138 Last updated (according to GEO): Dec 23 2005 67 52 descending colon Standard Affymetrix procedure Source GEO sample is GSM133019 Last updated (according to GEO): Aug 28 2007 Bone Marrow 1000 1705 in neurodegenerative disorders 1734 ER negative human primary breast tumor EA02014_41289_H133A_JA-1871 12 frontal Lobe 23 BPH-44 on UMich-10k Expression profiling of spinal cord section (T10) extracted from rats 14d following severe injury Source GEO sample is GSM31349 Last updated (according to GEO): May 27 2005 High Freezing Source GEO sample is GSM92432 Last updated (according to GEO): Jan 13 2006 MGJZ030228080Bpituitary brain 0 5 Adrenal Medulla 1000 Pulmonary Emphysema 1000 861 Brain Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18222.gif Source GEO sample is GSM91542 Last updated (according to GEO): Sep 22 2006 from cerebellum 1966 1980 I_U133A_56_CB Head and neck cancer Source GEO sample is GSM155678 Last updated (according to GEO): Apr 24 2007 GM07349_technical_rep_2 Spleen 0 5 cerebral cortex 7 21 prostate Source GEO sample is GSM203264 Last updated (according to GEO): Jun 21 2007 Epithelial Cells 1000 18 8 Cerebellum" Si9_2, mouse, SW, infected, 9 days post infection_rep 2 5 0 brain Dahl-Iwai Male LowSalt Cortex rat109 dahl_cortexr_k_109c_072001 Septum Source GEO sample is GSM107944 Last updated (according to GEO): Jun 06 2006 Laser capture lung cancer cells Source GEO sample is GSM191029 Last updated (according to GEO): May 25 2007 Frontal Cortex Source GEO sample is GSM107896 Last updated (according to GEO): Jun 06 2006 CNS-RM_Mod3mo-3B-s2 Dissection of E16.5 cortex for RNA extraction. Cortex Hemispheres of E16.5 mice were divided into the medial (R1), dorsal (R2), ventral (R3), lateral (R4), and occipital regions (R5). Preparation of RNA and Synthesis of cDNA. Poly A+ RNA was obtained through twice column procedures with oligo dT cellulose column (New England Biolabs, Beverly, MA) and was used for synthesis of cDNA. 1ug of polyA+ RNA was converted into double-stranded cDNA by reverse transcription using ReverTra Ace (ToYoBo, Japan) with oligo dT(24) primers containing the T7 RNA polymerase promotor sequence (Amersham Pharmacia Biotech, Japan). The integrity of RNA was confirmed by agarose electrophoresis and RNA contents were analyzed by measuring the optical density at 260 nm. Target preparation and array processing. The following procedures including preparation of cRNA targets, hybridization, washing, staining, and scanning were performed as described in the Expression Analysis Technical Manual (Affymetrix, CA). Briefly, biotin-labeled antisense cRNA targets were synthesized in in vitro transcription reaction system (IVT) using cDNA as template (ENZO BioArrayTM HighYieldTM RNA Transcription Labeling kit with T7 RNA polymerase, Enzo, NY). The cRNA targets were size-fragmented to 35-200 bp in a buffer containing potassium and magnesium acetate at 94 °C for 35 minutes and were used for hybridization as cRNA targets. The hybridization cocktail [containing 10 ug of target cRNA, control oligo BS (Affymetrix), and Eukaryotic Hybridization controls (Affymetrix)] was hybridized with a mouse U74A array at 42 °C for 16 hours in GeneChip Hybridization Oven 640. Washing and staining were performed after hybridization under the fluidics station protocol, EuGE-WS2, on GeneChip Fluidics Station 400. Then, we scanned the array twice on HP GeneArrayTM scanner. Experiments were repeated twice with independent dissection. Data analysis. To quantify the expression level of a transcript, the average difference value (Adv) was calculated from the intensities against the probe cells using the global methods of normalization by Microarray Suite ver. 4.0 (Affymetrix). Keywords = mouse Keywords = cortex Keywords = development Keywords = regional Keywords = gene expression Keywords = medial Keywords = dorsal Keywords = lateral Keywords = rostral Keywords = occipital Source GEO sample is GSM14594 Last updated (according to GEO): Oct 28 2005 Tissue-specific expression and regulation of sexually dimorphic genes in mice. 6 0 Leprosy 1000 Blood Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. 4h after sham surgery, a 4 mm diameter disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44505 Last updated (according to GEO): May 27 2005 SN12C hgu95e brain_DLPFC_bipolar B_mr646 HapMap CEU_parent Female Source GEO sample is GSM159571 Last updated (according to GEO): Feb 01 2007 Blood 1000 Parkinson Disease 861 GM19131 in the brain 150 162 Lymphoblastoid Cell Line for Individual 8113.5 log phase Overall study: Identification of PDGF-dependent patterns of gene expression in U87 glioblastoma cells. RNA was obtained from triplicate dishes of 5 different groups of U87 cells, each (total 15) analyzed with one U95 microarray chip. Three different comparisons were made: 1) Clone 3.1 (34580-34582) vs. clone 3.3 (34583-34585) vs. parent U87 (34592-34594). Purpose: demonstrate that the gene expression profiles between these 3 cell lines are not different, so they could be pooled as a single untreated group. 2) Pooled control group (34580-34585, 34592-34594) vs. clone 8.1 (34586-34588). Purpose: identify genes specifically controlled by autocrine PDGF activity. 3) Clone 8.1 (34586-34588) vs. clone 8.1 treated with PDGF (34589-34591) Purpose: Identify genes specifically induced by exogenous PDGF.. Date GSE1923 Last Updated: Dec 19 2005 Contributers: David M Kaetzel Catherine Nutt Xuejun Peng Piam Shanehsaz Deqin Ma David N Louis Includes GDS1730. Update date: May 02 2006. Dataset description GDS1730: Analysis of U87 glioblastoma (GBM) cell clones overexpressing a dominant-negative form of platelet-derived growth factor (PDGF) A subunit to inactive the PDGF autocrine signaling loop. The autocrine PDGF loop is a hallmark of GBM. Results identify genes regulated by oncogenic PDGF signaling.. 1000 Skeletal muscle structure Meningioma Recurrent Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108030 Last updated (according to GEO): Jun 06 2006 Tumor__Lung_Adeno_94_I_196 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A cingulate cortex 1000 Bone Marrow 1000 24M_A31103 1000 hindbrain 626 615 PCOS oocytes of rat soleus muscle 291 310 1241 1229 polymyositis 15 0 skeletal muscle 7 cerebral cortex 21 861 Blood accumbens_4 Source GEO sample is GSM80575 Last updated (according to GEO): Mar 31 2006 NA18609 22 0 Glioblastoma multiforme 91 from the bone marrow 72 Neoplasm 861 There is clinical and experimental evidence that elevated intraocular pressure (IOP), a mechanical stress, is involved in the pathogenesis of glaucomatous optic neuropathy. The mechanism by which astrocytes in the optic nerve head (ONH) respond to changes in IOP is under study. Gene transcription by ONH astrocytes exposed either to 60 mmHg hydrostatic pressure (HP) or control ambient pressure (CP) for 6, 24, and 48 h was compared using Affymetrix GeneChip microarrays to identify HP-responsive genes. Data were normalized across arrays within each gene. A linear regression model applied to test effect of time and HP on changes in expression level identified 596 genes affected by HP over time. Using GeneSpring analysis we selected genes whose average expression level increased or decreased more than 1.5-fold at 6, 24, or 48 h. Expression of selected genes was confirmed by real-time RT-PCR; protein levels were detected by Western blot. Among the genes highly responsive to HP were those involved in signal transduction, such as Rho nucleotide exchange factors, Ras p21 protein activator, tyrosine kinases and serine threonine kinases, and genes involved in transcriptional regulation, such as c-Fos, Egr2, and Smad3. Other genes that increased expression included ATP-binding cassettes, solute carriers, and genes associated with lipid metabolism. Among the genes that decreased expression under HP were genes encoding for dual activity phosphatases, transcription factors, and enzymes involved in protein degradation. These HP-responsive genes may be important in the establishment and maintenance of the ONH astrocyte phenotype under conditions of elevated IOP in glaucoma. 1000 Decapitation Ileum [JunctionChip 3 of 5] human frontal cortex Source GEO sample is GSM86999 Last updated (according to GEO): Feb 08 2006 91 from the bone marrow 72 1000 Lung "Sample 21,>5 yr survival(126 months) age 39 erp yes" on vantveer-oligo Bone marrow, Mesenchymal stem cells: T3-2-101103_e1_le1 Fibroblasts 1000 WGACON-162 Primary large cell neuroendocrine carcinoma 5020 Source GEO sample is GSM17329 Last updated (according to GEO): May 28 2005 Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Meningioma Primary Grade 2. Source GEO sample is GSM108036 Last updated (according to GEO): Jun 06 2006 Expression profiling of spinal cord section (T9) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM6671 Last updated (according to GEO): May 28 2005 Keywords = kidney 113 130 low gestational age Source GEO sample is GSM213075 Last updated (according to GEO): Jul 25 2007 Psychotic Disorders 1000 0 Human Cortex 11 A HID B D088 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108588 Last updated (according to GEO): Aug 22 2006 A2780_control_16h_2 cocaine naive, lateral hypothalamus, 0 hrs/day access to cocaine Source GEO sample is GSM93838 Last updated (according to GEO): Jan 26 2006 Heart 861 Hyperdip>50-C42 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A with myocardial infarction 313 339 Heart 1000 Ta gr2 tumour Source GEO sample is GSM2483 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92366 Last updated (according to GEO): Jan 13 2006 To investigate the gene program activated by serotonergic hallucinogens in mouse somatosensory cortex, the effects of the 5-HT2A agonist (±)2,5-dimethoxy 4-iodoamphetamine (DOI) on gene expression was studied. The 5-HT2A serotonin receptor is a member of the 5-HT2 receptor subfamily of G protein?coupled receptors. The 5-HT2A receptor is thought to modulate processes related to cognition, appetite, mood, anxiety, sleep, and sexual behavior. Abnormal function of this receptor has been implicated in neuropsychiatric disorders such as major depression and schizophrenia. In particular, the 5-HT2A receptor has been implicated in the modulation of the mechanisms related to psychosis. We compared gene response patterns in the somatosensory cortical brain area, which has a high density of 5-HT2A receptors and has been implicated in the action of hallucinogenic drugs. Mice (strain 129Sv) were injected with DOI (2 mg/kg or 10 mg/kg) or vehicle, animals were sacrificed after 1 h, and somatosensory cortex samples dissected on ice for RNA extraction. Seven independent microarray hybridizations from seven different DOI- or vehicle-treated mouse pairs were performed. In this particular hybridization, 15 µg of RNA was used. Keywords = somatosensory cortex 5-HT2A receptor DOI Source GEO sample is GSM3377 Last updated (according to GEO): Oct 28 2005 1530 1517 between tumors 17 7 hippocampus with some respiratory epithelium. 1039 1072 19 0 Head and neck cancer /testicles 152 162 115 101 Hyperthyroidism Cerebral cortex 1000 5 0 Tonsil 901 Lateral Sclerosis Gene expression data from human colon tumor tissue Source GEO sample is GSM173370 Last updated (according to GEO): Apr 20 2007 861 Retina 197 176 with coxsackievirus B3 861 Neoplasm Category: Lymphoma Classification Subcategory: Follicular Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n009 Source GEO sample is GSM2024 Last updated (according to GEO): Nov 21 2005 Bmi1 shRNA, biological rep2 5 0 brain Lymphoblastoid Cell Line for Individual 8205.4 log phase #2 nucleus accumbens ctrl replicate 1 Brain 1000 GSE4221 13 CN B 5 0 Kidney 1000 ovarian neoplasm with Parkinson's disease 27 50 Disease Source GEO sample is GSM175788 Last updated (according to GEO): Apr 09 2007 966 Hippocampus Acetaminophen 24hr Rat 0861 blood vs. Acetaminophen 24hr Rat Pooled Control blood Cerebral cortex 861 PGA-lv_1w_674 Prostate Gland 6 Normal 1000 Carcinoma 1000 Dermatitis, Allergic Contact fetallung Source GEO sample is GSM18806 Last updated (according to GEO): Sep 25 2006 brain, unknown: Sample55_e1_le1 spinal cord 0 11 Psychotic Disorders 1000 of neurodegenerative diseases 1372 1401 Gene expression data Source GEO sample is GSM183174 Last updated (according to GEO): Jul 30 2007 H9LMS00102610 dentate granule cells Source GEO sample is GSM35801 Last updated (according to GEO): May 27 2005 Brain (hippocampus) [JunctionChip 5 of 5] Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:248, Count:32 Corner- Avg:43803, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:17.496950,SFGene:All Background:Avg:346.00,Stdev:4.31,Max:359.2,Min:337.0 Noise:Avg:9.84,Stdev:0.35,Max:10.9,Min:8.9 RawQ:14.73 Keywords = ALL Source GEO sample is GSM3510 Last updated (according to GEO): May 28 2005 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188774 Last updated (according to GEO): Jun 06 2007 6626_Lung developed PGD Femur 1000 897 Neoplasm Metastasis Pressure-overload induced hypertrophy model. Mouse was sacrificed 24 hours after aortic banding. Keywords = Cardiac hypertrophy Source GEO sample is GSM2238 Last updated (according to GEO): May 27 2005 Heart 861 Nose 1000 M_U133A_6_CB Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141332 Last updated (according to GEO): Oct 26 2006 Exp A, Animal #2, 10mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours Source GEO sample is GSM246137 Last updated (according to GEO): Dec 03 2007 NA12740 growth 1 MLL_9 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A stria terminalis 901 Muscular Dystrophy, Duchenne 1000 1000 Intestines, Small osteoblast 627 637 Brain 861 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P21, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3222 Last updated (according to GEO): May 28 2005 Skeletal bone 861 G5 cornea no additional Source GEO sample is GSM199028 Last updated (according to GEO): Jun 08 2007 Gene expression data from mouse colon Source GEO sample is GSM198104 Last updated (according to GEO): Aug 22 2007 MPL13E_untreated_0.1% Nasal Epithelium Inhalation Formaldehyde 2ppm 24h ID214 Skeletal bone 861 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11317 Last updated (according to GEO): May 28 2005 28 24 Heart brain 0 5 GM18859_technical_rep_2 Expression profiling of spinal cord section (T10) extracted from rats 24h following severe injury Source GEO sample is GSM31352 Last updated (according to GEO): May 27 2005 Gene expression data from the right forebrain of C57BL mouse received Haloperidol oral treatment for twelve weeks. Source GEO sample is GSM148668 Last updated (according to GEO): Dec 12 2006 Medulla 861 TEL-AML1-2M#2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Normal Source GEO sample is GSM176260 Last updated (according to GEO): Apr 09 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withSLC (Secondary lymphoid-organ chemokine) for 240min Source GEO sample is GSM5777 Last updated (according to GEO): May 27 2005 Standard Affymetrix Protocol Source GEO sample is GSM16476 Last updated (according to GEO): May 28 2005 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28751 Last updated (according to GEO): May 27 2005 GSE846 Neostriatum 1000 Spleen 0 5 370 357 muscle groups Expression profiling of spinal cord section (T10) extracted from rats 30m following mild injury Source GEO sample is GSM31322 Last updated (according to GEO): May 27 2005 861 Glioblastoma Gene expression data from whole brain infected mouse, day 1 Source GEO sample is GSM189638 Last updated (according to GEO): May 16 2007 Dahl Salt Sensitive Rat Lung- Control 3 brain 0 5 RNA from muscle biopsy specimen Source GEO sample is GSM3718 Last updated (according to GEO): May 27 2005 Euploid sample 3 (cerebrum) RNA of Kidney was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 biological replicates were analyzed. Keywords = db/m mice Keywords = kidney Source GEO sample is GSM9929 Last updated (according to GEO): May 27 2005 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215064 Last updated (according to GEO): Aug 02 2007 1000 Coronary Arteriosclerosis Whole Brain 62 72 86 70 Fetal liver cells V5-P256 The nose 94 101 66 year old male Gene expression data from postmorten brain regions Source GEO sample is GSM145445 Last updated (according to GEO): Nov 20 2006 1000 Liver 12 0 ovarian tumor brain 0 5 861 Intestines post HCMV infection 71 89 901 Hepatocyte 1000 Malignant Neoplasms in the brain 150 162 M_95A_2978_CB_0_GS 88 68 with bicuspid valves Blood 1000 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156708 Last updated (according to GEO): Jan 22 2007 1000 Leukemia, Myelocytic, Acute Spleen 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145352 Last updated (according to GEO): Nov 20 2006 Fi9_2, mouse, FVB, infected, 9 days post infection_rep 2 Spinal Cord 901 dentate granule cells Source GEO sample is GSM35817 Last updated (according to GEO): May 27 2005 D_U133A_82_DLPFC 091243 OVR278E on Affymetrix GeneChip Human Full Length Array HuGeneFL of hypertension 267 282 Stria 861 trachea Source GEO sample is GSM18994 Last updated (according to GEO): Sep 25 2006 WGACON-177 Macrophage smi46 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120672 Last updated (according to GEO): May 14 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145546 Last updated (according to GEO): Nov 20 2006 CVB3_S-0h-4 38 21 from a hippocampus Myocardial Infarction 1000 Lungs 153 157 Nz1: Hippocampus_21PT-Y_rep9 Tumor__Lung_Adeno_93_I_146 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 6h mitotic selection total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with MIP3-alpha (Macrophage inflammatory protein-3) for 240min Source GEO sample is GSM5696 Last updated (according to GEO): May 27 2005 Primary Neoplasm 1000 N17__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 20 0 human caudate nucleus Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2671.gif Source GEO sample is GSM72167 Last updated (according to GEO): Sep 22 2006 Male 25.1 yr before antibody enrichment scan 1 (U133B) Gene expression data from postmorten brain regions Source GEO sample is GSM145020 Last updated (according to GEO): Nov 20 2006 Cerebral cortex 1000 Prosencephalon 861 154 147 in lung HCC (HBV+, HK14) 861 Alzheimer's Disease Whole blood 0 10 7 cerebral cortex 21 NA19093 ovary 45 50 of Huntington's disease 90 113 HNC2814 Pressure-overload induced hypertrophy model. Mouse was sacrificed 48 hours after aortic banding. Keywords = Cardiac hypertrophy Source GEO sample is GSM2239 Last updated (according to GEO): May 27 2005 na Source GEO sample is GSM181298 Last updated (according to GEO): Apr 10 2007 74 CB B 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113900 Last updated (according to GEO): Jun 16 2006 1000 Cerebellum 4525 4520 liver Spleen vs BAFF Treated B cell 240min (set3) 7 cerebral cortex 21 Joint Tissue Synovium 7 Normal nostrils 156 164 Lymphoblastoid Cell Line for Individual 8143.5 log phase 0 Human Cortex 11 1000 Brain Arteries 861 Gene expression data from skeletal muscle following 240 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230464 Last updated (according to GEO): Sep 19 2007 Utricle structure 1000 913 Fetal Diseases Primary tumor 19 32 brain, cerebellum: Lh-/-_Crb2_e1_le1 Pediatric septic shock Medulla 4 Normal of parieto-occipital cortex 118 144 Expression data from the abdominal aorta and abdominal aortic aneurysm 329 306 valvular cardiomyopathy Fibroblasts 861 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114186 Last updated (according to GEO): Jun 16 2006 Acetaminophen 6hr Rat 0948 blood vs. Acetaminophen 6hr Rat Pooled Control blood 49 30 (predominantly valve in the mammalian nervous system 110 141 in the brain 500 511 129Hippocampus(1)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B 913 Coronary heart disease Individual array of a bladder cancer expression experiment. Source GEO sample is GSM181002 Last updated (according to GEO): Apr 12 2007 1190 1171 on other chromosomes 129:23-7,8,9 superior colliculi Familial combined hyperlipidemia (FCHL), characterized by elevated levels of serum total cholesterol, triglycerides or both, is observed in about 20% of individuals with premature coronary heart disease. We previously identified a locus linked to FCHL on 1q21-q23 in Finnish families with the disease. This region has also been linked to FCHL in families from other populations as well as to type 2 diabetes mellitus. These clinical entities have several overlapping phenotypic features, raising the possibility that the same gene may underlie the obtained linkage results. Here, we show that the human gene encoding thioredoxin interacting protein (TXNIP) on 1q, which underlies combined hyperlipidemia in mice, is not associated with FCHL. We show that FCHL is linked and associated with the gene encoding upstream transcription factor 1 (USF1) in 60 extended families with FCHL, including 721 genotyped individuals (P = 0.00002), especially in males with high triglycerides (P = 0.0000009). Expression profiles in fat biopsy samples from individuals with FCHL seemed to differ depending on their carrier status for the associated USF1 haplotype. USF1 encodes a transcription factor known to regulate several genes of glucose and lipid metabolism. cardiac 746 752 S4_Muscle_Baseline_0min Epithelial Cells 1000 Whole Brain 73 83 Normal Source GEO sample is GSM176151 Last updated (according to GEO): Apr 09 2007 12096 on TGRI-6.5k 1000 Heart amygdala 887 895 6,18,30 month oculomotor nucleus and spinal cord Source GEO sample is GSM74342 Last updated (according to GEO): Sep 16 2005 to the nose 599 609 865 Disorder of artery Exp C, Animal #1, 10mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours Source GEO sample is GSM246168 Last updated (according to GEO): Dec 03 2007 Prosencephalon 861 V5-P374 M_U133Plus_126_AnCg 3AJZ02081484b_TemporalLobe rat hippocampus Treatment, type=time_course, measurement=72.0 h Source GEO sample is GSM32142 Last updated (according to GEO): May 27 2005 "Sample 78, <5 yr survival(44 months) age 54 erp yes" on vantveer-oligo 3AMH02082108_PB_CD19BCells 1000 Uterus CNS-SC_InjA24h-1C-s2 Cerebral cortex 1000 Nervous system structure 901 22 0 Normal epithelial cells IGR-OV1 hgu95c CNS-SpinalC-conAdult-30m-2B-s2 430A2_2045_83_control_sham_medulla Source GEO sample is GSM242706 Last updated (according to GEO): Nov 15 2007 5 0 brain Recurrent Carcinoma 875 Normal Source GEO sample is GSM176320 Last updated (according to GEO): Apr 09 2007 Gene expression data from the hippocampus of S1P2-knockout mouse Source GEO sample is GSM172968 Last updated (according to GEO): Mar 08 2007 from liver 21 30 Integumentary system 861 Abdominal aorta structure 865 Testes_022XACHX_113.txt The frontal cortex 572 589 Endometrium/Ovary 12 Disease in hearts 955 963 A VIS D031 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108618 Last updated (according to GEO): Aug 22 2006 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202667 Last updated (according to GEO): Jun 20 2007 861 Ganglia Y HID D003 901 Lupus Erythematosus 5 0 brain of insulin resistance 1775 1795 861 Stem cells brain, Left frontal Lobe: Extract32_le1 607 597 the rectum Whole blood 0 10 Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Meningioma Primary Grade 2. Source GEO sample is GSM108010 Last updated (according to GEO): Jun 06 2006 of the most anterior dorsal root ganglia 23 62 forebrain 7 15 of the heart 842 854 1000 Spinal Cord Injuries 5 0 Spleen dentate granule cells Source GEO sample is GSM35834 Last updated (according to GEO): May 27 2005 Rb-/- prostate epithelial cell line maintained in RPMI-1640 medium without fetal bovine serum for 48 hours Keywords = prostate Keywords = epithelial Source GEO sample is GSM14676 Last updated (according to GEO): May 28 2005 brain, forebrain: Sample13_e1_le1 Arteries 861 C57BL-6J mice were given intratracheal saline control and sacrificed at 24 hrs. Source GEO sample is GSM4168 Last updated (according to GEO): May 27 2005 709 699 in the skin M_U133Plus_120_DLPFC JMR-MurInj4h-3aAv2-s2 1000 Amygdaloid structure Amygdaloid structure 861 865 Disorder of artery of the heart 842 854 cerebellum Source GEO sample is GSM18758 Last updated (according to GEO): Sep 25 2006 NeverSmoker 45 5 0 brain at the Human Brain 744 761 NG108 rat neuronal cell culture exposed to 0.25% DMSO (control) for two hours. 10 µg total RNA hybridized per chip. RNA STAT 60 used to extract RNA. Standard Affymetrix chip scaling factors used. No other data transformation. Source GEO sample is GSM1659 Last updated (according to GEO): Oct 28 2005 ileum 1000 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 1 - Pair 5 - IML Source GEO sample is GSM49897 Last updated (according to GEO): Dec 20 2005 1000 jejunum GBM Treatment, type=remove Source GEO sample is GSM99563 Last updated (according to GEO): Apr 21 2006 Gene expression data from a neocortex of saline-injected mouse Source GEO sample is GSM147397 Last updated (according to GEO): Jan 03 2007 in seminoma 28 38 Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation. Source GEO sample is GSM228471 Last updated (according to GEO): Sep 10 2007 Parkinson's disease sample x092 of coronary artery disease 317 342 Laser captured visceral sensory neurons. Source GEO sample is GSM63680 Last updated (according to GEO): Dec 21 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145603 Last updated (according to GEO): Nov 20 2006 861 Pancreas /J mouse pituitary gland 25 48 Gene expression data from postmorten brain regions Source GEO sample is GSM144987 Last updated (according to GEO): Nov 20 2006 with mental retardation 241 263 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17079.gif Source GEO sample is GSM91593 Last updated (according to GEO): Sep 22 2006 in human mammary epithelial cells 37 69 bronchial epithelia 224 243 JejunTum2_022IAFCX_J1.txt 1000 Brain Mature B cells 9b Tumor__Breast_Adeno_09-B_005A on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Prostate 21 Normal GSE675 Nasal Epithelium Inhalation Formaldehyde 6ppm 8d ID299 SN:Human Glioblastoma Biopsy 06485 human frontal cortex Source GEO sample is GSM86951 Last updated (according to GEO): Feb 08 2006 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225355 Last updated (according to GEO): Aug 31 2007 Bladder sample 716-2 NB-C8 on NHGRI-6.5k_b CNS-SC_CtrA30m-1A-s2 brain, amygdala: Amygdala 5_le1 NFIA P16WT1 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5720.gif Source GEO sample is GSM76438 Last updated (according to GEO): Sep 22 2006 SQ-SQ10t1-A362-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A atrial septal defects 198 218 whole blood_100278 PGA-swim_4w_s907 plasma cells 332 344 861 Cardiomyopathies Hippocampus 2001 2 month Old Liver 1000 861 Cerebral cortex 861 Nerve 1000 Hippocampus 1000 Amygdaloid structure kidney 37 43 Total RNA was extracted from olfactory epithelium tissue from male C57Bl/6 mice (6 week old). Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol. Keywords = olfaction Keywords = neurogenesis Keywords = apoptosis Keywords = gene silencing Keywords = microarray, transcription factor Source GEO sample is GSM45675 Last updated (according to GEO): Oct 28 2005 MCF7 human breast cancer cells treated with 100 nM of dioxin to quantify RNA differences in a 2 platform, three replicate experiment Source GEO sample is GSM188018 Last updated (according to GEO): May 11 2007 with Alzheimer's disease 27 50 Expression profiling identifies novel candidate genes for ethanol sensitivity QTLs. 1000 Acquired Immunodeficiency Syndrome 901 frontal lobe Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184804 Last updated (according to GEO): Apr 26 2007 Plasma 861 Unsusceptible Group, Ventral tegmental area, Biological Replicate 2 f2#213 versus pool Mouse Brain tissue P46 non-deprived visual cortex replicate 3 1000 Hypothalamic structure 12 frontal Lobe 23 Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002. Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Part of the medium chain triacylglycerol oil in control diet was replaced with: 1.1% fungal oil and 1.9% fish oil. Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily. Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France). Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h. After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hepatic gene expression analysis. From these 5 mice, livers were dissected according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancourt, France), which consisted of carefully dissecting out the liver, rinsing with 70% EtOH to remove adhering blood, trimming of adhering connective tissue with scissors, cutting into 100-150 mg subsections, freezing in liquid N2, and storing at -80°C until gene expression and lipid analysis. Hepatic lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5). Liver tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hepatic RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips. Source GEO sample is GSM2573 Last updated (according to GEO): Oct 28 2005 Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18513.gif Source GEO sample is GSM91549 Last updated (according to GEO): Sep 22 2006 39 21 of substantia nigra on muscle fibres 1403 1418 865 Disorder of artery Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211248 Last updated (according to GEO): Jul 18 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11576 Last updated (according to GEO): May 28 2005 PGA-MCR-ctr-0h-2aAv2-s1 1000 Brain 78 66 Control blood 1000 Prostate C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 1 hour after the last shock treatment. Source GEO sample is GSM4529 Last updated (according to GEO): May 27 2005 Epithelial Cells 901 Myocardial Infarction 1000 ALL_20 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A no additional Source GEO sample is GSM199092 Last updated (according to GEO): Jun 08 2007 kidney 37 43 brain, unknown: C2B_e1_le1 19 0 human frontal cortex in the anteroventral cochlear nucleus 83 119 CNS-SpinalCsev-Adult-7d-4B-s2 Primary Neoplasm 1000 MGJZ030228093Bmedialolfactoryepithelium(MOE) Hippocampus 861 Blood 1000 19 0 human frontal cortex Head and neck cancer Source GEO sample is GSM155645 Last updated (according to GEO): Apr 24 2007 human frontal cortex Source GEO sample is GSM86986 Last updated (according to GEO): Feb 08 2006 NA Source GEO sample is GSM198909 Last updated (according to GEO): Jun 07 2007 ISR24 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153442 Last updated (according to GEO): Jan 11 2007 12 frontal Lobe 23 901 Mammary gland Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21272.gif Source GEO sample is GSM91562 Last updated (according to GEO): Sep 22 2006 861 Oocytes Sample Type: cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 15 ppm, 6 h time point Source GEO sample is GSM159772 Last updated (according to GEO): Apr 23 2007 Nose 1000 M_U133Plus_105_nAcc brain 0 5 966 Hippocampus Adenocarcinoma 861 TEL-AML1-2M#3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A /J pituitary gland rep2 1 23 5 0 brain Blood 861 Parkinson Disease 1000 human frontal cortex Source GEO sample is GSM87049 Last updated (according to GEO): Feb 08 2006 Spinal Cord 1000 861 Colon 492 475 in the PCOS oocyte 861 Cardiomyopathies Brn3a Knockout TG e13.5 U74Av2 1 Adult postmortem brain tissue (orbitofrontal cortex) from subjects with bipolar disorder and healthy controls Whole Brain 62 72 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68257 Last updated (according to GEO): Jul 07 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM144933 Last updated (according to GEO): Nov 20 2006 Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3881 Last updated (according to GEO): May 27 2005 1000 frontal lobe Expression profiling of spinal cord section (T10) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM4458 Last updated (according to GEO): May 28 2005 brain, ipsi Cortex: Trizol Extraction36_le1 Myometrium 9 Normal NA18620 966 Hippocampus f2#28 versus pool Mouse Brain tissue GSE611 Parkinson Disease 861 hippocampal glutamatergic CA3 pyramidal neurons Treatment, type=behavioral_stimulus, description=These are untreated animals. Source GEO sample is GSM35844 Last updated (according to GEO): May 27 2005 R642P00802 UBOC1 Exp A Day 2 (a) Hippocampus 1983 15 month Old CO_sham_med_4 Cerebellum Control (Alzheimer's disease control) MCF7_EtOH_24h_rep4 Type 1 Diabetes patient and the timepoint 1 month after diagnosis. Source GEO sample is GSM228653 Last updated (according to GEO): Sep 11 2007 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132560 Last updated (according to GEO): Feb 26 2007 B6 day 6, biological rep 1, tech rep 1 Expression profiling of spinal cord section (T8) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM6642 Last updated (according to GEO): May 28 2005 CAD_replicate50 Mouse Liver LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate C Gene expression data from postmorten brain regions Source GEO sample is GSM145793 Last updated (according to GEO): Nov 20 2006 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153436 Last updated (according to GEO): Jan 11 2007 Keywords = kidney 236 253 Expression profile of genes in mouse brain Source GEO sample is GSM21044 Last updated (according to GEO): May 27 2005 Total RNA was extracted from umbilical subcutaneous adipose tissue from an individual affected with FCHL and exhibiting the USF1 protective haplotype Source GEO sample is GSM9046 Last updated (according to GEO): May 28 2005 Parkinson Disease 1000 spinal cord 37 47 UBOC1 Exp A Day 1 (a) 1242 CP6_12 1000 Hyperthyroidism Obesity 1000 MGMH030211019Alung Sun212_TAV12 group 1000 Malignant neoplasm of breast Cnr1-/-/Cnr2-/- female number 1, DNFB-treated allergic ear (#10_Ko-Tr-4) Gene expression data from human prostate tissue with 90 percent tumor content Source GEO sample is GSM119312 Last updated (according to GEO): Feb 23 2007 brown fat; interscapular depression Source GEO sample is GSM18676 Last updated (according to GEO): May 27 2005 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15715 Last updated (according to GEO): May 28 2005 Cerebellum_nontransgenic control S46_10 months_replicate 3 Gene expression data from postmorten brain regions Source GEO sample is GSM145238 Last updated (according to GEO): Nov 20 2006 whole blood_100923 67 40 with coronary artery disease forebrain 7 15 Parkinson Disease 1000 virtaneva-aml8 1000 Brain 355 350 rectum 0 Human Cortex 11 M7TW00121815 Cerebral cortex 1000 Expression profiling of moderately injured raphe at 3 months in rats Source GEO sample is GSM41609 Last updated (according to GEO): May 27 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68220 Last updated (according to GEO): Jul 07 2006 with Parkinson's disease 27 50 901 frontal lobe 1000 Cardiomyopathy, Alcoholic Epithelial Cells 1000 M_U133Plus_89_HC Brain 861 1000 Brain Structure of entorhinal cortex 1000 human caudate nucleus Source GEO sample is GSM86806 Last updated (according to GEO): Feb 08 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145843 Last updated (according to GEO): Nov 20 2006 Cerebral cortex 861 FBooth-MDX-3Av2-s2 brain, hippocampus: Aldh5a1-/- #3389 Hippo_e1_le1 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD27 for 60min Source GEO sample is GSM5490 Last updated (according to GEO): May 27 2005 NHE1 null mutation cortex-1 861 Brain tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44888 Last updated (according to GEO): May 27 2005 Ganglia, Spinal 884 no additional Source GEO sample is GSM199370 Last updated (according to GEO): Jun 08 2007 HapMap CHB Male Source GEO sample is GSM159616 Last updated (according to GEO): Feb 01 2007 Carcinoma, Large Cell 884 the heart 987 996 Neuroglia 901 SCN2.2 Sample 8 (Exp#1-30 hr) corpus_callosum_10 Control frontal cortex 1 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53468 Last updated (according to GEO): Jul 06 2005 from the forebrain 20 37 468 459 the rectum Brain 861 10 Bone marrow 0 brain, cerebral cortex: Control 5_le1 20 0 human caudate nucleus Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68192 Last updated (according to GEO): Jul 07 2006 spinal cord, ventral spinal cord: D28WTMN1_e1_le1 7 0 prostate Brain 861 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:270, Count:32 Corner- Avg:37352, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:3.941622,SFGene:All Background:Avg:657.26,Stdev:6.43,Max:677.7,Min:641.9 Noise:Avg:12.21,Stdev:0.52,Max:14.7,Min:10.9 RawQ:16.85 Keywords = ALL Source GEO sample is GSM3393 Last updated (according to GEO): May 28 2005 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12376 Last updated (according to GEO): May 28 2005 brain, cerebellum: KCb12w#2_e1_le1 In intact animals, time of drug administration may be an important factor influencing drug response. Our general goal seeks to incorporate circadian time into the study of corticosteroid regulated gene expression. Since levels of endogenous steroid exhibit circadian fluctuations, it is our hypothesis that the expression of genes controlled by corticosteroids either directly or indirectly, will also exhibit a circadian pattern in normal animals. Last Updated (by provider): Sep 10 2007 Contributers: Richard Almon Gene expression data from biopsy of PBS treated skin of subject with pustule-former phenotype. (control) Source GEO sample is GSM128960 Last updated (according to GEO): Sep 13 2007 MV(LL) Spleen 4 Normal hrs nasal epithelium 1126 1146 ovary 45 50 Pineal gland 1000 esophagus_2 Source GEO sample is GSM80695 Last updated (according to GEO): Mar 31 2006 amygdala 886 894 Wild type P46 mouse visual cortex ipsilateral to monocular enucleation Source GEO sample is GSM97211 Last updated (according to GEO): Feb 17 2006 Macrophages, Exposed to Toxoplasma gondii - Repeat #2 Cerebral cortical contusion in rat, 1 and 4 dpi 829 813 between cirrhosis prostate Source GEO sample is GSM203300 Last updated (according to GEO): Jun 21 2007 0 Human Cortex 11 1000 Brain Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181134 Last updated (according to GEO): Jul 12 2007 Macrophage 14smi022 Normal Uterus 861 Immune system 05_0008_SepticShock_Day3_96 AML_16 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A with some respiratory epithelium. 1039 1072 861 Neoplasm 861 Malignant neoplasm of urinary bladder Plasma 861 cy5:WKY control, biological rep 1r; cy3:pool of 6 WKY control rats CH2127 Wild type 8 wk old male DBA/2J mouse bed nucleus of the stria terminalis Source GEO sample is GSM107001 Last updated (according to GEO): Mar 05 2007 Whole Brain 73 83 rat kidney at embryonic day 18, rep4 Adenocarcinoma 3 0 15 Keywords = kidney 113 130 237 214 with insulin resistance /Ovary 2 Disease 11 26 of metastasis 952 964 861 Colon Brain 861 mouse brain 478 489 Collagen 1000 861 Epithelial Cells 204 194 of retinal colon_cecum_1 in multiple myeloma 1037 1056 GM12044 KO_NP_mid_2 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5828 Last updated (according to GEO): May 27 2005 861 Neoplasm Heart 1000 Immature B cells 1 for liver 26 35 Hypertrophy, Left Ventricular 1000 Category: Cell-line Subcategory: HMEC This experiment was an out file converted from rana. The original files were not provided to load this experiment in Oracle. Category and Subcategories were made by curators. Scanning Software: unknown Software version: unknown Lot batch = 0376-5k Source GEO sample is GSM1929 Last updated (according to GEO): Nov 21 2005 M_U133A_109_nAcc 0 Human Cortex 11 Distinct gene expression profiles and reduced JNK signaling in retinitis pigmentosa caused by RP1 mutations. WGACON-29 D_U133Plus_38_nAcc Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188704 Last updated (according to GEO): Jun 06 2007 This dataset contains the gene expression profile of a CD11c high, CD8 positive splenic dendritic cell population. The cells were processed following 2 hour incubation in tissue culture medium at 37 C. Global scaling was applied to Avg Difference intensity values. Keywords = mouse, dendritic cells, spleen Source GEO sample is GSM4772 Last updated (according to GEO): May 27 2005 913 Acute leukemia none Source GEO sample is GSM149545 Last updated (according to GEO): Jan 03 2007 Heart 1000 861 Cancer of Neck brain, cerebellum: 3 hrs C LK_e1_le1 in chronic myeloid leukemia 373 400 Primary tumor 19 32 861 Cerebral cortex 1000 Spinal Cord Injuries 338 321 a Rhabdomyosarcoma Plasma 861 retina 5 10 Category: Cell-line Subcategory: Reproducibility Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp3306 Source GEO sample is GSM2136 Last updated (according to GEO): Nov 21 2005 901 Caudate nucleus structure 269813CD_4 1000 Infection Intestines, Small 1000 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114181 Last updated (according to GEO): Jun 16 2006 I_95Av2_3108_DLPFC_0_GS GM18858 R727P01204 HC62 CB A 901 Coronary artery 1500mg/kg APAP 24Hr rat 3624 blood vs. 3616 PC 24Hr (pool) Parkinson's disease sample x076 autism 0 5 CNS-SMTC_Mod7d-4B-s2 Congenital Abnormality 853 Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 8658 left_liver_lobe 901 Caudate nucleus structure outer medulla 31 43 1000 adenoma Parkinson Disease 1000 0029_1351_H95A2_KF-117_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 28 13 from spinal cord Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162158 Last updated (according to GEO): Jun 12 2007 TNF TG-13w-m-2 The current model to explain the organization of the mammalian nervous system is based on studies of anatomy, embryology, and evolution. To further investigate the molecular organization of the adult mammalian brain, we have built a gene expression-based brain map. We measured gene expression patterns for 24 neural tissues covering the mouse central nervous system and found, surprisingly, that the adult brain bears a transcriptional "imprint" consistent with both embryological origins and classic evolutionary relationships. Embryonic cellular position along the anterior-posterior axis of the neural tube was shown to be closely associated with, and possibly a determinant of, the gene expression patterns in adult structures. We also observed a significant number of embryonic patterning and homeobox genes with region-specific expression in the adult nervous system. The relationships between global expression patterns for different anatomical regions and the nature of the observed region-specific genes suggest that the adult brain retains a degree of overall gene expression established during embryogenesis that is important for regional specificity and the functional relationships between regions in the adult. The complete collection of extensively annotated gene expression data along with data mining and visualization tools have been made available on a publicly accessible web site (www.barlow-lockhartbrainmapnimhgrant.org). Last Updated (by provider): Nov 15 2005 Contributers: Matthew A Zapala Carrolee Barlow Includes GDS1490. Update date: May 08 2006. Dataset description GDS1490: Expression profiling of 24 neural tissues and 10 body regions from adult A/J, C57BL/6J, C3H/HeJ, DBA/2J, and 129S6/SvEvTac males. Relationship of regional gene expression in the brain to architecture and organization of the brain examined.. Normal Source GEO sample is GSM176224 Last updated (according to GEO): Apr 09 2007 I_U133A_10_CB ovary 45 50 Mouse Liver AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate D ER negative human primary breast tumor EA02014_41286_H133A_JA-1828 MP-11 brain, frontal cortex: Sham PM DR b_e1_le1 with myocardial infarction 313 339 22-oct-2002-BrainAsubA-ab150 Retroviral vectors for the four factors were transfected into Fbx15 bgeo-KI MEF. Cells were cultured with ES cell condition and selected with G418 for 16 days. Source GEO sample is GSM190224 Last updated (according to GEO): May 18 2007 Acetaminophen 3hr Rat 2698 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool 1000 Brain Stem Cerebral cortex 861 at the Human Brain 744 761 928 Endometrium Replicate1_Voxel C8 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68162 Last updated (according to GEO): Jul 07 2006 Epithelium 861 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15757 Last updated (according to GEO): May 28 2005 4h1 277 271 Retinas 20 0 human caudate nucleus 861 Colon 861 Brain T179 Cerebral cortex 861 This sample has two chips, therefore the values represent the average of the features from both chips. Source GEO sample is GSM227413 Last updated (according to GEO): Sep 12 2007 C57L/J Amygdala D Plasma 861 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211347 Last updated (according to GEO): Jul 18 2007 270 259 the amygdala seminoma specimen, pT1, patient age: 55y; W03 011 D_U133A_30_DLPFC Transplant Series 19 , Transplant # 4 Rat frontal cortex RNA - VH TTX Experiment Source GEO sample is GSM92320 Last updated (according to GEO): Jan 13 2006 plasma cells 332 344 40 21 from skeletal muscle Primary Carcinoma 876 Brain 861 Abdominal Aortic Aneurysm1-M f2#26 versus pool Mouse Brain tissue Met. Colon Carcinoid (SF11) 1000 Heart vehicle treatment, 1 hour time point, biological replicate 1 861 Ribosomal RNA Richard Almon-44-1133800610135 0029_1431_H95A2_T97-043_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Stromo vascular fraction from subcutaneous adipose tissue Source GEO sample is GSM210986 Last updated (according to GEO): Jul 17 2007 Infection 1000 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225763 Last updated (according to GEO): Nov 02 2007 D_U133A_22_nAcc CingulateCortex Source GEO sample is GSM18780 Last updated (according to GEO): Sep 25 2006 1000 Cerebral cortex 861 Cerebral cortex Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231041 Last updated (according to GEO): Sep 26 2007 Plasma 861 1000 Coronary Arteriosclerosis Liver Test (Blinded) Sample Source GEO sample is GSM130165 Last updated (according to GEO): Sep 18 2007 84 69 by heart failure 91 80 from bronchi 1000 frontal lobe Brain 861 bronchial epithelia 224 243 988 980 cerebella 7 0 prostate Post Natally excised CCAM 4 Wild type voxel E4 1000 Cerebral cortex Spleen vs Anti-IgM Treated B cell 240min (set1) GTP-Binding Proteins 901 Epithelial Cells 901 39 21 from mammary glands 91 from the bone marrow 72 7 frontal cortex 20 P21 cochlear nuclei 0 18 GSE6810 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225350 Last updated (according to GEO): Aug 31 2007 mouse brains 187 198 1000 Hippocampus putamen_2 BAL_18_A1B0 ovary 45 50 1000 Leukemia, Myelocytic, Acute 901 Caudate nucleus structure axons 294 298 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12342 Last updated (according to GEO): May 28 2005 901 Muscular Atrophy Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184801 Last updated (according to GEO): Apr 26 2007 Analysis of prefrontal cortex from 3 biological replicates of C57BL/6J mice at four Zeitgeber Times (ZT 3, 9, 15, and 21). Source GEO sample is GSM240419 Last updated (according to GEO): Oct 30 2007 15_0008_SepticShock_Day1_13 Bone Marrow 1000 S462_Mock_1 Stem cells 901 901 frontal lobe GBM: 69A34 #5 Bladder sample 919-1 Parkinson's disease sample x189 Small cell carcinoma of lung 867 861 Cerebral cortex of caudal 93 101 spinal cord 13 23 1000 Spleen emphysema. 257 267 Gene-expression profiles in hereditary breast cancer. to sex chromosomes 73 91 AMM_0_0_Male7_Olfact_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111850 Last updated (according to GEO): Nov 21 2006 bladder_T1GH_pool-3 913 Coronary heart disease Expression profiling of spinal cord section (T9) extracted from rats 28d following moderate injury Source GEO sample is GSM31545 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145176 Last updated (according to GEO): Nov 20 2006 GSE2880 Laser captured visceral sensory neurons. Source GEO sample is GSM63672 Last updated (according to GEO): Dec 21 2005 901 Muscle of orbit gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134612 Last updated (according to GEO): Jul 09 2007 1000 Communicable Diseases 1037 of transitional epithelium 1012 15 0 ciliary_ganglion 411 394 in blood pressure Neoplasm 861 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68322 Last updated (according to GEO): Jul 07 2006 Spinal Cord 861 Heart Atrium 4 Normal 861 Neurites 90 81 in stroke mouse brains 187 198 Expression profiling of spinal cord section (T9) extracted from rats 12h following moderate injury Source GEO sample is GSM31515 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 Female 24.4 yr before antibody enrichment scan 1 (U133B) Blood Test (Blinded) Sample Source GEO sample is GSM129975 Last updated (according to GEO): Sep 18 2007 1000 Huntington Disease ALS model Source GEO sample is GSM75479 Last updated (according to GEO): Mar 06 2006 Congenital Abnormality 853 Sun183_BAV13 group Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10036.gif Source GEO sample is GSM76411 Last updated (according to GEO): Sep 22 2006 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 24 h time point Source GEO sample is GSM159805 Last updated (according to GEO): Apr 23 2007 Preimplantation development is a crucial step for successful implantation and pregnancy. Although both compaction and blastocyst formation have been extensively studied, mechanisms regulating early cell division stages before compaction have remained unclear. Here, we show that ERK MAP kinase function is required for early embryonic cell division and normal cell-cell adhesion before compaction. Our analysis demonstrates that inhibition of ERK activation in the late 2-cell stage embryos leads to a reversible arrest in G2 phase in the 4-cell stage. The G2 arrested, 4-cell stage embryos show weakened cell-cell adhesion as compared to control embryos. Remarkably, microarray analyses show that most of the programmed changes of upregulated and downregulated gene expression during the 4- to 8-cell stages normally proceed in the 4-cell stage-arrested embryos, except for a portion of the genes whose expression profiles closely parallel the stages of embryonic development when arrested in G2 and released to resume development. These parallel genes include the genes encoding intercellular adhesion molecules, whose expression is found to be positively regulated by the ERK pathway. We also show that while ERK inactivation in the 8-cell stage embryos does not lead to cell division arrest, it does cause cell division arrest when cadherin-mediated cell-cell adhesion is disrupted. These results demonstrate an essential role of ERK function in the G2/M transition and the expression of adhesion molecules during the 2-cell to 8-cell stage embryos, and suggest a loose parallelism between the gene expression programs and the developmental stages before compaction. Last Updated (by provider): Mar 19 2007 Contributers: Momoko Maekawa Eisuke Nishida Takuya Yamamoto R436P00056 from liver 21 30 1000 Brain 861 Ganglia Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202670 Last updated (according to GEO): Jun 20 2007 12 0 ovarian tumor 865 Disorder of artery Gene expression data from controls Source GEO sample is GSM231004 Last updated (according to GEO): Sep 21 2007 hrs nasal epithelium 1127 1147 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n085 Source GEO sample is GSM2033 Last updated (according to GEO): Nov 21 2005 27_70603_SepticShock_Day1_6 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181092 Last updated (according to GEO): Jul 12 2007 Z4 biol repl 2 placenta-0649-uninflamed-past-rep1 Voxel G3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1433 Last updated (according to GEO): Nov 21 2005 hip_1067_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A (cortex 19 25 MGJZ030212027Bsalivarygland 12 frontal Lobe 23 Liver 1000 hippocampus 0 10 Neoplasm 861 10 0 Hippocampus DBA/2J_male_hypothalamus Source GEO sample is GSM184203 Last updated (according to GEO): Apr 26 2007 861 Chromosomes This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the lv samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12332 Last updated (according to GEO): May 28 2005 150 mg/kg X 24 hr Source GEO sample is GSM129832 Last updated (according to GEO): Sep 18 2007 Changes in mouse liver mRNA profiles following intra-peritoneal cytokine injection. One of 2 replicates of Interferon-gamma-/- mice, injected with phosphate-buffered saline, and killed after 4h. Source GEO sample is GSM5953 Last updated (according to GEO): May 27 2005 5 0 Spleen human frontal cortex Source GEO sample is GSM86942 Last updated (according to GEO): Feb 08 2006 at the Human Brain 724 741 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201289 Last updated (according to GEO): Jun 14 2007 Liver (fetal) [JunctionChip 2 of 5] 11 Bone marrow 0 901 Epithelial Cells Cell Culture: Hippocampal cells from E18 rat embryos were plated at a density of 500,000 cells per 60 mm poly-L-lysine (1mg/ml; Sigma) coated dish. Cultures were maintained at 37 C in 5% CO2 humidified incubator and used for experiments at 21 day in vitro (DIV). Control and experimental group cultures were incubated with 10 micro M TTX for 15 min followed by addition of 100 micro M baclofen or vehicle. Total RNA preparation: Each experimental group was compared as replicates of three. For each replicate cultured hippocampal neurones were harvested after 2 hours incubation +/- baclofen and total RNA was isolated using RNeasy Mini kit (Qiagen, UK) according to the manufacturer's protocol. Microarray Target Labelling and Hybridisation: Targets for cDNA microarrays were generated using 5 micro g of total RNA in a standard reverse transcription (RT) reaction. RNA was annealed, in 16 micro l water, with 1 micro g of 24-mer poly(dT) primer (Invitrogen, UK), by heating at 65oC for 10 min and cooling on ice for 2 min. The RT reaction was performed by adding 8 micro l of 5X first strand RT buffer (Life technologies, MD), 4 micro l of 20mM dNTPs minus dCTP (Pharmacia, UK), 4 micro l of 0.1M DTT, 40U of RNAse OUT (Life Technologies, MD), 6 micro l of 3000 Ci/mmol 33P-dCTP (ICN Biomedicals, UK) to the RNA/primer mixture to a final volume of 40 micro l. Two micro l (400 U) of Superscript II reverse transcriptase (Life Technologies, MD) was then added and the sample incubated for 30 min at 42oC followed by additional 2 micro l of Superscript II reverse transcriptase and another 30 min incubation. The reaction was stopped by addition of 5 micro l 0.5 M EDTA. Samples were incubated at 65oC for 30 min after addition of 10 micro l of 0.1M NaOH to hydrolyse and remove RNA. Samples were pH neutralized with 45 micro l 0.5M Tris, pH 8.0 and purified using Bio-Rad 6 purification columns (BioRad, UK). The NIA NeuroArray consists of 1152 cDNAs printed on nylon membrane in duplicate. The arrays were hybridised with alpha-33P-dCTP labelled cDNA probes overnight at 50oC in 4ml of hybridisation solution. Hybridised arrays were rinsed in 50ml of 2XSSC and 1%SDS twice at 55oC followed by two washes in 2X SSC and 1% SDS at 55oC for 15 min each. The microarrays were exposed to phosphorimager screens for 1-3 days. The screens were then scanned with Molecular Dynamics STORM PhosphorImager (Sunnyvale, CA) at 25 micro m resolution. Source GEO sample is GSM28538 Last updated (according to GEO): May 27 2005 1000 Amygdaloid structure hippocampus 7 17 CHIPEXP_NAME: 230_2_050531tpj_40h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Isoproterenol TREAT_TOX_MECHANISM1: Heart_Cardiotoxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0.5 SAMPLING_TIME: 3 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197617 Last updated (according to GEO): Jun 01 2007 hippocampus 7 17 Brain 861 comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247397 Last updated (according to GEO): Dec 11 2007 Coronary Arteriosclerosis 1000 1000 Hippocampus - Source GEO sample is GSM162901 Last updated (according to GEO): Aug 28 2007 Expression profiling of spinal cord section (T9) extracted from rats 24h following mild injury Source GEO sample is GSM31205 Last updated (according to GEO): May 27 2005 1000 Uterus low-grade dysplastic liver tissue Source GEO sample is GSM155978 Last updated (according to GEO): Jun 21 2007 Stem cells 901 673 659 by decapitation Liver Test (Blinded) Sample Source GEO sample is GSM130191 Last updated (according to GEO): Sep 18 2007 HC51 CB A 567 548 the descending colon 1000 Retina Deltoid Muscle 1 Normal 1000 Retina Sun194_TAV12 group cerebral cortex wistar ky 3912 all cortical minus the frontal cortex, individual animal, 10 weeks old, male Wistar Kyoto cerebral cortex file:p3912w Source GEO sample is GSM15149 Last updated (according to GEO): Oct 28 2005 Sensitized on days 0 and 3 with ragweed pollen protein and alum, challenged intratrecheally on days 10 and 17 with ragweed pollen protein and sacrificed after 72h. Lot batch = Source GEO sample is GSM1273 Last updated (according to GEO): May 28 2005 861 Malignant neoplasm of prostate no additional Source GEO sample is GSM199228 Last updated (according to GEO): Jun 08 2007 D04 3h TLR2/1L 1501 1481 a -myosin heavy chain heart 169 174 /J periaqueductal gray rep2 1 27 Fibroblasts 861 Spleen vs Lipopolysaccharide (LPS) Treated B cell 30min (set2) cingulate cortex 901 Leukemia, Lymphocytic, Chronic 1000 913 Acute leukemia 1000 Hippocampus 70 40 without coronary artery disease Mammary Gland @ Invo2, biological rep4 Epithelium 861 myotubes 826 833 The nose 94 101 0 Human Cortex 11 no additional Source GEO sample is GSM199146 Last updated (according to GEO): Jun 08 2007 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134632 Last updated (according to GEO): Jul 09 2007 129S1/SvImJ_male_hypothalamus Source GEO sample is GSM184189 Last updated (according to GEO): Apr 26 2007 861 HIV Infections The goal of this experiment was to compare mRNA isolated from synaptosomes (pre and post synaptic nerve endings) to total hippocampal mRNA in order to identify putative mRNAs that are enriched at the synapse. Source GEO sample is GSM126598 Last updated (according to GEO): Nov 22 2006 Osteoblasts 1000 1000 Coronary Arteriosclerosis CNS-SpinalC-conAdult-24h-1B-s2 Recurrent Squamous cell carcinoma 5 0 34 Chronic Lymphocytic Leukemia 19 47 861 Cochlear structure RR203_unifected_Skin_biopsy of the heart 842 854 3 0 Lung 5 0 brain /2J pituitary gland rep1 3 26 The genomic influcence of the combination of three reagents on cultured cortical neurons (9-11 DIV). Bursts of action potential firing were induced by the treatment of cultured cortical neurons with 50 ?M bicuculline (Bic) and 5 ?M 4-aminopyridine (4AP), which were abolished by the addition of the Ca2+ chelator EGTA (4 mM). Source GEO sample is GSM144059 Last updated (according to GEO): Nov 24 2006 osteoblast 627 637 AD control Treatment, type=dissect Source GEO sample is GSM119679 Last updated (according to GEO): Jul 10 2006 Keywords = Infectious diseases 1133 1163 Gene expression data from rat metanephric mesenchymes cultured for 2 days in the presence of LIF Source GEO sample is GSM126196 Last updated (according to GEO): Dec 08 2006 1100 1077 of Medulloblastoma - 8 - 5 0 brain Type 1 Diabetes patient and the timepoint 4 months after diagnosis. Source GEO sample is GSM228654 Last updated (according to GEO): Sep 11 2007 Hereditary Malignant Neoplasm 876 MP-DX-1 Heart Ventricle 1000 Some individuals are more vulnerable than others to chronic psychiatric illnesses, such as drug addiction or depression, but the neural and molecular mechanisms responsible for this are poorly understood. Although addiction and depression are known to have a strong genetic component, recent evidence has suggested that epigenetic mechanisms, such as histone acetylation, may also contribute. However, the mechanisms which integrate drugs of abuse or stress with changes in chromatin structure remain unclear. Here, we identify the activity-dependent class II histone deacetylase, HDAC5, as a central integrator of these stimuli with changes in chromatin structure and gene expression. We found that chronic, but not acute, exposure to cocaine or stress decreases HDAC5 function in the nucleus accumbens (NAc), a major brain reward region, which allows for increased histone acetylation and transcription of HDAC5 target genes. This regulation is behaviorally important, as loss of HDAC5 causes hypersensitive responses to chronic, not acute, cocaine or stress. Coupling gene expression microarrays and several bioinformatic approaches, we have gone on to identify the most likely HDAC5 target genes responsible for the behavioral maladaptations. One HDAC5 target, the Substance P Receptor, is upregulated in HDAC5 knockout mice, has increased histone acetylation on its promoter, and modulates cocaine reward, as measured by conditioned place preference. These findings suggest that proper balance of histone acetylation is a crucial factor in the saliency of a given emotional stimulus, and that disruption of this balance is involved in the transition from normal adaptive responses to chronic psychiatric illness. Last Updated (by provider): Sep 26 2007 Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM107999 Last updated (according to GEO): Jun 06 2006 Kidney YC-3A c_NY103 Primary tumor 19 32 114 101 brains quickly Plasma 861 Disease Source GEO sample is GSM176361 Last updated (according to GEO): Apr 09 2007 cardiac 763 769 Brain 861 Infection 1000 NA12750 growth 2 Gene expression data from human colon tumor tissue Source GEO sample is GSM173324 Last updated (according to GEO): Apr 20 2007 nostrils 156 164 858 Mesodermal cell 1000 Brain 315 312 left GC (HKG89N) Spleen vs IL10 Treated B cell 30min (set1) Glycosuria, Renal 873 Epithelium 861 JMR-MurInj8h-2bAv2-s2 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3336 Last updated (according to GEO): Mar 21 2006 GM19132 none Source GEO sample is GSM244639 Last updated (according to GEO): Nov 23 2007 nasal epithelial cells 28 49 plasma cells 50 61 Rett syndrome 0 12 5 0 brain cerebral cortex 7 21 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27672.gif Source GEO sample is GSM66557 Last updated (according to GEO): Sep 22 2006 none Source GEO sample is GSM244541 Last updated (according to GEO): Nov 23 2007 Central gray substance of midbrain 861 5 0 brain 1000 Hyperinsulinism 2500mg/kg APAP 12Hr rat 4136 blood vs. PC 12Hr rat 4126 blood 1000 Diabetes Mellitus, Non-Insulin-Dependent M_U133Plus_113_CB NA18856 14 7 amygdala 1000 ovarian neoplasm Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. 8h after sham surgery, a 4 mm diameter disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44506 Last updated (according to GEO): May 27 2005 467 458 the rectum A2780_oxa_IC90_16h_2 Parkinson's model voxel G1 901 Coronary artery 861 Skeleton SN:Human Glioblastoma Biopsy 10516 Ileum [JunctionChip 1 of 5] Blood 861 861 Skeletal bone These data were used as preliminary results for paper: Maternal Cocaine Administration Alters DNA Methylation in Hippocampal Neurons of Neonatal and Prepubertal Mice Svetlana I. Novikova, Fang He, Jie Bai, Nicholas J. Curtufello, Ashiwel S. Undie and Michael S. Lidow Source GEO sample is GSM154051 Last updated (according to GEO): Jan 19 2007 CNS-SpinalCsev-Adult-28d-4B-s2 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19259 Last updated (according to GEO): May 27 2005 Spleen vs Prostaglandin E2 Treated B cell 60min (set1) lung.1 1000 Structure of locus ceruleus Liver 1000 Disease Source GEO sample is GSM176257 Last updated (according to GEO): Apr 09 2007 1000 Ischemia GSE5019 861 Endometrium 3AMH02082801_BM_CD71EarlyErythroid 1000 Brain 1000 Spleen f2#151 versus pool Mouse Brain tissue plasma cells 50 61 CNS-SCsev_InjB4h-1C-s2 1000 Liver Brain 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145806 Last updated (according to GEO): Nov 20 2006 12 0 ovarian tumor Heart 861 Carcinoma of bladder 1000 of mouse brain 9 23 Infection 1000 Simple annotation: Metastatic tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12397.gif Source GEO sample is GSM79789 Last updated (according to GEO): Sep 22 2006 #24 (isolate H rich media PlGF 24hours) Lymphoblastoid Cell Line for Individual 8194.4 log phase Female3, Respiratory RNA_Nasal respiratory epithelium_Tissue was preserved in RNA Later and collected from nose Wild type 8 wk old male A/J mouse cingulate cortex Source GEO sample is GSM74944 Last updated (according to GEO): Feb 27 2007 Microarray analysis of NL and PCOS oocytes (NL2) Whole Brain 62 72 Prostate [JunctionChip 3 of 5] Coronary artery 901 Pooled EDL RNA samples from five 8 wk old male mdx5cv mice Source GEO sample is GSM13665 Last updated (according to GEO): May 28 2005 Primary Neoplasm 1000 R465P00426 1-4 Dentate Gyrus 7 23 no additional Source GEO sample is GSM199144 Last updated (according to GEO): Jun 08 2007 Large-scale analysis of the mouse transcriptome. Spinal cord, lower half C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 254.78 Stdv: 7.36 Min: 243.37 Max: 267.33 Source GEO sample is GSM2917 Last updated (according to GEO): May 27 2005 CC034B pfc_1017_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 861 Neoplasm ALL-B-cell-7 on Affymetrix GeneChip Human Full Length Array HuGeneFL cingulate cortex 861 AD-234t1(dup)-A155-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Prostatic Diseases 913 AD control Treatment, type=dissect Source GEO sample is GSM119624 Last updated (according to GEO): Jul 10 2006 outer medulla 31 43 901 Caudate nucleus structure M_U133A_106_nAcc To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.. Date GSE1145 Last Updated: May 29 2005 Contributers: Paul Allen Seigo Izumo Masako Tsubakihara Jozef Bartunek Jeffrey Brown Lauren E Riggi Martina Schinke Allen Paul Includes GDS651. Update date: Aug 02 2004. Dataset description GDS651: Examination of left ventricle in idiopathic dilated and ischemic cardiomyopathy. Diseased ventricles examined in reference to normal.. 5 0 brain Heart Atrium 1000 220 202 mental retardation brain, brainstem: PB7_e1_le1 Spleen vs Neuropeptide Y Treated B cell 913 Coronary heart disease human cerebellum Source GEO sample is GSM87101 Last updated (according to GEO): Feb 08 2006 861 Myositis Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:278, Count:32 Corner- Avg:40129, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:4.219163,SFGene:All Background:Avg:415.84,Stdev:15.46,Max:471.8,Min:386.3 Noise:Avg:9.28,Stdev:0.44,Max:11.1,Min:8.1 RawQ:12.67 Keywords = ALL Source GEO sample is GSM3442 Last updated (according to GEO): May 27 2005 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 2 hour after the last shock treatment. Source GEO sample is GSM4531 Last updated (according to GEO): May 27 2005 LT-Hematopoietic stem cell isolated by flow cytometry Source GEO sample is GSM149531 Last updated (according to GEO): Apr 27 2007 861 Adrenal Medulla Simple annotation: Adenoma, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10018.gif Source GEO sample is GSM79846 Last updated (according to GEO): Sep 22 2006 861 Cardiomyopathies NA18592 Prostate 861 S462_Infect_3 19 0 amygdala wistar 3723 Liver 1000 Posterior root of spinal nerve 861 D_U133Plus_97_Amy fetal lung fibroblast #2 , asynch repeat l 861 Cochlear structure CNS-SC_CtrA4h-2B-s2 Whole Brain 73 83 21 0 Rat vestibular ganglia ER-/LN-/Nevins24 on Affymetrix GeneChip Human Full Length Array HuGeneFL forebrain 7 15 Heart 861 I_U133Plus_94_AnCg Hippocampus 1000 1000 Hippocampus GTP-Binding Proteins 1000 cerebral_cortex_9 Source GEO sample is GSM80642 Last updated (according to GEO): Mar 31 2006 41 29 Control blood 661 649 how the liver Platelet activating factor receptor and innate immunity: 251186829677 1000 Retina 10 week mutant OMN rep 1 Whole neuroblastoma tumor_2181 Heart Ventricle 1000 338 333 brain Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM113534 Last updated (according to GEO): Jul 11 2006 15 7 brainstem D_U133A_5_DLPFC normal human skeletal muscle sample 4 Mouse_E13.5_Front_Middle_Back_16 Callosal Neurons P14 2 Myocardial Infarction 1000 134T 861 Neoplasm Hippocampus_Rasgrf1KO_rep3 VDXKIU_1708 PGA-RnSalt_h_3w_2-m5 5 0 brain ILS/ISS_cerebellum_naive_436 H9DKG00061403 861 Skeletal bone Spinal Cord 1000 PGA-Band_24h_5-m5 Exp A_3, 1mg/kg CPF 191 181 of ischemia 913 Lipid droplet D_U133A_43_DLPFC Gene expression data from postmorten brain regions Source GEO sample is GSM144951 Last updated (according to GEO): Nov 20 2006 stomach_fundus_3 skin 80 83 861 Cerebral cortex Gene expression data from postmorten brain regions Source GEO sample is GSM146039 Last updated (according to GEO): Nov 20 2006 Embryonic day 18 callosal projection neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription. Source GEO sample is GSM37082 Last updated (according to GEO): May 27 2005 Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep8 Y YOKE D060 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108655 Last updated (according to GEO): Aug 22 2006 Standard affymetrix protocol Source GEO sample is GSM119728 Last updated (according to GEO): Jul 31 2007 40 21 from skeletal muscle Gene expression data from colorectal adenoma. Source GEO sample is GSM215106 Last updated (according to GEO): Aug 02 2007 248-97_LCLC Tumor__CNS_Medulloblastoma_M49_A2 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Leukemia, Lymphocytic, Chronic 1000 Brain 1000 901 Muscular Atrophy Expression data from embryonic rat kidney timepoints and a budded WD-MM recombination tissue 901 Caudate nucleus structure Male Sprague-Dawley rats (400Ã?±25 g) were anesthetized with sodium pentobarbital. 21d after sham surgery, a 7 mm disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44495 Last updated (according to GEO): Oct 28 2005 Thyroid_022LAFBO_045.txt 913 Spinal Injuries 1000 Lung GSE7075 1000 Brain Forebrain 229 237 5 0 brain A Proposed Mechanism for the Protective Effect of Dioxin Against Breast Cancer: MECHANISM FOR CANCER PROTECTION BY DIOXIN. 0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point, biological rep 1 Communicable Diseases 1000 HMEC S1 day 7 sample 1 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160199 Last updated (according to GEO): Feb 08 2007 in the mouse small intestine 73 100 861 Parkinson Disease Nose 1000 71 56 by heart failure in blood 16 23 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211382 Last updated (according to GEO): Jul 18 2007 Mesenchymal Stem Cells 1000 Tumor__Lymphoma_Large_B-Cell_L_B_CELL_S98_17557_R on Affymetrix GeneChip Human 35K SubA Array Hu35k-A welsh-prostate PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls. All samples were normalized with quantile normalization and summarized using RMA. Source GEO sample is GSM135579 Last updated (according to GEO): Dec 19 2006 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225671 Last updated (according to GEO): Nov 02 2007 1000 Muscle none Source GEO sample is GSM149514 Last updated (according to GEO): Jan 03 2007 of coronary artery disease 258 284 Mouse_E13.5_Front_Middle_Back_3 Ovary_PD1_Foxo3 Wt_Replica 1 1000 Hypertensive disease The nose 94 101 Medulla 861 NA12751 growth 1, replicate 3 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211245 Last updated (according to GEO): Jul 18 2007 kidney 37 43 no additional Source GEO sample is GSM199361 Last updated (according to GEO): Jun 08 2007 lg_NY13 1000 Hypertrophic Cardiomyopathy 31 in the frontal cortex 51 DRG_control_5h_rep2 1000 ovarian neoplasm The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27021 Last updated (according to GEO): May 27 2005 A498 hgu95b from brain 21 30 E2A-PBX1-C8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A nasal epithelial cells 28 49 plasma cells 50 61 cerebral Source GEO sample is GSM67206 Last updated (according to GEO): Jan 19 2006 Mammary Gland @ Preg19, biological rep3 whole blood 34 44 1000 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145487 Last updated (according to GEO): Nov 20 2006 embryo_released_at_day4.5_rep2 31 21 spinal cord SN6h(2) 434_1 861 Brain Expression profiling of spinal cord section (T10) extracted from rats 28d following severe injury Source GEO sample is GSM31368 Last updated (according to GEO): May 27 2005 Wild type 8 wk old male A/J mouse bed nucleus of the stria terminalis Source GEO sample is GSM106995 Last updated (according to GEO): Mar 05 2007 865 Disorder of artery Primary tumor 19 32 Undifferentiated Carcinoma (HK17) 259_1 NA12813 361 335 hypertrophic cardiomyopathy GSE7309 858 Mesodermal cell of brain neurospheres 155 176 Chronic Lymphocytic Leukemia 19 47 brain 0 5 AML cDNA hybridization-ID70-L MLL_19 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Spleen 32 0 Neurodegenerative brain disorders To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Source GEO sample is GSM28448 Last updated (according to GEO): May 27 2005 Tumor__Breast_Adeno_93_I_250 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A UET-13TR-EWS/FLI1 24hr tet+ 1000 Spleen I_U133A_101_AnCg Healthy patient. Source GEO sample is GSM228566 Last updated (according to GEO): Sep 11 2007 Lung 861 Exp 2 (+TNFa) Parkinson Disease 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145612 Last updated (according to GEO): Nov 20 2006 1BJZ02060602_CardiacMyocytes RNA from muscle biopsy specimen Source GEO sample is GSM3721 Last updated (according to GEO): May 27 2005 Spleen vs Platelet activating factor Treated B cell Cells captured via Arcturus LCM system, amplified (RiboAmp, 2 rounds) and labeled (Enzo) for hybridizaton to Affymetrix MG_U74Av2 arrays, using manufacturers protocols in each step. Source GEO sample is GSM6197 Last updated (according to GEO): Mar 10 2006 none Source GEO sample is GSM123221 Last updated (according to GEO): Jul 26 2006 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211372 Last updated (according to GEO): Jul 18 2007 ATCC number CRL-1502 Source GEO sample is GSM6809 Last updated (according to GEO): May 27 2005 861 Brain prostate Source GEO sample is GSM203403 Last updated (according to GEO): Jun 21 2007 Ganglia, Spinal 1000 brain 0 5 Lymphoblastoid Cell Line for Individual 8132.4 log phase normal lung 1037 Source GEO sample is GSM17287 Last updated (according to GEO): May 28 2005 GM11994 M_U133Plus_124_DLPFC Visceral Afferents 1000 HC68 CB A ER+/LN-/Nevins38 on Affymetrix GeneChip Human Full Length Array HuGeneFL NA18992 Normal Source GEO sample is GSM176247 Last updated (according to GEO): Apr 09 2007 Dendrites 1000 1000 jejunum 983 nervous system disorder HC102 FC BA4 B none Source GEO sample is GSM149544 Last updated (according to GEO): Jan 03 2007 Nervous system structure 901 Plasma 861 NMDA 10 (7/8 RC) (Experiment NMDA1-Run 9136) Treatment, type=time_course, description=samples are treated for 10, 30 or 60 min with NMDA 1mM, the agonist is then washed out and the cells are harvested 24h later, measurement=10.0 m Source GEO sample is GSM96713 Last updated (according to GEO): Feb 14 2006 Gene expression data of substantia nigra from postmortem brain of PD patients Source GEO sample is GSM184373 Last updated (according to GEO): May 29 2007 Parkinson's disease sample x019 CNS-RM_Mod14d-4C-s2 DLCL-0024 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210413 Last updated (according to GEO): Jul 16 2007 5 0 Spleen peripheral blood-CD8TCells Source GEO sample is GSM18880 Last updated (according to GEO): Sep 25 2006 PMN_control_180min_Patient6 597 578 in the dentate gyrus 861 Dislocations **** Source GEO sample is GSM4316 Last updated (according to GEO): May 27 2005 Standard affymetrix protocol Source GEO sample is GSM119724 Last updated (according to GEO): Jul 31 2007 1037 of transitional epithelium 1012 151T n/a Source GEO sample is GSM178061 Last updated (according to GEO): Jun 11 2007 V5-P158 GM12752 Muscle Source GEO sample is GSM4298 Last updated (according to GEO): May 27 2005 Nerve 1000 Muscle 861 A/J Cingulate Cortex D WGACON-37 1000 Brain bc-ZT21-3 D_U133A_35_DLPFC Spinal Cord 901 Heart Ventricle 1000 V5-P107 Replicate3_Voxel B3 1BJZ02081484b_TemporalLobe Knockout cocaine, biological replicate 6 Chronic Lymphocytic Leukemia 19 47 YFPH-SomatosensoryCortex-replicate1 1000 frontal lobe GSE7578 D_U133A_64_DLPFC CNS-SpinalCsev-Adult-28d-2A-s2 1000 DNA, Mitochondrial 1000 Blood 11 0 Astrocytomas PBMCs-Type 1 Diabetes-IDDM11_T1D_New M_U133Plus_110_DLPFC HapMap CEU_parent Female Source GEO sample is GSM159521 Last updated (according to GEO): Feb 01 2007 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68152 Last updated (according to GEO): Jul 07 2006 Primary Neoplasm 1000 no additional Source GEO sample is GSM199309 Last updated (according to GEO): Jun 08 2007 1000 Brain no additional Source GEO sample is GSM199185 Last updated (according to GEO): Jun 08 2007 10 Bone marrow 0 Brain 1000 substantia nigra 0 15 Replicate2_Voxel D4 5 0 brain 1122 1108 muscle atrophy Blood 861 Malignant Neoplasms 861 CH2126 brain 1278 1283 15 0 human cerebellum Meningioma Primary Grade 2 U133A Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108014 Last updated (according to GEO): Jun 06 2006 12 0 ovarian tumor Plasma 861 Plasma 861 of mouse brain 9 23 Neuroglia 901 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225728 Last updated (according to GEO): Nov 02 2007 of mouse brain 9 23 Tongue Superior With Papillae 4 Normal HNC2914 no additional Source GEO sample is GSM199158 Last updated (according to GEO): Jun 08 2007 1000 Intestines, Small 1000 Mammary gland 861 Neoplasm Medulla 861 69 58 odontoblasts DRG010_b 136 131 Aortae 329 306 valvular cardiomyopathy Bladder sample 320-7 FSCC3 on Affymetrix GeneChip Human Full Length Array HuGeneFL Spleen 1000 Luminal breast tumor cell line BT474 Keywords = Agilent microarray, Expression analysis, EGFR, Breast cancer growth Source GEO sample is GSM29510 Last updated (according to GEO): Dec 13 2006 Left 1000 901 Contact Dermatitis gfp neg. sorted cells from 3 disected e14.5 cortecies Treatment, type=wait Source GEO sample is GSM135782 Last updated (according to GEO): Sep 12 2006 1000 Skeletal muscle structure BPH-37 on UMich-10k 1000 Hypertrophic Cardiomyopathy Whole Brain 62 72 GSE1294 brain, Left frontal Lobe: Extract15_le2 GSE7305 Endometrium 5 Normal E2A-PBX1-#4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Congenital Abnormality 853 Normal Source GEO sample is GSM176404 Last updated (according to GEO): Apr 09 2007 Sham 5 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107479 Last updated (according to GEO): May 01 2006 1000 Spleen lung Source GEO sample is GSM18654 Last updated (according to GEO): May 27 2005 Brain 1000 GSE395 Integumentary system 861 D_U133Plus_125_nAcc PS cDKO / Control, 6 months 28 that the cerebral cortex 51 Spleen vs Untreated B cell Time 0 (set14) Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n130 Source GEO sample is GSM2042 Last updated (according to GEO): Nov 21 2005 CNS-SC_Inj24h-3C-s2b of somatomotor cortex 21 41 Cerebellum 1000 to the nose 599 609 anatomy 1000 17 7 hippocampus 861 Cerebral cortex Spleen 0 5 none Source GEO sample is GSM241954 Last updated (according to GEO): Nov 29 2007 no_pre_LPS_restimulation_rep_A PBMCs-Type 1 Diabetes-IDDM6_T1D_New Medulla Oblongata 861 36 21 from hippocampus 1000 Brain brain 0 5 umbilical cord_bpd: 7H Blood 861 Wild type inbred mice Source GEO sample is GSM82940 Last updated (according to GEO): Nov 10 2005 mouse brain contralateral control Source GEO sample is GSM149750 Last updated (according to GEO): Mar 15 2007 Skeletal bone 861 Fibroblasts 1000 M_U133A_22_HC PC-3 hgu95e Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92296 Last updated (according to GEO): Jan 13 2006 CA95-198B Cerebral cortex 901 Brain 861 in the brain 150 162 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:523, Count:32 Corner- Avg:38268, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:10.581564,SFGene:All Background:Avg:529.04,Stdev:29.11,Max:602.6,Min:483.5 Noise:Avg:16.79,Stdev:1.70,Max:23.5,Min:13.4 RawQ:16.87 Keywords = ALL Source GEO sample is GSM3503 Last updated (according to GEO): May 27 2005 Muscle Fibers 1000 (No additional Information) Source GEO sample is GSM114393 Last updated (according to GEO): Jun 19 2006 n/a Source GEO sample is GSM178022 Last updated (according to GEO): Jun 11 2007 7 cerebral cortex 21 861 Acquired Immunodeficiency Syndrome 1000 Structure of superior frontal gyrus Fetal frontal cortex cocaine5 Prostaglandin J2 alters gene expression patterns and 26S proteasome assembly in human neuroblastoma cells Expression profiling of moderately injured raphe at 3 months in rats Source GEO sample is GSM41603 Last updated (according to GEO): May 27 2005 NA18853 C57BL10 gastroc sample 2 M_U133A_82_DLPFC HCC (HBV+, HK18) NoCAD_replicate2 130 111 of coxsackievirus B3 0 Human Cortex 11 midbrain_6 Source GEO sample is GSM80704 Last updated (according to GEO): Mar 31 2006 Blood Test (Blinded) Sample Source GEO sample is GSM129919 Last updated (according to GEO): Sep 18 2007 Expression profiling of spinal cord section (T10) extracted from rats 4h following laminectomy (sham) Lot batch = Source GEO sample is GSM4437 Last updated (according to GEO): May 28 2005 B220hi sIgM+ Mature B cells sorted out of mouse bone marrow, sort no. 3 Source GEO sample is GSM624 Last updated (according to GEO): Mar 17 2006 Expression profiling of somatomotor cortex extracted from rats at 14d following sham surgery Source GEO sample is GSM41635 Last updated (according to GEO): May 27 2005 Prostatic Diseases 913 1292 1263 within the CA1 neuronal field We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201796 Last updated (according to GEO): Jun 20 2007 Spleen vs MIP3-alpha Treated B cell 120min (set3) 673 659 by decapitation 1000 Structure of middle cerebral artery SCG_sema3A_5h_rep2 HCT-15 hgu95d Cultured_osteoblast-like_control_MC3T3-E1_cells_rep3 Human prostate cancer cells in different conditions Source GEO sample is GSM13095 Last updated (according to GEO): May 28 2005 AJ 14-4-1 Spleen Brain 1000 B10.PL mice with experimental autoimmune encephalomyelitis (MS model) were treated with either placebo or 200 ng 1,25(OH)2D3. Six hours later, the spinal cords were harvested and mRNA extracted for analysis. Naive mice served as controls. Keywords = Experimental autoimmune encephalomyelitis Keywords = multiple sclerosis Keywords = 1 Keywords = 25(OH)2D3 Source GEO sample is GSM13048 Last updated (according to GEO): May 28 2005 Total RNA from cultured stria vascularis, pool from 12 cochleas; used as control for hypoxia. Source GEO sample is GSM124841 Last updated (according to GEO): Aug 04 2006 human caudate nucleus Source GEO sample is GSM86906 Last updated (according to GEO): Feb 08 2006 Primary Neoplasm 1000 468 459 the rectum brainstem 7 15 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118353 Last updated (according to GEO): Jul 11 2006 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 6 hour after the last shock treatment. Source GEO sample is GSM4538 Last updated (according to GEO): May 27 2005 Male 73.5 yr before antibody enrichment scan 1 (U133A) Gene expression data from liver Source GEO sample is GSM243399 Last updated (according to GEO): Nov 16 2007 Adipose tissue 884 The aim of this study was to investigate whether the differences in memory decline associated with aging are a result of differences in gene expression. We first categorized age-unimpaired and age-impaired rats based on their performance in the Morris water maze, when compared to young rats. Then we isolated messenger RNA from the dentate gyrus of the hippocampus of each animal to interrogate Affymetrix RAE 230A rat genome microarrays. Supervised statistical analysis of the different groups of aged animals recognized 85 genes (p<0.005) that were significantly different in the dentate gyrus of aged rats that had learned the Morris water maze (MWM) paradigm when compared to learning impaired and a number of controls for stress, exercise and non-spatial learning. In addition, statistical analysis of the microarray data that included young and aged rats identified 1129 genes (p<0.005) that were differentially expressed between aged and young rats independent of behavior, but due to aging alone. Last Updated (by provider): Aug 22 2006 Contributers: Henry H Baker Nicholas Muzyczka Cecilia Lopez Corinna Burger Ron J Mandel outer medulla 31 43 GM18501 673 659 by decapitation in the brain 150 162 1000 Spleen NA12236 Cultured_cortical_astrocyte_Cx43_siRNA_rep1 214 210 uteri 861 Alzheimer's Disease human frontal cortex Source GEO sample is GSM86959 Last updated (according to GEO): Feb 08 2006 315 312 left 831 809 notably muscle atrophy Control rats 1h after injection with PBS Treatment, type=time_course, description=Control animals are treated with PBS, measurement=1.0 h Source GEO sample is GSM32072 Last updated (according to GEO): May 27 2005 H9LMS99102622 Skeletal muscle structure 1000 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12503.gif Source GEO sample is GSM79899 Last updated (according to GEO): Sep 22 2006 to the nose 599 609 Brain 1000 of spinal cord injury 695 716 NHF10-hTERT_M_C3_26595 E6.25_rep1 Brain 1000 7 cerebral cortex 21 1000 Skeletal muscle structure 14 days hindlimb suspended, 1 day reloaded RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis. Source GEO sample is GSM10058 Last updated (according to GEO): May 28 2005 no additional Source GEO sample is GSM199381 Last updated (according to GEO): Jun 08 2007 FBooth-MDX-5Av2-s2 Carcinoma 861 Balb/c to C57/BL6 Source GEO sample is GSM8928 Last updated (according to GEO): May 28 2005 1000 Brain in mouse hearts 40 54 B220+CD25+sIg- Large Pre BII cells sorted out of mouse bone marrow, sort no. 2 Source GEO sample is GSM644 Last updated (according to GEO): Mar 20 2006 Prefrontal Cortex 0 16 59 CN B salivary Source GEO sample is GSM67246 Last updated (according to GEO): Jan 19 2006 Expression profiling of moderately injured raphe at 7d in rats Source GEO sample is GSM41625 Last updated (according to GEO): May 27 2005 Brain 1000 brain, cerebellum: 6 hrs C LK_e1_le1 Utricle and 3 ampullae at E13.5, replicate1 embryonic hearts 1064 1079 human cerebellum Source GEO sample is GSM87153 Last updated (according to GEO): Feb 08 2006 To add Source GEO sample is GSM209390 Last updated (according to GEO): Jul 25 2007 RNA from three stroke patients was pooled. Source GEO sample is GSM239103 Last updated (according to GEO): Oct 29 2007 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8823.gif Source GEO sample is GSM76459 Last updated (according to GEO): Sep 22 2006 861 Cerebral cortex Brain 1000 H Fed Rep 3 Phenytoin frontal cortex 2 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53462 Last updated (according to GEO): Jul 06 2005 Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles. PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity. Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence. To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips. Source GEO sample is GSM136554 Last updated (according to GEO): Jun 05 2007 cerebellum 0 9 861 Malignant Neoplasms 1000 Skeletal muscle structure comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247393 Last updated (according to GEO): Dec 11 2007 with autism spectrum disorder 37 65 861 Heart ileum 861 Endometrium 10 Normal WGACON-44 Hyperdip>50-C14 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A In this time course pregnant CD-1 (outbred) dams were exposed to MeHg as monomethylmercuric chloride intraperitoneally on 9 d.p.c. The test dose of 5.0 mg/kg MeHg was selected as a dose with an estimated 20% increased risk for encephalopathy in term fetuses, with no evidence of maternal toxicosis. Sampling intervals ranged from 1.5h to 24.0h post-exposure. All measurements were on RNA from the embryonic forebrain (prosencephalon) using contemporous control embryos as a reference.. Date GSE1076 Last Updated: May 29 2005 Contributers: Thomas B Knudsen Amar V Singh Jeffrey H Charlap Kimberly R Nemeth Includes GDS636. Update date: Jul 14 2004. Dataset description GDS636: Temporal analysis of methylmercury (MeHg) exposure in embryos. Pregnant 9 days post coitum CD-1 dams injected with 5.0 mg/kg MeHg. Embryonic forebrain examined at 1.5 - 24 hours post-treatment. MeHg induces symptoms of fetal minamata disease (FMD).. Liver 1000 processed in batch 6 Source GEO sample is GSM90420 Last updated (according to GEO): Mar 20 2006 PL/J_male_hypothalamus Source GEO sample is GSM184214 Last updated (according to GEO): Apr 26 2007 M7TW00121354 1000 Hippocampus Prostate carcinoma 861 Mesenchymal Stem Cells 1000 P18 deprived visual cortex replicate 2 folatesufficientAs0ppm4 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211308 Last updated (according to GEO): Jul 18 2007 Brain 1000 45 CN B Plasma 861 289 280 infection 861 Malignant neoplasm of prostate Nasal Epithelium Inhalation Formaldehyde 07ppm 8d ID146 Pooled diaphragm RNA samples from five 8 wk old male mdx mice Source GEO sample is GSM13566 Last updated (according to GEO): May 28 2005 Olfactory Epithelium 1000 Spleen vs SDF1 alpha (Stromal cell derived factor-1) Treated B cell 30min (set2) Embryonal carcinoma, NCR-G2, non adherent Abdominal aortic aneurysm obtained from surgery to correct. Source GEO sample is GSM170551 Last updated (according to GEO): Jul 26 2007 WGACON-113 atrial septal defects 198 218 of Parkinson's disease 450 471 156-96_Adeno gene expression data from brain area 8/9 of a 6 year-old girl suffering from from Rett Syndrome (RTT) 6yr, RNA labeled and hybridized Aug. 2001 Source GEO sample is GSM160309 Last updated (according to GEO): Feb 05 2007 A VIS D033 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108620 Last updated (according to GEO): Aug 22 2006 This study explores the profiles of genes expressed during conditional differentiation of inner ear hair cell precursors in vitro. The cell line UB/OC-1 was derived from mouse embryonic organs of Corti (Rivolta et al, Proc. R. Soc. Lond. B 265: 1595-1603, 1998) and it can be induced to differentiate upon a temperature shift. The study has been replicated in two separate populations of cells, named Exp A and Exp B. Exp A includes daily time points from 0 to 9 days, then 11 and 14 days. Exp B includes days 0, 2, 4, and 9. The manuscript associated to this work is Rivolta et al., Genome Research 12(7):1091-1099, 2002.. Date GSE36 Last Updated: May 29 2005 Contributers: Marcelo N Rivolta Matthew C Holley Michael A Tones Claire M Johnson Antony Halsall Includes GDS51. Update date: Apr 04 2003. Dataset description GDS51: Gene expression profile of differentiation of inner ear hair cell precursors in vitro. A conditionally immortal cell line derived from the mouse cochlea, UB/OC-1, examined from 0 to 14 days.. Includes GDS45. Update date: Apr 04 2003. Dataset description GDS45: Gene expression profile of differentiation of inner ear hair cell precursors in vitro. A conditionally immortal cell line derived from the mouse cochlea, UB/OC-1, examined from 0 to 14 days.. RPMI8402 DMSO control 24h rep2 Gene expression data from human prostate tissue with 90 percent tumor content Source GEO sample is GSM119309 Last updated (according to GEO): Feb 23 2007 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134610 Last updated (according to GEO): Jul 09 2007 Macrophage 14smi071 from the spinal cord 14 33 5 0 Spleen brain, Entorhinal Cortex: Sample2_e1_le2 0 Human Cortex 11 DMSO-control NG108 neuronal cells 1 Expression profiling of spinal cord section (T9) extracted from rats 14d following severe injury Source GEO sample is GSM31590 Last updated (according to GEO): May 27 2005 Wild type fundic RNA Source GEO sample is GSM108485 Last updated (according to GEO): May 03 2007 dentate granule cells Treatment, type=acclimatization Source GEO sample is GSM35847 Last updated (according to GEO): May 27 2005 Donor 3 Time point 24 hours post Infection with HIV-1, RF Source GEO sample is GSM2622 Last updated (according to GEO): May 27 2005 Spinal Cord 901 5 0 Spleen Pool Eu_P0_hyb1 male MhmBN chip 25 BALB-c mice were given intratracheal bleomycin (1.5U per kg) or saline control. Lungs were harvested and frozen at 24h. Lot batch = Source GEO sample is GSM4156 Last updated (according to GEO): May 28 2005 Expression profiling of spinal cord section (T9) extracted from rats 28d following laminectomy (sham) Source GEO sample is GSM31269 Last updated (according to GEO): May 27 2005 H9RGV00102605 Mouse strain = BALB/c Age: Adult (>30 postnatal) One adult animal (postnatal 30 day or beyond) was used for each replicate adult sample Total RNA was extracted using RNeasy Midi Kit, according to manufacturerÆs instructions (Qiagen). The quality of the samples was checked with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA). Standard Affymetrix Protocol was used for RNA sample labeling with ENZO BioArray HighYield RNA Transcript Labeling Kit Keywords = Cerebellum, microarray, development, glycoconjugates, glycosyltransferases, proteoglycans, gene expression Lot batch = Source GEO sample is GSM29634 Last updated (according to GEO): Oct 28 2005 180minplus.3 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11236 Last updated (according to GEO): May 28 2005 861 Spinal Cord 1100 1087 heart failure 19 0 human frontal cortex Normal Source GEO sample is GSM176123 Last updated (according to GEO): Apr 09 2007 /NJ pituitary gland rep2 3 26 Small Pre-BII cells 10b Spleen vs Tumor necrosis factor-alpha Treated B cell 30min (set3) Osteoblasts 1000 HapMap CEU_parent Male Source GEO sample is GSM159540 Last updated (according to GEO): Feb 01 2007 114 105 hippocampi NSCLC_NCIH23 on Affymetrix GeneChip Human Full Length Array HuGeneFL CNS-SC_InjB30m-3cB-s2 vulva_3 Source GEO sample is GSM80897 Last updated (according to GEO): Mar 31 2006 VDXOXFU_544 infection 410 419 in mouse hearts 40 54 NCI60.31_LABEL35EXTRACT34SUB3 Source GEO sample is GSM134147 Last updated (according to GEO): Aug 06 2007 Myocardial Infarction 1000 ovarian tumor: serous Source GEO sample is GSM139471 Last updated (according to GEO): Apr 09 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114206 Last updated (according to GEO): Jun 16 2006 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184684 Last updated (according to GEO): Apr 26 2007 1959 1946 out the liver of their peripheral neurite 372 399 1000 Brain Blood 861 21 6 (caudate nucleus 1112 1104 in livers Normal__Germinal_Center_GC45 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Heart 861 861 Cerebral cortex 901 frontal lobe human frontal cortex Source GEO sample is GSM86935 Last updated (according to GEO): Feb 08 2006 Voxel I1 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1445 Last updated (according to GEO): Nov 21 2005 Hippocampus Source GEO sample is GSM107962 Last updated (according to GEO): Jun 06 2006 56 37 with chronic malaria 15 0 human cerebellum Chronic leukemia NOS 913 24 0 human prostate PC3 tumors 1000 Cerebral cortex Interatrial septum 865 983 Cor pulmonale dentate granule cells Source GEO sample is GSM35808 Last updated (according to GEO): May 27 2005 Brain 861 blood 0 5 The hypothalamic paraventricular (PVN) and supraoptic (SON) nuclei are important integrative structures that regulate co-ordinated responses to perturbations in cardiovascular homeostasis. Through descending projections from parvocellular neurons to the brainstem, the PVN acts as an autonomic 'premotor nucleus', regulating reflex changes in sympathetic nerve activity that are involved in blood pressure and blood volume regulation. Endocrine responses are mediated through axonal projections from SON and PVN magnocellular neurons (MCNs) to the capillaries of the posterior pituitary neural lobe. In response to dehydration, a massive release of the antidiuretic peptide hormone vasopressin (VP) into the circulation is accompanied by a dramatic functional remodelling of the HNS. We have used microarrays to comprehensively catalogue the genes expressed in the PVN, the SON and the neurointermediate lobe (NIL) of the pituitary gland. Further, we have identified transcripts that are regulated as a consequence of dehydration, as well as RNAs that are enriched in either the PVN or the SON. We suggest that these differentially expressed genes represent candidate regulators and effectors of HNS activity and remodelling. Last Updated (by provider): Jan 31 2006 Contributers: GEMMA BEIGHTON JULIAN PATON CHARLES C HINDMARCH SONG YAO to liver 484 492 BTBR T+ tf/tf Cingulate Cortex A LDMTX_MP-14 M_U133A_76_AnCg hippocampus Source GEO sample is GSM36008 Last updated (according to GEO): May 27 2005 Brain 861 NICM pool 2 (n=2) Neoplasm 1000 901 Ganglia, Sensory Gene expression data from postmorten brain regions Source GEO sample is GSM145493 Last updated (according to GEO): Nov 20 2006 80 68 Control blood Hypovolemia 861 861 Cerebral cortex 2_hypothalamus_12hrs_sleep_deprivation_#103 fertilized egg Source GEO sample is GSM18699 Last updated (according to GEO): May 27 2005 of the postmortem brains 2976 3000 D_U133A_76_Amy Expression profiling of spinal cord section (T9) extracted from rats 14d following severe injury Source GEO sample is GSM31614 Last updated (according to GEO): May 27 2005 Muscular Dystrophies 901 IGROV1_CL6010_Ovarian on Affymetrix GeneChip Human Full Length Array HuGeneFL Epithelium of bronchus 983 1000 Hippocampus Mouse Liver LRD Diet 5wk 10ppb As Food Exposure, biological replicate D fibroblast-like breast tumor cell line Hs578T Keywords = Agilent microarray, Expression analysis, EGFR, Breast cancer growth Source GEO sample is GSM29509 Last updated (according to GEO): Dec 13 2006 D_U133Plus_119_nAcc Wild type inbred mice Source GEO sample is GSM82949 Last updated (according to GEO): Nov 10 2005 Lymphoblastic Leukemia 901 6 month oculomotor nucleus rep 3 Cerebral cortex 861 healthy subject Source GEO sample is GSM211120 Last updated (according to GEO): Sep 10 2007 PGA-MurLungRag-pbs-24h-1aA-s2 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120691 Last updated (according to GEO): May 14 2007 Expression profiling of superficial bladder tumours to delineate the expression pattern differences between non-recurring and recurring tumours.. Date GSE88 Last Updated: May 29 2005 Contributers: Stephen Hamilton-Dutoit Thomas Thykjaer Niels Marcussen Hans Wolf Lars Dyrskjot Jens L Jensen Mogens Kruhoffer Torben F Orntoft Includes GDS184. Update date: Apr 09 2003. Dataset description GDS184: Expression profiling of superficial bladder tumors to delineate the differences between non-recurring and frequently recurring Ta tumors. Applied 32-gene molecular classification scheme to classify samples.. Spleen vs NGF (Nerve Growth Factor)Treated B cell 30min (set2) dorsal striatum sprague 3978 Lung tissue from C57BL/6 mice calorie restricted by 2/3 and sacrificed 2hrs after the onset of calorie restriction. Lot batch = Source GEO sample is GSM4025 Last updated (according to GEO): May 28 2005 Pre-BI cells 2 Breast Diseases 913 n/a Source GEO sample is GSM177995 Last updated (according to GEO): Jun 11 2007 Blood 1000 Medulla 861 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 16 hours after lights on. Original sample code = CM31A Source GEO sample is GSM227293 Last updated (according to GEO): Sep 10 2007 nasal epithelial cells 28 49 Lung 1000 Abdominal aorta structure 1000 Kidney 861 no additional Source GEO sample is GSM199376 Last updated (according to GEO): Jun 08 2007 Spleen vs Untreated B cell 120min (set3) mouse cerebral cortex from COX-2 WT Source GEO sample is GSM121428 Last updated (according to GEO): Jan 31 2007 cerebral cortex 7 21 NA Source GEO sample is GSM84321 Last updated (according to GEO): Dec 01 2005 Pineal 13 18 D_U133A_102_CB Expression profiling of spinal cord section (T9) extracted from rats 30m following laminectomy (sham) Source GEO sample is GSM31271 Last updated (according to GEO): May 27 2005 entorhinal cortex layer II stellate island cells Source GEO sample is GSM107526 Last updated (according to GEO): May 01 2006 106 95 from kidneys 861 Cerebellum Epithelium 861 Replicate1_Voxel D1 Neostriatum 1000 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201264 Last updated (according to GEO): Jun 14 2007 2hr post 3Gy IR HC61 CN B the heart 987 996 1000 Cerebral cortex E15 50 43 jejunum 7 0 prostate heart failure 583 595 Human Hypothalamus Female 3 (technical replicate) Heart Septal Defects, Atrial 1000 1546 1542 of Ig Suprachiasmatic Nucleus after 30-min dark pulse rep2 N/A Source GEO sample is GSM4329 Last updated (according to GEO): May 28 2005 1000 Impaired cognition We used DNA microarrays representing ~30,000 human genes to analyze gene expression in the cornea, lens, iris, ciliary body, retina, and optic nerve. Eight whole globes (G1-G8) were harvested from autopsy donors (age range=30-85 years-old) within 24 hours of death, and the tissues were immediately stored at 4? C in RNAlater (Ambion). Four of the globes were from female donors (G3, G6-8) and four were from male donors (G1, 2, 4, 5). Globes 4 and 5 were harvested as a set from a single donor, as were globes 6 and 7. No ophthalmologic clinical records were available for any of the globes at the time of harvest. Seven of the globes (G1-G7) were dissected into the following components: cornea, lens, iris, ciliary body, retina, and optic nerve, while only retinal tissue was available from G8. The maculas and the peripheral retinal tissues were further dissected from several of the retinal samples. The macula was defined as the visible xanthophyll-containing tissue temporal to the optic nerve, which encompassed an approximate area of 4 mm2. For comparison purposes, three post-mortem brain specimens were analyzed. Only those tissues that yielded adequate amounts of RNA were processed on the arrays. An organism part comparison experiment design type compares tissues, regions, organs within or between organisms. Differential gene expression in anatomical compartments of the human eye. Diehn et al. Genome Biology 2005, 6:R74 Last Updated (by provider): Sep 08 2006 Contributers: Jennifer Junkermeier [Switched to use SH-40k by Gemma] Using targeted gene deletion, we have firmly established that the Class IV POU domain transcription factor Brn-3.2 controls a developmental program regulating axon pathfinding in the mouse visual system. We have isolated and identified downstream gene targets of Brn-3.2, using Representational Difference Analysis (RDA), on cDNA populations derived from wildtype and Brn-3.2-/- retina at the appropriate embryonic stage. One of these candidate genes, the Homeodomain Interacting Protein Kinase 2 (HIPK2), is postulated to be a transcriptional coregulator, based on its in vitro interactions with repressor homeodomain proteins of the NK class, as well as other components of repressor complexes. HIPK2 has also been shown to be involved in post-translational modification of two major transcriptional regulators, p53 and CtBP. Expression of a dominant-negative form of HIPK2 in sensory neurons affects the innervation patterns of their target tissues, suggesting an axon pathfinding defect. The aim of this project is to identify targets for the Homeodomain Interacting Protein Kinase 2 (HIPK2), that we isolated as a downstream gene target of the class IV POU domain transcription factor Brn-3.2, and to investigate their function in the Brn-3.2 dependent pathway regulating axon pathfinding. We hypothesize that the genes regulated by HIPK2 will play a critical role in axon pathfinding and that the results of this study will provide novel insights into the molecular mechanisms of axon pathfinding, and possibly neural plasticity and regeneration, and therefore, be of great interest to the field of neurobiology in general. In order to uncover potential biological role(s) of HIPK2 in neural development, and particularly axon pathfinding, we generated transgenic mouse models for in vivo studies. Our preliminary observations in transgenic mice, indicate that a form of the molecule expected to act as a dominant-negative and designed to be expressed in sensory neurons, affects the innervation patterns of their target tissues, suggesting an axon pathfinding defect. We plan to take advantage of this model to identify genes regulated by HIPK2, and which are likely to be involved in axon pathfinding. To this end, we will compare gene expression profiles in sensory neurons isolated wild-type and transgenic mice. In our experimental paradigm, the trigeminal ganglion represents the ideal sensory structure in which to perform such an analysis: 1) High levels of transgene can be expressed in the trigeminal ganglion, as assessed by the expression of LacZ from the bicistronic construct which contains IRES-LacZ downstream of a dominant negative form of HIPK2. 2) The trigeminal ganglion can be dissected at embryonic day 13.5, when the phenotype is apparent, with ease and free of contamination from surrounding tissues. 3) The amounts of RNA that can be isolated from a single ganglion are in the range of 200-300 ng, which should be sufficient for microarray analysis following linear amplification of RNA. One series will be carried out with transgenic embryos and a control series will be carried out with wildtype littermates. Animals will be prepared and sacrificed by a standard protocol. Tissue will be rapidly dissected from E13.5 trigeminal ganglion, frozen in liquid nitrogen, and stored at -80C until RNA is extracted. RNA will be prepared using RNeasy Micro Kit. We will be providing 4 tissue samples for each of the wildtype and transgenic animals to mitigate any expression differences resulting from mouse to mouse variation.. Date GSE2869 Last Updated: Jul 06 2005 Contributers: M Rosenfeld Includes GDS1793. Update date: Jun 13 2006. Dataset description GDS1793: Analysis of the trigeminal ganglia of transgenics expressing a dominant-negative form of homeodomain interacting protein kinase 2 (HIPK2). HIPK2 is a downstream target of Brn-3.2, a class IV POU domain transcription factor that controls a developmental program regulating axon pathfinding.. DR12h(3) Neoplasm 861 cy3:SHR control, biological rep 2g; cy5:pool of 6 WKY control rats 65 24 from umbilical subcutaneous adipose tissue 5 0 brain brain, adrenal medulla: Sample#B3 (Ctrl Pt3)_e1_le1 Ptdsr-/- fibroblast_rep1 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68285 Last updated (according to GEO): Jul 07 2006 Arteries 861 the ventricular 1095 1109 osteoblast 627 637 1000 Parkinson Disease Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11494 Last updated (according to GEO): May 28 2005 195 with coxsackievirus B3 174 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195291 Last updated (according to GEO): Sep 13 2007 Amygdala Source GEO sample is GSM107956 Last updated (according to GEO): Jun 06 2006 1730 1719 hippocampus N/A Source GEO sample is GSM4333 Last updated (according to GEO): May 28 2005 Replicate2_Voxel B10 38 21 from a hippocampus Nrl ko 2 mon replicate 1 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28712 Last updated (according to GEO): May 27 2005 Acute leukemia 913 M_95A_2835_CB_1_GS C57BL10 diaphragm sample 1 1000 jejunum 5 0 Spleen 861 Gland structure 7 0 Synovium Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. /HeJ pituitary gland rep1 3 27 7 cerebral cortex 21 of the stria terminalis rep1 19 46 Treated Source GEO sample is GSM175965 Last updated (according to GEO): Apr 09 2007 913 Coronary heart disease 1500mg/kg APAP 6Hr rat 3591 blood vs. PC 6Hr rat 3586 blood striatum_Hdh4Q80_7S Spleen vs Prostaglandin E2 Treated B cell 120min (set1) 861 Medulla Measles 861 861 Juvenile Neuronal Ceroid Lipfuscinosis in the mouse brain 1160 1177 Primary tumor 19 32 prostate Source GEO sample is GSM203357 Last updated (according to GEO): Jun 21 2007 Primary tumor 19 32 PGA_PA-S_297 /extracellular matrix 873 893 Spleen 1000 Knockout 3 months old, female Source GEO sample is GSM154338 Last updated (according to GEO): Jan 09 2007 Stromo vascular fraction from subcutaneous adipose tissue Source GEO sample is GSM210988 Last updated (according to GEO): Jul 17 2007 Simple annotation: Reference verification, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs//9999.gif Source GEO sample is GSM78456 Last updated (according to GEO): Sep 22 2006 Mammary; Lactating Keywords = mouse gene expression database Source GEO sample is GSM29400 Last updated (according to GEO): May 27 2005 Prion Diseases 1000 Plasma 861 Paravertebral Muscle 6 Disease Lymphoblastoid Cell Line for Individual 8156.4 log phase Dendritic Cells, Exposed to Toxoplasma gondii - Repeat #1 no additional Source GEO sample is GSM199275 Last updated (according to GEO): Jun 08 2007 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:239, Count:32 Corner- Avg:38822, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:7.316926,SFGene:All Background:Avg:371.14,Stdev:5.69,Max:385.0,Min:359.1 Noise:Avg:10.15,Stdev:0.33,Max:11.2,Min:9.4 RawQ:12.76 Keywords = ALL Source GEO sample is GSM3497 Last updated (according to GEO): May 28 2005 164 136 of the middle cerebral artery B131 isotype treated DCs (cortex 19 25 Five different human MPNST cell lines, mock treated or infected with G207. Source GEO sample is GSM215816 Last updated (according to GEO): Aug 07 2007 1000 jejunum (cortex 19 25 Gene expression data from brain of adult rats Source GEO sample is GSM101005 Last updated (according to GEO): Feb 20 2007 Temporal Lobe 9 Normal 1705 1676 in medulloblastoma metastasis 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114236 Last updated (according to GEO): Jun 16 2006 cerebellum_4 no additional Source GEO sample is GSM199259 Last updated (according to GEO): Jun 08 2007 Whole brain gene expression was examined in the following strains of mice: 1. P0 maternal monosomic 39,Xm females, C57BL/6J x C3H/Paf 2. P0 paternal monosomic 39, Xp females, In(X)/C3H x C57BL/6J 3. P0 normal 40,XX females, In(X)/C3H x C57BL/6J 4. P0 normal 40,XX females, C57BL/6J x C3H/Paf. Date GSE1606 Last Updated: Jul 21 2005 Includes GDS1513. Update date: May 16 2006. Dataset description GDS1513: Analysis of neonatal brains of X-monosomic females that inherited either a maternal or a paternal X chromosome. X-monosomy is the basis of Turner's syndrome (TS). Expressivity of TS phenotypes depends partly on the parental origin of the single X. This expressivity may be due to imprinted X genes.. Parkinson Disease 861 BUB/BnJmale_hypothalamus PGA_PA-D_64 CAD_replicate4 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181131 Last updated (according to GEO): Jul 12 2007 kidney 37 43 brain 0 5 Adipose tissue 1000 Gene expression data from U0126 (20uM)-treated embryos at day 2.5. Source GEO sample is GSM176490 Last updated (according to GEO): Mar 19 2007 Category: Cell-line Subcategory: Pharmacogenomics This experiment was an out file converted from rana. The original files were not provided to load this experiment in Oracle. Category and Subcategories were made by curators. Scanning Software: unknown Software version: unknown Lot batch = dtp2827a Source GEO sample is GSM2146 Last updated (according to GEO): Nov 21 2005 Study of in vitro granulocyte differentiation Source GEO sample is GSM137481 Last updated (according to GEO): Jun 06 2007 brain, Superior Frontal Gyrus: Sample55_e1_le1 861 Oocytes 8 week old mice sacrificed after swimming for 10 minutes Keywords = exercise induced hypertrophy Source GEO sample is GSM2342 Last updated (according to GEO): May 27 2005 Ganglioneuroma 547 561 Wild type 8 wk old male C57BL/6J mouse pituitary gland Source GEO sample is GSM75002 Last updated (according to GEO): Feb 27 2007 healthy subject Source GEO sample is GSM211035 Last updated (according to GEO): Sep 10 2007 150 mg/kg X 12 hr Source GEO sample is GSM129895 Last updated (according to GEO): Sep 18 2007 Organotypic hippocampal slice cultures of male, postnatal day 15 mice (C57B6/SJL) were maintained in culture for 15 days and treated with 1 nM sAPPalpha (sAPPalpha) for an additional 24 h. Cultures were maintained on filter inserts in Neurobasal media with B-27 supplement (Invitrogen) and 1 mM glutamine. The sample consists of 12 slices from 4 mice. Data were analyzed with MAS 5.0 and scaled to 2500. Keywords = Alzheimer?s disease Keywords = neuroprotection Keywords = sAPPalpha Source GEO sample is GSM26703 Last updated (according to GEO): Oct 28 2005 1000 jejunum 1000 Pituitary Gland Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16363.gif Source GEO sample is GSM91528 Last updated (according to GEO): Sep 22 2006 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68165 Last updated (according to GEO): Jul 07 2006 Hypothalamic structure 861 23 0 Substantia nigra PD rep4 865 Disorder of artery Heart Septal Defects 884 988 980 cerebella LungP24_022IAF74_077d.txt 1000 Hippocampus atrial septal defects 198 218 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5814 Last updated (according to GEO): May 27 2005 Epithelium 861 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11522 Last updated (according to GEO): May 28 2005 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15752 Last updated (according to GEO): May 28 2005 cerebellum 7 16 V5-P208 PGA-Band_24h_4-m5 in the brain 150 162 GBM Treatment, type=remove Source GEO sample is GSM99586 Last updated (according to GEO): Apr 21 2006 CAD_replicate85 Levitiracetam hippocampus 7 Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53439 Last updated (according to GEO): Jul 06 2005 Skeletal bone 861 Primary small cell lung carcinoma 544 0 36 34 16 of stria vascularis KPeterson-Met-3box1G110-s2 Balb/c day 3, biological rep 3, tech rep 2 39 21 from mammary glands Kidney 1000 hippocampal glutamatergic CA3 pyramidal neurons Treatment, type=acclimatization Source GEO sample is GSM35842 Last updated (according to GEO): May 27 2005 Squamous epithelial cell 913 861 Bone Marrow Amino Terminated surface 32 hours T-ALL-C17 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 0.5 mg/kg/ml Isoproterenol treatment, 1 hour time point, biological rep 3 The nose 94 101 1000 frontal lobe 1000 Brain Gene expression data from retinas of two young SAMP8/Ta mice Source GEO sample is GSM143741 Last updated (according to GEO): Jan 24 2007 pituitary sprague1 Communicable Diseases 861 Heart Septal Defects, Atrial 1000 Epithelial Cells 901 Expression profiling of spinal cord section (T9) extracted from rats 4h following laminectomy (sham) Source GEO sample is GSM31264 Last updated (according to GEO): May 27 2005 The epithelial cells 962 981 Gene expression profile of the cell line UB/OC-1 grown for 9 days under differentiating conditions (39C). This data set is a replica experiment of sample GSM1542. Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1548 Last updated (according to GEO): May 27 2005 M_U133A_7_DLPFC_R /3T3 fibroblasts 295 310 D_U133A_42_DLPFC Blood 861 thalamus_5 AD-249t1x (d)-A165-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 0572 blood of gut neurospheres 39 57 PGA-RnSalt_c_6w_1-2-m5 1000 Tricuspid valve structure 19 0 Head and neck cancer nucleus raphe magnus 1000 Spleen 0 5 hrs nasal epithelium 1127 1147 861 Cerebral cortex H113 FC BA4 A left 35 38 n/a Source GEO sample is GSM178062 Last updated (according to GEO): Jun 11 2007 1000 Cochlear structure 861 Endometriosis, site unspecified Sprague-Dawley Male HighSalt Cortex rat710 sd_cortexr_k_710c_020802 Nervous System; Hippocampus Keywords = mouse gene expression database Source GEO sample is GSM29418 Last updated (according to GEO): May 27 2005 Cerebral cortex 1000 H123 FC BA4 A 91 from the bone marrow 72 Blood Test (Blinded) Sample Source GEO sample is GSM129958 Last updated (according to GEO): Sep 18 2007 NCI60.4_LABEL7EXTRACT6SUB3 Source GEO sample is GSM134011 Last updated (according to GEO): Aug 06 2007 in fibroblasts 1222 1236 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132484 Last updated (according to GEO): Feb 26 2007 Total RNA from iPS clone was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations. Source GEO sample is GSM231504 Last updated (according to GEO): Nov 22 2007 Expression profiling of moderately injured raphe at 7d in rats Source GEO sample is GSM41622 Last updated (according to GEO): May 27 2005 kidney 176 182 1000 Brain Female 21.5 yr before antibody enrichment scan 1 (U133B) Mechanisms of Aging in Senescence-Accelerated Mice accumbens rattus_norvegicus_strain iP animal_number 3 Antibodies 1000 861 Cerebral cortex days nasal epithelium 1127 1148 Stem cells 901 Medulla Oblongata 861 Brain 861 V5-P313 BT-549 hgu95e Normal Source GEO sample is GSM175994 Last updated (according to GEO): Apr 09 2007 Expression profiling of spinal cord section (T10) extracted from rats 4h following laminectomy (sham) Lot batch = Source GEO sample is GSM4436 Last updated (according to GEO): May 28 2005 1000 Brain Congenital Abnormality 853 Heart 861 Whole blood 0 10 frontal cortex wistar 3920 whole tissue, individual animal, 10 weeks old, male Wistar frontal cortex file:p3920w Source GEO sample is GSM15157 Last updated (according to GEO): Oct 28 2005 861 Brain Parkinson Disease 861 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215057 Last updated (according to GEO): Aug 02 2007 Muscle_adequate protein_female_rep5 1000 Hippocampus Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3282 Last updated (according to GEO): Mar 21 2006 human frontal cortex Source GEO sample is GSM87056 Last updated (according to GEO): Feb 08 2006 5 0 brain n/a Source GEO sample is GSM177942 Last updated (according to GEO): Jun 11 2007 Lymphoblastoid Cell Line for Individual 8054.4 log phase MAS 5.0, scaled to 500; Affymetrix data Mining Tool 3.0; dChip was used to determine differentially expressed genes (MBEI); Statistical Analysis of Microarrays(SAM), as described in Miller et al. 2004. Source GEO sample is GSM108081 Last updated (according to GEO): Sep 12 2006 22-oct-2002-liverA1-Mu11KsubAsc Cell source of DN2_1, DN3_1, and DN4_1 are identical. Cell source of DN2_2, DN3_2, and DN4_2 are identical. Cell source of DN2_3, DN3_3, and DN4_3 are identical. Cell source of DN2_4, DN3_4, and DN4_4 are identical. Each cell sorce was derived from four mice. Source GEO sample is GSM188616 Last updated (according to GEO): May 16 2007 Epithelium of bronchus 983 Muscle_inadequate protein_male_rep4 PBMCs-Type 1 Diabetes-IDDM57_T1D_New Cervix carcinoma 1000 Starvation 916 255 234 with HIV encephalitis Structure of olfactory bulb 861 Myometrium 50 Disease 1037 of transitional epithelium 1012 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92379 Last updated (according to GEO): Jan 13 2006 Cochlea at E14, replicate1 Melanoma xenograft, MA1_Lung_B (LeiATCC) GC (HKG28T) no additional Source GEO sample is GSM199358 Last updated (according to GEO): Jun 08 2007 Prosencephalon 861 Expression profiling of spinal cord section (T8) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM4450 Last updated (according to GEO): May 28 2005 Brain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM144938 Last updated (according to GEO): Nov 20 2006 Normal Source GEO sample is GSM176292 Last updated (according to GEO): Apr 09 2007 liver, wild type mice, treatment with WY14643 for 5d Source GEO sample is GSM205787 Last updated (according to GEO): Jul 24 2007 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162189 Last updated (according to GEO): Jun 12 2007 Subject code A25EB D_U133Plus_99_HC Olfactory Epithelium 1000 Neoplasm 861 in cervical cancer mainly 136 160 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132552 Last updated (according to GEO): Feb 26 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM146033 Last updated (according to GEO): Nov 20 2006 brain, hindbrain and spinal cord: P5KO1_e1_le1 MDA134_Untreated_0.1% Examining the effects of tTA expression in mouse hearts Source GEO sample is GSM15065 Last updated (according to GEO): May 28 2005 13 0 Brain Amygdala from liver 21 30 30 19 Solid tumor R749P01262 Liver (HBV+, HK39) NCI60.45_LABEL49EXTRACT48SUB3 Source GEO sample is GSM134223 Last updated (according to GEO): Aug 06 2007 901 Ciliary Body cocaine naive, nucleus accumbens, 0 hrs access to cocaine Source GEO sample is GSM93814 Last updated (according to GEO): Jan 26 2006 Gene expression profile of presenilin conditional double knockout cerebral cortex, comparing to control. Age of mice: 6 months Source GEO sample is GSM22353 Last updated (according to GEO): May 27 2005 ileum 0 4 C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 2hr after experimental mice received their last shock treatment. Source GEO sample is GSM4506 Last updated (according to GEO): May 27 2005 Plasma 861 Starvation 916 frontal lobe 1000 Osteoblasts 1000 Retina 1000 CNS_U251 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Hypertrophic Cardiomyopathy NA18573 Amyotrophic lateral sclerosis Hyperdip>50-C30 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A brain 0 5 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152017 Last updated (according to GEO): Feb 06 2007 M_U133A_7_nAcc 0 Lung tissue 10 861 Ventral Tegmental Area Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225926 Last updated (according to GEO): Nov 02 2007 Coronary Arteriosclerosis 1000 1000 Pancreas Epithelial Cells 1000 Kidney 861 Nasal Epithelium 865 1000 Brain Malignant neoplasm of urinary bladder 1000 Ovarian Diseases 877 Olfactory Epithelium 1000 Prostate 11 Disease Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174524 Last updated (according to GEO): Mar 14 2007 1000 Cerebral cortex 1000 L-Selectin 222-97_normal Mammary Gland @ Preg12, biological rep4 Identification of Primary Transcriptional Regulation of Cell-Cycle-Regulated Genes upon DNA Damage 281_2 4 0 Brain JMR-RatInj30m-4aA-s2 1200 1186 of chromosome 6 Cerebral cortex 901 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113971 Last updated (according to GEO): Jun 16 2006 BALB-RAG_PBS Replicate 2 LungP12_022AAF78_077c.txt with dystrophin 1448 1462 D_U133A_76_nAcc 72 54 of malignant glioma whole blood_100801 Carcinoma 861 AD-334t1 (d dup)-A221-8 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Parkinson Disease 861 Pancreas at e16.5, Chip C, rep 2 cerebral cortex 7 21 032801_HF_332MB in blood pressure 394 411 Myometrium 39 Disease Gene expression data from male mice. Source GEO sample is GSM115532 Last updated (according to GEO): Jun 13 2007 ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes(delta-hly)_A_5541 Source GEO sample is GSM161197 Last updated (according to GEO): Apr 23 2007 Lda3r 212 197 atherosclerosis Lymphoblastoid Cell Line for Individual 8180.3 log phase Gene expression data from postmorten brain regions Source GEO sample is GSM145443 Last updated (according to GEO): Nov 20 2006 59 35 out of mouse bone marrow 338 333 brain Primary Carcinoma 876 I_U133A_66_Amy Gene expression data from na?ve DIV 14 cortical neuron i.e. non activated state Source GEO sample is GSM100449 Last updated (according to GEO): Mar 15 2006 36 21 from whole brain Normal Source GEO sample is GSM175936 Last updated (according to GEO): Apr 09 2007 V5-P157 861 Cerebral cortex Carcinoma of lung 1000 Primary Carcinoma 875 1000 Cochlear structure pfc_1005_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 5 0 brain Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68172 Last updated (according to GEO): Jul 07 2006 3_cerebral_cortex_12hrs_sleep_#32 1000 Lipids Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210399 Last updated (according to GEO): Jul 16 2007 Retina 1000 2500mg/kg APAP 24Hr rat 3629 blood vs. 3616 PC 24Hr (pool) T-ALL-C7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Double KO 3 Thymus, Whole thymus: Amplified mRNA_le1 brain, unknown: C4C_e1_le1 861 Epithelial Cells Central gray substance of midbrain 861 no additional Source GEO sample is GSM199055 Last updated (according to GEO): Jun 08 2007 Expression profiling of laminectomized raphe at 4h in rats Source GEO sample is GSM41545 Last updated (according to GEO): May 27 2005 Heart 861 Mesenchymal Stem Cells 1000 20 0 human caudate nucleus 19 0 human frontal cortex Ta gr3 tumour Source GEO sample is GSM2537 Last updated (according to GEO): Mar 21 2006 YFP labeled neurons in amygdala. Source GEO sample is GSM63045 Last updated (according to GEO): Dec 01 2005 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11281 Last updated (according to GEO): May 28 2005 96 74 in experimental asthma 861 Adrenal Medulla Total RNA was extracted from umbilical subcutaneous adipose tissue from an individual affected with FCHL and exhibiting the USF1 susceptibility haplotype Source GEO sample is GSM9041 Last updated (according to GEO): May 28 2005 Wild type 2 Thymus, Whole thymus: Amplified mRNA_le1 CNS-SpinalC-conAdult-48h-1A-s2 in bipolar disorder 1392 1411 from somatosensory cortex 12 36 H9LMS00110807 Pituitary Gland 861 1000 Amygdaloid structure Medulla Oblongata 861 OVCAR-4 hgu95a 15 0 human cerebellum Hippocampus 861 of Parkinson's disease 450 471 Wild-type-hippocampus, biological rep6 (female) Brain 861 Brain 1000 Normal Source GEO sample is GSM175903 Last updated (according to GEO): Apr 09 2007 hippocampus 7 17 Backskin_DN-CLIM_P14_rep1 Head and neck cancer Source GEO sample is GSM155709 Last updated (according to GEO): Apr 24 2007 BC206B-AF plasma cells 50 61 Gene expression data from older male during 1 week of adequate protein intake Source GEO sample is GSM209815 Last updated (according to GEO): Jul 11 2007 CNS-SpinalCmod-Adult-24h-3A-s2 Cerebral cortex 1000 1000 Cerebellum 1000 frontal lobe Brain 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11267 Last updated (according to GEO): May 28 2005 861 Extracellular Matrix Sample # 1055-1 607 597 the rectum Meningioma 0 9 Disorder of artery 865 cerebellum 7 16 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198619 Last updated (according to GEO): Jun 06 2007 Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 1277 left_liver_lobe Medulla_Oblongata Source GEO sample is GSM18926 Last updated (according to GEO): Sep 25 2006 LiverAdult_022MACHG.txt 861 Cornea MGMH030228088Afertilizedegg Mature B cells 9 H132 CB A Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188739 Last updated (according to GEO): Jun 06 2007 D_U133A_62_Amy Cervix 8 Normal Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Source GEO sample is GSM15959 Last updated (according to GEO): May 28 2005 Medulla 861 of somatomotor cortex 21 41 1000 Brain Medulla Oblongata 861 of somatomotor cortex 21 41 Transitional epithelium 1000 in the cerebral cortex 1842 1864 GRP sample 12 1000 Retina 41 30 PCOS oocytes Seminoma 1000 AJ 14-1 WAT Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for twelve weeks. Source GEO sample is GSM148666 Last updated (according to GEO): Dec 12 2006 Ganglia, Spinal 923 VDXKIU_2889 WGACON-52 Skeletal muscle structure 901 861 Muscle 129:22-4 olfactory bulbs 41 37 Lungs 861 Cerebral cortex This is the third replicate for the SNc neurons which were captured using LCM. Source GEO sample is GSM19317 Last updated (according to GEO): May 27 2005 spinal cord 592 603 238 232 Retinas total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Tumor necrosis factor-alpha for 120min Source GEO sample is GSM5807 Last updated (according to GEO): May 27 2005 AD control Treatment, type=dissect Source GEO sample is GSM119660 Last updated (according to GEO): Jul 10 2006 1000 Cerebral cortex SCG explant cultured for 2 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246052 Last updated (according to GEO): Dec 03 2007 Intestines, Small 901 cardiac 763 769 Tumor__Lymphoma_Follicular_FSCC_S93_13188 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A B70 on NCI-7.6k 1000 Hypothalamic structure outer medulla 31 43 CNS-SpinalC-conAdult-28d-1A-s2 Cerebral Cortex 2 Normal 0 Lung tissue 10 H117 FC BA4 B none Source GEO sample is GSM239869 Last updated (according to GEO): Dec 07 2007 Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589?595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164?169.) Source GEO sample is GSM159479 Last updated (according to GEO): Jun 21 2007 901 Hepatocyte by primary human breast cancer 558 587 5 0 Spleen Alzheimer's Disease 861 1000 Dementia gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134619 Last updated (according to GEO): Jul 09 2007 D_U133A_35_HC 1000 Malignant neoplasm of breast Spleen vs Lysophosphatidic Acid Treated B cell 60min (set3) Cerebral cortex 861 bladder_T1GH_pool-1 cerebral cortex 7 21 GM12154 Head and neck cancer Source GEO sample is GSM155693 Last updated (according to GEO): Apr 24 2007 Bone Marrow 1000 Lateral Geniculate Body 1000 Parkinson Disease 1000 Sex Specific Transciption in Mouse Tissues Expression profiling of spinal cord section (T9) extracted from rats 28d following severe injury Source GEO sample is GSM31602 Last updated (according to GEO): May 27 2005 Phenytoin hippocampus 6 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53424 Last updated (according to GEO): Jul 06 2005 1000 Kidney Cerebral cortex 861 Study of in vitro granulocyte differentiation Source GEO sample is GSM137478 Last updated (according to GEO): Jun 06 2007 Spinal Cord 1000 Cerebral cortex 861 accumbens_8 Source GEO sample is GSM80598 Last updated (according to GEO): Mar 31 2006 from cingulate cortex 18 38 with primary hyperaldosteronism 52 82 1000 Hippocampus Mesenchymal Stem Cells 1000 Psychotic Disorders 1000 861 Cochlear structure in bronchial epithelia 311 332 1000 Brain 861 Cancer of Neck Tissue Source GEO sample is GSM67265 Last updated (according to GEO): Jan 19 2006 cornea Sprague2 with autism spectrum disorder 37 65 metanephric mesenchyme, NGAL, 2 days, biological rep1 Spleen vs Dimaprit Treated B cell 60min (set1) Endometrium 0 10 861 Neoplasm 5 0 brain brain, hippocampus: PR-DG-15_e1_le1 7 cortex 12 Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68038.gif Source GEO sample is GSM137413 Last updated (according to GEO): Sep 26 2006 HS 578T hgu95c Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15708 Last updated (according to GEO): May 28 2005 NA18964 acute myeloid leukemia Source GEO sample is GSM227446 Last updated (according to GEO): Sep 12 2007 307 in the cerebral cortex 328 Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Globin reduction was performed according to the Affymetrix technical note. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183400 Last updated (according to GEO): Apr 23 2007 2376 the trigeminal ganglion 2354 861 Cerebellum PGA-MAH-HeJAir-1bAv2-s1 Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 48 h to ambient pressure (CP48) and harvested with cells exposed for 48 h to hydrostatic pressure, pressure experiment # 1 (PE1). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11417 Last updated (according to GEO): Dec 15 2006 1000 frontal lobe Pool Ts1Cje_P30_hyb1 AD control Treatment, type=dissect Source GEO sample is GSM119666 Last updated (according to GEO): Jul 10 2006 Heart Atrium 1000 P1_KIDNEY_14 Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 5396 left_liver_lobe 1000 Coronary Arteriosclerosis 1000 Cerebral cortex Connexin-43 (Cx43) is the most abundant gap junction protein in brain, where it is found primarily between astrocytes. Although the morphology of astrocytes from Cx43-null (knockout, KO) mice is similar to that of wild-type (WT) astrocytes, KO astrocytes exhibit reduced growth rate in culture. To evaluate the impact of deletion of Cx43 on other genes, including those encoding cell cycle proteins, we used DNA arrays to determine expression patterns in cultured astrocytes from sibling Cx43-null and WT mice. RNA samples extracted from astrocytes cultured from WT and Cx43-null neonatal mice were dye labeled and individually cohybridized with a reference of labeled cDNAs pooled from a variety of tissues on 8 gene arrays containing 8,975 mouse DNA sequences. Normal variability in expression of each gene was evaluated and incorporated into "expression scores" to statistically compare expression levels between WT and KO samples. In Cx43-null astrocytes, 4.1% of the 4,998 adequately quantifiable spots were found to have significantly (P < 0.05) decreased hybridization compared with controls, and 9.4% of the spots showed significantly higher hybridization. The significantly different spots corresponded to RNAs encoding 252 known proteins, many not previously linked to gap junctions, including transcription factors, channels and transporters, cell growth and death signals, enzymes and cell adhesion molecules. These data indicate a surprisingly high degree of impact of deletion of Cx43 on other astrocyte genes, implying that gap junction gene expression alters numerous processes in addition to intercellular communication. 888 Large-Cell Lymphomas mouse brain 478 489 STHdhQ7/Q7-C 1000 Coronary Arteriosclerosis Lymphoblastoid Cell Line for Individual 8200.4 log phase brain, Entorhinal Cortex: Sample8_e1_le1 Gene expression data from a primary branch of the saphenous artery of 16 week old male Wistar-Kyoto rats Source GEO sample is GSM198858 Last updated (according to GEO): Nov 28 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28770 Last updated (according to GEO): May 27 2005 Leukemia, Lymphocytic, Chronic 1000 1000 Structure of trigeminal ganglion 901 Gallbladder Structure of parenchyma of lung 901 Skeletal bone 861 14 7 amygdala B6 JD2:1-4 CA1 1BMH02082906_BM_CD33myeloid brain, cerebral cortex: Rat_03-28_NroLep_Lipska_e1_le1 1000 Liver RNA samples extracted from astrocytes cultured from wild type and Cx43 null neonatal mice were dye labeled and individually co-hybridized with a reference of labeled cDNAs pooled from a variety of tissues on eight gene arrays containing 8975 mouse DNA sequences. Lot batch = 1 Source GEO sample is GSM8889 Last updated (according to GEO): May 27 2005 861 Blood Gene regulation and DNA damage in the aging human brain brain, amygdala: Amygdala 9_le1 Pre-BI cells 3b after traumatic brain injury 41 69 1 CN B Lung 1000 Gene expression data from whole brain infected mouse, day 1 Source GEO sample is GSM189640 Last updated (according to GEO): May 16 2007 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159732 Last updated (according to GEO): Apr 23 2007 Brain 1000 HC81 CN A DR12h(2) 861 Malignant Neoplasms 19 0 Head and neck cancer 67 40 with coronary artery disease Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184714 Last updated (according to GEO): Apr 26 2007 1BJZ02083089b_Uterus_Corpus Heart 1000 mouse cerebral cortex 0 20 1000 Intestines, Small 1000 Brain M_U133Plus_113_AnCg hippocampus_8 Source GEO sample is GSM80680 Last updated (according to GEO): Mar 31 2006 prostate_gland_2 Bone Marrow 1000 cingulate cortex 861 26 11 /Ovary-Disease 9 Thyroid carcinoma 901 GBM Treatment, type=remove Source GEO sample is GSM99445 Last updated (according to GEO): Apr 21 2006 We used the default settings of GCOS software to scan the chips. Source GEO sample is GSM146922 Last updated (according to GEO): Apr 16 2007 Transcriptional profiling of gastrin-regulated genes in mouse stomach. Brain 861 low-grade dysplastic liver tissue Source GEO sample is GSM155979 Last updated (according to GEO): Jun 21 2007 Blood 861 Transitional epithelium 1000 Heart 1000 Sarcolemma 1000 R741P00668 MO_LB_180min_Patient13 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=780620 LaserPower=2.341.29 Lot batch = LC17N148 Source GEO sample is GSM4841 Last updated (according to GEO): Nov 21 2005 1000 Amygdaloid structure 1000 Retina GM18856 19 0 Embryonal carcinoma Hippocampus 1000 V5-P092 60 CN A 1000 Parietal Lobe Pressure-overload induced hypertrophy model. Mouse was sacrificed 24 hours after aortic banding. Keywords = Cardiac hypertrophy Source GEO sample is GSM2236 Last updated (according to GEO): May 27 2005 human cerebellum Source GEO sample is GSM87092 Last updated (according to GEO): Feb 08 2006 osteoblast 627 637 brain, Left Temporal Lobe: Extract49_le1 from epididymal fat tissues 21 48 Gene expression data from postmorten brain regions Source GEO sample is GSM145457 Last updated (according to GEO): Nov 20 2006 Myocardial Infarction 1000 with myocardial infarction 313 339 19 0 Head and neck cancer Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210408 Last updated (according to GEO): Jul 16 2007 AD control Treatment, type=dissect Source GEO sample is GSM119688 Last updated (according to GEO): Jul 10 2006 338 333 brain b220+bcell Source GEO sample is GSM18671 Last updated (according to GEO): May 27 2005 9 0 Blood Test 29 18 after stroke Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120669 Last updated (according to GEO): May 14 2007 IFN_IFN_2 GSE8479 Prosencephalon 1000 Samp10 Hippocampus Old Sample 2 Parkinson Disease 861 Lipoproteins 1000 1000 Structure of middle cerebral artery saccule 275 282 Cerebral cortex 901 1000 ovarian neoplasm 19 0 Head and neck cancer Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141282 Last updated (according to GEO): Oct 26 2006 brain, brainstem: cRNA-SOD-2 Fibroblasts 861 Epithelium 861 334 320 Keywords = HIV Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 9388 left_liver_lobe Diet induced changes in mouse liver mRNA profiles. One of 3 replicates of LDL receptor deficient mice maintained for 12 weeks on low fat diet. Keywords = LDL receptor deficiency, high fat diet, atherosclerosis, liver Source GEO sample is GSM5412 Last updated (according to GEO): May 27 2005 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118543 Last updated (according to GEO): Jul 11 2006 S5_Muscle_Insulin_240min none Source GEO sample is GSM239891 Last updated (according to GEO): Dec 07 2007 1000 Temporal Lobe Muscle 861 C57 whole brain 5B 331 307 in central nervous system 861 Spinal Cord Stria 861 1000 Spleen 861 Cardiomyopathies RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above Source GEO sample is GSM160012 Last updated (according to GEO): Feb 05 2007 875 Cerebellar Diseases mild cognitive impairment - primary visual cortex 2 Gene expression data from brain of adult rats Source GEO sample is GSM101020 Last updated (according to GEO): Feb 20 2007 901 Caudate nucleus structure tibiae 115 120 1000 Brain pomeroy-embryonal Study of in vitro granulocyte differentiation Source GEO sample is GSM137454 Last updated (according to GEO): Jun 06 2007 none Source GEO sample is GSM123186 Last updated (according to GEO): Jul 26 2006 Pituitary Gland 861 Mouse ileum with L.innocua_B_5548 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12533.gif Source GEO sample is GSM79989 Last updated (according to GEO): Sep 22 2006 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs//9150.gif Source GEO sample is GSM93127 Last updated (according to GEO): Sep 22 2006 Blood B cells;anti-IgM+CD40L+IL-4 24h M_U133A_20_CB Cultured Dendritic Cells, CD4- CD8- subset - Expt #1 M7TW00122090 52 35 bone marrow cell 5 Stem cell fate is governed by the integration of intrinsic and extrinsic positive and negative signals upon inherent transcriptional networks. To identify novel embryonic stem cell (ESC) regulators and assemble transcriptional networks controlling ESC fate, we performed temporal expression microarray analyses of ESCs following the initiation of commitment and integrated these data with known genome-wide transcription factor binding. Effects of forced under- or over-expression of predicted novel regulators, defined as differentially expressed genes with potential binding sites for known regulators of pluripotency, demonstrated greater than 90% correspondence with predicted function, as assessed by functional and high content assays of self-renewal. We next assembled 43 theoretical transcriptional networks in ESCs, 82% (23 out of 28 tested) of which were supported by analysis of genome-wide expression in Oct4 knockdown cells. By using this integrative approach we have, for the first time, formulated novel networks describing gene repression of key developmental regulators in undifferentiated ESCs and successfully predicted the outcomes of genetic manipulation of these networks. Last Updated (by provider): Apr 12 2007 Contributers: Emily Walker Minako Ohishi Sandy D Der Peter W Zandstra Timothy R Hughes Quaid Morris Ryan E Davey William L Stanford Paul A Cassar Tetsuya S Tanaka Wen Zhang Pool Eu_P15_hyb1 Prosencephalon 1000 861 Cardiomyopathies brain, hippocampus: CON-CA1-10_e1_le1 adenoma 861 PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls. All samples were normalized with quantile normalization and summarized using RMA. Source GEO sample is GSM135590 Last updated (according to GEO): Dec 19 2006 umbilical cord_nobpd: 7I M_U133A_11_AnCg Visceral Afferents 901 Epithelial Cells 901 Fibroblasts 861 PGA-Csx_null_6a-m4 4_cerebral_cortex_9hrs_sleep_#29 at the synapse 193 207 Expression profiling of somatomotor cortex extracted from rats at 24h following moderate injury Source GEO sample is GSM41702 Last updated (according to GEO): May 27 2005 330 324 uterus Carcinoma, Neuroendocrine 861 Primary Neoplasm 1000 Spleen 0 5 1308 1284 after spinal cord injury UO-31 hgu95e 1000 Prostate in blood 16 23 Cerebral cortex 1000 17 7 hippocampus Menstrual phase - Follicular Source GEO sample is GSM175772 Last updated (according to GEO): Apr 09 2007 SCN2.2 Sample 7 (Exp#1-24 hr) Cerebral cortex 861 901 frontal lobe 1000 Cerebrovascular accident 5 0 Muscle AD-360t1-A176-A406 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 10 7 Left Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181081 Last updated (according to GEO): Jul 12 2007 Brain 1000 cy3:SHR treated w/ nifedipine, biological rep 2g; cy5:pool of 6 WKY control rats 861 Cardiomyopathies Brain 1000 Expression profiling of spinal cord section (T10) extracted from rats 24h following severe injury Source GEO sample is GSM31360 Last updated (according to GEO): May 27 2005 20 0 human caudate nucleus Mouse Liver Female 3 901 Myeloid Leukemia 901 Bone Marrow Gene expression data from postmorten brain regions Source GEO sample is GSM145844 Last updated (according to GEO): Nov 20 2006 Osteoblasts 1000 4 0 Brain 8 hr Hela Double Thymidine cardiac 763 769 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211327 Last updated (according to GEO): Jul 18 2007 1000 Optic Nerve A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism Source GEO sample is GSM5976 Last updated (according to GEO): Nov 21 2005 Treatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cells none Source GEO sample is GSM244528 Last updated (according to GEO): Nov 23 2007 pfc_1035_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Testis [JunctionChip 2 of 5] Brain 861 Bladder [JunctionChip 2 of 5] 166 156 of retinal Expression profiling of moderately injured raphe at 28d in rats Source GEO sample is GSM41591 Last updated (according to GEO): May 27 2005 39 21 of substantia nigra Gene expression profiles of human breast cancer progression. Kidney expression Normal Source GEO sample is GSM176171 Last updated (according to GEO): Apr 09 2007 Mouse Ovary 1 (technical replicate) 11 0 Hypothalamus brainstem 7 15 Transplant Series 19 , Transplant # 3 gene expression data from ODC mouse skin samples Source GEO sample is GSM216677 Last updated (according to GEO): Aug 09 2007 B6 day 6, biological rep 3, tech rep 2 proteoglycans 548 561 Category: Cell-line Subcategory: HMEC Scanning Software: unknown Software version: unknown Lot batch = 0095-5k Source GEO sample is GSM1940 Last updated (according to GEO): Nov 21 2005 901 Coronary artery Mid secretory endometrium from patient with endometriosis Source GEO sample is GSM150215 Last updated (according to GEO): Dec 14 2006 Bone Marrow 1000 Brain 1000 brain, cerebral cortex: Rat_02-139_TTX_Lipska_e1_le1 mouse cerebral cortex 0 20 LungP1_22UAFBF_077a.txt MuscleRegen-ctx9d-2LLbAv2-s2 M_U133A_106_DLPFC 1000 Brain Gene expression data from human prostate tissue with 90 percent tumor content Source GEO sample is GSM119319 Last updated (according to GEO): Feb 23 2007 861 Substantia nigra structure 861 Cerebral cortex PMN_LB_180min_Patient2 25 0 endothelial cells sprague1 Spleen vs Untreated B cell Time 0 (set24) D_U133A_47_Amy adaptive immune system 1463 1484 Epithelium 861 Spleen vs Platelet activating factor Treated B cell 120min (set2) Gastrin-CCK double Knockout replicate 3 Stria 861 Saphenous Vein 3 Normal Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. Source GEO sample is GSM112313 Last updated (according to GEO): Jun 06 2006 Mucous Membrane 861 Colorectal Adenocarcinoma (SW480) [JunctionChip 5 of 5] 7 cerebral cortex 21 1000 Substantia nigra structure 1000 Hippocampus PGA_PA-D_229 12 0 Nervous Sysem AML 66 on Affymetrix GeneChip Human Full Length Array HuGeneFL Primary tumor 19 32 AD control Treatment, type=dissect Source GEO sample is GSM119671 Last updated (according to GEO): Jul 10 2006 nostrils 156 164 Neostriatum 1000 Spleen 1000 Richard Almon-25-1138200270227 32h-DMSO replication 3 Keywords = preimplantation Keywords = development Source GEO sample is GSM14724 Last updated (according to GEO): May 28 2005 SON - Control Source GEO sample is GSM69838 Last updated (according to GEO): Aug 15 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68331 Last updated (according to GEO): Jul 07 2006 80 52 with congestive heart failure Somatic cell nuclear transfer allows trans-acting factors present in the mammalian oocyte to reprogram somatic cell nuclei to an undifferentiated state. Here we show that four factors (OCT4, SOX2, NANOG, and LIN28) are sufficient to reprogram human somatic cells to pluripotent stem cells that exhibit the essential characteristics of embryonic stem cells. These human induced pluripotent stem cells have normal karyotypes, express telomerase activity, express cell surface markers and genes that characterize human ES cells, and maintain the developmental potential to differentiate into advanced derivatives of all three primary germ layers. Such human induced pluripotent cell lines should be useful in the production of new disease models and in drug development as well as application in transplantation medicine once technical limitations (for example, mutation through viral integration) are eliminated. MCF7 pre-treated for 1h with cycloheximide, treated with vehicule for 24h Source GEO sample is GSM213322 Last updated (according to GEO): Jul 26 2007 Gastrin Knockout infused with saline fundic RNA Source GEO sample is GSM108488 Last updated (according to GEO): May 03 2007 Primary Carcinoma 875 Neoplasm 861 with some respiratory epithelium. 1039 1072 5 0 Spleen BC711A-AF A61 WT4 F24/5 A61 wild type Mouse 8 months Cerebellum Female Source GEO sample is GSM73199 Last updated (according to GEO): Sep 06 2005 no additional Source GEO sample is GSM199378 Last updated (according to GEO): Jun 08 2007 U87 glioblastoma cell, clone 8.1 (expresses PDGF-A dominant-negative) Keywords = bioinformatics Keywords = gene expression Keywords = cancer Keywords = platelet-derived growth factor Keywords = sterol regulatory element binding protein Keywords = glioblastoma multiformae Keywords = microarray Source GEO sample is GSM34588 Last updated (according to GEO): May 27 2005 in blood 16 23 1000 Cerebral cortex I_U133A_87_CB Muscle 861 trigeminal_ganglia_2 Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM107987 Last updated (according to GEO): Jun 06 2006 Nasal Epithelium 865 6 (cerebral cortex 21 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 4 hour after the last shock treatment. Source GEO sample is GSM4522 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T10) extracted from rats 28d following severe injury Source GEO sample is GSM31373 Last updated (according to GEO): May 27 2005 Human prostate cancer cells in different conditions Source GEO sample is GSM13093 Last updated (according to GEO): May 28 2005 861 Cerebral cortex P7 cochlear nuclei pooled from 5 pups for one replicate hybridization out of 3 replicates. Source GEO sample is GSM44852 Last updated (according to GEO): Jun 08 2005 meningiomas 885 896 from liver 21 30 LDMTX_MP-4 Muscular Dystrophies 901 HapMap CHB Female Source GEO sample is GSM159585 Last updated (according to GEO): Feb 01 2007 Blood Test (Blinded) Sample Source GEO sample is GSM129997 Last updated (according to GEO): Sep 18 2007 1000 Communicable Diseases 1000 Spleen 19 0 Head and neck cancer Gene expression data from human colon tumor tissue Source GEO sample is GSM173332 Last updated (according to GEO): Apr 20 2007 Skeletal Muscle_6wk_FVB_Female Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28708 Last updated (according to GEO): May 27 2005 brain, cerebral cortex: NMDA 360 2_le1 1000 Coronary Arteriosclerosis in bronchial epithelia 311 332 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215053 Last updated (according to GEO): Aug 02 2007 M7TW00121812 Adrenal cortex [JunctionChip 3 of 5] days nasal epithelium 1126 1147 Heart 1000 mouse cerebral cortex from COX-1 WT Source GEO sample is GSM121422 Last updated (according to GEO): Jan 31 2007 Leukemia, Lymphocytic, Chronic 1000 no additional Source GEO sample is GSM199377 Last updated (according to GEO): Jun 08 2007 of brain neurospheres 40 60 1000 Liver 1000 Lipids 861 Cardiomyopathies 331 307 in central nervous system 861 Cerebral cortex Neostriatum 1000 31 adrenal medulla 17 Plasma 861 D_U133Plus_38_Amy Normal human tissue:Normal Spinal Cord Keywords = Human, Normal Tissue, Normal Spinal Cord Source GEO sample is GSM44700 Last updated (according to GEO): May 27 2005 Skeletal bone 861 n/a Source GEO sample is GSM178006 Last updated (according to GEO): Jun 11 2007 Primary tumor 19 32 634 617 in the aged brain Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225923 Last updated (according to GEO): Nov 02 2007 D2_SleepDep_ZT 18_1 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with BAFF for 240min Source GEO sample is GSM5462 Last updated (according to GEO): May 27 2005 lateral hypothalamus 24 44 Olfactory Epithelium 1000 5 0 brain 1000 Spleen Monocular deprivation right cortex, biological rep1 CHC MD-2 Dorsal Root Ganglia 4 Normal substantia nigra Source GEO sample is GSM18585 Last updated (according to GEO): May 27 2005 Acetaminophen 6hr Rat 0644 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool 27 7 Medial Temporal Gyrus 75 48 with inflammatory myopathies PC9 Treatment, type=incubate, description=Hypoxic preconditioning Source GEO sample is GSM107483 Last updated (according to GEO): May 01 2006 Transitional epithelium 1000 1000 Hippocampus Parkinson Disease 861 Mesenchymal Stem Cells 1000 861 Cerebral cortex brain, cerebellum: Tg-/-_Crb3_e1_le1 Spleen 0 5 1000 Epithelial Cells Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell 30min (set2) metanephric mesenchyme, LIF, 4 days, biological rep1 HNC2774 1000 frontal lobe HapMap CEU_parent Male Source GEO sample is GSM159560 Last updated (according to GEO): Feb 01 2007 MGJZ030312065Adorsalrootganglion MSS-Ctr12moF-1aAv2-s2 Epithelial Cells 861 MCF10A_Untreated_#3 Cx43 KO cortical astrocytes 2 41 28 in mouse brain 715 705 from livers Wild type 8 wk old male C57BL/6J mouse pituitary gland Source GEO sample is GSM107045 Last updated (according to GEO): Mar 05 2007 UACC-62 hgu95d Cerebellum 1000 plasma cells 332 344 Disease Source GEO sample is GSM175922 Last updated (according to GEO): Apr 09 2007 Gene expression profile of the cell line UB/OC-1 grown for 8 days under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1541 Last updated (according to GEO): May 27 2005 983 Occipital lobe PGA_MI_nilv_4h_390 of the tumors 154 166 brain, Entorhinal Cortex: 01-22 tangle_e1_le1 1000 Brain Adrenal Medulla 1000 5 0 brain Brain 1000 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114226 Last updated (according to GEO): Jun 16 2006 Nasal Epithelium Inhalation Formaldehyde 07ppm 24h ID136 Clozapine treated 12weeks AffyGC RMA rep7 1000 Brain 83 60 hepatocellular carcinoma This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the lv samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12336 Last updated (according to GEO): May 28 2005 none Source GEO sample is GSM244566 Last updated (according to GEO): Nov 23 2007 1623 1613 hippocampus Brain 1000 Melanotransferrin (MTf) or melanoma tumor antigen p97 is an iron (Fe) binding transferrin homolog expressed highly on melanomas and at lower levels on normal tissues. It has been suggested that MTf is involved in a variety of processes such as Fe metabolism and cellular differentiation. Considering the crucial role of Fe in many metabolic pathways, for example, DNA synthesis, it is important to understand the function of MTf. To define the roles of MTf, two models were developed: (i) an MTf knockout (MTf-/-) mouse and (ii) downregulation of MTf expression in melanoma cells by post-transcriptional gene silencing (PTGS). Examination of the MTf-/- mice demonstrated no differences compared with wild-type littermates. However, microarray analysis showed differential expression of molecules involved in proliferation such as Mef2a, Tcf4, Gls and Apod in MTf-/- mice compared with MTf+/+ littermates. Considering the role of MTf in melanoma cells, PTGS was used to downregulate MTf mRNA and protein levels by >90 and >80%, respectively. This resulted in inhibition of proliferation and migration. As found in MTf-/- mice, in melanoma cells with suppressed MTf expression, hMEF2A and hTCF4 were upregulated compared with parental cells. Furthermore, when melanoma cells with decreased MTf expression were injected into nude mice, tumor growth was markedly reduced, suggesting a role for MTf in proliferation and tumorigenesis. Cerebral cortex 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145342 Last updated (according to GEO): Nov 20 2006 1000 Infection 23 14 from lungs Plasma 861 mouse hippocampus, cox-2 WT, rep3 456 452 lens 277 273 lungs Gene expression data from human colon tumor tissue Source GEO sample is GSM173331 Last updated (according to GEO): Apr 20 2007 Primary tumor 19 32 in seminoma 28 38 62 47 from 12 cochleas Gene expression data from postmorten brain regions Source GEO sample is GSM145400 Last updated (according to GEO): Nov 20 2006 861 Muscle Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132548 Last updated (according to GEO): Feb 26 2007 kidney 37 43 Liver (HBV+, SF12) WGACON-18 Occipital lobe 861 Neural tube, treated, GD9:12, T215585 156 145 Their livers Plasma 861 Heart 1000 Melanoma xenograft, MED1_Lung_C (LeiFidler) Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174516 Last updated (according to GEO): Mar 14 2007 between the LAD artery 266 287 Gene expression data from DAOY cells stably expressing Mel18 shRNA Source GEO sample is GSM182011 Last updated (according to GEO): Apr 23 2007 1344 1322 by cervical dislocation Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15700 Last updated (according to GEO): May 28 2005 osteoblast 627 637 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc68 Source GEO sample is GSM1878 Last updated (according to GEO): Nov 21 2005 1000 Hair follicle structure GRP sample 6 Expression profiling of spinal cord section (T9) extracted from rats 28d following laminectomy (sham) Source GEO sample is GSM31263 Last updated (according to GEO): May 27 2005 1000 Brain Ovarian_Tumor_Endometrioid_CHTN-OE-060 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy Keywords = pathological hypertrophy Keywords = rat Keywords = heart failure Keywords = cardiomyopathy Source GEO sample is GSM11882 Last updated (according to GEO): May 28 2005 Whole Brain 62 72 1000 Left pars nervosa of hypophysis 1000 /J mouse periaqueductal gray 25 52 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12684.gif Source GEO sample is GSM79794 Last updated (according to GEO): Sep 22 2006 D_U133Plus_112_nAcc WT cortical astrocyte 2 GSE3327 Cytotoxic activity of HTI-286 in prostate cancer EOM 14 Day mdx rep 2 osteoblast 627 637 12 0 ovarian tumor Disorder of artery 865 861 Cerebral cortex 861 Brain Nucleus Accumbends, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231035 Last updated (according to GEO): Sep 26 2007 Subject code A19EB D_U133A_93_DLPFC Kidney 861 1000 Brain prostate Source GEO sample is GSM18651 Last updated (according to GEO): May 27 2005 875 Acute leukemia PMN_control_180min_Patient9 Dissection of E16.5 cortex for RNA extraction. Cortex Hemispheres of E16.5 mice were divided into the medial (R1), dorsal (R2), ventral (R3), lateral (R4), and occipital regions (R5). Preparation of RNA and Synthesis of cDNA. Poly A+ RNA was obtained through twice column procedures with oligo dT cellulose column (New England Biolabs, Beverly, MA) and was used for synthesis of cDNA. 1ug of polyA+ RNA was converted into double-stranded cDNA by reverse transcription using ReverTra Ace (ToYoBo, Japan) with oligo dT(24) primers containing the T7 RNA polymerase promotor sequence (Amersham Pharmacia Biotech, Japan). The integrity of RNA was confirmed by agarose electrophoresis and RNA contents were analyzed by measuring the optical density at 260 nm. Target preparation and array processing. The following procedures including preparation of cRNA targets, hybridization, washing, staining, and scanning were performed as described in the Expression Analysis Technical Manual (Affymetrix, CA). Briefly, biotin-labeled antisense cRNA targets were synthesized in in vitro transcription reaction system (IVT) using cDNA as template (ENZO BioArrayTM HighYieldTM RNA Transcription Labeling kit with T7 RNA polymerase, Enzo, NY). The cRNA targets were size-fragmented to 35-200 bp in a buffer containing potassium and magnesium acetate at 94°C for 35 minutes and were used for hybridization as cRNA targets. The hybridization cocktail [containing 10 ug of target cRNA, control oligo BS (Affymetrix), and Eukaryotic Hybridization controls (Affymetrix)] was hybridized with a mouse U74A array at 42°C for 16 hours in GeneChip Hybridization Oven 640. Washing and staining were performed after hybridization under the fluidics station protocol, EuGE-WS2, on GeneChip Fluidics Station 400. Then, we scanned the array twice on HP GeneArrayTM scanner. Experiments were repeated twice with independent dissection. Data analysis. To quantify the expression level of a transcript, the average difference value (Adv) was calculated from the intensities against the probe cells using the global methods of normalization by Microarray Suite ver. 4.0 (Affymetrix). Source GEO sample is GSM14599 Last updated (according to GEO): Oct 28 2005 Sample is skeletal muscle from a morbidly obese patient undergoing elective abdominal surgery Source GEO sample is GSM3986 Last updated (according to GEO): May 28 2005 1000 Cerebral cortex Gene expression data from postmorten brain regions Source GEO sample is GSM145852 Last updated (according to GEO): Nov 20 2006 Multiple Myeloma 861 AML_18 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Immature B cells 2b Hippocampus 0 10 1000 Testis 861 Cerebral cortex 30 0 Skeletal Muscle [JunctionChip 2 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141309 Last updated (according to GEO): Oct 26 2006 19 0 The left hippocampus brain, Entorhinal Cortex: Sample7_e1_le1 Spleen vs Lipopolysaccharide (LPS) Treated B cell 30min (set3) M_U133A_87_nAcc Gene expression data from mouse colon Source GEO sample is GSM198115 Last updated (according to GEO): Aug 22 2007 IDC153 on harvard-12k NCI60.21_LABEL25EXTRACT24SUB3 Source GEO sample is GSM134099 Last updated (according to GEO): Aug 06 2007 861 Blood Nasal Epithelium 901 Lymphoblastoid Cell Line for Individual 8211.3 log phase 65 50 Cerebellum C57BL f2#188 versus pool Mouse Brain tissue CAKI-1 hgu95e LPS plus IL-10, 30 min, Rep_3 of target-ablated olfactory epithelium 34 71 mouse brain ipsilateral RU486 Source GEO sample is GSM149777 Last updated (according to GEO): Mar 15 2007 Adipocytes 861 21 0 acute myeloid leukemia 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114454 Last updated (according to GEO): Jun 16 2006 5 0 brain Blood Test (Blinded) Sample Source GEO sample is GSM129955 Last updated (according to GEO): Sep 18 2007 1000 Spleen Untreated versus treated (bortezomib) breast cancer cells. Source GEO sample is GSM120348 Last updated (according to GEO): Jul 20 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with BAFF for 240min Source GEO sample is GSM5460 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM176315 Last updated (according to GEO): Apr 09 2007 placenta-0702-uninflamed-infected-rep1 of parieto-occipital cortex 225 252 Large-scale analysis of the human transcriptome. Brain, cerebellum Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 184.69 Stdv: 14.25 Min: 162.22 Max: 220.89 Source GEO sample is GSM2849 Last updated (according to GEO): Mar 20 2006 Blood 1000 D_U133Plus_23_DLPFC healthy control sample x120 861 Cerebral cortex Bic/4AP/TTX Kidney 1000 Fear conditioning (FC) is a behavioral paradigm that measures an animal's ability to learn fear related information. FC is measured by pairing a mild foot-shock with the surroundings in which the shock was recieved. Upon being placed back in the context, mice exhibit freezing behavior, which is a species-specific response to fear. We have previously used selective breeding to produce lines of mice with high or low levels of freezing behavior. This experiment is a replication of a previous experiment that produced lines of mice with high or low levels of freezing behavior. These lines derive from different progenitor mouse strains. We are able to identify alleles that govern the genetic variability for FC by using chromosomal markers in these selected lines. Using microarrays, we will identify differences in gene expression in two key brain regions: amygdala and hippocampus. Gene expression differences and data regarding chromosomal regions involved in the behavior will be compared to identify particular genes that are both differentially expressed and whose expression is governed by alleles that fall into critical chromosomal regions. We will compare gene expresion in the amygdala and hippocampus (brain regions known to be relevant to fear behavior) from the these two lines of mice and to the those in the previous experiment. Bayesian statistics will be used in an effort to identify gene expression that affects fear behavior. We hypothesize that selection has acted in part by changing the frequency of alleles that cause differential expression of key genes in the amygdala and hippocampus of our selected lines. Slective breeding changes the frequency of trait relevand (FC) alleles. A relevant allele is expected to increas in one selected line and decrease in the oppositely selected line. Some trait relevant alleles are expected to cause changes in the level of expression at particular genes. Amygdala and hippocampus will be rapidly dissected out of experimentally naïve mice from each line. Naïve mice will be used for expression studies since the behavior of the mice in the FC test can be reliably anticipated due to their lineage. We have practiced these procedures, and can accurately and reproducibly remove these regions in less than 5 minutes. Different mice will be used to collect each brain region, since the dissection of hippocampus disrupts the removal of amygdala. We will collect enough samples from each region to accommodate a total of 6 microarrays per brain region, per line, thus we will use a total of 24 microarrays. We anticipate that a single brain region will be sufficient to for a microarray. However, we propose to utilize three samples per microarray, because this will reduce variability due to environmental factors and due to slight variability in our dissection procedures. Once this tissue is removed, we will isolate RNA for shipment to the Microarray consortium. We will also collect spleens from each subject as a source of genomic DNA, in order to permit direct comparison of genotype and expression phenotypes. Once we have the results of the microarray analysis, we use WebQTL.org to identify the chromosomal locations of alleles that are know to influence the expression of genes for which we have found differential expression. We will then superimpose this information on trait relevant chromosomal regions identified from our selected lines. This will allow us to rapidly identify genes which may account for genetic variability in FC due to differential expression. Such genes will then be subjected to further study.. Date GSE4034 Last Updated: Jan 13 2006 Contributers: Abraham A Palmer Includes GDS1901. Update date: Jun 09 2006. Dataset description GDS1901: Analysis of the amygdalae and hippocampi of strains exhibiting low or high freezing behavior in response to fear. Previous work identified alleles that contribute to the variability in freezing behavior, and the chromosomal location of these alleles.. 660 mesenchymal stem cell 639 D2_TP-48_I CNS-SMTC_Mod24h-2C-s2 Primary Neoplasm 1000 1000 Spleen Heart 1000 FNH (HK70) Nasal Epithelium Inhalation Formaldehyde 2ppm 8d ID221 Heart Septal Defects, Atrial 1000 C57/BL6 to C57/BL6 Source GEO sample is GSM8931 Last updated (according to GEO): May 28 2005 brain, forebrain: WCx4w#2_e1_le1 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68173 Last updated (according to GEO): Jul 07 2006 1000 Amygdaloid structure Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242061 Last updated (according to GEO): Dec 04 2007 Spleen 0 5 pfc_1022_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of DC, recombinant human (rh) IL-4 and rhGMCSF were added to the culture at 50 ng/ml on days 1, 3, and 5 of culture. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5138 Last updated (according to GEO): Mar 17 2006 Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 24h. Lot batch = Source GEO sample is GSM1240 Last updated (according to GEO): May 28 2005 CNS-SC_Inj24h-3A-s2 PGA_PA-D_225 Coronary Arteriosclerosis 1000 human caudate nucleus Source GEO sample is GSM86925 Last updated (according to GEO): Feb 08 2006 Trachea [JunctionChip 3 of 5] RNA isolated from post-mortem tissues Source GEO sample is GSM6826 Last updated (according to GEO): May 28 2005 78 66 Control blood putamen_4 Source GEO sample is GSM80571 Last updated (according to GEO): Mar 31 2006 Cerebral cortex 1000 Skeletal muscle structure 1000 C57BL/6ByJ strain, brain hemisphere, biological rep1 1BMH02082905_BM_CD33myeloid Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28815 Last updated (according to GEO): May 27 2005 861 Infection BXD31_M7SS02042210 Heart 1000 673 659 by decapitation Primary typical carcinoid 8512 Source GEO sample is GSM17326 Last updated (according to GEO): May 28 2005 acute myelogenous leukemia 761 787 Gene expression data from postmorten brain regions Source GEO sample is GSM145548 Last updated (according to GEO): Nov 20 2006 1000 Mitral Valve fibroblasts breast tumor cell line HDF-Skin Keywords = Agilent microarray, Expression analysis, EGFR, Breast cancer growth Source GEO sample is GSM29451 Last updated (according to GEO): Dec 13 2006 to the nose 599 609 50 41 mouse lung 861 Cerebral cortex 52 8 in docetaxel-refractory prostate cancer_docet 1000 Brain 7 cerebral cortex 21 1000 Brain HOXB4ERT_w/o TMX, 4hours, biological rep2 starved 143 149 AML_12 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Cerebellum Source GEO sample is GSM53377 Last updated (according to GEO): Jul 06 2005 Pressure-overload induced hypertrophy model. Mouse was sacrificed 8 weeks after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2265 Last updated (according to GEO): May 27 2005 The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76944 Last updated (according to GEO): Oct 11 2005 Backskin_WT_P23_rep1 Homozygous O377 mutant mouse line versus wildtype mice Source GEO sample is GSM86415 Last updated (according to GEO): Dec 08 2005 M_U133A_89_DLPFC nervous system function 44 66 1000 Brain Rat SCN Sample 7b (Exp 1 - 36 hr b) 47 30 of studying cancer 861 Cerebral cortex dentate granule cells Source GEO sample is GSM35829 Last updated (according to GEO): May 27 2005 901 Structure of locus ceruleus PGA-HBE-NormOz18h-1aA-S2 E7.25_rep2 1037 of transitional epithelium 1012 BXD11_M7SS02042205 Pituitary Gland 3 Normal Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28703 Last updated (according to GEO): May 27 2005 36 21 from whole brain Gene expression data from postmorten brain regions Source GEO sample is GSM145465 Last updated (according to GEO): Nov 20 2006 A1 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with fMLP for 60min Source GEO sample is GSM5571 Last updated (according to GEO): May 27 2005 Epithelium of bronchus 983 38 10 from cultured organ of Corti Breast Carcinoma 861 Spleen vs TGF-beta Treated B cell 120min (set2) Collagen 1000 Ts1Cje-2-MGU74B Isolated adipocytes 0 18 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184691 Last updated (according to GEO): Apr 26 2007 Gene regulation and DNA damage in the ageing human brain. 5 0 brain ISR3-WT TM1 RNA from 2 ug/ml tunicamycin treated (6 hr) wildtype cells. The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules. Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10886 Last updated (according to GEO): May 27 2005 0.5 mg/kg/ml Isoproterenol treatment, 3 hour time point, biological rep 1 913 Acute leukemia C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P28 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25138 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T9) extracted from rats 28d following severe injury Source GEO sample is GSM31600 Last updated (according to GEO): May 27 2005 to the lung 846 856 Blood 1000 MDA-MB-435 hgu95e palme-affy-mouse-198967 43 0 Chorionic mesoderm-derived mesenchymal cells Myocardial Infarction 1000 folatedeficientAs1ppm3 150mg/kg APAP 24Hr rat 3618 blood vs. 3616 PC 24Hr (pool) heart_atrium_3 Source GEO sample is GSM80655 Last updated (according to GEO): Mar 31 2006 Oat cell carcinoma 867 Nasal Epithelium 901 901 Epithelial Cells ovary 45 50 901 Caudate nucleus structure LungP12_022BAF73_077c.txt Heart_6wk_FVB_Female 60 45 of the Pituitary M_U133A_10_DLPFC Nucleus accumbens, male 10.5 week old c57bl/6J mouse, NON-DEFEATED control Source GEO sample is GSM224743 Last updated (according to GEO): Aug 31 2007 88 FC BA9 B Heart 861 Cultured_cortical_astrocyte_wild_type_rep1 Coronary heart disease 913 Utricle structure 1000 91 from the bone marrow 72 Malignant Neoplasms 861 1000 ovarian neoplasm LivRegen24hr022SAFAV_180.txt Muscle Source GEO sample is GSM4307 Last updated (according to GEO): May 27 2005 stria terminalis 901 Brain 861 Epithelial Cells 901 1000 Lens, Crystalline 101077 hippocampus 234 244 brain_DLPFC_bipolar C_mr284 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162177 Last updated (according to GEO): Jun 12 2007 5 0 brain brain, cerebral cortex: NIC + NMDA 4_le1 D_U133A_81_CB 80 68 Control blood human peripheral blood derived monocytes, 2 hour LPS stimulation, biological rep2 Source GEO sample is GSM126995 Last updated (according to GEO): Aug 15 2006 Circadian Time Treatment, type=time_course, measurement=12.0 h Source GEO sample is GSM53340 Last updated (according to GEO): Jul 06 2005 1000 Brain none Source GEO sample is GSM239873 Last updated (according to GEO): Dec 07 2007 brain, Left frontal Lobe: Extract21_le1 Plasma 861 the blood 393 402 Sun178_BAV13 group U937+HRF Brain 1000 5 0 Muscle Balb/c day 1, biological rep 2, tech rep 1 Inflammatory myopathy specimen GEIM21 861 Cerebral cortex Primary Neoplasm 1000 Plasma 861 AML cDNA hybridization-ID61-L Brain 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145049 Last updated (according to GEO): Nov 20 2006 with some respiratory epithelium. 1039 1072 467 459 seizures of Huntington's disease 226 248 AKR-J_male_hypothalamus Source GEO sample is GSM138576 Last updated (according to GEO): Apr 18 2007 4 0 Brain 24 0 Polycystic ovary syndrome processed in batch 6 Source GEO sample is GSM90421 Last updated (according to GEO): Mar 20 2006 cerebral cortex 7 21 Brain 1000 Lymphoblastoid Cell Line for Individual 8099.3 log phase 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201283 Last updated (according to GEO): Jun 14 2007 Control (6/24) (Experiment NMDA1-Run 9136) Treatment, type=time_course, measurement=0.0 m Source GEO sample is GSM96662 Last updated (according to GEO): Feb 14 2006 In order to more thoroughly investigate the mechanism of arsenate-induced NTDs we designed experiment in which highly sensitive Folr2 nullizygous mice were treated i.p. with teratogenic dose of sodium arsenate just at the beginning of the neural tube formation process. This specific knockout mouse and arsenic exposure conditions were chosen as they warranted high incidence of exencephaly in exposed embryos. We investigated the gene expression changes induced by arsenic in the anterior part of neural tube in order to discover patterns that might shed light on the mechanism of arsenic?s teratogenicity. Last Updated (by provider): Oct 11 2005 Contributers: Richard Finnell Denise Hill Daniel Bozinov Bogdan Wlodarczyk Robert Cabrera Epithelial Cells 901 119 111 cerebrum Primary Neoplasm 1000 pharyngeal_mucosa_4 Source GEO sample is GSM80751 Last updated (according to GEO): Mar 31 2006 nostrils 156 164 861 Cerebral cortex fibroblasts 39 49 Microdissected area # 3 of 2182 tumor brain 162 167 MSS-Ctr9moM-1bAv2-s2 Epithelium of bronchus 983 The nose 94 101 17 7 hippocampus (cortex 19 25 healthy subject Source GEO sample is GSM211072 Last updated (according to GEO): Sep 10 2007 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181105 Last updated (according to GEO): Jul 12 2007 95 year old male CAD_replicate60 Male 67.2 yr after antibody enrichment scan 2 (U133A) Cerebellum 861 Ventral Tegmental Area 1000 nasal epithelial cells 28 49 Spleen 1000 Epithelial Cells 1000 brain, cerebral cortex: Rat_03-39_NroLep_Lipska_e1_le1 WGACON-259 1000 Substantia nigra structure 13 7 cochlea ma-breast 0 8 /NJ mouse periaqueductal gray 27 55 E7, hTERT, neural differentiation, bone marrow cell 4 lateral hypothalamus short access to cocaine replicate 1 Skin 1000 Category: Cell-line Subcategory: HMEC Scanning Software: ScanAlyze Software version: 2.44 Lot batch = 0106-5k Source GEO sample is GSM1933 Last updated (according to GEO): Nov 21 2005 Recurrent tumor 861 129S6/SvEvTac periaqueductal gray rep1 901 Coronary artery 853 Acute leukemia 861 Acquired Immunodeficiency Syndrome Expression profiling of spinal cord section (T8) extracted from rats 30m following mild injury Source GEO sample is GSM31435 Last updated (according to GEO): May 27 2005 Cerebral cortex 1000 SmoothMuscle Source GEO sample is GSM18813 Last updated (according to GEO): Sep 25 2006 CAD_replicate56 left 22 25 GM12872 from colorectal adenoma 21 44 Gene profiling of the heart myocardium after a single dose administration of Isoproterenol hydrochloride brain, Entorhinal Cortex: Sample9_e1_le1 Communicable Diseases 861 210 204 ungual osteoblast 630 640 Cochlear structure 1000 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159810 Last updated (according to GEO): Apr 23 2007 Primary tumor 19 32 1000 Myopathy mouse brain 478 489 Female; Uterus - pregnant day4.5 Keywords = mouse gene expression database Source GEO sample is GSM29330 Last updated (according to GEO): May 27 2005 Leukemia Promyelocytic (HL-60) [JunctionChip 5 of 5] Cortex from rats with cerebral cortical contusion 4 days post injury, injured cortex (ipsilateral side) -uninjured cortex (contralateral side) were hybridised onto a 6240 cDNA probe microarray. Expression ratios were calculated using injured/ un-injured cortex Source GEO sample is GSM76023 Last updated (according to GEO): Sep 29 2005 966 Amygdaloid structure 1000 Mammary gland 3AJZ02031304_fetallung Macrophage smi117 Testis 1000 rotenone 4 weeks C Treatment, type=time_course, measurement=4.0 weeks Source GEO sample is GSM107867 Last updated (according to GEO): Jun 06 2006 211 190 with coxsackievirus B3 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68114 Last updated (according to GEO): Jul 07 2006 Diaphragm-skeletal muscle 0 25 /6J periaqueductal gray rep1 5 32 114 101 brains quickly 853 Malignant Neoplasms MD rep 3 Neoplasm 861 /NJ pituitary gland rep1 3 26 861 Cerebral cortex 861 Blood Arteries 861 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:201, Count:32 Corner- Avg:37367, Count:32 BF:testadult.CHP Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:8.311234,SFGene:All Background:Avg:442.52,Stdev:8.47,Max:475.3,Min:427.8 Noise:Avg:10.13,Stdev:0.36,Max:11.2,Min:9.2 RawQ:13.41 Keywords = ALL Source GEO sample is GSM3486 Last updated (according to GEO): May 28 2005 Pool of 11 cochlear tissues at E15 Source GEO sample is GSM182588 Last updated (according to GEO): Aug 14 2007 Brain 861 923 Leukemia, Lymphocytic, Acute Skin; Fetal Skin Day 16 Keywords = mouse gene expression database Source GEO sample is GSM29435 Last updated (according to GEO): May 27 2005 M_U133A_88_nAcc A HID B D057 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108584 Last updated (according to GEO): Aug 22 2006 none Source GEO sample is GSM123188 Last updated (according to GEO): Jul 26 2006 Wild type 8 wk old male 129S6/SvEvTac mouse bed nucleus of the stria terminalis Source GEO sample is GSM74927 Last updated (according to GEO): Feb 27 2007 caudatenucleus Source GEO sample is GSM18760 Last updated (according to GEO): Sep 25 2006 Wild-type-neocortex, biological rep5 (male) This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques P. Tremblay (jacques-p.tremblay@crchul.ulaval.ca; 2705 boulevard Laurier) for analysis. Stembase Experiment ID: E205 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205 SCGP Sample ID: S270 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205#SAMPLE_247 Short description: Cells from sphere were incubated in a differentiation medium. They differentiated into neurons after 7 days in culture. Analysis requested: mouse genechips RNA concentration: 0.689 ug/uL Sample volume: 15 uL total Source GEO sample is GSM93615 Last updated (according to GEO): Jan 23 2006 Neoplasm 861 Keywords = kidney 149 166 AKR/J_female_hypothalamus Source GEO sample is GSM138564 Last updated (according to GEO): Apr 18 2007 NCI60.17_LABEL21EXTRACT20SUB3 Source GEO sample is GSM134076 Last updated (according to GEO): Aug 06 2007 Cerebral cortex 861 DMN-CtrHippo32d-1aAv2-s2 CurrentSmoker 98 I_U133Plus_115_CB none Source GEO sample is GSM239858 Last updated (according to GEO): Dec 07 2007 12 0 ovarian tumor of somatomotor cortex 21 41 PGA-Band_Sham_1w_5-m5 861 Bladder A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism Source GEO sample is GSM5983 Last updated (according to GEO): Nov 21 2005 thyroid_gland_1 Source GEO sample is GSM80864 Last updated (according to GEO): Mar 31 2006 861 Medulla Probeset expression data from NA12740 growth 2 Source GEO sample is GSM201524 Last updated (according to GEO): Aug 08 2007 67 40 with coronary artery disease Average value of duplicate experiments of gut neurospheres (neurospheres of peripheral nervous system) of WT (wild type) mice (postnatal day 0). The cRNAs for hybridization were generated by two round RNA amplifications. Source GEO sample is GSM9241 Last updated (according to GEO): May 27 2005 GBM Treatment, type=remove Source GEO sample is GSM99493 Last updated (according to GEO): Apr 21 2006 spleen_4 Source GEO sample is GSM80826 Last updated (according to GEO): Mar 31 2006 Lymphoblastic Leukemia 901 Gene expression data from postmorten brain regions Source GEO sample is GSM145782 Last updated (according to GEO): Nov 20 2006 1000 Encephalitis Sample # 1285-1 Bone Marrow 1000 Wild Type, biological rep3 5 0 brain CNS Regeneration 14 7 amygdala Nasal Epithelium 865 in the brain 150 162 901 Cell phenotype 91 from the bone marrow 72 epidermis; dorsal skin without fur Source GEO sample is GSM18641 Last updated (according to GEO): May 27 2005 blood, Blood: 1432_1203_le1 Testis 1000 Ganglia, Spinal 923 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:239, Count:32 Corner- Avg:38822, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:7.316926,SFGene:All Background:Avg:371.14,Stdev:5.69,Max:385.0,Min:359.1 Noise:Avg:10.15,Stdev:0.33,Max:11.2,Min:9.4 RawQ:12.76 Keywords = ALL Source GEO sample is GSM3455 Last updated (according to GEO): May 28 2005 129T E10.5 craniofacial tissue, first branchial arch: KO_MXA-3_e1_le1 brain 0 5 healthy subject Source GEO sample is GSM211058 Last updated (according to GEO): Sep 10 2007 Jejunum 2 [JunctionChip 5 of 5] 15 0 human cerebellum 861 Cardiomyopathies Expression profiling of laminectomized raphe at 3mo in rats Source GEO sample is GSM41538 Last updated (according to GEO): May 27 2005 I_U133A_15_Amy Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211283 Last updated (according to GEO): Jul 18 2007 GSE398 901 Epithelial Cells Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120657 Last updated (according to GEO): May 14 2007 901 Bone Marrow HTI-286 in docetaxel-refractory prostate cancer Source GEO sample is GSM206170 Last updated (according to GEO): Jun 29 2007 1BJZ02061908_caudatenucleus 1000 Spleen NA18859 861 Colon Inflammatory myopathy 10 0 hippocampus 15 7 brainstem 5 0 brain Murine dermal burn wound Replicate3_Voxel E4 M_U133A_27_DLPFC 150 mg/kg X 24 hr Source GEO sample is GSM129831 Last updated (according to GEO): Sep 18 2007 19 0 human frontal cortex eye 0 3 Expression profiling of spinal cord section (T10) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31276 Last updated (according to GEO): May 27 2005 1000 frontal lobe T172 Pressure-overload induced hypertrophy model. Mouse was sacrificed 24 hours after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2254 Last updated (according to GEO): May 27 2005 Medulla 861 Whole Brain 62 72 1000 Hippocampus Expression profiling of moderately injured raphe at 4h in rats Source GEO sample is GSM41619 Last updated (according to GEO): May 27 2005 in the mammalian nervous system 110 141 Brain 861 foreskin fibroblast #2, serum starved 17 7 hippocampus 901 Cerebral cortex 660 mesenchymal stem cell 639 Infection 1000 of Parkinson's disease 450 471 Richard Almon-15-1138200269836 Gene expression data from postmorten brain regions Source GEO sample is GSM144915 Last updated (according to GEO): Nov 20 2006 Expression data from human donor lung biopsies GSE3063 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Platelet activating factor for 60min Source GEO sample is GSM5725 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM144981 Last updated (according to GEO): Nov 20 2006 861 Neoplasm 67 40 with coronary artery disease temporal_lobe_4 IDC88 on harvard-12k Parkinson 0 8 cerebral cortex wistar 3902 retina 7 12 330 324 uterus 8 0 Hindbrain 715 702 After the eyes Whole blood 0 10 AE318 Date : 4/13/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 6.0 hrs post-injection Intervention : none Risk: estimated 20% incraesed risk for encephalopathy Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Source GEO sample is GSM12250 Last updated (according to GEO): May 28 2005 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211405 Last updated (according to GEO): Jul 18 2007 CLL-59 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225749 Last updated (according to GEO): Nov 02 2007 1000 Hippocampus with mental retardation 241 263 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.4 Subject: 2978 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39040 Last updated (according to GEO): May 27 2005 brain_DLPFC_bipolar C_mr275 7 0 Melanoma Ganglia 861 Gloubus Pallidum External 3 Disease 430A2_1945_36_KO_neuropath_midbrain Source GEO sample is GSM242683 Last updated (according to GEO): Nov 15 2007 913 Coronary heart disease Anterior nares 1000 Spinal Cord 861 NFIA P16KO3 Nasal Epithelium Inhalation Formaldehyde 6ppm 5d ID294 5 0 Spleen Cultured_osteoblast-like_shear-stressed_MC3T3-E1_cells_rep1 park_1153_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Simple annotation: Cell-line, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3154.gif Source GEO sample is GSM79841 Last updated (according to GEO): Sep 22 2006 289 280 infection Expression profiling of spinal cord section (T10) extracted from rats 30m following mild injury Source GEO sample is GSM31325 Last updated (according to GEO): May 27 2005 Muscle 861 with Parkinson's disease 27 50 Lymphoblastoid Cell Line for Individual 8129.4 log phase 13 8 Retina Nasal Epithelium Instilation Formaldehyde 400mM 6h ID365 Normal Amygdala 1000 Hippocampus 861 Heart failure Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9983.gif Source GEO sample is GSM79860 Last updated (according to GEO): Sep 22 2006 1000 Pancreas Saccule at E14, replicate1 in seminoma 28 38 1000 Cerebral cortex Primary Neoplasm 1000 Heart 1000 HapMap CEU_parent Female Source GEO sample is GSM159537 Last updated (according to GEO): Feb 01 2007 Impaired cognition 1000 5 0 brain Cerebral cortex 861 Replicate two: differential expression analysis of CW vs Lyt44 treatment Source GEO sample is GSM128920 Last updated (according to GEO): Aug 16 2006 prostate Source GEO sample is GSM203282 Last updated (according to GEO): Jun 21 2007 Donor 3 Time point 48 hours post infection with HIV-1, RF Source GEO sample is GSM2624 Last updated (according to GEO): May 27 2005 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9964.gif Source GEO sample is GSM79805 Last updated (according to GEO): Sep 22 2006 the blood 393 402 Gene expression data from brain of adult rats Source GEO sample is GSM101010 Last updated (according to GEO): Feb 20 2007 4 0 Heart Whole blood 0 10 Malignant neoplasm of prostate 861 Cerebral cortex 1000 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225365 Last updated (according to GEO): Aug 31 2007 from colonic normal mucosa 21 47 5 0 brain 10 0 Small Bowel Virus Diseases 1000 Mouse Liver Male 3 (technical replicate) I_U133A_27_AnCg 10 7 left Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7776.gif Source GEO sample is GSM79964 Last updated (according to GEO): Sep 22 2006 AD control Treatment, type=dissect Source GEO sample is GSM119650 Last updated (according to GEO): Jul 10 2006 1000 Synovial Membrane Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174519 Last updated (according to GEO): Mar 14 2007 861 Cerebral cortex 21 0 Mammary Gland @ Lac9 Wild type inbred mice Source GEO sample is GSM83027 Last updated (according to GEO): Nov 10 2005 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n132 Source GEO sample is GSM2049 Last updated (according to GEO): Nov 21 2005 337 323 with adiposity GBM Treatment, type=remove Source GEO sample is GSM99567 Last updated (according to GEO): Apr 21 2006 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM119701 Last updated (according to GEO): Jul 11 2006 1000 Left Hepatocyte 1000 Liver Test (Blinded) Sample Source GEO sample is GSM130173 Last updated (according to GEO): Sep 18 2007 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23744.gif Source GEO sample is GSM66584 Last updated (according to GEO): Sep 22 2006 Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200617 Last updated (according to GEO): Jun 12 2007 Bic/4AP/MK801 CH2113 P18 deprived visual cortex replicate 4 1000 Rectum 1000 Spleen 1000 Cerebral cortex Leukemia, Lymphocytic, Chronic 1000 Sample is skeletal muscle from nonobese patient undergoing elective abdominal surgery Source GEO sample is GSM3994 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145523 Last updated (according to GEO): Nov 20 2006 GM19141 Gene expression data from postmorten brain regions Source GEO sample is GSM145520 Last updated (according to GEO): Nov 20 2006 esophagus_1 Source GEO sample is GSM80694 Last updated (according to GEO): Mar 31 2006 Hep2_42_rep2 of somatomotor cortex 21 41 /J Hippocampus A 3 18 861 Cerebellum human frontal cortex Source GEO sample is GSM87053 Last updated (according to GEO): Feb 08 2006 Recurrent Adenocarcinoma 7 Kidney 861 Ventral Tegmental Area 1000 Medulla 861 Bmi-1, bone marrow cell Plasma 861 73 54 of hyperinsulinaemic Small cell carcinoma of lung 901 Disease Source GEO sample is GSM175916 Last updated (according to GEO): Apr 09 2007 GSE833 861 Blood of regenerating Dorsal Root Ganglia 21 55 Whole Brain 62 72 NCI60.50_LABEL54EXTRACT53SUB3 Source GEO sample is GSM134246 Last updated (according to GEO): Aug 06 2007 Expression profile of genes in mouse brain Source GEO sample is GSM21058 Last updated (according to GEO): May 27 2005 (1 utricle 10 19 Stem cells 913 861 Cardiomyopathies Untreated versus treated (bortezomib) breast cancer cells. Source GEO sample is GSM120349 Last updated (according to GEO): Jul 20 2006 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28727 Last updated (according to GEO): May 27 2005 SkelMusc_022XAFC1_086.txt Defining a developmental path to neural fate by global expression profiling of mouse embryonic stem cells and adult neural stem/progenitor cells. Y HID D077 Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 72h. Lot batch = Source GEO sample is GSM1246 Last updated (according to GEO): May 28 2005 150 in the frontal cortex 170 in the mammalian nervous system 110 141 12 0 Blood B cells Coronary artery 901 Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181983 Last updated (according to GEO): Apr 13 2007 861 Lens, Crystalline Keywords = Heart 505 521 Intestines, Small 1000 Heart 1000 7 0 Amygdala brain, cerebellum: KCx12w#1_e1_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM145081 Last updated (according to GEO): Nov 20 2006 1000 Retina BACKGROUND: Previous genomic studies with human tissues have compared differential gene expression between 2 conditions (ie, normal versus diseased) to identify altered gene expression in a binary manner; however, a potentially more informative approach is to correlate the levels of gene expression with quantitative physiological parameters. METHODS AND RESULTS: In this study, we have used this approach to examine genes whose expression correlates with arterial stiffness in human aortic specimens. Our data identify 2 distinct groups of genes, those associated with cell signaling and those associated with the mechanical regulation of vascular structure (cytoskeletal-cell membrane-extracellular matrix). Although previous studies have concentrated on the contribution of the latter group toward arterial stiffness, our data suggest that changes in expression of signaling molecules play an equally important role. Alterations in the profiles of signaling molecules could be involved in the regulation of cell cytoskeletal organization, cell-matrix interactions, or the contractile state of the cell. CONCLUSIONS: Although the influence of smooth muscle contraction/relaxation on arterial stiffness could be controversial, our provocative data would suggest that further studies on this subject are indicated. G30-SomatosensoryCortex replicate3 Standard Affymetrix Protocol Source GEO sample is GSM16451 Last updated (according to GEO): May 28 2005 901 Connective Tissue 2269 2249 (Control-Hippocampus Gene expression data from liver Source GEO sample is GSM243400 Last updated (according to GEO): Nov 16 2007 TONGUE Source GEO sample is GSM18859 Last updated (according to GEO): Sep 25 2006 Spinal Cord 901 UBOC1 Exp A Day 0 (b) Profile of changes in gene expression in cultured hippocampal neurones evoked by the GABAB receptor agonist baclofen. MO_DH1b_SON_NCBI MGMH030212052Bstomach 1000 Maxilla Head and neck cancer Source GEO sample is GSM155663 Last updated (according to GEO): Apr 24 2007 Infection 1000 A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke. White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by 6 hours of reperfusion; first replicate; pooled mRNA from 6 brains. Source GEO sample is GSM2210 Last updated (according to GEO): May 27 2005 testis 52 58 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225916 Last updated (according to GEO): Nov 02 2007 NA12751 growth 2, replicate 3 55 with Down syndrome 38 Pineal gland 1000 Medulla 861 GM12864 27 7 Medial Temporal Gyrus Gene expression data from human colon tumor tissue Source GEO sample is GSM173336 Last updated (according to GEO): Apr 20 2007 COID-9794-A300-5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Hypertrophic Cardiomyopathy Large-scale analysis of the mouse transcriptome. Heart C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 263.13 Stdv: 7.97 Min: 250.68 Max: 278.01 Source GEO sample is GSM2909 Last updated (according to GEO): Mar 20 2006 Liver 0 4 Epithelial Cells 901 in the cerebellum 1017 1033 Brain 1000 1000 Encephalitis 3AMH02082806_PB_CD8TCells 1000 Infection 320 306 Keywords = HIV 140 134 soleus 78 66 Control blood 19 0 Head and neck cancer Replicate3_Voxel C8 a_NY7 1000 Stem cells na Source GEO sample is GSM181304 Last updated (according to GEO): Apr 10 2007 NoCAD_replicate10 AK_SleepDep_ZT 0_1 5 0 Spleen 18 month spinal cord rep 1 to the nose 599 609 post HCMV infection 5 23 15 7 brainstem Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28824 Last updated (according to GEO): May 27 2005 embryonic cortical neuron treated with NMDA Source GEO sample is GSM49620 Last updated (according to GEO): May 29 2005 high gestational age Source GEO sample is GSM213113 Last updated (according to GEO): Jul 25 2007 Structure of superior frontal gyrus 1000 1000 Hair follicle structure Gene expression data from postmorten brain regions Source GEO sample is GSM145300 Last updated (according to GEO): Nov 20 2006 1000 Congestive heart failure pfc_1041_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Disease Source GEO sample is GSM176360 Last updated (according to GEO): Apr 09 2007 Kainate-neocortex, biological rep1 Date 3/10/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : embryo proper Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 5.0 mg/kg Time : 3 hrs post-injection Intervention : none Risk: 25% increased risk of microphthalmia Conditional biomarker: p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 8-10 embryos pooled from same litter Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = embryo Keywords = microphthalmia Lot batch = AE195 Source GEO sample is GSM12061 Last updated (according to GEO): May 28 2005 Pancreas at e12.5, Chip B, rep 2 5 0 Spleen Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200618 Last updated (according to GEO): Jun 12 2007 1000 Structure of trigeminal ganglion of coronary artery disease 258 284 901 Caudate nucleus structure cDNAs were generated from 5ug of total RNA per sample by reverse transcription (RT) for two hours at 42oC using the 3DNA SubmicroTM Oligo Expression Array Detection Kit (Genisphere, Hatfield, PA) and Superscript II (Invitrogen, Carlsbad, CA). For each microarray chip two consecutive hybridizations were performed with cDNAs and the fluorescent probes following the manufacture?s specifications. Briefly, in the first hybridization reaction the solution containing the mixture of cDNAs obtained from control and treated cells was loaded onto the CAG Human 19K array and incubated overnight at 55oC in a hybridization chamber (Genemachines, San Carlos, CA). The human 19K array (www.cag.icph.org/microarray_facility.htm) contains 60-mer oligonucleotides (Compugen, San Jose, CA) representing 18,861 human genes spotted onto poly-l-lysine coated glass microscope slides. In the second hybridization reaction Cy3 (green) and Cy5 (red) fluorescent probes were used to label the cDNAs from control and PGJ2-treated cells, respectively. The second hybridization was carried out for 3 hours at 65oC in the hybridization chambers. The arrays were scanned using an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) with laser intensities adjusted to bring the brightest spot just below saturation and the data extracted with the Axon GenePix Pro software. Source GEO sample is GSM98762 Last updated (according to GEO): May 31 2006 Chromosomes 861 7 cerebral cortex 21 86 70 Fetal liver cells 1000 Left Endometrium 1000 10 week control spinal cord rep 3 861 Prostate carcinoma Lymphoblastoid Cell Line for Individual 8147.3 log phase Spleen vs CpG-oligodeoxynucleotide Treated B cell 120min (set2) 119 96 in embryonic stem cells Lymph Node || lc4b007 to the nose 599 609 1000 Rectum HRPC120_hormone resistant prostate cancer late stage Blood Test (Blinded) Sample Source GEO sample is GSM129984 Last updated (according to GEO): Sep 18 2007 Replicate1_Voxel A5 none Source GEO sample is GSM244543 Last updated (according to GEO): Nov 23 2007 CHIPEXP_NAME: 230_2_050531tpj_9h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Vehicle_Control TREAT_TOX_MECHANISM1: Liver_Non_Toxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0 SAMPLING_TIME: 3 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197614 Last updated (according to GEO): Jun 01 2007 Normal human tissue:Normal Pituitary Gland Keywords = Human, Normal Tissue, Normal Pituitary Gland Source GEO sample is GSM44699 Last updated (according to GEO): May 27 2005 LDMTX_MP-2 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153467 Last updated (according to GEO): Jan 11 2007 human caudate nucleus Source GEO sample is GSM86815 Last updated (according to GEO): Feb 08 2006 Epithelium 861 1000 medulloblastoma AT1-hTERT_sham_6h_C5_23978 1000 Skeletal muscle structure Recurrent Adenocarcinoma 11 1000 Congestive heart failure Nicotine-neocortex, biological rep1 Spleen vs SDF1 alpha Treated B cell 240min (set2) Wild type 8 wk old male C57BL/6J mouse hypothalamus Source GEO sample is GSM74974 Last updated (according to GEO): Feb 27 2007 no additional Source GEO sample is GSM199177 Last updated (according to GEO): Jun 08 2007 Heart [JunctionChip 2 of 5] Heart 1000 Hippocampus VC mice 1 week off dox 1 VDXIGRU_247243 1000 Structure of parenchyma of lung osteoblast 627 637 12 0 ovarian tumor labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156706 Last updated (according to GEO): Jan 22 2007 PGA-swim_10min_s992 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15747 Last updated (according to GEO): May 28 2005 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160320 Last updated (according to GEO): Feb 08 2007 861 Prostate /Ovary 3 Disease 11 26 Saccule structure 1000 CS-B wt-rescued cell UVC-irradiated (2hour) replicate 2 U133B M_U133A_104_AnCg 1000 Hippocampus 1000 Primary Neoplasm Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68166 Last updated (according to GEO): Jul 07 2006 39 21 of substantia nigra Wild-type-hippocampus, biological rep7 (female) NA18516 Olfactory epithelium of SR-A mutant mice following bilateral olfactory bulbectomy Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 5 day time point Source GEO sample is GSM159795 Last updated (according to GEO): Apr 23 2007 1100 1087 heart failure PGA-Csx_het_4a-m4 Spinal Cord 1000 Osteoblasts 1000 Spleen vs BLC Treated B cell 240min (set1) Primary tumor 19 32 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Platelet activating factor for 240min Source GEO sample is GSM5728 Last updated (according to GEO): May 27 2005 Whole Brain 62 72 Ta gr2 tumour Source GEO sample is GSM2488 Last updated (according to GEO): May 27 2005 CT62-1 861 Cardiomyopathies Kidney 861 858 Mesodermal cell ISR8 dorsal root ganglia 342 360 Mesenchymal Stem Cells 1000 brain 0 5 Primary Neoplasm 1000 brainThalamus Source GEO sample is GSM18935 Last updated (according to GEO): Sep 25 2006 (cortex 19 25 Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Source GEO sample is GSM15946 Last updated (according to GEO): May 28 2005 The nose 94 101 1000 ovarian neoplasm PBMCs-Healthy-H48_Healthy Stria 861 1000 Brain Heart 1000 1000 Hippocampus Two key paradigms for examining activity-dependent development of primary visual cortex (V1) involve either reduction of activity in both eyes via dark-rearing (DR) or imbalance of activity between the two eyes via monocular deprivation (MD). Combining DNA microarray analysis with computational approaches, RT-PCR, immunohistochemistry and physiological imaging, we find that DR leads to (i) upregulation of genes subserving synaptic transmission and electrical activity, consistent with a coordinated response of cortical neurons to reduction of visual drive, and (ii) downregulation of parvalbumin, implicating parvalbumin-expressing neurons as underlying the delay in cortical maturation after DR. MD partially activates homeostatic mechanisms but differentially upregulates gene systems related to growth factors and neuronal degeneration, consistent with reorganization of connections after MD. A binding protein of Insulin-like Growth Factor 1 is highly upregulated after MD, and exogenous application of IGF1 prevents the physiological effects of MD on ocular dominance plasticity examined in vivo. Last Updated (by provider): May 05 2006 Contributers: Sam Horng Daniela Tropea Mriganka Sur Gabriel Kreiman Hongbo Yu Includes GDS1983. Update date: Jun 15 2006. Dataset description GDS1983: Analysis of primary visual cortex (V1) under conditions of binocular deprivation by dark-rearing (DR) or monocular deprivation (MD). Animals subjected to DR from birth till postnatal day (P) 27 or to MD from P11-12 to P27. Results provide insight into the role of visual activity in V1 development.. Includes GDS1986. Update date: Jun 15 2006. Dataset description GDS1986: Analysis of primary visual cortex (V1) under conditions of binocular deprivation by dark-rearing (DR) or monocular deprivation (MD). Animals subjected to DR from birth till postnatal day (P) 27 or to MD from P11-12 to P27. Results provide insight into the role of visual activity in V1 development.. Includes GDS1984. Update date: Jun 15 2006. Dataset description GDS1984: Analysis of primary visual cortex (V1) under conditions of binocular deprivation by dark-rearing (DR) or monocular deprivation (MD). Animals subjected to DR from birth till postnatal day (P) 27 or to MD from P11-12 to P27. Results provide insight into the role of visual activity in V1 development.. Spleen 1000 Bone Marrow 1000 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153434 Last updated (according to GEO): Jan 11 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114211 Last updated (according to GEO): Jun 16 2006 Subject code A12EB Gene expression data from mouse primary visual cortex Source GEO sample is GSM101690 Last updated (according to GEO): Mar 27 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145403 Last updated (according to GEO): Nov 20 2006 4 0 Liver DBA/2J Cerebellum A 1000 Retina skeletal.muscle.4 Lymphoblastoid Cell Line for Individual 8198.3 log phase 1000 frontal lobe Ganglia, Spinal 923 Parkinson's model voxel B2 plasma cells 50 61 from the forebrain 20 37 mouse hippocampus 0 17 with some respiratory epithelium. 1039 1072 lymph_nodes_4 Cerebral cortex 1000 embryonic hearts 1064 1079 Cerebellum Alzheimer's disease 9 Normal Source GEO sample is GSM176290 Last updated (according to GEO): Apr 09 2007 long access to cocaine, amygdala, 6 hrs/day access to cocaine Source GEO sample is GSM93834 Last updated (according to GEO): Jan 26 2006 Epithelial Cells 1000 injured cortex 69 82 1000 Spleen Stomach [JunctionChip 2 of 5] MP-2 1639 of muscle tissue 1654 SVGR2 cells are glial cells which are derived from SVG-A cells. They were created by subjecting SVG-A cells to multiple rounds of lytic infection by the human polyomavirus JCV. SVGR2 cells are the cells that survived this process and are resistant to JCV infection. This experiment was designed to identify gene expression differences that may be responsible for SVGR2 resistance to JCV. Last Updated (by provider): May 16 2007 Contributers: Kate Manley Walter J Atwood 5 0 Spleen 660 mesenchymal stem cell 639 Subthalamic Nucleus 5 Normal Malignant neoplasm of breast 861 861 HIV Infections cingulate cortex 901 Expression data with no treatment Source GEO sample is GSM230911 Last updated (according to GEO): Sep 20 2007 peripheral blood-CD56NKCells Source GEO sample is GSM18875 Last updated (according to GEO): Sep 25 2006 865 Disorder of artery 1000 Muscular Atrophy Lung carcinoma (A549) [JunctionChip 1 of 5] 5 0 brain HC62 FC BA4 A 1000 Seizures 9 0 Blood Test AD control Treatment, type=dissect Source GEO sample is GSM119687 Last updated (according to GEO): Jul 10 2006 Parkinson Disease 1000 1000 Myeloid Leukemia, Chronic 861 Heart Large cell carcinoma of lung 937 Retina 1000 nasal epithelial cells 28 49 R522P00584 Blood 1000 Hippocampus_WildType_rep3 T-ALL-C25 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A U87 parent chip 3 IGROV1_CL6010_OVARIAN Heart 1000 195 with coxsackievirus B3 174 brain, unknown: Sample42_e1_le1 Epithelium of bronchus 983 Epithelium of bronchus 983 H128 FC BA4 B 1000 Spleen 5 0 Spleen 15_0008_SepticShock_Day3_12 Understanding preimplantation development is important both for basic reproductive biology and for practical applications including regenerative medicine and livestock breeding. Global expression profiles revealed and characterized the distinctive patterns of maternal RNA degradation and zygotic gene activation, including two major transient waves of de novo transcription. The first wave corresponds to zygotic genome activation (ZGA); the second wave, named mid-preimplantation gene activation (MGA), precedes the dynamic morphological and functional changes from the morula to blastocyst stage. Further expression profiling of embryos treated with inhibitors of transcription, translation, and DNA replication revealed that the translation of maternal RNAs is required for the initiation of ZGA. We propose a cascade of gene activation from maternal RNA/protein sets to ZGA gene sets and thence to MGA gene sets. The large number of genes identified as involved in each phase is a first step toward analysis of the complex gene regulatory networks. Last Updated (by provider): Mar 22 2007 Contributers: Mark G Carter Alexei A Sharov Toshio Hamatani Minoru S Ko Includes GDS579. Update date: May 07 2004. Dataset description GDS579: Characterization of zygotic gene activation (ZGA) and influence of maternal transcripts. Embryos cultured until 2-cell stage with inhibitors of transcription (α-amanitine), DNA replication (aphidicolin) and protein synthesis (cycloheximide).. From naive male Sprague-Dawley rats (400Ã?±25 g), a 7 mm disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44513 Last updated (according to GEO): Oct 28 2005 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27669.gif Source GEO sample is GSM66578 Last updated (according to GEO): Sep 22 2006 Heart 1000 Skeletal bone 861 The epithelial cells 962 981 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11490.gif Source GEO sample is GSM76421 Last updated (according to GEO): Sep 22 2006 1000 Coronary Arteriosclerosis 104 of mouse embryonic stem cells 76 5 0 brain no additional Source GEO sample is GSM199364 Last updated (according to GEO): Jun 08 2007 The epithelial cells 962 981 Ovary 1000 folatesufficientAs10ppm1 6 0 trachea Epithelium of bronchus 983 861 Muscle plasma cells 50 61 Peritoneum 861 32h-AC replication 1 f2#353 versus pool Mouse Brain tissue human peripheral blood derived monocytes, LPS stimulation time-series Pituitary Gland 8 Normal the ventricular 1095 1109 I_U133A_17_DLPFC 1916 1901 atherosclerosis CAD_replicate86 A HID U D018 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108607 Last updated (according to GEO): Aug 22 2006 861 Spinal Cord Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68208 Last updated (according to GEO): Jul 07 2006 Low Freezing Source GEO sample is GSM92411 Last updated (according to GEO): Jan 13 2006 858 Mesodermal cell 3AJZ02081484a_TemporalLobe embryonic hearts 1064 1079 with Parkinson's disease 27 50 42 30 Control blood liver_PPARa-knockout_control_6h_rep2 Squamous epithelial cell 861 Medulla Oblongata 861 861 Heart from colonic normal mucosa 21 47 7 frontal cortex 20 HDMTX-1 A2780_oxa_IC90_16h_3 326 319 jejunum 865 Disorder of artery mouse cerebral cortex from COX-1 WT Source GEO sample is GSM121423 Last updated (according to GEO): Jan 31 2007 314 292 of muscular dystrophy. PMN_control_0min_Patient1 Whole Genome array hippocampus_cocaine 24 skeletal muscle 10 no additional Source GEO sample is GSM199403 Last updated (according to GEO): Jun 08 2007 1BMH02082910_PB_CD56NKCells M-20-80-UN on UMich-10k Skin 1 Disease Parkinson's disease sample x024 0 30 D_U133A_10_HC 90 81 in stroke none Source GEO sample is GSM210348 Last updated (according to GEO): Jul 16 2007 442 415 in human Parkinsons disease adrenal_gland_cortex_2 7 cerebral cortex 21 Gene expression data from postmorten brain regions Source GEO sample is GSM145040 Last updated (according to GEO): Nov 20 2006 Femur 1000 Whole Brain 62 72 Gene expression data from postmorten brain regions Source GEO sample is GSM145239 Last updated (according to GEO): Nov 20 2006 CNS-SMTC_Mod3mo-1A-s2 Neoplasm 861 M_U133Plus_38_DLPFC C57BL/6J Saline treated, striatum, biological replicate 3 Source GEO sample is GSM187976 Last updated (according to GEO): Jun 14 2007 6 week mutant spinal cord rep 1 Blood Test (Blinded) Sample Source GEO sample is GSM129976 Last updated (according to GEO): Sep 18 2007 861 Blood Exp A_4, 10mg/kg CPF RNA extracted from brain Source GEO sample is GSM103420 Last updated (according to GEO): Sep 21 2006 HMVEC-L stimulated without LPS for 8 hours c08R1 901 Heart failure Prostate 1000 GM18861 12 0 basal ganglia 861 Heart Diseases Primary tumor 19 32 skeletal muscle sample 3 44 67 Nasal Epithelium 901 FVB/NJ hypothalamus rep2 (430 2.0 Array) Wild type inbred mice Source GEO sample is GSM82906 Last updated (according to GEO): Nov 10 2005 PBMC PMA+Ionomycin 1 Activated Gene expression of organ of Corti of newborn rats_cultivation_normoxia_repeat 2 inner ear 1000 Brain V5-P163 Hypothalamus 5 Normal 7 0 prostate 861 Cerebral cortex Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68268 Last updated (according to GEO): Jul 07 2006 Plasma 861 5 0 brain 1000 Corpus Callosum Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed for 6 h to hydrostatic pressure (HP24), pressure experiment # 2 (PE2). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11405 Last updated (according to GEO): Dec 15 2006 384 for occupational diseases 409 02_0001_SepticShock_Day3_107 Gene expression data from UET-13TR-EWS/ERG cells incubated in the presence of tetracycline for 72 hours Source GEO sample is GSM214930 Last updated (according to GEO): Aug 02 2007 1000 Malignant Neoplasms No_DHT_control_2 861 Brain tibiae 115 120 Blood 1000 Neoplasm 861 NH 16364A 736 730 retina Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118345 Last updated (according to GEO): Jul 11 2006 Tumor__Lymphoma_Large_B-Cell_L_B_CELL_S97_27534_G on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Differential expression: associative and nonassociative learning Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160717 Last updated (according to GEO): Sep 24 2007 hrs nasal epithelium 1127 1147 Semeralul_PFC_Development_Week5_Batch1_Animal_8 Mental Retardation 1000 GSE8218 9 CN A Plasma 861 5 0 brain Spleen 0 5 Bone Marrow 1000 139T with Alzheimer's disease 27 50 78 66 Control blood 228 219 Hippocampi Mesenchymal Stem Cells 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145375 Last updated (according to GEO): Nov 20 2006 CNS-SC_Inj14d-4C-s2 15_0001_Control_Day1_21 861 Neurofibromatoses Lymphoblastoid Cell Line for Individual 8189.3 log phase Fibroblasts 1000 145 134 hippocampus 1000 Mammary gland 15 0 human cerebellum like breast cancers 6 25 1000 Liver from liver 21 30 Heart 861 human caudate nucleus Source GEO sample is GSM86809 Last updated (according to GEO): Feb 08 2006 Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2659.gif Source GEO sample is GSM72208 Last updated (according to GEO): Sep 22 2006 Blood 7 11 Blood Vessels 861 Sample11, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53262 Last updated (according to GEO): Jul 06 2005 Macrophage 14smi085 Gene expression data from postmorten brain regions Source GEO sample is GSM144965 Last updated (according to GEO): Nov 20 2006 861 Spinal Cord M4 juvenile biol repl 2 GSE2869 human frontal cortex Source GEO sample is GSM87040 Last updated (according to GEO): Feb 08 2006 Marfan Syndrome 861 infection twice 324 338 863 Nerve of somatomotor cortex 21 41 Heart; Ventricle Keywords = mouse gene expression database Source GEO sample is GSM29348 Last updated (according to GEO): May 27 2005 468 459 the rectum NG026_a Whole Brain 62 72 with some respiratory epithelium. 1039 1072 1000 Cell Transformation, Neoplastic Macrophages treated with LPS plus IL-10, 20 min, Replicate 1 Source GEO sample is GSM241137 Last updated (according to GEO): Nov 02 2007 861 Lung Analysis of prefrontal cortex from 3 biological replicates of C57BL/6J mice at four Zeitgeber Times (ZT 3, 9, 15, and 21). Source GEO sample is GSM240415 Last updated (according to GEO): Oct 30 2007 B220+c-kit+ Pre BI cells sorted out of mouse bone marrow, sort no. 1 Source GEO sample is GSM610 Last updated (according to GEO): May 27 2005 43 0 Chorionic mesoderm-derived mesenchymal cells Prefrontal Cortex 0 16 brain, cortex: Sample20_e1_le1 861 Malignant Neoplasms Gene expression data from postmorten brain regions Source GEO sample is GSM145922 Last updated (according to GEO): Nov 20 2006 1000 Immune system Brain 861 of testicular seminoma 26 47 82 CB B 901 Mammary Neoplasms Prosencephalon 861 Expression profiling of spinal cord section (T9) extracted from rats 4h following severe injury Lot batch = Source GEO sample is GSM7585 Last updated (according to GEO): May 28 2005 861 Ganglia G42-CingulateCortex replicate1 V5-P397 Normal Source GEO sample is GSM176436 Last updated (according to GEO): Apr 09 2007 AR-bic-10miM 861 Nerve Neoplasm 861 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68246 Last updated (according to GEO): Jul 07 2006 of the colon 28 39 861 Cerebral cortex 0 Human Cortex 11 GSE2870 Primary adenocarcinoma Source GEO sample is GSM16562 Last updated (according to GEO): May 28 2005 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211411 Last updated (according to GEO): Jul 18 2007 Peripheral Nerves 851 DRG070_a Brain 1000 861 Neoplasm 135 116 by CO2 asphyxiation A HID B D021 861 Cerebral cortex /3T3 fibroblasts 743 759 0 Human Cortex 11 29 0 Salivary Gland [JunctionChip 2 Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. Moderate controlled cortical impact with pneumatic impactor, 6 m/s impact velocity and 1.5 mm deformation. 24h after surgery, a 4 mm diameter disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane then stored at â??80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44464 Last updated (according to GEO): Oct 28 2005 Heart 861 Integumentary system 1000 Non-defeated Control Group, Nucleus accumbens, Biological Replicate 3 20 0 Nicotine-hippocampus Cancers; Prox.Jejunum tumor Keywords = mouse gene expression database Source GEO sample is GSM29280 Last updated (according to GEO): May 27 2005 dorsal striatum sprague 3981 liver, PPARa-null mice, treatment with WY14643 for 6h Source GEO sample is GSM205781 Last updated (according to GEO): Jul 24 2007 To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132985 Last updated (according to GEO): Sep 12 2006 Skeletal bone 861 Mental Retardation 1000 Structure of olfactory bulb 861 ileum 861 HapMap YRI_parent Male Source GEO sample is GSM159693 Last updated (according to GEO): Feb 01 2007 Brain 1000 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs//9151.gif Source GEO sample is GSM93128 Last updated (according to GEO): Sep 22 2006 27 7 Medial Temporal Gyrus 913 Coronary heart disease 1000 frontal lobe Nose 1000 1000 Rectum 861 Brain Hyperdip>50-C28 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1083 1071 with diabetes Saccule at E15, replicate2 CNS-SCsev_InjB4h-4C-s2 VDXIGRU_246047 plasma cells 50 61 with some respiratory epithelium. 1039 1072 30 19 (Extra Renal of the small intestine 97 118 PC3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Ovarian Diseases 877 Primary Carcinoma 875 20 0 human caudate nucleus ventral_tegmental_area_3 128 113 such as dementia Gene expression data from UET-13TR-EWS/ERG cells incubated in the absence of tetracycline for 0 hours Source GEO sample is GSM214924 Last updated (according to GEO): Aug 02 2007 861 Substantia nigra structure GM19210 Ganglia, Spinal 923 15 7 hindbrain EWS-C-TEST-2 on NHGRI-6.5k_b VDXKIU_101B88 human frontal cortex Source GEO sample is GSM86992 Last updated (according to GEO): Feb 08 2006 BPH-18 on NHGRI-6.5k_c Epithelium 865 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11470 Last updated (according to GEO): May 28 2005 Subcutaneous Fat 1000 HA01-149B Prostate [JunctionChip 2 of 5] none Source GEO sample is GSM161905 Last updated (according to GEO): Feb 16 2007 10 7 left Expression profiling of spinal cord section (T9) extracted from rats 30m following mild injury Source GEO sample is GSM31230 Last updated (according to GEO): May 27 2005 HT29_II_CL4001_Colon on Affymetrix GeneChip Human Full Length Array HuGeneFL SR hgu95e 9 0 Blood Test seminoma specimen, pT1, patient age: 33y; W03 015 Brain 1000 jzo029-rp1-v5_u74av2-met pituitary sprague2 CC10B sample 1 5 0 brain at the Human Brain 744 761 substantia_nigra_8 861 Oocytes Congenital Abnormality 853 Fibroblasts 38 48 330 324 uterus 1000 Prostate carcinoma Day 3_L_-LIF_Achip Bone structure of tibia 1000 Gene Profile of RU486 effect on LPS induced gene expression in CNS. Ventral tegmental area 0 22 SN:1022905;Fetal Cartilage, biological rep1 BC117A-BE N/A Source GEO sample is GSM6681 Last updated (according to GEO): May 28 2005 MCF7_CHX_EtOH_24h_rep2 We analyzed the lumbar spinal cord tract of transplanted nmd mice (n=3), untransplanted nmd mice (n=3) and wild-type mice (n=3) (all mice are of male gender). The latter groups underwent surgical procedure with vehicle. The surgical procedure and spinal cord-derived neural stem cell transplantation (intratechal injection) were done at P1 and the animals were sacrificed at 6 weeks of age. Source GEO sample is GSM67532 Last updated (according to GEO): Dec 21 2005 1000 Spleen toe nail fibroblast, asynchronous Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27671.gif Source GEO sample is GSM66593 Last updated (according to GEO): Sep 22 2006 861 Blood VDXKIU_199B55 no additional Source GEO sample is GSM199151 Last updated (according to GEO): Jun 08 2007 901 Endothelial Cells of the actin cytoskeleton 850 875 1000 Hypothalamic structure Neoplasm 861 PLACENTA Source GEO sample is GSM18967 Last updated (according to GEO): Sep 25 2006 NSCLC_HOP62 on Affymetrix GeneChip Human Full Length Array HuGeneFL brain 0 5 1000 Muscular Dystrophy, Duchenne 861 Blood Replicate1_Voxel D4 Nasal Epithelium 901 mRNA was isolated after 8 hours of incubation from IMR-90 cells seeded onto a collagen/chondroitin sulfate tissue engineering scaffold mesh material. Cells were seeded at a density of 1 x 10^6 cells/ mesh, and this chip represents a pooling of cells from 4 meshes. Source GEO sample is GSM6064 Last updated (according to GEO): May 27 2005 S1P2-KO-neocortex, biological rep4 (male) 861 Muscle Primary large cell neuroendocrine carcinoma 5883 0 47 Cerebral cortex 1000 prostate Source GEO sample is GSM203390 Last updated (according to GEO): Jun 21 2007 142 126 Folate deficiency Liver 1000 VDXKIU_125B43 Gene expression data from biopsy of infected skin of subject with pustule former phenotype. Source GEO sample is GSM128963 Last updated (according to GEO): Sep 13 2007 on the ventricles 598 614 Circadian regulation in rat skeletal muscle 861 Blood PGA_MI_ilv_24h_360 n/a Source GEO sample is GSM177982 Last updated (according to GEO): Jun 11 2007 15 0 human cerebellum 338 333 brain prostate Source GEO sample is GSM203287 Last updated (according to GEO): Jun 21 2007 Collagen 1000 Gene expression data from the neocortex of S1P2-knockout mouse Source GEO sample is GSM172943 Last updated (according to GEO): Mar 08 2007 1000 Histones Phenytoin brainstem 3 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53414 Last updated (according to GEO): Jul 06 2005 seminoma specimen, pT2, patient age: 27y; W03 021 D_U133Plus_125_HC Gene expression data Source GEO sample is GSM183168 Last updated (according to GEO): Jul 30 2007 B6 day 1, biological rep 3, tech rep 1 1000 Skeletal muscle structure HapMap YRI_parent Male Source GEO sample is GSM159668 Last updated (according to GEO): Feb 01 2007 12 frontal Lobe 23 retina Source GEO sample is GSM18615 Last updated (according to GEO): May 27 2005 D_U133Plus_115_nAcc Monocular deprivation left cortex, biological rep3 CHB MD-6 Structure of vastus lateralis muscle 1000 Macrophages treated with LPS, 20 min, Replicate 2 Source GEO sample is GSM241135 Last updated (according to GEO): Nov 02 2007 5 0 brain 1000 Brain CNS-SCsev_InjB24h-3A-s2 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, air control, 6 h time point Source GEO sample is GSM159797 Last updated (according to GEO): Apr 23 2007 This is a wildtype littermate at postnatal day 5 pool of 5 animals Lot batch = Source GEO sample is GSM4063 Last updated (according to GEO): May 28 2005 ovarian tumor: mucinous Source GEO sample is GSM139427 Last updated (according to GEO): Apr 09 2007 278 255 ischemic cardiomyopathy Caudal 1000 Simple annotation: aging, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17545.gif Source GEO sample is GSM81564 Last updated (according to GEO): Sep 22 2006 861 Hippocampus mouse cerebral cortex, cox-1 knockout, rep3 1000 Hippocampus cells stimulated with lipoprotein prep 1, biological rep3 Disease Source GEO sample is GSM175920 Last updated (according to GEO): Apr 09 2007 Multiple System Atrophy 1000 UD rep 3 Primary Neoplasm 1000 3616 PC 24Hr (pool) vs. 150mg/kg APAP 24Hr rat 3618 blood ALL-B-cell-4 on Affymetrix GeneChip Human Full Length Array HuGeneFL NH 78h 19 0 human frontal cortex Gene expression data from postmorten brain regions Source GEO sample is GSM145461 Last updated (according to GEO): Nov 20 2006 11 Bone marrow 0 16 7 cerebellum Nrl ko P2 replicate 4 of mouse brain 9 23 Epithelial Cells 1000 cerebral cortex 7 21 CO_sham_med_3 vehicle treatment, 3 hour time point, biological replicate 1 1000 Female infertility of anovulatory origin NOS 1000 jejunum Lymphoblastoid Cell Line for Individual 8038.3 log phase Adrenal Medulla 1000 5 0 brain 1000 Neoplasm Blood 861 PGA-E18.5_3A Ovum 861 Brain 861 225635HG_4 Subject code A22 Interatrial septum 865 Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174531 Last updated (according to GEO): Mar 14 2007 Brain_MD_29_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL 63 47 from 12 cochleas 5 0 brain VDXIGRU_219139 ovarian tumor: endometrioid Source GEO sample is GSM139420 Last updated (according to GEO): Apr 09 2007 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181088 Last updated (according to GEO): Jul 12 2007 Expression profiling of spinal cord section (T9) extracted from rats 24h following moderate injury Source GEO sample is GSM31665 Last updated (according to GEO): May 27 2005 Macrophage smi68 plasma cells 332 344 NOS exp1 NitroArg Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12407.gif Source GEO sample is GSM79831 Last updated (according to GEO): Sep 22 2006 Liver_6wk_FVB_Female 10 7 Left 1000 frontal lobe AD-370t1x-A112-3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160220 Last updated (according to GEO): Feb 08 2007 Ganglia, Spinal 923 Bone structure of tibia 1000 human caudate nucleus Source GEO sample is GSM86795 Last updated (according to GEO): Feb 08 2006 Endometrium/Ovary-Disease 7 of regenerating Dorsal Root Ganglia 21 55 NCI-H226_CL1013__NSCLC ANIMALS Patched heterozygous mice (Goodrich et al., 1997) were obtained from Matthew Scott?s lab at Stanford, and maintained by breeding with 129X1/SvJ mice from Jackson Laboratories. Math1-GFP transgenic mice (Lumpkin et al., 2003) were provided by Jane Johnson at UT Southwestern Medical Center. Math1-GFP/patched+/- mice were generated by crossing patched heterozygotes with Math1-GFP mice, and then backcrossing to Math1-GFP mice three times before further analysis. All mice were maintained in the Cancer Center Isolation Facility at Duke University Medical Center. ISOLATION OF CELLS Granule cell precursors (GCPs) were isolated from 7-day-old (P7) patched+/- mice; preneoplastic cells were obtained from 6 week-old patched mutants; and tumor cells were obtained from 10-25-week old patched mutants displaying physical and behavioral signs of medulloblastoma. Cells were isolated from each source using a protocol described in (Wechsler- Reya and Scott, 1999). Briefly, cerebella were digested in solution containing 10 U/ml papain Oliver et al. Pre-Neoplastic Stage of Medulloblastoma - 8 - (Worthington, Lakewood, NJ) and 250 U/ml DNase (Sigma) and triturated to obtain a cell suspension. This suspension was centrifuged through a step gradient of 35% and 65% Percoll (Amersham Biosciences, Piscataway, NJ), and cells were harvested from the 35%-65% interface. Cells were resuspended in serum-free culture medium consisting of Neurobasal containing B27 supplement, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen, Carlsbad, California) and counted on a hemacytometer. Cells used for RNA isolation were centrifuged and flash frozen in liquid nitrogen. For proliferation assays or immunostaining, cells were plated on poly-D-lysine (PDL)-coated tissue culture vessels and incubated in serum-free culture medium. MICROARRAY HYBRIDIZATION AND ANALYSIS RNA from GCPs, pre-neoplastic cells and tumor cells (isolated as described above, but not FACS-sorted) and from normal adult cerebellum (not dissociated) was converted to cDNA using the Superscript Choice cDNA kit (Invitrogen) and a T7-dT(24) primer (Genset/Proligo, Boulder, CO). cRNA was generated using a T7-transcription/labeling kit from Enzo Life Sciences and hybridized to Affymetrix U74Av2 chips (Affymetrix, Santa Clara, CA). Chips were scanned, and hybridization data were acquired using Affymetrix Suite 5.0 software. Affymetrix CEL files were normalized and quantified using Bioconductor software with the gcRMA model to quantify gene expression levels (Gentleman and Carey, 2002). Unsupervised principal components analysis (PCA) was used to identify the relationships among normal adult cerebellum, GCPs, pre-neoplastic cells and tumor cells based on expression profiles. To identify genes that were differentially expressed among GCPs, pre-neoplastic cells and tumor cells, supervised analysis was carried out. A gene-by-gene ANOVA model with three groups (GCP, pre-neoplastic, tumor) was used to fit the log2-transformed intensities. To correct for multiple comparisons, the nominal p-value was adjusted using the false discovery rate (Benjamini and Hochberg, 1995). Genes were considered to be differentially expressed if they satisfied all of the following criteria: a difference in expression greater than 1.9-fold between any two groups, a maximum absolute intensity difference larger than 32 units, and an adjusted pvalue < 0.01. There were 118 genes that met these criteria. The identities of differentially expressed genes were verified by integrating data from the Affymetrix and Unigene databases. Gene functions were determined using information from Gene Ontology, Unigene, LocusLink and PubMed databases. Clustering was performed with Cluster and Treeview (Eisen et al., 1998). All statistical analysis was performed using R-1.7 software (Dalgaard, 2002). Results were visualized with Spotfire 6.0 (Somerville, MA). Keywords = medulloblastoma Keywords = pre-neoplastic Source GEO sample is GSM45619 Last updated (according to GEO): Oct 28 2005 1000 Spleen brain 0 5 spinal cord 0 11 Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002. Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Part of the medium chain triacylglycerol oil in control diet was replaced with: 1.9% fish oil (providing 0.5 dietary wt% DHA and 1.0en%). Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily. Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France). Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h. After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hippocampal gene expression analysis. From these same 5 mice, the hippocampus was dissected from the mice according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancourt, France), rinsed as described for livers, cut into 17-50 mg subsections, and frozen as described for livers. Hippocampal lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5). Hippocampal tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hippocampal RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips. Source GEO sample is GSM2562 Last updated (according to GEO): Mar 17 2006 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/5074.gif Source GEO sample is GSM93140 Last updated (according to GEO): Sep 22 2006 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188710 Last updated (according to GEO): Jun 06 2007 Fbx15 is specifically espressed in ES cells, but Fbx15-null ES cells do not show obvious phenotypes. Source GEO sample is GSM119300 Last updated (according to GEO): May 18 2007 Endometrium 23 Normal Primary tumor 19 32 gene expression of 3 day LIF differentiated ESCs Source GEO sample is GSM181953 Last updated (according to GEO): Apr 12 2007 861 Epithelial Cells 861 Cerebral cortex The epithelial cells 962 981 44 minus the frontal cortex 68 Brain_MD_49_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL Neoplasm 861 HC69 FC BA4 B Disease Source GEO sample is GSM176092 Last updated (according to GEO): Apr 09 2007 1000 Endometriosis, site unspecified brain, unknown: 03BY_e1_le1 896 Primary Neoplasm Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225360 Last updated (according to GEO): Aug 31 2007 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151975 Last updated (according to GEO): Feb 06 2007 Normal Source GEO sample is GSM176061 Last updated (according to GEO): Apr 09 2007 Vestibular organ 0 15 Gene expression data from postmorten brain regions Source GEO sample is GSM145912 Last updated (according to GEO): Nov 20 2006 Adipose tissue 901 testis 52 58 M-16-15-LN-ME on UMich-10k G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Source GEO sample is GSM9639 Last updated (according to GEO): May 28 2005 Nasal Epithelium Inhalation Formaldehyde 0ppm 8d ID65 33 17 tibialis anterior 61 49 mammary gland GM19171 of the postmortem brains 675 699 1000 Endometriosis, site unspecified 10 7 Left Rat Retina- chip number 251186834924; 5 weeks vs 20 weeks Liver 1000 P18, P24, P46, P104, and P46DR (dark reared) non-deprived vs. deprived visual cortex Gene expression data from SVGR2 glial cells. Source GEO sample is GSM189719 Last updated (according to GEO): May 16 2007 1000 Brain Hippocampus 1987 15 month Old adrenal gland Source GEO sample is GSM18948 Last updated (according to GEO): Sep 25 2006 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19234 Last updated (according to GEO): May 27 2005 91 from the bone marrow 72 pituitary_gland_10 Source GEO sample is GSM80804 Last updated (according to GEO): Mar 31 2006 15 7 brainstem osteoblast 627 637 kidney 37 43 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 72h after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44549 Last updated (according to GEO): May 27 2005 human cerebellum Source GEO sample is GSM87156 Last updated (according to GEO): Feb 08 2006 Osteoblasts 1000 Knockout 8 months old, male Source GEO sample is GSM154343 Last updated (according to GEO): Jan 09 2007 Disorder of artery 865 4525 4520 liver /SvEvTac mouse periaqueductal gray 29 62 861 Lens, Crystalline Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184741 Last updated (according to GEO): Apr 26 2007 CNS-SC_InjA30m-3A-s2 581 568 of the kidney 1000 Myositis Gene expression data from postmorten brain regions Source GEO sample is GSM145993 Last updated (according to GEO): Nov 20 2006 1000 Asthma Brain 861 M_U133A_77_nAcc Spinal Cord 901 861 Cancer of Neck total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Sphingosine-1-phosphate for 240min Source GEO sample is GSM5752 Last updated (according to GEO): May 27 2005 Heart 861 Brn3a Heterozygote DRG e13.5 430A v2.0 Wild-type-hippocampus, biological rep8 (female) Aorta 861 Brain 861 A comparison of prion infected and non-infected samples from neuroblastoma cells (N2a), and a comparison of prion infected and non-infected samples from hypothalmus cells (GT1). 11 dual-color DNA-chip hybridizations of cDNAs were made. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Aug 24 2005 Contributers: Marion Horsch Alex Greenwood Mesenchymal stem cells 13 34 Gene expression data from postmorten brain regions Source GEO sample is GSM145064 Last updated (according to GEO): Nov 20 2006 rat cortex Treatment, type=time_course, measurement=7.0 d Source GEO sample is GSM53219 Last updated (according to GEO): Jul 06 2005 42 minus the frontal cortex 66 kidney 37 43 BrE18_5wt022EAFBN.txt 9 0 Blood Test Saccule structure 1000 brain, SNc and VTA: VTA3_e1_le1 brain, cerebellum: 6 hrs A GW_e3_le1 n/a Source GEO sample is GSM177906 Last updated (according to GEO): Jun 11 2007 Cerebral cortex 1000 Osteoblasts 1000 Heart 1000 Gene expression data from the hippocampus of wild-type mouse Source GEO sample is GSM172958 Last updated (according to GEO): Mar 08 2007 49 30 (predominantly valve PGA-RnSalt_h_6w_3-m5 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211426 Last updated (according to GEO): Jul 18 2007 Pool of 10 cochlear tissues at E14 Source GEO sample is GSM182584 Last updated (according to GEO): Aug 14 2007 GSE7929 Wild type voxel J4 SN:1010401 Source GEO sample is GSM115384 Last updated (according to GEO): Jun 20 2006 SN:1010391 Source GEO sample is GSM115375 Last updated (according to GEO): Jun 20 2006 40 21 from skeletal muscle 1000 Thalamic structure 3488 3466 medial temporal gyrus 4 Cerebral cortex 861 HUVEC isolate 9 low serum media VEGF-A 24hours cf. #13 Source GEO sample is GSM12907 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145525 Last updated (according to GEO): Nov 20 2006 913 Acute leukemia Brain, Right Motor Cortex KT10_AR1 Subject code A17EB 1000 Brain 7 0 Amygdala 861 Immunoglobulins Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198646 Last updated (according to GEO): Jun 06 2007 PGA_PA-D_206 Cerebral cortex 861 C57BL/6 benchmark dataset: Embryonic day 13.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25163 Last updated (according to GEO): May 27 2005 PMN_LB_180min_Patient16 to the nose 599 609 Pyramidal Cells 1000 HC103 FC BA4 A IM-1_POST Motor Neuron Disease 1000 Leg 7 Day Control rep 2 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195333 Last updated (according to GEO): Jun 04 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11544 Last updated (according to GEO): May 28 2005 57 39 with endometriosis to the nose 599 609 Abnormal development 0 19 Inflammatory myopathy specimen GEIM3 1000 Aorta Gene expression data from human colon tumor tissue Source GEO sample is GSM173338 Last updated (according to GEO): Apr 20 2007 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141279 Last updated (according to GEO): Oct 26 2006 NA Source GEO sample is GSM84330 Last updated (according to GEO): Dec 01 2005 NA12745 growth 1 bronchial epithelia 224 243 Brain 1000 spinal_cord_10 1000 Brain Gingival Epithelial Cell Transcriptional Responses to Commensal and Opportunistic Oral Microbial Species. CNS-SC_InjB24h-1bA-s2 liver damage 134 145 Date 2/26/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : headfold Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 2.5 mg/kg Time : 3.0 hrs post-injection Intervention : 4.0 mg/kg PK11195 co-administered Risk: remediated Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 16-20 headfolds pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = PK11195 Keywords = embryo Keywords = microphthalmia Lot batch = AM039 Source GEO sample is GSM12203 Last updated (according to GEO): May 28 2005 150 mg/kg X 6 hr Source GEO sample is GSM129871 Last updated (according to GEO): Sep 18 2007 WGACON-100 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.94 Subject: 1905 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM38998 Last updated (according to GEO): May 27 2005 -_6257_batch1 on NHGRI-6.7k Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153359 Last updated (according to GEO): Dec 27 2006 Large-scale analysis of the human transcriptome. Dorsal root ganglia Source: Analytical Biological Services; http://www.absbioreagents.com Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 158.42 Stdv: 4.91 Min: 148.08 Max: 169.81 Source GEO sample is GSM2889 Last updated (according to GEO): Mar 20 2006 1000 Spinal Cord Substantia Nigra MME Sample4 RMA, MAS 5, dChip Skeletal bone 861 913 Coronary heart disease 304 280 alcoholic cardiomyopathy Cell source of DN2_1, DN3_1, and DN4_1 are identical. Cell source of DN2_2, DN3_2, and DN4_2 are identical. Cell source of DN2_3, DN3_3, and DN4_3 are identical. Cell source of DN2_4, DN3_4, and DN4_4 are identical. Each cell sorce was derived from four mice. Source GEO sample is GSM188618 Last updated (according to GEO): May 16 2007 f2#34 versus pool Mouse Brain tissue D_U133A_50_nAcc 1000 jejunum Biopsy of the normal mucosa of the colon from patient #31 5 0 brain Hoxb1 is required for proper specification of rhombomere 4 and the facial motor neurons. This study analyzed gene expression in the corresponding hindbrain segment of E10.5 mutant embryos. Several genetic pathways were found altered, including transcription factors such as Phox2b, Gata3, Nkx2-2 and Nkx6-1. Last Updated (by provider): Aug 28 2006 Contributers: Robert B Weiss Petr Tvrdik Benjamin R Arenkiel Mario R Capecchi Gary O Gaufo 43 0 Chorionic mesoderm-derived mesenchymal cells 2500 mg/kg X 12 hr Source GEO sample is GSM129882 Last updated (according to GEO): Sep 18 2007 Sample represents the Neurointermediate lobe of the Pituitary from 5 control animals Source GEO sample is GSM69791 Last updated (according to GEO): Dec 15 2005 861 Acquired Immunodeficiency Syndrome na Source GEO sample is GSM181297 Last updated (according to GEO): Apr 10 2007 total RNA from biosource CC#2 Source GEO sample is GSM92462 Last updated (according to GEO): Jan 13 2006 Blood 1000 human caudate nucleus Source GEO sample is GSM86852 Last updated (according to GEO): Feb 08 2006 C57BLKS/J_male_hypothalamus Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92330 Last updated (according to GEO): Jan 13 2006 brain, Left frontal Lobe: Extract30_le1 663 mesenchymal stem cell 642 in obese 185 192 cardiac 763 769 1000 Brain hypothalamus sa hyp Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184734 Last updated (according to GEO): Apr 26 2007 R485P00308 1000 Brain nico 18h 9/06/02 (Experiment Neuroprotection3- Run 13276) Treatment, type=timepoint, description=primary cortical neurons were treated for 18 h with nicotine 10uM then were harvested, measurement=18.0 h Source GEO sample is GSM96724 Last updated (according to GEO): Feb 14 2006 SCG_reference_pool Gene expression data from postmorten brain regions Source GEO sample is GSM145573 Last updated (according to GEO): Nov 20 2006 Heart 861 Primary Carcinoma 876 Mouse Liver LRD Diet 5wk Control, biological replicate B AD control Treatment, type=dissect Source GEO sample is GSM119616 Last updated (according to GEO): Jul 10 2006 1000 Hippocampus brain, cochlea: [12] Sample #12_le1 Pressure-overload induced hypertrophy model. Mouse was sacrificed 1 week after aortic banding. Keywords = Cardiac Hypertrophy Source GEO sample is GSM2244 Last updated (according to GEO): May 27 2005 Corticospinal Motor Neurons P3 2 SN:1006712 Source GEO sample is GSM115349 Last updated (according to GEO): Jun 20 2006 control 2 weeks B Treatment, type=time_course, measurement=2.0 weeks Source GEO sample is GSM107857 Last updated (according to GEO): Jun 06 2006 Myocardium 861 Large cell carcinoma of lung 901 GM19127 cerebellum wistar 3884 whole tissue, individual animal, 10 weeks old, male Wistar cerebellum file:p3884w Source GEO sample is GSM15127 Last updated (according to GEO): Oct 28 2005 in the postnatal forebrain 150 175 between the LAD artery 266 287 Normal Source GEO sample is GSM176262 Last updated (according to GEO): Apr 09 2007 25 7 Right Parietal Lobe Category: Cell-line Subcategory: HMEC Scanning Software: unknown Software version: unknown Lot batch = 0134-5k Source GEO sample is GSM1930 Last updated (according to GEO): Nov 21 2005 amygdala 336 343 Gene expression data from postmorten brain regions Source GEO sample is GSM145302 Last updated (according to GEO): Nov 20 2006 Gene expression data from a neocortex from mouse injected 10 mg/kg nicotine Source GEO sample is GSM147410 Last updated (according to GEO): Jan 03 2007 Coronary Arteriosclerosis 1000 Myocardium 861 928 Endometrium 5 0 blood 1206 1184 by cervical dislocation Tissue Source GEO sample is GSM67210 Last updated (according to GEO): Jan 19 2006 The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76947 Last updated (according to GEO): Oct 11 2005 Sprague-Dawley Male LowSalt Cortex rat708 sd_cortexr_k_708c_020802 liver_wildtype_WY14643_6h_rep4 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11255 Last updated (according to GEO): May 28 2005 P18 non-deprived visual cortex replicate 3 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3495.gif Source GEO sample is GSM93147 Last updated (according to GEO): Sep 22 2006 4 0 Brain Brain 1000 Voxel C2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1392 Last updated (according to GEO): Nov 21 2005 brain, cerebellum: RNA#8S_le1 Parkinson's disease sample x205 SMCL-SMCL4t1-A354-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Iris with some respiratory epithelium. 1039 1072 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 20 hours after lights on. Original sample code = CM51A Source GEO sample is GSM227343 Last updated (according to GEO): Sep 10 2007 861 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145345 Last updated (according to GEO): Nov 20 2006 353 331 of the pituitary gland foreskin fibroblast #1, serum starved' brain, amygdala: Stress-Amygdala_e1_le2 Richard Almon-42-1138200270711 ovarian tumor: mucinous Source GEO sample is GSM139429 Last updated (according to GEO): Apr 09 2007 Gene expression data from brain of adult rats Source GEO sample is GSM101046 Last updated (according to GEO): Feb 20 2007 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM119699 Last updated (according to GEO): Jul 11 2006 tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44877 Last updated (according to GEO): Nov 18 2005 Pineal gland 861 1000 frontal lobe GM19222 Expression profiling of spinal cord section (T9) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM6665 Last updated (according to GEO): May 28 2005 ER+/LN+/Nevins41 on Affymetrix GeneChip Human Full Length Array HuGeneFL This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195258 Last updated (according to GEO): Sep 13 2007 Disorder of artery 865 861 Cerebellum 166 156 of retinal Richard Almon-16-1138200269883 f2#335 versus pool Mouse Brain tissue AD control Treatment, type=dissect Source GEO sample is GSM119659 Last updated (according to GEO): Jul 10 2006 Murine Rat Brain Injury - Mus musculus 861 Oocytes PMN_control_0min_Patient9 1000 Colon 861 Neoplasm HNC2725 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 9 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM11040 Last updated (according to GEO): May 28 2005 We carried out a global survey of age-related changes in mRNA levels in the C57BL/6NIA mouse hippocampus and found a difference in the hippocampal gene expression profile between 2-month-old young mice and 15-month-old middle-aged mice correlated with an age-related cognitive deficit in hippocampal-based explicit memory formation. Middle-aged mice displayed a mild but specific deficit in spatial memory in the Morris water maze. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Jun 19 2006 Contributers: Miguel Verbitsky Conrad Gilliam Gael Malleret Eric Kandel Amanda Yonan Paul Pavlidis (cerebellum 1982 1992 brain_DLPFC_bipolar B_mr304 Expression profiling of somatomotor cortex extracted from rats at 14d following moderate injury Source GEO sample is GSM41693 Last updated (according to GEO): May 27 2005 with increased obesity 996 1017 1000 Cerebrovascular accident PGA-swim_10min_n996 861 Umbilicus Neoplasm 861 Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22571 Last updated (according to GEO): Sep 14 2005 HNC017 Whole Brain 62 72 Isoflurane 10 exposures-3 Parkinson Disease 861 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17160.gif Source GEO sample is GSM91516 Last updated (according to GEO): Sep 22 2006 Cochlear nucleus structure 901 1000 Brain Posterior root of spinal nerve 861 Time-course and concentration-effect experiments with multiple time points and drug concentrations provide far more valuable information than experiments with just two design-points (treated vs. control), as commonly performed in most microarray studies. Analysis of the data from such complex experiments, however, remains a challenge. Here we present a semi-automated method for fitting time profiles and concentration-effect patterns, simultaneously, to gene expression data. The submodels for time-course included exponential increase and decrease models with parameters such as initial expression level, maximum effect, and rate-constant (or half-time). The submodel for concentration-effect was a 4-parameter Hill model. The method was applied to an Affymetrix HG-U95Av2 dataset consisting of 51 arrays. The specific study focused on the effects of two platinum drugs, cisplatin and oxaliplatin, on A2780 human ovarian carcinoma cells. Replicates were available at most time points and concentrations. Eighteen genes were selected; time-course and concentration-effect were modeled simultaneously. Comparisons of model parameters helped distinguish genes with different expression patterns between the two drug treatments. This overall paradigm can help in understanding the molecular mechanisms of the agents, and the timing of their actions. Last Updated (by provider): Jun 07 2007 Contributers: William Greco Ramakumar Tummala Yseult F Brun Ram Varma Suzanne M Hector Lakshmi Pendyala 113T Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92283 Last updated (according to GEO): Jan 13 2006 AML_1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A rad001 12h, biological rep4 NMDA360 (Experiment shortNMDA: Run 19222) Treatment, type=time_course, description=primary cortical neurons were treated with 1 mM NMDA for increasing periods of time (10 to 360 min)., measurement=360.0 m Source GEO sample is GSM96772 Last updated (according to GEO): Feb 14 2006 56 32 out of mouse bone marrow 50 F arm fibroblast LS28, asynchronous SCG_control_40h_rep1 Gene expression data from postmorten brain regions Source GEO sample is GSM146001 Last updated (according to GEO): Nov 20 2006 striatum 33 41 Thymus [JunctionChip 4 of 5] 1000 Heart Mouse old heart w/ a-tocopherol aT-Ht-1 hydrocephalus 279 292 Myocardial Infarction 1000 861 Cerebral cortex PGA-Band_Sham_48h_15-m5 1000 Brain Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 24h. Lot batch = Source GEO sample is GSM1235 Last updated (according to GEO): May 28 2005 22 19 left Gene expression data from postmorten brain regions Source GEO sample is GSM146065 Last updated (according to GEO): Nov 20 2006 Spinal Cord 1000 Liver (HBV+, HK67) Gene expression data for comparing calorie restricted-fed 30-month-old to control-fed 30-month-old for investigating effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7447 Last updated (according to GEO): May 27 2005 129:24-5 medulla Nose 1000 EOM 14 Day Control rep 1 Large-scale analysis of the human transcriptome. Lymphoma Burkitt's, Daudi Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 259.98 Stdv: 8.04 Min: 246.43 Max: 276.51 Source GEO sample is GSM2875 Last updated (according to GEO): Mar 20 2006 Keywords = Heart 505 521 ovarian tumor: endometrioid Source GEO sample is GSM139391 Last updated (according to GEO): Apr 09 2007 none Source GEO sample is GSM244557 Last updated (according to GEO): Nov 23 2007 21 0 Heart failure sample 2 from ventral prostate 21 41 Ng1: Hippocampus_NT-Y_rep5 adenocarcinoma 3806 0 18 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211435 Last updated (according to GEO): Jul 18 2007 Pool of 10 saccules at E14 Source GEO sample is GSM182616 Last updated (according to GEO): Aug 14 2007 1000 Left 91 from the bone marrow 72 C57L/J Frontal Cortex C Eye 1000 21 0 Mammary Gland @ Lac1 ventral tegmental area cocaine naive replicate 2 Brain_MD_35_Medulloblastoma_Desmoplastic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL D13 12h Media 1000 Leukemia, Myelocytic, Acute cerebral cortex 7 21 between the LAD artery 266 287 861 Stria Blood T cells;Adult Naove CD4+ Unstimulated 1000 Prostate Suppressor of cytokine signaling (SOCS) proteins are feedback inhibitors of the Janus kinase (JAK) and signal transducer and activator of transcription (STAT) signaling pathway. SOCS3 is upregulated by several signals in macrophages and has been implicated as a regulator of various signaling pathways. Here we show that phosphorylation of STAT3 is prolonged in mouse Socs3-deficient macrophages after stimulation with interleukin-6 (IL-6) but not IL-10, indicating that SOCS3 specifically affects signaling mediated by IL-6 and gp130. IL-6 induces a wider transcriptional response in Socs3-deficient macrophages than in wild-type cells; this response is dominated by interferon (IFN)-regulated genes owing to an excess of STAT1 phosphorylation. Thus, SOCS3 functions to control the quality of the response to IL-6 and prevents the activation of an IFN-induced program of gene expression. Midbrain 5 Normal X50 WT1 F2/8 X50 wild type Mouse 16 months Cerebellum Male Source GEO sample is GSM73196 Last updated (according to GEO): Sep 06 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM146076 Last updated (according to GEO): Nov 20 2006 5 0 Spleen human cerebellum Source GEO sample is GSM87111 Last updated (according to GEO): Feb 08 2006 FETALTHYROID Source GEO sample is GSM18804 Last updated (according to GEO): Sep 25 2006 WGACON-201 254 240 the endometrium Affymetrix MG430 2.0 expression levels of wild-type (STHdhQ7/Q7), 3NP-treated wild-type (STHdhQ7/Q7+3-NP), and mutant (STHdhQ111/Q111) striatal cells Last Updated (by provider): Sep 05 2007 Contributers: Jong-Min Lee Marcy E MacDonald in the brain 150 162 834 820 in hypothalamus male C57BL6, double amplification Source GEO sample is GSM5433 Last updated (according to GEO): Mar 17 2006 1000 Spleen Day 1_M_+RA_Bchip 861 Chromosomes 660 mesenchymal stem cell 639 M_U133Plus_93_nAcc M_U133A_29_HC human caudate nucleus Source GEO sample is GSM86913 Last updated (according to GEO): Feb 08 2006 TEL-AML1-#7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Cerebral cortex To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18483 Last updated (according to GEO): May 27 2005 MLL-2M#2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Fibroblasts 861 Infection 1000 osteoblast 627 637 CNS BMI-1 KO brain, cerebral cortex: PC14_e1_le1 of the saphenous artery 43 65 none Source GEO sample is GSM239938 Last updated (according to GEO): Dec 07 2007 966 Hippocampus Gene expression data from rat metanephric mesenchymes cultured for 4 days in the presence of the ANX fraction Source GEO sample is GSM126224 Last updated (according to GEO): Dec 08 2006 V5-P510 24 skeletal muscle 10 1000 Brain osteoblast 627 637 Gene expression data from postmorten brain regions Source GEO sample is GSM145209 Last updated (according to GEO): Nov 20 2006 Mislabeled (was labeled Heart (interventricular septum)) [JunctionChip 5 of 5] mammary_gland_10 43h-AC replication 1 brain, brainstem: D60WTFNMN2_e1_le1 884 Structure of intestinal epithelium MP-DX-5 Cerebral cortex 861 28 17 brain injury testis Source GEO sample is GSM18822 Last updated (according to GEO): Sep 25 2006 mouse brains 187 198 The most common congenital cardiac abnormalities 50 97 brain, cerebral cortex: Rat_03-45_NroLep_Lipska_e1_le1 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Neuropeptide Y labeled with Cy5- time course with repeats. Date GSE393 Last Updated: May 29 2005 Contributers: Yun Anna Cao Jong-Woo Kim Rebecca Hart Zhen Yan Robert Hsueh Angela Alexander Sun Young Lee Sangdun Choi Mi Sook Chang Joella Grossoehme Includes GDS314. Update date: Nov 18 2003. Dataset description GDS314: Temporal analysis of effects induced by 1 uM neuropeptide Y in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. BL-C8 on NHGRI-6.5k_b 861 Chromosomes N/A Source GEO sample is GSM96293 Last updated (according to GEO): Feb 13 2006 of bipolar disorder 25 43 1000 Rectum DMSO-control NG108 neuronal cells 4 GIN (Gad1 inhibitory ref. (pubmed id:10777798) ) neurons from hippocampus Source GEO sample is GSM63015 Last updated (according to GEO): Dec 01 2005 14 0 Normal Thalamus 86 70 Fetal liver cells human caudate nucleus Source GEO sample is GSM86807 Last updated (according to GEO): Feb 08 2006 2022 1994 of adhering connective tissue KO_IL-6_100_rep2 R466P00431 Osteoblasts 1000 DLCL-0003 1000 Primary carcinoma of the liver cells Brain 861 901 Epithelial Cells Type 2 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228672 Last updated (according to GEO): Sep 11 2007 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201813 Last updated (according to GEO): Jun 20 2007 Cerebral cortex 1000 Endometrium-Normal 9 human cerebellum Source GEO sample is GSM87142 Last updated (according to GEO): Feb 08 2006 BC118A-AF Obesity 0 7 MDA-N_CL5012_Breast on Affymetrix GeneChip Human Full Length Array HuGeneFL infection 432 441 861 Cerebral cortex gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134622 Last updated (according to GEO): Jul 09 2007 468 462 basally sensorimotor cortex 200 218 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50646.gif Developmental Stage: E9 Source GEO sample is GSM229817 Last updated (according to GEO): Nov 06 2007 Skeletal bone 861 1000 Lung 114 cortex 120 1000 Infection Standard Affymetrix Protocol on total RNA extracted from brain tissue Source GEO sample is GSM101413 Last updated (according to GEO): Mar 28 2006 stellate cells 284 297 Category: Lymphoma Classification Subcategory: Hematopoetic cell lines Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc5b004 Source GEO sample is GSM1956 Last updated (according to GEO): Nov 21 2005 Disorder of artery 865 RNA isolated from fetal cerebrum Keywords = trisomy Keywords = brain Keywords = Down syndrome Source GEO sample is GSM22509 Last updated (according to GEO): May 27 2005 Fat RYGB-Success Repl3 861 Oocytes 24 19 (Brain Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) mice exhibit a large difference in a number of alcohol and drug related behaviors. This study examined the expression levels of transcripts in these strains in the cerebellum, which is a major target of ethanol?s actions in the CNS, in order to find differentially expressed candidate genes for these phenotypes. Cerebellum was specifically chosen due to the fact that Purkinje cell sensitivity to ethanol in these strains is highly correlated to "sleep time", the measure of ethanol sensitivity used with these strains. Naive mice were used because differences in sensitivity are observed upon initial exposure to ethanol. Last Updated (by provider): Apr 20 2006 Contributers: Beth Bennett Thomas E Johnson James M Sikela Erik J MacLaren Includes GDS1609. Update date: Aug 22 2006. Dataset description GDS1609: Comparison of cerebella of Inbred Long Sleep (ILS) and Inbred Short Sleep (ISS) animals. ILS animals are more sensitive than ISS animals to ethanol. Initial sensitivity to ethanol is a predictor of alcohol abuse. Results provide insight into the molecular basis of differential ethanol sensitivity.. Includes GDS1610. Update date: Aug 22 2006. Dataset description GDS1610: Comparison of cerebella of Inbred Long Sleep (ILS) and Inbred Short Sleep (ISS) animals. ILS animals are more sensitive than ISS animals to ethanol. Initial sensitivity to ethanol is a predictor of alcohol abuse. Results provide insight into the molecular basis of differential ethanol sensitivity.. 1000 Prostate Mammary Gland @ Preg17, biological rep4 Heart 861 Muscle 861 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211392 Last updated (according to GEO): Jul 18 2007 8-cell embryo replication 3 Keywords = preimplantation Keywords = development Source GEO sample is GSM14685 Last updated (according to GEO): May 28 2005 R623P01188 Gene expression data from postmorten brain regions Source GEO sample is GSM145657 Last updated (according to GEO): Nov 20 2006 861 Oocytes Renal clear cell carcinoma (RCC) is the most common histological cancer in which has been proved an anti-tumor response and a spontaneous regression of metastatic lesions. In vitro studies demonstrated that selected subpopulations of T cells or even T cell clones can eradicate or reduce a large tumor mass that expresses antigens recognized by these effectors cells. In the present study, we generated and induced in vitro autologous and allogeneic antigen-specific T cell responses against RCC cell line by MLTC. The expansion of tumor-specific cytotoxic lymphocytes (CTL) allowed the analysis of the phenotypic, functional and genomic profiles of unstimulated and activated CD8+ T cells. The autologous and MLTC responder cells recognized the RCC cell line in IFN-g Elispot assay and antibody blocking assay defined that tumor-reactive CD8+ T cell response was HLA class I restricted. CD8+ T lymphocytes showed cytotoxic activity against RCC tumor cells with a phenotype of CD45RA- CD45RO+ CCR7- CD69+ memory T cells. Comparison of gene expression data, using microarray, in normal activated T cells versus RCC CD8+ T cells, demonstrated differential expressed genes involved in proliferation, signaling pathways, apoptosis associated to phenotypic and functional changes in responder T cells. Among the genes involved in intracellular signaling, JAK3 gene expression was down-regulated in RCC CD8+ T cells and up-regulated in normal subjects upon activation. Interestingly, also MCL-1 gene, an antiapoptotic member of the BCL-2 family, was decreased in activated RCC CD8+ T cells and increased in healthy donors. These mechanisms of defective cellular signaling and their relationship on induction of apoptosis in effector T cell subset is critical for the identification of alterations in T cell responses in RCC and might be useful to set up strategies to overcome tumor induced-immune suppression. Last Updated (by provider): Apr 16 2007 mouse hippocampus 0 16 gfp pos. sorted cells from 3 disected e14.5 cortecies Treatment, type=wait Source GEO sample is GSM135784 Last updated (according to GEO): Sep 12 2006 Human endometriosis vs normal endometrium study - transcriptional profiling 1000 Integumentary system to the nose 599 609 Cx43 cortical astrocytes 3 Testis 861 CNS-RM_Ctr3mo-2C-s2 1000 Communicable Diseases SHR rep1 966 Hippocampus Analysis of clinical bladder cancer classification according to microarray expression profiles Gene expression data from dorsal pancreas at e13.5, MG-U74B version2 Source GEO sample is GSM199455 Last updated (according to GEO): Jun 08 2007 CNS-SpinalCmod-Adult-48h-4A-s2 YP1 Wild type inbred mice Source GEO sample is GSM82927 Last updated (according to GEO): Nov 10 2005 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12414.gif Source GEO sample is GSM79856 Last updated (according to GEO): Sep 22 2006 midbrain_4 none Source GEO sample is GSM210334 Last updated (according to GEO): Jul 16 2007 Cerebral cortex 1000 15 0 human cerebellum 41 29 Control blood GC (HKG64T) GSE2361 GSE1572 cortex from B6 mice at ZT3 rep3 Source GEO sample is GSM160454 Last updated (according to GEO): Feb 05 2007 Mouse old brain w/ a-tocopherol aT-Br-4 ScN2a_3 861 Epithelial Cells Congenital Abnormality 853 jzo028-rp1-v5-u74av2-met NFIA E18WT1 9 0 Blood Test Normal Source GEO sample is GSM175880 Last updated (according to GEO): Apr 09 2007 Type 2 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228676 Last updated (according to GEO): Sep 11 2007 GC (HKG70T) 1000 Uterus Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) mice exhibit a large difference in a number of alcohol and drug related behaviors. This study examined the expression levels of transcripts in these strains in the cerebellum, which is a major target of ethanol?s actions in the CNS, in order to find differentially expressed candidate genes for these phenotypes. Cerebellum was specifically chosen due to the fact that Purkinje cell sensitivity to ethanol in these strains is highly correlated to "sleep time", the measure of ethanol sensitivity used with these strains. Naive mice were used because differences in sensitivity are observed upon initial exposure to ethanol. Last Updated (by provider): Apr 20 2006 Contributers: Erik J MacLaren Beth Bennett Thomas E Johnson James M Sikela Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. Moderate controlled cortical impact with pneumatic impactor, 6 m/s impact velocity and 1.5 mm deformation. 8h after surgery, a 4 mm diameter disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44512 Last updated (according to GEO): May 27 2005 176 166 bone marrow Liver Test (Blinded) Sample Source GEO sample is GSM130129 Last updated (according to GEO): Sep 18 2007 Inhaled anesthetics produce many effects and bind to a large number of brain proteins, but it is not yet clear if this is accompanied by widespread changes in gene expression of the biological targets. Such changes in expression might implicate functionally important targets from the large pool of binding targets. Isolated primary cortical neurons were exposed to anesthetics and DNA oligonucleotide microarrays were used to detect and quantify transcriptional changes in neuronal tissue. Last Updated (by provider): Mar 24 2006 Contributers: Maryellen F Eckenhoff John W Tobias James G Hecker Roderic G Eckenhoff Huafeng Wei Jonathan Z Pan Includes GDS1398. Update date: Jan 27 2006. Dataset description GDS1398: Expression profiling of primary cortical neuron cultures exposed to 1 or 3% halothane or 4% isoflurane for 6 hours. Cells allowed to recover for an additional 6 hours. Results provide insight into effect of inhaled anesthetics on global gene expression.. Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228625 Last updated (according to GEO): Sep 11 2007 234-97_Adeno no additional Source GEO sample is GSM199238 Last updated (according to GEO): Jun 08 2007 none Source GEO sample is GSM123238 Last updated (according to GEO): Jul 26 2006 Fibroblasts 861 Pituitary Gland 9 Normal in the tumours 942 955 1000 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145720 Last updated (according to GEO): Nov 20 2006 24 0 human prostate PC3 tumors 861 Skin M7TW01010638 pfc_1028_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Spleen vs CpG-oligodeoxynucleotide Treated B cell 30min (set2) 19 0 human frontal cortex nasal epithelial cells 28 49 Heart failure 1000 brain 0 5 DBA 1-1-1 Heart 913 Hereditary Malignant Neoplasm Biopsy of the normal mucosa of the colon from patient #13 A HID U D054 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108613 Last updated (according to GEO): Aug 22 2006 Expression profiling of moderately injured raphe at 14d in rats Source GEO sample is GSM41568 Last updated (according to GEO): May 27 2005 C2C12_0_hr Bladder sample 925-1 4_cerebral_cortex_9hrs_sleep_deprivation_#21 129/SvImJ Hippocampus B Nose 1000 28 17 brain injury Expression profiling of spinal cord section (T9) extracted from rats 12h following moderate injury Source GEO sample is GSM31514 Last updated (according to GEO): May 27 2005 Gene expression data Source GEO sample is GSM230360 Last updated (according to GEO): Sep 19 2007 of rat oculomotor nucleus 40 64 Five different human MPNST cell lines, mock treated or infected with G207. Source GEO sample is GSM215803 Last updated (according to GEO): Aug 07 2007 cardiac 763 769 8 0 Pituitary Ovarian Diseases 877 Creatine-treated, biological rep3 C2C12_2.0_hr ES_129b #2(16012165010073) NA19143 experiment II untransduced replicate 1 Wild type voxel F2 Cells were either prestimulated (1_X) or not (0_X) for 18h with 100 ng/ml LPS. Media was exchanged and after 2h rest, cells either restimulated (X_1) or not (X_0) with again 100 ng/ml LPS. This resulted in 4 experimental conditions: 0_0, 0_1, 1_0 and 1_1. There were 3 biological replicates done, resulting in 12 arrays altogether. Source GEO sample is GSM213697 Last updated (according to GEO): Aug 01 2007 901 Coronary artery Bicalutamide treated LNCaP cells not stimulated with DHT, biological replicate 2 Source GEO sample is GSM187375 Last updated (according to GEO): May 04 2007 Heart 861 RMS-C2 on NHGRI-6.5k_b Neoplasm 1000 1000 Aorta Midbrain 2 Normal Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225740 Last updated (according to GEO): Nov 02 2007 CNS-SC_CtrA24h-1B-s2 Large-scale analysis of the mouse transcriptome. Bladder C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 342.12 Stdv: 18.37 Min: 313.81 Max: 371.22 Source GEO sample is GSM2946 Last updated (according to GEO): Mar 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145964 Last updated (according to GEO): Nov 20 2006 901 Coronary artery human frontal cortex Source GEO sample is GSM87023 Last updated (according to GEO): Feb 08 2006 Nrl ko samples were compared to wt at postnatal 2. Source GEO sample is GSM227452 Last updated (according to GEO): Sep 07 2007 Coronary artery 901 1000 Solid tumor brain, hippocampus: Sample14_e1_le1 HapMap CHB Female Source GEO sample is GSM159599 Last updated (according to GEO): Feb 01 2007 861 Oocytes Wild type olfactory epithlium 8 hpO replicate3 40 21 from the hippocampus tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44863 Last updated (according to GEO): May 27 2005 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141315 Last updated (according to GEO): Oct 26 2006 Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35385 Last updated (according to GEO): May 27 2005 330 324 uterus Gene expression data from postmorten brain regions Source GEO sample is GSM145721 Last updated (according to GEO): Nov 20 2006 Mature B cells 1_2 901 Spinal Cord Spleen vs CpG-oligodeoxynucleotide Treated B cell 60min (set1) 1000 Spleen 36 21 from whole brain Primary tumor 19 32 Blood Test (Blinded) Sample Source GEO sample is GSM130027 Last updated (according to GEO): Sep 18 2007 f2#337 versus pool Mouse Brain tissue CAD_replicate67 1BJZ02022751_testis HapMap JPT Male Source GEO sample is GSM159655 Last updated (according to GEO): Feb 01 2007 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225750 Last updated (according to GEO): Nov 02 2007 46 8 in docetaxel-refractory prostate cancer 78 73 rectum 1000 Spleen of regenerating Dorsal Root Ganglia 21 55 Skeletal bone 861 228 219 Hippocampi Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22558 Last updated (according to GEO): May 27 2005 Category: Cell-line Subcategory: HMEC Scanning Software: unknown Software version: unknown Lot batch = 0386-5k Source GEO sample is GSM1952 Last updated (according to GEO): Nov 21 2005 25 0 frontal cortex wistar 3660 21 0 acute myeloid leukemia Skeletal bone 861 Medulla 861 in the mammalian nervous system 110 141 736 727 in tumors to the nose 599 609 R6/1 wildtype, brain hemisphere Source GEO sample is GSM83872 Last updated (according to GEO): Apr 20 2007 468 459 the rectum aa_NY234 Trigeminal Ganglion Source GEO sample is GSM53317 Last updated (according to GEO): Jul 06 2005 HapMap JPT Female Source GEO sample is GSM159649 Last updated (according to GEO): Feb 01 2007 none Source GEO sample is GSM123266 Last updated (according to GEO): Jul 27 2006 Heart 1000 320 306 Keywords = HIV 112 77 Keywords = congenital heart disease 1000 Skeletal muscle structure Brain 1000 CNS-SCsev_InjA24h-2C-s2 Whole blood from a healthy control Source GEO sample is GSM153448 Last updated (according to GEO): Jan 11 2007 Blood 1000 Nothing in line. Source GEO sample is GSM154238 Last updated (according to GEO): Jul 05 2007 Sample7, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53258 Last updated (according to GEO): Jul 06 2005 M_U133Plus_118_HC tibiae 115 120 osteoblast 630 640 brain, frontal cortex: Sample58_e1_le1 myocardial infarction 383 403 DIF 1, chip MOE430A human frontal cortex Source GEO sample is GSM87045 Last updated (according to GEO): Feb 08 2006 adipose_tissue_5 V5-P063 43 0 Chorionic mesoderm-derived mesenchymal cells Gene expression data from colorectal adenoma. Source GEO sample is GSM215090 Last updated (according to GEO): Aug 02 2007 Blood 861 human caudate nucleus Source GEO sample is GSM86803 Last updated (according to GEO): Feb 08 2006 with autism spectrum disorder 37 65 brain, cochlea: [17] Sample #17_le1 Cancer cells 462 473 V5-P056 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184753 Last updated (according to GEO): Apr 26 2007 Brain 861 vestibular_nuclei_superior_6 Source GEO sample is GSM80893 Last updated (according to GEO): Mar 31 2006 Arteries 861 trachea Source GEO sample is GSM18835 Last updated (according to GEO): Sep 25 2006 1_hypothalamus_3hrs_sleep_#135 1000 Bone Marrow D_U133Plus_107_CB in bronchial epithelia 311 332 901 Impaired cognition CurrentSmoker 12 Fibroblasts 1000 Colon 1000 1BJZ02052111_TestiLeydigCell Osteoblasts 1000 1000 Liver Expression profiling of spinal cord section (T8) extracted from rats 0h following laminectomy (naive) Source GEO sample is GSM31418 Last updated (according to GEO): May 27 2005 with some respiratory epithelium. 1039 1072 680 668 of the tumor Gene expression data from postmorten brain regions Source GEO sample is GSM144967 Last updated (according to GEO): Nov 20 2006 3885 3874 spinal cords Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11306 Last updated (according to GEO): May 28 2005 1000 Encephalitis heart failure 583 595 Wild-type-neocortex, biological rep6 (female) Normal Source GEO sample is GSM176230 Last updated (according to GEO): Apr 09 2007 Cerebral cortex 861 Whole Genome array hippocampus_cocaine5 plasma cells 50 61 Parkinson Disease 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Leukotriene B4 (LTB4) for 120min Source GEO sample is GSM5680 Last updated (according to GEO): May 27 2005 901 Coronary artery Donor 3 Time point 48 hours Autologous control (uninfected) Source GEO sample is GSM2623 Last updated (according to GEO): May 27 2005 KO_NP_mid_1 Astrocytoma 861 abd skin fibroblast , asynchronous l 901 Intestines, Small Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184764 Last updated (according to GEO): Apr 26 2007 28 13 from fetal heart 861 Brain M_U133Plus_38_AnCg Brain 1000 17 7 hippocampus Parkinson's disease pathogenesis proceeds through several phases, culminating in the loss of dopaminergic neurons of the substantia nigra (SN). Although the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) model of oxidative SN injury is frequently used to study degeneration of dopaminergic neurons in mice and non-human primates, an understanding of the temporal sequence of molecular events from inhibition of mitochondrial complex 1 to neuronal cell death is limited. Here, microarray analysis and integrative data mining were used to uncover pathways implicated in the progression of changes in dopaminergic neurons after MPTP administration. This approach enabled the identification of small, yet consistently significant, changes in gene expression within the SN of MPTP-treated animals. Such an analysis disclosed dysregulation of genes in three main areas related to neuronal function: cytoskeletal stability and maintenance, synaptic integrity, and cell cycle and apoptosis. The discovery and validation of these alterations provide molecular evidence for an evolving cascade of injury, dysfunction, and cell death. Coronary heart disease 913 Urethra 5 Normal Large-scale analysis of the mouse transcriptome. Trachea C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 289.50 Stdv: 6.72 Min: 277.68 Max: 299.19 Source GEO sample is GSM2989 Last updated (according to GEO): Mar 20 2006 Liver 1000 NA18994 prostate Source GEO sample is GSM203295 Last updated (according to GEO): Jun 21 2007 High-density progenitors Source GEO sample is GSM47541 Last updated (according to GEO): Jun 10 2005 3AMH02082106_BM_CD33Myeloid Heart 1000 CONTEXT: Polycystic ovary syndrome (PCOS), the most common cause of anovulatory infertility, is characterized by increased ovarian androgen production and arrested follicle development and is frequently associated with insulin resistance. These PCOS phenotypes are associated with exaggerated ovarian responsiveness to FSH and increased pregnancy loss. OBJECTIVE: The objective of this study was to examine whether the perturbations in follicle growth and the intrafollicular environment affect gene expression and ultimately development of the PCOS oocyte. DESIGN: Oocyte cDNA was subjected to microarray and PCR analysis. SETTING: This study was conducted at a university laboratory. PATIENTS: The study comprised 10 normal ovulatory women and nine women with PCOS. INTERVENTION: The intervention was GnRH analog/recombinant human FSH therapy for in vitro fertilization. MAIN OUTCOME MEASURE: The main outcome measure was mRNA abundance of oocyte-expressed genes. RESULTS: Cluster analysis revealed differences in global gene expression profiles between normal and PCOS oocytes. Of the 8123 transcripts expressed in the oocytes, 374 genes showed significant differences in mRNA abundance in PCOS oocytes. Annotation of the data demonstrated that a subset of these genes was associated with chromosome alignment and segregation during mitosis and/or meiosis. Furthermore, 68 of the differentially expressed genes contained putative androgen receptor and/or peroxisome proliferating receptor gamma binding sites. CONCLUSIONS: These analyses demonstrated that normal and PCOS oocytes that are morphologically indistinguishable and of high quality exhibit different gene expression profiles. Promoter analysis suggests that androgens and other activators of nuclear receptors may play a role in differential gene expression in the PCOS oocyte. Likewise, annotation of the differentially expressed genes suggests that defects in meiosis or early embryonic development may contribute to reduced developmental competency of PCOS oocytes. 278 255 ischemic cardiomyopathy Whole Brain 62 72 1000 Liver Normal Source GEO sample is GSM176021 Last updated (according to GEO): Apr 09 2007 15 0 human cerebellum Putamen P4 Disease Muscular Atrophy 901 bronchial epithelia 224 243 Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep6 hippocampus Source GEO sample is GSM36007 Last updated (according to GEO): May 27 2005 2500 mg/kg X 6 hr Source GEO sample is GSM129845 Last updated (according to GEO): Sep 18 2007 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 11 hours after lights on. Original sample code = CM26A Source GEO sample is GSM227336 Last updated (according to GEO): Sep 10 2007 Brain 1000 brain, unknown: Sample50_e1_le1 54 37 with acute malaria pull-downSD_3, ZT6 plasma cells 332 344 spinal cord 0 11 Brain 861 2376 2368 18S rRNA Cardiac 523 530 HC53 CN B osteoblast 627 637 Normal Spleen for liver 26 35 Cochlear nuclei 0 14 Standard affymetrix protocol Source GEO sample is GSM119731 Last updated (according to GEO): Jul 31 2007 the blood 393 402 TUMOR 8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A plasma cells 332 344 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with SDF1 alpha (Stromal cell derived factor-1) for 60min Source GEO sample is GSM5760 Last updated (according to GEO): May 27 2005 eye 0 3 in NSCLC 41 48 861 Cerebral cortex cingulate cortex 1000 V5-P121 Exp A, Animal #4, control (0mg/kg) CPF Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours Source GEO sample is GSM246131 Last updated (according to GEO): Dec 03 2007 human caudate nucleus Source GEO sample is GSM86819 Last updated (according to GEO): Feb 08 2006 intestine_PPARa_kockout_24hfasted_rep1 5 0 brain Hypertensive disease 861 Liver Source GEO sample is GSM18954 Last updated (according to GEO): Sep 25 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145004 Last updated (according to GEO): Nov 20 2006 Large-scale analysis of the mouse transcriptome. Brown fat, interscapular depression C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 275.32 Stdv: 12.26 Min: 259.37 Max: 301.19 Source GEO sample is GSM2922 Last updated (according to GEO): Mar 20 2006 Myometrium 3 Normal GSE5547 intestine_wildtype_control_rep3 with some respiratory epithelium. 1039 1072 D_U133A_96_CB Gene expression data from postmorten brain regions Source GEO sample is GSM145042 Last updated (according to GEO): Nov 20 2006 Bladder sample 942-1 B6 day 0, biological rep 1, tech rep 2 5 0 brain Cerebellum Alzheimer's disease 2 shRNA-mediated knock down of Bmi-1 and Mel-18 in medulloblastoma cells Epithelial Cells 901 adenoma 861 1000 Hypertrophic Cardiomyopathy 5 0 brain HC86 CB A spleen 0 5 mouse cerebral cortex from COX-1 Knockout Source GEO sample is GSM121425 Last updated (according to GEO): Jan 31 2007 JMR-MurInj72h-3cAv2-s2 5 0 brain 1000 Down Syndrome SN:Human Glioblastoma Biopsy 07081 the spinal cords 144 159 A fundamental feature of the architecture and functional design of vertebrate animals is a stroma , composed of xtracellular matrix and mesenchymal cells, which provides a structural scaffold and conduit for blood and lymphatic vessels, nerves, and leukocytes. Reciprocal interactions between mesenchymal and epithelial cells are known to play a critical role in orchestrating the development and morphogenesis of tissues and organs, but the roles played by specific stromal cells in controlling the design and function of tissues remain poorly understood. The principal cells of stromal tissue are called fibroblasts, a catch-all designation that belies their diversity. We characterized genome-wide patterns of gene expression in cultured fetal and adult human fibroblasts derived from skin at different anatomical sites. Fibroblasts from each site displayed distinct and characteristic transcriptional patterns, suggesting that fibroblasts at different locations in the body should be considered distinct differentiated cell types. Notablegroups of differentially expressed genes included some implicated in extracellular matrixsynthesis, lipid metabolism, and cell signaling pathways that control proliferation, cellmigration, and fate determination. Several genes implicated in genetic diseases werefound to be expressed in fibroblasts in an anatomic pattern that paralleled the phenotypicdefects. Finally, adult fibroblasts maintained key features of Hox gene expressionpatterns established during embryogenesis, suggesting that Hox genes may directtopographic differentiation and underlie the detailed positional memory in fibroblasts. Last Updated (by provider): Dec 29 2005 [Switched to use SH-40k by Gemma] in primary human breast tumors 151 181 1000 Uterus Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188855 Last updated (according to GEO): Jun 06 2007 Bronchus 3 Normal no additional Source GEO sample is GSM199186 Last updated (according to GEO): Jun 08 2007 861 Hippocampus Exp C_3, 5mg/kg CPF The Dlx homeobox genes have central roles in controlling patterning and differentiation of the brain and craniofacial primordia. In the brain, loss of Dlx function results in defects in the production, migration and differentiation of GABAergic neurons, that can lead to epilepsy. In the branchial arches, loss of Dlx function leads to craniofacial malformations that include trigeminal axon pathfinding defects. To determine how these genes function, we wish to identify the transcriptional circuitry that lies downstream of these transcription factors by comparing gene expression in wild type with Dlx mutant CNS and craniofacial tissues. 1) Compare gene expression in the maxillay branch of the first branchial arch (BA) of E10.5 wild type and Dlx2 -/- mutants. 2) Compare gene expression in the maxillary branch of the first BA of E10.5 wild type and Dlx1/2 -/- mutants. 3) Compare gene expression in wild type maxillary and mandibular branchial arches. 4) Compare gene expressionin mandibular branch of Dlx5/6 -/- mutants with wild type mandibular branch. The Dlx transcription factors are essential for controlling patterning of the brain and craniofacial primordia. In the brain, they control differentiation of GABAergic neurons of the basal ganglia. In the branchial arches, they control regional patterning. I hypothesize that there will be some conserved and some divergent mechanisms that the Dlx genes use in controlling brain and craniofacial development. We have already performed array analyses on Dlx function in the developing basal ganglia (with TGEN) by comparing expressed genes in wild type and Dlx1/2 mutants. Here we will compare gene expression in the brachial arches of wild type and Dlx mutant mice. 1) Generate E10.5 mouse embryos that are either wild type, Dlx2-/-, Dlx1/2 -/- or Dlx5/6 -/-. 2) Determine genotype by PCR. 3) Dissect branchial arches from the different genotypes. 4) Separate maxillary and mandibular branch of each branchial arch. 5) Prepare total RNA from the specimens. Obtain sufficient tissue to obtain 10 ug of total RNA - based on previous experience we anticipate that this will require ~ 10 branchial arches. We will pool the tissue from different embryos of the same genotype. 6) Send total RNA to TGEN for probe preparation, hybridization and array result analysis. Last Updated (by provider): Jun 06 2006 Contributers: John L Rubenstein Normal Source GEO sample is GSM176249 Last updated (according to GEO): Apr 09 2007 of Parkinson's disease 450 471 to cardiovascular disease 299 323 in the mammalian nervous system 110 141 23 11 of the kidney Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc58 Source GEO sample is GSM1862 Last updated (according to GEO): Nov 21 2005 41 28 in mouse brain HairCat_0220ACIC_039.txt Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184792 Last updated (according to GEO): Apr 26 2007 RNA isolated from fetal cerebellum Keywords = trisomy Keywords = brain Keywords = Down syndrome Source GEO sample is GSM22588 Last updated (according to GEO): May 27 2005 Infection 1176 1185 Ovarian_Tumor_Serous_CHTN-OS-018 Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation. Source GEO sample is GSM228465 Last updated (according to GEO): Sep 10 2007 Standard Affymetrix Protocol Source GEO sample is GSM16472 Last updated (according to GEO): May 28 2005 GSE8921 14 on NHGRI-13.8k no additional Source GEO sample is GSM199278 Last updated (according to GEO): Jun 08 2007 na Source GEO sample is GSM181275 Last updated (according to GEO): Apr 10 2007 Tumor__Ovary_Adeno_HCTN_19120 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Plasma 861 frontal_lobe_8 Source GEO sample is GSM80676 Last updated (according to GEO): Mar 31 2006 Normal Source GEO sample is GSM176117 Last updated (according to GEO): Apr 09 2007 B380 on Affymetrix GeneChip Human Full Length Array HuGeneFL Cortex 0 5 heart 1169 1173 Gene expression data from postmorten brain regions Source GEO sample is GSM145704 Last updated (according to GEO): Nov 20 2006 of the most anterior dorsal root ganglia 23 62 Primary small cell lung carcinoma 3170 0 37 within the hippocampal dentate gyrus 96 132 Brain 861 1000 Brain Ventral Tegmental Area 1000 of paediatric cancers 114 134 Biopsy of a colorectal adenoma from patient #25 Ganglioneuroblastoma 1000 placebo 48h, biological rep4 GSE1069 Macrophage smi75 Female 20.1 yr before antibody enrichment scan 1 (U133B) Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11467 Last updated (according to GEO): May 28 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CGS for 60min Source GEO sample is GSM5514 Last updated (according to GEO): May 27 2005 medial motoneurons (MMN) 10 Hyperdip>50-C11 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Rat vestibular ganglia_calretinin_positive_rep1. 1000 Cardiomyopathy, Alcoholic Nasal Epithelium 901 Whole Brain 62 72 Liver 1000 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc70 Source GEO sample is GSM1887 Last updated (according to GEO): Nov 21 2005 1000 Hippocampus days nasal epithelium 1127 1148 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159780 Last updated (according to GEO): Apr 23 2007 861 Neurofibromatoses 1000 Structure of parenchyma of lung 338 333 brain Ldn2 Normal Source GEO sample is GSM175944 Last updated (according to GEO): Apr 09 2007 Structure of horn of uterus 983 Transitional epithelium 1000 861 Gastrocnemius muscle structure Plasma 861 21 0 acute myeloid leukemia HapMap CHB Male Source GEO sample is GSM159605 Last updated (according to GEO): Feb 01 2007 Gene expression data from experimental treatment D-CD = Differentiated and control decoy transfected cells. Source GEO sample is GSM102883 Last updated (according to GEO): May 11 2006 Our laboratory has developed the first mouse model overexpressing a RNA-binding protein, the ELAV-like protein HuD, in the CNS under the control of the CaMKinII alpha promoter. Initial behavioral characterization of the mice revealed that they had significant learning deficits together with abnormalities in prepulse inhibition (PPI). At the molecular level, we found that the expression of the growth-associated protein GAP-43, one of the targets of HuD, was increased in the hippocampus of HuD transgenic mice. To characterize these mice further and to evaluate the utility of these animals in understanding human diseases, we propose to use DNA microarray methods. To test our hypothesis we propose 3 specific aims: 1) To characterize the pattern of gene expression in the hippocampus of HuD overexpressor mice 2) To compare the pattern of gene expression in our mouse model with that in the hippocampus of rats prenatally exposed to alcohol (FAS model) and 3) To compare the pattern of gene expression in our mouse model with that shown in post-mortem tissues of patients with schizophrenia. In our previous protocols we examined the pattern of gene expression in our HuD transgenic mice and in rats prenaltally exposed to alcohol. A report by another group (Hakak et al, 2001) showed that three of the HuD targets were upregulated in the prefrontal cortex of patients with schizophrenia. To evaluate whether other target of HuD may be affected in this illness, in the current protocol, we want to compare the pattern of expression in our transgenic mice with in tissue from patients with schizophrenia Based on the behavioral and molecular properties of our HuD transgenic mice we hypothesize that these animals may be good models for the studying the basis of learning disabilities and of diseases that show deficits in PPI such as fetal alcohol syndrome and schizophrenia. All 28 samples are derived from cerebellar tissues for patients with schizophrenia and matched controls. The specimens were obtained from the Maryland Brain Collection according to NIH guidelines for confidentially and privacy. The protocol used in these studies was reviewed by our HRRC which found that our studies do not fall within the category of protocols monitored by the IRB (see attached letter form the HRRC). Specimens from 14 patients with a diagnosis of schizophrenia performed according to DSM-IV criteria and 14 sex-, age- and PMI-matched controls was included in this study. No differences were found between patients and control subjects in the average age (45±12 versus 43±10 years, p=0.86) or PMI (12±5 versus 16±6 hours, p=0.11). We will provide 28 samples containing 5 ug of RNA each in DEPC water (see validation of the quality of the RNA below). In addition, we include in our study animals treated with haloperidol as control for medication. These samples will be submitted in a separate protocol.. Date GSE4036 Last Updated: Jan 13 2006 Contributers: Nora I Perrone-Bizzozero Includes GDS1917. Update date: Jun 14 2006. Dataset description GDS1917: Analysis of cortical samples corresponding to the crus I/VIIa area of the cerebellum from schizophrenia patients. A study indicates that targets of the RNA-binding ELAV-like protein HuD are overexpressed in the prefrontal cortex of patients with schizophrenia.. Mammary Gland @ Preg17, biological rep1 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Prostaglandin E2 for 60min Source GEO sample is GSM5735 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM146070 Last updated (according to GEO): Nov 20 2006 Cerebral cortex 1000 1hr post 3Gy IR 432_2 CVB3_S-9h-4 WGACON-186 on the ventricles 598 614 875 Refractory Carcinoma Spleen 0 5 Category: Cell-line Subcategory: Breast Human umbilical vein endothelial cells obtained from Clonetics Scanning Software: unknown Software version: unknown Lot batch = svcc42 Source GEO sample is GSM1923 Last updated (according to GEO): Nov 21 2005 PROSTATE 15 22 Hyperdip>50-C43 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Normal Source GEO sample is GSM175942 Last updated (according to GEO): Apr 09 2007 1000 Mitral Valve 1000 Mammary gland Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs//27678.gif Source GEO sample is GSM66565 Last updated (according to GEO): Sep 22 2006 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68147 Last updated (according to GEO): Jul 07 2006 39 21 of substantia nigra 1000 Skeletal muscle structure 1000 Liver The epithelial cells 962 981 Hindlimb muscle, comparison of wild type and mdx mice, 7 to 112 Day (Porter lab) Disease Source GEO sample is GSM175787 Last updated (according to GEO): Apr 09 2007 with Parkinson's disease 27 50 801 782 The B cell phenotype ovarian tumor: clear cell Source GEO sample is GSM139383 Last updated (according to GEO): Apr 09 2007 Infection 1000 270 257 from 6 brains 99 94 heart 1000 Kidney Probeset expression data from NA12743 growth 1 Source GEO sample is GSM201528 Last updated (according to GEO): Aug 08 2007 Fibroblasts 38 48 861 Cerebral cortex total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD40 for 120min Source GEO sample is GSM5505 Last updated (according to GEO): May 27 2005 human frontal cortex Source GEO sample is GSM86998 Last updated (according to GEO): Feb 08 2006 Lymphoblastoid Cell Line for Individual 8177.4 log phase Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy Keywords = pathological hypertrophy Keywords = rat Keywords = heart failure Keywords = cardiomyopathy Source GEO sample is GSM11895 Last updated (according to GEO): May 28 2005 HapMap CEU_parent Male Source GEO sample is GSM159556 Last updated (according to GEO): Feb 01 2007 cerebral cortex 7 21 from rat lungs 21 34 Melanoma (G361) [JunctionChip 1 of 5] Bladder sample 1062-2 Spleen 1000 176 166 bone marrow 1BMH02022701_Colorectal Adenocarc NA18570 Large-scale analysis of the mouse transcriptome. placenta from females with E18 embryos C57BL/6L, female, 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 313.61 Stdv: 13.16 Min: 292.71 Max: 337.19 Source GEO sample is GSM2972 Last updated (according to GEO): Mar 20 2006 Microarray analyses during adipogenesis: understanding the effects of Wnt signaling on adipogenesis and the roles of liver X receptor alpha in adipocyte metabolism. Transcription profiling involves H3 methyltransferase G9a-deleted MEFs reconstituted with empty vector (delta), wild type FLAG-G9a (WT), FLAG-G9a K165A (K165A) or FLAG-G9a H1093K catalytic mutant (H1093K). Source GEO sample is GSM197744 Last updated (according to GEO): Jul 16 2007 HMVEC-L stimulated with LPS for 8 hours L08R3 1000 Spleen 11_0008_Control_Day1_52 861 Neoplasm Sample is skeletal muscle from a morbidly obese patient undergoing elective abdominal surgery Source GEO sample is GSM3980 Last updated (according to GEO): May 28 2005 Gene expression data for comparing calorie restricted-fed 30-month-old to control-fed 30-month-old for investigating effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7449 Last updated (according to GEO): May 27 2005 Disease Source GEO sample is GSM176376 Last updated (according to GEO): Apr 09 2007 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM119694 Last updated (according to GEO): Jul 11 2006 1000 Hippocampus Primary Neoplasm 1000 Cerebral cortex 1000 Nipple Cross Section 4 Normal 70 40 without coronary artery disease Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184725 Last updated (according to GEO): Apr 26 2007 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188714 Last updated (according to GEO): Jun 06 2007 Compare the brain transcriptomes of Gja9 (-/-) and Gja9 (+/-) mice with that of wildtype mice to detect transcriptomic alterationss induced by total or partial ablation of Gja9 Source GEO sample is GSM146901 Last updated (according to GEO): Nov 29 2006 GSE2572 in normal testes 162 178 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11059.gif Source GEO sample is GSM76415 Last updated (according to GEO): Sep 22 2006 Muscle 861 cerebellum 7 16 929 921 of tumors G4 lens 901 Mammary gland CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of DC, recombinant human (rh) IL-4 and rhGMCSF were added to the culture at 50 ng/ml on days 1, 3, and 5 of culture. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5135 Last updated (according to GEO): Mar 21 2006 Control male 8 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114467 Last updated (according to GEO): Jun 16 2006 Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19201 Last updated (according to GEO): May 27 2005 861 Integumentary system Entorhinal Cortex 7 23 Skeletal bone 861 Skin Sg Normal male C57BL6, double amplification Source GEO sample is GSM5429 Last updated (according to GEO): Mar 10 2006 very advanced HCC Source GEO sample is GSM155957 Last updated (according to GEO): Jun 21 2007 ATCC number CRL-1502 Source GEO sample is GSM6804 Last updated (according to GEO): May 27 2005 Expression profiling of laminectomized raphe at 3mo in rats Source GEO sample is GSM41539 Last updated (according to GEO): May 27 2005 0 Human Cortex 11 no doxycycline, wt Source GEO sample is GSM213389 Last updated (according to GEO): Jul 26 2007 Muscle 1000 1000 Structure of trigeminal ganglion Gene expression data from the hippocampus of S1P2-knockout mouse Source GEO sample is GSM172966 Last updated (according to GEO): Mar 08 2007 trachea 0 6 cerebral cortex 7 21 Papillary renal cell carcinoma 0 29 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11294 Last updated (according to GEO): May 28 2005 hg_NY55 Coordinated regulation of gene expression by Brn3a in developing sensory ganglia 7 0 Lymphoma 27 0 cerebral cortex sprague 3919 367 364 left 1000 Cerebral cortex brain 0 5 1000 Structure of middle cerebral artery Brain_Wild-type_MiceNoB4395 Skeletal bone 861 NA Source GEO sample is GSM198895 Last updated (according to GEO): Jun 07 2007 1000 Cerebral cortex GSE9442 Plasma 861 861 Cerebellum 861 Heart 129:3-1 -3-5 pituitary Colonic mucous membrane 913 1000 Amygdaloid structure A number of human neurodegenerative diseases result from the expansion of a glutamine repeat within the disease-causing protein. Spinocerebellar ataxia type1 is one such disease, caused by expansion of a polyglutamine tract in the novel protein ataxin-1. To faithfully model SCA1 in the mouse, we generated knock-in mice carrying 154 CAG repeats in the mouse Sca1 locus. These mice reproduced many aspects of the human disease. Despite ubiquitous expression of the mutant protein, they developed slowly progressive selective neurodegeneration , which is most distinct in Purkinje cells and spinal cord. Alterations in gene expression have been proposed to be involved in the pathogenesis of polyglutamine disease including SCA1, but the changes of gene expression in an authentic disease model have not been characterized. We believe that knowledge of these genes will give insight into the pathophysiology of SCA1 and may ultimately be relevant to the treatment of SCA1. We will determine gene expression patterns in the cerebellum and forebrain at three different time points. We propose that the genes whose expression is affected by mutant ataxin-1 expression are effectors for neuronal dysfunction and neuronal degeneration in the knock-in mice. We also hypothesize the difference in the expression levels of these genes accounts for selective vulnerability of neurons. We will examine three time points: 4 weeks, 11 weeks, and 20 weeks of age. We have shown that the mice developed motor incoordination as revealed by rotating rod test as early as 5 weeks of age but it was not until 10 weeks that they start showing clear neurological phenotype such as clasping. At each point, we will compare the pattern between the mutant and wild-type littermate. Animals will be prepared and sacrificed by a standard procedure. Cerebellum and spinal cord are the most affected areas whereas forebrain shows less neurodegeneration. Tissue will be rapidly dissected from cerebellum and forebrain, frozen in liquid nitrogen, and stored at ?80 C until analysis. Tissues will be sent to the centers (as opposed to RNA). We will be providing 9 tissue samples from three litters for each time point to mitigate any expression differences resulting from subtle differences of procedure or environment where the mice grow.. Date GSE2867 Last Updated: Jul 06 2005 Contributers: H Zoghbi Includes GDS1756. Update date: May 02 2006. Dataset description GDS1756: Analysis of cerebellum and forebrain tissue of knock-in mice carrying 154 CAG repeats in the spinocerebellar ataxia type 1 (SCA1) locus at 4 and 12 weeks of age. Results provide insight into the pathophysiology of the neurodegenerative disease SCA1.. 17 0 Most somatic cells 5 0 brain that the adult brain 1022 1041 NRS-1 intestine_PPARa-knockout_treated_rep1 traumatic brain injury 642 663 Prosencephalon 1000 Keywords = Heart 505 521 amygdala_9 Heart 1000 Y SIT D074 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108643 Last updated (according to GEO): Aug 22 2006 lateral hypothalamus short access to cocaine replicate 4 858 Prostatic Neoplasms from ventral prostate 21 41 Leukemia, Lymphocytic, Chronic 1000 M_U133A_103_DLPFC human caudate nucleus Source GEO sample is GSM86854 Last updated (according to GEO): Feb 08 2006 38 12 of congenital heart disease Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11565 Last updated (according to GEO): May 28 2005 brain_OFC_bipolar B_mr89 106 77 of epithelial ovarian cancers Coronary Arteriosclerosis 1000 the blood 393 402 Gene expression data from postmorten brain regions Source GEO sample is GSM145254 Last updated (according to GEO): Nov 20 2006 Neoplasm 1000 Parkinson Disease 861 918 910 ischemia DLCL-0032 H124 FC BA4 A CNS-SC_CtrB7d-1B-s2 Malignant neoplasm of prostate 901 Epithelial Cells 901 861 Breast Head and neck cancer Source GEO sample is GSM155727 Last updated (according to GEO): Apr 24 2007 osteoblast 627 637 M_U133A_3_DLPFC Female infertility 1000 Prostate 861 306-99_node the mammalian forebrain 50 72 901 Coronary artery 861 Rett Syndrome A/J Basal Ganglia D Arteries 861 Parkinson Disease 861 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2780 Source GEO sample is GSM2099 Last updated (according to GEO): Nov 21 2005 112 98 from the kidney cin_NY50 AD-AD4T1-A386-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Interatrial septum 865 Adenocarcinoma, Clear Cell 923 84 69 by heart failure 19 0 human frontal cortex Small Intestine; d1 small intestine Keywords = mouse gene expression database Source GEO sample is GSM29293 Last updated (according to GEO): May 27 2005 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211241 Last updated (according to GEO): Jul 18 2007 913 Dermatitis, Atopic Gene expression data from postmorten brain regions Source GEO sample is GSM146038 Last updated (according to GEO): Nov 20 2006 f2#221 versus pool Mouse Brain tissue total RNA from biosource CC#10S Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92486 Last updated (according to GEO): Jan 13 2006 trigeminal_ganglia_8 41 CB B 1000 Heart failure Lung 861 1000 Solid tumor brain 0 5 1829 1819 for livers 1000 Temporal Lobe 861 Nerve Breast 6 Normal Ischemia-reperfusion with AEOL 10150 #1 onto a collagen 72 86 CC243 Myocardial Infarction 1000 cy5:SHR control, biological rep 4r; cy3:pool of 6 WKY control rats 861 Cardiomyopathies Parkinson's disease sample x098 0 30 acute lymphoblastic leukemia 498 525 V5-P446 femur 6 10 Liver 1000 24h +TGF-beta odontoblasts 0 Human Cortex 11 Alzheimer's Disease 901 Prostate 8 Disease 0 17 2175 2157 of medulloblastoma 861 Brain Brain 861 861 medulloblastoma Spleen 1000 8h1 1000 Spleen human caudate nucleus Source GEO sample is GSM86891 Last updated (according to GEO): Feb 08 2006 Y SIT D071 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108641 Last updated (according to GEO): Aug 22 2006 of parieto-occipital cortex 118 144 of the atrial 647 659 GBM Treatment, type=remove Source GEO sample is GSM99482 Last updated (according to GEO): Apr 21 2006 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211341 Last updated (according to GEO): Jul 18 2007 1000 Brain 33 9 Polycystic ovary syndrome Neostriatum 1000 A39 WT7 F2/14 A39 wild type Mouse 10 months Cerebellum Male Source GEO sample is GSM73191 Last updated (according to GEO): Sep 06 2005 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195357 Last updated (according to GEO): Jun 04 2007 2045 2017 of adhering connective tissue 861 Cerebral cortex 1000 ovarian neoplasm 861 Cerebellum 1000 Coronary Arteriosclerosis SR-A mutant olfactory epithlium 16 hpO replicate3 Endometrium 2 Normal mouse brain ipsilateral RU486 Source GEO sample is GSM149776 Last updated (according to GEO): Mar 15 2007 OAC:_1A24 Spleen 1000 1000 Heart 1000 Coronary Arteriosclerosis Brain 1000 SCG_control_2h_rep2 858 Prostatic Neoplasms tumors 976 981 10 7 Left ovary 45 50 Organ 966 cerebellum_2 Source GEO sample is GSM80617 Last updated (according to GEO): Mar 31 2006 29 0 cerebral cortex wistar ky 3911 A498 hgu95a in oculomotor nuclei 618 637 Spleen vs 2-Methyl-thio-ATP Treated B cell 240min (set3) HapMap CEU_parent Female Source GEO sample is GSM159569 Last updated (according to GEO): Feb 01 2007 1000 Liver on the Y chromosome 678 696 Menstruation blood, primary E6 901 Coronary artery D_U133A_12_HC hippocampus_2 Source GEO sample is GSM80665 Last updated (according to GEO): Mar 31 2006 96 13 from fetal cerebrum Keywords = trisomy 13 Keywords = brain Keywords = Patau syndrome metanephric mesenchyme, NGAL, 1 day, biological rep1 Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22567 Last updated (according to GEO): May 27 2005 1302 1295 in brain 923 Optic Disk lateral hypothalamus no access to cocaine replicate 2 NINDS-RNP-SNC-4aA-s2 A2780_cis_IC75_16h_1 1000 Encephalitis Obesity 1000 5 0 Spleen Sample was obtained from a 46 years old male subject with congestive heart failure after LVAD support. Good quality sample. Keywords = Congestive heart failure, left ventricular assist device, eNOS, gene, dimethylarginine dimethylaminohydrolase Source GEO sample is GSM6552 Last updated (according to GEO): May 28 2005 Simple annotation: Normal tissue, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3496.gif Source GEO sample is GSM76466 Last updated (according to GEO): Sep 22 2006 Acute leukemia 913 Whole blood 0 10 913 Hereditary Malignant Neoplasm NoCAD_replicate46 861 Colon 1000 Prostate 1000 Dermatitis, Allergic Contact with myocardial infarction 313 339 867 Large-Cell Lymphomas atrial septal defects 198 218 1000 Cornea Infection 1000 D_U133A_30_HC Cerebral cortex 861 total RNA from biosource CC#41 Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92468 Last updated (according to GEO): Jan 13 2006 Category: Cell-line Subcategory: Pharmacogenomics This experiment was an out file converted from rana. The original files were not provided to load this experiment in Oracle. Category and Subcategories were made by curators. Scanning Software: unknown Software version: unknown Lot batch = dtp3676 Source GEO sample is GSM2152 Last updated (according to GEO): Nov 21 2005 Spleen 0 5 I_U133A_91_AnCg Epithelial Cells 901 Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 24h. Lot batch = Source GEO sample is GSM1239 Last updated (according to GEO): May 28 2005 32 21 from retinas Heart 1000 Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 2344 blood Parkinson Disease 1000 Pregnant females fed with maltose dextrin, PF06 (Pair Fed) corresponds to replicate 6 Haloperidol treated 12weeks AffyGC RMA rep4 Autistic Disorder 877 from the femurs 95 109 4089 4084 liver 38 10 from cultured organ of Corti 26 11 /Ovary-Disease 4 13 0 Nervous System Mental Retardation 1000 Neostriatum 861 (cortex 19 25 Primary Neoplasm 1000 40 21 from skeletal muscle heart 1169 1173 1000 Spleen Whole blood from a patient with progressive supranuclear palsy Source GEO sample is GSM153507 Last updated (according to GEO): Jan 11 2007 Primary Neoplasm 1000 1000 Brain CVB3_S-9h-3 Expression profiling of spinal cord section (T10) extracted from rats 24h following laminectomy (sham) Lot batch = Source GEO sample is GSM4435 Last updated (according to GEO): May 28 2005 aggressive tumors 1117 1134 the heart 987 996 in fibroblasts 1222 1236 corpus_callosum_7 Source GEO sample is GSM80644 Last updated (according to GEO): Mar 31 2006 Cerebral cortex 1000 1000 Retina Spleen vs Untreated B cell 60min (set3) 31 0 Cerebellum Alzheimer's disease 7 901 Coronary artery seminoma specimen, pT2, patient age: 34y; W03 031 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3331 Last updated (according to GEO): Mar 21 2006 PGA-MurLungRag-rwp-72h-1aBv2-s2 136 131 Aortae Gene expression data from postmorten brain regions Source GEO sample is GSM145017 Last updated (according to GEO): Nov 20 2006 1861 1832 such as fetal alcohol syndrome 19 0 human frontal cortex ISR15-Fv2E-PERK AP20187 4hr1 RNA from an 2nm AP20187 treated (4hr) Fv2E-PERK expressing mouse fibroblast cell line in an eIF2 alpha SS (wildtype), PERK-/- background. AP20187 activates the kinase activity of the Fv2E-PERK chimera. The PERK-/- background was used in order to obtain a cell line that expressed high levels of the Fv2E-PERK transgene. (We were unable to obtain clones with high levels of expression in wildtype cells.) The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules. Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10898 Last updated (according to GEO): May 28 2005 prostate Source GEO sample is GSM203280 Last updated (according to GEO): Jun 21 2007 Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2675.gif Source GEO sample is GSM72172 Last updated (according to GEO): Sep 22 2006 78 73 rectum 19 0 Head and neck cancer Spinal Cord 1000 striatum 33 41 olfactory epithelium tissue 85 111 Neoplasm 861 Expression profiling of spinal cord section (T9) extracted from rats 21d following moderate injury Source GEO sample is GSM31527 Last updated (according to GEO): May 27 2005 865 Disorder of artery Organ 966 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114178 Last updated (according to GEO): Jun 16 2006 brain, frontal cortex: Sample55_e1_le1 488_7d Vestibular organ 0 15 1000 Liver B_AK_SleepDep_ZT 6_3 P1_KIDNEY_4 NAP-105 on UMich-10k 861 Encephalitis [prefrontal cortex 813 831 Gene expression data from postmorten brain regions Source GEO sample is GSM144922 Last updated (according to GEO): Nov 20 2006 Tolerizing allografts 70 days No.2 C57BL/6J bed nucleus of the stria terminalis rep2 (430 2.0 Array) ER+/LN+/Nevins13 on Affymetrix GeneChip Human Full Length Array HuGeneFL GM07029_technical_rep_2 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16709.gif Source GEO sample is GSM91597 Last updated (according to GEO): Sep 22 2006 Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3877 Last updated (according to GEO): May 27 2005 435_1 1000 Hypothalamic structure 901 Heart failure AK_SleepDep_ZT 12_1 3AJZ02022107_ spinal cord 5 0 Spleen Myocardium 861 Disorder of artery 865 Autistic Disorder 877 Nothing in line. Source GEO sample is GSM154236 Last updated (according to GEO): Jul 05 2007 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225963 Last updated (according to GEO): Nov 02 2007 30 0 ventral tegmental area sprague2 acute myeloid leukemia Source GEO sample is GSM227438 Last updated (according to GEO): Sep 12 2007 Plasma 861 Cerebral cortex 861 Neoplasm 861 Molecular classification of familial non-BRCA1/BRCA2 breast cancer. Primary small cell lung carcinoma 8526 1BJZ02022104_leukemiapromyelocytic(hl60) f2#52 versus pool Mouse Brain tissue Cochlear nucleus structure 901 154 147 in lung 901 Spinal Cord 5 0 Testis 12 0 ovarian tumor 334 320 Keywords = HIV M_U133Plus_70_HC HCC (HBV+, HK43) 1000 Brain Stem Normal Skeletal Muscle jzo031-rp1-v5_u74av2-met Bronchoalveolar lavage samples collected from lung transplant recipients. Numeric portion of sample name is an arbitrary patient ID and AxBx number indicates the perivascular (A) and bronchiolar (B) scores from biopsies collected on the same day as the BAL fluid was collected. Several patients have more than one sample in this series and can be determined by patient number followed by a lower case letter. Acute rejection state is determined by the combined A and B score - specifically, a combined AB score of 2 or greater is considered an acute rejection.. Control 1 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 2 - Pair 2 - MMN Source GEO sample is GSM49878 Last updated (according to GEO): Dec 20 2005 329 306 valvular cardiomyopathy Gene expression data from human colon tumor tissue Source GEO sample is GSM173323 Last updated (according to GEO): Apr 20 2007 CNS-SC_InjB30m-2A-s2 brain 0 5 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11498 Last updated (according to GEO): May 28 2005 The rod photoreceptor-specific neural retina leucine zipper protein Nrl is essential for rod differentiation and plays a critical role in regulating gene expression. In the mouse retina, rods account for 97% of the photoreceptors; however, in the absence of Nrl (Nrl-/-), no rods are present and a concomitant increase in cones is observed. A functional all-cone mouse retina represents a unique opportunity to investigate, at the molecular level, differences between the two photoreceptor subtypes. Using mouse GeneChips (Affymetrix), we have generated expression profiles of the wild-type and Nrl-/- retina at three time-points representing distinct stages of photoreceptor differentiation. Comparative data analysis revealed 161 differentially expressed genes; of which, 78 exhibited significantly lower and 83 higher expression in the Nrl-/- retina. Hierarchical clustering was utilized to predict the function of these genes in a temporal context. The differentially expressed genes primarily encode proteins associated with signal transduction, transcriptional regulation, intracellular transport and other processes, which likely correspond to differences between rods and cones and/or retinal remodeling in the absence of rods. A significant number of these genes may serve as candidates for diseases involving rod or cone dysfunction. Chromatin immunoprecipitation assay showed that in addition to the rod phototransduction genes, Nrl might modulate the promoters of many functionally diverse genes in vivo. Our studies provide molecular insights into differences between rod and cone function, yield interesting candidates for retinal diseases and assist in identifying transcriptional regulatory targets of Nrl. Lymphoblastoid Cell Line for Individual 8025.4 log phase GSE1782 55 29 Undifferentiated bone tumor of IR-induced DNA damage 872 896 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225949 Last updated (according to GEO): Nov 02 2007 collagen 303 311 N06__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Spleen 0 5 114 101 brains quickly gene expression data from melanoma xenografts following ILI with melphalan Source GEO sample is GSM213640 Last updated (according to GEO): Jul 27 2007 1000 Hippocampus 861 Blood Ganglia 1000 Wild type 8 wk old male C57BL/6J mouse hippocampus Source GEO sample is GSM74959 Last updated (according to GEO): Feb 27 2007 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188785 Last updated (according to GEO): Jun 06 2007 Y YOKE D059 prostate Source GEO sample is GSM203327 Last updated (according to GEO): Jun 21 2007 875 Blood Cells from colorectal adenoma 21 44 Trauma 1000 Laser capture lung cancer cells Source GEO sample is GSM190993 Last updated (according to GEO): May 25 2007 MDA Mb231 6h + 10 nM Cxcl12 1 Treated M_U133A_21_CB T-ALL-#1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28754 Last updated (according to GEO): May 27 2005 Disease Source GEO sample is GSM176227 Last updated (according to GEO): Apr 09 2007 HMEC X HMEC -EGF for 2days RNA samples extracted from astrocytes cultured from wild type and Cx43 null neonatal mice were dye labeled and individually co-hybridized with a reference of labeled cDNAs pooled from a variety of tissues on eight gene arrays containing 8975 mouse DNA sequences. Date GSE580 Last Updated: May 29 2005 Contributers: Dumitru A Iacobas Sanda Iacobas David C Spray Eliana Scemes Marcia Urban-Maldonado Includes GDS455. Update date: Nov 19 2003. Dataset description GDS455: Analysis of cultured cortical astrocytes isolated from neonatal wild type and connexin-43 (Cx43) knockout mice. Results imply that gap junction gene expression alters numerous processes in addition to intercellular communication.. This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12351 Last updated (according to GEO): May 28 2005 of the postmortem brains 676 700 I_U133A_37_DLPFC CON(DR)(3) 46 8 in docetaxel-refractory prostate cancer Brain 1000 5 0 brain Expression profiling of spinal cord section (T9) extracted from rats 7d following laminectomy (sham) Lot batch = Source GEO sample is GSM1335 Last updated (according to GEO): May 28 2005 14 7 amygdala ER negative human primary breast tumor EA02014_41277_H133A_JA-1593 cerebellum wistar 3889 whole tissue, individual animal, 10 weeks old, male Wistar cerebellum file:p3889w Source GEO sample is GSM15132 Last updated (according to GEO): Oct 28 2005 Atypical antipsychotic Clozapine has a superior antipsychotic and antimanic effects compared to other antisphicotics. Its widespread use was limited by the side effects of agranulocytosis, cardiomyopathy and metabolic anomalies such as weight gain, and diabetes. Very little is known about mechanisms by which Clozapine works. The aim of this experiment is to compare the chronic gene expression profile of the atypical antipsychotic Clozapine to the typical antipsychotic drug Haloperidol using gene expression Microarray in order to understand the intercellular mechanism behind the therapeutic and the toxic effects of Clozapine. Last Updated (by provider): Dec 12 2006 Contributers: Mie A Rizig Hugh M Gurling CT26-1 456_1 CAD_replicate2 Medulla 861 39 21 from mammary glands DLBC37 on Affymetrix GeneChip Human Full Length Array HuGeneFL stria terminalis 901 Skeletal bone 861 Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22559 Last updated (according to GEO): May 27 2005 36 21 from hippocampus 1000 Prostate HCC (HBV+, HK63, T1) 129S1-SvImJ_male_hypothalamus 901 Temporal Lobe Liver 1000 1000 Spleen processed in batch 7 Source GEO sample is GSM90426 Last updated (according to GEO): Mar 20 2006 5 0 brain Expression profiling of moderately injured raphe at 14d in rats Source GEO sample is GSM41570 Last updated (according to GEO): May 27 2005 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114225 Last updated (according to GEO): Jun 16 2006 11_0019_Control_Day1_38 f2#165 versus pool Mouse Brain tissue prostate Source GEO sample is GSM203321 Last updated (according to GEO): Jun 21 2007 1000 Brain Neoplasms GM10851_technical_rep_1 861 Cancer of Neck Schizophrenia 1000 WGACON-70 Mesenchymal Stem Cells 1000 brain, cerebral cortex: NMDA10 7/8_le1 Olfactory epithelium 0 19 Mesenchymal Stem Cells 1000 288 275 hyperglycemia Large-scale analysis of the mouse transcriptome. Digits C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 286.06 Stdv: 8.56 Min: 274.79 Max: 300.96 Source GEO sample is GSM2982 Last updated (according to GEO): Mar 20 2006 Osteoblasts 1000 VDXRHU_5228 of underlying brain 174 193 Transplant Series 10 , Transplant # 3 Expression profiling of medulloblastoma: PDGFRA and the RAS/MAPK pathway as therapeutic targets for metastatic disease. /3T3 fibroblasts 295 310 Gene expression data from postmorten brain regions Source GEO sample is GSM145960 Last updated (according to GEO): Nov 20 2006 1829 1819 for livers EOM 28 Day mdx rep 2 Delineation of prognostic biomarkers in prostate cancer. 100319 Brain 1000 PGA-MPF-BALB-bleo-14d-1bAv2-s2 228 219 Hippocampi Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181222 Last updated (according to GEO): Jul 12 2007 Intestines, Small 1000 Fibroblasts 861 Chronic leukemia NOS 913 865 Disorder of artery Job's patient Source GEO sample is GSM211151 Last updated (according to GEO): Sep 10 2007 Brain 861 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=1 (Non-acute rejection). One of three samples from the same patient, different visits. Source GEO sample is GSM36455 Last updated (according to GEO): May 27 2005 Gene expression data from mouse colon Source GEO sample is GSM198110 Last updated (according to GEO): Aug 22 2007 36 21 from whole brain 1000 Rectum D_U133Plus_16_DLPFC Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for four weeks. Source GEO sample is GSM149806 Last updated (according to GEO): Dec 12 2006 23 11 of the kidney mouse brain 478 489 1000 Amyotrophic Lateral Sclerosis Lymphoblastoid Cell Line for Individual 8106.4 log phase cells stimulated with lipoprotein prep 2, biological rep3 Bic/4AP/Nif 42 30 Control blood 1513 1486 central innate immune system Primary tumor 19 32 Adenocarcinoma 10 0 16 1000 Cerebral cortex total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Neuropeptide Y for 120min Source GEO sample is GSM5716 Last updated (according to GEO): May 27 2005 GSE776 1000 Obesity this sample is from a 16-week-old male normal mouse gastrocnemius muscle Source GEO sample is GSM4375 Last updated (according to GEO): May 28 2005 1000 Cerebellum Epithelium of bronchus 983 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188727 Last updated (according to GEO): Jun 06 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM146008 Last updated (according to GEO): Nov 20 2006 8-cell embryo replication 3 Neoplasm 861 Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. 1000 Brain 2-cell embryo replication 3 Heart 861 Adenocarcinoma 861 Prostaglandin J2 alters pro-survival and pro-death gene expression patterns and 26 S proteasome assembly in human neuroblastoma cells. 1000 Spleen brain_Down_syndrome_sampleid_jg1740 HIGK cells infected with Streptococcus gordonii, biological rep2 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92341 Last updated (according to GEO): Jan 13 2006 Cerebellum 1000 nostrils 156 164 liver, wild type mice, control conditions Source GEO sample is GSM205767 Last updated (according to GEO): Jul 24 2007 brain, cerebral cortex: Sham14_e1_le1 Control VZ13 of the brain primarily 506 527 Gene expression data from postmorten brain regions Source GEO sample is GSM145144 Last updated (according to GEO): Nov 20 2006 337 324 from 6 brains Simple annotation: Normal tissue, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3502.gif Source GEO sample is GSM76426 Last updated (according to GEO): Sep 22 2006 GSE1837 9 0 Blood Test cells stimulated with lipoprotein prep 3, biological rep3 77 62 of non-cartilage Ventral tegmental area 28 50 Epithelium 861 CNS-SMTC_Mod7d-3C-s2 bronchial epithelia 224 243 Brain 861 Cerebrovascular accident 1000 CD3 beads 00.00 hr. T-Cell 861 Blood 901 Cerebral cortex 901 frontal lobe total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Prostaglandin E2 for 240min Source GEO sample is GSM5742 Last updated (according to GEO): May 27 2005 67 40 with coronary artery disease vehicle treatment, 1 hour time point, biological replicate 2 ovary 45 50 Primary Neoplasm 884 Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. Source GEO sample is GSM112310 Last updated (according to GEO): Jun 06 2006 PriG_Expt1_Day0_rep1 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Insulin-like growth factor 1 for 120min Source GEO sample is GSM5621 Last updated (according to GEO): May 27 2005 861 Heart failure Stom Mucos Keywords = mouse gene expression database Source GEO sample is GSM39100 Last updated (according to GEO): May 27 2005 Bone marrow, Mesenchymal stem cells: T4-2-101103_e1_le1 Pre Natal CCAM 3 HapMap CEU_parent Male Source GEO sample is GSM159544 Last updated (according to GEO): Feb 01 2007 Spleen 0 5 PMN_control_180min_Patient13 SNB-75 hgu95b 861 Muscle no additional Source GEO sample is GSM199195 Last updated (according to GEO): Jun 08 2007 901 Coronary artery beta-thymosin 706 719 1000 Nervous system structure I_U133A_41_AnCg Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92332 Last updated (according to GEO): Jan 13 2006 Examination of gene expression profiles from liver of C57BL/6 mice and LDL receptor deficient mice fed on either a low fat diet or a high fat Western-style diet for 12 weeks. Three replicates of each condition analyzed.. Date GSE363 Last Updated: May 29 2005 Contributers: Adrian Recinos Allan Brasier Includes GDS279. Update date: Dec 08 2003. Dataset description GDS279: Examination of gene expression profiles from liver of C57BL/6 wild type mice and LDL receptor deficient mice fed on either a low fat diet or a high fat, western-style diet for 12 weeks.. Simple annotation: Drug_treatment, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8764.gif Source GEO sample is GSM78474 Last updated (according to GEO): Sep 22 2006 Superior_Cervical_Ganglion Source GEO sample is GSM19011 Last updated (according to GEO): Sep 25 2006 91 from the bone marrow 72 Disease Source GEO sample is GSM176450 Last updated (according to GEO): Apr 09 2007 adenocarcinoma 3216 861 Occipital lobe 901 frontal lobe Olfactory Epithelium 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28707 Last updated (according to GEO): May 27 2005 WGACON-22 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15397.gif Source GEO sample is GSM84179 Last updated (according to GEO): Sep 22 2006 101038 Myocardial Infarction 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145173 Last updated (according to GEO): Nov 20 2006 Skin 1000 M_U133A_20_HC Prosencephalon 1000 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25637.gif Source GEO sample is GSM81562 Last updated (according to GEO): Sep 22 2006 "20h Thy-Noc, Exp4" Fi9_3, mouse, FVB, infected, 9 days post infection_rep 3 Craniocerebral Trauma 861 HapMap CHB Male Source GEO sample is GSM159603 Last updated (according to GEO): Feb 01 2007 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153408 Last updated (according to GEO): Jan 11 2007 865 Disorder of artery ALS model Source GEO sample is GSM75505 Last updated (according to GEO): Mar 06 2006 Gap junction and purinergic P2 receptor proteins as a functional unit: insights from transcriptomics 861 Muscle 1 CN A B262 on Affymetrix GeneChip Human Full Length Array HuGeneFL human caudate nucleus Source GEO sample is GSM86835 Last updated (according to GEO): Feb 08 2006 experimental autoimmune encephalomyelitis 38 78 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114485 Last updated (according to GEO): Jun 16 2006 Gene expression data from a primary branch of the saphenous artery of 16 week old male Wistar-Kyoto rats Source GEO sample is GSM198857 Last updated (according to GEO): Nov 28 2007 K562_I_CL7005_Leukemia on Affymetrix GeneChip Human Full Length Array HuGeneFL peripheral blood-CD8TCells Source GEO sample is GSM18720 Last updated (according to GEO): Sep 25 2006 UO-31_CL9004__RENAL Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153438 Last updated (according to GEO): Jan 11 2007 7 cortex 12 Wild type inbred mice Source GEO sample is GSM82979 Last updated (according to GEO): Nov 10 2005 78 66 Control blood T40__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A GSE6791 715 705 from livers brain 0 5 frontal lobe 1000 GSE6453 Gene expression data from postmorten brain regions Source GEO sample is GSM145744 Last updated (according to GEO): Nov 20 2006 5 0 Spleen Blood 1000 HNC004 A HID I D050 aa_NY224 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9969.gif Source GEO sample is GSM79810 Last updated (according to GEO): Sep 22 2006 Lymph Nodes 2 Normal CNS-SpinalCmod-Adult-4h-1A-s2 leukemia 861 Ok2: Hippocampus_NT-A_rep7 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225730 Last updated (according to GEO): Nov 02 2007 16 7 cerebellum 913 Coronary heart disease R435P00262 SCLC cell line Source GEO sample is GSM17195 Last updated (according to GEO): May 28 2005 1000 Decapitation Macrophage smi58 R563P00723 Wild type hippocampus region Source GEO sample is GSM88935 Last updated (according to GEO): Jan 04 2006 901 Coronary artery Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92285 Last updated (according to GEO): Jan 13 2006 M_U133Plus_126_DLPFC nasal epithelial cells 28 49 HCC (HBV+, HK67, T3) Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181971 Last updated (according to GEO): Apr 13 2007 Cerebellum_naive_ILS51 Pancreas at e15.5, Chip C, rep 1 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184790 Last updated (according to GEO): Apr 26 2007 HCT-15 hgu95a 861 Heart Diseases Whole Brain 62 72 861 Ribosomal RNA 1000 Integumentary system from the femurs 95 109 21 0 Mammary Gland @ Preg7 861 Neoplasm M_U133Plus_108_nAcc Exp A_5, 10mg/kg CPF Oat cell carcinoma 867 D_U133A_85_DLPFC G8 optic nerve n/a Source GEO sample is GSM177909 Last updated (according to GEO): Jun 11 2007 Day 1_L_-LIF_Achip days nasal epithelium 1126 1147 861 Anterior 861 Brain M_U133Plus_123_CB Primary large cell carcinoma 4319 0 32 861 Brain Primary tumor 19 32 8 hr vehicle repl 1 Cerebral cortex 1000 Gene expression data from PD14 Foxo3 wild-type ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203833 Last updated (according to GEO): Aug 02 2007 24h +TGF-beta pulp tissu Brain 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM146018 Last updated (according to GEO): Nov 20 2006 861 Acquired Immunodeficiency Syndrome 1000 Rectum Gene expression data from purified granule neuron precursors. Source GEO sample is GSM148574 Last updated (according to GEO): Mar 14 2007 Replicate2_Voxel B3 BXD 14_M7SS02080621 N53__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A HapMap YRI_parent Female Source GEO sample is GSM159678 Last updated (according to GEO): Feb 01 2007 Acetaminophen 3hr Rat 8030 blood vs. Acetaminophen 3hr Rat Pooled Control blood 583 563 to other chromosomes whole brain from wild-type littermate of nicotinic acetylcholine receptor subunit mutant mice Source GEO sample is GSM120579 Last updated (according to GEO): Sep 22 2006 Wild type P46 (dark reared to P42) mouse visual cortex contralateral to monocular enucleation Source GEO sample is GSM97226 Last updated (according to GEO): Feb 17 2006 Spinal Cord 1000 5 0 brain Small cell carcinoma of lung 867 861 Cerebellum Lda3 Skeletal muscle structure 1000 Cardiac-specific TNF-alpha transgenic mouse is an excellent model to study the pathologenesis of heart failure. Affytrix U74V2A was used to analyzed the gene expression profile of mice at the time point of compensated hypertrophy and dilated heart failure. Source GEO sample is GSM8993 Last updated (according to GEO): May 28 2005 Semeralul_PFC_Development_Week10_Batch1_Animal_6 (cortex 19 25 Prostate 861 mouse cerebral cortex 0 20 the heart 987 996 26 15 endometrioid Brain 861 1000 Pontine structure NHF3-hTERT_G0_C5_26551 Medulla Oblongata 861 24 0 human prostate PC3 tumors brain, cerebellum: 3 hrs C GW_e1_le1 Large-scale analysis of the human transcriptome. Thyroid Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 123.40 Stdv: 4.93 Min: 115.06 Max: 130.09 Source GEO sample is GSM2848 Last updated (according to GEO): Mar 20 2006 249 224 peripheral blood stem cell cirrhotic liver 630 645 1000 Eye Expression profiling of spinal cord section (T9) extracted from rats 24h following laminectomy (sham) Lot batch = Source GEO sample is GSM4479 Last updated (according to GEO): May 28 2005 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50641.gif Developmental Stage: E7.75 Source GEO sample is GSM229809 Last updated (according to GEO): Nov 06 2007 963 940 medulloblastomas arising f2#290 versus pool Mouse Brain tissue brain 0 5 Bone Marrow 1000 Liver (HBV+, HK17) 1000 Structure of trigeminal ganglion 152 117 Keywords = congenital heart disease Normal human tissue:Normal Salivary Gland Keywords = Human, Normal Tissue, Normal Salivary Gland Source GEO sample is GSM44687 Last updated (according to GEO): May 27 2005 Acetaminophen 6hr Rat 9476 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool Primary Neoplasm 1000 hind Source GEO sample is GSM67219 Last updated (according to GEO): Jan 19 2006 Nasal Epithelium Inhalation Formaldehyde 2ppm 8d ID220 Heart 1000 861 Spinal Cord Exposure to high levels of arsenic in drinking water is associated with several types of cancers including lung, bladder and skin, as well as vascular disease and diabetes. Drinking water standards are based primarily on epidemiology and extrapolation from higher dose experiments, rather than measurements of phenotypic changes associated with chronic exposure to levels of arsenic similar to the current standard of 10ppb, and little is known about the difference between arsenic in food as opposed to arsenic in water. Measurement of phenotypic changes at low doses may be confounded by the effect of laboratory diet, in part because of trace amounts of arsenic in standard laboratory chows, but also because of broad metabolic changes in response to the chow itself. Finally, this series contrasts 8hr, 1mg/kg injected arsenic with the various chronic exposures, and also contrasts the acute effects of arsenic, dexamethasone or their combination. Male C57BL/6 mice were fed on two commercially available laboratory diets (LRD-5001 and AIN-76A) were chronically exposed, through drinking water or food, to environmentally relevant concentrations of sodium arsenite, or acutely exposed to dexamethasone. Last Updated (by provider): Nov 16 2007 Contributers: Michael A Ihnat Joshua W Hamilton Spleen vs ELC Treated B cell 240min (set2) Mucous Membrane 861 DLBC23 on Affymetrix GeneChip Human Full Length Array HuGeneFL human cerebellum Source GEO sample is GSM87096 Last updated (according to GEO): Feb 08 2006 A HID B D012 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108580 Last updated (according to GEO): Aug 22 2006 GSE1148 Creatine-treated, biological rep6 78 66 Control blood from mouse colon 21 36 Macrophage 14smi076 861 Occipital lobe 20 0 hypothalamus sprague1 Epithelial Cells 901 cerebral cortex 7 21 of Parkinson's disease 450 471 803 780 of autoimmune antibodies GC (HKG49L) 3_cerebral_cortex_3hrs_sleep_#58 infection 433 442 human frontal cortex Source GEO sample is GSM87054 Last updated (according to GEO): Feb 08 2006 901 Caudate nucleus structure 5 0 brain VDXRHU_2320 KT80_AR1 858 Mesodermal cell Spleen vs CGS Treated B cell 30min (set1) 861 Prostate occipital_lobe_8 Source GEO sample is GSM80766 Last updated (according to GEO): Mar 31 2006 861 Brain ventral_tegmental_area_4 Source GEO sample is GSM80873 Last updated (according to GEO): Mar 31 2006 6,18,30 month oculomotor nucleus and spinal cord Source GEO sample is GSM74349 Last updated (according to GEO): Sep 16 2005 Colon 1000 861 Cancer of Neck Male 69.2 yr after antibody enrichment scan 2 (U133B) Tumor__Bladder_TCC_11520 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A NCI60.42_LABEL46EXTRACT45SUB3 Source GEO sample is GSM134207 Last updated (according to GEO): Aug 06 2007 prostate Source GEO sample is GSM203312 Last updated (according to GEO): Jun 21 2007 Liver 1000 liver 0 5 NA12892 PGA-MurLungRag-pbs-24h-1bCv2-s2 AMM_0_0_Female6_Olfact_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111855 Last updated (according to GEO): Nov 21 2006 570 554 from sporadic ALS 1000 Hippocampus brain, unknown: 5634-99_e1_le1 M_U133Plus_38_CB Sample details: Three pools of rostral (R1-3), three pools of middle (M1-3), and three pools of caudal (C1-3) E13.5 MF1 neocortex were collected from 4 embryos. All possible 18 comparisons were carried out. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. Source GEO sample is GSM62829 Last updated (according to GEO): Aug 26 2005 Two 90 minute exposures (3 hr recovery in between) to 1.0% isoflurane every day for 2.5 days, for a total of 5 exposures Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5118 Last updated (according to GEO): Mar 17 2006 Soleus muscle structure 901 Melanoma xenograft, MA2_Sub_B (LeiATCC) Large Pre-BII cells 9b Bladder sample 1264-1 of the stria terminalis 49 71 amygdala short access to cocaine replicate 2 SN:1030148 Source GEO sample is GSM115420 Last updated (according to GEO): Jun 20 2006 50 Cortex C57BL 61 none Source GEO sample is GSM239874 Last updated (according to GEO): Dec 07 2007 tongue_main_corpus_2 Source GEO sample is GSM80844 Last updated (according to GEO): Mar 31 2006 Primary tumor 19 32 1000 Heart failure HapMap JPT Male Source GEO sample is GSM159636 Last updated (according to GEO): Feb 01 2007 861 Brain Fertilized egg replication 1 Wild type voxel F4 Wild type voxel H3 Neural tube, treated, GD9:00, T215571 entorhinal cortex layer II stellate island cells Source GEO sample is GSM107528 Last updated (according to GEO): May 01 2006 Arteries 861 G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Source GEO sample is GSM9646 Last updated (according to GEO): May 28 2005 Wild type inbred mice Source GEO sample is GSM82939 Last updated (according to GEO): Nov 10 2005 UBOC1 Exp A Day 9 (a) 5 0 brain 84 69 by heart failure Gastrin-CCK double Knockout fundic RNA Source GEO sample is GSM108492 Last updated (according to GEO): May 03 2007 36 21 from whole brain 6625_Lung developed PGD 5 0 Spleen 901 Mammary gland Gene expression data from postmorten brain regions Source GEO sample is GSM145370 Last updated (according to GEO): Nov 20 2006 430A2_2045_77_control_neuropath_medulla Source GEO sample is GSM242704 Last updated (according to GEO): Nov 15 2007 "22h Thy-Noc, Exp4" 861 Neoplasm Skeletal muscle structure 901 1hr post 10Gy IR 239 202 of the peripheral innate immune system 144 114 from a single adult spinal cord of parieto-occipital cortex 117 143 ovarian tumor: endometrioid Source GEO sample is GSM139395 Last updated (according to GEO): Apr 09 2007 ER-/LN+/Marks216 on Affymetrix GeneChip Human Full Length Array HuGeneFL /NJ pituitary gland rep1 3 26 1000 Brain Brain 861 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=790650 LaserPower=1.881.33 Lot batch = LC17N063 Source GEO sample is GSM4802 Last updated (according to GEO): Nov 21 2005 Balb/c day 1, biological rep 4, tech rep 1 Cerebral cortex 861 parietal_lobe_7 ovarian tumor: endometrioid Source GEO sample is GSM139408 Last updated (according to GEO): Apr 09 2007 organs 28 33 Neoplasm 861 9 CN B 23 6 (postcentral gyrus 1037 of transitional epithelium 1012 human frontal cortex Source GEO sample is GSM86989 Last updated (according to GEO): Feb 08 2006 Osteoblasts 1000 Pool of 12 non-inner ear tissue samples at E9.5; 6 at E10; 6 at E10.5 Source GEO sample is GSM182625 Last updated (according to GEO): Aug 14 2007 901 Myeloid Leukemia brain, cerebral cortex: Rat_03-50_NroLep_Lipska_e1_le1 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11569 Last updated (according to GEO): May 28 2005 B6:17-7,8,9 superior colliculi 0 Human Cortex 11 M_U133A_30_nAcc Mouse Liver Female 2 (technical replicate) Parkinson Disease 861 Gene expression data from the neocortex of S1P2-knockout mouse Source GEO sample is GSM172945 Last updated (according to GEO): Mar 08 2007 MuscleRegen-ctx4d-8RLA-s2 1000 Coronary Arteriosclerosis Duoden22VAFBA_066.txt D_U133A_75_DLPFC JMR-MurInj4h-2aAv2-s2 Ovary 50 55 1000 Amygdaloid structure Lung; Fetal Day 13.5 Keywords = mouse gene expression database Source GEO sample is GSM29386 Last updated (according to GEO): May 27 2005 NA12739 growth 2 CNS-SC_InjA30m-4A-s2 Normal Source GEO sample is GSM176207 Last updated (according to GEO): Apr 09 2007 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225917 Last updated (according to GEO): Nov 02 2007 brain, cerebral cortex: 9150_e3_le1 Normal Source GEO sample is GSM176154 Last updated (according to GEO): Apr 09 2007 Plasma 861 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225956 Last updated (according to GEO): Nov 02 2007 autism 0 5 of somatomotor cortex 21 41 M_U133A_37_DLPFC 858 Mesodermal cell GBM: 52A28 folatedeficientAs1ppm1 Clone 3.3 chip 3 Simple annotation: Cell-cycle, Mitotic selection Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16452.gif Source GEO sample is GSM79710 Last updated (according to GEO): Sep 22 2006 20 0 human caudate nucleus 354 Epithelial cells 369 MCF7 cells were treated with DMSO or 100 nM Dioxin for 16 hr. Gene expression changes were quantified by microarray analyses. Last Updated (by provider): May 31 2007 Contributers: Oliver Hankinson Diana Yoon 4016 0b 861 Cancer of Neck plasma cells 50 61 Hippocampus 861 DLBC36 on Affymetrix GeneChip Human Full Length Array HuGeneFL MDA Mb231 + Cxcr4 + Sdf 3 Treated 23 0 large intestine sprague2 865 Disorder of artery 91 from the bone marrow 72 Gene expression data from postmorten brain regions Source GEO sample is GSM145019 Last updated (according to GEO): Nov 20 2006 CurrentSmoker 106 RIIIS/J_female_hypothalamus Source GEO sample is GSM138572 Last updated (according to GEO): Apr 18 2007 Mouse Liver AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate C CNS-SpinalCmod-Adult-4h-3C-s2 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184698 Last updated (according to GEO): Apr 26 2007 Nose 1000 Malignant Neoplasms 1000 Normal__Pancreas_OV_1 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 861 Malaria Primary Carcinoma 876 MammLac_022JACHV_053.txt 861 Cerebral cortex plasma cells 50 61 Epithelium 861 Neoplasm 861 861 HIV Infections R431P00183 H Fast Rep 1 Gene expression data from U0126 (20uM)-treated embryos at day 2.5. Source GEO sample is GSM176489 Last updated (according to GEO): Mar 19 2007 Heart 861 266 257 infection DIF 1, chip MOE430B brain 0 5 36 21 from whole brain Duchenne muscular dystrophy (DMD) patient?s skeletal muscle sample 9 healthy subject Source GEO sample is GSM211061 Last updated (according to GEO): Sep 10 2007 The nose 94 101 Brain_Rhab_4_AT/RT (Brain) on Affymetrix GeneChip Human Full Length Array HuGeneFL 10 week mutant spinal cord rep 2 7 cerebral cortex 21 Structure of horn of uterus 983 C57BL/6 benchmark dataset: Embryonic day 15.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25179 Last updated (according to GEO): May 27 2005 Neocortical and cerebellar astrocytes Mouse old brain w/ a-tocopherol aT-Br-5 BALB/cByJ Hippocampus B Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211346 Last updated (according to GEO): Jul 18 2007 brain, cerebral cortex: Nico + NMDA 8/23_le1 19 0 human frontal cortex Mouse ileum 0 10 1000 Cardiomyopathy, Alcoholic B6Hippocampus(2)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14967 Last updated (according to GEO): Oct 28 2005 Bone Marrow 1000 18 0 Experimental asthma 61 41 from postmortem brain 1000 Liver damage Neoplasm 1000 e14-6 from the femurs 95 109 AD-379t1-A116-3 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 7 cerebral cortex 21 Total RNA was extracted from umbilical subcutaneous adipose tissue from an individual affected with FCHL and exhibiting the USF1 susceptibility haplotype Source GEO sample is GSM9044 Last updated (according to GEO): May 28 2005 Job's patient Source GEO sample is GSM211092 Last updated (according to GEO): Sep 10 2007 901 Bone Marrow MLL-#5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A from colorectal adenoma 21 44 Gene expression data from purified granule neuron precursors. Source GEO sample is GSM148573 Last updated (according to GEO): Mar 14 2007 10 7 Left human caudate nucleus Source GEO sample is GSM86840 Last updated (according to GEO): Feb 08 2006 CNS-SMTC_Mod14d-3C-s2 no additional Source GEO sample is GSM199380 Last updated (according to GEO): Jun 08 2007 heart failure 583 595 Mouse Liver AIN Diet 8hr Saline Injection, biological replicate F AKR/J Olfactory Bulb E 40 17 mammary epithelial cells Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hrs per day, 24 h time point Source GEO sample is GSM159764 Last updated (according to GEO): Apr 23 2007 adenoma 861 C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P20 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25131 Last updated (according to GEO): May 27 2005 The epithelial cells 962 981 Brain 1000 Brain 861 DBA 11-2 WAT Gene expression data from postmorten brain regions Source GEO sample is GSM145547 Last updated (according to GEO): Nov 20 2006 (cortex 19 25 5 0 Spleen Spleen vs Insulin-like growth factor 1 Treated B cell 30min (set2) 3263 3253 in dementia comparison of olfactory-bulbectomized and sham-operated rats with depressive-like behaviour Source GEO sample is GSM247198 Last updated (according to GEO): Dec 11 2007 861 Oocytes 161 148 for metastases WGACON-124 Coronary Arteriosclerosis 1000 brain, unknown: 03CQ_e1_le1 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.4 Subject: 2978 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39045 Last updated (according to GEO): May 27 2005 healthy subject Source GEO sample is GSM211144 Last updated (according to GEO): Sep 10 2007 NoCAD_replicate49 cerebral cortex 7 21 913 Coronary heart disease Expression profiling of moderately injured raphe at 3 months in rats Source GEO sample is GSM41608 Last updated (according to GEO): May 27 2005 RNA obtained from vastus lateralis biopsies from 7 healthy men, 66-77 years old. RNA was pooled before cDNA synthesis. Analysis done with Affymetrix Microarray Suite 5.0 software. Keywords = muscle, aging Source GEO sample is GSM2400 Last updated (according to GEO): May 27 2005 the spinal cords 144 159 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118336 Last updated (according to GEO): Jul 11 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145529 Last updated (according to GEO): Nov 20 2006 Myocardial Infarction 1000 brain, Left Temporal Lobe: Extract44_le2 processed in batch 7 Source GEO sample is GSM90428 Last updated (according to GEO): Mar 20 2006 CNS-SpinalC-conAdult-7d-1B-s2b Immune; Spleen(C57) Keywords = mouse gene expression database Source GEO sample is GSM29356 Last updated (according to GEO): May 27 2005 esophagus_3 Source GEO sample is GSM80696 Last updated (according to GEO): Mar 31 2006 CNS-SC_CtrB24h-1B-s2 861 Neoplasm 1000 Cardiomyopathies This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12344 Last updated (according to GEO): May 28 2005 12 Temporal Lobe 24 861 Bone Marrow Cortex_Control_rep5 (06SE461) SMARD1 is an infantile autosomal recessive motor neuron (MN) disease, caused by mutations in the Immunoglobulin mu binding protein 2 (IGHMBP2). We investigated the potential of a spinal cord neural stem cell population isolated on the basis of aldehyde dehydrogenase activity (ALDH) to modify disease progression of nmd mice, an animal model of SMARD1. ALDHhiSSClo stem cells are self-renewing and multipotent and when intratechally transplanted in nmd mice generate motor neurons properly localized in the spinal cord ventral horns. Transplanted nmd animals presented delayed disease progression, sparing of motor neurons and ventral root axons and increased life-span. To further investigate the molecular events responsible for these differences, microarray and Real time RT-PCR analysis of wild-type, mutated and transplanted nmd spinal cord were undertaken. We demonstrated a down-regulation of genes involved in excitatory amino acid toxicity and oxidative stress handling, as well as an up-regulation of genes related to the chromatin organization in nmd compared to wild-type mice, suggesting that they may play a role in SMARD1 pathogenesis. Spinal cord of nmd transplanted mice expressed high transcript levels for genes related to neurogenesis such as Doublecortin (DCX), LIS1 and drebrin. The presence of DCX-expressing cells in adult nmd spinal cord suggests that both exogenous and endogenous neurogenesis may contribute to the observed nmd phenotype amelioration. Last Updated (by provider): Dec 21 2005 Contributers: Roberto Del Bo Andreina Bordoni Sabrina Salani Sandra Strazzer Stefania Corti Federica Locatelli Dimitra Papadimitriou Giacomo P Comi Nereo Bresolin Marco Crimi Chiara Donadoni Francesco Fortunato Giorgia Menozzi Includes GDS1468. Update date: Aug 23 2006. Dataset description GDS1468: Analysis of neuromuscular degeneration mutant (nmd) spinal cords transplanted with ALDHhiSSClo neural stem cells. nmd is a model for spinal muscular atrophy with respiratory distress type 1. Results provide insight into the mechanisms underlying neuromuscular improvements in stem cell recipients.. HCC (HBV+, HK85, T1) Aortic aneurysm without mention of rupture NOS 901 861 Malignant Glioma 1000 Left Normal Source GEO sample is GSM175868 Last updated (according to GEO): Apr 09 2007 Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002. Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Part of the medium chain triacylglycerol oil in control diet was replaced with: 1.1% fungal oil (providing 0.5 dietary wt% AA and 1.0en%). Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily. Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France). Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h. After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hippocampal gene expression analysis. From these same 5 mice, the hippocampus was dissected from the mice according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancourt, France), rinsed as described for livers, cut into 17-50 mg subsections, and frozen as described for livers. Hippocampal lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5). Hippocampal tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hippocampal RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips. Source GEO sample is GSM2560 Last updated (according to GEO): Mar 10 2006 ventral tegmental area sprague2 obtained with a 16 gauge punch from coronal brain slices from 5.0-6.3 mm posterior to bregma, pool of 5 animals, 16 weeks old, male Sprague Dawley ventral tegmental area file:R3KJF02012264 Source GEO sample is GSM15220 Last updated (according to GEO): May 28 2005 Plasma 861 Primary large cell neuroendocrine carcinoma 2144 0 47 G1E_30_C 5 0 brain BC208B-AF 901 GTP-Binding Proteins Occipital region 983 Cortex_Bulbectomized_rep2 A SIT D099 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108616 Last updated (according to GEO): Aug 22 2006 21 0 acute myeloid leukemia Mental Retardation 1000 1100 1087 heart failure Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188747 Last updated (according to GEO): Jun 06 2007 Brain (corpus callosum) [JunctionChip 1 of 5] 865 Disorder of artery Gene expression data from mouse primary visual cortex Source GEO sample is GSM101706 Last updated (according to GEO): Mar 27 2006 AD control Treatment, type=dissect Source GEO sample is GSM119618 Last updated (according to GEO): Jul 10 2006 Brain 861 Lymphoblastoid Cell Line for Individual 8010.4 log phase liver_PPARa-knockout_control_5d_rep2 in bronchial epithelia 311 332 1000 Brain I_U133A_56_AnCg "28 hr Hela Double Thymidine, exp3" 91 from the bone marrow 72 of familial Alzheimer's disease 58 89 brain, hippocampus: PR-DG-A25_e1_le1 CNS-SC_InjA14d-1A-s2 Epithelial Cells 861 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12373 Last updated (according to GEO): May 28 2005 CLL-15 of damaged fibers 1223 1239 in cervical cancer 2109 2127 436 416 Keywords = Alzheimer? Brain 861 brain, hippocampus: PH3_e1_le1 DMN-CtrHippo15d-2cAv2-s2 861 Alzheimer's Disease PC 6Hr rat 3586 blood vs. 1500mg/kg APAP 6Hr rat 3592 blood normal 1050 48 35 hair follicles Parkinson Disease 861 Timecourse of TLR2/1 stimulated human dendritic cells with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225878 Last updated (according to GEO): Aug 31 2007 NA19116 Ventral tegmental area 19 41 1000 Mammary gland 928 Endometrium Spleen 1000 Heart 1000 129S1-SvImJ_male_hypothalamus Source GEO sample is GSM138574 Last updated (according to GEO): Apr 18 2007 KPeterson-Met-20G110-s2 865 Gingival epithelium prostate Source GEO sample is GSM203334 Last updated (according to GEO): Jun 21 2007 trigeminal_ganglia_5 Source GEO sample is GSM80891 Last updated (according to GEO): Mar 31 2006 Prostate Gland BD Normal I_U133Plus_16_Amy Blood 1000 329 306 valvular cardiomyopathy beta-thalassemia 352 367 Primary Carcinoma 876 ND014 Pancreas at e12.5, Chip B, rep 1 17 7 hippocampus 343 adrenocorticotropic hormone 317 of coronary artery disease 317 342 spinal cord 21 31 Gene Expression Changes in Peripheral Blood Mononuclear Cells During Measles. Neural tube, treated, GD8:15, T216803 embryonic cortical neuron treated with NMDA Source GEO sample is GSM49560 Last updated (according to GEO): May 29 2005 Anterior nares 1000 1000 frontal lobe cingulate cortex 1000 Saccule structure 861 Gene expression data from epididymal fat tissues. Source GEO sample is GSM215573 Last updated (according to GEO): Aug 07 2007 1000 Colon 43 29 from the kidney Contusion - 35 Day Epicenter Rep1 10 7 left none Source GEO sample is GSM149649 Last updated (according to GEO): Jan 03 2007 CAD_replicate40 Ta gr2 tumour Source GEO sample is GSM2486 Last updated (according to GEO): May 27 2005 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153417 Last updated (according to GEO): Jan 11 2007 Tumor__Uterus_Adeno_5116 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A in the mammalian nervous system 110 141 M_U133A_56_nAcc no additional Source GEO sample is GSM199354 Last updated (according to GEO): Jun 08 2007 21h-Control replication 3 Keywords = preimplantation Keywords = development Source GEO sample is GSM14696 Last updated (according to GEO): May 28 2005 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211357 Last updated (according to GEO): Jul 18 2007 Liver 1000 1000 Neoplasm 861 Neuronal Ceroid-Lipofuscinosis Mice were a mixed background between 129/SvEv and C57BL/6. Rp1 knockout mice (Rp1-/-) and wildtype littermates examined. At P7, P10, P14, P18 and P21, mice were sacrificed and retinas removed. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm.. Date GSE128 Last Updated: Mar 28 2006 Contributers: Jian Zuo Wei Liu Cheng Cheng Jiewu Liu Kyeogmi Cheon Jason Higdon Qian Huang total RNA from biosource CC#31 Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92465 Last updated (according to GEO): Jan 13 2006 T21__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A mouse hippocampus from COX-2 heterozygous Source GEO sample is GSM121450 Last updated (according to GEO): Jan 31 2007 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181107 Last updated (according to GEO): Jul 12 2007 1000 Rectum Adipose tissue 884 Primary large cell neuroendocrine carcinoma 571 Source GEO sample is GSM17327 Last updated (according to GEO): May 28 2005 eye, retina: 2 Retina at ZT 6_e1_le1 seminoma specimen, pT1, pN1, patient age: 34y; W99 113 Nasal Epithelium 901 KT138_AR1 Ovary 1000 metanephric mesenchyme, ANX, 3 days, biological rep1 858 Mesodermal cell none Source GEO sample is GSM244538 Last updated (according to GEO): Nov 23 2007 01_0019_SepticShock_Day3_121 Epithelium of bronchus 983 84 69 by heart failure Parkinson 0 8 MF-16 Richard Almon-37-1133800609932 274 257 in ovarian cancers Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12411.gif Source GEO sample is GSM79854 Last updated (according to GEO): Sep 22 2006 this sample is from a 16-week-old male mdx mice gastrocnemius muscle Source GEO sample is GSM4381 Last updated (according to GEO): May 28 2005 36 21 from whole brain Primary Neoplasm 1000 with ALDHhiSSClo neural stem cells 155 189 outer medulla 31 43 861 Blood Plasma 861 861 Encephalitis E10.5 craniofacial tissue, first branchial arch: 5_6_MNA-3_e1_le1 Bmi1 Mel18 shRNA, biological rep1 Gene expression data from a placenta without malaria Source GEO sample is GSM183608 Last updated (according to GEO): Apr 23 2007 Feeder-independent ES cell line was grown using standard culture conditions. RNA was isolated using RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol. Data were normalized by AffyMetrix MAS5.0 using defaults. Keywords = embryonic stem cholesterol transport Source GEO sample is GSM9280 Last updated (according to GEO): May 27 2005 5 0 blood Gene expression data from colorectal adenoma. Source GEO sample is GSM215114 Last updated (according to GEO): Aug 02 2007 Retina 1000 with mental retardation 241 263 cingulate cortex 1000 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n107 Source GEO sample is GSM2050 Last updated (according to GEO): Nov 21 2005 1000 Cerebral cortex 861 Liver The Early Growth Response (Egr) family of transcription factors consists of 4 members (Egr1-4) that are expressed in a wide variety of cell types. A large body of evidence point to a role for Egr transcription factors in growth, survival, and differentiation. A major unanswered question is whether Egr transcription factors serve similar functions in diverse cell types by activating a common set of target genes. Signal transduction cascades in neurons and lymphocytes show striking parallels. Activation of either cell type activates the Ras-MAPK pathway and, in parallel, leads to increases in intracellular calcium stimulating the calcineurin-NFAT pathway. In both cell types, the strength of the activation signal affects the cellular outcomes and very strong stimuli lead to cell death. Notably both these pathways converge on the induction of Egr genes. We believe that downstream targets of Egr transcription factors in lymphocytes may also be activated by Egr factors in activated neurons. There is precedence for common target gene activation in these two cell types: apoptosis in both activated T cells and methamphetamine stimulated neurons occurs via FasL induction by NFAT transcription factors. We propose to use developing T lymphocytes (thymocytes) as a model system for discovery of Egr-dependent target genes for several reasons. First, we have observed a prominent survival defect in thymocytes from mice deficient in both Egr1 and Egr3 (1/3 DKO) and a partial differention block in the immature double negative (DN) stage. In addition, thymocytes are an easily manipulatable cell type, and the DN subpopulation affected in 1/3 DKO mice can be isolated to very high purity. We anticipate that 1/3 DKO thymocytes will provide an excellent experimental system that will provide insight into Egr-dependent transcription in neuronal development, activation, and death. To identify Egr transcription factor target genes in developing thymocytes. Egr1/3 DKO mice show a profound defect in thymocyte survival and differentiation, but the target genes downstream of Egr1 and Egr3 are unknown. Using Egr1/3 double knockout and wild type littermate mice, we will compare gene expression profiles from DN thymocytes to identify genes that are deregulated in Egr1/3 DKO cells. Egr1 and Egr3 expression is necessary for the proper survival and differentiation of developing thymocytes. We hypothesize that we will be able to identify crucial target genes of Egr1 and Egr3 by comparing gene expression profiles from wild type and 1/3 DKO thymocytes. Egr1 and Egr3 are first expressed in the immature double negative (DN) thymocytes. We will isolate DN thymocytes by FACS sorting which allows isolation of cell populations of >99% purity. We will perform microarray analysis using the Mouse 430 2.0 gene array with thymocyte RNA samples from 3 wild type and 3 1/3 DKO mice (6 arrays total). Differentially regulated genes (up-regulated and down-regulated) will be identified from the list of genes with significantly altered expression greater than or equal to 2-fold by paired T test. Interesting genes will be validated by real-time PCR in wild type and 1/3 DKO thymocytes. Recognizing that both direct and indirect target genes may be identified in the list of differentially expressed genes, real-time PCR validated target genes will be further screened using chromatin immunoprecipitation coupled with PCR (ChIP-PCR) to determine whether Egr1 and/or Egr3 are bound to potential regulatory regions of the putative target genes. Last Updated (by provider): Aug 24 2006 Contributers: Warren G Tourtellotte Gene expression data from postmorten brain regions Source GEO sample is GSM145787 Last updated (according to GEO): Nov 20 2006 901 Bone Marrow 861 Cerebral cortex 1000 ovarian neoplasm large cell lung carcinoma 4222 Source GEO sample is GSM17355 Last updated (according to GEO): May 28 2005 5 0 brain 861 Spinal Cord Plasma 861 brain, cerebral cortex: Rat_02-128_TTX_Lipska_e1_le1 135 117 on chromosome 17q21 60 45 of the Pituitary striatum 32 40 861 Infection 91 from the bone marrow 72 Cochlear structure 1000 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 7365 left_liver_lobe 0029_1483_H95A2_T96-94_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A this sample is from a 16-week-old male normal mouse gastrocnemius muscle Source GEO sample is GSM4376 Last updated (according to GEO): May 28 2005 TAp63 alpha Q540L 24h without induction s2 cy5:SHR treated w/ nifedipine, biological rep 5r; cy3:pool of 6 WKY control rats NCI60.46_LABEL50EXTRACT49SUB3 Source GEO sample is GSM134228 Last updated (according to GEO): Aug 06 2007 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 1 hour after lights on. Original sample code = CM2A Source GEO sample is GSM227338 Last updated (according to GEO): Sep 10 2007 1000 Brain Acetaminophen 24hr Rat 7075 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool Primary tumor 19 32 13 0 Nervous System 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201268 Last updated (according to GEO): Jun 14 2007 Parkinson Disease 861 Communicable Diseases 1000 Muscle Source GEO sample is GSM4280 Last updated (according to GEO): May 27 2005 None Source GEO sample is GSM214187 Last updated (according to GEO): Aug 01 2007 Sun215_TAV12 group Muscle 861 NA Source GEO sample is GSM198891 Last updated (according to GEO): Jun 07 2007 CNS-SCsev_InjB24h-2A-s2 861 Cerebral cortex 2869 tumor cells 2880 Utricle structure 861 19 0 human frontal cortex 0029_1210_H95A2_KF0079_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Standard Affymetrix Protocol Source GEO sample is GSM16457 Last updated (according to GEO): May 28 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with fMLP for 30min Source GEO sample is GSM5568 Last updated (according to GEO): May 27 2005 CLL-50 875 Structure of cingulate gyrus cy5:WKY treated w/ angtiotensin, biological rep 6r; cy3:pool of 6 WKY control rats M_U133Plus_73_HC AD control Treatment, type=dissect Source GEO sample is GSM119657 Last updated (according to GEO): Jul 10 2006 861 Hippocampus 1000 Ventral Tegmental Area MSE_D_G72A Dark rearing, biological rep2 CHC DR-2 Plasma 861 Mesenchymal Stem Cells 1000 metanephric mesenchyme, ANX, 7 days, biological rep1 CNS-SpinalCsev-Adult-14d-1A-s2 PMN_control_360min_Patient4 Standard Affymetrix procedure Source GEO sample is GSM132988 Last updated (according to GEO): Aug 28 2007 Primary Carcinoma 876 NG008_b 17 7 hippocampus D_U133Plus_119_HC Plasma 861 M_U133A_77_DLPFC 366 354 encephalitis DLBC55 on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression data from postmorten brain regions Source GEO sample is GSM145808 Last updated (according to GEO): Nov 20 2006 12 0 ovarian tumor 5 0 Spleen Whole blood 0 10 Cultured_cortical_astrocyte_wild_type_rep4 901 Structure of locus ceruleus placenta-0543-inflamed-infected-rep1 164 136 of the middle cerebral artery Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159781 Last updated (according to GEO): Apr 23 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28763 Last updated (according to GEO): May 27 2005 546 525 of melanoma metastases 901 Stem cells A_2m25 Utricle 0 6 Cerebral cortex 861 1000 Spinal Cord Injuries spinal cord 0 11 913 Coronary heart disease 5 0 brain Liver; day 14 postnatal_liver Keywords = mouse gene expression database Source GEO sample is GSM29369 Last updated (according to GEO): May 27 2005 Olfactory Epithelium 1000 M_U133A_109_AnCg Laser captured visceral sensory neurons. Source GEO sample is GSM63664 Last updated (according to GEO): Dec 21 2005 C57 whole brain 2B 901 Stem cells Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184784 Last updated (according to GEO): Apr 26 2007 Brain 861 5 0 brain the ventricular 1095 1109 lateral hypothalamus 25 45 36 21 from whole brain PriG_5%O2_Expt2_Day4_rep1 hypothalamus_10 Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589?595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164?169.) Source GEO sample is GSM159487 Last updated (according to GEO): Jun 21 2007 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201294 Last updated (according to GEO): Jun 14 2007 Small Intestine; ileum short bowel resection Keywords = mouse gene expression database Source GEO sample is GSM29301 Last updated (according to GEO): May 27 2005 CNS-SpinalCsev-Adult-7d-3B-s2 between the LAD artery 266 287 3AJZ02022750_fetal liver infection 278 287 2478 2451 from the ganglionic eminence Testis 1000 204 194 of retinal 1000 Descending colon nasal epithelial cells 28 49 GC (HKG47L) VDXGUYU_4036 umbilical cord_bpd: 7F The epithelial cells 962 981 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11531 Last updated (according to GEO): May 28 2005 between the LAD artery 265 286 Gene expression data from postmorten brain regions Source GEO sample is GSM145871 Last updated (according to GEO): Nov 20 2006 1000 Coronary Arteriosclerosis Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27674.gif Source GEO sample is GSM66561 Last updated (according to GEO): Sep 22 2006 f2#149 versus pool Mouse Brain tissue Rats 6h after injection with dose kainate. Treatment, type=time_course, description=KA animals are treated with kainate., measurement=6.0 h Source GEO sample is GSM32074 Last updated (according to GEO): May 27 2005 Gene expression data from whole brain infected mouse, day 3 Source GEO sample is GSM189617 Last updated (according to GEO): May 16 2007 N2_d2 #2(16012165010075) 7 cerebral cortex 21 M7TW01010682 861 Pituitary Gland 8-cell embryo replication 4 Keywords = preimplantation Keywords = development Source GEO sample is GSM14686 Last updated (according to GEO): May 28 2005 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15758 Last updated (according to GEO): May 28 2005 Conventional Descending colon 2 FSCC4 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Brain 1000 Palatine Tonsil I_U133A_11_CB 1000 Brain cocaine naive, lateral hypothalamus, 0 hrs/day access to cocaine Source GEO sample is GSM93839 Last updated (according to GEO): Jan 26 2006 Gene expression of modiolus of newborn rats_cultivation_hypoxia_repeat 2 inner ear nmd treated 1 Neural tube, control, GD9:12, C215584 Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203995 Last updated (according to GEO): Aug 02 2007 1000 Liver NMDA30 (Experiment shortNMDA: Run 19222) Treatment, type=time_course, description=primary cortical neurons were treated with 1 mM NMDA for increasing periods of time (10 to 360 min)., measurement=30.0 m Source GEO sample is GSM96756 Last updated (according to GEO): Feb 14 2006 Biopsy of the normal mucosa of the colon from patient #22 0029_1246_H95A2_KF0139_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 7 0 prostate 861 Cerebral cortex D_U133Plus_124_Amy Cerebral cortex 1000 Sham 6 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107485 Last updated (according to GEO): May 01 2006 Testis 861 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211408 Last updated (according to GEO): Jul 18 2007 5 0 Spleen 861 Fibroblasts ER negative human primary breast tumor EA02014_41271_H133A_JA-1524 Stromo vascular fraction from intraabdominal adipose tissue Source GEO sample is GSM210990 Last updated (according to GEO): Jul 17 2007 Brain 1000 AD-185t2-A232-8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from postmorten brain regions Source GEO sample is GSM145746 Last updated (according to GEO): Nov 20 2006 Heart 861 Epithelial Cells 1000 Plasma 861 short access to cocaine, lateral hypothalamus, 1 hr/day access to cocaine Source GEO sample is GSM93843 Last updated (according to GEO): Jan 26 2006 73 year old male 3AJZ02083092a_Skeletal_Muscle_Psoas total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with 2-Methyl-thio-ATP for 240min Source GEO sample is GSM5438 Last updated (according to GEO): May 27 2005 AD-183t1-A215-8 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A short access to cocaine, lateral hypothalamus, 1 hr/day access to cocaine Source GEO sample is GSM93842 Last updated (according to GEO): Jan 26 2006 brain, hippocampi, left: Sham PM Hypo_e1_le1 none Source GEO sample is GSM123274 Last updated (according to GEO): Jul 27 2006 Liver 1000 control wild-type prostate epithelial cell line maintained in RPMI-1640 medium supplemented with 5% fetal bovine serum Keywords = prostate Keywords = epithelial Source GEO sample is GSM14670 Last updated (according to GEO): May 28 2005 Epithelium 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145339 Last updated (according to GEO): Nov 20 2006 I_U133Plus_124_CB in the brain 150 162 HapMap CHB Male Source GEO sample is GSM159588 Last updated (according to GEO): Feb 01 2007 BTBR T+ tf/tf Hippocampus B brain, hippocampus: Ctr-24h-P15-II_e1_le1 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 9 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM11041 Last updated (according to GEO): May 28 2005 Germ free Jejenum 3 on the Y chromosome 677 695 17 7 hippocampus 865 Disorder of artery Tonsil Source GEO sample is GSM18902 Last updated (according to GEO): Sep 25 2006 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211412 Last updated (according to GEO): Jul 18 2007 861 Cardiomyopathies Normal Source GEO sample is GSM176066 Last updated (according to GEO): Apr 09 2007 21 0 acute myeloid leukemia 861 Brain human caudate nucleus Source GEO sample is GSM86914 Last updated (according to GEO): Feb 08 2006 Spleen 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145231 Last updated (according to GEO): Nov 20 2006 39 21 from mammary glands umbilical cord_bpd: 5C NH 28892A f2#249 versus pool Mouse Brain tissue 7 0 Lymphoma n/a Source GEO sample is GSM177939 Last updated (according to GEO): Jun 11 2007 14_360plus2 no additional Source GEO sample is GSM199171 Last updated (according to GEO): Jun 08 2007 453 434 The descending colon C57BL/6J_male_hypothalamus Source GEO sample is GSM184197 Last updated (according to GEO): Apr 26 2007 Total RNA from iPS clone was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations. Source GEO sample is GSM239967 Last updated (according to GEO): Nov 22 2007 Spleen 1000 cocaine naive, septum, 0 hrs/day access to cocaine Source GEO sample is GSM93851 Last updated (according to GEO): Jan 26 2006 797 cortex 803 G30-SomatosensoryCortex replicate2 Epithelium 861 Normal Source GEO sample is GSM175795 Last updated (according to GEO): Apr 09 2007 861 Prostate carcinoma NCI60.2_LABEL125EXTRACT64SUB3 Source GEO sample is GSM134002 Last updated (according to GEO): Aug 06 2007 rat model organism with depression left untreated or treated with reserpine Source GEO sample is GSM247180 Last updated (according to GEO): Dec 11 2007 HMEC X HMEC + TGFbeta 24hrs Disease Source GEO sample is GSM175933 Last updated (according to GEO): Apr 09 2007 Cells were either prestimulated (1_X) or not (0_X) for 18h with 100 ng/ml LPS. Media was exchanged and after 2h rest, cells either restimulated (X_1) or not (X_0) with again 100 ng/ml LPS. This resulted in 4 experimental conditions: 0_0, 0_1, 1_0 and 1_1. There were 3 biological replicates done, resulting in 12 arrays altogether. Source GEO sample is GSM213695 Last updated (according to GEO): Aug 01 2007 61 41 from postmortem brain gfp pos. sorted cells from 3 disected e14.5 cortecies Treatment, type=wait Source GEO sample is GSM135778 Last updated (according to GEO): Sep 12 2006 nmda4 (Experiment Neuroprotection4- Run 14985) Treatment, type=timepoint, description=primary cortical neurons were treated for 30 m wiht NMDA 1mM. The agonist was then washed out and the cells were harvested 24h later, measurement=30.0 m Source GEO sample is GSM96752 Last updated (according to GEO): Feb 14 2006 901 Epithelial Cells 1000 Spinal Cord NHE1 null mutation cerebellum-2 gut neurospheres 243 258 brain, cerebral cortex: NIC + NMDA 2_le1 Recurrent Squamous cell carcinoma 5 861 Heart Diseases Wild type 1 Thymus, Whole thymus: Amplified mRNA_le1 1 in fibroblasts 1627 1641 peripheral blood-CD4TCells Source GEO sample is GSM18718 Last updated (according to GEO): Sep 25 2006 E6.25_rep2 861 Cerebral cortex Communicable Diseases 1000 1000 Left of motor neuron diseases 785 809 Neoplasm 861 Lymph node metastasis 19 40 Replicate1_Voxel F8 T-ALL-#9 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Brain Sample # 1178-1 5 0 brain PriG_5%O2_Expt2_Day9_rep1 5 0 brain brain, cortex: Sample13_e1_le1 Hippocampus 861 256 235 dilated heart failure 355 342 in the tumors PGA-Band_Sham_4h_2-m5 Expression profiling of spinal cord section (T8) extracted from rats 30m following laminectomy (sham) Source GEO sample is GSM31409 Last updated (according to GEO): May 27 2005 Eye 1000 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198663 Last updated (according to GEO): Jun 06 2007 SN:Human Glioblastoma Biopsy 30145 Alzheimer's Disease 861 Lung 1000 Prefrontal Cortex 0 16 of the colon 28 39 skeletal.muscle.1 Head and neck cancer Source GEO sample is GSM155711 Last updated (according to GEO): Apr 24 2007 Skeletal bone 861 GM11832 Wild type inbred mice Source GEO sample is GSM82988 Last updated (according to GEO): Nov 10 2005 f2#164 versus pool Mouse Brain tissue PBMCs-Healthy-H171_Healthy /J Basal Ganglia A 4 21 Brain 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Dimaprit for 30min Source GEO sample is GSM5534 Last updated (according to GEO): May 27 2005 12 frontal Lobe 23 (hypothalamus 1036 1048 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc77 Source GEO sample is GSM1899 Last updated (according to GEO): Nov 21 2005 1000 Left ventricular structure Liver 861 Hippocampus Treatment, type=pharmacogenomic_treatment, description=Chronic Immobilization Stress Source GEO sample is GSM53303 Last updated (according to GEO): Jul 06 2005 Structure of horn of uterus 983 101 CN A PP164_infected_Skin biopsy Chronic Lymphocytic Leukemia 19 47 Hair; Awn Hair (back) catagen Keywords = mouse gene expression database Source GEO sample is GSM29338 Last updated (according to GEO): May 27 2005 R6/1 18 week wildtype_DFFC Plasma 861 Expression profiling of moderately injured raphe at 28d in rats Source GEO sample is GSM41589 Last updated (according to GEO): May 27 2005 human frontal cortex Source GEO sample is GSM87030 Last updated (according to GEO): Feb 08 2006 1000 Structure of parenchyma of lung Osteoblasts 1000 861 Skeletal bone Kidney 1000 Muscular Dystrophy, Duchenne 1000 of somatomotor cortex 21 41 of uterine horns 365 380 Replicate3_Voxel A6 15 0 human cerebellum ALL-B-cell-16 on Affymetrix GeneChip Human Full Length Array HuGeneFL 41 36 spleen Menstruation blood, primary E5 1000 nervous system disorder 1000 jejunum HOXB4const-LSK+ cells_ 1 hour after TMX withdrawal Source GEO sample is GSM228753 Last updated (according to GEO): Sep 13 2007 of other neurotransmitters 150 176 831 813 to any other tumor ISR3 861 Cerebral cortex Parkinson Disease 861 Expression profiling of somatomotor cortex extracted from rats at 24h following sham surgery Source GEO sample is GSM41643 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T9) extracted from rats 28d following mild injury Source GEO sample is GSM31229 Last updated (according to GEO): May 27 2005 Cerebral cortex 1000 Primary Neoplasm 1000 Skeletal muscle biopsy was obtained after a 3-hour hyperinsulinemic (infusion rate 40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172167 Last updated (according to GEO): Feb 28 2007 testis 0 5 1000 Brain Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16204.gif Source GEO sample is GSM84190 Last updated (according to GEO): Sep 22 2006 D_U133Plus_46_nAcc Head and neck cancer Source GEO sample is GSM155671 Last updated (according to GEO): Apr 24 2007 Primary tumor 19 32 Isograft 7 days No.3 wild-type mouse cerebellum Treatment, type=time_course, measurement=11.0 weeks Source GEO sample is GSM53355 Last updated (according to GEO): Jul 06 2005 cortices 122 129 Communicable Diseases 1000 Spleen 0 5 8 0 Ligament Heart 861 NG003_c 495 of bone 489 114 101 brains quickly Gene expression data from postmorten brain regions Source GEO sample is GSM145186 Last updated (according to GEO): Nov 20 2006 Transcriptional profiling and ontology tools were utilized to define the biological pathways of gingival epithelial cells modulated by coculture with the oral commensal Streptococcus gordonii and the opportunistic commensal Fusobacterium nucleatum. Overall, F. nucleatum and S. gordonii perturbed the gingival epithelial cell transcriptome much less significantly than the oral pathogens Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans perturbed the transcriptome, indicating that there was a greater degree of host adaptation by the commensal species (M. Handfield, J. J. Mans, G. Zheng, M. C. Lopez, S. Mao, A. Progulske-Fox, G. Narasimhan, H. V. Baker, and R. J. Lamont, Cell. Microbiol. 7:811-823, 2005). The biological pathways significantly impacted by F. nucleatum and S. gordonii included the mitogen-activated protein kinase (MAPK) and Toll-like receptor signaling pathways. Differential regulation of GADD45 and DUSP4, key components of the MAPK pathway, was confirmed at the protein level by Western blotting. Modulation of the MAPK pathway is likely to affect host cell proliferation and differentiation. In addition, both the MAPK and Toll-like receptor pathways ultimately converge on cytokine gene expression. An enzyme-linked immunosorbent assay of secreted interleukin-6 (IL-6) and IL-8 demonstrated that F. nucleatum induced production of these cytokines, whereas S. gordonii inhibited secretion from the epithelial cells. Stimulation of secretion of proinflammatory cytokines from epithelial cells may reflect the invasive phenotype of F. nucleatum and contribute to the greater pathogenic potential of F. nucleatum than of S. gordonii. brain, forebrain: Sample14_e1_le1 Normal human tissue:Normal Fetal Lung Keywords = Human, Normal Tissue, Normal Fetal Lung Source GEO sample is GSM44705 Last updated (according to GEO): May 27 2005 /3T3 fibroblasts 743 759 Sample # 1044-1 D_U133A_51_DLPFC Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15284.gif Source GEO sample is GSM91544 Last updated (according to GEO): Sep 22 2006 1000 Left 73 35 with several human hereditary disorders 14 days hindlimb suspended, 5 day reloaded Source GEO sample is GSM17360 Last updated (according to GEO): May 28 2005 Bladder 1000 NCI60.4_LABEL7EXTRACT6SUB3 Source GEO sample is GSM134013 Last updated (according to GEO): Aug 06 2007 38 21 from a hippocampus SCG explant cultured for 24 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246055 Last updated (according to GEO): Dec 03 2007 no additional Source GEO sample is GSM199285 Last updated (according to GEO): Jun 08 2007 Spleen 1000 146 110 of the substantia nigra pars compacta 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114448 Last updated (according to GEO): Jun 16 2006 1000 Modiolus anguli oris The effect of sleep deprivation on gene expression in the brain and the liver of three inbred mouse strains 798 773 localized prostate cancer 1000 Mitral Valve whole blood_100265 Sporadic_s1324 on NHGRI-6.5k Testis 861 31 0 Conventional Descending colon 3 Fibroblasts 1000 861 Adipose tissue 1000 Descending colon 1000 Cerebrovascular accident 353 331 of the pituitary gland Gene expression data from dorsal pancreas at e16.5, MG-U74C version2 Source GEO sample is GSM199471 Last updated (according to GEO): Jun 08 2007 Expression profiling of laminectomized raphe at 14d in rats Source GEO sample is GSM41521 Last updated (according to GEO): May 27 2005 91 from the bone marrow 72 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195334 Last updated (according to GEO): Jun 04 2007 The mammalian forebrain 0 22 Samp8 Hippocampus Old Sample 1 Medulla Oblongata 861 /J cingulate cortex rep1 1 24 of 1761 tumor 50 62 Gene expression data from human prostate tissue with 90 percent tumor content Source GEO sample is GSM119311 Last updated (according to GEO): Feb 23 2007 Primary tumor 19 32 626 615 PCOS oocytes 1000 Primary carcinoma of the liver cells 5 0 brain Primary Neoplasm 1000 B6 day 0, biological rep 4, tech rep 2 PBMCs-Type 1 Diabetes-IDDM23_T1D_New 861 Down Syndrome Replicate two: differential expression analysis of CW treatment on RBEC6 cells Source GEO sample is GSM128925 Last updated (according to GEO): Aug 16 2006 Olfactory Epithelium 1000 Pineal gland 1000 IRTGFBd8_13 861 Blood Biopsy of a colorectal adenoma from patient #23 in the brain 51 62 861 Ganglia 861 Breast kidney 37 43 Gene expression data from postmorten brain regions Source GEO sample is GSM146066 Last updated (according to GEO): Nov 20 2006 5 0 brain cortex 7 12 Normal Source GEO sample is GSM176063 Last updated (according to GEO): Apr 09 2007 Expression profiling of spinal cord section (T10) extracted from rats 7dh following severe injury Source GEO sample is GSM31388 Last updated (according to GEO): May 27 2005 PBMCs-Type 2 Diabetes-T2D_7_New Biopsy of the normal mucosa of the colon from patient #27 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28821 Last updated (according to GEO): May 27 2005 Parkinson Disease 861 1000 Cerebral cortex ovary 197 201 X-ray irradiation (2 Gy). Source GEO sample is GSM203986 Last updated (according to GEO): Jun 25 2007 Communicable Diseases 861 GC (HKG43T) 39 21 of substantia nigra 5 0 brain Parkinson 0 8 Gene expression data from postmorten brain regions Source GEO sample is GSM145932 Last updated (according to GEO): Nov 20 2006 Nasal Epithelium Inhalation Formaldehyde 2ppm 19d ID232 4 0 Brain This mouse is non-transgenic to be used as a control for caPI3k and dnPI3k. These arrays were scanned at a PMT of 10%. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/pi3k_home.html Keywords = cardiac, pi3k, hypertrophy Source GEO sample is GSM8525 Last updated (according to GEO): May 27 2005 Small Intestinejejunum 6 Normal Nodose Ganglion 901 1000 Brain 204-97_Adeno Gene expression data from PD3 Foxo3 wild-type ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203848 Last updated (according to GEO): Aug 02 2007 Although cancer classification has improved over the past 30 years, there has been no general approach for identifying new cancer classes (class discovery) or for assigning tumors to known classes (class prediction). Here, a generic approach to cancer classification based on gene expression monitoring by DNA microarrays is described and applied to human acute leukemias as a test case. A class discovery procedure automatically discovered the distinction between acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) without previous knowledge of these classes. An automatically derived class predictor was able to determine the class of new leukemia cases. The results demonstrate the feasibility of cancer classification based solely on gene expression monitoring and suggest a general strategy for discovering and predicting cancer classes for other types of cancer, independent of previous biological knowledge. 19 olanzapine Colonic mucous membrane 901 861 Heart 901 Coronary artery Gene expression data from B6xBALB F2 mouse lung Source GEO sample is GSM133466 Last updated (according to GEO): Apr 05 2007 GSE5342 spinal cord 13 23 Heart failure sample 6 HCT-116 hgu95a stomach_fundus_2 Hippocampus 1000 CNS-SC_Inj24h-1A-s2c Gene expression data from skeletal muscle following 240 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230443 Last updated (according to GEO): Sep 19 2007 1000 Rectum with Alzheimer's disease 27 50 14 7 amygdala Alzheimer's Disease 861 254 238 of neural retinas 861 Dislocations olfactory epithelium tissue 54 80 Integumentary system 1000 Gap Junctions 1000 1500 mg/kg X 12 hr Source GEO sample is GSM129886 Last updated (according to GEO): Sep 18 2007 Cardiac-specific TNF-alpha transgenic mouse is an excellent model to study the pathologenesis of heart failure. Affytrix U74V2A was used to analyzed the gene expression profile of mice at the time point of compensated hypertrophy and dilated heart failure. Source GEO sample is GSM8998 Last updated (according to GEO): May 28 2005 with Alzheimer's disease 27 50 WGACON-208 no additional Source GEO sample is GSM199301 Last updated (according to GEO): Jun 08 2007 38 21 of medulloblastoma NO_KIDNEY_1 Richard Almon-38-1133800609964 901 Coronary artery 33 17 tibialis anterior prostate Source GEO sample is GSM203360 Last updated (according to GEO): Jun 21 2007 22-oct-2002-BrainEsubA-ab150 mdx5cv gastroc sample 1 Spleen vs Interferon-gamma (IFN gamma) Treated B cell 120min (set2) Nose 1000 7 cerebral cortex 21 cardiac 763 769 Donor B, prior to G-CSF Source GEO sample is GSM178550 Last updated (according to GEO): Aug 09 2007 brain, cortex: Sample18_e1_le1 5 0 Spleen RR216_infected_skin_biopsy GI_canc, Duodenal Tumor Keywords = mouse gene expression database Source GEO sample is GSM29271 Last updated (according to GEO): May 27 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68190 Last updated (according to GEO): Jul 07 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145178 Last updated (according to GEO): Nov 20 2006 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19215 Last updated (according to GEO): May 27 2005 B6Amygdala(1a)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B CNS-RM_Mod28d-4C-s2 Normal__Kidney_Norm_613NPS on Affymetrix GeneChip Human 35K SubA Array Hu35k-A total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withTerbutaline for 120min Source GEO sample is GSM5787 Last updated (according to GEO): May 27 2005 B220+CD25+sIg- Small Pre BII cells sorted out of mouse bone marrow, sort no. 10 Source GEO sample is GSM660 Last updated (according to GEO): Mar 20 2006 61 41 from postmortem brain 1037 of transitional epithelium 1012 1000 Hypothalamic structure 1000 Brain adipose tissue; mesenteric Source GEO sample is GSM18625 Last updated (according to GEO): May 27 2005 Rat frontal cortex RNA - VH TTX Experiment Source GEO sample is GSM92305 Last updated (according to GEO): Jan 13 2006 D_U133A_42_nAcc 1000 Retina Chronic Obstructive Airway Disease 1000 Gene expression data from liver Source GEO sample is GSM243352 Last updated (according to GEO): Nov 16 2007 Brain 861 RNA isolated from fetal cerebrum Keywords = trisomy 13 Keywords = brain Keywords = Patau syndrome Source GEO sample is GSM22624 Last updated (according to GEO): May 27 2005 D_U133A_34_nAcc Basal Ganglia 901 67 40 with coronary artery disease Expression profiling of spinal cord section (T10) extracted from rats 4h following severe injury Source GEO sample is GSM31381 Last updated (according to GEO): May 27 2005 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134628 Last updated (according to GEO): Jul 09 2007 to atherosclerosis 112 130 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL10 for 240min Source GEO sample is GSM5648 Last updated (according to GEO): May 27 2005 DRG Source GEO sample is GSM19009 Last updated (according to GEO): Sep 25 2006 Probeset expression data from NA12751 growth 3, replicate 1 Source GEO sample is GSM195213 Last updated (according to GEO): Aug 08 2007 bone_marrow_2 Source GEO sample is GSM80577 Last updated (according to GEO): Mar 31 2006 861 Aneurysm 21 0 Heart failure sample 6 nostrils 156 164 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3337 Last updated (according to GEO): Mar 21 2006 Mouse young heart C5-Ht-4 EWS-T-TEST-19 on NHGRI-6.5k_b 1000 Brain Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22573 Last updated (according to GEO): May 27 2005 early HCC Source GEO sample is GSM155986 Last updated (according to GEO): Jun 21 2007 mild cognitive impairment - posterior cingulate cortex 2 VDXKIU_248C91 G1E_3_B 1933 tumor cells 1943 Viscera 1000 Kidney CR-4A Gene expression data from postmorten brain regions Source GEO sample is GSM146028 Last updated (according to GEO): Nov 20 2006 Gene expression data from human colon tumor tissue Source GEO sample is GSM173337 Last updated (according to GEO): Apr 20 2007 zhang-affy-mouse-308606 in acute myeloid leukemia 64 88 TEL-AML1-C27 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Keywords = Infectious diseases 1069 1099 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15457.gif Source GEO sample is GSM84152 Last updated (according to GEO): Sep 22 2006 none Source GEO sample is GSM123273 Last updated (according to GEO): Jul 27 2006 DCIS179 on harvard-12k 052401_HF_332CB in multiple myeloma patients. 221 250 of hindbrain 1511 1522 BC37-FA Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13113.gif Source GEO sample is GSM79974 Last updated (according to GEO): Sep 22 2006 1000 Brain 19 0 Head and neck cancer with some respiratory epithelium. 1039 1072 NOS exp2 CONTROL Simple annotation: Reference verification, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10005.gif Source GEO sample is GSM78457 Last updated (according to GEO): Sep 22 2006 brain, cerebellum: WCx12w#2_e1_le1 9 0 Trisomy 21 myocardial infarction 383 403 in the mammalian nervous system 110 141 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213468 Last updated (according to GEO): Jul 31 2007 901 Nervous system structure 10 weeks Source GEO sample is GSM147465 Last updated (according to GEO): Dec 01 2006 D2_SleepDep_ZT 12_2 Wild type inbred mice Source GEO sample is GSM82915 Last updated (according to GEO): Nov 10 2005 Nicotinic Receptors 1000 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202679 Last updated (according to GEO): Jun 20 2007 no additional Source GEO sample is GSM199067 Last updated (according to GEO): Jun 08 2007 2CdA: PK11195 intervention at 6.0h RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above Source GEO sample is GSM160004 Last updated (according to GEO): Feb 05 2007 1100 1087 heart failure 1000 Hippocampus Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211323 Last updated (according to GEO): Jul 18 2007 ileum 861 314-99_normal Infection 1000 Transplant Series 32 , Transplant # 4 901 Coronary artery 1000 Organ olfactory epithelium tissue 54 80 in the mammalian nervous system 110 141 none Source GEO sample is GSM149540 Last updated (according to GEO): Jan 03 2007 LDMTX_MP-DX-11 1000 Brain 12 0 ovarian tumor 227 223 Brain nostrils 156 164 Simple annotation: Normal tissue, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs//3741.gif Source GEO sample is GSM76463 Last updated (according to GEO): Sep 22 2006 PCA-409 on UMich-10k Cerebral cortex 861 occipital regions 163 179 none Source GEO sample is GSM246001 Last updated (according to GEO): Dec 03 2007 861 Lung Head and neck cancer Source GEO sample is GSM155686 Last updated (according to GEO): Apr 24 2007 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 11.75 hours after lights on. Original RNA code = LC45A. Source GEO sample is GSM227396 Last updated (according to GEO): Sep 10 2007 Skeletal bone 861 Lymphoblastoid Cell Line for Individual 8026.4 log phase spinal cord 21 31 1000 Brain Pituitary Gland 861 with some respiratory epithelium. 1039 1072 none Source GEO sample is GSM244622 Last updated (according to GEO): Nov 23 2007 Brain 1000 9 0 Blood Test of the postmortem brains 674 698 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225930 Last updated (according to GEO): Nov 02 2007 olfactory epitheliumSR-A mutant mouse 16 hpO Source GEO sample is GSM80207 Last updated (according to GEO): Oct 26 2005 Plasma 861 BAL_20b_A1B1 cingulate cortex 1000 Low-density CCg progenitors treated with FBS to derive Astrocytes Source GEO sample is GSM47552 Last updated (according to GEO): Jun 10 2005 Liver 1000 Spleen 0 5 Nose 1000 Exp A, Animal #4, 50mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 50mg/kg of CPF for 96 hours Source GEO sample is GSM246144 Last updated (according to GEO): Dec 03 2007 Cerebral cortex 1000 HCC (HBV+, HK15) Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO + U0126(10?M) overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 9 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10961 Last updated (according to GEO): Sep 08 2006 Nose 1000 Ovarian_Tumor_Serous_KU-OS-021 Richard Almon-50-1133800610292 Tumor__Lymphoma_Follicular_FSCC_S98_11020 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Expression profiling of spinal cord section (T8) extracted from rats 24h following severe injury Source GEO sample is GSM31473 Last updated (according to GEO): May 27 2005 1000 Muscular Dystrophy, Duchenne osteoblast 627 637 1000 Structure of locus ceruleus 1469 1457 in glomeruli 0 Human Cortex 11 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28720 Last updated (according to GEO): May 27 2005 Female 70.7 yr after antibody enrichment scan 2 (U133A) 1000 Structure of parenchyma of lung This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis. Stembase Experiment ID: E189 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189 SCGP Sample ID: S232 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_190 Short description: RNA isolated from first passage retinal sphere cells. Estimated purity: > 90% RNA concentration: > 0.15ug/ul Num cells for RNA prep: ~1.7x10e6 Sample volume: 10.0 ul Source GEO sample is GSM87195 Last updated (according to GEO): Jan 19 2006 1000 Hippocampus 106 FC BA9 A AD-178T2-A22-1 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 20 0 human caudate nucleus mouse brains 187 198 861 Huntington Disease PGA-RnSalt_c_3w_3-m5 901 Caudate nucleus structure processed in batch 4 Source GEO sample is GSM90424 Last updated (according to GEO): Mar 20 2006 CNS-SCsev_InjA28d-4A-s2 861 Spinal Cord Replicate1_Voxel D9 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with NGF (Nerve Growth Factor) for 120min Source GEO sample is GSM5703 Last updated (according to GEO): May 27 2005 Prostate tumors 0 14 Spinal Cord 901 EKVX hgu95b Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc55 Source GEO sample is GSM1909 Last updated (according to GEO): Nov 21 2005 Macrophage 14smi035 Sample 115 on vantveer-oligo Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_3 months_replicate 3 Primary small cell lung carcinoma 3424 Source GEO sample is GSM17345 Last updated (according to GEO): May 28 2005 n/a Source GEO sample is GSM178076 Last updated (according to GEO): Jun 11 2007 whole blood_101291 1000 Hippocampus 861 Encephalitis 1000 ovarian neoplasm Plasma 861 Epithelium 861 D01 3h Media Appendix Source GEO sample is GSM18840 Last updated (according to GEO): Sep 25 2006 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181118 Last updated (according to GEO): Jul 12 2007 Primary Neoplasm 1000 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array.Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188687 Last updated (according to GEO): Jun 06 2007 21 7 adrenal medulla Gene expression profile of the cell line UB/OC-1 grown at 33C (undifferentiated, day 0) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1517 Last updated (according to GEO): May 27 2005 Gene expression data from human colon tumor tissue Source GEO sample is GSM173345 Last updated (according to GEO): Apr 20 2007 no additional Source GEO sample is GSM199240 Last updated (according to GEO): Jun 08 2007 861 Neoplasm testis 52 58 43h-DMSO replication 3 plasma cells 332 344 LCCS vs control comparison Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM Source GEO sample is GSM207682 Last updated (according to GEO): Jul 09 2007 Bone structure of tibia 1000 861 Malignant Glioma Amygdaloid structure 1000 B6 day 3, biological rep 2, tech rep 1 1000 Retina Autistic Disorder 877 Nervous system structure 901 Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 3565 blood between the LAD artery 266 287 Entorhinal Cortex 7 23 retina 5 10 of underlying brain 171 190 MGJZ030212072Asubstantianigra Expression profiling of somatomotor cortex extracted from rats at 72h following sham surgery Source GEO sample is GSM41667 Last updated (according to GEO): May 27 2005 to the nose 599 609 Putamen P7 Normal Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 4258 blood Gene expression data from postmorten brain regions Source GEO sample is GSM145550 Last updated (according to GEO): Nov 20 2006 Parkinson Disease 1000 1000 Huntington Disease Coronary heart disease 913 Gene expressions affected by TNF alpha Source GEO sample is GSM189808 Last updated (according to GEO): May 21 2007 human frontal cortex Source GEO sample is GSM86971 Last updated (according to GEO): Feb 08 2006 56 32 out of mouse bone marrow 1000 Brain Male 25.2 yr before antibody enrichment scan 1 (U133B) Addictive Behavior 861 114 cortex 120 Epithelium of bronchus 983 Whole blood 0 10 healthy subject Source GEO sample is GSM211034 Last updated (according to GEO): Sep 10 2007 Circadian Time Treatment, type=time_course, measurement=12.0 h Source GEO sample is GSM53337 Last updated (according to GEO): Jul 06 2005 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip.. Date GSE974 Last Updated: Jun 28 2005 Contributers: Schuchong Pan David Fermin Judith Graziano Shireen E de Sam Lazaro Sofia Ormaza Robert D Simari Leslie W Miller Xinqiang Han Yingjie Chen Ami Mariash Soon Park Jennifer Hall Robert J Bache Zhanjun Guan Suzanne M Grindle Jeanne Thompson Includes GDS558. Update date: Apr 20 2004. Dataset description GDS558: Analysis of paired left ventricular apex samples harvested at implant of left ventricular assist device (LVAD) and at explant. Patients classified as ischemic, non-ischemic or acute myocardial infarction within 10 days of implant.. 884 Myosin Heavy Chains GC (HKG34T) Changes in mouse liver mRNA profiles following intra-peritoneal cytokine injection. One of 2 replicates of albumin-cre(+) Socs3(-/fl) mice, injected with phosphate-buffered saline (PBS), and killed after 4h. Source GEO sample is GSM5950 Last updated (according to GEO): May 27 2005 1000 Neoplasm Brain_MD_23_Medulloblastoma_Desmoplastic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114210 Last updated (according to GEO): Jun 16 2006 97 FC BA9 A Tissue Source GEO sample is GSM67260 Last updated (according to GEO): Jan 19 2006 67 52 descending colon 5 0 Spleen oksen-affy-mouse-212956 human frontal cortex Source GEO sample is GSM86948 Last updated (according to GEO): Feb 08 2006 R7E 8 Communicable Diseases 1000 CNS-SC_InjB4h-3B-s2 ColonTumor022RAFBU_cta.txt brain, forebrain: Sample4_e1_le1 Skeletal muscle biopsy was obtained before a 3-hour hyperinsulinemic (infusion rate 40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172156 Last updated (according to GEO): Feb 28 2007 Category: Cell-line Subcategory: HMEC Scanning Software: unknown Software version: unknown Lot batch = 0132-5k Source GEO sample is GSM1944 Last updated (according to GEO): Nov 21 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68248 Last updated (according to GEO): Jul 07 2006 7 CN A Bone Marrow 1000 Job's patient Source GEO sample is GSM211051 Last updated (according to GEO): Sep 10 2007 X-ray irradiation (2 Gy) and TGFB added. Source GEO sample is GSM203979 Last updated (according to GEO): Jun 25 2007 861 Blood Neostriatum 1000 GSE7023 502 496 organs 331 307 in central nervous system Expression profiling of moderately injured raphe at 24h in rats Source GEO sample is GSM41576 Last updated (according to GEO): May 27 2005 Brain 1000 Category: Cell-line Subcategory: HMEC Scanning Software: unknown Software version: unknown Lot batch = 0387-5k Source GEO sample is GSM1953 Last updated (according to GEO): Nov 21 2005 human caudate nucleus Source GEO sample is GSM86877 Last updated (according to GEO): Feb 08 2006 R533P00403 Kidney 1000 1000 Spleen mod089_10nM-1 278 255 ischemic cardiomyopathy cerebral cortex 7 21 Voxel I4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1452 Last updated (according to GEO): Nov 21 2005 "18h Thy-Noc, Exp4" GSE4537 Matrigel culture, 14B3, rep 2 1000 Left tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44875 Last updated (according to GEO): May 27 2005 CVB3_V-0.5h-3 10 Bone marrow 0 Wild type 8 wk old male C3H/HeJ mouse hypothalamus Source GEO sample is GSM74977 Last updated (according to GEO): Feb 27 2007 26 0 Bone marrow [JunctionChip 1 567 548 the descending colon 861 Intestines Trigeminal Ganglion Source GEO sample is GSM53319 Last updated (according to GEO): Jul 06 2005 861 Blood VDXOXFU_37 plasma cells 50 61 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225378 Last updated (according to GEO): Aug 31 2007 861 Cerebellum Prostate 13 Disease 150 mg/kg X 24 hr Source GEO sample is GSM129861 Last updated (according to GEO): Sep 18 2007 352 340 encephalitis SR-A mutant olfactory epithlium 48 hpO replicate3 untreated localized prostate cancer 175 209 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181080 Last updated (according to GEO): Jul 12 2007 striatum 23 31 41 29 Control blood 1000 Brain 861 Cerebral cortex 492 475 in the PCOS oocyte After 2 week acclimation to 12 hr/12 hr light/dark regimen, c57/Bl6 mice were subjected to a 36 hour period of constant darkness. Aortae were subsequently harvested at 4 hour intervals to 48 hours. Duplicate microarrays were hybridized with biotin-labeled probes derived from aorta tissue (6 pooled aortae/timepoint). Source GEO sample is GSM6092 Last updated (according to GEO): May 27 2005 brain, unknown: 00DLR_e1_le1 861 Neoplasm Large-scale analysis of the human and mouse transcriptomes. nostrils 156 164 5 0 brain Rat frontal cortex RNA - VH TTX Experiment Source GEO sample is GSM92314 Last updated (according to GEO): Jan 13 2006 Islet Source GEO sample is GSM18979 Last updated (according to GEO): Sep 25 2006 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b017 Source GEO sample is GSM1996 Last updated (according to GEO): Nov 21 2005 Low-density CCg progenitors Source GEO sample is GSM47548 Last updated (according to GEO): Jun 10 2005 mouse brain 478 489 861 frontal lobe GSE5594 Epithelium 861 Gene expression of stria vascularis of newborn rats_cultivation_normoxia_repeat 1 inner ear 865 Disorder of artery Epithelium 861 626 615 PCOS oocytes 31 0 Cerebellum Alzheimer's disease 3 D10 24h Media HDMTX-18 Skeletal bone 861 mild cognitive impairment - superior frontal gyrus 5 Brain Stem 1000 GSE5478 1000 Brain 861 Brain 1000 Solid tumor Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118548 Last updated (according to GEO): Jul 11 2006 D5 aggregate culture, 14B3, rep 1 Brain 1000 Brain 1000 TUMOR 3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Hippocampus from the femurs 95 109 1000 Hippocampus bronchial epithelia 224 243 Parkinson Disease 861 277 271 Retinas HMVEC-L stimulated with LPS for 8 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114556 Last updated (according to GEO): Sep 20 2006 861 Brain cerebral cortex 7 21 in human breast cancers 817 840 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118340 Last updated (according to GEO): Jul 11 2006 Timed pregnant C57Bl6 mice were exposed to ethanol during gestational day 15 to day 18 and ethanol exposed fetuses were delivered by cessarian section on gestational day 19. Alcohol exposed fetuses were compared to control timed preg Source GEO sample is GSM116855 Last updated (according to GEO): Jul 03 2006 Baclofen treated 3 Spleen vs Insulin-like growth factor 1 Treated B cell 240min (set1) Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28818 Last updated (according to GEO): May 27 2005 Evidence for a role of developmental genes in the origin of obesity and body fat distribution. Alterations of gene expression in failing myocardium following left ventricular assist device support. 5 0 brain Skeletal bone 861 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68284 Last updated (according to GEO): Jul 07 2006 7 cerebral cortex 21 10 week control OMN rep 3 1581 such as Alzheimer disease 1605 pull-downSD_1, ZT6 194 Raphe magnus 183 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201736 Last updated (according to GEO): Jun 20 2007 brain, unknown: 04HM_e1_le1 Brain 861 700 679 by Brucella infection 99 96 (HIV Primary tumor 19 32 of 13 childhood astrocytomas to 318 348 Replicate3_Voxel C10 Whole blood 0 10 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=0 (Non-acute rejection). Source GEO sample is GSM36446 Last updated (according to GEO): May 27 2005 1000 medulloblastoma Skeletal bone 861 1000 Brain 5 0 brain 901 Prostate carcinoma rat hippocampus Treatment, type=time_course, measurement=72.0 h Source GEO sample is GSM32144 Last updated (according to GEO): May 27 2005 Parkinson Disease 861 HMVEC-L stimulated without LPS for 4 hours c04R2 12 0 Blood B cells Peripheral Nervous System 1000 Group 3 NMBA treated, pool #EP4 vs. reference pool Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188715 Last updated (according to GEO): Jun 06 2007 none Source GEO sample is GSM239947 Last updated (according to GEO): Dec 07 2007 20 0 human caudate nucleus Donor 1 Time point 48 hours Autologous control (uninfected) Source GEO sample is GSM2603 Last updated (according to GEO): May 27 2005 Cerebral cortex 1000 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153407 Last updated (according to GEO): Jan 11 2007 of underlying brain 171 190 Sample details: Three pools of rostral (R1-3), three pools of middle (M1-3), and three pools of caudal (C1-3) E13.5 MF1 neocortex were collected from 4 embryos. All possible 18 comparisons were carried out. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. Source GEO sample is GSM62823 Last updated (according to GEO): Aug 26 2005 T2+ gr3 tumour Source GEO sample is GSM2515 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 tibiae 115 120 Prostate 5 Disease 0 17 14 9 Retina 861 Cerebral cortex T-ALL-C6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A D_U133A_68_HC 40 21 from the hippocampus 861 Gland structure Primary tumor 19 32 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13136.gif Source GEO sample is GSM79656 Last updated (according to GEO): Sep 22 2006 Trauma 861 human cerebellum Source GEO sample is GSM87185 Last updated (according to GEO): Feb 08 2006 901 Mammary gland 5 0 brain Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200616 Last updated (according to GEO): Jun 12 2007 CNS-SCsev_InjB24h-4B-s2 (1 utricle 10 19 with mental retardation 241 263 brain 0 5 91 from the bone marrow 72 Medulla Oblongata 861 fetallung Source GEO sample is GSM18966 Last updated (according to GEO): Sep 25 2006 61 41 from postmortem brain Infection 861 in human cancers 1232 1247 1000 Rectum M_U133A_74_DLPFC 861 Blood Expression profiling of somatomotor cortex extracted from rats at 24h following moderate injury Source GEO sample is GSM41703 Last updated (according to GEO): May 27 2005 Paravertebral Muscle 1 Disease 0 29 Bone structure of tibia 1000 Carcinoma, Large Cell 867 Ovary 1000 320 306 Keywords = HIV A YOKE D093 715 702 After the eyes 7 cerebral cortex 21 Squamous cell carcinoma 875 FVB/NJ Olfactory Bulb B V5-P226 mouse diaphragm 65 79 brain, brainstem: CB4_e1_le1 123 111 ciliary body B6 9:1-3 CA1 Normal__Bladder_BL_5 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 833 812 muscle-invasive tumors TK-10 hgu95d Standard Affymetrix Protocol Source GEO sample is GSM16479 Last updated (according to GEO): May 28 2005 861 HIV Infections e_M75 R682P00687 spinal cord 0 11 Pressure-overload induced hypertrophy model. Mouse was sacrificed 24 hours after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2256 Last updated (according to GEO): May 27 2005 GBM Treatment, type=remove Source GEO sample is GSM99453 Last updated (according to GEO): Apr 21 2006 877 Diabetes Mellitus, Non-Insulin-Dependent human caudate nucleus Source GEO sample is GSM86864 Last updated (according to GEO): Feb 08 2006 VDXGUYU_4097 C99 on NCI-7.6k 861 Descending colon Mental Retardation 1000 AD-202t2-A139-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Expression profiling of spinal cord section (T9) extracted from rats 7d following severe injury Lot batch = Source GEO sample is GSM7600 Last updated (according to GEO): May 28 2005 660 mesenchymal stem cell 639 prostate Source GEO sample is GSM203299 Last updated (according to GEO): Jun 21 2007 liver Source GEO sample is GSM18696 Last updated (according to GEO): May 27 2005 AK_Control_ZT 18_3 Lymphoblastoid Cell Line for Individual 8058.3 log phase Epithelium 861 Kidney 1000 Thalamus 1 Normal 50 43 jejunum 861 Cerebral cortex IGF1 and IGF1 receptors (IGF1R) are present in the adult heart and have been shown to be essential for myocardial performance. Insulin-like growth factor 1 (IGF1) is produced in numerous tissues particularly by the liver in response to growth hormone stimulation and is an important factor in the regulation of post-natal growth and development. We have generated and characterized transgenic mice over-expressing the IGF1R. We crossed IGF1R transgenic mice with dominant negative (dn)PI3K (p110) and with constitutively active (ca)PI3K(p110) transgenic mice. Expression profiling was performed on the ventricles of IGF1R, IGF1R-caPI3K, IGF1R-dnPI3K, caPI3K, dnPI3K transgenic female mice at 3 months of age. Non-transgenic littermates were used as controls. Keywords = insulin growth factor, IGF, cardiac, hypertrophy Source GEO sample is GSM18368 Last updated (according to GEO): May 27 2005 BTBR T+ tf/tf Basal Ganglia C 913 frontal lobe CNS-RM_Mod3mo-3A-s2 GSE7506 Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3876 Last updated (according to GEO): May 27 2005 hg_NY28 Dahl Salt Sensitive Rat Lung- Hypoxia, SU-5416, and Sorafenib rep1 173 165 blindness B158 DCs treated with isotype antibody Brain 861 58 41 with endometriosis CNS-SpinalCmod-Adult-28d-2A-s2 20 0 human caudate nucleus iron biological rep1 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lipopolysaccharide (LPS) for 30min Source GEO sample is GSM5661 Last updated (according to GEO): May 27 2005 Colon 110 115 Human papillomaviruses (HPVs) are associated with nearly all cervical cancers (CCs), 20-30% of head and neck cancers (HNCs), and other cancers. Because HNCs also arise in HPV-negative patients, this type of cancer provides unique opportunities to define similarities and differences of HPV-positive versus HPV-negative cancers arising in the same tissue. Here, we describe genome-wide expression profiling of 84 HNCs, CCs and site-matched normal epithelial samples in which we used laser capture microdissection to enrich samples for tumor-derived versus normal epithelial cells. This analysis revealed that HPV+HNCs and CCs differed in their patterns of gene expression yet shared many changes compared to HPV-HNCs. Some of these shared changes were predicted, but many others were not. Notably, HPV+HNCs and CCs were found to be upregulated in their expression of a distinct and larger subset of cell cycle genes than observed in HPV-HNC. Moreover, HPV+ cancers over-expressed testis-specific genes that are normally expressed only in meiotic cells. Many, though not all, of the hallmark differences between HPV+HNC and HPV-HNC were a direct consequence of HPV and in particular the viral E6 and E7 oncogenes. This included a novel association of HPV oncogenes with testes specific gene expression. These findings in primary human tumors provide novel biomarkers for early detection of HPV+ and HPV- cancers, and emphasize the potential value of targeting E6 and E7 function, alone or combined with radiation and/or traditional chemotherapy, in the treatment of HPV+ cancers. Last Updated (by provider): May 31 2007 Contributers: Elaine M Smith Thomas H Haugen Lubomir P Turek Paul Ahlquist Joseph P Connor Johan A den Boon Dohun Pyeon Karl T Kelsey Michael A Newton Carmen J Marsit Paul F Lambert Srikumar Sengupta nucleus accumbens, whole wistar1 Obtained with a 1.5 mm diameter punch, using a 2mm thick slice, and anterior commisure was in dorsolateral portion of punch, pool of 5 animals, 16 weeks old, male Wistar whole nucleus accumbens file:R3JV01080105 Source GEO sample is GSM15197 Last updated (according to GEO): May 28 2005 eye 0 3 PMN_control_180min_Patient5 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc119 Source GEO sample is GSM1871 Last updated (according to GEO): Nov 21 2005 Spleen vs MIP3-alpha Treated B cell 30min (set3) The cerebellar transcriptome during postnatal development of the Ts1Cje mouse, a segmental trisomy model for Down syndrome. 1236 CP0_11 Diet-induced changes in serum lipoproteins are a major risk factor for the development of atherosclerosis, the leading cause of mortality in Westernized countries. Atherosclerosis is now appreciated to be a systemic inflammatory disease where increased synthesis of inducible proteins by the liver, such as C-reactive protein (CRP) and others, may play roles in accelerating the disease process. To systematically investigate the genetic response of the liver to diet-induced atherosclerosis, we applied high-density microarray technology in a mouse model of atherosclerosis (LDLR-/- mouse). LDLR-/- mice and congenic (LDLR+/+) controls were placed on low-fat (LF) or high-fat (HF) Western-style diets. The Western diet produced sustained elevations in total cholesterol (2.5-fold for LDLR+/+, 5.0-fold LDLR-/-) relative to the respective LF groups. Tissues were harvested after 12 wk when significant atherosclerotic lesion development was first detectable by en face histomorphometry of oil red O-stained aortas. Diet, rather than genotype, was most highly associated with development of atherosclerotic lesions. Liver mRNA expression profiles of triplicate animals from each group were determined by high-density oligonucleotide microarrays; and genes with transcript levels influenced by genotype and diet were identified by two-way ANOVA. Approximately one-third of the 102 genes identified to be altered by diet [Pr(F) < 0.0005] were involved in lipid metabolism. In addition, we identified components of the alternative complement pathway, including C3, properdin, and factor D, for which mRNA levels were independently confirmed by quantitative real-time RT-PCR analysis, and C3 protein was demonstrated in aortic lesions by immunostaining. These findings suggest that induction of the alternative complement pathway may be an additional mechanism by which a high-fat/Western diet accelerates atherosclerosis. mild cognitive impairment - middle temporal gyrus 2 starved 30 36 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11273 Last updated (according to GEO): May 28 2005 PE_N_562 GSE5682 Day 3 Mouse #31 - 1st replicate hippocampus: Sample #5_e1_le1 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162190 Last updated (according to GEO): Jun 12 2007 861 Cardiomyopathies Epithelium of bronchus 983 spinal_cord_4 Spinal Cord 1000 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b039 Source GEO sample is GSM1968 Last updated (according to GEO): Nov 21 2005 Gastrointestinal Neoplasms 896 healthy control sample x117 Brain_C57 Wildtype_affs275-1099 tibiae 115 120 PBMCs-Type 1 Diabetes-IDDM18_T1D_New male C57BL6, double amplification Source GEO sample is GSM5431 Last updated (according to GEO): Mar 17 2006 861 Prostate Gene expression data from postmorten brain regions Source GEO sample is GSM145751 Last updated (according to GEO): Nov 20 2006 861 Acquired Immunodeficiency Syndrome Ovarian_Tumor_ClearCell_CHTN-OC-028 I_95Av2_1871_Cg_0_GS Stem cells 1000 CNS-SpinalC-conAdult-T0-2C-s2 Expression profiling of spinal cord section (T8) extracted from rats 4h following severe injury Source GEO sample is GSM31484 Last updated (according to GEO): May 27 2005 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html. Date GSE776 Last Updated: Jun 15 2005 Contributers: Jeffrey Brown Seigo Izumo Peter Kang Includes GDS489. Update date: May 03 2004. Dataset description GDS489: Analysis of physiologic hypertrophy (induced via exercise) and pathologic hypertrophy (induced via high salt diet) in Dahl salt-sensitive (DS) rats. Left heart ventricle examined at 3, 6 and 15 weeks. Pathologic hypertrophy leads to heart failure.. RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above Source GEO sample is GSM160013 Last updated (according to GEO): Feb 05 2007 200 in the frontal cortex 220 5 0 brain visceral adipose tissue 635 658 Pituitary Gland 1000 Transitional epithelium 1000 Mouse Ovary 3 (technical replicate) 62 38 out of mouse bone marrow AD control Treatment, type=dissect Source GEO sample is GSM119631 Last updated (according to GEO): Jul 10 2006 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159808 Last updated (according to GEO): Apr 23 2007 Neostriatum 1000 R6/2 (untreated) 5227 5 0 Spleen Spleen vs CGS Treated B cell 120min (set1) Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68317 Last updated (according to GEO): Jul 07 2006 of mouse brain 9 23 RNA obtained from vastus lateralis muscle biopsies from 8 healthy men, 62-72 years old. RNA was pooled before cDNA synthesis. Analysis done with Affymetrix Microarray Suite 5.0 software. Keywords = muscle, aging Source GEO sample is GSM2401 Last updated (according to GEO): May 27 2005 28 in the prefrontal cortex 51 2032 2022 for livers Expression profiling of spinal cord section (T10) extracted from rats 28d following severe injury Source GEO sample is GSM31371 Last updated (according to GEO): May 27 2005 A HID I D083 Bladder tumours used to construct a tumour stage classifier. Date GSE89 Last Updated: May 29 2005 Contributers: Niels Marcussen Thomas Thykjaer Jens L Jensen Hans Wolf Lars Dyrskjot Torben F Orntoft Stephen Hamilton-Dutoit Mogens Kruhoffer Includes GDS183. Update date: Apr 09 2003. Dataset description GDS183: Identification of clinically relevant subclasses of bladder carcinoma. Three major stages identified, Ta, T1 and T2-4. Ta tumors further classified into subgroups. A 32-gene molecular classifier was built.. pfc_1024_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A HOP-62 hgu95e Central gray substance of midbrain 861 Liver Test (Blinded) Sample Source GEO sample is GSM130132 Last updated (according to GEO): Sep 18 2007 Heart 861 Brain 1000 LungE135_022WAF76_076.txt The adult somatosensory cortex undergoes reorganization in response to changes in peripheral input, such as limb usage patterns or denervation/amputation. This reorganization underlies important phenomena, such as phantom pain, recovery after stroke, and certain forms of learning. Although cellular processes, such as LTP, receptor regulation, axonal growth and synaptic formation have been theorized and studied in relation to cortical reorganization, conclusive evidence remains elusive. The identification of genes up- and down-regulated during reorganization will provide clues for which processes underlie reorganization. Reorganization is likely to involve forms of signaling between cortical neurons (e.g. release of growth factors), which could be identified through gene chip studies. Identification of genes modulated during reorganization will provide specific direction for further studies in the elucidation of the mechanism(s) underlying cortical reorganization. To identify those genes with altered regulation during the cortical reorganization process. We hypothesize that genes regulated during cortical reorganization will be components of the mechanism(s) underlying this important process, and that identification of these genes will provide insight for the design of further studies of cortical plasticity. Cortical reorganization in rat somatosensory cortex (S1) will be induced at the forepaw/lower jaw border by partially denervating the paw. The animals will be recovered and the reorganization allowed to proceed for 3, 7, 14 and 28 days. Control animals will receive a sham denervation. Following the allotted time, the border between the lower jaw and the now silent forepaw cortex will be mapped in vivo. A 500 um wide strip of cortex surrounding the border area will be excised and stored in RNAlater (Qiagen) at 20oC until processed for RNA extraction. The tissue will be dispersed using a disposable pestle and microcentrifuge tube and then homogenized in Qiashredder (Qiagen) columns. RNA will be extracted using a RNeasy Micro Kit. However, if the UCLA center has a rotor/stator homogenizer with a microcentrifuge tube sized probe, we would like to discuss the possibility of performing the RNA extraction there (we would expect a better yield, and cannot locate this equipment at UCR). An initial portion of this study will done for 3 day experimental and sham control animals, plus non-operated animals, with four animals per group. This will be to determine the variability among our samples and to familiarize our personnel with the process. The number of samples/group necessary for the remaining time points may be modified based on the results of the 3 day study. Last Updated (by provider): Jul 06 2005 Contributers: P A Steen Includes GDS1840. Update date: Jun 14 2006. Dataset description GDS1840: Analysis of the adult somatosensory cortex at the forepaw/lower jaw border at various time points up to 28 days after partial paw denervation. The adult somatosensory cortex undergoes reorganization in response to changes in peripheral input, such as limb usage patterns or denervation.. D01 6h Media 5 0 brain 1000 Brain NCI60.32_LABEL36EXTRACT35SUB3 Source GEO sample is GSM134152 Last updated (according to GEO): Aug 06 2007 Laser captured visceral sensory neurons. Source GEO sample is GSM63687 Last updated (according to GEO): Dec 21 2005 normal testis 54 66 Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 6930 left_liver_lobe Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 22 hours after lights on. Original RNA code = LC34A. Source GEO sample is GSM227391 Last updated (according to GEO): Sep 10 2007 1037 of transitional epithelium 1012 Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.4 Subject: 2978 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39048 Last updated (according to GEO): May 27 2005 786-0__CL9018_RENAL Gene expression data from dorsal pancreas at e13.5, MG-U74A version2 Source GEO sample is GSM199446 Last updated (according to GEO): Jun 08 2007 861 leukemia MCF7_CHX_EtOH_24h_rep3 /3T3 fibroblasts 743 759 NeverSmoker 94 NCI60.10_LABEL13EXTRACT12SUB3 Source GEO sample is GSM134040 Last updated (according to GEO): Aug 06 2007 5 0 Spleen Heart Ventricle 1000 brain, hippocampus: ADX PM Hip b_e1_le1 HCC (HBV+, HK29) 1000 Tonsil 3AJZ02060514_OlfactoryBulb human frontal cortex Source GEO sample is GSM86940 Last updated (according to GEO): Feb 08 2006 913 Coronary heart disease Control #1 embryo_at_day3.5_rep2 Mouse old heart w/ a-tocopherol aT-Ht-3 Recurrent Squamous cell carcinoma 1 0 34 660 mesenchymal stem cell 639 Brain 1000 BALB/cByJ Cingulate Cortex A 1BMH02082901_BM_CD34 brain 0 5 Gene expression data from whole brain of uninfected mouse Source GEO sample is GSM189628 Last updated (according to GEO): May 16 2007 228 219 Hippocampi 888 Extracellular Matrix 901 Mammary Neoplasms Normal Thyroid 865 Disorder of artery 43 0 Chorionic mesoderm-derived mesenchymal cells 5 0 brain small cell lung carcinoma 4567 0 29 861 Cerebral cortex I_U133A_98_AnCg post HCMV infection 18 36 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141275 Last updated (according to GEO): Oct 26 2006 861 Cerebral cortex Cerebral cortex 1000 Adrenal Medulla 1000 Primary Neoplasm 1000 5 0 brain Heart 1000 Nasal Epithelium 901 Keywords = muscle 123 140 whole blood_100689 Hyperdip>50-2M#1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 0089 blood 11 0 spinal cord 3_hypothalamus_9hrs_sleep_deprivation_#83 MCF7 hgu95c Cerebellum 1000 43 0 Chorionic mesoderm-derived mesenchymal cells 1000 Brain 1000 Cerebral cortex HUVEC isolate C rich media VEGF-A 24hours cf. #5 Source GEO sample is GSM12899 Last updated (according to GEO): May 28 2005 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16994.gif Source GEO sample is GSM91577 Last updated (according to GEO): Sep 22 2006 1000 Primary carcinoma of the liver cells V5-P271 41 25 of the Rat Retina Multiple Myeloma 901 CNS-RM_Mod24h-3B-s2 whole brain from nicotinic acetylcholine receptor beta4 subunit null mutant mouse Source GEO sample is GSM120584 Last updated (according to GEO): Sep 22 2006 5 0 Spleen pharyngeal_mucosa_2 Source GEO sample is GSM80748 Last updated (according to GEO): Mar 31 2006 Expression profiling of somatomotor cortex extracted from rats at 28d following sham surgery Source GEO sample is GSM41649 Last updated (according to GEO): May 27 2005 5 0 brain Parkinson Disease 861 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188816 Last updated (according to GEO): Jun 06 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145473 Last updated (according to GEO): Nov 20 2006 Colorectal Adenocarc Source GEO sample is GSM18707 Last updated (according to GEO): Sep 25 2006 Infection 1000 Posterior root of spinal nerve 861 Liver 1000 C3H/HeJ Cerebellum D M_U133Plus_120_AnCg Blood 1000 Heart Ventricle 1000 n/a Source GEO sample is GSM177920 Last updated (according to GEO): Jun 11 2007 M_U133A_96_DLPFC Brain 861 2M_120502 H9LMS99090504 861 Neoplasm Metastasis EOM 112 Day mdx rep 3 We used manual macrodissection or laser capture microdissection (LCM) to isolate tissue sections of the hippocampus area of Ras-GRF1 wild type and knockout mice brains, and analyzed their transcriptional patterns using commercial oligonucleotide microarrays. Comparison between the transcriptomes of macrodissected and microdissected samples showed that the LCM samples allowed detection of significantly higher numbers of differentially expressed genes, with higher statistical rates of significance. These results validate LCM as a reliable technique for in vivo genomic studies in the brain hippocampus, where contamination by surrounding areas (not expressing Ras-GRF1) increases background noise and impairs identification of differentially expressed genes. Comparison between wild type and knockout LCM hippocampus samples revealed that Ras-GRF1 elimination caused significant gene expression changes, mostly affecting signal transduction and related neural processes. The list of 36 most differentially expressed genes included loci concerned mainly with Ras/G protein signaling and cytoskeletal organization (i.e. 14-3-3?/?, Kcnj6, Clasp2) or related, cross-talking pathways (i.e. jag2, decorin, strap). Consistent with the phenotypes shown by Ras-GRF1 knockout mice, many of these differentially expressed genes play functional roles in processes such as sensory development and function (i.e. Sptlc1, antiquitin, jag2) and/or neurological development/neurodegeneration processes affecting memory and learning. Indeed, potential links to neurodegenerative diseases such as Alzheimer disease (AD) or Creutzfeldt-Jacobs disease (CJD), have been reported for a number of differentially expressed genes identified in this study (Ptma, Aebp2,Clasp2, Hebp1, 14-3-3?/?, Csnk1?, etc.). These data, together with the previously described role of IRS and insulin (known Ras-GRF1 activators) in AD, warrant further investigation of a potential functional link of Ras-GRF1 to neurodegenerative processes. Last Updated (by provider): Jul 12 2007 Contributers: J De Las Rivas A Porteros A Nuñez A Fernández-Medarde E Santos J J Fuster 901 Intestines, Small Universal Mouse Reference RNA Source GEO sample is GSM93431 Last updated (according to GEO): Jan 23 2006 with mental retardation 241 263 Expression profiling of somatomotor cortex extracted from rats at 7d following moderate injury Lot batch = Source GEO sample is GSM44718 Last updated (according to GEO): May 27 2005 1000 Left GSE4192 NA Source GEO sample is GSM109470 Last updated (according to GEO): May 22 2006 Epithelium 861 HUVEC isolate V low serum media control for #28 Source GEO sample is GSM12919 Last updated (according to GEO): May 28 2005 1124 1103 of the pituitary gland Blood 861 CH1802 Colonic mucous membrane 913 Accumbens 10 Normal 27 0 H9 Human Embryonic Stem cell Expression profiling of spinal cord section (T8) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31398 Last updated (according to GEO): May 27 2005 Brain 861 T3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A PGA-MFD-CtrPD5-2aBv2-s2 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68346 Last updated (according to GEO): Jul 07 2006 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225651 Last updated (according to GEO): Aug 31 2007 Osteoblasts 1000 CNS-SMTC_Mod24h-2A-s2 861 Cerebral cortex Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b025 Source GEO sample is GSM2016 Last updated (according to GEO): Nov 21 2005 4 0 Brain 1000 Spinal Cord 20 0 human caudate nucleus NCI-H322 hgu95c 91 from the bone marrow 72 Gene expression data from PD14 Foxo3 Null ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203839 Last updated (according to GEO): Aug 02 2007 1000 Heart failure 1000 Liver High Freezing Source GEO sample is GSM92416 Last updated (according to GEO): Jan 13 2006 ADH-1 ip saline ILI 4hrs post ILI sample B NSCLC_A549/ATCC_CL1004 on Affymetrix GeneChip Human Full Length Array HuGeneFL 329 306 valvular cardiomyopathy Prosencephalon 861 Standard Affymetrix Protocol Keywords = microarray Keywords = muscle Source GEO sample is GSM15934 Last updated (according to GEO): May 28 2005 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188726 Last updated (according to GEO): Jun 06 2007 1000 Lung 1000 Rectum NA18944 Epithelial Cells 1000 cerebellum wistar ky 3893 whole tissue, individual animal, 10 weeks old, male Wistar Kyoto cerebellum file:p3893w Source GEO sample is GSM15136 Last updated (according to GEO): Oct 28 2005 Time point 48h post HCMV infection mouse brain 478 489 1000 Hippocampus Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.86 Subject: 2822 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39021 Last updated (according to GEO): May 27 2005 To add Source GEO sample is GSM207580 Last updated (according to GEO): Jul 25 2007 BT-549 hgu95c Left 1000 CS-B cell unirradiated replicate 3 U133A 1000 Spleen Category: Tissue Rejection Subcategory: Kidney UTI/Pyelonephritis also Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=690660 LaserPower=2.141.28 Lot batch = LC17N111 Source GEO sample is GSM4829 Last updated (according to GEO): Nov 21 2005 no additional Source GEO sample is GSM199145 Last updated (according to GEO): Jun 08 2007 CNS-SMTC_Ctr3mo-1B-s2 30 19 Solid tumor PGA-Csx_wt_5a-m4 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141328 Last updated (according to GEO): Oct 26 2006 Autistic Disorder 877 GM07048 Saccule structure 1000 eye, retina: 2 Retina at CT 12_e1_le1 Epithelium 861 Gene expression data of substantia nigra from postmortem brain of normal controls Source GEO sample is GSM184359 Last updated (according to GEO): May 29 2007 WGACON-111 Disease Source GEO sample is GSM176455 Last updated (according to GEO): Apr 09 2007 MF-33 Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2644.gif Source GEO sample is GSM72184 Last updated (according to GEO): Sep 22 2006 1000 frontal lobe Large-scale analysis of the human transcriptome. Brain, caudate nucleus Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 233.03 Stdv: 9.77 Min: 206.76 Max: 246.58 Source GEO sample is GSM2885 Last updated (according to GEO): Mar 20 2006 plasma cells 50 61 1000 Cardiomyopathy, Alcoholic The Affymetrix GeneChip MgU74Av2 was used to analyze expression profiles of mice that had cardiac hypertrophy induced by swimming training. More information of this model can be obtained at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/swim_home.html. Date GSE77 Last Updated: May 29 2005 Contributers: Iuan Chen Martina Schinke Lauren E Riggi Seigo Izumo Includes GDS144. Update date: Apr 06 2003. Dataset description GDS144: Effects of chronic conditioning by swimming which increases left ventricular mass and induces myocyte hypertrophy. 8 week old FVB mice swum in tanks 7 days a week for 4 weeks. Animals sacrificed at several time points up to 28 days.. 861 Cerebral cortex Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92331 Last updated (according to GEO): Jan 13 2006 none Source GEO sample is GSM239961 Last updated (according to GEO): Dec 07 2007 Bone marrow, Mesenchymal stem cells: T1-210404_e1_le1 prostate_gland_2 Source GEO sample is GSM80806 Last updated (according to GEO): Mar 31 2006 1000 frontal lobe Cerebral cortex 861 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47529 Last updated (according to GEO): May 29 2005 with the control muscles 1507 1531 Meningioma Primary Grade 1 Source GEO sample is GSM108025 Last updated (according to GEO): Jun 06 2006 3 week Post Natally excised Human lung tissue Source GEO sample is GSM107825 Last updated (according to GEO): May 04 2006 brain, Posterior Singulate: Sample44_e1_le1 V5-P457 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Leukotriene B4 (LTB4) labeled with Cy5- time course with repeats. Date GSE390 Last Updated: May 29 2005 Contributers: Angela Alexander Joella Grossoehme Mi Sook Chang Sangdun Choi Yun Anna Cao Zhen Yan Sun Young Lee Jong-Woo Kim Robert Hsueh Rebecca Hart Includes GDS311. Update date: Nov 18 2003. Dataset description GDS311: Temporal analysis of effects induced by 1 uM leukotriene B4 in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. Pool of 12 saccules at E12.5 Source GEO sample is GSM182610 Last updated (according to GEO): Aug 14 2007 5 0 brain 091265 Pool1(dup) on Affymetrix GeneChip Human Full Length Array HuGeneFL CHIPEXP_NAME: 230_2_050531tpj_8h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Vehicle_Control TREAT_TOX_MECHANISM1: Liver_Non_Toxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0 SAMPLING_TIME: 3 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197613 Last updated (according to GEO): Jun 01 2007 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181211 Last updated (according to GEO): Jul 12 2007 HapMap CEU_parent Male Source GEO sample is GSM159553 Last updated (according to GEO): Feb 01 2007 861 Cancer of Neck 255 234 with HIV encephalitis 0 Human Cortex 11 4 0 Brain plasma cells 50 61 the heart 987 996 117 112 Lipids SN:1010406 Source GEO sample is GSM115389 Last updated (according to GEO): Jun 20 2006 Subcutaeous isolated adipocytes, rep3 RR216_uninfected_DC total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Sphingosine-1-phosphate for 30min Source GEO sample is GSM5744 Last updated (according to GEO): May 27 2005 The vascular endothelium 0 23 5 0 brain Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11573 Last updated (according to GEO): May 28 2005 with Parkinson's disease 27 50 32 12 frontal temporal lobe doxycycline, mutant Source GEO sample is GSM213381 Last updated (according to GEO): Jul 26 2007 Genome-wide gene expression in HDAC5 wildtype and knockout mice treated with chronic cocaine or saline total spinal cord 0 16 Cerebral cortex 861 Posterior root of spinal nerve 861 Mesenchymal Stem Cells 1000 human caudate nucleus Source GEO sample is GSM86842 Last updated (according to GEO): Feb 08 2006 Amygdaloid structure 861 Spinal Cord 1000 1BJZ02022108_spinalcord S46 WT6 F5/54 S46 wild type Mouse 10 months Cerebellum Female Source GEO sample is GSM73223 Last updated (according to GEO): Sep 06 2005 vagina_10 Source GEO sample is GSM80904 Last updated (according to GEO): Mar 31 2006 Bone marrow, Mesenchymal stem cells: T2-1-101103_e1_le1 Testis 1000 Whole brain 0 10 1M_B31103 P46 non-deprived visual cortex replicate 2 Control_long-term 9 of prefrontal cortex 28 Transitional epithelium 1000 861 Cerebral cortex 77 67 cecum C57BL Gene expression data from postmorten brain regions Source GEO sample is GSM145092 Last updated (according to GEO): Nov 20 2006 865 Disorder of artery 913 frontal lobe Female mice used were 129/SvImJ wildtype (Jackson Lab), 10-16 weeks of age. 14 days after ovariectomy, mice were injected subcutaneously with progesterone dissolved in sesame oil (Sigma; 0.2mg/0.1mL/mouse), followed by sacrifice and removal of uterine horns at 1 hour after injection. 8 uterine horns from 4 mice were pooled to form one sample. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix. Source GEO sample is GSM3054 Last updated (according to GEO): May 27 2005 with some respiratory epithelium. 1039 1072 861 Encephalitis of somatomotor cortex 21 41 1000 Pituitary Gland Carcinoma, Large Cell 867 no additional Source GEO sample is GSM199219 Last updated (according to GEO): Jun 08 2007 Expression profiling of spinal cord section (T9) extracted from rats 24h following severe injury Lot batch = Source GEO sample is GSM7567 Last updated (according to GEO): May 28 2005 Normal Source GEO sample is GSM176139 Last updated (according to GEO): Apr 09 2007 Low-density CCg progenitors treated with RA/Fsk to derive Neurons Source GEO sample is GSM47558 Last updated (according to GEO): Jun 10 2005 Plasma 861 Knockout saline, biological replicate 6 Colon (transverse) [JunctionChip 4 of 5] Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198640 Last updated (according to GEO): Jun 06 2007 1000 Hypertrophic Cardiomyopathy human cerebellum Source GEO sample is GSM87073 Last updated (according to GEO): Feb 08 2006 RENAL_RXF393 on Affymetrix GeneChip Human Full Length Array HuGeneFL Brain 861 Coronary artery 901 cardiac 763 769 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 6 hour after the last shock treatment. Source GEO sample is GSM4533 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145766 Last updated (according to GEO): Nov 20 2006 861 Neoplasm 304 280 alcoholic cardiomyopathy Cultured_osteoblast-like_control_MC3T3-E1_cells_rep6 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152001 Last updated (according to GEO): Feb 06 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD27 for 60min Source GEO sample is GSM5488 Last updated (according to GEO): May 27 2005 in the cerebellum 29 45 1000 Muscle brain 0 5 923 Congestive heart failure Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b056 Source GEO sample is GSM1958 Last updated (according to GEO): Nov 21 2005 983 Muscle C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 6 hour after the last shock treatment. Source GEO sample is GSM4528 Last updated (according to GEO): May 27 2005 rat hippocampus Treatment, type=time_course, measurement=1.0 h Source GEO sample is GSM32125 Last updated (according to GEO): May 27 2005 Sample29, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53280 Last updated (according to GEO): Jul 06 2005 Congenital Abnormality 853 76 45 with nearly all cervical cancers 146 134 encephalitis spinal cord 46 56 Anterior nares 1000 61 50 Bone marrow of Parkinson's disease 450 471 231 222 this organ spinal cord 0 11 1000 pars nervosa of hypophysis CAD_replicate18 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153456 Last updated (according to GEO): Jan 11 2007 Y HID D039 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108634 Last updated (according to GEO): Aug 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145192 Last updated (according to GEO): Nov 20 2006 cerebral cortex 7 21 ISR10-PERK UT2 RNA from untreated PERK-/- cells. The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules. Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10893 Last updated (according to GEO): May 27 2005 kidney 37 43 Total RNA from cultured stria vascularis, pool from 12 cochleas; used as control for hypoxia. Source GEO sample is GSM124837 Last updated (according to GEO): Aug 04 2006 1000 Stem cells In the classical form of a1antitrypsin deficiency a mutant protein accumulates in a polymerized form in the ER of liver cells causing liver damage and carcinogenesis by a gain-of-toxic function mechanism. Recent studies have indicated that the accumulation of mutant a1antitrypsin Z in the ER specifically activates the autophagic response but not the unfolded protein response and that autophagy plays a critical role in disposal of insoluble a1antitrypsin Z. In this study, we used genomic analysis of the liver in a novel transgenic mouse model with inducible expression to screen for changes in gene expression that would potentially define how the liver responds to accumulation of this mutant protein. There was no unfolded protein response . Of several distinct gene expression profiles, marked upregulation of regulator of G signaling (RGS16) was particularly notable. RGS16 did not increase when model systems were exposed to classical inducers of ER stress including tunicamycin and calcium ionophore or when a nonpolymerogenic a1antitrypsin mutant accumulated in the ER. RGS16 was upregulated in livers from patients with a1antitrypsin deficiency and the degree of upregulation correlated with the hepatic levels of insoluble a1antitrypsin Z protein. Taken together, these results indicate that expression of RGS16 is an excellent marker for the distinct form of 'ER stress' that occurs in a1antitrypsin deficiency, presumably determined by the aggregation-prone properties of the mutant protein that characterizes the deficiency. at the Human Brain 744 761 Malignant Neoplasms 861 Brain 861 4 0 Ovary Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19202 Last updated (according to GEO): May 27 2005 7 cerebral cortex 21 Structure of horn of uterus 884 23 11 of the kidney Small cell carcinoma of lung 937 heart failure 583 595 Blood Test (Blinded) Sample Source GEO sample is GSM129922 Last updated (according to GEO): Sep 18 2007 (cortex 19 25 RNAtotC_25, ZT6 Time point at 60min post HCMV infection Cerebral cortex 861 hippocampal glutamatergic CA1 pyramidal neurons Source GEO sample is GSM35818 Last updated (according to GEO): May 27 2005 15 0 human cerebellum Gene expression data from human colon tumor tissue Source GEO sample is GSM173364 Last updated (according to GEO): Apr 20 2007 0 Human Cortex 11 whole blood_100214 259 252 (Adenoma Fibroblasts 861 Carcinoma, Large Cell 867 to the nose 599 609 of tumor growth 670 684 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28768 Last updated (according to GEO): May 27 2005 988 980 cerebella Nucleus accumbens, male 10.5 week old c57bl/6J mouse, SUSCEPTIBLE group Source GEO sample is GSM224744 Last updated (according to GEO): Aug 31 2007 from liver 21 30 Malignant neoplasm of stomach 901 Nj13: Hippocampus_21PT-AI_rep5 Skeletal muscle structure 1000 Normal Source GEO sample is GSM175940 Last updated (according to GEO): Apr 09 2007 NA18961 Spleen 1000 human caudate nucleus Source GEO sample is GSM86870 Last updated (according to GEO): Feb 08 2006 Pituitary Gland 861 Gastrocnemius muscle 2 days after 100ul 10uM cardiotoxin injection Source GEO sample is GSM4276 Last updated (according to GEO): May 27 2005 CVB3_S-3h-4 parietal_lobe_3 Source GEO sample is GSM80746 Last updated (according to GEO): Mar 31 2006 Brain 1000 39 12 of congenital heart disease from the olfactory epithelium tissue 171 207 335 325 The jejunum M_U133Plus_89_nAcc Gene expression in PBMCs from children with diabetes Spleen vs 2-Methyl-thio-ATP Treated B cell 240min (set2) human frontal cortex Source GEO sample is GSM86985 Last updated (according to GEO): Feb 08 2006 1000 Amygdaloid structure Heart 1000 Large-scale analysis of the mouse transcriptome. Lymph node, mesenteric C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 284.59 Stdv: 16.72 Min: 260.70 Max: 315.90 Source GEO sample is GSM2940 Last updated (according to GEO): Mar 20 2006 Malignant Neoplasms 1000 Gene expression data from brain of adult rats Source GEO sample is GSM101056 Last updated (according to GEO): Feb 20 2007 2.5 mg/kg 2CdA headfold at 6.0h Heart Septal Defects, Atrial 1000 Seminoma of testis 1000 Lymphoblastoid Cell Line for Individual 8188.3 log phase Normal Source GEO sample is GSM176032 Last updated (according to GEO): Apr 09 2007 Brain 861 861 Carcinoma Brain 1000 40 21 from the hippocampus vulva_10 Source GEO sample is GSM80900 Last updated (according to GEO): Mar 31 2006 861 Blood 1000 Folic Acid Deficiency 861 Spinal Cord frontal_lobe_10 Source GEO sample is GSM80678 Last updated (according to GEO): Mar 31 2006 R569P00764 Skeletal muscle structure 1000 1000 Brain of the stria terminalis 49 71 NA12743 growth 1 Expression profiling of spinal cord section (T8) extracted from rats 7d following severe injury Source GEO sample is GSM31494 Last updated (according to GEO): May 27 2005 Spleen 0 5 4 0 Heart Gene expression data from postmorten brain regions Source GEO sample is GSM145357 Last updated (according to GEO): Nov 20 2006 Spleen 1000 healthy subject Source GEO sample is GSM211043 Last updated (according to GEO): Sep 10 2007 to endothelial cells 1113 1132 spinal cord, spinal cord: G6C_le1 Blood Test (Blinded) Sample Source GEO sample is GSM129995 Last updated (according to GEO): Sep 18 2007 Date : 10/4/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 4.5 hrs post-injection Intervention : none Risk: estimated 20% increased risk for encephalopathy Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AG673 Source GEO sample is GSM12249 Last updated (according to GEO): May 28 2005 Basal-like breast tumor cell line Sum102 Keywords = Agilent microarray, Expression analysis, EGFR, Breast cancer growth Source GEO sample is GSM29450 Last updated (according to GEO): Dec 13 2006 913 Fetal Diseases Pool of 8 non-inner ear tissue samples at E9 Source GEO sample is GSM182622 Last updated (according to GEO): Aug 14 2007 cortex from B6 mice at ZT15 rep1 Source GEO sample is GSM160458 Last updated (according to GEO): Feb 05 2007 AD-266t1-A90-3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Spleen 1000 D3_TP-24_C in mdx skeletal muscle 1079 1101 of somatomotor cortex 21 41 Gene expression data from human colon tumor tissue Source GEO sample is GSM173375 Last updated (according to GEO): Apr 20 2007 Gastrocnemius muscle 4 days after 100ul 10uM cardiotoxin injection Source GEO sample is GSM4291 Last updated (according to GEO): May 27 2005 Alzheimer's Disease 861 17 7 hippocampus Balb/c day 0, biological rep 4, tech rep 1 To investigate the gene program activated by serotonergic hallucinogens in mouse somatosensory cortex, the effects of the 5-HT2A agonist (±)2,5-dimethoxy 4-iodoamphetamine (DOI) on gene expression was studied. The 5-HT2A serotonin receptor is a member of the 5-HT2 receptor subfamily of G protein?coupled receptors. The 5-HT2A receptor is thought to modulate processes related to cognition, appetite, mood, anxiety, sleep, and sexual behavior. Abnormal function of this receptor has been implicated in neuropsychiatric disorders such as major depression and schizophrenia. In particular, the 5-HT2A receptor has been implicated in the modulation of the mechanisms related to psychosis. We compared gene response patterns in the somatosensory cortical brain area, which has a high density of 5-HT2A receptors and has been implicated in the action of hallucinogenic drugs. Mice (strain 129Sv) were injected with DOI (2 mg/kg or 10 mg/kg) or vehicle, animals were sacrificed after 1 h, and somatosensory cortex samples dissected on ice for RNA extraction. Seven independent microarray hybridizations from seven different DOI- or vehicle-treated mouse pairs were performed.. Date GSE138 Last Updated: Oct 28 2005 Contributers: Elisa Wurmbach Jay A Gingrich Alena Lira Stuart C Sealfon Barbara J Ebersole Tony Yuen Javier González-Maeso Includes GDS346. Update date: Nov 03 2005. Dataset description GDS346: Effect of 5-HT2A seratonin receptor agonist (±)2,5-dimethoxy 4-iodoamphetamine (DOI) in somatosensory cortex. 129Sv mice injected with DOI (2 mg/kg or 10 mg/kg), 1 hour. Abnormal 5-HT2A receptor function implicated in depression and schizophrenia.. 861 Heart Diseases Gene expression data from postmorten brain regions Source GEO sample is GSM145073 Last updated (according to GEO): Nov 20 2006 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162159 Last updated (according to GEO): Jun 12 2007 Autistic Disorder 1000 141 106 Keywords = Congestive heart failure Brain 1000 Nasal Epithelium 901 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201768 Last updated (according to GEO): Jun 20 2007 Epithelial Cells 1000 HNC018 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n131 Source GEO sample is GSM2053 Last updated (according to GEO): Nov 21 2005 BXD 21_M7SS02080604 small intestine 0 14 Cerebellum 1000 mouse brain ipsilateral control Source GEO sample is GSM149765 Last updated (according to GEO): Mar 15 2007 1000 Heart Testis (NL075) Hybe #1 Collection of data from ´mRNA obtained from the spinal cord of hree human fetuses suffering from Lethal Congenital Contracture Syndrome and two age-matched human fetuses aborted to unrelated causes. Last Updated (by provider): Nov 10 2005 Contributers: Niklas Pakkasjärvi Includes GDS1295. Update date: Nov 09 2005. Dataset description GDS1295: Analysis of spinal cord from fetuses with lethal congenital contracture syndrome (LCCS). LCCS is autosomal recessive, causes death in 32nd gestational week, and involves degeneration of anterior horn motor neurons in spinal cord. Results provide insight into pathways active in motoneuron disease.. Gastrointestinal Stromal Tumors 966 Accumbens 9 Normal Muscle Source GEO sample is GSM4309 Last updated (according to GEO): May 27 2005 PGA-MAH-OuJAir-1bAv2-s1 WT 2 mon replicate 1 33 17 tibialis anterior Abdominal aorta structure 865 298 in skeletal muscle 281 Colon (transverse) [JunctionChip 5 of 5] Normal__Whole_Brain_BRAIN_3 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Utricle structure 861 1000 Liver Spleen 1000 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5157.gif Source GEO sample is GSM79934 Last updated (according to GEO): Sep 22 2006 SN:Human Glioblastoma Biopsy 29154 Macrophage smi48 striatum_Hdh4Q80_9S Liver 1000 MuscleRegen-ctx4d-2RLAv2-s2 no additional Source GEO sample is GSM199387 Last updated (according to GEO): Jun 08 2007 Skeletal bone 861 184Aa Parkinson's disease sample x114 Neoplasm 861 Epithelial Cells 1000 9 0 Blood Test Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19236 Last updated (according to GEO): May 27 2005 Ganglia, Spinal 884 1868 1854 adhering blood Alzheimer's Disease 861 -_5937_batch1 on NHGRI-6.7k Proliferating normal human peripheral blood mononuclear cells infected with HIV type 1 RF Spinal Cord 861 prostate Source GEO sample is GSM203363 Last updated (according to GEO): Jun 21 2007 Uterus 1000 Melanoma xenograft, MEA3_Lung_B (LeiFidler) Blood 861 3AJZ02022764_cerebellum HDMTX_MP-DX-9 corpus_callosum_1 32 16 of organ of Corti S7_Muscle_Insulin_30min Gene expression data from postmorten brain regions Source GEO sample is GSM145604 Last updated (according to GEO): Nov 20 2006 GSE432 1000 Neuraxis 1387 1365 that cognitive symptoms GSE1144 Within the vertebrate nervous system, the presence of many different lineages of neurons and glia complicates the molecular characterization of single neuronal populations. In order to elucidate molecular mechanisms underlying the specification and development of corticospinal motor neurons (CSMN), we purified CSMN at distinct stages of development in vivo and compared their gene expression to two other pure populations of cortical projection neurons: callosal projection neurons and corticotectal projection neurons. We found genes that are potentially instructive for CSMN development, as well as genes that are excluded from CSMN and are restricted to other populations of neurons, even within the same cortical layer. Loss-of-function experiments in null mutant mice for Ctip2 (also known as Bcl11b), one of the newly characterized genes, demonstrate that it plays a critical role in the development of CSMN axonal projections to the spinal cord in vivo, confirming that we identified central genetic determinants of the CSMN population. A control group consisting of nine C57/BL/6J mice was maintained on a normal diet consisting of Purina Rodent Chow (Harlan Teklad, catalog #5008, 6.5% fat, 49% carbohydrate, 23% protein, 3.5 kcal/ g). The experimental group consisted of nine mice grown on a specialty high-fat diet (Harlan Teklad, catalog #TD88137, 42.16% fat, 42.81% carbohydrate, 15.02% protein, 4.53 kcal/ g). Mice were maintained for ten weeks on their respective diets in a controlled environment with standard light and feeding schedule. Two days before tissue harvest, the experimental group on the high-fat diet was divided into one group of five and one group of four mice. The first group continued on the high-fat diet for the final two days, while the second group fasted. Mouse weights were recorded two days prior, and the day of tissue harvest. At the end of the fasting period liver tissue samples were harvested from each mouse. RNA was purified from the liver tissue samples. Each tissue was homogenized in 1 mL of STAT-60 (Tel-Test, Inc., Friendswood, TX) and the homogenate was mixed with 200 uL of chloroform. The aqueous phase was removed, and mixed with 500 uL of isopropanol to precipitate the RNA. The resulting RNA pellet was washed with 500 uL of 70% ethanol and allowed to air dry. The pellet was dissolved in RNase free water (Ambion, TX), quantified by UV spectroscopy, and stored at -80C. Total RNA control samples (Universal Mouse Reference RNA, catalog # 740100, Stratagene) were labeled using Cy3 dCTP (Perkin-Elmer), and liver total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). The control RNA samples were additionally mixed with 2 uL of random hexamers. The reaction mixtures were incubated at 42 C for two hours. After the reverse transcription reactions, the RNA templates were degraded by addition of 2 uL of 1 N NaOH and incubation at 65 C for 10 minutes. The alkaline conditions were neutralized by addition of 2 uL of 1 N HCl. Liver cDNA samples were then mixed with a control cDNA sample, and the mixtures were cleaned using a QIAquick Nucleotide Removal kit (Qiagen) as described by the manufacturer's instructions. The cleaned samples were concentrated in a speed vacufuge (Eppendorf) for 20 minutes at 65 C, and were dissolved in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), quantified, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 C using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), then in 1X SSC, and finally in 0.1X SSC. The arrays were dried by centrifugation and scanned using a GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and analyzed using Matlab (The MathWorks, Inc.). Microarrays were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). Arrays contained 16,847 features, printed from a synthesized oligonucleotide mouse library (Operon). The library was suspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed at approximately 50% humidity. Once printed, the probes were crosslinked using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride (Fluka AG), 239 mL 1-methyl-2-pyrrolidinone (EM Science), and 10.7 mL of 1 M boric acid (Fisher), pH 8.0. They were cleaned by rinsing twice in 250 mL of milli-Q water, followed by 250 mL of 95% ethanol (Pharmco Products). After blocking, they were dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, energy homeostasis, gene expression, microarrays Source GEO sample is GSM6595 Last updated (according to GEO): Nov 21 2005 Prostate Gland 2 Normal Tissue transferred into RNAlater within 30 minutes of removal, and frozen at -20C Source GEO sample is GSM9093 Last updated (according to GEO): May 28 2005 Normal Source GEO sample is GSM176235 Last updated (according to GEO): Apr 09 2007 cerebral cortex sprague 3919 Spinal Cord 901 Affymetrix GeneChip® Mouse Genome 430 2.0 Array Source GEO sample is GSM197124 Last updated (according to GEO): May 31 2007 10 7 Left Malignant neoplasm of ovary 901 Healthy patient. Source GEO sample is GSM228578 Last updated (according to GEO): Sep 11 2007 1000 Microphthalmos of somatomotor cortex 21 41 JMR-Sham21d-1aA-s2 HUVEC isolate V rich media PlGF 24hours cf. #19 Source GEO sample is GSM12913 Last updated (according to GEO): May 28 2005 To understand the mechanisms underlying autosomal dominant progressive retinitis pigmentosa (RP) caused by the mutations of the RP1 gene and to identify molecules that play roles in the early disease process, we used Affymetrix U74Av2 microarrays to compare the gene expression profiles of retinas from Rp1-/- and Rp1+/+ mice at postnatal days (P) 7, 10, 14, 18 and 21. These profiles were independently verified by comparison with results of retinal serial analysis of gene expression, U74Av2 array studies of mouse retinas, real-time PCR and in situ hybridization. We found that the disruption of Rp1 significantly affected the expression of multiple clusters of genes whose products were involved in diverse biological pathways. The molecular responses to the disruption of Rp1 changed dramatically during development and were distinct from responses to the disruption of photoreceptor transcription factors (Crx-/- or Nrl-/-) and a phototransduction molecule (Pde6brd1). We found specific alterations of gene expression in the c-Jun N-terminal kinase (JNK) signaling cascades. Western analysis confirmed that the phosphorylation of key members in the JNK signaling cascades (i.e. JNK1, JNK2, MAP2, MKK4 and c-Jun) is reduced, whereas phospho-ERK and phospho-p38 are unchanged, in Rp1-/- retinas at P18-21. Immunostaining demonstrated that, like Rp1, phospho-JNKs and phospho-MAP2 are present in outer segments of photoreceptors. Our studies reveal unique molecular phenotypes in multiple biological pathways and the specific reduction of JNK signaling cascades in RP1 diseases, and suggest that RP1, a doublecortin-containing microtubule associated protein, and JNK signaling cascades play integral roles in photoreceptor development and maintenance. Our studies further suggest JNK-related therapeutic strategies for RP1 diseases. 7 0 prostate ColonProx_0227AFAS_070.txt GSE587 Meningioma Recurrent Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108002 Last updated (according to GEO): Jun 06 2006 Normal Source GEO sample is GSM175831 Last updated (according to GEO): Apr 09 2007 913 Autistic Disorder 1000 Brain CNS-SpinalC-4hAdult-3C-s2 Wild type inbred mice Source GEO sample is GSM83039 Last updated (according to GEO): Nov 10 2005 54h-Control replication 1 861 Cerebral cortex Gene expression data from whole brain infected mouse, day 6 Source GEO sample is GSM189654 Last updated (according to GEO): May 16 2007 901 Coronary artery Cochlea_WT_9mo_3 SVGR2 subclone 4-E12 GeneChip U133A a unique leukemia 81 98 forebrain 7 15 between the LAD artery 266 287 D3_TP-12_I with some respiratory epithelium. 1039 1072 Nervous system structure 901 Profile of gene expression in lungs of ovalbumen sensitized and challenged C3H mice.. Date GSE446 Last Updated: May 29 2005 Includes GDS347. Update date: Mar 22 2004. Dataset description GDS347: Lungs of ovalbumin sensitized/challenged C3H mice compared with controls. C3H are ovalbumin resistant. Attempt to identify genes involved in antigen-induced airway hyperresponsiveness.. 93 77 (hippocampus CA1 3792 12b of peripheral nervous system 73 100 Ovarian_Tumor_Serous_KU-OS-007 To facilitate high-throughput 3D imaging of brain gene expression, a new method called voxelation has been developed. Spatially registered voxels (cubes) are analyzed, resulting in multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems. Using microarrays, 40 voxel images for 9000 genes were acquired from brains of both normal mice and mice in which a pharmacological model of Parkinson's disease (PD) had been induced by methamphetamine. Quality-control analyses established the reproducibility of the voxelation procedure. The investigation revealed a common network of coregulated genes shared between the normal and PD brain, and allowed identification of putative control regions responsible for these networks. In addition, genes involved in cell/cell interactions were found to be prominently regulated in the PD brains. Finally, singular value decomposition (SVD), a mathematical method used to provide parsimonious explanations of complex data sets, identified gene vectors and their corresponding images that distinguished between normal and PD brain structures, most pertinently the striatum. of Parkinson's disease 450 471 A control group consisting of nine C57/BL/6J mice was maintained on a normal diet consisting of Purina Rodent Chow (Harlan Teklad, catalog #5008, 6.5% fat, 49% carbohydrate, 23% protein, 3.5 kcal/ g). The experimental group consisted of nine mice grown on a specialty high-fat diet (Harlan Teklad, catalog #TD88137, 42.16% fat, 42.81% carbohydrate, 15.02% protein, 4.53 kcal/ g). Mice were maintained for ten weeks on their respective diets in a controlled environment with standard light and feeding schedule. Two days before tissue harvest, the experimental group on the high-fat diet was divided into one group of five and one group of four mice. The first group continued on the high-fat diet for the final two days, while the second group fasted. Mouse weights were recorded two days prior, and the day of tissue harvest. At the end of the fasting period liver tissue samples were harvested from each mouse. RNA was purified from the liver tissue samples. Each tissue was homogenized in 1 mL of STAT-60 (Tel-Test, Inc., Friendswood, TX) and the homogenate was mixed with 200 uL of chloroform. The aqueous phase was removed, and mixed with 500 uL of isopropanol to precipitate the RNA. The resulting RNA pellet was washed with 500 uL of 70% ethanol and allowed to air dry. The pellet was dissolved in RNase free water (Ambion, TX), quantified by UV spectroscopy, and stored at -80C. Total RNA control samples (Universal Mouse Reference RNA, catalog # 740100, Stratagene) were labeled using Cy3 dCTP (Perkin-Elmer), and liver total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). The control RNA samples were additionally mixed with 2 uL of random hexamers. The reaction mixtures were incubated at 42 C for two hours. After the reverse transcription reactions, the RNA templates were degraded by addition of 2 uL of 1 N NaOH and incubation at 65 C for 10 minutes. The alkaline conditions were neutralized by addition of 2 uL of 1 N HCl. Liver cDNA samples were then mixed with a control cDNA sample, and the mixtures were cleaned using a QIAquick Nucleotide Removal kit (Qiagen) as described by the manufacturer's instructions. The cleaned samples were concentrated in a speed vacufuge (Eppendorf) for 20 minutes at 65 C, and were dissolved in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), quantified, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 C using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), then in 1X SSC, and finally in 0.1X SSC. The arrays were dried by centrifugation and scanned using a GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and analyzed using Matlab (The MathWorks, Inc.). Microarrays were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). Arrays contained 16,847 features, printed from a synthesized oligonucleotide mouse library (Operon). The library was suspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed at approximately 50% humidity. Once printed, the probes were crosslinked using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride (Fluka AG), 239 mL 1-methyl-2-pyrrolidinone (EM Science), and 10.7 mL of 1 M boric acid (Fisher), pH 8.0. They were cleaned by rinsing twice in 250 mL of milli-Q water, followed by 250 mL of 95% ethanol (Pharmco Products). After blocking, they were dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, energy homeostasis, gene expression, microarrays Source GEO sample is GSM6593 Last updated (according to GEO): Nov 21 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145282 Last updated (according to GEO): Nov 20 2006 ALL_22 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 111 by the trigeminal ganglion 86 RR203_infected_skin_biopsy Cerebral cortex 861 Plasma 861 Cochlear nuclei 0 14 Cerebral cortex 861 1000 Neoplasm small cell lung carcinoma 8526 0 29 Tumor__Mesothelioma_31_T10 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A plasma cells 50 61 Coronary Arteriosclerosis 1000 ALL B-cell41 on Affymetrix GeneChip Human Full Length Array HuGeneFL NCI60.26_LABEL30EXTRACT29SUB3 Source GEO sample is GSM134120 Last updated (according to GEO): Aug 06 2007 AR-R-810pM HeLa CD4+ cells were transfected with an epitope-tagged eTat plasmid and selected with hygromycin. Cells were treated with nocodazole and collected @6 hours. Source GEO sample is GSM8707 Last updated (according to GEO): May 27 2005 1345 1323 by cervical dislocation HMVEC-L stimulated with LPS for 4 hours L04R4 Liver 861 Mesenchymal Stem Cells 1000 9 0 Blood Test Cerebellum 1000 320 306 Keywords = HIV Lymphoblastoid Cell Line for Individual 8010.3 log phase Primary small cell lung carcinoma 2229 Bone Marrow 1000 861 Blood 861 Substantia nigra structure 1000 Brain SCN2.2 Sample 25 (Exp#3-30 hr) EWS-T-TEST-6 on NHGRI-6.5k_b PGA-swim_2.5d_s1002 Neural tube, treated, GD8:15, T216804 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201251 Last updated (according to GEO): Jun 14 2007 5 0 Spleen in the adult brain 51 68 Melanoma xenograft, MA2_Sub_C (LeiATCC) Pregnant females fed with maltose dextrin, PF05 (Pair Fed) corresponds to replicate 5 that mesenchimal stem cells 905 931 Liver 1000 mRNA was isolated after 2 hours of incubation from IMR-90 cells seeded onto a collagen/chondroitin sulfate tissue engineering scaffold mesh material. Cells were seeded at a density of 1 x 10^6 cells/ mesh, and this chip represents a pooling of cells from 4 meshes. Source GEO sample is GSM6050 Last updated (according to GEO): May 27 2005 Gene expression data from rat lungs exposed to FiO2 of ~9.5% and SU-5416 (hypoxia-SU-5416). Source GEO sample is GSM201489 Last updated (according to GEO): Jun 14 2007 MAS 5.0, scaled to 500; Affymetrix data Mining Tool 3.0; dChip was used to determine differentially expressed genes (MBEI); Statistical Analysis of Microarrays(SAM), as described in Miller et al. 2004. Source GEO sample is GSM108088 Last updated (according to GEO): Sep 12 2006 901 Bone Marrow MO_control_0min_Patient14 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47521 Last updated (according to GEO): May 29 2005 20 0 Nicotine-hippocampus brain_control_sampleid_mr275 nasal epithelial cells 28 49 **** Source GEO sample is GSM4303 Last updated (according to GEO): May 27 2005 2 on NHGRI-13.8k of the cerebellum 1656 1672 Nasal Epithelium 865 from epididymal fat tissues 16 42 "Sample 81, BRCA1 mutation(69 months) age 49 erp no" on vantveer-oligo none Source GEO sample is GSM161889 Last updated (according to GEO): Feb 16 2007 453 433 to the neurofibromas spinal cord 0 11 861 Brain liver 0 5 Skeletal muscle biopsy was obtained before a 3-hour hyperinsulinemic (infusion rate 40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172161 Last updated (according to GEO): Feb 28 2007 stria terminalis 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145835 Last updated (according to GEO): Nov 20 2006 from aorta 100 110 ExpressionLevel:GXN-00529 on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 8 hours after lights on. Original RNA code = LC24A. Source GEO sample is GSM227385 Last updated (according to GEO): Sep 10 2007 14 0 Prostate cancer small intestine PPARalpha knockout mice, control diet. Source GEO sample is GSM124314 Last updated (according to GEO): Jun 28 2007 D_U133Plus_111_nAcc 1000 Spleen Heart 1000 264 230 from hippocampus neural stem cells LD1a 14 7 amygdala 7 0 prostate Mouse Testis 2 Nose 1000 M_U133A_42_DLPFC 861 Amygdaloid structure Epithelial Cells 901 1000 Spleen 1000 Brain Stem 7 frontal cortex 20 Wild type hippocampus region Source GEO sample is GSM88933 Last updated (according to GEO): Jan 04 2006 normal lung 3208 Source GEO sample is GSM17304 Last updated (according to GEO): May 28 2005 pooled RNA of the kidney of 36 day old rats Source GEO sample is GSM86653 Last updated (according to GEO): Jun 12 2006 17 7 hippocampus the blood 393 402 TS21 sample 1 (cerebellum) Leukemia, Lymphocytic, Chronic 1000 7 0 Prostate 2869 tumor cells 2880 Infection 861 Aorta 861 Epithelial Cells 901 Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22574 Last updated (according to GEO): May 27 2005 M7TW00122041 VDXIGRU_256975 of mouse brain 9 23 Richard Almon-9-1138200269649 91 from the bone marrow 72 of Parkinson's disease 450 471 MK C: MK control. Young male C57BL/6J mice received an injection of MK-801 (300 micro-g per g body weight). No other treatment administered. RNA from control mice were extracted 2 hours after experimental mice received their last shock treatment. Source GEO sample is GSM4563 Last updated (according to GEO): May 27 2005 DRG008_c none Source GEO sample is GSM149520 Last updated (according to GEO): Jan 03 2007 SN:Human Glioblastoma Biopsy 06488 Hyponatremia 1000 1000 Structure of parenchyma of lung CAD_replicate32 brain_DLPFC_bipolar B_mr403 in primary tumors 1011 1027 Diabetes Mellitus 1000 1000 Malignant neoplasm of prostate Cytoskeletal Proteins 1000 861 Hippocampus osteoblast 627 637 Obesity, Morbid 928 none Source GEO sample is GSM149626 Last updated (according to GEO): Jan 03 2007 "Sample 17,>5 yr survival(94 months) age 48 erp yes" on vantveer-oligo 861 Cerebral cortex Murine_NK_IL-15_24h_2 Brain 1000 To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18451 Last updated (according to GEO): May 27 2005 Neural tube, treated, GD8:15, T216802 78 66 Control blood Gene expression data from postmorten brain regions Source GEO sample is GSM144995 Last updated (according to GEO): Nov 20 2006 of spinal cords 84 98 brain, frontal cortex: pADX AM FC b_e1_le1 Lung 861 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211349 Last updated (according to GEO): Jul 18 2007 hip_1024_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 406 395 whose hearts M_U133A_117_DLPFC Infection 861 1000 Ischemia Pooled diaphragm RNA samples from five 8 wk old male mdx mice Source GEO sample is GSM13565 Last updated (according to GEO): May 28 2005 I_U133A_74_CB 901 Coronary artery CT38-1 861 Neoplasm Bic/4AP(1) n/a Source GEO sample is GSM178038 Last updated (according to GEO): Jun 11 2007 119 82 of the peripheral innate immune system 865 Disorder of artery 861 Brain Squamous cell carcinoma 875 CNS-SMTC_Ctr7d-2B-s2 46 8 in docetaxel-refractory prostate cancer 3AMH02082109_PB_CD56NKCells 861 Cerebral cortex 129:4-3 striatum during measles 265 279 Heart 1000 861 Brain Gene expression data from aneurismal tissues obtained from patients with bicuspid valves. Source GEO sample is GSM116784 Last updated (according to GEO): Jun 28 2006 19 0 Head and neck cancer Brain_PNET_2_PNET on Affymetrix GeneChip Human Full Length Array HuGeneFL Pool Ts1Cje_P0_hyb1 129S6/SvEvTac bed nucleus of the stria terminalis rep1 (430 2.0 Array) I_U133A_30_AnCg 758 740 to any other tumor 901 Coronary artery Nasal Epithelium Inhalation Formaldehyde 2ppm 5d ID219 hedenfalk-breast 4525 4520 liver Brain 861 1000 Lung HCC (HBV+, HK66, T2) Spleen vs Anti-IgM Treated B cell 60min (set2) 861 Cerebral cortex 861 Blood Resting Source GEO sample is GSM175999 Last updated (according to GEO): Apr 09 2007 Bone Marrow 1000 A control group consisting of nine C57/BL/6J mice was maintained on a normal diet consisting of Purina Rodent Chow (Harlan Teklad, catalog #5008, 6.5% fat, 49% carbohydrate, 23% protein, 3.5 kcal/ g). The experimental group consisted of nine mice grown on a specialty high-fat diet (Harlan Teklad, catalog #TD88137, 42.16% fat, 42.81% carbohydrate, 15.02% protein, 4.53 kcal/ g). Mice were maintained for ten weeks on their respective diets in a controlled environment with standard light and feeding schedule. Two days before tissue harvest, the experimental group on the high-fat diet was divided into one group of five and one group of four mice. The first group continued on the high-fat diet for the final two days, while the second group fasted. Mouse weights were recorded two days prior, and the day of tissue harvest. At the end of the fasting period liver tissue samples were harvested from each mouse. RNA was purified from the liver tissue samples. Each tissue was homogenized in 1 mL of STAT-60 (Tel-Test, Inc., Friendswood, TX) and the homogenate was mixed with 200 uL of chloroform. The aqueous phase was removed, and mixed with 500 uL of isopropanol to precipitate the RNA. The resulting RNA pellet was washed with 500 uL of 70% ethanol and allowed to air dry. The pellet was dissolved in RNase free water (Ambion, TX), quantified by UV spectroscopy, and stored at -80C. Total RNA control samples (Universal Mouse Reference RNA, catalog # 740100, Stratagene) were labeled using Cy3 dCTP (Perkin-Elmer), and liver total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). The control RNA samples were additionally mixed with 2 uL of random hexamers. The reaction mixtures were incubated at 42 C for two hours. After the reverse transcription reactions, the RNA templates were degraded by addition of 2 uL of 1 N NaOH and incubation at 65 C for 10 minutes. The alkaline conditions were neutralized by addition of 2 uL of 1 N HCl. Liver cDNA samples were then mixed with a control cDNA sample, and the mixtures were cleaned using a QIAquick Nucleotide Removal kit (Qiagen) as described by the manufacturer's instructions. The cleaned samples were concentrated in a speed vacufuge (Eppendorf) for 20 minutes at 65 C, and were dissolved in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), quantified, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 C using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), then in 1X SSC, and finally in 0.1X SSC. The arrays were dried by centrifugation and scanned using a GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and analyzed using Matlab (The MathWorks, Inc.). Microarrays were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). Arrays contained 16,847 features, printed from a synthesized oligonucleotide mouse library (Operon). The library was suspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed at approximately 50% humidity. Once printed, the probes were crosslinked using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride (Fluka AG), 239 mL 1-methyl-2-pyrrolidinone (EM Science), and 10.7 mL of 1 M boric acid (Fisher), pH 8.0. They were cleaned by rinsing twice in 250 mL of milli-Q water, followed by 250 mL of 95% ethanol (Pharmco Products). After blocking, they were dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, energy homeostasis, gene expression, microarrays Source GEO sample is GSM6597 Last updated (according to GEO): Nov 21 2005 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184689 Last updated (according to GEO): Apr 26 2007 Communicable Diseases 1000 Heart 1000 the heart 987 996 1000 Liver 1000 Pancreas Gene expression data from a placenta with acute malaria Source GEO sample is GSM183613 Last updated (according to GEO): Apr 23 2007 84 69 by heart failure Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc92 Source GEO sample is GSM1905 Last updated (according to GEO): Nov 21 2005 with myocardial infarction 313 339 CNS-SC_InjA24h-4B-s2 525 512 mel-14 antigen nasal epithelial cells 28 49 Dystrophin 1000 brain, hippocampus: CON-CA1-A5_e1_le1 11_0001_SepticShock_Day3_55 901 Caudate nucleus structure labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156711 Last updated (according to GEO): Jan 22 2007 861 Muscle 1392 1382 to vascular 853 Refractory Carcinoma none Source GEO sample is GSM210304 Last updated (according to GEO): Jul 16 2007 981-1 Standard affymetrix protocol Source GEO sample is GSM119713 Last updated (according to GEO): Jul 31 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28765 Last updated (according to GEO): May 27 2005 Heart 861 Epithelium 861 AMM_0_0_Female6_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111836 Last updated (according to GEO): Nov 21 2006 nodose_nucleus_9 liver, PPARa-null mice, treatment with WY14643 for 6h Source GEO sample is GSM205780 Last updated (according to GEO): Jul 24 2007 trachea Source GEO sample is GSM18618 Last updated (according to GEO): May 27 2005 brain 0 5 midbrain_3 Source GEO sample is GSM80701 Last updated (according to GEO): Mar 31 2006 913 Coronary heart disease 1000 Neoplasm 1000 Coronary Arteriosclerosis from brain 21 30 Epithelial Cells 901 453 418 with newly diagnosed type 2 diabetes human frontal cortex Source GEO sample is GSM87022 Last updated (according to GEO): Feb 08 2006 2869 tumor cells 2880 1BMH02083009_721_Blymphoblasts hypothalamus_5 129S6/SvEvTac hippocampus rep1 (430 2.0 Array) Many neurodegenerative disorders are characterized by two pathological hallmarks: progressive loss of neurons and occurrence of inclusion bodies containing ubiquitinated proteins. Inflammation may be critical to neurodegeneration associated with ubiquitin-protein aggregates. We previously showed that prostaglandin J2 (PGJ2), one of the endogenous products of inflammation, induces neuronal death and the accumulation of ubiquitinated proteins into distinct aggregates. We now report that temporal microarray analysis of human neuroblastoma SK-N-SH revealed that PGJ2 triggered a "repair" response including increased expression of heat shock, protein folding, stress response, detoxification and cysteine metabolism genes. PGJ2 also decreased expression of cell growth/maintenance genes and increased expression of apoptotic genes. Over time pro-death responses prevailed over pro-survival responses, leading to cellular demise. Furthermore, PGJ2 increased the expression of proteasome and other ubiquitin-proteasome pathway genes. This increase failed to overcome PGJ2 inhibition of 26 S proteasome activity. Ubiquitinated proteins are degraded by the 26 S proteasome, shown here to be the most active proteasomal form in SK-N-SH cells. We demonstrate that PGJ2 impairs 26 S proteasome assembly, which is an ATP-dependent process. PGJ2 perturbs mitochondrial function, which could be critical to the observed 26 S proteasome disassembly, suggesting a cross-talk between mitochondrial and proteasomal impairment. In conclusion neurotoxic products of inflammation, such as PGJ2, may play a role in neurodegenerative disorders associated with the aggregation of ubiquitinated proteins by impairing 26 S proteasome activity and inducing a chain of events that culminates in neuronal cell death. Temporal characterization of these events is relevant to understanding the underlying mechanisms and to identifying potential early biomarkers. 1000 Liver 861 Blood BCR-ABL-R3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM Source GEO sample is GSM207684 Last updated (according to GEO): Jul 09 2007 Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.43 Subject: 2846 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39039 Last updated (according to GEO): May 27 2005 861 HIV Infections A2780_oxa_IC25_16h_2 brain, unknown: UTB_e1_le1 Cerebral cortex 861 Simple annotation: Normal tissue, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3720.gif Source GEO sample is GSM76434 Last updated (according to GEO): Sep 22 2006 innervated tibialis anterior muscles from runx1f/- control mice Treatment, type=add, description=runx1f/- Source GEO sample is GSM99431 Last updated (according to GEO): Mar 08 2006 osteoblast 630 640 12 0 ovarian tumor Myocardium 861 Myometrium 27 Disease 861 hair 1 of 3 replicates in treatment group Source GEO sample is GSM206044 Last updated (according to GEO): Jun 29 2007 91 from the bone marrow 72 Myocardial Infarction 1000 5 0 Spleen Array representing the response of Human foreskin fibroblasts at 16h post HCMV infection Source GEO sample is GSM10350 Last updated (according to GEO): May 28 2005 861 Nerve M_U133A_84_nAcc Bone structure of tibia 1000 7 frontal cortex 20 861 Cardiomyopathies Normal Source GEO sample is GSM176310 Last updated (according to GEO): Apr 09 2007 cerebellum wistar ky 3890 Heart 861 Normal Source GEO sample is GSM176233 Last updated (according to GEO): Apr 09 2007 Conventional Descending colon 1 bc-ZT21-1 26 16 of modiolus 901 Mammary gland perro-affy-human-186940 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118328 Last updated (according to GEO): Jul 11 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM144941 Last updated (according to GEO): Nov 20 2006 Extracellular Matrix 1000 Interatrial septum 865 1000 Hippocampus Entorhinal Cortex 7 23 of breast cancer 727 743 12 hr Hela Double Thymidine Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132504 Last updated (according to GEO): Feb 26 2007 Brain 861 Cerebral cortex 861 4 0 Ovary human cerebellum Source GEO sample is GSM87117 Last updated (according to GEO): Feb 08 2006 stomach_fundus_1 Source GEO sample is GSM80809 Last updated (according to GEO): Mar 31 2006 284 273 of epilepsy U87 glioblastoma cell, clone 8.1 (expresses PDGF-A dominant-negative) Keywords = bioinformatics Keywords = gene expression Keywords = cancer Keywords = platelet-derived growth factor Keywords = sterol regulatory element binding protein Keywords = glioblastoma multiformae Keywords = microarray Source GEO sample is GSM34590 Last updated (according to GEO): May 27 2005 ALL-B-cell-18 on Affymetrix GeneChip Human Full Length Array HuGeneFL Breast 1 Disease 861 Retina 239-97_SCC 0 Lung tissue 10 Nose 1000 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26622.gif Source GEO sample is GSM81545 Last updated (according to GEO): Sep 22 2006 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 2 hour after the last shock treatment. Source GEO sample is GSM4540 Last updated (according to GEO): May 27 2005 Macrophage 14smi011 67 40 with coronary artery disease abd skin fibroblast (1.4BF), asynch PGA-lv_48h_520 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213491 Last updated (according to GEO): Jul 31 2007 1BJZ022987A_TONGUE 13 salivary gland 0 41 29 Control blood Substantia nigra normal rep8 861 Cerebral cortex infection 755 763 Spleen 0 5 Mouse Liver AIN Diet 5wk 10ppb As Food Exposure, biological replicate D Normal Source GEO sample is GSM175967 Last updated (according to GEO): Apr 09 2007 5 0 Kidney Wild type 8 wk old male C3H/HeJ mouse hypothalamus Source GEO sample is GSM107024 Last updated (according to GEO): Mar 05 2007 Large-scale analysis of the mouse transcriptome. Cortex C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 261.21 Stdv: 7.59 Min: 250.89 Max: 279.65 Source GEO sample is GSM2948 Last updated (according to GEO): Mar 20 2006 Liver (HBV+, HK42) Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=1 (Acute rejection) Source GEO sample is GSM36423 Last updated (according to GEO): May 27 2005 cerebellum sprague 3896 Frontal_Cerebrocortex_Vehicle_6hr_rep12 Structure of trigeminal ganglion 1000 1000 Kidney adenoma 861 DMN-CtrHippo20d-2aAv2-s2 I_U133A_76_AnCg Site: University of California, Davis Cohort: Male/Female Control Set Diagnosis: Control pH: 6.12 Subject: 3108 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39072 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 Lymphoblastoid Cell Line for Individual 8172.3 log phase Heart 861 E2A-PBX1-R1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1259 1239 of the basal ganglia 10_0012_SepticShock_Day3_63 567 548 the descending colon in the brain 150 162 Communicable Diseases 1000 T02__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Left SCG_sema3A_2h_rep1 brain 0 5 C Fast Rep 2 Normal__Pancreas_Pan_8N on Affymetrix GeneChip Human 35K SubA Array Hu35k-A G42-Homogenate-CingulateCortex replicate1 SN:Human Glioblastoma Biopsy 10390 Gene Expression Profiles of HPV-Positive and -Negative Head/Neck and Cervical Cancers Experimental Autoimmune Encephalomyelitis 1000 Ganglia, Spinal 1000 119T Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184774 Last updated (according to GEO): Apr 26 2007 Gene expression data for comparing calorie restricted-fed 30-month-old to control-fed 30-month-old for investigating effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7452 Last updated (according to GEO): May 27 2005 Wildtype saline, biological replicate 5 Primary tumor 19 32 1000 Pain cerebral.hemisphere.2 Fibroblasts 861 Category: Cell-line Subcategory: HMEC Scanning Software: ScanAlyze Software version: 2.44 Lot batch = 0119-5k Source GEO sample is GSM1935 Last updated (according to GEO): Nov 21 2005 42 minus the frontal cortex 66 C57BL/6J periaqueductal gray rep1 (430 2.0 Array) Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11571 Last updated (according to GEO): May 28 2005 Muscular Dystrophy, Duchenne 1000 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114435 Last updated (according to GEO): Jun 16 2006 861 Neoplasm cerebellum 813 823 Gene expression data from postmorten brain regions Source GEO sample is GSM146025 Last updated (according to GEO): Nov 20 2006 Anterior nares 1000 Duchenne muscular dystrophy 0 26 361 335 hypertrophic cardiomyopathy Neoplasm 861 I_U133A_37_CB 913 Coronary heart disease human frontal cortex Source GEO sample is GSM87017 Last updated (according to GEO): Feb 08 2006 of coronary artery disease 258 284 Frontal_Cerebrocortex_Vehicle_6hr_rep11 between hepatocellular carcinoma 933 964 1000 Amyotrophic Lateral Sclerosis Primary large cell neuroendocrine carcinoma 6065 Cells captured via Arcturus LCM system, amplified (RiboAmp, 2 rounds) and labeled (Enzo) for hybridizaton to Affymetrix MG_U74Av2 arrays, using manufacturers protocols in each step. Source GEO sample is GSM6198 Last updated (according to GEO): Mar 17 2006 901 Lateral Sclerosis Cardiovascular Diseases 1000 M_U133A_17_CB Parkinson's disease sample x019 0 30 brain, SNc and VTA: VTA2_e1_le1 1BJZ02081482b_Appendix Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225712 Last updated (according to GEO): Aug 31 2007 Nasal Epithelium Inhalation Formaldehyde 07ppm 24h ID132 SKBR3_Treated D_U133A_62_nAcc Frontal_Cerebrocortex_Vehicle_6hr_rep5 1000 Substantia nigra structure 1000 Prostate Cerebral cortex 861 Spleen 1000 861 Cancer of Neck 861 Esophagus I_95Av2_2835_DLPFC_1_GS Epithelium 861 Ky2: Hippocampus_21PT-Y_rep2 660 mesenchymal stem cell 639 Phenytoin brainstem 6 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53417 Last updated (according to GEO): Jul 06 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM146080 Last updated (according to GEO): Nov 20 2006 Bone Marrow 1000 Primary Neoplasm 1000 861 Mammary gland Parkinson Disease 861 1000 Malignant Glioma liver 0 5 plasma cells 332 344 Simple annotation: Reference verification, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10003.gif Source GEO sample is GSM78472 Last updated (according to GEO): Sep 22 2006 861 Leprosy IGF1 and IGF1 receptors (IGF1R) are present in the adult heart and have been shown to be essential for myocardial performance. Insulin-like growth factor 1 (IGF1) is produced in numerous tissues particularly by the liver in response to growth hormone stimulation and is an important factor in the regulation of post-natal growth and development. We have generated and characterized transgenic mice over-expressing the IGF1R. We crossed IGF1R transgenic mice with dominant negative (dn)PI3K (p110) and with constitutively active (ca)PI3K(p110) transgenic mice. Expression profiling was performed on the ventricles of IGF1R, IGF1R-caPI3K, IGF1R-dnPI3K, caPI3K, dnPI3K transgenic female mice at 3 months of age. Non-transgenic littermates were used as controls. Keywords = insulin growth factor, IGF, cardiac, hypertrophy Source GEO sample is GSM18369 Last updated (according to GEO): May 27 2005 Nicotinic receptors 0 18 PMN_control_360min_Patient11 in Duchenne muscular dystrophy 137 166 m2 Posterior root of spinal nerve 861 489 470 of bladder carcinoma nucleus accumbens long access to cocaine replicate 4 Gonadectomized Dahl-Iwai Male LowSalt OuterMedulla rat9 gdahl_medullar_k_GX_9om_rh_051402 Gene expression data from brain of adult rats Source GEO sample is GSM101012 Last updated (according to GEO): Feb 20 2007 2283 in skeletal muscle 2266 Spleen 1000 adenoma 861 DLBC6 on Affymetrix GeneChip Human Full Length Array HuGeneFL 861 Amygdaloid structure 11 0 Hypothalamus 43 0 Chorionic mesoderm-derived mesenchymal cells Epithelium of bronchus 983 132T Liver 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11301 Last updated (according to GEO): May 28 2005 embryonic hearts 1064 1079 Tissue Source GEO sample is GSM67238 Last updated (according to GEO): Jan 19 2006 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184688 Last updated (according to GEO): Apr 26 2007 none Source GEO sample is GSM123251 Last updated (according to GEO): Jul 26 2006 861 Neoplasm 1000 Spleen to chronic obstructive pulmonary disease 253 292 Stem cells 861 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18925.gif Source GEO sample is GSM84123 Last updated (according to GEO): Sep 22 2006 Male 24.2 yr after antibody enrichment scan 2 (U133A) GM18859_technical_rep_1 Brain 861 Whole Brain 62 72 Squamous cell carcinoma 923 Sample 117 on vantveer-oligo hindlimb muscle groups 771 792 The virB operon, encoding a Type IV secretion system (T4SS), is essential for intracellular survival and persistent infection of Brucella spp. To better understand the role of the T4SS in evading host defense mechanisms and establishing chronic infection, we compared transcriptional profiles of the host response to infection with wild type Brucella strains and strains that fail to express the virB genes. Analysis of host gene expression profiles three days after inoculation with wild type Brucella strains revealed an inflammatory response dominated by interferon-induced genes. This analysis found that not only the type II but also type I interferon pathway was elicited by Brucella infection. Real time RT-PCR showed that a group of genes from these pathways was induced by day 3 post-infection and declined to baseline levels by day 7. In contrast, neither of the two virB mutant strains elicited expression of interferon-induced genes, demonstrating that the T4SS was required to trigger an inflammatory response early during infection. Last Updated (by provider): Aug 08 2007 Contributers: Renee M Tsolis Christelle M Roux V5-P508 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection). One of three samples from the same patient, different visits. Source GEO sample is GSM36454 Last updated (according to GEO): May 27 2005 /SvEvTac mouse cingulate cortex 29 59 The application of human embryonic stem (ES) cells in medicine and biology has an inherent reliance on understanding the starting cell population. Human ES cells differ from mouse ES cells and the specific embryonic origin of both cell types is unclear. Previous work suggested that mouse ES cells could only be obtained from the embryo before implantation in the uterus1?5. Here we show that cell lines can be derived from the epiblast, a tissue of the postimplantation embryo that generates the embryo proper. These cells, which we refer to as EpiSCs (post-implantation epiblastderived ES cells), express transcription factors known to regulate pluripotency, maintain their genomic integrity, and robustly differentiate into the major somatic cell types as well as primordial germ cells. The EpiSC lines are distinct from mouse ES cells in their epigenetic state and the signals controlling their differentiation. Furthermore, EpiSC and human ES cells share patterns of gene expression and signalling responses that normally function in the epiblast. These results show that epiblast cells can be maintained as stable cell lines and interrogated to understand how pluripotent cells generate distinct fates during early development. *Note: EpiSCs were previously referred to as post-ES cells Last Updated (by provider): Jun 25 2007 Contributers: Paul J Tesar Josh G Chenoweth Ron McKay 861 Asphyxia Brain 861 DRG_reference_pool C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 2 hour after the last shock treatment. Source GEO sample is GSM4545 Last updated (according to GEO): May 27 2005 Hyperdip>50-#3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Communicable Diseases 901 CNS-SCsev_InjA4h-1B-s2 VDXRHU_1496 AD-287t1-A101-3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152000 Last updated (according to GEO): Feb 06 2007 Caudal 1000 Parkinson Disease 861 254 226 the expected hypersensitivity Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for twelve weeks.. Source GEO sample is GSM148661 Last updated (according to GEO): Dec 12 2006 Monocyte-derived dendritic cells (DC) and macrophages (M?) generated in vitro from the same individual blood donors were exposed to five different pathogens, and gene expression profiles were assessed by microarray analysis. Responses to Mycobacterium tuberculosis and to phylogenetically distinct protozoan (Leishmania major, L. donovani, Toxoplasma gondii) and helminth (Brugia malayi) parasites were examined, each of which produces chronic infections in humans yet vary considerably in the nature of the immune responses they trigger. Last Updated (by provider): Sep 08 2006 Contributers: D Sacks D Chaussabel R T Semnani T B Nutman A Sher M A McDowell Includes GDS260. Update date: Mar 22 2004. Dataset description GDS260: Gene expression in macrophages and dendritic cells following exposure to a variety of pathogens that produce variable chronic infections. Pathogens include Mycobacterium tuberculosis, helminths and three phylogenetically distinct protozoa.. total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Bombesin for 240min Source GEO sample is GSM5483 Last updated (according to GEO): May 27 2005 45 42 (ALS 28 0 Adult frontal cortex cocaine1 Plasma 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145758 Last updated (according to GEO): Nov 20 2006 0 Human Cortex 11 Heart 1000 Exp 2 Time point 6 561 in the cortex 573 8 0 G4 cornea RNAtotC_22, ZT6 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153499 Last updated (according to GEO): Jan 11 2007 MCF7 treated with vehicule for 24h Source GEO sample is GSM213331 Last updated (according to GEO): Jul 26 2007 70 40 without coronary artery disease GSE7764 0 cortex 5 cerebellum wistar ky 3891 human caudate nucleus Source GEO sample is GSM86800 Last updated (according to GEO): Feb 08 2006 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7821.gif Source GEO sample is GSM76423 Last updated (according to GEO): Sep 22 2006 861 Stria Expression profiling of spinal cord section (T9) extracted from rats 28d following severe injury Source GEO sample is GSM31611 Last updated (according to GEO): May 27 2005 Communicable Diseases 901 0029_1375_H95A2_KF-094_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 33 17 tibialis anterior 1896 1886 for livers High Fat Mouse 1 141 137 Brain Gene expression data from experimental treatment D-UT = 48h after PMA induced differentiated SH-SY5Y cells. Source GEO sample is GSM102877 Last updated (according to GEO): May 11 2006 cin_NY42B 23 13 spinal cord CO (Experiment 4Rlong: Run 19283) Treatment, type=timepoint, measurement=0.0 m Source GEO sample is GSM96677 Last updated (according to GEO): Feb 14 2006 9 0 Blood Test Array representing the response of Human foreskin fibroblasts at 6h post HCMV infection Source GEO sample is GSM10373 Last updated (according to GEO): May 27 2005 Heart 861 no additional Source GEO sample is GSM199420 Last updated (according to GEO): Jun 08 2007 5 0 brain Heart Ventricle 1000 healthy subject Source GEO sample is GSM211044 Last updated (according to GEO): Sep 10 2007 Primary Neoplasm 983 Bone marrow, Mesenchymal stem cells: T3-1-101103_e1_le1 67 50 Hypothalamus C57BL Liver 1000 1000 Brain Measles 861 Leukemia Promyelocytic (HL-60) [JunctionChip 1 of 5] MuscleRegen-ctx12d-1RLAv2-s2 Heart Septal Defects, Atrial 1000 GSE8081 865 Disorder of artery 5 0 Spleen mouse brain 478 489 "29 hr Hela Double Thymidine, exp3" Brain 861 1000 ovarian neoplasm 1000 Hippocampus Epithelium of bronchus 983 ci_NY19 19 0 Head and neck cancer Mouse ileum 0 10 Spinal Cord 1000 Intestines 861 923 Subcutaneous Fat Primary tumor 19 32 Adrenal Medulla 1000 24hr post 3Gy IR Normal Source GEO sample is GSM176149 Last updated (according to GEO): Apr 09 2007 Mesenchymal Stem Cells 1000 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11473 Last updated (according to GEO): May 28 2005 nostrils 156 164 proteoglycans 563 576 AML_25 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Cerebral cortex 9 0 cerebellum shld1 effect on 3T3 cell NHE1 null mutation brain stem-diencephalon-DS2 Neoplasm 861 861 Immune system 12 0 ovarian tumor 8 week old mice that did NOT undergo swimming. Used as a control for the 10 minute, 2.5 day, 1 week, and 2 week time points. Keywords = exercise induced hypertrophy Source GEO sample is GSM2343 Last updated (according to GEO): May 27 2005 I_95Av2_2822_AnCg_1_GS_B Normal Source GEO sample is GSM176108 Last updated (according to GEO): Apr 09 2007 We used the default settings of GCOS software to scan the chips. Source GEO sample is GSM148484 Last updated (according to GEO): Apr 16 2007 1000 Liver brain 0 5 651 629 in the caudate nucleus Localized Carcinoma 875 M_U133A_7_DLPFC ES_129b #1(16012165010066) Heart 1000 Gene expression data from the hippocampus of S1P2-knockout mouse Source GEO sample is GSM172965 Last updated (according to GEO): Mar 08 2007 none Source GEO sample is GSM210317 Last updated (according to GEO): Jul 16 2007 sAPPalpha #1 861 Malignant Neoplasms Brain_Wild-type_MiceNoLT340 The nose 94 101 242 230 of the heart no additional Source GEO sample is GSM199128 Last updated (according to GEO): Jun 08 2007 from colorectal adenoma 21 44 Coronary artery 901 in hippocampus 18 32 Bilateral olfactory bulbectomies were performed on male C57Bl/6 mice(6 week old) and olfactory epithelium tissue collected 5 days post-bulbectomy. Total RNA was extracted from the olfactory epithelium tissue. Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol. Keywords = olfaction Keywords = neurogenesis Keywords = apoptosis Keywords = gene silencing Keywords = microarray, transcription factor Source GEO sample is GSM45684 Last updated (according to GEO): Oct 28 2005 Lymphoblastoid Cell Line for Individual 8048.3 log phase Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. Source GEO sample is GSM112314 Last updated (according to GEO): Jun 06 2006 40 21 from the hippocampus Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15743 Last updated (according to GEO): May 28 2005 Squamous cell carcinoma 853 Interatrial septum 865 1000 Cerebral cortex 5 0 brain Bone Marrow 1000 Replicate two: differential expression analysis of CW vs Lyt44 treatment Source GEO sample is GSM128918 Last updated (according to GEO): Aug 16 2006 brain, Left Temporal Lobe: Extract46_le1 H9LMS00061303 B220+c-kit+ Pre BI cells sorted out of mouse bone marrow, sort no. 2 Source GEO sample is GSM628 Last updated (according to GEO): Mar 10 2006 in fibroblasts 1222 1236 Skeletal bone 861 GSE7952 from colonic normal mucosa 21 47 983 Epiphysial cartilage Human Sural Nerve Schwann Cell Donor 317 Passage 1 Treatment, type=add, description=growth factors heregulin and forskolin added Source GEO sample is GSM92235 Last updated (according to GEO): Jan 13 2006 1000 Brain GC (HKG33T) Recommended Affymetrix protocols were followed. Source GEO sample is GSM148465 Last updated (according to GEO): May 01 2007 Female 68.4 yr after antibody enrichment scan 2 (U133B) Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231044 Last updated (according to GEO): Sep 26 2007 26 12 of the pancreas I_U133A_114_CB CNS-RM_Ctr28d-2A-s2 hippocampal glutamatergic CA1 pyramidal neurons Source GEO sample is GSM35827 Last updated (according to GEO): May 27 2005 1000 Hippocampus Gene expression data from mouse primary visual cortex Source GEO sample is GSM101692 Last updated (according to GEO): Mar 27 2006 861 Cerebellum MCF7_CHX_E2_24h_rep4 Replicate3_Voxel C4 Myometrium 24 Disease of chromosome 16 61 76 f2#64 versus pool Mouse Brain tissue Brain 861 Brain 1000 Cochlear nucleus structure 1000 1000 Bronchi n/a Source GEO sample is GSM177919 Last updated (according to GEO): Jun 11 2007 36 21 from mouse brain none Source GEO sample is GSM239878 Last updated (according to GEO): Dec 07 2007 861 Neoplasm 861 Cardiomyopathies Seizures 1000 Disorder of artery 865 204 194 of retinal CNS-SpinalC-4hAdult-4A-s2 C77 on NCI-7.6k Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15469.gif Source GEO sample is GSM84177 Last updated (according to GEO): Sep 22 2006 Ischemia-reperfusion with AEOL 10150 #13 Bladder 861 Whole blood 0 10 83 69 Normal Pancreas 89 80 in stroke 1000 Heart Motor neurons from the spinal cord of SOD1 mutant mice Treatment, type=linear_amplification, description=T7-based RNA amplification Source GEO sample is GSM113706 Last updated (according to GEO): Jun 09 2006 0029_1428_H95A2_T96-250_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 3_cerebral_cortex_9hrs_sleep_deprivation_#4 901 Coronary artery Hippocampus 1000 3070 3040 specific endoplasmic reticulum- Tissue homogenate from cingulate cortex from GIN mouse (Gad1 inhibitory ref. (pubmed id:10777798) ). Source GEO sample is GSM64186 Last updated (according to GEO): Dec 01 2005 HOP-92 hgu95a adenoma 861 Normal__Pancreas_Pan_43N on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Brain JMR-RatSham4h-4aA-s2 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159952 Last updated (according to GEO): Feb 01 2007 Diaphragm 23 Day control rep 1 Normal Source GEO sample is GSM175879 Last updated (according to GEO): Apr 09 2007 CNS_SF295 on Affymetrix GeneChip Human Full Length Array HuGeneFL of mouse brain 9 23 1000 Cerebellum Bone Marrow 1000 1000 Brain metanephric mesenchyme, NGAL, 3 days, biological rep1 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13157.gif Source GEO sample is GSM79730 Last updated (according to GEO): Sep 22 2006 Genome-wide association analysis in diverse inbred mice: power and population structure none Source GEO sample is GSM244594 Last updated (according to GEO): Nov 23 2007 Pooled gastroc RNA samples from five 8 wk old male mdx5cv mice Source GEO sample is GSM13684 Last updated (according to GEO): May 28 2005 Metastatic tumor 19 35 Brain 1000 Medulla 861 AK_SleepDep_ZT 18_1 923 Neuronal Ceroid-Lipofuscinosis GSE1133.2 GC (HKG61T) Ganglia, Spinal 923 independent of SCLC 1975 1993 Spinal Cord 1000 Nasal Epithelium 901 1000 Myopathies, Nemaline plasma cells 50 61 Blood Test (Blinded) Sample Source GEO sample is GSM130014 Last updated (according to GEO): Sep 18 2007 Heart 861 Expression profiling of spinal cord section (T8) extracted from rats 24h following severe injury Source GEO sample is GSM31481 Last updated (according to GEO): May 27 2005 brain, hippocampus: PH4_e1_le1 546 525 of melanoma metastases 71 cortex 77 of the postmortem brains 676 700 Female 20.1 yr after antibody enrichment scan 2 (U133B) 18 olanzapine Multiple sclerosis (MS) is a neuroinflammatory disease of the central nervous system (CNS) with a well documented genetic component. Significant advances in the identification of the genetic component of MS have yet to be realized. The recent success that genetical genomics has shown in the identification of new QTL in plants and mice hold significant promise that this method can now be systematically applied in humans. Encouraging results indicate that even normal variation in gene expression could be genetically encoded. Characteristic patterns of gene expression have been already identified in PBMC from MS patients, and a high-resolution map of the human genome is readily available. We are combining these two powerful sources of information towards the identification of the long-time elusive genetic component of MS. The study proposed herein of ten individuals is a pilot study to ensure that gene expression variation is detectable in selected samples from our lymphoblastoid cell line collection to warrart a larger genetical genomics study. Pilot: Verify that there is sufficient variation in lymphoblastoid cell lines to warrant a full study. The full study will have the following specific aim: To explore and identify genomic regions responsible for the gene expression signature characteristic of multiple sclerosis patients. Gene expression patterns across lymphoblastoid cell lines from MS patients are sufficiently variable. Following validation of the above hypothesis, the following hypothesis will be addressed in a full study: Some of the genetic determinants of multiple sclerosis can be identified through the combination of studying gene expression and genomic mutations associated with this gene expression. Ten human lymphoblastoid cell line samples from our repository have been selected for this pilot study. Lymphoblastoid cell lines have been established by infection with the Epstein-Barr virus, and RNA has been isolated with the Rneasy kit (Qiagen, CA). RNA was quantitated using the RibogreenTM reagent (Molecular Probes, Eugene, OR) and its integrity was evaluated by agarose gel electrophoresis. BRB Arraytools, Bioconductor in R, and JMP Genomics (SAS Institute, Cary, NC) will be used to evaluate the expression variance of the samples by comparing them to already existing human microarray data. Last Updated (by provider): Jul 26 2007 Contributers: Jorge R Oksenberg V5-P103 901 Myeloid Leukemia Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118563 Last updated (according to GEO): Jul 11 2006 61 50 Testis C57BL 1000 Substantia nigra structure 861 Brain 304 280 alcoholic cardiomyopathy Alzheimer's Disease 1000 Epithelium of bronchus 983 2045 2017 of adhering connective tissue NA19131 CS-B cell UVC-irradiated (2hour) replicate 1 U133B 1000 Neurobehavioral Manifestations Patient1D days nasal epithelium 1126 1147 5 0 Spleen 24 0 human prostate PC3 tumors 861 Skin Gene expression data from skeletal muscle following 240 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230449 Last updated (according to GEO): Sep 19 2007 861 Cerebral cortex Probeset expression data from NA12745 growth 1 Source GEO sample is GSM201530 Last updated (according to GEO): Aug 08 2007 Bone Marrow 1000 861 Intestines Mouse model of congenital heart disease in Csx/Nkx2.5 mutant embryos. Heterozygous embyronic day 9.5 mouse. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2269 Last updated (according to GEO): May 27 2005 Type 1 Diabetes patient and the timepoint 4 months after diagnosis. Source GEO sample is GSM228621 Last updated (according to GEO): Sep 11 2007 Brain 861 Primary tumor 19 32 Cerebral cortex 861 Nose 1000 M7TW00121816 lateral motoneurons (LMN) 8 861 Encephalitis 861 Neoplasm Nose 1000 29 year old male 861 Infection vantveer-breast Epithelial Cells 901 11 0 Brain trauma brain, hippocampus: KA72-II_e1_le1 Ovarian_Tumor_Mucinous_CHTN-OM-035 Mammary Gland @ Preg3, biological rep3 Epithelium 861 Gonadectomized Dahl-Iwai Female LowSalt Cortex rat2 gdahl_cortexr_k_GX_2c_051702 Coronary Arteriosclerosis 1000 the heart 987 996 plasma cells 50 61 Infection 861 Immune; Lymph Node_Comprlete Freunds Adjuvant stimulated Keywords = mouse gene expression database Source GEO sample is GSM29351 Last updated (according to GEO): May 27 2005 Coronary heart disease 913 861 Cholinergic Receptors Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184821 Last updated (according to GEO): Apr 26 2007 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188849 Last updated (according to GEO): Jun 06 2007 20 0 human caudate nucleus Skeletal muscle structure 1000 Expression profiling of spinal cord section (T9) extracted from rats 12h following moderate injury Source GEO sample is GSM31516 Last updated (according to GEO): May 27 2005 bronchial epithelia 224 243 plasma cells 332 344 901 Coronary artery liver, wild type mice, treatment with WY14643 for 6h Source GEO sample is GSM205770 Last updated (according to GEO): Jul 24 2007 Exp 1 (-TNFa) brain, hippocampus: CON-CA3-A8_e1_le1 1000 Liver for liver 26 35 Neocortical astrocyte chip 3. CHIP ID 10488 Source GEO sample is GSM130361 Last updated (according to GEO): Mar 14 2007 osteoblast 627 637 27 0 Substantia nigra normal rep1 Spleen vs IL4 Treated B cell 120min (set2) Saccule 0 6 Cerebral cortex 1000 mouse control, liver, RNA B6477A Coronary Arteriosclerosis 1000 5 0 brain Spinal Cord 1000 olfactory epithelium wild type mouse 8 hpO Source GEO sample is GSM80191 Last updated (according to GEO): Oct 26 2005 nasal epithelial cells 28 49 19 0 Head and neck cancer Autistic Disorder 877 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188721 Last updated (according to GEO): Jun 06 2007 HeartE145_227AFIG_td1.txt Epithelial Cells 1000 861 Neoplasm Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15953.gif Source GEO sample is GSM84132 Last updated (according to GEO): Sep 22 2006 FVB-3w-f-1 1000 jejunum 861 HIV Infections BXD 34_M7SS02080617 Laser capture lung cancer cells Source GEO sample is GSM191050 Last updated (according to GEO): May 25 2007 Endometrium/Ovary-Disease 1 14 0 Large Intestine Cortex Source GEO sample is GSM53369 Last updated (according to GEO): Jul 06 2005 HCC (HBV+, CH2) R481P00302 the blood 393 402 Gene expression data from postmorten brain regions Source GEO sample is GSM146011 Last updated (according to GEO): Nov 20 2006 861 HIV Infections Cerebellum Control (AD) 10 vantveer-breast Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174529 Last updated (according to GEO): Mar 14 2007 861 Ganglia Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228583 Last updated (according to GEO): Sep 11 2007 the blood 393 402 Infection 861 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184802 Last updated (according to GEO): Apr 26 2007 861 Bladder 1000 Neuraxis embryonic hearts 1064 1079 1000 Hypertrophic Cardiomyopathy 861 Ganglia Colon 861 Ta gr3 tumour Source GEO sample is GSM2535 Last updated (according to GEO): Mar 21 2006 113 104 IV gliomas SN:Human Glioblastoma Biopsy 07096 Gastrocnemius muscle 2 days after 100ul 10uM cardiotoxin injection Source GEO sample is GSM4277 Last updated (according to GEO): May 27 2005 ventral tegmental area short access to cocaine replicate 1 Laser capture lung cancer cells Source GEO sample is GSM191013 Last updated (according to GEO): May 25 2007 1281_32d Spleen vs Untreated B cell Time 0 (set1) 1 of 3 replicates in treatment group Source GEO sample is GSM206041 Last updated (according to GEO): Jun 29 2007 Exp C, Animal #4, 10mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours Source GEO sample is GSM246171 Last updated (according to GEO): Dec 03 2007 Phenytoin hippocampus 2 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53420 Last updated (according to GEO): Jul 06 2005 200 164 of bronchiolitis obliterans syndrome n/a Source GEO sample is GSM177975 Last updated (according to GEO): Jun 11 2007 of the postmortem brains 654 678 Arteries 861 Osteoblasts 1000 GC (HKG39N) B. abortus 2308 ADH4.2 replicate 2 Spleen 251 256 Accumbens 5 Normal Paravertebral Muscle 3 Disease 0 29 861 Prostate Prostate 19 Normal brain 0 5 1000 Brain osteoblast 627 637 1000 Turner's Syndrome The most common congenital cardiac abnormalities 50 97 Gene expression data from postmorten brain regions Source GEO sample is GSM145269 Last updated (according to GEO): Nov 20 2006 Occipital lobe 861 hippocampus_4 Source GEO sample is GSM80663 Last updated (according to GEO): Mar 31 2006 Plasma 861 1000 Structure of superior frontal gyrus 10 0 whole brain cerebral cortex 7 21 Expression profiling of laminectomized raphe at 3mo in rats Source GEO sample is GSM41537 Last updated (according to GEO): May 27 2005 parietal_lobe_10 Source GEO sample is GSM80763 Last updated (according to GEO): Mar 31 2006 5 0 Uterus Epithelial Cells 1000 Expression profiling of spinal cord section (T10) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM6649 Last updated (according to GEO): May 28 2005 Z1 biol repl 2 Gene expression data from the neocortex of S1P2-knockout mouse Source GEO sample is GSM172946 Last updated (according to GEO): Mar 08 2007 91 from the bone marrow 72 Mouse Liver LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate E B. melitensis 16M replicate 1 Fibroblasts 1000 Brazil 22613(LL) T2+ gr4 tumour Source GEO sample is GSM2513 Last updated (according to GEO): Mar 21 2006 102T Tumor__CNS_Medulloblastoma_M50_D7 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene expression data from postmorten brain regions Source GEO sample is GSM145076 Last updated (according to GEO): Nov 20 2006 LymphomaRaji Source GEO sample is GSM18732 Last updated (according to GEO): Sep 25 2006 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184726 Last updated (according to GEO): Apr 26 2007 Heart 1000 1000 Communicable Diseases 24 0 human prostate PC3 tumors M_U133A_27_AnCg HapMap JPT Female Source GEO sample is GSM159647 Last updated (according to GEO): Feb 01 2007 CNS-SCsev_InjB7d-4C-s2 865 Disorder of artery 670 664 muscle Parkinson Disease 1000 Fibroblasts 861 NINDS-RNP-SNC-2aA-s2 Gene expression data from postmorten brain regions Source GEO sample is GSM144918 Last updated (according to GEO): Nov 20 2006 HDMTX-DX-17 32 12 frontal temporal lobe 2 hrs Post-clamp sample 6 of osteoblasts 71 85 Cerebral cortex 861 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181227 Last updated (according to GEO): Jul 12 2007 Heart 861 in blood 16 23 NA12891 67 40 with coronary artery disease 901 Bone Marrow Gene expression data from postmorten brain regions Source GEO sample is GSM144889 Last updated (according to GEO): Nov 20 2006 901 Coronary artery 861 Cerebral cortex Nose 1000 1500 mg/kg X 12 hr Source GEO sample is GSM129884 Last updated (according to GEO): Sep 18 2007 Epithelium 861 Liver 1000 117 112 Lipids brain, Posterior Singulate: Sample41_e1_le1 407 400 of axons brain, cerebral cortex: Rat_03-05_NroLep_Lipska_e1_le1 BACKGROUND: Germline mutations in BRCA1 and BRCA2 are responsible for 5%-10% of epithelial ovarian cancers, but the molecular pathways affected by these mutations are unknown. We used complementary DNA (cDNA) microarrays to compare gene expression patterns in ovarian cancers associated with BRCA1 or BRCA2 mutations with gene expression patterns in sporadic epithelial ovarian cancers and to identify patterns common to both hereditary and sporadic tumors. METHODS: Tumor samples from 61 patients with pathologically confirmed epithelial ovarian adenocarcinoma with matched clinicopathologic features were studied, including 18 with BRCA1 founder mutations, 16 with BRCA2 founder mutations, and 27 without either founder mutation (termed sporadic cancers). The cDNA microarrays contained 7651 sequence-verified features. Gene expression data were analyzed with a modified two-sided F test, with P<.0001 considered statistically significant. The expression level of six genes was also studied with reverse transcription-polymerase chain reaction. RESULTS: The greatest contrast in gene expression was observed between tumors with BRCA1 mutations and those with BRCA2 mutations; 110 genes showed statistically significantly different expression levels (P<.0001). This group of genes could segregate sporadic tumors into two subgroups, "BRCA1-like" and "BRCA2-like," suggesting that BRCA1-related and BRCA2-related pathways are also involved in sporadic ovarian cancers. Fifty-three genes were differentially expressed between tumors with BRCA1 mutations and sporadic tumors; six of the 53 mapped to Xp11.23 and were expressed at higher levels in tumors with BRCA1 mutations than in sporadic tumors. Compared with the immortalized ovarian surface epithelial cells used as reference, several interferon-inducible genes were overexpressed in the majority of tumors with a BRCA mutation and in sporadic tumors. CONCLUSIONS: Mutations in BRCA1 and BRCA2 may lead to carcinogenesis through distinct molecular pathways that also appear to be involved in sporadic cancers. Sporadic carcinogenic pathways may result from epigenetic aberrations of BRCA1 and BRCA2 or their downstream effectors. acute myeloid leukemia Source GEO sample is GSM227416 Last updated (according to GEO): Sep 12 2007 861 Brain tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44890 Last updated (according to GEO): May 27 2005 12 0 Blood B cells Gene expression data from dorsal pancreas at e14.5, MG-U74A version2 Source GEO sample is GSM199448 Last updated (according to GEO): Jun 08 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145174 Last updated (according to GEO): Nov 20 2006 Colon 861 VDXIGRU_307506 The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76943 Last updated (according to GEO): Oct 11 2005 Fibroblasts 861 Liver 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with SDF1 alpha (Stromal cell derived factor-1) for 120min Source GEO sample is GSM5762 Last updated (according to GEO): May 27 2005 none Source GEO sample is GSM244545 Last updated (according to GEO): Nov 23 2007 Nose 1000 Putamen P1 Disease in the adult heart 44 61 ALS model Source GEO sample is GSM75488 Last updated (according to GEO): Mar 06 2006 NHF10-hTERT_S_C3_26578 experimental autoimmune encephalomyelitis 563 603 e_NY44 861 Brain Endometrium 14 Normal Myocardial Infarction 1000 liver 0 5 Neoplasm 861 tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44889 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T10) extracted from rats 14d following severe injury Source GEO sample is GSM31346 Last updated (according to GEO): May 27 2005 of Parkinson's disease 432 453 144 114 from a single adult spinal cord 10 7 left 901 frontal lobe Dorsal Raphe Source GEO sample is GSM107970 Last updated (according to GEO): Jun 06 2006 Blood Test (Blinded) Sample Source GEO sample is GSM129926 Last updated (according to GEO): Sep 18 2007 TEL-AML1-#1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 5 0 Kidney GSE4458 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD16 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD16 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36706 Last updated (according to GEO): May 27 2005 Hippocampus 1992 15 month Old 32 16 of organ of Corti Expression profiling of spinal cord section (T9) extracted from rats 4h following moderate injury Source GEO sample is GSM31567 Last updated (according to GEO): May 27 2005 1262 1247 dermatomyositis Brain 861 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11553 Last updated (according to GEO): May 28 2005 leukemia lymphoblastic (MOLT-4) Source GEO sample is GSM18888 Last updated (according to GEO): Sep 25 2006 Keywords = kidney 113 130 Cerebral cortex 1000 PMN_control_360min_Patient9 15 0 human cerebellum frontal lobe 1000 861 HIV Infections spinal_cord_1 Source GEO sample is GSM80784 Last updated (according to GEO): Mar 31 2006 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10148.gif Source GEO sample is GSM79633 Last updated (according to GEO): Sep 22 2006 Trachea BD Normal 2737 tumor cells 2747 with Parkinson's disease 27 50 1000 Mitral Valve Spleens 129 135 Ganglia 1000 Squamous cell carcinoma 923 adenoma 861 Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging and comparing calorie restricted-fed 30-month-old to control-fed 30-month-old to investigate effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7459 Last updated (according to GEO): May 27 2005 861 Blood VDXGUYU_4011 861 Oocytes Breast cancer patients with the same stage of disease can have markedly different treatment responses and overall outcome. The strongest predictors for metastases (for example, lymph node status and histological grade) fail to classify accurately breast tumours according to their clinical behaviour. Chemotherapy or hormonal therapy reduces the risk of distant metastases by approximately one-third; however, 70-80% of patients receiving this treatment would have survived without it. None of the signatures of breast cancer gene expression reported to date allow for patient-tailored therapy strategies. Here we used DNA microarray analysis on primary breast tumours of 117 young patients, and applied supervised classification to identify a gene expression signature strongly predictive of a short interval to distant metastases ('poor prognosis' signature) in patients without tumour cells in local lymph nodes at diagnosis (lymph node negative). In addition, we established a signature that identifies tumours of BRCA1 carriers. The poor prognosis signature consists of genes regulating cell cycle, invasion, metastasis and angiogenesis. This gene expression profile will outperform all currently used clinical parameters in predicting disease outcome. Our findings provide a strategy to select patients who would benefit from adjuvant therapy. 70 40 without coronary artery disease prostate Source GEO sample is GSM203406 Last updated (according to GEO): Jun 21 2007 To identify patterns of change in gene expression that correlated with drug treatment (saline control, ADH-1 alone, melphalan alone and ADH-1 plus melphalan) in our animal model of regional therapy for extremity melanoma we evaluated gene expression using microarray genechips and a Pearson correlation analysis. Genes were ranked according to the degree to which expression correlated with systemic ADH-1 treatment alone or in combination with regional melphalan. Tissue samples were harvested at 4, 24 and 48 hours after treatment with melphalan. Specific cellular pathways associated with drug treatment were identified using gene set enrichment analysis (GSEA). Last Updated (by provider): Jul 27 2007 Contributers: Christina K Augustine Douglas S Tyler Sample8, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53259 Last updated (according to GEO): Jul 06 2005 4089 4084 liver 1000 ovarian neoplasm Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO + U0126 (10?M) overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 9 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10963 Last updated (according to GEO): Sep 08 2006 Seminoma 1000 Low-density CCg progenitors Source GEO sample is GSM47549 Last updated (according to GEO): Jun 10 2005 Hippocampus 1000 Brain 861 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12408.gif Source GEO sample is GSM79833 Last updated (according to GEO): Sep 22 2006 Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242054 Last updated (according to GEO): Dec 04 2007 CNS-SC_Inj24h-4B-s2b Large-scale analysis of the human transcriptome. Lymphoma Burkitt's Daudi Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 344.37 Stdv: 16.95 Min: 316.61 Max: 376.49 Source GEO sample is GSM2890 Last updated (according to GEO): Mar 20 2006 Occipital lobe 861 Spleen 0 5 7 0 prostate Tissue Source GEO sample is GSM67241 Last updated (according to GEO): Jan 19 2006 Accumbens 1 Normal Spinal Cord 1000 none Source GEO sample is GSM161908 Last updated (according to GEO): Feb 16 2007 CNS-SpinalC-4hAdult-4C-s2 Wild type 8 wk old male 129S6/SvEvTac mouse hippocampus Source GEO sample is GSM107005 Last updated (according to GEO): Mar 05 2007 E7.5_rep1 1000 Neoplasm n/a Source GEO sample is GSM177900 Last updated (according to GEO): Jun 11 2007 brain 0 5 Head and neck cancer Source GEO sample is GSM155715 Last updated (according to GEO): Apr 24 2007 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181097 Last updated (according to GEO): Jul 12 2007 598 590 in urine Gene expression data from brain of adult rats Source GEO sample is GSM100999 Last updated (according to GEO): Feb 20 2007 of Parkinson's disease 450 471 Gene expression data from postmorten brain regions Source GEO sample is GSM145330 Last updated (according to GEO): Nov 20 2006 none Source GEO sample is GSM149546 Last updated (according to GEO): Jan 03 2007 Plasma 861 39 27 the maxillary Olfactory Epithelium 1000 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113970 Last updated (according to GEO): Jun 16 2006 Olfactory Epithelium 1000 The goal of these experiments was to identify the genes that are regulated by CCAT, a novel transcription factor derived from the C-terminus of CaV1.2. Neuro2A neuroblastoma cells were transfected with the last 503 AA of CaV1.2 which is full length CCAT (CCAT FL) or with the last 280 AA of CaV1.2, a form of CCAT that lacks the transcriptional activation domain (CCAT DTA). The mRNA from either CCAT FL or CCAT DTA expressing cells was hybridized to Agilent mouse genome microarrays along with mRNA from untransfected neuro2A cells. The microarray data was subsequently analyzed with the Rossetta Luminator gene expression data analysis system. Subsequent investigation revealed that CCAT DTA can still activate transcription albeit at much lower levels than CCAT FL. Source GEO sample is GSM95644 Last updated (according to GEO): Feb 07 2006 Human muscle cultures were prepared from progenitor satellite cells isolated from a muscle biopsy of a 16-donor subject through an explant-reexplant technique (5). Biopsies were obtained with informed consent and approval of the Human Use Committee of the Hospital Vall d?Hebrón, Barcelona. A batch of cells isolated after 1 explant and 4 consecutive subcultures at dilution (1:3) were induced to differentiate for 15 days and then weekly monitored for the stated parameters. Growth medium was DMEM:MEM-199 3:1, supplemented with 10 % fetal bovine serum (FBS), 10 µg/ml insulin, 2 mM glutamine, 25 ng/ml fibroblast growth factor (FGF) and 10 ng/ml epidermal growth factor (EGF). Differentiating medium had the same composition except FGF and EGF. Cultures were kept at 37ºC in a humidified 5% CO2 atmosphere. Source GEO sample is GSM19154 Last updated (according to GEO): Oct 28 2005 Breast Diseases 913 1000 Hippocampus 278 231 with previously untreated acute myeloid leukemia 660 mesenchymal stem cell 639 1000 frontal lobe Ovary_Normal_UM-NO-3 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153412 Last updated (according to GEO): Jan 11 2007 Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19192 Last updated (according to GEO): May 27 2005 SVGR2 subclone 4-E12 GeneChip U133B 5 0 brain ovary 45 50 Adipocytes 861 Replicate2_Voxel F8 from ventral prostate 21 41 Tissue Source GEO sample is GSM67229 Last updated (according to GEO): Jan 19 2006 RNA samples extracted from astrocytes cultured from wild type and Cx43 null neonatal mice were dye labeled and individually co-hybridized with a reference of labeled cDNAs pooled from a variety of tissues on eight gene arrays containing 8975 mouse DNA sequences Lot batch = 1 Source GEO sample is GSM8893 Last updated (according to GEO): May 27 2005 amygdala_2 in Human Skeletal Muscle 35 58 Colon 861 Examining the effects of tTA expression in mouse hearts Source GEO sample is GSM15063 Last updated (according to GEO): May 28 2005 Heart 861 Obesity 1000 Communicable Diseases 901 1000 Ventricular septum plasma cells 332 344 Structure of hemidiaphragm 861 on human airway epithelial cells 1114 1145 Localized Carcinoma 853 We used the default settings of GCOS software to scan the chips. Source GEO sample is GSM148486 Last updated (according to GEO): Apr 16 2007 Cortex 0 5 Normal Source GEO sample is GSM175838 Last updated (according to GEO): Apr 09 2007 of the colon 28 39 To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132995 Last updated (according to GEO): Sep 12 2006 1500 mg/kg X 6 hr Source GEO sample is GSM129840 Last updated (according to GEO): Sep 18 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11464 Last updated (according to GEO): May 28 2005 in seminoma 28 38 7 cerebral cortex 21 To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18443 Last updated (according to GEO): May 27 2005 autism 0 5 stria terminalis 1000 978 969 carcinomas embryonic hearts 1064 1079 Small Intestine Jejunum 3 Normal plasma cells 332 344 NCI-H322 hgu95e 24 a genetic disease 40 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=700630 LaserPower=2.191.29 Lot batch = LC17N042 Source GEO sample is GSM4793 Last updated (according to GEO): Nov 21 2005 Liver 1000 129:28-11-20 choroid plexus 708 704 lens 1000 Hypothalamic structure Anterior nares 1000 1123 1116 tubulin Brain 861 Replicate1_Voxel A7 Transitional epithelium 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145251 Last updated (according to GEO): Nov 20 2006 nostrils 156 164 865 Disorder of artery Cerebellum 1000 1000 frontal lobe Osteoblasts 1000 166 156 of retinal EpiTl_022WACI3_114b.txt Polyamide 2 treated LNCaP cells not stimulated with DHT, biological replicate 1 Source GEO sample is GSM187380 Last updated (according to GEO): May 04 2007 1000 Rectum Colon 861 20 0 human caudate nucleus Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12969.gif Source GEO sample is GSM79982 Last updated (according to GEO): Sep 22 2006 human frontal cortex Source GEO sample is GSM86965 Last updated (according to GEO): Feb 08 2006 1000 Medulla ISS/ILS_cerebellum_naive_416 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 24h after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44477 Last updated (according to GEO): May 27 2005 278 255 ischemic cardiomyopathy PGA-HBE-AsthOz18h-1aA-S2 1000 Brain CNS-SC_CtrB30m-1B-s2 nostrils 156 164 Anterior nares 1000 14 0 Locus Coeruleus A/J cingulate cortex rep2 Colonic mucous membrane 913 from brain 21 30 pfc_1046_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A HA01-57A Timecourse of TLR2/1 stimulated human dendritic cells with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225875 Last updated (according to GEO): Aug 31 2007 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=730610 LaserPower=2.041.31 Lot batch = LC17N094 Source GEO sample is GSM4817 Last updated (according to GEO): Nov 21 2005 Embryonic day 18.5 corticospinal motor neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription. Source GEO sample is GSM37090 Last updated (according to GEO): May 27 2005 861 Kidney cy5:SHR control, biological rep 2r; cy3:pool of 6 WKY control rats Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Subject code A29 861 Kidney Coronary heart disease 913 Nervous system structure 901 CNS-RM_Mod14d-1B-s2 ER negative human primary breast tumor EA02014_41295_H133A_JA-1976 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3292 Last updated (according to GEO): Mar 21 2006 17 7 hippocampus Gene expression data from postmorten brain regions Source GEO sample is GSM145684 Last updated (according to GEO): Nov 20 2006 brain, cochlea: [8] Sample #8_le1 mouse brain contralateral LPS.RU486 Source GEO sample is GSM149761 Last updated (according to GEO): Mar 15 2007 long access to cocaine, ventral tegmental area, 6 hrs/day access to cocaine Source GEO sample is GSM93864 Last updated (according to GEO): Jan 26 2006 34 CB B Gene expression data from postmorten brain regions Source GEO sample is GSM145424 Last updated (according to GEO): Nov 20 2006 Cerebellum 1000 Liver; Adult Fed Keywords = mouse gene expression database Source GEO sample is GSM29366 Last updated (according to GEO): May 27 2005 large cell lung carcinoma 1934 Source GEO sample is GSM17350 Last updated (according to GEO): May 28 2005 Plasma 861 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 6161 left_liver_lobe DLBC56 on Affymetrix GeneChip Human Full Length Array HuGeneFL Epithelial Cells 901 19 0 human frontal cortex n/a Source GEO sample is GSM177932 Last updated (according to GEO): Jun 11 2007 Leukemia, Lymphocytic, Chronic 1000 Lymphoblastoid Cell Line for Individual 8075.5 log phase Mouse Liver AIN Diet 5wk 10ppb As Food Exposure, biological replicate A 901 Caudate nucleus structure Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210422 Last updated (according to GEO): Jul 16 2007 Skeletal bone 861 861 Femur brain, cortex: Sample6_e1_le1 Standard affymetrix protocol Source GEO sample is GSM119500 Last updated (according to GEO): Jul 31 2007 These data were used as preliminary results for paper: Maternal Cocaine Administration Alters DNA Methylation in Hippocampal Neurons of Neonatal and Prepubertal Mice Svetlana I. Novikova, Fang He, Jie Bai, Nicholas J. Cutrufello, Ashiwel S. Undie and Michael S. Lidow Source GEO sample is GSM154045 Last updated (according to GEO): Jan 19 2007 gfp pos. sorted cells from 3 disected e14.5 cortecies Treatment, type=wait Source GEO sample is GSM135781 Last updated (according to GEO): Sep 12 2006 7 0 prostate P2B_KIDNEY_9 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13081.gif Source GEO sample is GSM76473 Last updated (according to GEO): Sep 22 2006 861 Epithelial Cells NCI60.34_LABEL38EXTRACT37SUB3 Source GEO sample is GSM134164 Last updated (according to GEO): Aug 06 2007 Spleen 1000 15 0 human cerebellum gene expression data from melanoma xenografts following ILI with saline Source GEO sample is GSM213636 Last updated (according to GEO): Jul 27 2007 15 0 human cerebellum Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225725 Last updated (according to GEO): Nov 02 2007 Brain 861 Conn Syndrome 1000 4 0 Heart 1000 Cerebellum 1000 Amygdaloid structure 27 7 Medial Temporal Gyrus 145T frontal lobe 901 striatum 30 38 79 58 of murine bone marrow Serum 20 Neoplasm 861 CNS-RM_Mod4h-3C-s2 1000 Brain 1000 Pituitary Gland 777 760 in skeletal muscle Job's patient Source GEO sample is GSM211032 Last updated (according to GEO): Sep 10 2007 Spleen 0 5 PE_D_594 160T Heart Septal Defects, Atrial 1000 1596 in neurodegenerative disorders 1625 861 Antibodies none Source GEO sample is GSM123224 Last updated (according to GEO): Jul 26 2006 Expression profiling of spinal cord section (T9) extracted from rats 28d following mild injury Source GEO sample is GSM31225 Last updated (according to GEO): May 27 2005 Performed by UCI Microarray Facility. Source GEO sample is GSM203589 Last updated (according to GEO): Jun 22 2007 Isolated adipocytes 0 18 Y HID D037 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108632 Last updated (according to GEO): Aug 22 2006 "Sample 11,>5 yr survival(70 months) age 37 erp yes" on vantveer-oligo M_U133A_91_nAcc Heart 1000 Effects of SOCS3 on transcriptional response of macrophages to IL-6. Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Replicate 1 after stimulation for 400 minutes with 10 ng/ml IL-6. Source GEO sample is GSM6077 Last updated (according to GEO): Mar 17 2006 SM-J_male_hypothalamus total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL4 for 240min Source GEO sample is GSM5642 Last updated (according to GEO): May 27 2005 1000 frontal lobe 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114459 Last updated (according to GEO): Jun 16 2006 human caudate nucleus Source GEO sample is GSM86881 Last updated (according to GEO): Feb 08 2006 Rat frontal cortex RNA - VH TTX Experiment Source GEO sample is GSM92315 Last updated (according to GEO): Jan 13 2006 1000 Muscle 861 Cerebral cortex 1000 Hippocampus 861 Heart brain 0 5 901 frontal lobe none Source GEO sample is GSM239870 Last updated (according to GEO): Dec 07 2007 901 frontal lobe 928 Endometrium Studies in the developing spinal cord suggest that different motoneuron (MN) cell types express very different genetic programs, but the degree to which adult programs differ is unknown. To compare genetic programs between adult MN columnar cell types, we used laser capture microdissection (LCM) and Affymetrix microarrays to create expression profiles for three columnar cell types: lateral and medial MNs from lumbar segments and sympathetic preganglionic motoneurons located in the thoracic intermediolateral nucleus. A comparison of the three expression profiles indicated that approximately 7% (813/11,552) of the genes showed significant differences in their expression levels. The largest differences were observed between sympathetic preganglionic MNs and the lateral motor column, with 6% (706/11,552) of the genes being differentially expressed. Significant differences in expression were observed for 1.8% (207/11,552) of the genes when comparing sympathetic preganglionic MNs with the medial motor column. Lateral and medial MNs showed the least divergence, with 1.3% (150/11,552) of the genes being differentially expressed. These data indicate that the amount of divergence in expression profiles between identified columnar MNs does not strictly correlate with divergence of function as defined by innervation patterns (somatic/muscle vs. autonomic/viscera). Classification of the differentially expressed genes with regard to function showed that they underpin all fundamental cell systems and processes, although most differentially expressed genes encode proteins involved in signal transduction. Mining the expression profiles to examine transcription factors essential for MN development suggested that many of the same transcription factors participate in combinatorial codes in embryonic and adult neurons, but patterns of expression change significantly. 135T FVB-3w-f-2 heart 1169 1173 Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 0460 blood Whole Brain 62 72 Aortic Aneurysm 901 Prostate 861 Parkinson 0 8 5 0 brain 468 459 the rectum Gene expression data from postmorten brain regions Source GEO sample is GSM145737 Last updated (according to GEO): Nov 20 2006 D2_SleepDep_ZT 18_3 Infection 1000 14 days hindlimb suspended RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis Source GEO sample is GSM10052 Last updated (according to GEO): May 28 2005 Plasma 861 406 395 whose hearts Brain 1000 in mouse hearts 40 54 PMN_LB_360min_Patient16 total RNA from biosource CC#17 Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92460 Last updated (according to GEO): Jan 13 2006 Nose 1000 hrs nasal epithelium 1126 1146 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181055 Last updated (according to GEO): Jul 12 2007 Head and neck cancer Source GEO sample is GSM155703 Last updated (according to GEO): Apr 24 2007 5 0 brain Testis 1000 3 min exposure to halothane prior to immediate perfusion with ice cold saline Keywords = Eckenhoff Keywords = anesthetics Source GEO sample is GSM11381 Last updated (according to GEO): May 28 2005 Balb/c day 3, biological rep 1, tech rep 1 hip_1015_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Cnr1-/-/Cnr2-/- female number 2, DNFB-treated allergic ear (#11_Ko-Tr-5) Skeletal bone 861 91 from the bone marrow 72 of the postmortem brains 656 680 306 293 from asthmatic Replicate2_Voxel D11 9 0 Blood Test High Freezing Source GEO sample is GSM92428 Last updated (according to GEO): Jan 13 2006 89 68 with tricuspid valves 206 188 of the spinal cord vestibular_nuclei_superior_3 861 Oocytes CNS-SMTC_CtrT0-4A-s2 brain 0 5 mammary epithelial cells transduced with hTERT Source GEO sample is GSM5174 Last updated (according to GEO): May 27 2005 861 medulloblastoma leukemiachronicmyelogenous(k562) Source GEO sample is GSM18739 Last updated (according to GEO): Sep 25 2006 "13 hr Hela Double Thymidine, exp3" Temporal neocortex mTLE 1 567 548 the descending colon 861 Occipital lobe Richard Almon-26-1138200270258 861 Blood WT biol repl2 Keywords = Heart 505 521 Cerebellum 1000 Type 2 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228667 Last updated (according to GEO): Sep 11 2007 TUMOR 4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Prostate carcinoma Brain 861 5 0 brain 861 Cerebral cortex 1000 Malignant neoplasm of urinary bladder Lymphoblastoid Cell Line for Individual 8036.4 log phase JMR-RatInj30m-3aA-s2 B6 day 0, biological rep 4, tech rep 1 na Source GEO sample is GSM180458 Last updated (according to GEO): Apr 04 2007 Whole blood 0 10 Date : 3/21/2002 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 3.0 hrs post-injection Intervention : 4.0 mg/kg PK11195 co-administered Risk: anticipated remediation to <10% malformations Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots Keywords = methylmercury Keywords = PK11195 Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = SC856 Source GEO sample is GSM12259 Last updated (according to GEO): May 28 2005 1000 Cerebral cortex Cerebellum 1000 GSE7329 Normal Source GEO sample is GSM176272 Last updated (according to GEO): Apr 09 2007 m1-carcinoma5 D_U133A_30_nAcc Normal Source GEO sample is GSM176258 Last updated (according to GEO): Apr 09 2007 Meningioma Recurrent Grade 1 Treatment, type=harvest, description=There is no treatment. Tumors were flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108008 Last updated (according to GEO): Jun 06 2006 aa_NY74 Gene expression data from postmorten brain regions Source GEO sample is GSM145191 Last updated (according to GEO): Nov 20 2006 none Source GEO sample is GSM239860 Last updated (according to GEO): Dec 07 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM146081 Last updated (according to GEO): Nov 20 2006 Bone Marrow 1000 Femur 1000 861 Cancer of Neck Ta gr2 tumour Source GEO sample is GSM2475 Last updated (according to GEO): Mar 16 2006 Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 3 MO_LB_180min_Patient17 1000 ovarian neoplasm Mesenchymal Stem Cells 1000 Cerebellum 1000 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155056 Last updated (according to GEO): Jun 04 2007 in cortex 160 168 CS-B wt-rescued cell unirradiated replicate 3 U133B brain, amygdala: Stress-Hippocampus_e1_le1 the blood 393 402 Gene expression data of substantia nigra from postmortem brain of PD patients Source GEO sample is GSM184363 Last updated (according to GEO): May 29 2007 with autism spectrum disorder 37 65 Large-scale analysis of the mouse transcriptome. Lung C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 271.63 Stdv: 11.08 Min: 254.33 Max: 291.48 Source GEO sample is GSM2936 Last updated (according to GEO): May 27 2005 1037 of transitional epithelium 1012 peripheral blood-CD14Monocytes Source GEO sample is GSM18871 Last updated (according to GEO): Sep 25 2006 Localized Malignant Neoplasm 853 861 Patau's syndrome NOS Neoplasm 1000 4 0 Liver adrenal gland Source GEO sample is GSM18947 Last updated (according to GEO): Sep 25 2006 brain, Right Temporal Parietal: Extract83_le2 VDXGUYU_4022 1000 Heart failure 5 0 Kidney 913 Acute leukemia 1000 Heart failure 5 0 Spleen D07 6h Media Low-density CCg progenitors treated with RA/Fsk to derive Neurons Source GEO sample is GSM47557 Last updated (according to GEO): Jun 10 2005 Basal-like breast tumor cell line HME-CC Keywords = Agilent microarray, Expression analysis, EGFR, Breast cancer growth Source GEO sample is GSM29519 Last updated (according to GEO): Dec 13 2006 19 0 Kainate-hippocampus Stem cells 901 Endometrium/Ovary 18 Disease Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. organs 28 33 21 0 acute myeloid leukemia temporal_lobe_10 Source GEO sample is GSM80861 Last updated (according to GEO): Mar 31 2006 1000 Spleen 861 Cerebral cortex brain, cerebellum: RNA#35_le1 Neurites 861 1st 4hr C-CA1 Richard Almon-26-1133800609573 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141286 Last updated (according to GEO): Oct 26 2006 12 frontal Lobe 23 1.25 mg/kg MeHg forebrain at 3.0h GSE1133.1 913 Blood Cells gfp pos. sorted cells from 3 disected e14.5 cortecies Treatment, type=wait Source GEO sample is GSM135767 Last updated (according to GEO): Sep 12 2006 of the brain 1345 1356 10 7 Left HCC (HBV+, HK51) Cerebral cortex 861 control lean rat A8 HC102 CB A Muscle Fibers 1000 Background: Recently a 76-gene prognostic signature able to predict distant metastases in lymph node-negative (N-) breast cancer patients was reported. The aims of this study conducted by TRANSBIG were to independently validate these results and to compare the outcome with clinical risk assessment. Materials and Methods: Gene expression profiling of frozen samples from 198 N- systemically untreated patients was performed at the Bordet Institute, blinded to clinical data and independent of Veridex. Genomic risk was defined by Veridex, blinded to clinical data. Survival analyses, done by an independent statistician, were performed with the genomic risk and adjusted for the clinical risk, defined by Adjuvant!Online. Results: The actual 5- and 10-year time to distant metastasis (TDM) were 98% (88%-100%) and 94% (83%-98%) respectively for the good profile group and 76% (68%- 82%) and 73% (65%-79%) for the poor profile group. The actual 5- and 10-year overall survival (OS) were 98% (88%-100%) and 87% (73%-94%) respectively for the good profile group and 84% (77%-89%) and 72% (63%-78%) for the poor profile group. We observed a strong time-dependency of this signature, leading to an adjusted HR of 13.58 (1.85-99.63) and 8.20 (1.10-60.90) at 5 years, and 5.11 (1.57-16.67) and 2.55 (1.07-6.10) at 10 years for TDM and OS respectively. Conclusion: This independent validation confirmed the performance of the 76-gene signature and adds to the growing evidence that gene expression signatures are of clinical relevance, especially for identifying patients at high risk of early distant metastases. Last Updated (by provider): Jun 11 2007 Contributers: John A Foekens Christos Sotiriou Yhi Zhang Rosette Lidereau Mahasti Saghatchian Sherene Loi Jan G Klijn Christine Desmedt Fanny Piette Paul Ellis Martine J Piccart Benjamin Haibe-Kains Francoise Lallemand Fatima Cardoso Mauro Delorenzi Marc Buyse Adrian Harris Jonas Bergh Yixin Wang Giuseppe Viale Transitional epithelium 1000 Cells were either prestimulated (1_X) or not (0_X) for 18h with 100 ng/ml LPS. Media was exchanged and after 2h rest, cells either restimulated (X_1) or not (X_0) with again 100 ng/ml LPS. This resulted in 4 experimental conditions: 0_0, 0_1, 1_0 and 1_1. There were 3 biological replicates done, resulting in 12 arrays altogether. Source GEO sample is GSM213701 Last updated (according to GEO): Aug 01 2007 Communicable Diseases 901 Lymphoblastoid Cell Line for Individual 8076.3 log phase VDXIGRU_307327 gene expression from allergen stimulated mouse lung Source GEO sample is GSM158142 Last updated (according to GEO): Jan 25 2007 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141285 Last updated (according to GEO): Oct 26 2006 Richard Almon-51-1138200270961 Gene expression data from DAOY cells stably expressing Bmi1 and Mel18 shRNA Source GEO sample is GSM182013 Last updated (according to GEO): Apr 23 2007 861 Heart failure Adenocarcinoma 8 tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44885 Last updated (according to GEO): May 27 2005 Lymphoblastic Leukemia 901 FVB/NJ Cerebellum A brain, cerebral cortex: Rat_03-15_NroLep_Lipska_e1_le1 HC66 CN B ovarian tumor: serous Source GEO sample is GSM139469 Last updated (according to GEO): Apr 09 2007 14 7 amygdala Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184797 Last updated (according to GEO): Apr 26 2007 5 0 brain Normal Source GEO sample is GSM176178 Last updated (according to GEO): Apr 09 2007 Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles. PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity. Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence. To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips. Source GEO sample is GSM136512 Last updated (according to GEO): Jun 05 2007 15 0 human cerebellum 1000 Left 1000 Muscle of orbit R6/1 transgenic, brain hemisphere Source GEO sample is GSM83864 Last updated (according to GEO): Apr 20 2007 861 Malignant Neoplasms 901 Bone Marrow Activation of human CD8+ T cells in renal cell carcinoma Anterior nares 1000 Resting murine bulk splenocytes were lysed in Trizol and assessed for gene expression on Affy MOE430_2 microarray Source GEO sample is GSM188181 Last updated (according to GEO): May 09 2007 SCG explant cultured for 5 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246053 Last updated (according to GEO): Dec 03 2007 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132545 Last updated (according to GEO): Feb 26 2007 contralateral Cortex 7 27 660 mesenchymal stem cell 639 Gene expression data from brain of adult rats Source GEO sample is GSM101048 Last updated (according to GEO): Feb 20 2007 861 Blood 1000 Retina Osteoblasts 1000 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15481.gif Source GEO sample is GSM84128 Last updated (according to GEO): Sep 22 2006 hip_1010_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A cirrhotic liver tissue Source GEO sample is GSM155965 Last updated (according to GEO): Jun 21 2007 PC-3 hgu95d Normal Source GEO sample is GSM176343 Last updated (according to GEO): Apr 09 2007 brain, Right Anterior Temporal: Extract52_le2 Replicate2_Voxel F9 Identification of genes periodically expressed in the human cell cycle and their expression in tumors. 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201304 Last updated (according to GEO): Jun 14 2007 ALS model Source GEO sample is GSM75467 Last updated (according to GEO): Mar 06 2006 1000 Hypertrophic Cardiomyopathy 1 of 3 replicates in treatment group Source GEO sample is GSM206050 Last updated (according to GEO): Jun 29 2007 1000 Structure of superior frontal gyrus of brain neurospheres 39 59 19 0 human frontal cortex Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. 4h after sham surgery, a 7 mm disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44511 Last updated (according to GEO): May 27 2005 Adenocarcinoma 861 Brn3a Heterozygote TG e13.5 U74Bv2 2 Muscle 861 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181191 Last updated (according to GEO): Jul 12 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114200 Last updated (according to GEO): Jun 16 2006 GSE9751 Oj11: Hippocampus_5T-AI_rep6 AD-382t1-A117-3 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Left skin 80 83 Prostate 861 5 0 brain H120 FC BA4 B DBA/2J hippocampus rep1 1000 Nervous system structure 1000 frontal lobe NA18608 1000 Endometriosis, site unspecified Prosencephalon 1000 leukemia, chronic Myelogenous K-562 Source GEO sample is GSM18897 Last updated (according to GEO): Sep 25 2006 of the postmortem brains 673 697 Parkinson Disease 1000 Myocardium 861 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19227 Last updated (according to GEO): May 27 2005 healthy control sample x112 1933 tumor cells 1943 PBMCs-Type 1 Diabetes-IDDM45_T1D_1MO Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68202 Last updated (according to GEO): Jul 07 2006 861 Prostate carcinoma in blood 16 23 G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Source GEO sample is GSM9649 Last updated (according to GEO): May 28 2005 1000 Cerebral cortex total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with BLC for 240min Source GEO sample is GSM5473 Last updated (according to GEO): May 27 2005 28 24 Heart Oocytes 861 Male Sprague-Dawley albino rats (Charles River) initially weighting approximately 200 grams were randomly assigned to one of the following: 1) olanzapine (2 mg/kg/day, I.P.) (N=20) or 2) Saline (N=20) and administered olanzapine or saline for 21 days. Frontal cortex (N=4/group) was dissected and homogenized for microarray, QPCR and western blotting following previous methods (Fatemi et al. 2003; Brooks et al. 2003). RNA isolation, cDNA preparation, microarray hybridization and QPCR followed previous methods (Brooks et al. 2003). Keywords = olanzapine Keywords = frontal cortex Source GEO sample is GSM48578 Last updated (according to GEO): Apr 10 2006 Isolated adipocytes 0 18 Mice were swum for 4 weeks and then allowed 1 week of rest before they were sacrificed. Keywords = exercise induced hypertrophy Source GEO sample is GSM2366 Last updated (according to GEO): May 27 2005 Genome-Wide Expression Analysis of Placental Malaria Reveals Features of Lymphoid Neogenesis during Chronic Infection. ADH193 on harvard-12k Ovarian_Tumor_ClearCell_KU-OC-006 456_2 IL-10 regulates anti-inflammatory signaling via the activation of STAT3, which in turn controls the induction of a gene expression program whose products execute inhibitory effects on pro-inflammatory mediator production. Here we show that IL-10 induces the expression of an ETS family transcriptional repressor, ETV3 and a helicase family co-repressor, SBNO2 (Strawberry notch homolog 2) in mouse and human macrophages. IL-10-mediated induction of ETV3 and SBNO2 expression was dependent upon both STAT3, and co-stimulus through the TLR pathway. We also observed that ETV3 expression was strongly induced by the STAT3 pathway induced by IL-10 but not STAT3 signaling activated by IL-6, which cannot activate the anti-inflammatory signaling pathway. ETV3 and SBNO2 specifically repressed NF-kB-mediated transcription and can physically interact. Collectively our data suggest that ETV3 and SBNO2 are components of the pathways that contribute to the downstream anti-inflammatory effects of IL-10. We compared expression profiles of macrophages isolated from IL-10 -/- mice. Macrophages were treated with either LPS or LPS plus IL-10. Treatment times were 10, 20 and 30 minutes. Last Updated (by provider): Nov 02 2007 Contributers: Peter J Murray Tumor__Prostate_Adeno_P_0033 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Fibroblasts 1000 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18378.gif Source GEO sample is GSM91566 Last updated (according to GEO): Sep 22 2006 Cerebellum 1000 Spleen vs IL10 Treated B cell 120min (set3) 901 Caudate nucleus structure 334 320 Keywords = HIV 1000 Communicable Diseases Skeletal bone 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145622 Last updated (according to GEO): Nov 20 2006 Melanoma xenograft, SM_Lung_C (LeiFidler) Skeletal bone 861 brain, cerebellum: RNA#39*_le1 LDMTX_MP-DX-14 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Sphingosine-1-phosphate for 60min Source GEO sample is GSM5747 Last updated (according to GEO): May 27 2005 To identify genes dysregulated in bipolar disorder (BD1) we carried out global gene expression profiling using whole-genome microarrays. To minimize genetic variation in gene expression levels between cases and controls we compared expression profiles in lymphoblastoid cell lines from monozygotic twin pairs discordant for the disease. We identified 82 genes that were differentially expressed by ? 1.3-fold in 3 BD1 cases compared to their co-twins, and which were statistically (p ? 0.05) differentially expressed between the groups of BD1 cases and controls. Using qRT-PCR we confirmed the differential expression of some of these genes, including: KCNK1, MAL, PFN2, TCF7, PGK1, and PI4KCB, in at least 2 of the twin pairs. In contrast to the findings of a previous study by Kakiuchi and colleagues with similar discordant BD1 twin design1 our data do not support the dysregulation of XBP1 and HSPA5. From pathway and gene ontology analysis we identified up-regulation of the WNT signalling pathway and the biological process of apoptosis. The differentially regulated genes and pathways identified in this study may provide insights into the biology of BD1. Last Updated (by provider): Jun 20 2007 Contributers: Louisa Windus Nicholas Matigian Bryan Mowry Cheryl Filippich John McGrath Heather Smith Nicholas Hayward Christos Pantelis 968 956 neuropathies 10 Bone marrow 0 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198633 Last updated (according to GEO): Jun 06 2007 plasma cells 332 344 Tissue Source GEO sample is GSM67262 Last updated (according to GEO): Jan 19 2006 Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Meningioma Primary Grade 2. Source GEO sample is GSM108033 Last updated (according to GEO): Jun 06 2006 861 Heart 1000 Spleen Day 7 Mouse #52 - 1st replicate ci_NY30 Ganglia, Spinal 923 Epithelium 861 Wild type 8 wk old male DBA/2J mouse hypothalamus Source GEO sample is GSM107026 Last updated (according to GEO): Mar 05 2007 Primary Neoplasm 1000 Epithelium of bronchus 983 Tumor__Leukemia_ALL-B_ALL_(21302)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Infection 1000 NoCAD_replicate35 Bipolar Disorder 861 Disease Source GEO sample is GSM176396 Last updated (according to GEO): Apr 09 2007 Brain of P10 Gja9 (-/-) C57Bl/6j mouse, replica K2 Gene expression data from postmorten brain regions Source GEO sample is GSM145157 Last updated (according to GEO): Nov 20 2006 I_U133A_22_CB Tumor__CNS_Glioblastoma_GlioB_6 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Standard Affymetrix Protocol Source GEO sample is GSM15854 Last updated (according to GEO): May 28 2005 Nose 1000 plasma cells 50 61 Pulmonary hypertension (PH) and cancer pathophysiology share common signal transduction pathways leading to abnormal endothelial and smooth muscle cell interactions and angioproliferative vasculopathy. Sorafenib (Sor) a drug in clinical trials for cancer treatment, is an inhibitor of multiple kinases important in angiogenesis (Raf-1 kinase, VEGFR-2, VEGFR-3, PDGFR-?)?. In this study, we assessed the efficacy of Sor as a potential therapy for PH, and hypothesized that Sor prevents the development of both a conventional and an augmented rodent model of PH. We performed studies in Dahl Salt-Sensitive rats (SS) exposed to hypoxia alone and in combination with the VEGFR-2 inhibitor, SU5416, known to induce a well-characterized augmented PH phenotype. Rats were, thus, divided into 5 groups: normoxia/vehicle (Norm), hypoxia/vehicle (H), hypoxia/ SU5416 (H-SU), hypoxia/Sorafenib (H-Sor) and hypoxia/ SU5416/ Sorafenib (H-SU-Sor). Except for the Norm group, all rats were maintained in a hypoxia chamber with a FiO2 of 10%. Rats received a single injection of SU5416 on Day 1 (20 mg/kg) and Sor solution was administered daily by gavage (2.5mg/kg). After 3.5 weeks, all rats were assessed by open chest catheterizations for pulmonary vascular and right ventricular pressures. Lung and heart tissue were harvested for histological and microarray analyses. Our results showed H-SU rats developed severe PH with changes in hemodynamic and histologic parameters when compared to Norm controls while rats exposed to H alone only displayed mildly elevated pressures compared with Norm. There was no significant change in pressures in the H-Sor or H-SU-Sor compared to Norm. Histopathology demonstrated a dramatic prevention of the PH phenotype in the H-SU-Sor rats with no significant remodeling compared with H-SU rats. Expression profiling data from H (n=4) and H-SU (n=3) rat lungs were compared to Norm (n=4) using normalization in R and SAM (?>.639,) (minimum fold change >1.4). With false discovery rates (FDR) of 6.5% in hypoxia and 1.6% in H-SU, 1019 and 465 genes, respectively, were differentially-regulated compared to Norm. In addition, 38 genes were differentially expressed between H-SU and H-SU-Sor (n=4, FDR 6.7%) revealing a molecular signature with potentially novel target genes of Sor. Five differentially expressed genes (Tgf?3, C1qg, Nexn, Frzb, and Plaur) were examined by real-time RT-PCR and three were further validated by immunohistochemistry confirming the regulation on protein level. Based on the known pathways of hypoxic-induced PH and Sor, we further utilized immunohistochemistry to show the up-regulation of mediators of the MAPK cascade in the H and H-SU models of PH with subsequent, down-regulation by Sor. We therefore present Sor as a novel treatment for the development of severe PH and theorize that the MAPK cascade is a canonical pathway involved both in the development of PH and in the attenuation by Sor. This SuperSeries is composed of the following subset Series: GSE8078: A Multi- Kinase Inhibitor Modulates Pulmonary Hypertension in a Rodent Model 1 GSE8132: A Multi- Kinase Inhibitor Modulates Pulmonary Hypertension in a Rodent Model 2 Last Updated (by provider): Jun 14 2007 1000 Hippocampus Exp 3 Time point 4 Gene expression data from postmorten brain regions Source GEO sample is GSM145143 Last updated (according to GEO): Nov 20 2006 Primary tumor 19 32 Suprachiasmatic Nucleus after 30-min dark pulse rep1 Large-scale analysis of the mouse transcriptome. Gall bladder C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 403.13 Stdv: 17.80 Min: 379.85 Max: 443.91 Source GEO sample is GSM2984 Last updated (according to GEO): Mar 20 2006 DR12h(5) This is 8-week-old mouse untreated gastrocnemius muscle Source GEO sample is GSM4247 Last updated (according to GEO): May 27 2005 Epithelium 861 Spleen 0 5 Kidney 861 Fibroblasts 38 48 GSE1025 Brain 861 Pituitary Gland 861 20 12 Cartilage Cultured Dendritic Cells, CD4- CD8- subset - Expt #2 550 537 in the kidney 9 0 Blood Test Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151983 Last updated (according to GEO): Feb 06 2007 WGACON-117 12 frontal Lobe 23 M7TW00121819 Spleen 0 5 human_hepatocytes_control_pooled 6hr Hela Double Thymidine Medulla Oblongata 861 Total RNA from cultured modiolus, pool from 12 cochleas. Source GEO sample is GSM124846 Last updated (according to GEO): Aug 04 2006 901 Coronary artery 125 103 of early osteoarthritis Replicate2_Voxel B11 861 Posterior root of spinal nerve Biopsy of a colorectal adenoma from patient #17 Plasma 861 Brain 1000 Ptdsr-/- fibroblast_rep13 964 Body of uterus D11 24h TLR2/1L brain, cerebral cortex: PC13_e1_le1 Myocardium 861 Stria 861 Mesenchymal Stem Cells 1000 901 Coronary artery f2#202 versus pool Mouse Brain tissue Brain 861 Brain 861 striatum 32 40 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD27 for 120min Source GEO sample is GSM5498 Last updated (according to GEO): May 27 2005 913 Coronary heart disease Expression profiling of spinal cord section (T9) extracted from rats 7d following moderate injury Source GEO sample is GSM31592 Last updated (according to GEO): May 27 2005 Expression data after reversal of DNA methylation Source GEO sample is GSM230910 Last updated (according to GEO): Sep 20 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11440 Last updated (according to GEO): May 28 2005 AEOL 10150 control #2 663 mesenchymal stem cell 642 Ng12: Hippocampus_NT-Y_rep7 468 459 the rectum StomMucos_0225AF6W_064.txt Examining the effects of tTA expression in mouse hearts Source GEO sample is GSM15073 Last updated (according to GEO): May 28 2005 Cerebral cortex 861 26 15 endometrioid MuscleRegen-ctx10d-9RLA-s2 like tumor 309 318 no additional Source GEO sample is GSM199305 Last updated (according to GEO): Jun 08 2007 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225657 Last updated (according to GEO): Aug 31 2007 Cy5-labeled cDNA was obtained from RNA sample reference, prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice. Keywords = wildtype mouse brain Source GEO sample is GSM34859 Last updated (according to GEO): Jun 19 2007 9 0 Blood Test Tumor__Uterus_Adeno_3226 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A f2#278 versus pool Mouse Brain tissue Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P10, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3228 Last updated (according to GEO): May 28 2005 cerebral cortex 7 21 Category: Lymphoma Classification Subcategory: Hematopoetic cell lines Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc5b007 Source GEO sample is GSM1955 Last updated (according to GEO): Nov 21 2005 MLL-C4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Parkinson Disease 861 Heart Atrium 1000 M_U133A_101_DLPFC Malignant Neoplasms 1000 NCI60.22_LABEL26EXTRACT25SUB3 Source GEO sample is GSM134102 Last updated (according to GEO): Aug 06 2007 Whole blood 0 10 skeletal_muscle_2 the blood 393 402 none Source GEO sample is GSM239955 Last updated (according to GEO): Dec 07 2007 Hep2_41_rep3 Macrophage smi100 1BJZ02081478a_Superior_Cervical_Ganglion Lymphoblastoid Cell Line for Individual 8156.5 log phase GBM: 64A34 #5 Muscle 861 1000 Retina 261 255 asthma Femur 1000 Saccule structure 1000 Pre-BI cells 9b V5-P354 Bone Marrow_6wk_FVB_Female Brain 1000 BAL_15b_A0B0 AT3-hTERT_1.5Gy_6h_C3_27046 N/A Source GEO sample is GSM96290 Last updated (according to GEO): Feb 13 2006 Fibroblasts 861 with some respiratory epithelium. 1039 1072 7 cerebral cortex 21 Gene expression data from mouse primary visual cortex Source GEO sample is GSM101691 Last updated (according to GEO): Mar 27 2006 Expression of VP16-CREB, a constitutively active form of CREB, in hippocampal neurons of the CA1 region lowers the threshold for eliciting the late, persistent phase of long-term potentiation (L-LTP) in the Schaffer collateral pathway. This VP16-CREB-mediated L-LTP differs from the conventional late phase of LTP in not being dependent on new transcription. This finding suggests that in the transgenic mice the mRNA transcript(s) encoding the protein(s) necessary for this form of L-LTP might already be present in CA1 neurons in the basal condition. We used high-density oligonucleotide arrays to identify the mRNAs differentially expressed in the hippocampus of transgenic and wild-type mice. Last Updated (by provider): Jan 04 2006 Contributers: Susan Patterson Eric R Kandel Alexei Morozov Angel Barco Manuel Mata-Roig Petra Gromova Juan M Alarcon Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Enghigh 1 BladdD1_022YAC3A_043.txt brain_DLPFC_bipolar C_mr700 10 on NHGRI-13.8k in blood 16 23 brain, frontal cortex: Sham PM FC_e1_le1 human cerebellum Source GEO sample is GSM87129 Last updated (according to GEO): Feb 08 2006 120 93 of gingival epithelial cells 1000 Brain B220+c-kit+ Pre BI cells sorted out of mouse bone marrow, sort no. 8 Source GEO sample is GSM657 Last updated (according to GEO): Mar 17 2006 352 347 brain Retina 1000 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181217 Last updated (according to GEO): Jul 12 2007 10 0 hippocampus 1545 to neurodegenerative diseases 1573 1000 Basal Ganglia Spinal Cord 1000 Category: Cell-line Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.31 Lot batch = svcc67 Source GEO sample is GSM1925 Last updated (according to GEO): Nov 21 2005 1000 Prostate 479 452 from the embryonic forebrain striatum 35 43 Myocardium 861 MuscleRegen-ctx4.5d-2LLAv2-s2 9 0 Blood Test ACHN_CL9023_Renal on Affymetrix GeneChip Human Full Length Array HuGeneFL GM11829 Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. P1_KIDNEY_8 doxycycline, mutant Source GEO sample is GSM213364 Last updated (according to GEO): Jul 26 2007 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188807 Last updated (according to GEO): Jun 06 2007 Multiplex three dimensional brain gene expression mapping in a mouse model of Parkinson's disease NoCAD_replicate17 Bone Marrow 1000 861 Brain 901 frontal lobe 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113972 Last updated (according to GEO): Jun 16 2006 Amygdaloid structure 1000 Adipocytes 1000 Lymphoblastic Leukemia 901 861 Hippocampus 568 559 to seizure Macrophage smi62 17 7 hippocampus 17 7 hippocampus in bronchial epithelia 311 332 Spleen 0 5 Communicable Diseases 861 cocaine naive, amygdala, 0 hrs/day access to cocaine Source GEO sample is GSM93827 Last updated (according to GEO): Jan 26 2006 Mammary Gland @ Preg3, biological rep4 Deltoid Muscle 4 Normal to the nose 599 609 endothelial cells sprague2 whole tissue, individual animal, 10 weeks old, male Sprague Dawley endothelial cells file:R3JW02103022 Source GEO sample is GSM15218 Last updated (according to GEO): May 28 2005 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16948.gif Source GEO sample is GSM91538 Last updated (according to GEO): Sep 22 2006 861 Heart Diseases FSCC19 on Affymetrix GeneChip Human Full Length Array HuGeneFL 889 884 muscle human caudate nucleus Source GEO sample is GSM86858 Last updated (according to GEO): Feb 08 2006 Compare the brain transcriptomes of Gja9 (-/-) and Gja9 (+/-) mice with that of wildtype mice to detect transcriptomic alterationss induced by total or partial ablation of Gja9 Source GEO sample is GSM146904 Last updated (according to GEO): Nov 29 2006 M7TW00122037 embryonic hearts 1064 1079 mouse brain 478 489 saphenous_vein_3 Source GEO sample is GSM80789 Last updated (according to GEO): Mar 31 2006 861 Intestines Large-scale analysis of the mouse transcriptome. Tongue epidermis, dorsal tongue surface C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 427.46 Stdv: 23.58 Min: 375.50 Max: 469.31 Source GEO sample is GSM2959 Last updated (according to GEO): Mar 20 2006 1000 jejunum Expression profiling of spinal cord section (T9) extracted from rats 28d following severe injury Source GEO sample is GSM31608 Last updated (according to GEO): May 27 2005 Large-scale analysis of the mouse transcriptome. Lung C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 250.14 Stdv: 11.39 Min: 234.07 Max: 267.68 Source GEO sample is GSM2935 Last updated (according to GEO): Mar 20 2006 Job's patient Source GEO sample is GSM211150 Last updated (according to GEO): Sep 10 2007 Leukemia, Lymphocytic, Chronic 1000 V5-P487 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15529.gif Source GEO sample is GSM84149 Last updated (according to GEO): Sep 22 2006 D_U133A_17_DLPFC rad001 15d, biological rep2 Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203894 Last updated (according to GEO): Aug 02 2007 MDA Mb231 6h + 10 nM Cxcl12 2 Treated Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 5027 blood Gene expression profile of the cell line UB/OC-1 grown for 11 days under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1543 Last updated (according to GEO): May 27 2005 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n123 Source GEO sample is GSM2062 Last updated (according to GEO): Nov 21 2005 861 Cerebral cortex D_U133Plus_107_Amy Brain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145158 Last updated (according to GEO): Nov 20 2006 L_AK_SleepDep_ZT 6_3 Hippocampus 1000 mouse brains 161 172 Brain of P10 wildtype C57Bl/6j mouse, replica W2 Abdominal Aortic Aneurysm2-F no additional Source GEO sample is GSM199199 Last updated (according to GEO): Jun 08 2007 437 417 Keywords = Alzheimer? 5 0 blood This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12369 Last updated (according to GEO): May 28 2005 CNS-SpinalCsev-Adult-4h-4A-s2 Small cell carcinoma of lung 888 Liver 1000 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169486 Last updated (according to GEO): Feb 21 2007 D_U133A_54_CB CNS-SCsev_InjA28d-4B-s2 Cerebral cortex 1000 984 952 in more posterior sensory ganglia 215 199 of neural retinas Pooled TA RNA samples from five 8 wk old male mdx mice Source GEO sample is GSM13747 Last updated (according to GEO): May 28 2005 no additional Source GEO sample is GSM199274 Last updated (according to GEO): Jun 08 2007 Expression profiling of spinal cord section (T8) extracted from rats 28d following severe injury Source GEO sample is GSM31476 Last updated (according to GEO): May 27 2005 9 0 Blood Test between the LAD artery 266 287 A Survey of Genetic Human Cortical Gene Expression no additional Source GEO sample is GSM199102 Last updated (according to GEO): Jun 08 2007 Cerebral cortex 861 osteoblast 627 637 875 Blood Cells Prosencephalon 861 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211335 Last updated (according to GEO): Jul 18 2007 stria terminalis 901 1000 Hippocampus BRCA1_s1714 on NHGRI-6.5k 1000 Brain Replicate3_Voxel E8 Parkinson's model voxel F2 prostate Source GEO sample is GSM203369 Last updated (according to GEO): Jun 21 2007 outer medulla 31 43 32 10 from cultured modiolus VDXOXFU_360 Nasal Epithelium 865 NH 66h Bone Marrow 1000 120T total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withSLC (Secondary lymphoid-organ chemokine) for 60min Source GEO sample is GSM5770 Last updated (according to GEO): May 27 2005 I_U133A_41_Amy Brain 1000 425_2 CNS-SMTC_Mod4h-4A-s2 Tumor__Leukemia_ALL-T_ALL_(9186)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Plasma 861 n/a Source GEO sample is GSM177965 Last updated (according to GEO): Jun 11 2007 Subcutaneous stromo vascular fraction, rep3 Breast 861 HUVEC isolate Z low serum media control for #26 Source GEO sample is GSM12918 Last updated (according to GEO): May 28 2005 1000 Prostate Posterior root of spinal nerve 861 861 Cerebral cortex Bone Marrow 1000 Blood 861 8 hr Hela Double Thymidine, exp2 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159981 Last updated (according to GEO): Feb 01 2007 GSE8607 5 0 Spleen C3H/HeJ periaqueductal gray rep1 Plasma 861 M14 hgu95d 5 0 brain 191 181 of ischemia Anterior interpositus nucleus-centered deep cerebellar nuclei were sampled using syringe needles Source GEO sample is GSM84987 Last updated (according to GEO): Mar 29 2006 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD21 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD21 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36696 Last updated (according to GEO): May 27 2005 861 HIV Infections 884 Leukemia, Myelocytic, Acute Blood 1000 skin 80 83 Primary Neoplasm 1000 none Source GEO sample is GSM244592 Last updated (according to GEO): Nov 23 2007 BT-549_CL5013_Breast on Affymetrix GeneChip Human Full Length Array HuGeneFL Cerebral cortex 861 post HCMV infection 17 35 plasma cells 332 344 "Sample 79, <5 yr survival(28 months) age 53 erp no" on vantveer-oligo P21CN1 FSCC14 on Affymetrix GeneChip Human Full Length Array HuGeneFL (cortex 19 25 25 7 Right Parietal Lobe bronchial epithelia 224 243 CurrentSmoker 36 966 Hippocampus 1000 Spinal Cord 861 Brain 1000 Retina AML cDNA hybridization-ID71-L p53 +/-, 12 hour, replicate a Source GEO sample is GSM2552 Last updated (according to GEO): May 27 2005 Starvation 916 liver_1 Source GEO sample is GSM80728 Last updated (according to GEO): Mar 31 2006 66 50 Hippocampus C57BL CNS-SpinalC-conAdult-72h-1A-s2 861 Brain Myocardial Infarction 1000 human frontal cortex Source GEO sample is GSM87033 Last updated (according to GEO): Feb 08 2006 MSM/Ms_male_hypothalamus Source GEO sample is GSM184209 Last updated (according to GEO): Apr 26 2007 GSE1555 1207 1189 in the hippocampus Expression profiling of spinal cord section (T9) extracted from rats 0 following laminectomy (naïve) Lot batch = Source GEO sample is GSM4486 Last updated (according to GEO): Oct 28 2005 1000 Lung Bone Marrow 1000 GM12144 RNA isolated from post-mortem tissues Source GEO sample is GSM6831 Last updated (according to GEO): May 28 2005 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12676.gif Source GEO sample is GSM79965 Last updated (according to GEO): Sep 22 2006 in bronchial epithelia 311 332 with myocardial infarction 313 339 901 Muscular Dystrophies Gene expression data from human colon tumor tissue Source GEO sample is GSM173372 Last updated (according to GEO): Apr 20 2007 962 939 medulloblastomas arising Congenital Abnormality 853 330 324 uterus 658 651 adipose Low-density CCg progenitors treated with FBS to derive Astrocytes Source GEO sample is GSM47553 Last updated (according to GEO): Jun 10 2005 Systematic variation in gene expression patterns in human cancer cell lines. Primary tumor 19 32 Balb/c day 6, biological rep 4, tech rep 1 Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell 240min (set1) Brain 861 Macrophage 14smi084 901 Caudate nucleus structure The frontal cortex 572 589 861 Myocardium Cardiac tTA expression JMR-RatInj8h-2aA-s2 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195325 Last updated (according to GEO): Jun 04 2007 R668P01211 Plasma 861 Cerebral cortex 861 30 0 Adrenal medulla [JunctionChip 5 plasma cells 50 61 1000 frontal lobe MO_DH3c_SON_NCBI cerebral cortex 7 21 frontal lobe 1000 "6 hr Hela Double Thymidine, exp3" 1000 prostatitis brain, amygdala: Control-Hippocampus_e1_le3 Female 26.5 yr after antibody enrichment scan 2 (U133B) V5-P568 C57L/J Frontal Cortex B Parkinson Disease 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145623 Last updated (according to GEO): Nov 20 2006 Low Freezing Source GEO sample is GSM92425 Last updated (according to GEO): Jan 13 2006 Myocardial Infarction 1000 G42-CingulateCortex replicate3 Ovary 1000 Spinal Cord 1000 861 Dislocations /2J cingulate cortex rep1 3 27 Nasal Epithelium Inhalation Formaldehyde 6ppm 24h ID288 Heart 861 42 15 dedifferentiated chondrocyte Structure of entorhinal cortex 1000 Bladder sample 1146-1 Communicable Diseases 1000 Addictive Behavior 861 Expression profiling of somatomotor cortex extracted from rats at T0 naive Source GEO sample is GSM41674 Last updated (according to GEO): May 27 2005 901 frontal lobe from whole tumor 21 36 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68164 Last updated (according to GEO): Jul 07 2006 none Source GEO sample is GSM244626 Last updated (according to GEO): Nov 23 2007 brain 0 5 Job's patient Source GEO sample is GSM211017 Last updated (according to GEO): Sep 10 2007 SJL/J_male_hypothalamus 7 cerebral cortex 21 D_U133A_26_HC Epithelial Cells 1000 Intestines 861 Spleen 1000 Cardiomyopathies 1000 HapMap CEU_parent Male Source GEO sample is GSM159572 Last updated (according to GEO): Feb 01 2007 5 0 brain Brain (amygdala) [JunctionChip 1 of 5] Brain 861 1000 Heart failure FormerSmoker 41 861 Cerebellum Brain 1000 159 150 carcinomas Coronary artery 901 1000 Liver 861 Malaria 3AMH02030702_Heart 91 from the bone marrow 72 Standard Affymetrix Protocol Source GEO sample is GSM16460 Last updated (according to GEO): May 28 2005 HC65 CN A Occipital lobe 861 Liver 1000 Brain 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM146013 Last updated (according to GEO): Nov 20 2006 Expression profiling of somatomotor cortex extracted from rats at 7d following moderate injury Source GEO sample is GSM48634 Last updated (according to GEO): May 29 2005 1329 1317 in cirrhosis NA Source GEO sample is GSM84335 Last updated (according to GEO): Dec 01 2005 5 0 Spleen 5 0 Spleen human frontal cortex Source GEO sample is GSM87034 Last updated (according to GEO): Feb 08 2006 10 7 Left Tissue Culture Polystyrene 32 hours Parkinson Disease 1000 none Source GEO sample is GSM241963 Last updated (according to GEO): Nov 29 2007 Zeitgeber Time Treatment, type=time_course, measurement=12.0 h Source GEO sample is GSM53334 Last updated (according to GEO): Jul 06 2005 EKVX hgu95c Wild-type control striatal Source GEO sample is GSM82445 Last updated (according to GEO): Jun 26 2007 928 Endometrium Patient3E Cerebral cortex 861 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Lysophosphatidic Acid labeled with Cy5- time course with repeats. Date GSE388 Last Updated: May 29 2005 Contributers: Yun Anna Cao Zhen Yan Rebecca Hart Robert Hsueh Sun Young Lee Mi Sook Chang Joella Grossoehme Sangdun Choi Jong-Woo Kim Angela Alexander Includes GDS309. Update date: Nov 18 2003. Dataset description GDS309: Temporal analysis of effects induced by 1 uM lysophosphatidic acid in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. P21_cy5_2 Nasal Epithelium 901 Communicable Diseases 1000 1000 Brain 39 21 of substantia nigra AA Treatment, type=remove Source GEO sample is GSM99501 Last updated (according to GEO): Apr 21 2006 V5-P511 868 850 of medulloblastoma Brain 1000 1000 Amygdaloid structure Mesenchymal Stem Cells 1000 Gene expression of organ of Corti (OC), modiolus (MOD) and stria vascularis (SV) of newborn rats ileum (pool of 4 animals)_72h monoassociation with L.innocua(inlA)_A_5557 Source GEO sample is GSM161586 Last updated (according to GEO): Apr 23 2007 Spleen 0 5 861 Cancer of Neck AT3-hTERT_sham_6h_C3_27042 Gene expression data from postmorten brain regions Source GEO sample is GSM145462 Last updated (according to GEO): Nov 20 2006 MO_LB_180min_Patient5 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188835 Last updated (according to GEO): Jun 06 2007 1000 frontal lobe I_U133A_2_AnCg 1000 Brain 3AJZ02081483b_Trigeminal_Ganglion Nasal Epithelium Inhalation Formaldehyde 6ppm 24h ID292 NMDA60 (Experiment shortNMDA: Run 19222) Treatment, type=time_course, description=primary cortical neurons were treated with 1 mM NMDA for increasing periods of time (10 to 360 min)., measurement=60.0 m Source GEO sample is GSM96766 Last updated (according to GEO): Feb 14 2006 in the brain 150 162 247 242 Spleen E6, E7, hTERT, endometrial cell EPC100 HNC2719 Blood 1000 660 mesenchymal stem cell 639 10 week mutant OMN rep 3 of early Parkinson's disease 18 45 Simple annotation: Cell-line, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2873.gif Source GEO sample is GSM79877 Last updated (according to GEO): Sep 22 2006 of the most anterior dorsal root ganglia 23 62 heart failure 583 595 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy, pathological hypertrophy, rat, heart failure, cardiomyopathy Source GEO sample is GSM12309 Last updated (according to GEO): May 28 2005 oral_mucosa_4 1BMH02083005_PB_CD8TCells Lung; Day 5 postnatal Keywords = mouse gene expression database Source GEO sample is GSM29385 Last updated (according to GEO): May 27 2005 1000 Spleen 715 702 After the eyes DLCL-0018 39 21 of substantia nigra from the cerebellum 20 38 Primary tumor 19 32 Primary Neoplasm 1000 Gene expression data from dorsal pancreas at e16.5, MG-U74C version2 Source GEO sample is GSM199472 Last updated (according to GEO): Jun 08 2007 hippocampus 7 17 C107 on NCI-7.6k brain 0 5 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114458 Last updated (according to GEO): Jun 16 2006 C57BL/6J pituitary gland rep2 (430 2.0 Array) 91 from the bone marrow 72 Female mice used were SvJ/129, 10-16 weeks of age, with both copies of the Hoxa-10 gene (GenBank # NM_008263) present (wildtype). These mice were littermates of Hoxa-10-/- mice used in parallel experiments. 14 days after ovariectomy, mice were injected subcutaneously with progesterone dissolved in sesame oil (Sigma; 0.2mg/0.1mL/mouse), followed by sacrifice and removal of uterine horns at 6 hours after injection. 8 uterine horns from 4 mice were pooled to form one sample. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix. Source GEO sample is GSM3042 Last updated (according to GEO): May 27 2005 of hormone resistant prostate cancer 81 116 Secondary malignant neoplasm of lymph node 1000 the heart 987 996 Ovary 1000 1000 Spleen CNS-SMTC_Ctr4h-1C-s2 Sample Type: cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde instilation exposure, 400 mM formaldehyde, single exposure, 6 h time point Source GEO sample is GSM159753 Last updated (according to GEO): Apr 23 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145670 Last updated (according to GEO): Nov 20 2006 HOP-92 hgu95d 861 Aortic valve structure Gene expression data from normal adrenal gland Source GEO sample is GSM211447 Last updated (according to GEO): Jul 18 2007 brain, unknown: 03DE_e1_le1 1500mg/kg APAP 6Hr rat 3592 blood vs. PC 6Hr rat 3586 blood 25 7 Right Temporal Lobe PC 13 Treatment, type=incubate, description=Hypoxic preconditioning Source GEO sample is GSM107492 Last updated (according to GEO): May 01 2006 none Source GEO sample is GSM123264 Last updated (according to GEO): Jul 27 2006 1000 Infection 1000 Brain nasal epithelial cells 28 49 Epithelial Cells 1000 Basal- 0 5 Medulla 861 spinal cord, spinal cord: G4C_le1 of mouse brain 9 23 204 194 of retinal bonemarrow Source GEO sample is GSM18910 Last updated (according to GEO): Sep 25 2006 of the small intestine 97 118 Fibroblasts 861 091254 PRSC on Affymetrix GeneChip Human Full Length Array HuGeneFL Spleen vs IL10 Treated B cell 60min (set3) Prefrontal Cortex 0 16 103 85 of a past infection /cByJ Frontal Cortex A 4 25 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113946 Last updated (according to GEO): Jun 16 2006 Spleen vs fMLP Treated B cell 60min (set3) Medulla Oblongata 861 B6 day 1, biological rep 4, tech rep 1 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11259 Last updated (according to GEO): May 28 2005 Spinal Cord 1000 Mesenchymal Stem Cells 1000 osteoblast 627 637 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92335 Last updated (according to GEO): Jan 13 2006 913 Blood Cells B384 on Affymetrix GeneChip Human Full Length Array HuGeneFL Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3886 Last updated (according to GEO): May 27 2005 5 0 brain 861 Liver Brain 1000 Wild type olfactory epithlium 48 hpO replicate3 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 2 - Pair 3 - MMN Source GEO sample is GSM49884 Last updated (according to GEO): Dec 20 2005 Cerebral cortex 1000 Mek exp1 control treatment Donor C, post G-CSF 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201247 Last updated (according to GEO): Jun 14 2007 thymocytes_DN3_3 Abdominal aortic aneurysm 0 24 M7TW00121471 Alzheimer's Disease 1000 WT_PBS_1 Liver (HCV+, SF3) neurotoxicity 108 120 GSE3761 1000 Prostate Prosencephalon 1000 SMCL-SMCL3t1-A290-10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A occipital_lobe_5 1000 Brain /2J Cerebellum A 3 18 from ventral prostate 21 41 forebrain 7 15 To examine irreversible changes in the developing brain following seizures, juvenile inbred mice were intraperitoneally injected with kainate and nicotine. Last Updated (by provider): Jan 03 2007 Contributers: Noriyuki Akahoshi Isao Ishii 1000 Neuraxis 1000 Lipofuscin a Duchenne muscular dystrophy 148 176 Cerebral cortex 1000 Brain 861 ipsi Cortex 7 17 seminoma specimen, pT1, patient age: 43y; W02 003 Gene expression data from colorectal adenoma. Source GEO sample is GSM215097 Last updated (according to GEO): Aug 02 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113897 Last updated (according to GEO): Jun 16 2006 A HID I D047 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108594 Last updated (according to GEO): Aug 22 2006 Olfactory Epithelium 1000 Backskin_WT_P23_rep2 Wild type 8 wk old male C57BL/6J mouse pituitary gland Source GEO sample is GSM107046 Last updated (according to GEO): Mar 05 2007 861 Cancer of Neck CLL-53 gene expression of 3 day LIF differentiated ESCs Source GEO sample is GSM181954 Last updated (according to GEO): Apr 12 2007 KPeterson-NonMet-2box2-2G110-s2 esophagus_4 Mesenchymal Stem Cells 1000 1668 1650 in the bone marrow 1000 medulloblastoma To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18433 Last updated (according to GEO): May 27 2005 Cochlear nuclei pooled from 20 pups to generate one sample for one replicate hybridization out of 5 replicates. In this replicate, dyes were flipped. Cohybridized with P21_cy3. Source GEO sample is GSM44978 Last updated (according to GEO): Jun 08 2005 Study the transcriptomic effects of the shear stress on cultured osteoblast-like MC3T3 cells Source GEO sample is GSM201206 Last updated (according to GEO): Jun 19 2007 of mouse brain 9 23 Colonic mucous membrane 913 896 Ewings sarcoma Nose 1000 861 Muscle Muscle 861 C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 6hr after experimental mice received their last shock treatment. Source GEO sample is GSM4496 Last updated (according to GEO): May 27 2005 CNS-SMTC_Mod14d-1C-s2 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28717 Last updated (according to GEO): May 27 2005 Mesentery 1000 1933 tumor cells 1943 901 frontal lobe Whole Brain 73 83 660 mesenchymal stem cell 639 Liver 0 4 MuscleRegen-ctx10d-1RLAv2-s2 brain, unknown: C1A_e1_le1 Epithelium 865 861 Eminence 1000 Hippocampus Brain 861 schizophrenia 559 572 901 Heart Diseases CLL-39 || lc7b070 of mouse brain 9 23 Primary small cell lung carcinoma 4567 Plasma 861 Standard Affymetrix procedure Source GEO sample is GSM132994 Last updated (according to GEO): Aug 28 2007 Spleen 1000 1000 Coronary Arteriosclerosis Sample Type: cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, air control, 6 h time point Source GEO sample is GSM159786 Last updated (according to GEO): Apr 23 2007 1000 medulloblastoma MDA-MB-231 transfected with EGRE3-VgRXR and pIND-DACH1, selected by Zeocin and G418. Induced DACH1 expression was confirmed by western blot. Source GEO sample is GSM11368 Last updated (according to GEO): May 28 2005 none Source GEO sample is GSM190785 Last updated (according to GEO): Jun 25 2007 1000 Endometriosis, site unspecified 1000 Brain 1494 1471 of learning disabilities Macrophage 14smi060 MO_LB_180min_Patient7 autism 0 5 ISR17 NCI60.39_LABEL43EXTRACT42SUB3 Source GEO sample is GSM134185 Last updated (according to GEO): Aug 06 2007 861 Blood Genomic and Phenotypic Evidence for a Causative Role of Calcineurin in the Astrogliosis of Aging and Alzheimer's Disease Wild type 8 wk old male FVB/NJ mouse hippocampus Source GEO sample is GSM107015 Last updated (according to GEO): Mar 05 2007 Blood 1000 1100 1087 heart failure brain, hippocampus: Aldh5a1-/- #3389 Cort_e1_le1 mES_ESF58/2 striatum_wildtype_4S CNS-SpinalC-30mAdult-4B-s2 5 0 brain gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134634 Last updated (according to GEO): Jul 09 2007 Oat cell carcinoma 867 567 548 the descending colon 19 0 Head and neck cancer Nasal Epithelium 901 Anterior nares 1000 Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242083 Last updated (according to GEO): Dec 04 2007 Brain Injuries 1000 020102_HF_328FL Exp A_4, 1mg/kg CPF 10 Bone marrow 0 Wild type 8 wk old male DBA/2J mouse pituitary gland Source GEO sample is GSM107049 Last updated (according to GEO): Mar 05 2007 Communicable Diseases 1000 Cerebral cortex 861 HeLa CD4+ cells were transfected with an epitope-tagged eTat plasmid and selected with hygromycin. Cells were treated with nocodazole and collected @0 hours. Source GEO sample is GSM8703 Last updated (according to GEO): May 27 2005 HDMTX-DX-4 no additional Source GEO sample is GSM199227 Last updated (according to GEO): Jun 08 2007 Dark rearing, biological rep2 CHB DR-2 861 Decapitation D2_TP-12_I 1000 Neoplasm Gene expression data from postmorten brain regions Source GEO sample is GSM145463 Last updated (according to GEO): Nov 20 2006 Primary large cell neuroendocrine carcinoma 5020 0 47 Rat SCN Sample 2 (Exp 1 - 6 hr) 6 0 Cancers WBM_2Months_A Sample Matching by Inferred Agonal Stress in Gene Expression Analyses of the Brain Ventral Tegmental Area 1000 WGACON-85 1000 Hippocampus 1000 Cerebellum kidney 37 43 STHdhQ7/Q7-A 1000 Neoplasm 1037 of transitional epithelium 1012 Plasma 861 brain, hippocampus: C24-I_e1_le1 12 0 ovarian tumor 901 Heart failure Standard Affymetrix Protocol Keywords = microarray Keywords = muscle Source GEO sample is GSM15848 Last updated (according to GEO): May 28 2005 Cerebral cortex 1000 Autistic Disorder 877 c-Jun (cellular Jun) is a transcription factor activated by phosphorylation by the stress activated protein kinase/c-Jun-N-terminal-kinase pathway in response to extracellular signals and cytokines. We show that adenovirus mediated gene transfer of dn-c-Jun (dominant negative form of c-Jun) in C57BL/6 mice increased greatly apoE (apolipoprotein E) hepatic mRNA and plasma levels, increased plasma cholesterol, triglyceride and VLDL (very low density lipoprotein) levels and resulted in the accumulation of discoidal HDL (high density lipoprotein). A similar but more severe phenotype was generated by overexpression of the mouse apoE in C57BL/6 mice, suggesting that dyslipidemia induced by dn-c-Jun was the result of apoE overexpression. Unexpectedly, infection of apoE-/- mice with adenovirus expressing dn-c-Jun reduced by 70% plasma cholesterol, suggesting that dn-c-Jun affected other genes that control plasma cholesterol levels. To identify these genes we performed whole genome expression analysis (34,000 genes) of isolated livers from two groups of five apoE-/- mice, infected with adenoviruses expressing either the dn-c-Jun or the green fluorescence protein. Bioinformatical analysis and Northern blotting validation revealed that dn-c-Jun increased 40-fold the apoE mRNA and reduced by 70% the Scd-1 (stearoyl-CoA-desaturase 1) mRNA. The involvement of Scd-1 in lowering plasma cholesterol was confirmed by restoration of high cholesterol levels of apoE-/- mice following coinfection with adenoviruses expressing dn-c-Jun and Scd-1. In conclusion, dn-c-Jun appears to trigger two opposing events in mice that affect plasma cholesterol and triglyceride levels: One results in apoE overexpression and triggers dyslipidemia and the other results in inhibition of Scd-1 and offsets dyslipidemia. 32h-Control replication 3 25_70603_SepticShock_Day3_8 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226044 Last updated (according to GEO): Nov 02 2007 Aortic Aneurysm 901 5 0 Spleen Breast 4 Disease 0 15 D2_SleepDep_ZT 6_2 The epithelial cells 962 981 Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2669.gif Source GEO sample is GSM72141 Last updated (according to GEO): Sep 22 2006 U251 hgu95e none Source GEO sample is GSM244582 Last updated (according to GEO): Nov 23 2007 861 Ovary Expression profiling of spinal cord section (T9) extracted from rats 0 following laminectomy (naïve) Lot batch = Source GEO sample is GSM1338 Last updated (according to GEO): Oct 28 2005 1000 Coronary Arteriosclerosis Cerebellum 1000 striatum_Q92_3m_439 Expression profiling of spinal cord section (T8) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM6639 Last updated (according to GEO): May 28 2005 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11370.gif Source GEO sample is GSM76470 Last updated (according to GEO): Sep 22 2006 R624P00744 Lymphoblastoid Cell Line for Individual 8028.4 log phase Pressure-overload induced hypertrophy model. Mouse was sacrificed 1 hour after aortic banding. Keywords = Cardiac Hypertrophy Source GEO sample is GSM2230 Last updated (according to GEO): May 27 2005 brain, ipsi Cortex: Trizol Extraction7_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM145005 Last updated (according to GEO): Nov 20 2006 Stomach Pyloric 3 Normal 24 0 human prostate PC3 tumors Neoplasm 861 Heart 1000 2nd 6hr C-DG Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18172.gif Source GEO sample is GSM91497 Last updated (according to GEO): Sep 22 2006 left 22 25 Cerebral cortex 861 D_U133Plus_97_nAcc Gene expression data from postmorten brain regions Source GEO sample is GSM145867 Last updated (according to GEO): Nov 20 2006 CNS-SpinalCmod-Adult-24h-4A-s2 Cochlear structure 1000 5 0 Spleen left 22 25 091242 OVR233 on Affymetrix GeneChip Human Full Length Array HuGeneFL Neoplasm 861 Small cell carcinoma of lung 901 embryo_at_day2.5_rep2 human caudate nucleus Source GEO sample is GSM86848 Last updated (according to GEO): Feb 08 2006 Normal Source GEO sample is GSM176211 Last updated (according to GEO): Apr 09 2007 D_U133A_42_HC 181-96_Adeno 21 0 acute myeloid leukemia 861 Neoplasm GSE937 Liver 1000 Normal Source GEO sample is GSM176136 Last updated (according to GEO): Apr 09 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11511 Last updated (according to GEO): May 28 2005 Bipolar Disorder 1000 Medulla 861 Cerebral cortex 1000 A/J Frontal Cortex E Carcinoma, Non-Small-Cell Lung 890 nodose_nucleus_2 brain, cortex: norm1_e1_le1 861 Neoplasm HSC_2Months_B Using Affymetrix microarray technology we analyzed the gene expression profiles of the most important pathological categories of bladder cancer in order to detect potential marker genes. Applying an unsupervised cluster algorithm we observed clear differences between tumor and control samples, as well as between superficial and muscle invasive tumors. According to cluster results, the T1 high grade tumor type presented a global genetic profile which could not be distinguished from invasive cases. We described a new measure to classify differentially expressed genes and we compared it against the B-rank statistic as a standard method. According to this new classification method, the biological functions overrepresented in top differentially expressed genes when comparing tumor versus control samples were associated with growth, differentiation, immune system response, communication, cellular matrix and enzyme regulation. Comparing superficial versus invasive samples, the most important overrepresented biological category was growth and, specifically, DNA synthesis and mitotic cytoskeleton. On the other hand, some under expressed genes have been clearly related to muscular tissue contamination in control samples. Finally, we demonstrated that a pool strategy could be a good option to detect the best differentially expressed genes between two compared conditions. Last Updated (by provider): Apr 12 2007 that the oculomotor nuclei actively 1344 1378 501 490 optic nerve frontal lobe 901 Brain 861 COID-COID14t1-A351-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Liver Test (Blinded) Sample Source GEO sample is GSM130087 Last updated (according to GEO): Sep 18 2007 20 0 human caudate nucleus prostate Source GEO sample is GSM203383 Last updated (according to GEO): Jun 21 2007 of the X chromosome 1034 1053 Squamous cell carcinoma 875 4 0 Liver 1000 Soleus muscle structure Wild type P24 mouse visual cortex contralateral to monocular enucleation Source GEO sample is GSM97208 Last updated (according to GEO): Feb 17 2006 Primary Neoplasm 1000 861 Heart frontal cortex sprague 3936 whole tissue, individual animal, 10 weeks old, male Sprague Dawley frontal cortex file:p3936w Source GEO sample is GSM15173 Last updated (according to GEO): Oct 28 2005 Total RNA extracted from the forebrain of a Lh-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144406 Last updated (according to GEO): Nov 14 2006 Probeset expression data from NA12750 growth 2, replicate 4 Source GEO sample is GSM195198 Last updated (according to GEO): Aug 08 2007 Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell 60min (set3) Macrophage smi38 To elucidate the pathways involved in the SCA7 retinal degeneration, we used DNA GeneChips and compared the gene expression profiles of the mutant mice (R7E) and the control ones (R7N). We performed these experiments at the onset stage of the disease (3w) as well as on the moderate one (9w) in order to correlate the transcriptional deregulations with the phenotype progression. We also compared the R6/2 mice vs wild type (wt) ones to identify between the deregulated transcripts the ones that were also differentially expressed in the R7E vs R7N mice. These common changes are likely caused by polyQ expansion independently of the protein context. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Nov 29 2006 Primary Neoplasm 896 1000 Cartilage Neoplasm 861 B2-4 on NCI-7.6k Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28776 Last updated (according to GEO): May 27 2005 101 86 of the amygdalae 24 0 human prostate PC3 tumors CA96-116B Gene expression data from aneurismal tissues obtained from patients with bicuspid valves. Source GEO sample is GSM116780 Last updated (according to GEO): Jun 28 2006 1000 Midbrain structure in seminoma 28 38 S1P2-KO-hippocampus, biological rep10 (female) 18 0 Trisomy 21 sample 3 41 36 spleen 1000 Prostate Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28721 Last updated (according to GEO): May 27 2005 GSE1611 cDNAs were generated from 5ug of total RNA per sample by reverse transcription (RT) for two hours at 42oC using the 3DNA SubmicroTM Oligo Expression Array Detection Kit (Genisphere, Hatfield, PA) and Superscript II (Invitrogen, Carlsbad, CA). For each microarray chip two consecutive hybridizations were performed with cDNAs and the fluorescent probes following the manufacture?s specifications. Briefly, in the first hybridization reaction the solution containing the mixture of cDNAs obtained from control and treated cells was loaded onto the CAG Human 19K array and incubated overnight at 55oC in a hybridization chamber (Genemachines, San Carlos, CA). The human 19K array (www.cag.icph.org/microarray_facility.htm) contains 60-mer oligonucleotides (Compugen, San Jose, CA) representing 18,861 human genes spotted onto poly-l-lysine coated glass microscope slides. In the second hybridization reaction Cy3 (green) and Cy5 (red) fluorescent probes were used to label the cDNAs from control and PGJ2-treated cells, respectively. The second hybridization was carried out for 3 hours at 65oC in the hybridization chambers. The arrays were scanned using an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) with laser intensities adjusted to bring the brightest spot just below saturation and the data extracted with the Axon GenePix Pro software. Source GEO sample is GSM98758 Last updated (according to GEO): May 31 2006 Primary tumor 19 32 Blood 1000 spinal cord, spinal cord: G3C_le1 Adipocytes 861 Gene expression data from a placenta with acute malaria Source GEO sample is GSM183611 Last updated (according to GEO): Apr 23 2007 Peripheral Nervous System 1000 197 176 with coxsackievirus B3 Normal Source GEO sample is GSM176296 Last updated (according to GEO): Apr 09 2007 Cerebral cortex 861 cerebral cortex 7 21 Tumor__Lung_Adeno_HCTN_LUT4_(18870_A1C) on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 129 122 in brain 28 13 from spinal cord HMVEC-L stimulated without LPS for 4 hours c04R1 Fibroblasts 1000 N28__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from postmorten brain regions Source GEO sample is GSM145271 Last updated (according to GEO): Nov 20 2006 NOS exp2 NitroArg 97 75 8 clear cell carcinomas Heart 861 A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke. White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by treatment (IV) with the catalytic antioxidant AEOL 10150 and then 6 hours of reperfusion; first replicate; pooled mRNA from 6 brains. Source GEO sample is GSM2214 Last updated (according to GEO): May 27 2005 HDMTX-14 2535 2522 of spinal cord 901 Bone Marrow cerebral_cortex_4 Source GEO sample is GSM80653 Last updated (according to GEO): Mar 31 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Leukotriene B4 (LTB4) for 30min Source GEO sample is GSM5673 Last updated (according to GEO): May 27 2005 Spinal Cord 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145264 Last updated (according to GEO): Nov 20 2006 SN72h(3) Primary large cell carcinoma 1485 0 32 861 Lung diseases Brain 1000 V5-P569 CNS-SC_CtrA4h-1B-s2 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132556 Last updated (according to GEO): Feb 26 2007 43 0 Chorionic mesoderm-derived mesenchymal cells 29 0 cerebral cortex wistar ky 3910 1000 Coronary Arteriosclerosis 4-cell embryo replication 1 cDNAs were generated from 5ug of total RNA per sample by reverse transcription (RT) for two hours at 42oC using the 3DNA SubmicroTM Oligo Expression Array Detection Kit (Genisphere, Hatfield, PA) and Superscript II (Invitrogen, Carlsbad, CA). For each microarray chip two consecutive hybridizations were performed with cDNAs and the fluorescent probes following the manufacture?s specifications. Briefly, in the first hybridization reaction the solution containing the mixture of cDNAs obtained from control and treated cells was loaded onto the CAG Human 19K array and incubated overnight at 55oC in a hybridization chamber (Genemachines, San Carlos, CA). The human 19K array (www.cag.icph.org/microarray_facility.htm) contains 60-mer oligonucleotides (Compugen, San Jose, CA) representing 18,861 human genes spotted onto poly-l-lysine coated glass microscope slides. In the second hybridization reaction Cy3 (green) and Cy5 (red) fluorescent probes were used to label the cDNAs from control and PGJ2-treated cells, respectively. The second hybridization was carried out for 3 hours at 65oC in the hybridization chambers. The arrays were scanned using an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) with laser intensities adjusted to bring the brightest spot just below saturation and the data extracted with the Axon GenePix Pro software. Source GEO sample is GSM98764 Last updated (according to GEO): May 31 2006 80 CB B A/J hippocampus rep2 (430 2.0 Array) 129 2000-1 BAT The genomic consequences of bursts of action potential firing induced by the treatment of cultured cortical neurons (9-11 DIV) with the GABAA receptor antagonist bicuculline (Bic, 50 ?M) and the potassium channel blocker 4-aminopyridine (4AP, 5 ?M). Source GEO sample is GSM144062 Last updated (according to GEO): Nov 24 2006 1000 Rectum The Huntington's disease 0 23 AD-355t2-A174-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A seminoma specimen, pT2, patient age: 34y; W03 013 Tumor__Colorectal_Adeno_mCRT1_(8936) on Affymetrix GeneChip Human 35K SubA Array Hu35k-A liver, PPARa-null mice, fasting conditions (24h) Source GEO sample is GSM205752 Last updated (according to GEO): Jul 24 2007 Carcinoma of lung 1000 Brain_6wk_FVB_Male 39 27 the maxillary Brain_Adult_Salineip_4hr_mouse2 (YP2_#59) 1000 Brain prostate Source GEO sample is GSM203278 Last updated (according to GEO): Jun 21 2007 Normal Source GEO sample is GSM175842 Last updated (according to GEO): Apr 09 2007 TNF-alpha, 24.00 hr. T-cell. 52 25 in hereditary breast cancer MDA Mb231 1 Control D_U133Plus_110_nAcc 7 0 prostate GBM: 41A31 in the mammalian nervous system 110 141 cerebral 0 7 Tacrine 2.7mg/kg/day from 5 weeks Moclobemide 10mg/kg/day Creatine 1%w/v added to wet mash Lot batch = 5289 Source GEO sample is GSM13359 Last updated (according to GEO): May 28 2005 10 7 left 861 Acquired Immunodeficiency Syndrome Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11462 Last updated (according to GEO): May 28 2005 To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18426 Last updated (according to GEO): May 27 2005 1000 Brain Pre Natal CCAM 1 Ta gr3 tumour Source GEO sample is GSM2518 Last updated (according to GEO): May 27 2005 in bronchial epithelia 311 332 Myometrium 17 Normal Acute lymphoblastic leukemias carrying a chromosomal translocation involving the mixed-lineage leukemia gene (MLL, ALL1, HRX) have a particularly poor prognosis. Here we show that they have a characteristic, highly distinct gene expression profile that is consistent with an early hematopoietic progenitor expressing select multilineage markers and individual HOX genes. Clustering algorithms reveal that lymphoblastic leukemias with MLL translocations can clearly be separated from conventional acute lymphoblastic and acute myelogenous leukemias. We propose that they constitute a distinct disease, denoted here as MLL, and show that the differences in gene expression are robust enough to classify leukemias correctly as MLL, acute lymphoblastic leukemia or acute myelogenous leukemia. Establishing that MLL is a unique entity is critical, as it mandates the examination of selectively expressed genes for urgently needed molecular targets. AD-261t1b-A173-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Supranuclear Palsy, Progressive 1000 Brain 1000 Occipital Lobe 8 Normal Neoplasm Metastasis 861 Large-scale analysis of the human transcriptome. Prostate cancer Source: University of Virginia, see PMID 11507037 Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 133.07 Stdv: 5.06 Min: 123.99 Max: 141.08 Source GEO sample is GSM2861 Last updated (according to GEO): Mar 20 2006 Nose 1000 Chronic leukemia NOS 913 861 Malignant Neoplasms 15 0 skeletal muscle Isoflurane 5 exposures-1 Keywords = Infectious diseases 1135 1165 Plasma 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145195 Last updated (according to GEO): Nov 20 2006 Colon Tumor Keywords = mouse gene expression database Source GEO sample is GSM39416 Last updated (according to GEO): May 27 2005 7 frontal cortex 20 Activated Source GEO sample is GSM176006 Last updated (according to GEO): Apr 09 2007 CNS-SC_CtrB24h-2A-s2 gene expression from allergen stimulated mouse lung Source GEO sample is GSM158132 Last updated (according to GEO): Jan 25 2007 Plasma 861 Brain 861 accumbens_5 Source GEO sample is GSM80587 Last updated (according to GEO): Mar 31 2006 Lymphoma (Burkitts Raji) [JunctionChip 5 of 5] primary cortical neurons sprague2 pool of several animals, 16 days gestation, unknown gender Sprague Dawley primary cortical neurons file:R3RS01062216 Source GEO sample is GSM15236 Last updated (according to GEO): May 28 2005 The epithelial cells 962 981 861 Fibroblasts Experimental Autoimmune Encephalomyelitis 1000 TGFbeta added. Source GEO sample is GSM203991 Last updated (according to GEO): Jun 25 2007 861 Left Lymphoblastoid Cell Line for Individual 8199.4 log phase CCRF-CEM hgu95a 861 Retina 861 Blood The functional relationships and properties of different sub-types of dendritic cells (DC) remain largely undefined. We used a global gene profiling approach to determine gene expression patterns among murine splenic CD11c high DC subsets in an effort to better characterise these cells. Last Updated (by provider): Jun 15 2005 Contributers: S Tomlinson A D Edwards C Reis E Sousa O Schulz D Chaussabel A Sher Includes GDS352. Update date: Jun 16 2003. Dataset description GDS352: Profiling of murine splenic CD11c high dendritic cell subtypes. CD4+, CD8+ and CD8- CD4- cells analyzed both directly after sorting and after 2 hours cultivation.. Parkinson's disease sample x100 0 30 T1 gr3 tumour Source GEO sample is GSM2543 Last updated (according to GEO): Mar 21 2006 nucleus accumbens_core sprague2 580 557 normal epithelial cells no additional Source GEO sample is GSM199217 Last updated (according to GEO): Jun 08 2007 Stria 861 Neoplasm 861 Heart 1000 574 542 in the spared extraocular muscles ventral spinal cord 13 31 for multiple sclerosis 179 200 of somatomotor cortex 21 41 C3H/HeJ Cingulate Cortex E 972 Structure of middle temporal gyrus GSE8988 Brain 50 55 9 0 rat kidney 1000 Cerebral cortex 1000 Pulmonary alveolar structure Parkinson 0 8 Gene expression data from colorectal adenoma. Source GEO sample is GSM215099 Last updated (according to GEO): Aug 02 2007 1000 Brain Experimental Autoimmune Encephalomyelitis 1000 Epithelial Cells 901 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114268 Last updated (according to GEO): Jun 16 2006 cerebellum_1 Source GEO sample is GSM80616 Last updated (according to GEO): Mar 31 2006 6wkB EWS-T-TEST-20 on NHGRI-6.5k_b 901 Temporal Lobe Epithelium of bronchus 983 infection 64 72 Arteries 861 Bladder sample 928_1 UD rep 2 Ovary 1000 Plasma 861 D_U133A_82_CB KT32_N I_U133A_44_CB 861 Brain HCC (HBV+, HK59) Job's patient Source GEO sample is GSM211116 Last updated (according to GEO): Sep 10 2007 0 Huntington's disease 19 1000 Heart VDXKIU_121 1000 Olfactory Epithelium Brain 861 Intestines 861 1000 hindbrain Ts1Cje-1-MGU74B Locus Coeruleus Source GEO sample is GSM107936 Last updated (according to GEO): Jun 06 2006 Parkinson Disease 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145170 Last updated (according to GEO): Nov 20 2006 Epithelial Cells 1000 P12-ICHIKAWA DMSO control 24h rep1 156 145 Their livers 589 578 hippocampus Paravertebral Muscle 10 Disease for nicotinic receptors 163 185 1000 Malignant neoplasm of prostate nerve 0 5 Liver 1000 CAD_replicate46 901 Stem cells Gene expression data from rat lungs exposed to FiO2 of ~9.5% (hypoxia). Source GEO sample is GSM184878 Last updated (according to GEO): Jun 14 2007 NH 299141A 861 Mesentery 110 94 of heart failure 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113956 Last updated (according to GEO): Jun 16 2006 HC57 FC BA4 B Normal Source GEO sample is GSM175891 Last updated (according to GEO): Apr 09 2007 none Source GEO sample is GSM239904 Last updated (according to GEO): Dec 07 2007 1000 Cerebellum C57BL10 soleus sample 1 I_U133A_37_AnCg Recurrent Carcinoma 875 861 Spinal Cord Peritoneum 861 D_U133A_21_nAcc Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM Source GEO sample is GSM207691 Last updated (according to GEO): Jul 09 2007 carcinogenic 755 767 Gene expression data of substantia nigra from postmortem brain of PD patients Source GEO sample is GSM184374 Last updated (according to GEO): May 29 2007 Obesity 1000 Bone Marrow 1000 R529P00609 238 232 Retinas A HID U D054 901 frontal lobe Measles 861 3 min exposure to halothane, immediate perfusion with ice cold saline Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5084 Last updated (according to GEO): Mar 10 2006 136 131 Aortae 901 Caudate nucleus structure ER+/LN-/Marks212 on Affymetrix GeneChip Human Full Length Array HuGeneFL normal testis 54 66 mouse hippocampus 0 16 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Sphingosine-1-phosphate for 30min Source GEO sample is GSM5743 Last updated (according to GEO): May 27 2005 Spleen 0 5 Spleen vs Interferon-gamma (IFN gamma) Treated B cell 30min (set1) General Paralysis 885 1000 Hippocampus Replicate2_Voxel B5 of mouse brain 9 23 Plasma 861 Mammary Gland @ Preg1, biological rep3 Gene expression data from whole brain infected mouse, day 3 Source GEO sample is GSM189645 Last updated (according to GEO): May 16 2007 liver.3 DLBC29 on Affymetrix GeneChip Human Full Length Array HuGeneFL Endometrium 0 10 PE_D_508 plasma cells 332 344 861 Cardiomyopathies 1BMH02082904_BM_CD105endothelia nucleus accumbens, whole wistar2 Obtained with a 1.5 mm diameter punch, using a 2mm thick slice, and anterior commisure was in dorsolateral portion of punch. Wistar whole nucleus accumbens file:R3JV01080106 Source GEO sample is GSM15198 Last updated (according to GEO): May 28 2005 Prefrontal Cortex AB Normal 861 Cerebral cortex Gene expression data from human colon tumor tissue Source GEO sample is GSM173373 Last updated (according to GEO): Apr 20 2007 1000 Muscle brain, cerebral cortex: 4R 1 (4/14)_le1 1000 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145441 Last updated (according to GEO): Nov 20 2006 - Source GEO sample is GSM216537 Last updated (according to GEO): Aug 09 2007 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226149 Last updated (according to GEO): Nov 02 2007 901 Coronary artery 861 Cardiomyopathies 861 Ribosomal RNA 196 177 from the bone marrow umbilical cord_nobpd: 4B Gene expressions affected by TNF alpha Source GEO sample is GSM189814 Last updated (according to GEO): May 21 2007 for these two carcinomas 429 452 DMN-NF1Hippo18d-1bAv2-s2 Liver 0 4 brain, cerebral cortex: 4R 3 (4/28)_le1 "Sample 15,>5 yr survival(63 months) age 46 erp yes" on vantveer-oligo 1000 Lung Liver Test (Blinded) Sample Source GEO sample is GSM130060 Last updated (according to GEO): Sep 18 2007 Spleen 0 5 Mucous Membrane 861 in seminoma 245 255 Nose 1000 100 73 of gingival epithelial cells nasal epithelial cells 28 49 1000 Ataxia Telangiectasia pfc_1002_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Blood Cells 875 Expression profiling of moderately injured raphe at 24h in rats Source GEO sample is GSM41578 Last updated (according to GEO): May 27 2005 180 157 tibialis anterior muscle testis Source GEO sample is GSM18982 Last updated (according to GEO): Sep 25 2006 Multiple sclerosis (MS) begins as an inflammatory/demyelinating disease but axon injury and neurodegeneration underlie chronic progression. Extracellular matrix (ECM) heparan sulfate proteoglycans (HSPG) are catabolized in acute inflammatory MS lesions and HSPG catabolic products may contribute to failure of neuron repair. Neurite outgrowth and axon elongation of PC12 cells are inhibited when these cells are grown on heparanase-digested HSPG. This inhibition of differentiation is counteracted by nerve growth factor (NGF) but failure to completely reverse inhibition may be due to loss of other growth factors affected by HSPG breakdown. To understand effects of the digested ECM in this model, expression of genes that control differentiation in PC12 cells grown on digested and undigested HSPG will be analyzed. This will permit identification of new potential therapeutic targets for specifically counteracting inhibitory effects of ECM breakdown on neuron regrowth/regeneration in MS. We will compare gene expression patterns of PC12 cells grown on undigested and digested HSPG in the presence and in the absence of NGF over a two week time course to identify the alterations induced by the catabolized HSPG on expression of genes involved in their acquisition of a neuronal phenotype and to determine which genes are and are not targeted by NGF. We are studying ECM HSPG breakdown in human and experimental demyelinating diseases and have developed an in vitro model of ECM catabolism-induced inhibition of neuronal differentiation. Our data indicate that: 1) the numbers of PC12 cells that exhibit neurite outgrowth are decreased when the ECM contains digested, as opposed to intact HSPG; and 2) in the presence of NGF, neurite outgrowth inhibition is counteracted, but complete axonal growth/elongation is not achieved. We will use gene microarray analysis to identify the specific gene expression alterations that digested ECM HSPG induces in PC12 cells in this model of inhibition of neural differentiation. We hypothesize that the genes that are critical for PC12 cell differentiation will be altered by the pathologically altered ECM. Rat pheochromocytoma PC12 cell lines are widely used for analyzing neuronal differentiation. Microarray analyses have identified gene expression patterns associated with their differentiation and response to growth factors. We developed a model of catabolized HSPG inhibition of PC12 cell differentiation that mimics the ECM in MS lesions. HSPG coated on tissue culture dishes is digested with heparanases prior to plating of the PC12 cells. Cells grown on digested ECM without NGF show inhibition of neuronal differentiation (decreased numbers with neurite outgrowth) from days 7 to 14. NGF can partially, but not completely counteract the inhibition, suggesting that signaling pathways in addition to those affected by NGF may be affected by the ECM HSPG digestion. Therefore, we will compare gene expression patterns in samples of cells grown on digested and undigested HSPG ECM both in the presence and absence of NGF. The cells are plated on washed, undigested or digested HSPG-coated 100 mm Petri dishes and grown with or without NGF. Total RNA will be extracted from cells grown in the 4 conditions (w/without digestion; w/without NGF) on 100mm Petri dishes using the RNeasy extraction kit (Qiagen). We propose: 2 duplicate samples/culture condition (8 samples) per time point X 5 time points (days 1, 5, 7, 10, and 14 of culture) = 40 samples/experiment. The RNA will be sent to the Microarray Consortium center for QC check and microarray analysis. Previous analyses of PC12 cells have used the NIA Mouse 15K cDNA clone set scanned with the Agilent Oligo array platform (Vaudry, 2002; Grumolato, 2003). Therefore, this methodology will be useful for comparisons to published studies. (Number of experiments to be determined). Vaudry D, et al, 2002. J Neurochem 83:1272-1284 Grumolato L, et al, 2003. Endocrinology 144:2368-2379 Last Updated (by provider): Jun 07 2006 Contributers: Raymond A Sobel Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002. Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Part of the medium chain triacylglycerol oil in control diet was replaced with: 1.9% fish oil (providing 0.5 dietary wt% DHA and 1.0en%). Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily. Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France). Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h. After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hepatic gene expression analysis. From these 5 mice, livers were dissected according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancourt, France), which consisted of carefully dissecting out the liver, rinsing with 70% EtOH to remove adhering blood, trimming of adhering connective tissue with scissors, cutting into 100-150 mg subsections, freezing in liquid N2, and storing at -80°C until gene expression and lipid analysis. Hepatic lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5). Liver tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hepatic RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips. Source GEO sample is GSM2572 Last updated (according to GEO): Oct 28 2005 Normal and diseased human tissues were profiled for gene expression using the Affymetrix U133 plus 2.0 array In total 20 samples were processed Last Updated (by provider): Apr 09 2007 Contributers: Richard Roth Nose 1000 1000 Descending colon for liver 26 35 GPX-000046 Ta gr3 tumour Source GEO sample is GSM2534 Last updated (according to GEO): Mar 21 2006 1000 Descending colon Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Source GEO sample is GSM15958 Last updated (according to GEO): May 28 2005 GIN-Hippocampus replicate1 5 0 Spleen Parkinson Disease 1000 Immune_Peripheral Blood Mononuclear Cells (ficoll)_1 Keywords = mouse gene expression database Source GEO sample is GSM29445 Last updated (according to GEO): May 27 2005 p53 +/+, 12 hour, replicate b Source GEO sample is GSM2557 Last updated (according to GEO): May 27 2005 1004 996 in tumors Liver 861 Gene expression data from embryos released from the U0126-induced arrest at day 4.5. Source GEO sample is GSM176493 Last updated (according to GEO): Mar 19 2007 This is the mutant littermate at postnatal day 5 pooled 4 animals Lot batch = Source GEO sample is GSM4083 Last updated (according to GEO): May 28 2005 HCT-116 hgu95c 151 to genetic disorders 170 1000 Hippocampus Hoxb1 wt E10.5, rep 1 (W5) GBM Treatment, type=remove Source GEO sample is GSM99531 Last updated (according to GEO): Apr 21 2006 mouse brain 478 489 Female infertility syndromes are among the most prevalent chronic health disorders in women, but their molecular basis remains unknown because of the complexity of oogenesis and uncertainty regarding the number and identity of ovarian factors controlling the assembly, preservation, and maturation of ovarian follicles. To systematically discover such ovarian fertility factors en masse, we employed a mouse model (Foxo3), where follicles are assembled normally but are then synchronously activated. Gene expression profiling of mutant and normal ovaries led to the identification a surprisingly large set of ovarian factors. The set included the vast majority of known ovarian factors, many of which when mutated produce female sterility phenotypes, but most were novel. Subsequent analyses revealed novel classes of ovarian factors and significant overrpresentation on the X chromosome, among other insights into the general properties of oogenesis genes and their patterns of expression. Last Updated (by provider): Aug 02 2007 Contributers: Esra Akbay Meredith Schidler George B John Diego H Castrillon Cristina M Contreras Marshall Haynie Samuel Ward Lane Shirley Teresa D Gallardo human frontal cortex Source GEO sample is GSM87025 Last updated (according to GEO): Feb 08 2006 by basal progenitor cells 702 726 D_U133A_50_Amy f2#88 versus pool Mouse Brain tissue brain, cerebellum: RNA#11S_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM145128 Last updated (according to GEO): Nov 20 2006 Brain 1000 CLL-49 Expression profiling of moderately injured raphe at 14d in rats Source GEO sample is GSM41569 Last updated (according to GEO): May 27 2005 1000 Impaired cognition 254 238 of neural retinas 1000 Malignant Neoplasms healthy control sample x072 Macrophage 14smi023 adipose_tissue_subcutaneous_6 Source GEO sample is GSM80590 Last updated (according to GEO): Mar 31 2006 Brain 861 1000 Neuraxis NCI60.28_LABEL32EXTRACT31SUB3 Source GEO sample is GSM134130 Last updated (according to GEO): Aug 06 2007 Date : 5/30/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 10 mg/kg Time : 3 hrs post-injection Intervention : none Risk: 40% increased risk for encephalopathy Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AO092 Source GEO sample is GSM12243 Last updated (according to GEO): May 28 2005 901 Coronary artery 1000 Prostate Standard affymetrix protocol Source GEO sample is GSM119733 Last updated (according to GEO): Jul 31 2007 Lymphoblastoid Cell Line for Individual 8127.5 log phase human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155050 Last updated (according to GEO): Jun 04 2007 Liver 3 Normal Normal Source GEO sample is GSM176326 Last updated (according to GEO): Apr 09 2007 Aorta 2 Normal 146 134 encephalitis AO Treatment, type=remove Source GEO sample is GSM99512 Last updated (according to GEO): Apr 21 2006 861 Neoplasm no additional Source GEO sample is GSM199113 Last updated (according to GEO): Jun 08 2007 284 276 in aortas Oat cell carcinoma 888 brain, cerebral cortex: CO3_le1 1000 Encephalopathies of coronary artery disease 317 342 B283 on Affymetrix GeneChip Human Full Length Array HuGeneFL Normal__Uterus_UT_4 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 861 Muscle 1000 Prostate Vulva 10 Normal M_U133A_37_CB 1000 Brain 1000 Spleen urethra_4 LEUK_MOLT4 on Affymetrix GeneChip Human Full Length Array HuGeneFL Neoplasm 861 B220+CD25+sIg- Small Pre BII cells sorted out of mouse bone marrow, sort no. 9 Source GEO sample is GSM663 Last updated (according to GEO): May 27 2005 Donor 3 Time point 24 hours Autologous control (uninfected) Source GEO sample is GSM2621 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T10) extracted from rats 24h following severe injury Source GEO sample is GSM31363 Last updated (according to GEO): May 27 2005 Control rats 1h after injection with PBS Treatment, type=time_course, description=Control animals are treated with PBS, measurement=1.0 h Source GEO sample is GSM32071 Last updated (according to GEO): May 27 2005 gene expression of 1 day LIF differentiated ESCs Source GEO sample is GSM181948 Last updated (according to GEO): Apr 12 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM146067 Last updated (according to GEO): Nov 20 2006 Total RNA was extracted from umbilical subcutaneous adipose tissue from an individual affected with FCHL and exhibiting the USF1 susceptibility haplotype Source GEO sample is GSM9040 Last updated (according to GEO): May 28 2005 Primary small cell lung carcinoma 2229 0 37 246 219 of parieto-occipital cortex MGJZ030211071Adorsalstriatum VDXRHU_4188 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11599 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145827 Last updated (according to GEO): Nov 20 2006 WGACON-90 Primary Neoplasm 1000 1000 jejunum 861 Cardiomyopathies nodose_nucleus_1 Source GEO sample is GSM80768 Last updated (according to GEO): Mar 31 2006 3AMH02082805_PB_CD8TCells 1000 Tongue Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide Source GEO sample is GSM225348 Last updated (according to GEO): Aug 31 2007 brain 0 5 Pool of 13 cochlear tissues at E11.5 Source GEO sample is GSM182574 Last updated (according to GEO): Aug 14 2007 1000 Brain 67 40 with coronary artery disease from brain 21 30 none Source GEO sample is GSM239832 Last updated (according to GEO): Dec 07 2007 Normal Corpus brain, Medial Temporal Gyrus: Sample29_e1_le1 Coxsackievirus Infections 861 rat cortex Treatment, type=time_course, measurement=28.0 d Source GEO sample is GSM53232 Last updated (according to GEO): Jul 06 2005 287_2 4 0 Liver NCI60.29_LABEL33EXTRACT32SUB3 Source GEO sample is GSM134136 Last updated (according to GEO): Aug 06 2007 SN:Human Glioblastoma Biopsy 10405 133 by the trigeminal ganglion 108 1000 Leukemia, Myelocytic, Acute B240 on Affymetrix GeneChip Human Full Length Array HuGeneFL Normal__Germinal_Center_GC44 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Retina Central gray substance of midbrain 861 C57BL/6J female number 2, untreated control ear (#2_Wt-C-4) to gap junctions 1276 1292 skin Source GEO sample is GSM19001 Last updated (according to GEO): Sep 25 2006 with skeletal muscle atrophy 26 53 Lymphoblastoid Cell Line for Individual 8114.3 log phase Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160727 Last updated (according to GEO): Sep 24 2007 VDXRHU_2393 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 4176 left_liver_lobe in cardiac ventricle 148 167 Wild type P104 mouse visual cortex contralateral to monocular enucleation Source GEO sample is GSM97222 Last updated (according to GEO): Feb 17 2006 Wild type 8 wk old male FVB/NJ mouse hypothalamus Source GEO sample is GSM107027 Last updated (according to GEO): Mar 05 2007 Large-scale analysis of the mouse transcriptome. Hypothalamus C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 258.13 Stdv: 7.82 Min: 246.78 Max: 280.71 Source GEO sample is GSM2908 Last updated (according to GEO): Mar 20 2006 It is suggested that the stress induced activation of the HPA axis and associated increases in plasma ACTH and glucocorticoids (corticosterone, B in the rat) are contributing factors in the development of many psychopathologies. However, the circadian fluctuation of the HPA axis activity (characterized by a zenith in the plasma ACTH and B, before the beginning of the active awake state and the nadir during the inactive sleeping period) occurs throughout the life and is important for normal physiological and behavioral functioning. A blunting or enhancement of this rhythm through changes in the trough or in the peak is a characteristic feature of many pathological states. At the CNS level, the circadian fluctuation of the HPA axis activity is associated with changes in the expression profile of structural, functional, and immediate early genes. However, little is known about the specific role of B in the modulation of the circadian pattern of gene regulation in the CNS. Thus, during the circadian cycle B is a major factor, which could influence the expression profile of a large family of genes. Accordingly, the microarray technology, because of its characteristic feature that facilitates the identification of the expression profiles of a wide range of genes simultaneously, is an ideal technique. Because the B status of animals can be easily manipulated by adrenalectomy (ADX) surgery with or without B replacement, this model will be used in these studies. Thus, the proposed studies are intended to characterize, by the use of the microarray technique, the effects of the B milieu on diurnal gene expression profiles in selected rat brain regions strongly influenced by: a.) B status: amygdala, hippocampus, hypothalamus, and septum; and b.) Circadian Activity: dorsal raphe, frontal Cortex and locus coeruleus. The gradient of the B response during the circadian cycle implies that at the beginning of the sleep cycle MR are predominantly occupied while at the end of the sleep cycle, both MR and GR are occupied. Thus, we propose that differing ratios of activation of these nuclear receptors could differentially modulate gene expression and impart temporal characteristics in the expression profile of a large family of genes. Furthermore, we propose that these effects may be region specific, reflecting regional differences in GR and MR distribution, B uptake, and neural activity. B may exert these circadian effects on regional gene expression profiles either directly or indirectly via interneurons. However, little is known about the circadian effect of B on gene expression profiles in different brain regions. Such knowledge is important to identify the specific role of B in circadian differences in CNS function and, potentially, the development of psychopathologies. After arrival at the facility the rats (male Long Evans) will be maintained on 12:12 h LD cycle ('lights-on" at 0700 h) with food and water ad libitum. One week after, they will undergo bilateral ADX under survival anesthetics (day-0). The study will include three groups (n=10); (a) ADX: rats with no adrenals, (b) pADX: ADX rats with subcutaneous 40 percent B pellet (fused cholesterol and B), and (c) SHAM: rats undergoing flank incisions without the removal of the adrenals. After surgery, rats will be housed individually. The ADX rats will receive 0.5 percent saline in addition to regular tap water. On post-surgical day-7, 15 rats (five/group) will be sacrificed by decapitation 2h after 'lights-on", and the remaining 15, 2h after "lights-off". The brains will be removed immediately, frozen on dry ice, and stored at -80 C. The trunk blood will be collected with EDTA and plasma frozen for ACTH and B RIA. The brains from rats with confirmed ADX will be used for free hand dissection of brain regions: frontal cortex, septum, hypothalamus, amygdala, hippocampus, dorsal raphe, and locus coeruleus. Tissue will be stored at -80 C. Total RNA will be extracted from individual brain regions using Qiagen RNeasy Lipid Tissue kit. Initial evaluation of quality and quantity of the RNA will be done by the absorbance method. Frozen samples containing 0.5 ul total RNA or higher will be sent to the NINDS-NIMH Microarray Consortium in dry ice for evaluation of the integrity of 28S and 18S RNA on an Agilent Bioanalyzer. If the integrity of RNA is not good, the experiment will be repeated and new RNA samples will be provided. Replicates of each brain region with 28S/18S ratio of 1.7 and higher will be selected for assay using Affymetrix Rat U34A array. The RNA samples from one region from all the brains will be processed together. A total of 84 chips may be utilized in these studies, however the final number will depend upon integrity of the total RNA. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Jun 06 2006 Contributers: K. V Thrivikraman 901 Coronary artery Plasma 861 28 hr Hela Double Thymidine, exp2 Acetaminophen 6hr Rat 8066 blood vs. Acetaminophen 6hr Rat Pooled Control blood m1-WT6 1000 Uterus Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:160, Count:32 Corner- Avg:26213, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:5.273146,SFGene:All Background:Avg:392.26,Stdev:13.62,Max:427.1,Min:369.8 Noise:Avg:9.71,Stdev:0.44,Max:11.0,Min:8.7 RawQ:12.69 Keywords = ALL Source GEO sample is GSM3444 Last updated (according to GEO): May 27 2005 Wild type olfactory epithelium 16 hpO replicate1 brain, cerebral cortex: Rat_03-22_NroLep_Lipska_e1_le1 1000 Endometriosis, site unspecified n/a Source GEO sample is GSM178040 Last updated (according to GEO): Jun 11 2007 CVB3_V-9h-2 vomeral nasal organ Source GEO sample is GSM18653 Last updated (according to GEO): May 27 2005 NA Source GEO sample is GSM84334 Last updated (according to GEO): Dec 01 2005 Transplant Series 33 , Transplant # 2 Adenocarcinoma 861 M_U133Plus_38_HC Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211239 Last updated (according to GEO): Jul 18 2007 5 0 brain Gene expression data from postmorten brain regions Source GEO sample is GSM145383 Last updated (according to GEO): Nov 20 2006 for liver 26 35 19 0 The left hippocampus 0 cortex 5 Respiratory Distress Syndrome, Adult 1000 Cardiac 523 530 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68230 Last updated (according to GEO): Jul 07 2006 /NJ cingulate cortex rep1 3 27 T-ALL-R6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Studies using mice with beta4 nicotinic acetylcholine receptor (nAChR) subunit deficiency (beta4-/- mice) helped reveal the roles of this subunit in bradycardiac response to vagal stimulation, nicotine-induced seizure activity and anxiety. In order to identify genes that might be related to beta4-containing nAChRs activity, we compared the mRNA expression profiles of brains from beta4-/- and wild-type mice using Affymetrix U74Av2 microarray. Seventy-seven genes significantly differentiated between these two experimental groups. Of them, the two most down-regulated were Spg21 and Pts genes. Since the targeted mutagenesis of beta4 nAChR subunit was done by using two mouse strains, 129SvEv and C57BL/6J, it is possible that genes closely linked to the mutated beta4 gene represent the 129SvEv allele and not the control C57BL/6J-driven allele. We examined this possibility by using public database and quantitative RT-PCR. The expression levels of Spg21 and Pts genes that, like beta4 gene, are localized on chromosome 9, as well as the expression levels of other genes located on this chromosome, were dependent on the mouse background strain. The 67 differentially expressed genes that are not located on chromosome 9 were further analyzed for over-represented functional annotations and transcription regulatory elements compared to the entire microarray. Genes encoding for proteins involved in tyrosine phosphatase activity, calcium ion binding, cell growth and/or maintenance and chromosome organization were over-represented. Our data enhance the understanding of the molecular interactions involved in beta4 nAChR subunit function. They also emphasize the need for careful interpretation of expression microarray studies done on genetically manipulated animals. Key words: Nicotinic acetylcholine receptor 4 subunit, Knockout mice, Microarray, Gene expression, Background mouse strain. M_U133Plus_116_DLPFC to psychosis 673 685 Muscle_adequate protein_male_rep1 Bone Marrow 1000 1000 lymph nodes Category: Cell-line Subcategory: HMEC Scanning Software: unknown Software version: unknown Lot batch = 0164-5k Source GEO sample is GSM1936 Last updated (according to GEO): Nov 21 2005 Brain 1000 brain_healthy_control_sampleid_jg1744 1000 Hippocampus hippocampus 7 17 Normal Source GEO sample is GSM176043 Last updated (according to GEO): Apr 09 2007 1000 Brain Entorhinal Cortex 7 23 Neonatal (P0) whole brain mRNA from 39,Xm (XmO) C57BL/6J x C3H/Paf Source GEO sample is GSM27448 Last updated (according to GEO): May 27 2005 Female mice used were 129/SvImJ wildtype (Jackson Lab), 10-16 weeks of age. 14 days after ovariectomy, mice were injected subcutaneously with progesterone dissolved in sesame oil (Sigma; 0.2mg/0.1mL/mouse), followed by sacrifice and removal of uterine horns at 9 hours after injection. 8 uterine horns from 4 mice were pooled to form one sample. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix. Source GEO sample is GSM3057 Last updated (according to GEO): May 27 2005 from the olfactory epithelium tissue 140 176 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Bombesin for 60min Source GEO sample is GSM5479 Last updated (according to GEO): May 27 2005 ICM pool 3 (n=4) Mouse model of congenital heart disease. Wild-type embyronic day 9.5 mouse. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2268 Last updated (according to GEO): May 27 2005 CNS-SMTC_Mod28d-2A-s2 Infection 1000 D09 12h TLR2/1L Spleen 1000 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50637.gif Developmental Stage: E6.75 Source GEO sample is GSM229816 Last updated (according to GEO): Nov 06 2007 Neoplasm 861 in the adult heart 44 61 Kidney YC-5B 1000 Spleen Lung Diseases, Obstructive 905 SR hgu95b 861 Heart Diseases of the postmortem brains 676 700 Primary tumor 19 32 Cerebral cortex 861 12 0 ovarian tumor Kidney 1000 Normal Source GEO sample is GSM176060 Last updated (according to GEO): Apr 09 2007 Nose 1000 Blood 1000 VDXGUYU_4073 Gene expression data from postmorten brain regions Source GEO sample is GSM145066 Last updated (according to GEO): Nov 20 2006 252 225 in human neurofibromatosis. labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156164 Last updated (according to GEO): Jan 22 2007 from colonic normal mucosa 21 47 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 22 hours after lights on. Original sample code = CM16A Source GEO sample is GSM227313 Last updated (according to GEO): Sep 10 2007 1000 Descending colon of cognitive decline 41 60 Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell 1571 1557 sporadic tumors Gene expression data from postmorten brain regions Source GEO sample is GSM145776 Last updated (according to GEO): Nov 20 2006 in seminoma 28 38 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM80009 Last updated (according to GEO): Oct 26 2005 Whole blood 0 10 from liver 21 30 V5-P241 whole blood_100812 /Ovary 11 Disease 11 27 Lymphoblastoid Cell Line for Individual 8195.3 log phase Duchenne muscular dystrophy 0 26 3AJZ02022222_ leukemia, chronic Myelogenous K-562 M_U133Plus_122_AnCg Polycystic ovary syndrome (PCOS), the most common cause of anovulatory infertility, is characterized by increased ovarian androgen production, arrested follicle development, and is frequently associated with insulin resistance. These PCOS phenotypes are associated with exaggerated ovarian responsiveness to FSH and increased pregnancy loss. To examine whether the perturbations in follicle growth and the intrafollicular environment affects development of the mature PCOS oocyte, genes that are differentially expressed in PCOS compared to normal oocytes were defined using microarray analysis. This analysis detected approximately 8000 transcripts. Hierarchical clustering and principal component analysis revealed differences in global gene expression profiles between normal and PCOS oocytes. 374 genes had a statistically-significant increase or decrease in mRNA abundance in PCOS oocytes. A subset of these genes was associated with chromosome alignment and segregation during mitosis and/or meiosis, suggesting that increased mRNAs for these proteins may negatively affect oocyte maturation and/or early embryonic development. Of the 374 differentially expressed genes, 68 contained putative androgen receptor, retinoic acid receptor, and/or peroxisome proliferating receptor gamma binding sites, including 9 of the genes involved in chromosome alignment and segregation. These analyses demonstrated that normal and PCOS oocytes that are morphologically indistinguishable and of high quality exhibit different gene expression profiles. Furthermore, altered mRNA levels in the PCOS oocyte may contribute to defects in meiosis and/or mitosis which might impair oocyte competence for early development and therefore contribute to poor pregnancy outcome in PCOS. Last Updated (by provider): Jun 05 2007 Contributers: David H Abbott Daniel A Dumesic Jerome F Strauss III Jennifer R Wood Whole Brain 73 83 cerebellum sprague 3900 D_U133A_51_Amy CNS-SC_InjA4h-3C-s2 brain, hippocampus: LH3_e1_le1 Brain 1000 GBM Treatment, type=remove Source GEO sample is GSM99538 Last updated (according to GEO): Apr 21 2006 of 24 neural tissues 98 117 Whole brain 0 10 brain, Left frontal Lobe: Extract7_le1 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226040 Last updated (according to GEO): Nov 02 2007 GBM: 46A15 Adenocarcinoma 9 0 15 CT6-CingulateCortex-replicate1 HapMap CHB Male Source GEO sample is GSM159617 Last updated (according to GEO): Feb 01 2007 3ARS02080774b_globus_pallidus 1000 Endometriosis, site unspecified Expression profiling of spinal cord section (T10) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM6648 Last updated (according to GEO): May 28 2005 of the normal mucosa 7 26 Chronic Lymphocytic Leukemia 19 47 Cerebral cortex 861 TEL-AML1-#12 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Cerebral cortex brain, Left frontal Lobe: Extract32_le2 1000 Endometrium Liver (HBV+, HK28) n/a Source GEO sample is GSM178031 Last updated (according to GEO): Jun 11 2007 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 3 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM11034 Last updated (according to GEO): May 28 2005 Melanoma xenograft, MEA2_Lung_C (LeiFidler) WGACON-112 Abdomen 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145972 Last updated (according to GEO): Nov 20 2006 Spleen 0 5 Mouse ileum 0 10 This is replicate 1 of the 3 hour sample from passive avoidance trained rats. Source GEO sample is GSM17400 Last updated (according to GEO): Aug 22 2007 pfc_1034_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1-Englow 1 cortex 7 12 Haloperidol treated 12weeks AffyGC RMA rep3 1000 Prostate 1000 Myeloid Leukemia, Chronic Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 8002 blood C57BL/6J periaqueductal gray rep2 I_U133Plus_110_CB Dorsal Raphe Source GEO sample is GSM107928 Last updated (according to GEO): Jun 06 2006 Dysregulation of gene expression in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-lesioned mouse substantia nigra. Control 8/23/02 (Experiment Neuroprotection3- Run 13276) Treatment, type=timepoint, measurement=0.0 h Source GEO sample is GSM96666 Last updated (according to GEO): Feb 14 2006 7 frontal cortex 20 21h-Control replication 4 861 Neoplasm Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162182 Last updated (according to GEO): Jun 12 2007 7 frontal cortex 20 Small cell carcinoma of lung 867 Brain 861 rat hippocampus Treatment, type=time_course, measurement=240.0 h Source GEO sample is GSM32149 Last updated (according to GEO): May 27 2005 3535 3514 superior frontal gyrus 78 66 Control blood mesenteric 11 20 Rejecting allografts 7 days No.3 of coronary artery disease 258 284 17 7 hippocampus Pool of 8 (1 utricle and 3 ampullae) at E13.5 Source GEO sample is GSM182603 Last updated (according to GEO): Aug 14 2007 Acetaminophen 24hr Rat 8194 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool Adenocarcinoma 861 AD control Treatment, type=dissect Source GEO sample is GSM119685 Last updated (according to GEO): Jul 10 2006 GSE697 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155040 Last updated (according to GEO): Jun 04 2007 plasma cells 332 344 This mouse is transgenic for constitutively active PI3k. caPI3K transgenic animals have hearts 20% larger than those of wild type littermates. These arrays were scanned at a PMT of 10%. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/pi3k_home.html Keywords = hypertrophy, pi3k, cardiac Source GEO sample is GSM8519 Last updated (according to GEO): May 27 2005 brain, Left frontal Lobe: Extract13_le1 1000 Brain GSE8615 24 7 Right Frontal Lobe CNS-SCsev_InjB4h-1A-s2 Mental Retardation 1000 861 Anterior 1000 Hypertrophic Cardiomyopathy 1146_24d Gene expression data from postmorten brain regions Source GEO sample is GSM145214 Last updated (according to GEO): Nov 20 2006 31 0 Cerebellum Alzheimer's disease 8 5 0 brain DBA/2J bed nucleus of the stria terminalis rep2 1BJZ02022634_fetalliver 186 167 In the mouse retina 144 114 from a single adult spinal cord Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211351 Last updated (according to GEO): Jul 18 2007 To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18449 Last updated (according to GEO): May 27 2005 Replicate3_Voxel A4 primary hepatocytes, rat, control condition Source GEO sample is GSM205898 Last updated (according to GEO): Jul 24 2007 Ganglia, Spinal 923 24 skeletal muscle 10 D_U133Plus_38_HC Microarray analyses support a role for Nurr1 in resistance to oxidative stress and neuronal differentiation in neural stem cells. Acetaminophen 24hr Rat 5480 blood vs. Acetaminophen 24hr Rat Pooled Control blood cells stimulated with lipoprotein prep 3, biological rep2 Primary Neoplasm 1000 CNS-SpinalC-4hAdult-2C-s2 D_U133Plus_19_DLPFC Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16559.gif Source GEO sample is GSM91555 Last updated (according to GEO): Sep 22 2006 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156169 Last updated (according to GEO): Jan 22 2007 hippocampus rattus_norvegicus_strain iP animal_number 3 1000 Spleen Heart 1000 865 Disorder of artery Brain 861 12 0 ovarian tumor 110 94 of heart failure Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P18, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3236 Last updated (according to GEO): May 28 2005 hindbrain 861 CNS-SMTC_Mod3mo-2B-s2 2389 2376 of hippocampus f2#348 versus pool Mouse Brain tissue for hereditary non-polyposis colon cancer 340 380 99 86 of hippocampus DLBC49 on Affymetrix GeneChip Human Full Length Array HuGeneFL Hypertensive disease 1000 1000 Hippocampus DLCL-0028 || lc7b025 Multiple sclerosis 0 17 Nervous system structure 901 ER negative human primary breast tumor EA02014_41279_H133A_JA-1650 Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM182002 Last updated (according to GEO): Apr 13 2007 brain, unknown: Sample45_e1_le1 Effect of SOCS3 on the transcriptional response of bone marrow-derived macrophages to IL-6 Epithelium 861 4525 4520 liver 1000 Coronary Arteriosclerosis Nrf2 +/+ mice (C57B6/SJL) were crossed with nrf2 -/- mice (C57B6/129SVJ) to generate mice heterozygous for nrf2. Interbreeding these heterozygotes generated the double-knockout mice (nrf2 -/-) as well as the corresponding littermate controls (nrf2 +/+). Mice were housed in plastic cages on a bedding of wood chips and maintained at ~22C, ~60% relative humidity, and a 12 hr light/dark cycle. The animals were fed with mouse diet 5015, which includes 30 IU/g of vitamin A and 35 IU/kg of vitamin E, (LabDiet, Richmond, IN) and drinking water ad libitum. All animal protocols were approved by the Institutional Animal Use and Care Committee at the University of Wisconsin-Madison. Total RNA was extracted from livers and spleens isolated from male and female nrf2 wildtype and knockout mice at 5 months of age (prior to the development of severe autoimmune disease). Keywords = Nrf2 Keywords = liver Source GEO sample is GSM13437 Last updated (according to GEO): May 28 2005 Nasal Epithelium 901 1000 Cerebral cortex 1000 Spinal Cord Injuries in amygdala 20 31 SQ-2572-A321-5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A P46DR (dark reared) non-deprived visual cortex replicate 1 KT1008c_DT/IN 19 0 human frontal cortex Cigarette smoke is the major cause of lung cancer, the leading cause of cancer death, and of chronic obstructive pulmonary disease, the fourth leading cause of death in the United States. Using high-density gene expression arrays, we describe genes that are normally expressed in a subset of human airway epithelial cells obtained at bronchoscopy (the airway transcriptome), define how cigarette smoking alters the transcriptome, and detail the effects of variables, such as cumulative exposure, age, sex, and race, on cigarette smoke-induced changes in gene expression. We also determine which changes in gene expression are and are not reversible when smoking is discontinued. The persistent altered expression of a subset of genes in former smokers may explain the risk these individuals have for developing lung cancer long after they have discontinued smoking. The use of gene expression profiling to explore the normal biology of a specific subset of cells within a complex organ across a broad spectrum of healthy individuals and to define the reversible and irreversible genetic effects of cigarette smoke on human airway epithelial cells has not been previously reported. The left hippocampus was dissected out of a male, 12 month-old mouse overexpressing amyloid precursor protein with the Swedish mutation (Tg2576; APPSw). Total RNA was extracted and the data were analyzed with MAS 5.0 and scaled to 2500. Source GEO sample is GSM26708 Last updated (according to GEO): May 27 2005 861 Gland structure Expression profiling of spinal cord section (T9) extracted from rats 14d following mild injury Source GEO sample is GSM31200 Last updated (according to GEO): May 27 2005 Replicate3_Voxel F8 MGJZ030312066Bplacenta 54h-Control replication 2 Keywords = preimplantation Keywords = development Source GEO sample is GSM14705 Last updated (according to GEO): May 28 2005 with mental retardation 241 263 TS13 sample 2 (cerebrum) Animal models represent a very useful tool for the study of depressive-like behaviour and for the evaluation of the therapeutic efficacy of antidepressants. Nevertheless, gene expression patterns of these different animal models and whether genes classically associated to human major depression are present in these genetic profiles remain unknown. Gene expression was evaluated in an animal model of depression: olfactory-bulbectomized rats. Gene expression analyses were carried out using the Affymetrix® GeneChip® technology. Last Updated (by provider): Dec 11 2007 Contributers: Marcel Ferrer-Alcon Javier Meana Alvaro Diaz David Arteta Angel Pazos Rebeca Diez-Alarcia Leyre Uriguen Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy Keywords = pathological hypertrophy Keywords = rat Keywords = heart failure Keywords = cardiomyopathy Source GEO sample is GSM11888 Last updated (according to GEO): May 28 2005 97 upon DNA Damage 83 20 0 human caudate nucleus 19 0 Head and neck cancer 1000 Brain hip_1009_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 12 Parietal Lobe 24 Leukemic fractions of ID10 AML patient have been hybridized. Source GEO sample is GSM103099 Last updated (according to GEO): Feb 26 2007 with heart failure 125 143 853 Blood Cells Gonadectomized Dahl-Iwai Male LowSalt Cortex rat8 gdahl_cortexr_k_GX_8c_051702 Voxel D2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1407 Last updated (according to GEO): Nov 21 2005 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13151.gif Source GEO sample is GSM79717 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145652 Last updated (according to GEO): Nov 20 2006 C3H/HeJ Hippocampus B hypothalamus Source GEO sample is GSM18591 Last updated (according to GEO): May 27 2005 5 0 Spleen RNA was amplified and converted into cDNA with the NuGEN Ovation? Biotin RNA Amplification and Labeling System {http://www.nugentechnologies.com/html/03_products2.html} Source GEO sample is GSM83046 Last updated (according to GEO): Jun 22 2006 Activated Source GEO sample is GSM176002 Last updated (according to GEO): Apr 09 2007 CBA/J_male_hypothalamus CLL-68 || lc4b068 Head and neck cancer Source GEO sample is GSM155704 Last updated (according to GEO): Apr 24 2007 Tunica submucosa 1000 D_U133Plus_70_nAcc Hypertensive disease 1000 Control Source GEO sample is GSM175962 Last updated (according to GEO): Apr 09 2007 Colon 1000 B6:2-5 retina PC 6Hr rat 3586 blood vs. 150mg/kg APAP 6Hr rat 3590 blood -_6503_batch1 on NHGRI-6.7k 1000 Brain RNA isolated from post-mortem tissues Source GEO sample is GSM6834 Last updated (according to GEO): May 28 2005 IGF1 and IGF1 receptors (IGF1R) are present in the adult heart and have been shown to be essential for myocardial performance. Insulin-like growth factor 1 (IGF1) is produced in numerous tissues particularly by the liver in response to growth hormone stimulation and is an important factor in the regulation of post-natal growth and development. We have generated and characterized transgenic mice over-expressing the IGF1R. We crossed IGF1R transgenic mice with dominant negative (dn)PI3K (p110) and with constitutively active (ca)PI3K(p110) transgenic mice. Expression profiling was performed on the ventricles of IGF1R, IGF1R-caPI3K, IGF1R-dnPI3K, caPI3K, dnPI3K transgenic female mice at 3 months of age. Non-transgenic littermates were used as controls. Keywords = insulin growth factor, IGF, cardiac, hypertrophy Source GEO sample is GSM18361 Last updated (according to GEO): May 27 2005 39 21 from mammary glands Impact of commensal microbiota on murine gastrointestinal tract gene ontologies. 17 7 hippocampus Brain 1000 660 mesenchymal stem cell 639 31 20 Whole thymus Brain 861 Primary Neoplasm 1000 4089 4084 liver PGA-HBE-AsthAir0h-1aA-S2 of somatomotor cortex 21 41 human frontal cortex Source GEO sample is GSM86932 Last updated (according to GEO): Feb 08 2006 Fertilized egg replication 4 865 Disorder of artery 1000 Coronary Arteriosclerosis Frontal Cortex Source GEO sample is GSM107897 Last updated (according to GEO): Jun 06 2006 861 Colon BAL_40_A0B0 1000 Brain 861 Neoplasm JF1/Ms_male_hypothalamus 1000 Brain Lung tissue from C57BL/6 mice that were always fed by 2/3 and sacrificed 2hrs after the onset of calorie-restriction in calorie-restricted mice. Lot batch = Source GEO sample is GSM4040 Last updated (according to GEO): May 28 2005 Cytoplasm 1000 of parieto-occipital cortex 64 90 Primary tumor 19 32 HUVEC isolate 55 rich media VEGF-A 24hours cf. #3 Source GEO sample is GSM12897 Last updated (according to GEO): May 28 2005 Tissue transferred into RNAlater within 30 minutes of removal, and frozen at -20C Source GEO sample is GSM9099 Last updated (according to GEO): May 28 2005 861 Communicable Diseases 320 291 of human oral epithelial cells /NJ periaqueductal gray rep2 3 30 91 from the bone marrow 72 Male Sprague-Dawley albino rats (Charles River) initially weighting approximately 200 grams were randomly assigned to one of the following: 1) olanzapine (2 mg/kg/day, I.P.) (N=20) or 2) Saline (N=20) and administered olanzapine or saline for 21 days. Frontal cortex (N=4/group) was dissected and homogenized for microarray, QPCR and western blotting following previous methods (Fatemi et al. 2003; Brooks et al. 2003). RNA isolation, cDNA preparation, microarray hybridization and QPCR followed previous methods (Brooks et al. 2003). Keywords = olanzapine Keywords = frontal cortex Source GEO sample is GSM48580 Last updated (according to GEO): Apr 10 2006 the ventricular 1095 1109 Heart Ventricle 1000 1000 Kidney E6, E7, bone marrow cell Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell 60min (set1) 567 548 the descending colon Heart Atrium 1000 Normal Source GEO sample is GSM176312 Last updated (according to GEO): Apr 09 2007 3240 tumor cells 3250 Control 10 3 0 Skin Saphenous Vein 1 Normal Brain 861 spleen_4 5 0 brain 861 Cerebellum Expression profiling of somatomotor cortex extracted from rats at 28d following moderate injury Source GEO sample is GSM41710 Last updated (according to GEO): May 27 2005 1000 Cerebellum CAD_replicate21 Lymphoma (Burkitts Daudi) [JunctionChip 4 of 5] Endometrium-Normal 7 Primary Neoplasm 1000 HDMTX-7 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-beta (IFN beta) for 120min Source GEO sample is GSM5596 Last updated (according to GEO): May 27 2005 20 0 human caudate nucleus Cockayne syndrome B wt-rescued cell Source GEO sample is GSM226623 Last updated (according to GEO): Sep 04 2007 Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM182005 Last updated (according to GEO): Apr 13 2007 total RNA from biosource CC#4* Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92475 Last updated (according to GEO): Jan 13 2006 wild type placebo 48h, biological rep1 spinal cord 13 23 Cerebral cortex 1000 872 Blood Cells from the buccal mucosa 584 606 M_U133A_14_DLPFC_R CNS-SpinalCmod-Adult-48h-3B-s2 Brain 1000 2737 tumor cells 2747 of mouse brain 9 23 Cerebral cortex 1000 Time course analysis of response to HCMV infection human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155052 Last updated (according to GEO): Jun 04 2007 "Sample 68, <5 yr survival(14 months) age 50 erp no" on vantveer-oligo parietal_lobe_4 5 0 brain brain, cerebellum: RNA#34*_le1 Erythrocytes 1000 C57 whole brain 3B M_U133Plus_121_AnCg Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour.This animal was sacrificed at 8 hours after lights on.Original sample code = CM42A Source GEO sample is GSM227317 Last updated (according to GEO): Sep 10 2007 B382 on Affymetrix GeneChip Human Full Length Array HuGeneFL Plasma 861 AKR/J Amygdala D Epithelial cells from Astmatic subject were removed by dissection and digestion from bronchi of donor long tissue from normal subject. Source GEO sample is GSM3909 Last updated (according to GEO): May 27 2005 Ovarian Diseases 877 PGA-E14.5_2 of the postmortem brains 676 700 spinal_cord_4 Source GEO sample is GSM80787 Last updated (according to GEO): Mar 31 2006 B6:4-5 striatum DBA/2J_female_hypothalamus of somatomotor cortex 21 41 978 971 amygdala 1000 Demyelinating Diseases Brain 861 human caudate nucleus Source GEO sample is GSM86865 Last updated (according to GEO): Feb 08 2006 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15392.gif Source GEO sample is GSM84170 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145801 Last updated (according to GEO): Nov 20 2006 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12956.gif Source GEO sample is GSM79938 Last updated (according to GEO): Sep 22 2006 db/db 16 wk 3 Diabetes Mellitus 1000 901 Caudate nucleus structure Small cell carcinoma of lung 888 7 cortex 12 Monocyte-derived dendritic cells (DCs) and macrophages (Ms) generated in vitro from the same individual blood donors were exposed to 5 different pathogens, and gene expression profiles were assessed by microarray analysis. Responses to Mycobacterium tuberculosis and to phylogenetically distinct protozoan (Leishmania major, Leishmania donovani, Toxoplasma gondii) and helminth (Brugia malayi) parasites were examined, each of which produces chronic infections in humans yet vary considerably in the nature of the immune responses they trigger. In the absence of microbial stimulation, DCs and Ms constitutively expressed approximately 4000 genes, 96% of which were shared between the 2 cell types. In contrast, the genes altered transcriptionally in DCs and Ms following pathogen exposure were largely cell specific. Profiling of the gene expression data led to the identification of sets of tightly coregulated genes across all experimental conditions tested. A newly devised literature-based clustering algorithm enabled the identification of functionally and transcriptionally homogenous groups of genes. A comparison of the responses induced by the individual pathogens by means of this strategy revealed major differences in the functionally related gene profiles associated with each infectious agent. Although the intracellular pathogens induced responses clearly distinct from the extracellular B malayi, they each displayed a unique pattern of gene expression that would not necessarily be predicted on the basis of their phylogenetic relationship. The association of characteristic functional clusters with each infectious agent is consistent with the concept that antigen-presenting cells have prewired signaling patterns for use in the response to different pathogens. OBX Day 5,# 3 1000 Brain Normal Source GEO sample is GSM176323 Last updated (according to GEO): Apr 09 2007 M_U133A_44_HC Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A61_8 months_replicate 2 1000 Pancreas Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118542 Last updated (according to GEO): Jul 11 2006 ileum 0 4 ATCC number CRL-1502 Source GEO sample is GSM6817 Last updated (according to GEO): May 27 2005 to the spinal cord 46 63 865 Disorder of artery V5-P564 B305 Immature DCs treated with IFNa Wild type voxel A1 Statistical analysis of MPSS measurements: application to the study of LPS-activated macrophage gene expression. 1000 Prostate G30 neurons from somatosensory cortex Source GEO sample is GSM63028 Last updated (according to GEO): Dec 01 2005 dorsal root ganglion fisher1 whole tissue, pool of 5 animals, 16 weeks old, male Fisher dorsal root ganglion file:p3970w Source GEO sample is GSM15187 Last updated (according to GEO): May 28 2005 Lung tissue from C57BL/6 mice calorie restricted by 2/3 and sacrificed 96hrs after the onset of calorie restriction. Lot batch = Source GEO sample is GSM4032 Last updated (according to GEO): May 28 2005 ileum 1000 Trigeminal ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until enough tissue was harvested to be pooled by genotype. Approximately 10-12 ganglia were pooled for a single analysis, which was extracted using the RNeasy system (Qiagen). Source GEO sample is GSM89134 Last updated (according to GEO): Dec 23 2005 Osteoblasts 1000 Sample 109 on vantveer-oligo Cells were either prestimulated (1_X) or not (0_X) for 18h with 100 ng/ml LPS. Media was exchanged and after 2h rest, cells either restimulated (X_1) or not (X_0) with again 100 ng/ml LPS. This resulted in 4 experimental conditions: 0_0, 0_1, 1_0 and 1_1. There were 3 biological replicates done, resulting in 12 arrays altogether. Source GEO sample is GSM213693 Last updated (according to GEO): Aug 01 2007 CVB3_V-7h M_95A_2846_CB_1_GS M_U133A_28_HC Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:198, Count:32 Corner- Avg:34063, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:16.661921,SFGene:All Background:Avg:350.18,Stdev:6.94,Max:371.2,Min:338.0 Noise:Avg:9.79,Stdev:0.45,Max:11.9,Min:8.8 RawQ:13.14 Keywords = ALL Source GEO sample is GSM3487 Last updated (according to GEO): May 27 2005 Lamina Propria 1000 48 33 for 72hrs- lungs Testis 861 Blood 861 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11298 Last updated (according to GEO): May 28 2005 861 Brain Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11510 Last updated (according to GEO): May 28 2005 PBMCs-Type 2 Diabetes-T2D_3_New Heart 1000 Basal- 0 5 brain 0 5 Epithelial ovarian cancer 1000 Osteoblasts 1000 CNS-SpinalC-30mAdult-1A-s2 0 Lung tissue 10 brain 0 5 Nose 1000 Neostriatum 1000 Spleen vs BLC Treated B cell 240min (set2) Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226164 Last updated (according to GEO): Nov 02 2007 pfc_1009_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 1000 Amygdaloid structure Gene expression data from mouse colon Source GEO sample is GSM198114 Last updated (according to GEO): Aug 22 2007 of parieto-occipital cortex 222 249 901 frontal lobe Medulla 861 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15560.gif Source GEO sample is GSM84146 Last updated (according to GEO): Sep 22 2006 AT1-hTERT_1.5Gy_2h_C3_21711 Liver 1000 plasma cells 50 61 Five different human MPNST cell lines, mock treated or infected with G207. Source GEO sample is GSM215812 Last updated (according to GEO): Aug 07 2007 865 Disorder of artery Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28800 Last updated (according to GEO): May 27 2005 HTI-286 in docetaxel-refractory prostate cancer_docet (Biological Replicate2) Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM107994 Last updated (according to GEO): Jun 06 2006 none Source GEO sample is GSM149521 Last updated (according to GEO): Jan 03 2007 Changes in mouse liver mRNA profiles following intra-peritoneal cytokine injection. One of 2 replicates of Interferon-Gamma-/- mice, injected with Interferon Gamma, and killed after 4h. Source GEO sample is GSM5951 Last updated (according to GEO): May 27 2005 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92347 Last updated (according to GEO): Jan 13 2006 1000 Ovary Expression profiling of laminectomized raphe at 28d in rats Source GEO sample is GSM41533 Last updated (according to GEO): May 27 2005 of testicular seminoma 25 46 the ventricular 1095 1109 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68336 Last updated (according to GEO): Jul 07 2006 of multiple sclerosis 1593 1613 129S6/SvEvTac amygdala rep1 67 44 from Human Somatic Cells Muscle Source GEO sample is GSM4261 Last updated (according to GEO): May 27 2005 embryonic cortical neuron treated with CSS Source GEO sample is GSM49559 Last updated (according to GEO): May 29 2005 Blood Test (Blinded) Sample Source GEO sample is GSM130041 Last updated (according to GEO): Sep 18 2007 199-97_Adeno_p DRG_control_12h_rep2 WGACON-79 gene expression data from ODC mouse skin samples Source GEO sample is GSM216663 Last updated (according to GEO): Aug 09 2007 HNC2907 f2#78 versus pool Mouse Brain tissue Blood 861 A/J Amygdala E Liver Test (Blinded) Sample Source GEO sample is GSM130078 Last updated (according to GEO): Sep 18 2007 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120683 Last updated (according to GEO): May 14 2007 Gene expression data from PD14 Foxo3 wild-type ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203832 Last updated (according to GEO): Aug 02 2007 Timed pregnant C57Bl6 mice were exposed to ethanol during gestational day 15 to day 18 and ethanol exposed fetuses were delivered by cessarian section on gestational day 19. Alcohol exposed fetuses were compared to control timed preg Source GEO sample is GSM116856 Last updated (according to GEO): Jul 03 2006 Muscle 861 78 66 Control blood 73 54 of malignant glioma 40 21 from the hippocampus Midbrain 6 Normal Gene expression data from rat lungs exposed to FiO2 of ~9.5% and SU-5416 (hypoxia-SU-5416). Source GEO sample is GSM184880 Last updated (according to GEO): Jun 14 2007 Recurrent Carcinoma 875 plasma cells 50 61 Malignant neoplasm of cervix uteri 1000 B226 Immature DCs treated with anti-FcgRIIB antibody for 24 hrs 40 21 from dorsal pancreas U937 x SR21 #2 KO_sham_med_2 Normal Source GEO sample is GSM176121 Last updated (according to GEO): Apr 09 2007 RNA sample 2 from motor neurons of SOD1 mice Treatment, type=double_round_amplification, description=T7-based two round of RNA amplification Source GEO sample is GSM92522 Last updated (according to GEO): Jan 13 2006 194 168 the ventral tegmental area human cerebellum Source GEO sample is GSM87132 Last updated (according to GEO): Feb 08 2006 CF knockout LFCF CHN309 amygdala 0 7 rat kidney at week 4 post birth, rep1 1000 Cerebral cortex CCAT Full Length Rep A2 f2#313 versus pool Mouse Brain tissue 861 Cardiomyopathies Gene expression data from aneurismal tissues obtained from patients with bicuspid valves. Source GEO sample is GSM116786 Last updated (according to GEO): Jun 28 2006 of underlying brain 171 190 no additional Source GEO sample is GSM199200 Last updated (according to GEO): Jun 08 2007 15 0 human cerebellum 40 21 from skeletal muscle C57BL/6J CHR, Rep1 Hippocampus 1000 D_U133A_71_DLPFC 9 0 cerebellum Lymphoblastoid Cell Line for Individual 8121.3 log phase Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10168.gif Source GEO sample is GSM79681 Last updated (according to GEO): Sep 22 2006 Microdissected area # 2 of 1589 tumor GSE7826 29 0 cerebral cortex wistar ky 3913 861 Blood normal testis 54 66 5 0 testis NA12847 growth 1 CNS-SMTC_Mod4h-1A-s2 NCI60.30_LABEL34EXTRACT33SUB3 Source GEO sample is GSM134143 Last updated (according to GEO): Aug 06 2007 Ovarian Diseases 877 Lung 1000 1000 Amygdaloid structure Epithelial Cells 901 660 mesenchymal stem cell 639 Gene expression data from postmorten brain regions Source GEO sample is GSM145117 Last updated (according to GEO): Nov 20 2006 Cerebral cortex 1000 1000 Mammary Neoplasms NCI60.37_LABEL41EXTRACT40SUB3 Source GEO sample is GSM134177 Last updated (according to GEO): Aug 06 2007 pfc_1031_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Plasma 861 Parkinson Disease 1000 Normal Source GEO sample is GSM175866 Last updated (according to GEO): Apr 09 2007 Transitional epithelium 1000 spleen 299 304 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13425.gif Source GEO sample is GSM79663 Last updated (according to GEO): Sep 22 2006 "Sample 62, <5 yr survival(10 months) age 36 erp no" on vantveer-oligo 5 0 brain Patient2F 5 0 brain Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225380 Last updated (according to GEO): Aug 31 2007 Gonadectomized Dahl-Iwai Female LowSalt OuterMedulla rat3 gdahl_medullar_k_GX_3om_050702 1000 Pancreas GC (HKG6T) 5 0 brain Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151992 Last updated (according to GEO): Feb 06 2007 Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Malignant Neoplasms 861 occipital_lobe_1 Source GEO sample is GSM80772 Last updated (according to GEO): Mar 31 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145846 Last updated (according to GEO): Nov 20 2006 mouse cerebral cortex from COX-2 knockout Source GEO sample is GSM121431 Last updated (according to GEO): Jan 31 2007 MO_control_0min_Patient15 Gene expression data from the right forebrain of C57BL mouse received Haloperidol oral treatment for twelve weeks. Source GEO sample is GSM148671 Last updated (according to GEO): Dec 12 2006 Aldosterone-producing adenoma (APA1) Heart Septal Defects, Atrial 1000 CNS-SpinalCmod-Adult-48h-1A-s2 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153362 Last updated (according to GEO): Dec 27 2006 Primary tumor 19 32 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 3 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM11035 Last updated (according to GEO): May 28 2005 brain, hippocampus: Hippocampus 8_le1 Macrophage 14smi058 "Sample 95, BRCA1 mutation(49 months) age 45 erp yes" on vantveer-oligo Fibroblasts 861 1000 Brain human cerebellum Source GEO sample is GSM87169 Last updated (according to GEO): Feb 08 2006 VDXOXFU_1373 861 Cerebral cortex myometrium_10 Source GEO sample is GSM80720 Last updated (according to GEO): Mar 31 2006 1BJZ02083092a_Skeletal_Muscle_Psoas Liver 1000 hg_NY58 861 Heart 3AJZ02053101_HBEC 7 0 prostate spinal cord 0 11 Conventional Jejenum 2 Hep2_37_rep1 none Source GEO sample is GSM149565 Last updated (according to GEO): Jan 03 2007 Normal Breast Thyroid Gland 3 Normal PriG_Expt2_Day0_rep1 Nasal Epithelium 901 none Source GEO sample is GSM244564 Last updated (according to GEO): Nov 23 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145057 Last updated (according to GEO): Nov 20 2006 Plasma 861 861 Brain Heart 1000 C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P10 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25128 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145599 Last updated (according to GEO): Nov 20 2006 Analysis of prefrontal cortex from 3 biological replicates of C57BL/6J mice at four Zeitgeber Times (ZT 3, 9, 15, and 21). Source GEO sample is GSM240420 Last updated (according to GEO): Oct 30 2007 Gene expression data Source GEO sample is GSM183179 Last updated (according to GEO): Jul 30 2007 /3T3 fibroblasts 295 310 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 1009 left_liver_lobe KT1013_N none Source GEO sample is GSM149612 Last updated (according to GEO): Jan 03 2007 1000 Malignant Neoplasms MO_control_0min_Patient16 ovarian tumor: endometrioid Source GEO sample is GSM139413 Last updated (according to GEO): Apr 09 2007 0 Human Cortex 11 29 0 Adrenal cortex [JunctionChip 3 Wild type inbred mice Source GEO sample is GSM83041 Last updated (according to GEO): Nov 10 2005 27 0 Substantia nigra normal rep9 bunge-affy-arabi-162779 Microarray technology was used to examine gene expression changes following contusive injury of the adult rat spinal cord. To obtain a global understanding of the changes triggered by the injury, differential gene expression was examined spatially, using tissue samples from the epicenter of injury as well as 1 cm rostral and 1 cm caudal to the epicenter, and temporally, at 3 h, 24 h, 7 days, and 35 days post-injury. To filter out gene expression changes that were due to the laminectomy, samples of contused tissue were compared to laminectomy-only controls. We took advantage of four different, complementary methods of data analysis to detect differentially expressed genes. We have identified functional groups of genes that are differentially regulated in our model, including those associated with apoptosis, cell cycle, inflammation, and cholesterol metabolism. Our analysis has led to the identification of novel potential therapeutic targets within each group of genes that is discussed. 79 60 in human fibroblasts Lymphoblastoid Cell Line for Individual 8174.4 log phase Spleen vs Interferon-beta (IFN beta) Treated B cell 30min (set2) Epithelium 861 Understanding patterns of gene-expression variation within and among human populations will provide important insights into the molecular basis of phenotypic diversity and the interpretation of patterns of expression variation in disease. However, little is known about how gene-expression variation is apportioned within and among human populations. Here, we characterize patterns of natural gene-expression variation in 16 individuals of European and African ancestry. We find extensive variation in gene-expression levels and estimate that approximately 83% of genes are differentially expressed among individuals and that approximately 17% of genes are differentially expressed among populations. By decomposing total gene-expression variation into within- versus among-population components, we find that most expression variation is due to variation among individuals rather than among populations, which parallels observations of extant patterns of human genetic variation. Finally, we performed allele-specific quantitative polymerase chain reaction to demonstrate that cis-regulatory variation in the lymphocyte adaptor protein (SH2B adapter protein 3) contributes to differential expression between European and African samples. These results provide the first insight into how human population structure manifests itself in gene-expression levels and will help guide the search for regulatory quantitative trait loci. 1000 Hippocampus brain, hippocampus: LH1_e1_le1 HCC (HK46) 9 0 Blood Test 1000 Spleen DLBC44 on Affymetrix GeneChip Human Full Length Array HuGeneFL Expression profiling of moderately injured raphe at 28d in rats Source GEO sample is GSM41594 Last updated (according to GEO): May 27 2005 We demonstrate that expression of key markers of keratinocyte differentiation is suppressed by exposure to sodium arsenite. Folate deficiency exacerbates this effect. In addition, cancer-related cell movement genes, and growth and proliferation genes are altered. Several redox-sensitive transcription factors are implicated in mediating these gene expression changes due to arsenic treatment and folate deficiency. Last Updated (by provider): Aug 09 2007 Contributers: James W Allen Don A Delker Gail M Nelson William O Ward Barbara C Roop Thomas O'Brien Yan Chen Kirk T Kitchin Gene J Ahlborn Michael J Kohan none Source GEO sample is GSM149650 Last updated (according to GEO): Jan 03 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11465 Last updated (according to GEO): May 28 2005 GSE7956 na Source GEO sample is GSM181279 Last updated (according to GEO): Apr 10 2007 Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242060 Last updated (according to GEO): Dec 04 2007 Timepoint8 861 Muscle Human aging is associated with skeletal muscle atrophy and functional impairment (sarcopenia). Multiple lines of evidence suggest that mitochondrial dysfunction is a major contributor to sarcopenia. We evaluated whether healthy aging was associated with a transcriptional profile reflecting mitochondrial impairment and whether resistance exercise could reverse this signature to that approximating a younger physiological age. Skeletal muscle biopsies from healthy older (N = 25) and younger (N = 26) adult men and women were compared using gene expression profiling, and a subset of these were related to measurements of muscle strength. 14 of the older adults had muscle samples taken before and after a six-month resistance exercise-training program. Before exercise training, older adults were 59% weaker than younger, but after six months of training in older adults, strength improved significantly (P<0.001) such that they were only 38% lower than young adults. As a consequence of age, we found 596 genes differentially expressed using a false discovery rate cut-off of 5%. Prior to the exercise training, the transcriptome profile showed a dramatic enrichment of genes associated with mitochondrial function with age. However, following exercise training the transcriptional signature of aging was markedly reversed back to that of younger levels for most genes that were affected by both age and exercise. We conclude that healthy older adults show evidence of mitochondrial impairment and muscle weakness, but that this can be partially reversed at the phenotypic level, and substantially reversed at the transcriptome level, following six months of resistance exercise training. Ventral tegmental area 21 43 Replicate2_Voxel C8 Coronary artery 901 861 Retina total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Sphingosine-1-phosphate for 240min Source GEO sample is GSM5754 Last updated (according to GEO): May 27 2005 40 21 from dorsal pancreas VP16-CREB hippocampus region Source GEO sample is GSM88938 Last updated (according to GEO): Jan 04 2006 Standard Affymetrix Protocol Source GEO sample is GSM16474 Last updated (according to GEO): May 28 2005 GBM Treatment, type=remove Source GEO sample is GSM99590 Last updated (according to GEO): Apr 21 2006 O377 mutant mouseline with progressive lens opacity. Mutation mapped to distal chromosome 5 and finally characterized by an A - T bp substiution at the end of intro 5 of Crybb2. Crybb2 expression also found in olfactory bulb, pyramidal cells of the cortex, hippocampus, Purkinje and stellate cells of cerebellum. Last Updated (by provider): Dec 07 2005 Contributers: Johannes Beckers Marion Horsch Graw Jochen Koustav Ganguly Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13142.gif Source GEO sample is GSM79682 Last updated (according to GEO): Sep 22 2006 013102_HF_289FL UV radiation-induced DNA damage Prefrontal Cortex Source GEO sample is GSM105450 Last updated (according to GEO): Apr 17 2006 67 40 with coronary artery disease Date 2/13/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : headfold Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 2.5 mg/kg Time : 6.0 hrs post-injection Intervention : none Risk: benchmark dose modeled for 5% increased risk of microphthalmia Conditional biomarker: post-injection interval beyond p53 protein induction Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 16-20 headfolds pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = embryo Keywords = microphthalmia Lot batch = AM036 Source GEO sample is GSM12076 Last updated (according to GEO): May 28 2005 Lymphoblastoid Cell Line for Individual 8161.3 log phase Neostriatum 1000 Parkinson Disease 1000 D_U133Plus_117_HC Macrophage 14smi046 AMM_0_0_Male2_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111845 Last updated (according to GEO): Nov 21 2006 26 15 endometrioid Primary Neoplasm 1000 CN530 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15722 Last updated (according to GEO): May 28 2005 861 Uterus brain 0 5 1 of 3 replicates in treatment group Source GEO sample is GSM206043 Last updated (according to GEO): Jun 29 2007 861 Encephalitis 1000 Spleen Gene expression data from postmorten brain regions Source GEO sample is GSM145229 Last updated (according to GEO): Nov 20 2006 DCN_P3_C Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132549 Last updated (according to GEO): Feb 26 2007 in mouse hearts 40 54 none Source GEO sample is GSM149610 Last updated (according to GEO): Jan 03 2007 Brain 861 Central gray substance of midbrain 861 545 533 in cirrhosis Fibroblasts 861 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD12 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD12 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36680 Last updated (according to GEO): May 27 2005 plasma cells 50 61 17 7 hippocampus 1000 Retina n/a Source GEO sample is GSM177957 Last updated (according to GEO): Jun 11 2007 129:4-3 -4-5 BNST OA 3 626 605 of the nervous system 1000 Retina hrs nasal epithelium 1127 1147 Lung tissue from C57BL/6 mice calorie restricted by 2/3 and sacrificed 48hrs after the onset of calorie restriction. Lot batch = Source GEO sample is GSM4026 Last updated (according to GEO): May 28 2005 Cardiac 523 530 brain 0 5 1000 Kidney Epidermis 1000 Brain 1000 171 156 Alzheimer's mice Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3519.gif Source GEO sample is GSM93117 Last updated (according to GEO): Sep 22 2006 861 Cerebral cortex HDMTX-DX-8 Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Enghigh 3 MDA Mb231 1h 1 Control Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68349 Last updated (according to GEO): Jul 07 2006 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50634.gif Developmental Stage: E6.25 Source GEO sample is GSM229811 Last updated (according to GEO): Nov 06 2007 861 Blood olfactory bulb 0 13 EAE, placebo treated #5 Neoplasm 861 Normal Source GEO sample is GSM176231 Last updated (according to GEO): Apr 09 2007 Lymphoblastoid Cell Line for Individual 8080.3 log phase of the stria terminalis rep2 21 48 no additional Source GEO sample is GSM199299 Last updated (according to GEO): Jun 08 2007 SK-MEL-28 hgu95a 430A2_2045_43_KO_sham_medulla Source GEO sample is GSM242699 Last updated (according to GEO): Nov 15 2007 cy5:SHR treated w/ nifedipine and then washed out, biological rep 1r; cy3:pool of 6 WKY control rats Heart 861 1000 Structure of superior cervical ganglion 724-1 Skeletal muscle biopsy was obtained before a two-hours of hyperinsulinaemic (40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172136 Last updated (according to GEO): Feb 28 2007 10 0 hippocampus I_U133Plus_38_AnCg na Source GEO sample is GSM181283 Last updated (according to GEO): Apr 10 2007 861 Cerebral cortex Normal Source GEO sample is GSM176012 Last updated (according to GEO): Apr 09 2007 32 12 frontal temporal lobe 19 0 human frontal cortex with autism spectrum disorder 37 65 Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200629 Last updated (according to GEO): Jun 12 2007 4 Treatment groups: A) Uninfected B) Infected 6 weeks prior with GFP-expressing recombinant lentivirus C) Infected 6 weeks prior with Htt-N171-19Q-expressing recombinant lentivirus D)Infected 6 weeks prior with Htt-N171-82Q-expressing recombinant lentivirus Last Updated (by provider): Oct 16 2006 Contributers: Beate Sick Patrick Aebischer Diana Zala Ruth Luthi-Carter Etienne Regulier Nicole Deglon CNS-SMTC_Mod4h-3C-s2 in papillary thyroid carcinoma 16 45 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195298 Last updated (according to GEO): Sep 13 2007 acute myeloid leukemia Source GEO sample is GSM227434 Last updated (according to GEO): Sep 12 2007 Brain Injuries 1000 861 Cerebral cortex FVB/NJ Frontal Cortex A Brain 1000 5_hypothalamus_6hrs_sleep_deprivation_#149 1000 Solid tumor 19 of muscle tissue 34 Brn3a Heterozygote TG e13.5 U74Av2 1 Whole blood 0 10 heart 1169 1173 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188823 Last updated (according to GEO): Jun 06 2007 1000 Cardiomyopathies 10 Bone marrow 0 Aortic stiffness Whole blood 0 10 olfactory epithelium wild type mouse 16 hpO Source GEO sample is GSM80192 Last updated (according to GEO): Oct 26 2005 Transitional epithelium 1000 Skeletal muscle structure 901 861 Neoplasm Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19233 Last updated (according to GEO): May 27 2005 861 Brain human frontal cortex Source GEO sample is GSM87020 Last updated (according to GEO): Feb 08 2006 Brain 861 Ovary 10 Normal Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231049 Last updated (according to GEO): Sep 26 2007 CurrentSmoker 29 1000 Spleen T7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A lateral hypothalamus no access to cocaine replicate 4 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155046 Last updated (according to GEO): Jun 04 2007 Brain 861 BCR-ABL-#5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Ovary 1000 861 Brain 1000 Hippocampus Wild type P104 mouse visual cortex ipsilateral to monocular enucleation Source GEO sample is GSM97219 Last updated (according to GEO): Feb 17 2006 Nerve 1000 Spleen 1000 Infection 861 B40 on NCI-7.6k Antibodies 1000 111 89 by ectodermal dysplasia Eye 966 GSE4037 7 0 prostate Female reproductive neoplasm malignant NOS 1000 Ovarian_Tumor_Mucinous_CHTN-OM-007 Heart Ventricle 1000 14 0 G3 Ciliary Body PriG_5%O2_Expt3_Day17_rep1 "14 hr Hela Double Thymidine, exp3" Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188817 Last updated (according to GEO): Jun 06 2007 1000 Neoplasm Metastasis Myocardium 861 Prefrontal Cortex Source GEO sample is GSM105467 Last updated (according to GEO): Apr 17 2006 brain, Left frontal Lobe: Extract11_le1 Control rat 7 substantia nigra Source GEO sample is GSM32169 Last updated (according to GEO): May 27 2005 Sample12, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53263 Last updated (according to GEO): Jul 06 2005 1000 Heart failure AD control Treatment, type=dissect Source GEO sample is GSM119676 Last updated (according to GEO): Jul 10 2006 55 31 out of mouse bone marrow eTat - Hu6hr - 2 5 0 brain Subject code A22EB this sample is from a 16-week-old male normal mouse gastrocnemius muscle Source GEO sample is GSM4373 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145475 Last updated (according to GEO): Nov 20 2006 5 0 brain Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242059 Last updated (according to GEO): Dec 04 2007 B6 day 1, biological rep 3, tech rep 2 Carcinoma, Transitional Cell 923 861 Blood 14 7 amygdala Brain 1000 Liver (HCV+, SF30) 16 CN A 1000 Blood Vessels Communicable Diseases 1000 Whole Brain 62 72 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc121 Source GEO sample is GSM1857 Last updated (according to GEO): Nov 21 2005 Voxel F1 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1421 Last updated (according to GEO): Nov 21 2005 plasma cells 332 344 brain, Entorhinal Cortex: 00 28 normal_e1_le1 B10.PL mice with experimental autoimmune encephalomyelitis (MS model) were treated with either placebo or 200 ng 1,25(OH)2D3. Six hours later, the spinal cords were harvested and mRNA extracted for analysis. Naive mice served as controls. Keywords = Experimental autoimmune encephalomyelitis Keywords = multiple sclerosis Keywords = 1 Keywords = 25(OH)2D3 Source GEO sample is GSM13052 Last updated (according to GEO): May 28 2005 Hippocampus 1000 /Ovary 10 Disease 11 27 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201814 Last updated (according to GEO): Jun 20 2007 CVB3_S-5h 660 mesenchymal stem cell 639 Neoplasm 861 Virus Diseases 1000 Gene expression profiling of bronchoalveolar lavage cells in acute lung rejection. dentate granule cells Source GEO sample is GSM35836 Last updated (according to GEO): May 27 2005 Bone marrow, Mesenchymal stem cells: T2-2-101103_e1_le1 AD-228t2-A152-4 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A female mhm chip 42 F9_3, mouse, FVB, control (non-infected), 9 day time matched control_rep 3 Accumbens 7 Normal in mdx skeletal muscle. 1080 1103 861 Brain 12 Temporal Lobe 24 of schizophrenia 1798 1813 brain 0 5 5 0 Spleen Brain_MGlio_10_Malignant Glioma on Affymetrix GeneChip Human Full Length Array HuGeneFL Heart 861 1000 Brain no doxycycline, mutant Source GEO sample is GSM213369 Last updated (according to GEO): Jul 26 2007 I_U133A_49_CB C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P28 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25142 Last updated (according to GEO): May 27 2005 861 Blood Colorectal Adenocarcinoma Source GEO sample is GSM18866 Last updated (according to GEO): Sep 25 2006 H117 CN B olfactory epithelium wild type mouse 48 hpO Source GEO sample is GSM80197 Last updated (according to GEO): Oct 26 2005 no additional Source GEO sample is GSM199298 Last updated (according to GEO): Jun 08 2007 Untreated versus treated (bortezomib) breast cancer cells. Source GEO sample is GSM120346 Last updated (according to GEO): Jul 20 2006 1000 Amyotrophic Lateral Sclerosis The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169495 Last updated (according to GEO): Feb 21 2007 861 Skin Abdominal Cavity 1000 f2#230 versus pool Mouse Brain tissue Tumor__Leukemia_AML_AML_(3,PK)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 861 Neoplasm of prion disease 19 34 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 2698 left_liver_lobe CHIPEXP_NAME: 230_2_050531tpj_54h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Isoproterenol TREAT_TOX_MECHANISM1: Heart_Cardiotoxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0.5 SAMPLING_TIME: 24 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197623 Last updated (according to GEO): Jun 01 2007 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181079 Last updated (according to GEO): Jul 12 2007 PLA2G2A and human gastric cancers Medulla Oblongata 861 1000 Brain Oat cell carcinoma 867 23 0 mammary epithelial cells Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162157 Last updated (according to GEO): Jun 12 2007 MGMH030212051Asmallintestine 13 0 Nervous System 50 41 mouse lung KHG-LG-9Av2-s2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gonadectomized Dahl-Iwai Female HighSalt OuterMedulla rat5 gdahl_medullar_k_GX_5om_050702 cerebellum wistar ky 3892 whole tissue, individual animal, 10 weeks old, male Wistar Kyoto cerebellum file:p3892w Source GEO sample is GSM15135 Last updated (according to GEO): Oct 28 2005 861 Cerebral cortex none Source GEO sample is GSM239843 Last updated (according to GEO): Dec 07 2007 VDXIGRU_306818 67 40 with coronary artery disease 254 238 of neural retinas between the LAD artery 266 287 Lymphoblastoid Cell Line for Individual 8044.4 log phase 1581 1570 PCOS oocytes 861 Cerebellum 861 Heart 207 199 infection SN:Human Glioblastoma Biopsy 10403 1000 Cerebellum Skeletal bone 861 Carcinoma, Large Cell 884 T-ALL-R5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Infection 1000 861 Cerebral cortex lung 141 145 kidney_cortex_1 Source GEO sample is GSM80686 Last updated (according to GEO): Mar 31 2006 352 347 brain MammLac_022RACIL_053.txt 376 367 Cerebellum Neoplasm 861 brain, Left frontal Lobe: Extract5_le1 Cerebellum 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145692 Last updated (according to GEO): Nov 20 2006 74 55 of hyperinsulinaemic amygdala 25 33 eTat - Hu9hr - 1 FVB/NJ bed nucleus of the stria terminalis rep2 1000 Mammary gland 1000 Brain Spleen vs Neuropeptide Y Treated B cell 60min (set2) 0029_1397_H95A2_KF-207_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Prostate Thyroid; Thyroid Keywords = mouse gene expression database Source GEO sample is GSM29444 Last updated (according to GEO): May 27 2005 Cochlear nucleus structure 901 83 of Turner syndrome 100 I_U133A_47_Amy 129:23-1,2,3 amygdala 1000 Aorta H9LMS00111002 1000 Skin Male C57Bl/6 mice (6 week old) were sham-operated and olfactory epithelium tissue collected 5 days post-operation. Total RNA was extracted from the olfactory epithelium tissue. Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol. Keywords = olfaction Keywords = neurogenesis Keywords = apoptosis Keywords = gene silencing Keywords = microarray, transcription factor Source GEO sample is GSM45678 Last updated (according to GEO): Oct 28 2005 032801_HF_321MB in ALS 165 171 human peripheral blood derived monocytes, 24 hour LPS stimulation, biological rep1 Source GEO sample is GSM127011 Last updated (according to GEO): Aug 15 2006 884 Glomerular Basement Membrane Primary tumor 19 32 n/a Source GEO sample is GSM178005 Last updated (according to GEO): Jun 11 2007 Spleen 0 5 Cardiac transgenesis with the tetracycline transactivator changes myocardial function and gene expression. 0 Lung tissue 10 Normal__Prostate_NLP10N on Affymetrix GeneChip Human 35K SubA Array Hu35k-A HMEC X HB2 (0164) Peripheral Nerves 851 post HCMV infection 68 86 Normal Source GEO sample is GSM175850 Last updated (according to GEO): Apr 09 2007 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211362 Last updated (according to GEO): Jul 18 2007 1000 Brain no additional Source GEO sample is GSM199263 Last updated (according to GEO): Jun 08 2007 SCG explant cultured for 65 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246057 Last updated (according to GEO): Dec 03 2007 ES cell line, RNA 68 Anterior nares 1000 1000 Amygdaloid structure Exp A_2, control (0mg/kg) CPF whole blood_101007 Lymphoblastoid Cell Line for Individual 8187.3 log phase 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14966 Last updated (according to GEO): Oct 28 2005 Spleen vs Neuropeptide Y Treated B cell 30min (set1) forebrain 7 15 HCC (HBV+, HK48) 1000 Structure of locus ceruleus CNS-SpinalCmod-Adult-12h-1A-s2 prostate Source GEO sample is GSM203323 Last updated (according to GEO): Jun 21 2007 Gene expression data from the neocortex of S1P2-knockout mouse Source GEO sample is GSM172938 Last updated (according to GEO): Mar 08 2007 861 Prostate 14 days age control RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis Source GEO sample is GSM10047 Last updated (according to GEO): May 28 2005 PGC-1a KO 2 RNA was amplified and converted into cDNA with the NuGEN Ovation? Biotin RNA Amplification and Labeling System {http://www.nugentechnologies.com/html/03_products2.html} Source GEO sample is GSM82892 Last updated (according to GEO): Jun 22 2006 Gene expression data from the neocortex of S1P3-knockout mouse Source GEO sample is GSM172951 Last updated (according to GEO): Mar 08 2007 212 201 of chromatin GSE7958 1000 Liver Heart 1000 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 6474 left_liver_lobe Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3878 Last updated (according to GEO): May 27 2005 Trigeminal_Ganglion Source GEO sample is GSM19005 Last updated (according to GEO): Sep 25 2006 Infection 1000 Skeletal bone 861 109 FC BA9 A Blood 1000 Infected with B. abortus 2308 and euthanized 3 days post-infection Source GEO sample is GSM155249 Last updated (according to GEO): Aug 08 2007 901 frontal lobe ventral_tegmental_area_4 E8.75_rep1 CNS-SpinalCmod-Adult-12h-1B-s2 CT3 Whole blood 0 10 Gene expression data from postmorten brain regions Source GEO sample is GSM145014 Last updated (according to GEO): Nov 20 2006 052401_HF_357CB male C57BL6, double amplification Source GEO sample is GSM5417 Last updated (according to GEO): Mar 17 2006 Gene expression data from mouse primary visual cortex Source GEO sample is GSM101726 Last updated (according to GEO): Jun 15 2006 Kidney CR-3B Uterus [JunctionChip 4 of 5] from the right forebrain 21 44 013102_HF_328FL 20 0 human caudate nucleus Neoplasm 861 liver_4 prostate Source GEO sample is GSM203322 Last updated (according to GEO): Jun 21 2007 Blood 1000 BC114B-AF 1402 1398 lens B6Amygdala(1b)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B GSE8316.2 Communicable Diseases 1000 Nasal Epithelium 901 Clone 3.3 chip 2 150mg/kg APAP 24Hr rat 3619 blood vs. 3616 PC 24Hr (pool) of the small intestine 97 118 Malignant Neoplasms 1000 1000 Brain 861 Femur Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132506 Last updated (according to GEO): Feb 26 2007 PGA-Pi3k_ca_2818v2 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 2 - Pair 2 - IML Source GEO sample is GSM49880 Last updated (according to GEO): Dec 20 2005 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181165 Last updated (according to GEO): Jul 12 2007 Cerebral cortex 861 3AJZ02053103_HBEC 1000 Fibroid Tumor 338 333 brain ALL_13 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Control, biological rep1 726 718 in brain of the human brain 11 28 Gene expression data from postmorten brain regions Source GEO sample is GSM145267 Last updated (according to GEO): Nov 20 2006 Communicable Diseases 1000 Saline control-neocortex, biological rep3 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210382 Last updated (according to GEO): Jul 16 2007 1000 Prostate 1000 Integumentary system Spleen 1000 Huntington? 0 10 Lymphoblastoid Cell Line for Individual 8059.3 log phase plasma cells 332 344 NCI60.36_LABEL40EXTRACT39SUB3 Source GEO sample is GSM134173 Last updated (according to GEO): Aug 06 2007 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151971 Last updated (according to GEO): Feb 06 2007 865 Disorder of artery 3AJZ02060603_SmoothMuscle CAF 1303 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Hereditary Malignant Neoplasm 876 861 Malaria Prosencephalon 861 1000 Aorta osteoblast 627 637 MO_LB_180min_Patient12 Sample5, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53256 Last updated (according to GEO): Jul 06 2005 SN:1029152 Source GEO sample is GSM115416 Last updated (according to GEO): Jun 20 2006 861 Muscle of a polyglutamine tract 200 223 Undifferentiated Carcinoma 0 25 901 Bone Marrow 40 21 from the hippocampus Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226053 Last updated (according to GEO): Nov 02 2007 Carcinoma, Transitional Cell 875 NCI60.21_LABEL25EXTRACT24SUB3 Source GEO sample is GSM134097 Last updated (according to GEO): Aug 06 2007 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188826 Last updated (according to GEO): Jun 06 2007 brain, cerebral cortex: NMDA 3_le1 Normal Source GEO sample is GSM176402 Last updated (according to GEO): Apr 09 2007 Plasma 861 Aorta 861 C3H-HeJ mice were exposed to filtered air. Lungs were removed-frozen in liquid nitrogen-RNA extraction. Lot batch = Source GEO sample is GSM4013 Last updated (according to GEO): May 28 2005 861 Muscle 1000 Spleen AD-123T1-A25-1 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Dendritic Cells, CD8+ subset - Expt #1 f2#66 versus pool Mouse Brain tissue Blood Test (Blinded) Sample Source GEO sample is GSM130048 Last updated (according to GEO): Sep 18 2007 lateral hypothalamus long access to cocaine replicate 4 Lymphoblastic Leukemia 901 Macrophage smi49 Liver 1000 4089 4084 liver 861 Cerebral cortex 22 14 (cerebrum 861 Kidney 1000 Testis onto a collagen 71 85 Unlike adults, kainic acid (KA)-induced status epilepticus (SE) in immature rats causes neither cell death nor recurrent spontaneous seizures. To elucidate the mechanisms of these distinct responses, transcriptional changes in neuropeptides were examined following KA-induced SE. We aimed to determine whether neuropeptides with anticonvulsant/neuroprotective properties were preferentially increased in immature rats while those with a proconvulsant/neurotoxic role were elevated to a greater extent in mature rats. We used high-density oligonucleotide gene arrays and directly compared transcriptional regulation of seven select neuropeptides at P15 and P30 over five time points. Total RNAs were isolated from hippocampi of 12 animals and pooled to hybridize to triplicate Affymetrix Genechips. Microarray results were validated by real-time quantitative RT-PCR (qRT-PCR). Independent individual RNA samples were purified for triplicate runs of qRT-PCR. Neuropeptides are significantly regulated by seizures in both immature and mature hippocampus. The magnitude of increase is significantly higher at P30 compared with that at P15, not only for neuropeptides with neurotoxic/proconvulsant properties but also for those with neuroprotective/ anticonvulsant properties. Galanin is induced at 24 h only in P30 rats. CST shows high expression in immature hippocampus and is further increased after KA-induced SE only in P15. The expression trends seen in the microarray data are confirmed by qRT-PCR for all six neuropeptides analyzed. CST might play a neuroprotective role in immature rats, and its overexpression might prevent neuronal loss after seizure in adults. Also, suppression of tachykinin and corticotropin-releasing hormone might be effective in alleviating seizure-induced neuronal damage. Gene expression data from postmorten brain regions Source GEO sample is GSM145273 Last updated (according to GEO): Nov 20 2006 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152006 Last updated (according to GEO): Feb 06 2007 Tissue fiber 861 Post infection 28 41 Abdominal aorta structure 1000 GSE8117 in brains 419 427 Disease Source GEO sample is GSM176042 Last updated (according to GEO): Apr 09 2007 Cockayne syndrome B cell Source GEO sample is GSM226609 Last updated (according to GEO): Sep 04 2007 1000 Hippocampus 1000 Substantia nigra structure Parkinson 0 8 Bilateral olfactory bulbectomies were performed on male C57Bl/6 mice(6 week old) and olfactory epithelium tissue collected 5 days post-bulbectomy. Total RNA was extracted from the olfactory epithelium tissue. Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol. Keywords = olfaction Keywords = neurogenesis Keywords = apoptosis Keywords = gene silencing Keywords = microarray, transcription factor Source GEO sample is GSM45686 Last updated (according to GEO): Oct 28 2005 Analysis of prefrontal cortex from 3 biological replicates of C57BL/6J mice at four Zeitgeber Times (ZT 3, 9, 15, and 21). Source GEO sample is GSM240421 Last updated (according to GEO): Oct 30 2007 Genomewide association analysis in diverse inbred mice: power and population structure. Nervous system structure 901 Category: Lymphoma Classification Subcategory: Follicular Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n016 Source GEO sample is GSM2026 Last updated (according to GEO): Nov 21 2005 861 Nerve 84 69 by heart failure AML_28 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Untreated versus treated (bortezomib) breast cancer cells. Source GEO sample is GSM120359 Last updated (according to GEO): Jul 20 2006 Skeletal bone 861 no additional Source GEO sample is GSM199066 Last updated (according to GEO): Jun 08 2007 861 Kidney PBMCs-Type 1 Diabetes-IDDM41_T1D_New 10 Bone marrow 0 3_hypothalamus_3hrs_sleep_#151 Human spinal cord development is still poorly understood and detailed molecular analyses of human motoneuron diseases could improve our understanding of the normal developmental processes of the spinal cord. Lethal Congenital Contracture Syndrome (LCCS, MIM 253310) provides a human model to study the early motoneuronal development. A typical phenotype of LCCS fetuses consists of multiple joint contractures, distinct facial features, and hydrops. Tissue pathology is characterized by severe muscle atrophy, lung hypoplasia, and degeneration of the anterior horn of the spinal cord as the hallmark of the syndrome. In this study we performed a global transcript analysis of LCCS spinal cords. The RNA expression profiles of these spinal cords were compared to age-matched healthy control fetuses, aborted for nonrelated causes. In addition, we applied phylogenetic footprinting methods to decipher the mechanisms of transcriptional regulation in the affected transcripts. Changes in transcripts involved with the development of the CNS and oligodendrocytes were obvious and the transcription factor PAX6 was identified as a key regulator during spinal cord development. In addition, transcript pathway analysis clearly indicated genes belonging to groups with neuronal functions to be affected. Our findings support the hypothesis that human motoneurons and oligodendrocytes are dependent on each other during their development and are influenced by distinct transcription factors previously known to act during murine and chick motoneuron development. These data provide valuable information about the molecular pathways putatively active in motoneuron diseases. 1000 Retina Gene expression data from postmorten brain regions Source GEO sample is GSM145423 Last updated (according to GEO): Nov 20 2006 96 for metastatic disease 118 tissue-specific pattern of mRNA expression - Mus musculus VDXKIU_266C51 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour.This animal was sacrificed at 8 hours after lights on.Original sample code = CM6A Source GEO sample is GSM227345 Last updated (according to GEO): Sep 10 2007 901 frontal lobe CNS-RM_Mod14d-2C-s2 1000 Spleen 1000 Liver Nervous system structure 901 913 Coronary heart disease mouse cerebral cortex 0 20 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68256 Last updated (according to GEO): Jul 07 2006 C57BL-6J were given intratracheal saline control. Lungs were harvested and frozen at 14d. Lot batch = Source GEO sample is GSM4165 Last updated (according to GEO): May 28 2005 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 6 hour after the last shock treatment. Source GEO sample is GSM4548 Last updated (according to GEO): May 27 2005 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213499 Last updated (according to GEO): Jul 31 2007 Pituitary Gland 1000 901 Bone Marrow Epithelial Cells 901 Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22566 Last updated (according to GEO): May 27 2005 Osteoblasts 1000 Fibroblasts 861 Gene expression data from aneurismal tissues obtained from patients with tricuspid valves. Source GEO sample is GSM116793 Last updated (according to GEO): Jun 28 2006 901 Bone Marrow 33 17 tibialis anterior Lymphoblastoid Cell Line for Individual 8158.4 log phase 56 year old female 114 FC BA9 A N01__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Myocardium 861 Nerve 861 861 HIV Infections Array representing the response of Human foreskin fibroblasts at 20h post HCMV infection Source GEO sample is GSM10352 Last updated (according to GEO): May 27 2005 thalamus_2 R7E 10 N34__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3296 Last updated (according to GEO): Mar 21 2006 Brain 861 22-oct-2002-BrainDsubA-ab150 Kidney CR-2A Gene expression data from rat metanephric mesenchymes cultured for 2 days in the presence of NGAL Source GEO sample is GSM126208 Last updated (according to GEO): Dec 08 2006 Cerebral cortex 861 Category: Serum-response Subcategory: Fibroblasts Scanning Software: unknown Software version: unknown Lot batch = 415 Source GEO sample is GSM2164 Last updated (according to GEO): Nov 21 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM146000 Last updated (according to GEO): Nov 20 2006 D_U133Plus_120_DLPFC FormerSmoker 104 Myocardium 861 in bronchial epithelia 311 332 MO_LB_180min_Patient8 861 Cerebral cortex 112 77 Keywords = congenital heart disease 703 680 from other brain tumours in cigulate cortex 26 44 1000 Aorta Brain 861 Diet induced changes in mouse liver mRNA profiles. One of 3 replicates of C57BL/6 mice maintained for 12 weeks on low fat diet. Keywords = LDL receptor deficiency, high fat diet, atherosclerosis, liver Source GEO sample is GSM5406 Last updated (according to GEO): May 27 2005 32h-Control replication 3 Keywords = preimplantation Keywords = development Source GEO sample is GSM14700 Last updated (according to GEO): May 28 2005 Liver 1000 brain, cortex: 7dexp4_e1_le1 no additional Source GEO sample is GSM199160 Last updated (according to GEO): Jun 08 2007 Control 12 Disease Source GEO sample is GSM175786 Last updated (according to GEO): Apr 09 2007 Timed pregnant C57Bl6 mice were exposed to ethanol during gestational day 15 to day 18 and ethanol exposed fetuses were delivered by cessarian section on gestational day 19. Alcohol exposed fetuses were compared to control timed preg Source GEO sample is GSM116861 Last updated (according to GEO): Jul 03 2006 Infection 1000 Heart 1000 Spleen vs Tumor necrosis factor-alpha Treated B cell 60min (set3) control for Abca1 +/- ES, RNA 77 Voxel E4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1419 Last updated (according to GEO): Nov 21 2005 Communicable Diseases 901 Unfertilized egg replication 3 Keywords = preimplantation Keywords = development Source GEO sample is GSM14661 Last updated (according to GEO): May 28 2005 743 723 of these spinal cords spinal cord, ventral spinal cord: D60SODSPMN1_e1_le1 in blood 16 23 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16950.gif Source GEO sample is GSM91560 Last updated (according to GEO): Sep 22 2006 I_U133A_23_AnCg Abdominal aorta structure 1000 607 597 the rectum SK-MEL-5 hgu95b autism 0 5 GM10860_technical_rep_1 brain 0 5 D_U133Plus_113_HC 3AJZ02022752_testis 1000 Left total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-gamma (IFN gamma) for 240min Source GEO sample is GSM5611 Last updated (according to GEO): May 27 2005 7 0 prostate cingulate cortex 861 901 frontal lobe Wild type inbred mice Source GEO sample is GSM82972 Last updated (according to GEO): Nov 10 2005 Transplant Series 19 , Transplant # 5 NMDA10 (Experiment shortNMDA: Run 19222) Treatment, type=time_course, description=primary cortical neurons were treated with 1 mM NMDA for increasing periods of time (10 to 360 min)., measurement=10.0 m Source GEO sample is GSM96716 Last updated (according to GEO): Feb 14 2006 Dendritic Cells, Exposed to Brugia malayi (5) - Repeat #2 Nasal Epithelium Inhalation Formaldehyde 07ppm 6h ID131 Whole Brain Source GEO sample is GSM18762 Last updated (according to GEO): Sep 25 2006 1000 Brain Cerebral cortex 1000 G30-SomatosensoryCortex replicate1 hippocampus 222 233 GSE4675 Brain 861 placenta-0409-uninflamed-past-rep1 Normal Source GEO sample is GSM175818 Last updated (according to GEO): Apr 09 2007 Standard Affymetrix Protocol Source GEO sample is GSM16481 Last updated (according to GEO): May 28 2005 Somatic cell 1000 B158 DCs treated with inflammatory cytokines for 24 hrs 1BJZ02053106_SmoothMuscle 14 0 Large Intestine 1000 Cerebral cortex the vasculature 1243 1257 A bioinformatics analysis of memory consolidation reveals involvement of the transcription factor c-rel. 101049 Gene expression data from postmorten brain regions Source GEO sample is GSM145338 Last updated (according to GEO): Nov 20 2006 in seminoma 28 38 Mental Retardation 1000 osteoblast 630 640 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Neuropeptide Y for 60min Source GEO sample is GSM5713 Last updated (according to GEO): May 27 2005 5 0 Spleen Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b062 Source GEO sample is GSM2007 Last updated (according to GEO): Nov 21 2005 Liver 1000 Parkinson's disease sample x007 0 30 Molecular heterogeneity in acute renal allograft rejection identified by DNA microarray profiling. Skeletal muscle structure 1000 Lmna H222P heterozygous male 1 the blood 393 402 Epithelium of bronchus 983 brain 0 5 in amygdala 20 31 frontal lobe 1000 Metabolic and transcriptional patterns accompanying glutamine depletion and repletion in mouse hepatoma cells: a model for physiological regulatory networks. Pregnant females fed with maltose dextrin, PF01 (Pair Fed) corresponds to replicate 1 PGA-HMO-Obese-5aUA-s2 HL-60(TB) hgu95c I_U133Plus_73_CB Plasma 861 BT-549 hgu95d brain 0 5 Mesenchymal Stem Cells 1000 Adipose tissue 901 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14955 Last updated (according to GEO): Oct 28 2005 Adenocarcinoma 7 0 15 861 Prostate carcinoma NCI60.15_LABEL19EXTRACT18SUB3 Source GEO sample is GSM134069 Last updated (according to GEO): Aug 06 2007 Lymphoblastoid Cell Line for Individual 8202.4 log phase 4525 4520 liver Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153770 Last updated (according to GEO): Jan 19 2007 cocaine naive, septum, 0 hrs/day access to cocaine Source GEO sample is GSM93850 Last updated (according to GEO): Jan 26 2006 Pressure-overload induced hypertrophy model. Mouse was sacrificed 4 hours after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2252 Last updated (according to GEO): May 27 2005 Interferon gamma, 02.00 hr. T-cell * 861 Brain ileum 0 4 Nucleus Accumbends, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231030 Last updated (according to GEO): Sep 26 2007 NCI60.18_LABEL22EXTRACT21SUB3 Source GEO sample is GSM134081 Last updated (according to GEO): Aug 06 2007 of Parkinson's disease 450 471 Structure of trigeminal ganglion 1000 Gene expression data from liver Source GEO sample is GSM243385 Last updated (according to GEO): Nov 16 2007 10 Bone marrow 0 ER negative human primary breast tumor EA02014_41246_H133A_JA-401 Heart failure_LVAD_7 Cerebral cortex 861 Control brainstem 6 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53445 Last updated (according to GEO): Jul 06 2005 865 Disorder of artery Control, biological rep2 CHB Con-2 of somatomotor cortex 21 41 Simple annotation: Cell-line, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/3099.gif Source GEO sample is GSM79875 Last updated (according to GEO): Sep 22 2006 861 Blood 861 Blood Conventional Jejenum 3 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11564 Last updated (according to GEO): May 28 2005 Parkinson 0 8 271 258 from 6 brains Donor 1 Time point 72 hours post infection with HIV-1, RF Source GEO sample is GSM2606 Last updated (according to GEO): May 27 2005 Large Pre-BII cells 9 Wild type inbred mice Source GEO sample is GSM82947 Last updated (according to GEO): Nov 10 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with SDF1 alpha (Stromal cell derived factor-1) for 240min Source GEO sample is GSM5766 Last updated (according to GEO): May 27 2005 Cerebral cortex 1000 NA12742 growth 1 CNS-SC_InjB30m-2B-s2 BC1369 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141303 Last updated (according to GEO): Oct 26 2006 22 0 Mammary Gland @ Preg19 Gene expression profile of the cell line UB/OC-1 grown for 4 days under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1537 Last updated (according to GEO): May 27 2005 Luminal breast tumor cell line MCF7 Keywords = Agilent microarray, Expression analysis, EGFR, Breast cancer growth Source GEO sample is GSM29520 Last updated (according to GEO): Dec 13 2006 GC (HKG58T) Leg 23 Day control rep 3 spleen 214 220 19 0 Head and neck cancer 1000 jejunum This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12356 Last updated (according to GEO): May 28 2005 /testicles 204 214 RMS-T4 on NHGRI-6.5k_b ScGT1_2 Expression profiling of spinal cord section (T10) extracted from rats 4h following moderate injury Source GEO sample is GSM29449 Last updated (according to GEO): May 27 2005 Neoplasm Metastasis 1000 Normal__Colon_CR_4 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184775 Last updated (according to GEO): Apr 26 2007 69 in the skeletal muscle 48 Tissue homogenate from cingulate cortex from G42 mouse (Ref. Pubmed:15509747 ). Source GEO sample is GSM64189 Last updated (according to GEO): Dec 01 2005 eTat - Noco6hr - 2 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5815 Last updated (according to GEO): May 27 2005 Starvation 916 1000 Brain Tumor__Lung_Adeno_95_I_117 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A of ovarian cancers 267 285 striatum 31 39 607 596 the rectum. 26 15 endometrioid vestibular_nuclei_superior_8 20 0 human caudate nucleus Heart Septal Defects, Atrial 1000 Coronary Arteriosclerosis 1000 5 0 Spleen brain, Entorhinal Cortex: Sample4_e1_le1 Female 67.9 yr after antibody enrichment scan 2 (U133B) n/a Source GEO sample is GSM178046 Last updated (according to GEO): Jun 11 2007 5 0 Muscle in amygdala 20 31 ovarian tumor: endometrioid Source GEO sample is GSM139421 Last updated (according to GEO): Apr 09 2007 1000 ovarian neoplasm 345 of skeletal muscle 328 Muscle 861 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs//7273.gif Source GEO sample is GSM79722 Last updated (according to GEO): Sep 22 2006 brain, contralateral Cortex: Trizol Extraction41_le1 Spleen 1000 Neurodegenerative Disorders 901 GC (HKG41N) Euploid sample 2 (cerebrum_TS13) liver_wildtype_WY14643_5d_rep4 861 Longitudinal GSE3016 7 0 Amygdala ileum 1000 NOD/LtJ_male_hypothalamus 340 326 Hyperthyroidism PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls. All samples were normalized with quantile normalization and summarized using RMA. Source GEO sample is GSM135580 Last updated (according to GEO): Dec 19 2006 Haloperidol treated 12weeks AffyGC RMA rep8 861 Blood "Sample 96, BRCA1 mutation(55 months) age 62 erp no" on vantveer-oligo 1000 Transverse IleumSBR_022LAF6O_177.txt PBMCs-Type 1 Diabetes-IDDM53_T1D_1MO The most common congenital cardiac abnormalities 50 97 Gene expression data from dorsal pancreas at e12.5, MG-U74A version2 Source GEO sample is GSM199443 Last updated (according to GEO): Jun 08 2007 858 Prostatic Neoplasms Richard Almon-30-1133800609682 Endometrium 7 Normal Expression profiling of spinal cord section (T8) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM4445 Last updated (according to GEO): May 28 2005 1000 Liver Prostate 861 M_U133Plus_97_HC Exp B, Animal #2, control (0mg/kg) CPF Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours Source GEO sample is GSM246146 Last updated (according to GEO): Dec 03 2007 Testis 861 Brain 861 SK-MEL-2 hgu95a 7 cerebral cortex 21 none Source GEO sample is GSM239865 Last updated (according to GEO): Dec 07 2007 715 702 After the eyes cerebral cortex 7 21 Parkinson's disease sample x029 0 30 changes in cardiac transcription profiles brought about by heart failure skin 80 83 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134624 Last updated (according to GEO): Jul 09 2007 22 0 Mammary Gland @ Preg12 1624 1607 in the spinal cord Spleen 1000 foreskin fibroblast #3, asynchronous plasma cells 50 61 in bronchial epithelia 311 332 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17327.gif Source GEO sample is GSM91586 Last updated (according to GEO): Sep 22 2006 Expression profiling of somatomotor cortex extracted from rats at 4h following moderate injury Source GEO sample is GSM41698 Last updated (according to GEO): May 27 2005 Compare the brain transcriptomes of Gja9 (-/-) and Gja9 (+/-) mice with that of wildtype mice to detect transcriptomic alterationss induced by total or partial ablation of Gja9 Source GEO sample is GSM146903 Last updated (according to GEO): Nov 29 2006 cy5:SHR treated w/ nifedipine and then washed out, biological rep 2r; cy3:pool of 6 WKY control rats total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL10 for 120min Source GEO sample is GSM5643 Last updated (according to GEO): May 27 2005 DCIS131 on harvard-12k Muscle 1000 Huntington's disease 0 19 Organ 966 Cerebral cortex 861 Olfactory Epithelium 1000 no additional Source GEO sample is GSM199423 Last updated (according to GEO): Jun 08 2007 C57BL/6 benchmark dataset: Embryonic day 14.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25172 Last updated (according to GEO): May 27 2005 GBM Treatment, type=remove Source GEO sample is GSM99593 Last updated (according to GEO): Apr 21 2006 RPMI-8226 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12361 Last updated (according to GEO): May 28 2005 in the cerebellum 741 758 914 904 cerebellum olfactory epithelium 194 213 Plasma 861 Liver 1000 Primary Neoplasm 1000 none Source GEO sample is GSM161890 Last updated (according to GEO): Feb 16 2007 861 Mammary gland Cochlea at E11, replicate1 1000 Cerebral cortex bc-ZT15-1 at the Human Brain 733 750 Expression profiling of somatomotor cortex extracted from rats at 4h following sham surgery Source GEO sample is GSM41660 Last updated (according to GEO): May 27 2005 Myocardial Infarction 1000 288 261 at the longitudinal fissure EAE, 1,25(OH)2D2 treated #6 MucOlfEpith_022VACJ2_030.txt Ventral Tegmental Area 1000 1000 Liver Pancreas at e14.5, Chip A, rep 1 NA19171 Male 26.2 yr before antibody enrichment scan 1 (U133B) 30 month oculomotor nucleus rep 1 Job's patient Source GEO sample is GSM211097 Last updated (according to GEO): Sep 10 2007 gene expression of 1 day LIF differentiated ESCs Source GEO sample is GSM181946 Last updated (according to GEO): Apr 12 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lipopolysaccharide (LPS) for 60min Source GEO sample is GSM5664 Last updated (according to GEO): May 27 2005 113 78 Keywords = congenital heart disease Spleen vs Sphingosine-1-phosphate Treated B cell 240min (set3) brain, Right Temporal Lobe: Extract82_le1 28 7 Superior Frontal Gyrus 23 11 of the kidney Mesenchymal Stem Cells 1000 966 Hippocampus Expression profiling of spinal cord section (T9) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM4472 Last updated (according to GEO): May 28 2005 Day 11 Mouse #71 - 1st replicate C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 1 hour after the last shock treatment. Source GEO sample is GSM4544 Last updated (according to GEO): May 27 2005 Ovarian_Tumor_Serous_KU-OS-013 the blood 393 402 21 6 (corpus callosum 16 6 (cerebellum 861 Cerebellum 5.0 mg/kg 2CdA embryo at 3.0h 20 0 human caudate nucleus 4 0 Brain Subcutaeous isolated adipocytes, rep1 umbilical cord_nobpd: 3D Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141312 Last updated (according to GEO): Oct 26 2006 hippocampus sprague 3957 Left 1000 Replicate1_Voxel E4 /2J mouse pituitary gland 27 51 Gene expression data from a primary branch of the saphenous artery of 16 week old spontaneously hypertensive (SHR) rats Source GEO sample is GSM198864 Last updated (according to GEO): Nov 28 2007 GM12146 Brain_MD_33_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL healthy subject Source GEO sample is GSM211137 Last updated (according to GEO): Sep 10 2007 brain 0 5 Cerebral cortex 861 1008 990 to the optic nerve ALL_12 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Neoplasm 861 Skeletal bone 861 861 Breast Universal Mouse Reference RNA Source GEO sample is GSM93425 Last updated (according to GEO): Jan 23 2006 brain, brainstem: D60WTFNMN3_e1_le1 Spinal Cord 1000 25 0 Superior_Cervical_Ganglion 901 Structure of trigeminal ganglion SCN2.2 Sample 23 (Exp#3-18 hr) Samp8 Hippocampus Young Sample 2 1000 Liver Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162169 Last updated (according to GEO): Jun 12 2007 127 111 of chromosome 21 Spleen vs Terbutaline Treated B cell 60min (set1) NMDA30 (Experiment shortNMDA: Run 19222) Treatment, type=time_course, description=primary cortical neurons were treated with 1 mM NMDA for increasing periods of time (10 to 360 min)., measurement=30.0 m Source GEO sample is GSM96754 Last updated (according to GEO): Feb 14 2006 Whole blood 0 10 Spleen 1000 Foreskin Microarray data set (Sample 3) 660 mesenchymal stem cell 639 park_1147_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12412.gif Source GEO sample is GSM79855 Last updated (according to GEO): Sep 22 2006 /NJ mouse periaqueductal gray 27 55 WGACON-56 352 340 encephalitis 457 447 in pancreas 27 7 Medial Temporal Gyrus 1000 Bipolar Disorder 1000 Infection large cell lung carcinoma 4222 0 29 28 0 frontal cortex wistar ky 3931 5 0 Spleen 67 40 with coronary artery disease 861 Down Syndrome To add Source GEO sample is GSM209454 Last updated (according to GEO): Jul 25 2007 Oculomotor nucleus 1000 Resting Source GEO sample is GSM176285 Last updated (according to GEO): Apr 09 2007 1000 Endometrium thalamus_8 5 0 brain 7 cerebral cortex 21 experiment IV, hTERT transduced, replicate 1 PriG_5%O2_Expt3_Day9_rep1 1037 of transitional epithelium 1012 Fibroblasts 38 48 Ovary_6wk_FVB Wt rat cortex Treatment, type=time_course, measurement=3.0 d Source GEO sample is GSM53207 Last updated (according to GEO): Jul 06 2005 Adenocarcinoma 861 spleen.3 129:3-1 + 3-2 hypothalamus mefloquine-treated NG108 neuronal cells 3 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Prostaglandin E2 for 30min Source GEO sample is GSM5732 Last updated (according to GEO): May 27 2005 1000 Solid tumor Brain 861 Normal Source GEO sample is GSM176416 Last updated (according to GEO): Apr 09 2007 Simple annotation: Chronic Lymphocytic Leukemia, Fludarabine chemotherapy Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2856.gif Source GEO sample is GSM72173 Last updated (according to GEO): Sep 22 2006 3 0 Pons Mouse Liver AIN Diet 8hr 1mg/kg As Injection, biological replicate A Gap Junctions 1000 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184815 Last updated (according to GEO): Apr 26 2007 Diaphragm 112 Day mdx rep 1 Plasma 861 62 49 prostate C57BL 091213 OVR11 on Affymetrix GeneChip Human Full Length Array HuGeneFL 861 Mammary gland of gut neurospheres 39 57 with essential tremor 27 47 of somatomotor cortex 21 41 of muscular dystrophy 159 180 Myocardium 861 The goal of these experiments was to identify the genes that are regulated by CCAT, a novel transcription factor derived from the C-terminus of CaV1.2. Neuro2A neuroblastoma cells were transfected with the last 503 AA of CaV1.2 which is full length CCAT (CCAT FL) or with the last 280 AA of CaV1.2, a form of CCAT that lacks the transcriptional activation domain (CCAT DTA). The mRNA from either CCAT FL or CCAT DTA expressing cells was hybridized to Agilent mouse genome microarrays along with mRNA from untransfected neuro2A cells. The microarray data was subsequently analyzed with the Rossetta Luminator gene expression data analysis system. Subsequent investigation revealed that CCAT DTA can still activate transcription albeit at much lower levels than CCAT FL. Source GEO sample is GSM95631 Last updated (according to GEO): Feb 07 2006 Wild type voxel B3 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:285, Count:32 Corner- Avg:33775, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:9.132693,SFGene:All Background:Avg:254.61,Stdev:1.76,Max:260.0,Min:249.4 Noise:Avg:6.85,Stdev:0.19,Max:7.4,Min:6.3 RawQ:9.74 Keywords = ALL Source GEO sample is GSM3479 Last updated (according to GEO): May 28 2005 Mesenchymal Stem Cells 1000 Brain 1000 861 Prostate carcinoma pfc_1036_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 861 HIV Infections Cochlea at E13.5, replicate1 stria terminalis 1000 human frontal cortex Source GEO sample is GSM86980 Last updated (according to GEO): Feb 08 2006 Bone Marrow 1000 Testis [JunctionChip 1 of 5] in the brain 150 162 of somatomotor cortex 21 41 plasma cells 50 61 adenocarcinoma 3088 40 21 from skeletal muscle Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242057 Last updated (according to GEO): Dec 04 2007 C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P20 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25125 Last updated (according to GEO): May 27 2005 Parkinson Disease 1000 cerebral cortex 7 21 Cerebral cortex 901 1000 Spleen Primary small cell lung carcinoma 2425 0 37 I_95Av2_2822_DLPFC_1_GS 861 Brain Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28769 Last updated (according to GEO): May 27 2005 spleen 338 343 129Cerebellum(1)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B Testis 1000 Osteoblasts 1000 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132554 Last updated (according to GEO): Feb 26 2007 Interatrial septum 865 865 Disorder of artery BXD 16_M7SS02080613 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL4 for 30min Source GEO sample is GSM5628 Last updated (according to GEO): May 27 2005 Hereditary Nonpolyposis Colorectal Neoplasms 947 861 Retina 1000 Substantia nigra structure small intestine PPARa knockout mice, fasted for 24 hours Source GEO sample is GSM154800 Last updated (according to GEO): Jul 04 2007 of NIH3T3 Fibroblasts 20 40 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198639 Last updated (according to GEO): Jun 06 2007 Normal Source GEO sample is GSM176026 Last updated (according to GEO): Apr 09 2007 Reduced beta-amyloid production and increased inflammatory responses in presenilin conditional knock-out mice. Epithelium 861 ovarian tumor: endometrioid Source GEO sample is GSM139405 Last updated (according to GEO): Apr 09 2007 430A2_2045_3_KO_sham_medulla Source GEO sample is GSM242697 Last updated (according to GEO): Nov 15 2007 395 366 to other embryonal CNS tumours 21 7 caudate nucleus Nose 1000 GM12763 901 Nervous system structure Epithelium of bronchus 983 Normal Source GEO sample is GSM176393 Last updated (according to GEO): Apr 09 2007 ventral spinal cord 13 31 Pituitary Gland 861 Basal- 0 5 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188775 Last updated (according to GEO): Jun 06 2007 Gene expression data from biopsy of infected skin of subject with pustule former phenotype. Source GEO sample is GSM128964 Last updated (according to GEO): Sep 13 2007 51 31 in failing myocardium mouse cerebral cortex 0 21 Nose 1000 human frontal cortex Source GEO sample is GSM86927 Last updated (according to GEO): Feb 08 2006 861 Cerebellum Occipital region 983 Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200642 Last updated (according to GEO): Jun 12 2007 1000 Cardiomyopathy, Alcoholic 330 324 uterus Parkinson Disease 1000 Site: University of California, Davis Cohort: Male/Female Control Set Diagnosis: Control pH: 6.86 Subject: 2822 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39015 Last updated (according to GEO): May 27 2005 Cockayne syndrome B cell Source GEO sample is GSM225389 Last updated (according to GEO): Sep 04 2007 Stomach Pyloric 4 Normal Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151968 Last updated (according to GEO): Feb 06 2007 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27042 Last updated (according to GEO): May 27 2005 human caudate nucleus Source GEO sample is GSM86902 Last updated (according to GEO): Feb 08 2006 R663P00904 spinal cord, spinal cord: G4F_le1 Colorectal Adenocarc Source GEO sample is GSM18706 Last updated (according to GEO): Sep 25 2006 In an effort to develop a genomics-based approach to the prediction of drug response, we have developed an algorithm for classification of cell line chemosensitivity based on gene expression profiles alone. Using oligonucleotide microarrays, the expression levels of 6,817 genes were measured in a panel of 60 human cancer cell lines (the NCI-60) for which the chemosensitivity profiles of thousands of chemical compounds have been determined. We sought to determine whether the gene expression signatures of untreated cells were sufficient for the prediction of chemosensitivity. Gene expression-based classifiers of sensitivity or resistance for 232 compounds were generated and then evaluated on independent sets of data. The classifiers were designed to be independent of the cells' tissue of origin. The accuracy of chemosensitivity prediction was considerably better than would be expected by chance. Eighty-eight of 232 expression-based classifiers performed accurately (with P < 0.05) on an independent test set, whereas only 12 of the 232 would be expected to do so by chance. These results suggest that at least for a subset of compounds genomic approaches to chemosensitivity prediction are feasible. Brain 861 861 Endometrium 8814_Mock_2 73 35 with several human hereditary disorders VDXIGRU_246919 M_U133A_107_DLPFC Exp B_2, 0.5mg/kg CPF Biopsy skeletal muscle sample obtained from 17-year-old female individual Keywords = gene expression profile of normal human skeletal muscle Keywords = Affymetrix HG-U95A Source GEO sample is GSM15807 Last updated (according to GEO): May 28 2005 39 27 the maxillary Epithelium of bronchus 983 Replicate2_Voxel B4 Communicable Diseases 901 mild cardiomyopathy 1174 1193 200 in the frontal cortex 220 of the heart 842 854 This sample has two chips, therefore the values represent the average of the features from both chips. Source GEO sample is GSM227425 Last updated (according to GEO): Sep 12 2007 Leukemia Promyelocytic (HL-60) [JunctionChip 2 of 5] in blood 16 23 Gene expression data from postmorten brain regions Source GEO sample is GSM145509 Last updated (according to GEO): Nov 20 2006 LCM 800 biological rep2 421 412 infection Liver (HBV+, HK85) Brain 861 Gene expression data from skeletal muscle following 30 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230451 Last updated (according to GEO): Sep 19 2007 Osteoblasts 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145194 Last updated (according to GEO): Nov 20 2006 I_U133A_44_AnCg Amygdaloid structure 1000 732 715 during metastasis Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92321 Last updated (according to GEO): Jan 13 2006 Transitional epithelium 1000 861 Neoplasm normal testis 54 66 Epithelial Cells 901 Seminoma 1000 M_95A_1905_CB_1_GS 5 0 Spleen DCN_SHAM_B C57BL/6J_female_hypothalamus Epithelium 861 313 302 brain damage "Sample 87, BRCA1 mutation(46 months) age 40 erp no" on vantveer-oligo with some respiratory epithelium. 1039 1072 1000 Brain Cerebral cortical contusion in rat, 4 dpi #4 Communicable Diseases 1000 Vimentin 1000 mouse hippocampus 0 17 short access to cocaine, amygdala, 1 hr/day access to cocaine Source GEO sample is GSM93832 Last updated (according to GEO): Jan 26 2006 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225688 Last updated (according to GEO): Nov 05 2007 Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68039.gif Source GEO sample is GSM137414 Last updated (according to GEO): Sep 26 2006 9 0 Blood Test brain_DLPFC_bipolar C_mr682 starved 34 40 1000 frontal lobe CNS-SpinalCmod-Adult-28d-5C-s2 Neoplasm 861 Gonadectomized Dahl-Iwai Male HighSalt Cortex rat12 gdahl_cortexr_k_GX_12c_051702 eyes 135 138 CS 85h 861 Prostate carcinoma 430A2_2045_78_control_neuropath_midbrain Source GEO sample is GSM242705 Last updated (according to GEO): Nov 15 2007 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153413 Last updated (according to GEO): Jan 11 2007 80 68 Control blood spinal cord 37 47 Lymphoblastic Leukemia 901 Amygdaloid structure 1000 SPRET/EiJ_male_hypothalamus Source GEO sample is GSM184220 Last updated (according to GEO): Apr 26 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113908 Last updated (according to GEO): Jun 16 2006 1000 Hippocampus Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68282 Last updated (according to GEO): Jul 07 2006 1000 Ischemia A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism Source GEO sample is GSM5992 Last updated (according to GEO): Nov 21 2005 Whole Brain 62 72 Ta gr2 tumour Source GEO sample is GSM2484 Last updated (according to GEO): May 27 2005 no additional Source GEO sample is GSM199218 Last updated (according to GEO): Jun 08 2007 TestiSeminiferousTubule Source GEO sample is GSM18831 Last updated (according to GEO): Sep 25 2006 VDXGUYU_4076 84 69 by heart failure Sample 8 Treatment, type=pharmacogenomic_treatment, description=Neuronal cultures from cultures of rat cerebellar granule neurons will be treated with the chemical compound GW5074. Source GEO sample is GSM53240 Last updated (according to GEO): Jul 06 2005 SAMR1 Retina Old Sample 2 at the Human Brain 743 760 into hepatocyte- 503 518 cortex 7 12 Brain 861 858 Mesodermal cell gene expression data from the Superior Frontal Gyrus of 10year-old normal girl, RNA labeled and hybridized Dec. 2001 Source GEO sample is GSM160310 Last updated (according to GEO): Feb 05 2007 Blood 1000 V5-P451 901 Neuroectodermal Tumors #28 (isolate V low serum media PlGF 24hours) Nose 1000 mouse brains 187 198 1000 Brain 225 207 in the hypothalamus Serum cyc 4 hours Brain 861 ILS/ISS_cerebellum_naive_459 Osteoblasts 1000 12 0 ovarian tumor CurrentSmoker 58 715 702 After the eyes FL-5;CD19+ Structure of horn of uterus 884 2524 CP6_31 from liver 21 30 11_0018_Control_Day1_39 Solid tumor 983 Dioxin treated MCF7 breast cancer cells [HG-U133A] Exp 3 olfactory epithelium 194 213 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118346 Last updated (according to GEO): Jul 11 2006 ileum 1000 R6/1 22 week transgenic_BBB4 Exp A_1, control (0mg/kg) CPF neurological disease control sample x155 861 Retina Brain 1000 Erythroid Differentiation: G1E Model 12hr post 3Gy IR 43h-AM replication 2 fetal liver Source GEO sample is GSM18905 Last updated (according to GEO): Sep 25 2006 D_U133Plus_106_Amy 41 28 in mouse brain dorsal striatum wistar 3966 Cerebral cortex 1000 280_1 1000 Spleen aa_NY226 BPH-2 on UMich-10k Brain 861 7 CN B Tumor__Colorectal_Adeno_95_I_175 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A NH 64h Nose 1000 Cerebral cortex 861 amygdala wistar 3721 whole tissue, individual animal, 10 weeks old, male Wistar amygdala file:p3946w Source GEO sample is GSM15176 Last updated (according to GEO): Oct 28 2005 CNS-SMTC_Mod4h-1C-s2 861 Cerebellum 0 Human Cortex 11 cerebral cortex 7 21 295 274 ventral tegmental area Disorder of artery 865 m1-WT2 Tissue fiber 861 861 Cardiomyopathies 67 40 with coronary artery disease I_U133A_32_AnCg /Ovary 12 Disease 11 27 1000 Pancreas 861 Neoplasm Heart Ventricle 1000 Normal Source GEO sample is GSM176365 Last updated (according to GEO): Apr 09 2007 Coronary artery 901 total RNA derived from a leprosy lesion Source GEO sample is GSM6774 Last updated (according to GEO): May 27 2005 Infection 1000 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225715 Last updated (according to GEO): Nov 05 2007 Peripheral blood 99 114 14 NT control Source GEO sample is GSM92500 Last updated (according to GEO): Jan 13 2006 D_U133A_77_DLPFC low gestational age Source GEO sample is GSM213103 Last updated (according to GEO): Jul 25 2007 Cerebellum 1000 We build a model for the molecular and cellular events underlying phenotypic discordance in glycine receptor defects (beta subunit). Some mice progress and die, while their littermates recover and get better, despite the same mutation on an inbred genetic background. We find evidence for glycine neurotransmitter toxicity and loss of glycinergic interneurons early in the disease, but some mice are able to keep things going until they can over-express homomeric alpha1 channels, whereupon they recover. In the mice progressing towards lethality, neurotransmitter toxicity too quickly extends to GABAergic interneurons and motorneurons, and they lose their window of time to upregulate the alpha1 glycine receptor, and they crash and burn. Importantly, human patients with glycine receptor defects typically show a resolution of their phenotype with age, and we propose that the same remodeling events are occuring in human patients. Source GEO sample is GSM31005 Last updated (according to GEO): May 27 2005 Large Intestine; Cecum Keywords = mouse gene expression database Source GEO sample is GSM29287 Last updated (according to GEO): May 27 2005 12 0 ovarian tumor 1000 Descending colon Bone Marrow 1000 7 cerebral cortex 21 in seminoma 28 38 olfactory epithelium 194 213 091212 OVR10 on Affymetrix GeneChip Human Full Length Array HuGeneFL brain 0 5 WGACON-64 Wild type P46 (dark reared to P42) mouse visual cortex ipsilateral to monocular enucleation Source GEO sample is GSM97227 Last updated (according to GEO): Feb 17 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM146086 Last updated (according to GEO): Nov 20 2006 Nose 1000 f2#113 versus pool Mouse Brain tissue 861 medulloblastoma V5-P463 Gene expression data from postmorten brain regions Source GEO sample is GSM145756 Last updated (according to GEO): Nov 20 2006 Heart Septal Defects 884 of neurodegenerative disease 2046 2074 Y VIS D029 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108646 Last updated (according to GEO): Aug 22 2006 spinal cord 0 11 rat model organism with depression left untreated or treated with reserpine Source GEO sample is GSM247184 Last updated (according to GEO): Dec 11 2007 SN6h(1) WT_IL-6_400_rep1 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195342 Last updated (according to GEO): Jun 04 2007 Ventral Tegmental Area 1000 T177 Lmna H222P heterozygous male 6 PGA_MI_nilv_1h_394 Brain 1000 Trachea 1000 Epithelium 861 5_cerebral_cortex_3hrs_sleep_#73 brain 0 5 P14CN2 embryonic hearts 1064 1079 861 Neoplasm Tissue Source GEO sample is GSM67211 Last updated (according to GEO): Jan 19 2006 861 Lung PGA-MurLungRag-pbs-72h-1bAv2-s2 MO_control_180min_Patient10 1000 Brain Macrophage 14smi095 hormone sensitive prostate cancer 215 248 Chronic Lymphocytic Leukemia 19 47 Z1 juvenile biol repl 1 1000 Epithelial Cells starved 30 36 Lymphoblastic Leukemia 901 Spleen 1000 Liver 1000 Patient3D Cortex_reserpine_treated_rep6 brain, amygdala: pADX PM A_e1_le1 3 0 Lung of prostate cancer 226 243 5 0 blood AML58 on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132540 Last updated (according to GEO): Feb 26 2007 Neoplasm 861 the blood 393 402 Gene expression patterns in human liver cancers 335 325 The jejunum M_U133A_80_nAcc M_U133A_15_DLPFC_R 45 CN A Gene expression data from whole tumor Source GEO sample is GSM182296 Last updated (according to GEO): Apr 16 2007 266 257 infection CC701 Tumor__Leukemia_AML_AML_(7,PK)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Richard Almon-43-1133800610104 Replicate 3 of 3 (same genotype, same age). All replicates were individual animals. Source GEO sample is GSM138273 Last updated (according to GEO): Sep 29 2006 MCF7 hgu95e 1000 Lipids Temporal Cortex Control (AD) 3 Tissue Source GEO sample is GSM67215 Last updated (according to GEO): Jan 19 2006 Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. 72h after sham surgery, a 4 mm diameter disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44501 Last updated (according to GEO): May 27 2005 Posterior root of spinal nerve 1000 B Cells Resting 30h 1 Resting Gene expression data from postmorten brain regions Source GEO sample is GSM145287 Last updated (according to GEO): Nov 20 2006 861 Cardiomyopathies blood, Blood: 1442_0002_le1 DCIS102 on harvard-12k Category: Cell-line Subcategory: Breast Scanning Software: unknown Software version: unknown Lot batch = svcc17 Source GEO sample is GSM1924 Last updated (according to GEO): Nov 21 2005 in the submucosa 764 779 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201263 Last updated (according to GEO): Jun 14 2007 110 94 of heart failure Prosencephalon 861 R7N 4 861 Prostate carcinoma 1BJZ02051609_OccipitalLobe fetal buttock-thigh fibroblast #2, asynch Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225727 Last updated (according to GEO): Nov 02 2007 Gene expression profiling of anti-GBM glomerulonephritis model: the role of NF-kappaB in immune complex kidney disease. Tissue Source GEO sample is GSM67259 Last updated (according to GEO): Jan 19 2006 Primary Neoplasm 1000 Vestibular Nuclei Superior 3 Normal YP2 Normal Source GEO sample is GSM176218 Last updated (according to GEO): Apr 09 2007 accumbens rattus_norvegicus_strain iNP animal_number 7 vulva_10 f2#109 versus pool Mouse Brain tissue 1BJZ02052319_WHOLEBLOOD(JJV) Liver Test (Blinded) Sample Source GEO sample is GSM130059 Last updated (according to GEO): Sep 18 2007 DNA microarray profiling identifies molecular heterogeneity and suggests a role of B-cells in acute renal allograft rejection. Description of Appendix 1: Last Updated (by provider): May 29 2005 Contributers: S C Hsieh O Salvatierra T Satterwhite M Sarwal M S Chua M Masek N Kambham Includes GDS365. Update date: Jul 01 2003. Dataset description GDS365: Molecular heterogeneity and role of B-cells in acute renal allograft rejection.. 861 Blood I-7_POST brain, cerebellum: 6hrs C GW_e1_le1 Neoplasm 861 in synapses 27 37 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114432 Last updated (according to GEO): Jun 16 2006 1000 Prostate Parkinson Disease 1000 PGA-Csx_het_8a-m4 5 0 brain brain, cortex: 28dexp2_e1_le1 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68338 Last updated (according to GEO): Jul 07 2006 VDXIGRU_307251 108 86 of brain frontal cortex GSE7002 1000 medulloblastoma 1000 Spleen Prostate 861 V5-P025 KHG-HG-2Av2-s2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A GC (HKG51T) ISS/ILS_cerebellum_naive_417 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28796 Last updated (according to GEO): May 27 2005 Exp C_2, 30mg/kg CPF Gene expression data from postmorten brain regions Source GEO sample is GSM145881 Last updated (according to GEO): Nov 20 2006 Anterior nares 1000 Exp 3 (+TNFa) Disease Source GEO sample is GSM175798 Last updated (according to GEO): Apr 09 2007 376 358 prostatic neoplasms 0 Human Cortex 11 frontal cortex 206 220 Animals were sacrificed and organs were rapidly frozen in liquid nitrogen, and subsequently stored at <ETH>80oC. Tissues were mechanically homogenized with a polytron and total cellular RNA was extracted using a commercially available reagent (TMTRIzol; Invitrogen). The poly-(A)+ fraction of the RNA was isolated by chromatography with oligo d(T) cellulose beads. For cDNA labeling, either 25 mg of total RNA or 2.5 mg of poly-(A) RNA was converted into cDNA using reverse transcriptase (RT; Super Script II, Invitrogen) and alternatively Cy5 or Cy3-labeled dCTP (1mM, Perkin Elmer-Cetus/NEN, Boston) in a reaction mixture containing 1.5 mL oligo (dT) (100pmol/ mL), 3 mL dNTP-dCTP (6.67mM each), 1 mL dCTP (2mM), 4 mL DTT (100mM), 8 mL 5 X RT Buffer (Invitrogen, California). The reactions were carried out at 42¼C for 3 hrs, after which the RNA was degraded by the addition of 0.5 mL RNase A (1 mg/mL) and 1.5 mL RNaseH 5 units/mL). Labeled cDNA was separated from unincorporated nucleotides (Qiagen column) and further concentrated by evaporation under vacuum. The arrays were pre-hybridized for 1-2hrs with DIGEasy hybridization buffer (Roche) containing 10ug/ml denatured salmon sperm DNA, and 10ug/ml yeast tRNA. The Cy5 and Cy3 labelled cDNAs were combined and hybridized in the same medium and incubated with the arrays for 16-18hrs at 37Co. Finally, the arrays were washed 3 x 10 mins in 0.1 x SSC (20 X SSC is 3M sodium chloride, 0.3 M sodium citrate, pH 7.0), 0.1%SDS at 50Co, and 4 x 3min in 0.1 x SSC at room temperature, and dried by centrifugation. Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray fluorescent scanner and image intensity data were extracted and analyzed with QuantArray 3.0 analysis software. Quantification data was imported in GeneSpring (Silicon Genetics). The import format was modified to maintain information relevant to user-contributed flagging as well as QC parameter furnished by the array manufacturer. Dye swap and Intensity-based normalization (Lowess) were performed using the default settings. Keywords = spleen Keywords = malaria Source GEO sample is GSM11006 Last updated (according to GEO): Oct 28 2005 861 Blood small cell lung carcinoma 8526 Source GEO sample is GSM17349 Last updated (according to GEO): May 28 2005 Expression profiling of somatomotor cortex extracted from rats at 14d following moderate injury Source GEO sample is GSM41692 Last updated (according to GEO): May 27 2005 A2780_oxa_IC90_6h_1 1000 Neuraxis V5-P482 Epithelium of bronchus 983 38 21 from a hippocampus Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225955 Last updated (according to GEO): Nov 02 2007 contralateral Cortex 7 27 at the Human Brain 746 763 N38__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A OVCAR-3 hgu95d 1037 of transitional epithelium 1012 D_95Av2_2822_DLPFC_1_GS Communicable Diseases 1000 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68228 Last updated (according to GEO): Jul 07 2006 861 Neoplasm A Bioinformatics Analysis of Memory Consolidation Reveals Involvement of the Transcription Factor c-Rel 875 Refractory Carcinoma stomach_pyloric_1 Source GEO sample is GSM80813 Last updated (according to GEO): Mar 31 2006 Expression profiling of laminectomized raphe at 3mo in rats Source GEO sample is GSM41540 Last updated (according to GEO): May 27 2005 1000 Spleen D_U133A_56_DLPFC umbilical cord_nobpd: 2D WGACON-190 nostrils 156 164 1000 jejunum brain, cerebral cortex: Rat_02-138_TTX_Lipska_e1_le1 human cerebellum Source GEO sample is GSM87088 Last updated (according to GEO): Feb 08 2006 prostate Source GEO sample is GSM203303 Last updated (according to GEO): Jun 21 2007 861 Cerebellum none Source GEO sample is GSM123206 Last updated (according to GEO): Jul 26 2006 PBMCs-Type 2 Diabetes-T2D_2_New nostrils 156 164 Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14344.gif Source GEO sample is GSM79697 Last updated (according to GEO): Sep 22 2006 DLBC4 on Affymetrix GeneChip Human Full Length Array HuGeneFL whole blood_100374 Anterior nares 1000 861 Carcinoma human frontal cortex Source GEO sample is GSM87057 Last updated (according to GEO): Feb 08 2006 -_10684_batch1 on NHGRI-6.7k brain, hippocampus: C240-I_e1_le1 1000 Spleen 901 Epithelial Cells Epithelium 861 861 Mammary gland DRG084_a of the olfactory bulb 25 45 TUMOR 19 0 7 Infection 1000 Transplant Series 42 , Transplant # 5 861 Cancer of Neck 884 Neuronal Ceroid-Lipofuscinosis 1000 Asthma the blood 393 402 GSE5126 861 Retina Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51120.gif Developmental Stage: E Source GEO sample is GSM229825 Last updated (according to GEO): Nov 06 2007 Immune; normal adult(2X+) Keywords = mouse gene expression database Source GEO sample is GSM29354 Last updated (according to GEO): May 27 2005 861 Cerebral cortex Brain_MD_45_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL Diaphragm 23 Day control rep 2 Osteoblasts 1000 pituitary_gland_9 Source GEO sample is GSM80803 Last updated (according to GEO): Mar 31 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-gamma (IFN gamma) for 240min Source GEO sample is GSM5612 Last updated (according to GEO): May 27 2005 Subject code A18 28 13 from spinal cord advanced HCC Source GEO sample is GSM155941 Last updated (according to GEO): Jun 21 2007 H9LMS99102620 post infection 29 42 861 Muscle Mk2: Hippocampus_21PT-AI_rep2 of mouse brain 9 23 Osteoblasts 1000 Cultured_osteoblast-like_shear-stressed_MC3T3-E1_cells_rep5 901 Caudate nucleus structure frontal lobe 901 Bicalutamide treated LNCaP cells not stimulated with DHT, biological replicate 3 Source GEO sample is GSM187376 Last updated (according to GEO): May 04 2007 78 73 rectum Collagen 1000 1000 Testis 1000 Brain PHG-PCM-1aAv2-s2 Saline control-hippocampus, biological rep5 Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6 hr Rat 8960 Blood Chronic leukemia NOS 913 1000 Cerebrum HDMTX-DX-13 Allergic contact dermatitis affects about 5% of men and 11% of women in industrialized countries and is one of the leading causes for occupational diseases. In an animal model for cutaneous contact hypersensitivity, we show that mice lacking both known cannabinoid receptors display exacerbated allergic inflammation. In contrast, fatty acid amide hydrolase-deficient mice, which have increased levels of the endocannabinoid anandamide, displayed reduced allergic responses in the skin. Cannabinoid receptor antagonists exacerbated allergic inflammation, whereas receptor agonists attenuated inflammation. These results demonstrate a protective role of the endocannabinoid system in contact allergy in the skin and suggest a target for therapeutic intervention. in the mdx muscle 609 625 MLL-#4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A HUVEC isolate 22 rich media untreated Source GEO sample is GSM12923 Last updated (according to GEO): May 28 2005 Deltoid Muscle 3 Normal Inadequate dietary protein intake causes adverse changes in the morphology and function of skeletal muscle. These changes may be reflected in early alterations in muscle mRNA levels. Microarray analysis was used to assess whether inadequate protein intake differentially affects skeletal muscle transcript levels and expression profiles in older adults. Last Updated (by provider): Jul 11 2007 Contributers: James C Fleet Bruce A Craig Anna E Thalacker-Mercer Wayne W Campbell Nadine S Carnell 861 Chromosomes 14 7 amygdala CHIPEXP_NAME: 230_2_050531tpj_59h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Isoproterenol TREAT_TOX_MECHANISM1: Heart_Cardiotoxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0.5 SAMPLING_TIME: 72 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197630 Last updated (according to GEO): Jun 01 2007 A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke. White and grey matter in the distribution on the middle cerebral artery 6 hours after administration of saline (control); second replicate; pooled mRNA from 6 brains. Source GEO sample is GSM2205 Last updated (according to GEO): May 27 2005 S25 WT3 F41/391 S25 wild type Mouse 2.5 months Cerebellum Female Source GEO sample is GSM73209 Last updated (according to GEO): Sep 06 2005 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10013.gif Source GEO sample is GSM79840 Last updated (according to GEO): Sep 22 2006 913 Coronary heart disease PNS WT Chip C Primary Neoplasm 1000 The most common congenital cardiac abnormalities 50 97 21 0 Mammary Gland @ Lac1 granule neuron precursors infected with retroviruses that express Cyclin D1; array A Gene expression data from dorsal pancreas at e14.5, MG-U74C version2 Source GEO sample is GSM199468 Last updated (according to GEO): Jun 08 2007 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210393 Last updated (according to GEO): Jul 16 2007 1000 Brain Prosencephalon 1000 Wild type inbred mice Source GEO sample is GSM82961 Last updated (according to GEO): Nov 10 2005 rat hippocampus Treatment, type=pharmacogenomic_treatment, description=Fed control diet Source GEO sample is GSM35872 Last updated (according to GEO): May 27 2005 Probeset expression data from NA12750 growth 1, replicate 1 Source GEO sample is GSM195191 Last updated (according to GEO): Aug 08 2007 Parkinson Disease 861 corpus_callosum_7 Platelet activating factor receptor and innate immunity: 251186821865 Brain 1000 102 91 in melanoma Blood 861 861 Cerebral cortex 12 Parietal Lobe 24 Sham 1 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107475 Last updated (according to GEO): May 01 2006 861 Cerebellum starved 33 39 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11329 Last updated (according to GEO): May 28 2005 928 Hyperinsulinism 1079 1067 PCOS oocytes Spleen 1000 Coronary Arteriosclerosis 1000 none Source GEO sample is GSM239896 Last updated (according to GEO): Dec 07 2007 Heart 1000 Epithelium 861 AML 53 on Affymetrix GeneChip Human Full Length Array HuGeneFL Cardiac-specific TNF-alpha transgenic mice is an excellent model to study the pathologenesis of heart failure. Affymetrix U74V2A was used to analyzed the genes expression profile of mice at the time point of compensated hypertrophy and dilated heart failure. Source GEO sample is GSM8979 Last updated (according to GEO): May 28 2005 ventral tegmental area 25 47 861 Oocytes plasma cells 332 344 1000 Brain CNS-SpinalCsev-Adult-24h-1C-s2 atrial septal defects 198 218 901 Mammary gland Timepoint5 1000 Prostate Gene expression data from postmorten brain regions Source GEO sample is GSM145152 Last updated (according to GEO): Nov 20 2006 Gene expression data from whole tumor Source GEO sample is GSM182300 Last updated (according to GEO): Apr 16 2007 Cerebral cortex 861 brain, hindbrain and spinal cord: P0WT3_e1_le1 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15395.gif Source GEO sample is GSM84176 Last updated (according to GEO): Sep 22 2006 The sample is a part of a series describing gene expression changes during postnatal development of the small intestine Source GEO sample is GSM198882 Last updated (according to GEO): Jun 11 2007 Parkinson Disease 861 plasma cells 50 61 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with TGF-beta (transforming growth factor-beta) for 30min Source GEO sample is GSM5792 Last updated (according to GEO): May 27 2005 GSE4236 substantia_nigra_4 Source GEO sample is GSM80833 Last updated (according to GEO): Mar 31 2006 Brain 1000 D_U133Plus_94_nAcc 1000 Spinal Cord Isolated adipocytes 0 18 865 Disorder of artery Whole Brain 62 72 1000 Brain Structure of horn of uterus 983 Normal epidermal keratinocyte, neonate, primary Malignant neoplasm of ovary 901 Bone Marrow 1000 861 Hypothalamic structure Pressure-overload induced hypertrophy model. Mouse was sacrificed 24 hours after aortic banding. Keywords = Cardiac hypertrophy Source GEO sample is GSM2237 Last updated (according to GEO): May 27 2005 Wnt signaling maintains preadipocytes in an undifferentiated state. When Wnt signaling is enforced, 3T3-L1 preadipocytes no longer undergo adipocyte conversion in response to adipogenic medium. Here we used microarray analyses to identify subsets of genes whose expression is aberrant when differentiation is blocked through enforced Wnt signaling. Furthermore, we used the microarray data to identify potentially important adipocyte genes and chose one of these, the liver X receptor alpha (LXR alpha), for further analyses. Our studies indicate that enforced Wnt signaling blunts the changes in gene expression that correspond to mitotic clonal expansion, suggesting that Wnt signaling inhibits adipogenesis in part through dysregulation of the cell cycle. Experiments designed to uncover the potential role of LXR alpha in adipogenesis revealed that this transcription factor, unlike CCAAT/enhancer binding protein alpha and peroxisome proliferator-activated receptor gamma, is not adipogenic but rather inhibits adipogenesis if inappropriately expressed and activated. However, LXR alpha has several important roles in adipocyte function. Our studies show that this nuclear receptor increases basal glucose uptake and glycogen synthesis in 3T3-L1 adipocytes. In addition, LXR alpha increases cholesterol synthesis and release of nonesterified fatty acids. Finally, treatment of mice with an LXR alpha agonist results in increased serum levels of glycerol and nonesterified fatty acids, consistent with increased lipolysis within adipose tissue. These findings demonstrate new metabolic roles for LXR alpha and increase our understanding of adipogenesis. 156 145 Their livers 17 7 hippocampus Large-scale analysis of the mouse transcriptome. Snout epidermis, vibrissa epidermal region C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 268.83 Stdv: 8.11 Min: 255.17 Max: 283.85 Source GEO sample is GSM2954 Last updated (according to GEO): Mar 20 2006 185-96_Adeno IMR90 from the ES(IMR90)-4 sample Skin; Skin postnatal Day 2-3 Keywords = mouse gene expression database Source GEO sample is GSM29433 Last updated (according to GEO): May 27 2005 GSE4773 N2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A CVB3_V-9h-3 Total RNA from brain sample of wild type mice at P5. Treatment, type=purify, measurement=0.0 years Source GEO sample is GSM113686 Last updated (according to GEO): Jun 09 2006 Transitional epithelium 1000 1000 Brain 61 41 from postmortem brain CNS-SMTC_Mod3mo-1B-s2 Paravertebral Muscle 7 Disease 0 29 PC 18 Treatment, type=incubate, description=Hypoxic preconditioning Source GEO sample is GSM107502 Last updated (according to GEO): May 01 2006 Posterior root of spinal nerve 861 1000 Brain Control rat 8 ventral tegmental area Source GEO sample is GSM32171 Last updated (according to GEO): May 27 2005 Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35375 Last updated (according to GEO): May 27 2005 1000 Bronchi Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198647 Last updated (according to GEO): Jun 06 2007 bronchial epithelia 224 243 1000 Congestive heart failure 1100 1077 of Medulloblastoma - 8 - Brain 861 NG108 rat neuronal cell culture exposed to 4400 ng/ml mefloquine (treated) for two hours. 10 µg total RNA hybridized per chip. RNA STAT 60 used to extract RNA. Standard Affymetrix chip scaling factors used. No other data transformation. Source GEO sample is GSM1663 Last updated (according to GEO): Oct 28 2005 n/a Source GEO sample is GSM177964 Last updated (according to GEO): Jun 11 2007 901 Gallbladder in human cancers 1324 1339 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188841 Last updated (according to GEO): Jun 06 2007 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162163 Last updated (according to GEO): Jun 12 2007 G1E_14_B 1000 Brain Brain 861 1000 Brain Nervous system structure 950 Penis SG Normal Retina 1000 1000 Pancreas HapMap JPT Male Source GEO sample is GSM159629 Last updated (according to GEO): Feb 01 2007 80 66 bicuspid valves olfactory epithelium 83 102 861 Asthma Expression profiling of naive raphe (T0) in rats Source GEO sample is GSM41558 Last updated (according to GEO): May 27 2005 rat cortex Treatment, type=time_course, measurement=28.0 d Source GEO sample is GSM53233 Last updated (according to GEO): Jul 06 2005 M_95A_3076_AnCg_1_GS 1000 Endometriosis, site unspecified 1000 Tonsil 1206 1184 by cervical dislocation AD-AD5T1-A387-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Blood Test (Blinded) Sample Source GEO sample is GSM130030 Last updated (according to GEO): Sep 18 2007 1000 Heart 861 Neoplasm CH2117 108 83 metastatic medulloblastoma Tissue fiber 1000 GSE8325 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153450 Last updated (according to GEO): Jan 11 2007 Whole blood from a healthy control Source GEO sample is GSM153477 Last updated (according to GEO): Jan 11 2007 1000 Brain 923 Subcutaneous Fat of coronary artery disease 317 342 of uterine horns 375 390 Chromosomes 861 Summary: Spinal cord injury (SCI) is a damage to the spinal cord induced by trauma or disease resulting in a loss of mobility or feeling. SCI is characterized by a primary mechanical injury followed by a secondary injury in which several molecular events are altered in the spinal cord often resulting in loss of neuronal function. Analysis of the areas directly (spinal cord) and indirectly (raphe and sensorimotor cortex) affected by injury will help understanding mechanisms of SCI. Hypothesis: Areas of the brain primarily affected by spinal cord injury are the Raphe and the Sensorimotor cortex thus gene expression profiling these two areas might contribute understanding the mechanisms of spinal cord injury. Specific Aim: The project aims at finding significantly altered genes in the Raphe and Sensorimotor cortex following an induced moderate spinal cord injury in T9. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Aug 23 2005 Contributers: Alan Faden Includes GDS1292. Update date: Nov 09 2005. Dataset description GDS1292: Temporal analysis of Sprague-Dawley males subjected to moderate spinal cord injury (SCI) at vertebral T9. Raphe magnus and sensorimotor cortex examined at various time points up to 3 months following trauma. Analysis of areas indirectly affected by injury helps understanding the mechanisms of SCI.. Includes GDS1294. Update date: Nov 09 2005. Dataset description GDS1294: Temporal analysis of Sprague-Dawley males subjected to moderate spinal cord injury (SCI) at vertebral T9. Raphe magnus and sensorimotor cortex examined at various time points up to 3 months following trauma. Analysis of areas indirectly affected by injury helps understanding the mechanisms of SCI.. Includes GDS1293. Update date: Nov 09 2005. Dataset description GDS1293: Temporal analysis of Sprague-Dawley males subjected to moderate spinal cord injury (SCI) at vertebral T9. Raphe magnus and sensorimotor cortex examined at various time points up to 3 months following trauma. Analysis of areas indirectly affected by injury helps understanding the mechanisms of SCI.. Seminoma of testis 1000 Leukemia Lymphoblastic (MOLT-4) [JunctionChip 4 of 5] GSE106 7 cerebral cortex 21 Tumor__Breast_Adeno_9912c068_CC on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Liver Brain 861 1000 Uterus processed in batch 1 Source GEO sample is GSM90446 Last updated (according to GEO): Mar 20 2006 Blood 1000 Cerebral cortex 901 Autistic Disorder 877 Spinal Cord 1000 861 Leprosy 901 Autoimmune Diseases from the femurs 95 109 129P3/J Acute morphine treated, striatum, biological replicate 1 Source GEO sample is GSM187968 Last updated (according to GEO): Jun 14 2007 Basal Ganglia 901 Heart Ventricle 1000 N/A Source GEO sample is GSM4313 Last updated (according to GEO): May 28 2005 132 121 among tumors 17 7 hippocampus of motor neuron diseases 784 808 Nasal Epithelium 865 204 194 of retinal NCI60.17_LABEL21EXTRACT20SUB3 Source GEO sample is GSM134079 Last updated (according to GEO): Aug 06 2007 492 475 in the PCOS oocyte innervated tibialis anterior muscles from runx1f/-; MCK::cre mice Treatment, type=remove, description=MCK::cre; runx1f/- Source GEO sample is GSM99424 Last updated (according to GEO): Mar 08 2006 Wild type fundic RNA Source GEO sample is GSM108483 Last updated (according to GEO): May 03 2007 Alzheimer's Disease 901 Homozygous O377 mutant mouse line versus wildtype mice Source GEO sample is GSM86420 Last updated (according to GEO): Dec 08 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM146057 Last updated (according to GEO): Nov 20 2006 ileum 861 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7552.gif Source GEO sample is GSM79949 Last updated (according to GEO): Sep 22 2006 WGACON-173 cy5:SHR control, biological rep 5r; cy3:pool of 6 WKY control rats 673 659 by decapitation Brain 1000 in blood 16 23 folatedeficientAs1ppm2 Lymphoblastoid Cell Line for Individual 8036.3 log phase Parkinson's disease sample x036 WGACON-62 1000 Coronary Arteriosclerosis 861 Cardiomyopathies Brain 861 861 Cerebral cortex Mouse model of congenital heart disease in Csx/Nkx2.5 mutant embryos. Heterozygous embyronic day 9.5 mouse. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2270 Last updated (according to GEO): May 27 2005 MDA-MB-231-NCI plasma cells 50 61 1000 Spleen Cerebral cortex 861 Parkinson Disease 861 31 21 spinal cord 34 21 in mouse liver Skeletal Muscle Superior Quadracep 2 Normal of a colorectal adenoma 7 29 liver_PPARa-knockout_control_5d_pooled 861 Brain in the frontal cortex 269 290 The hypothesis was tested that differential, coregulated transcriptional adaptations of various cellular pathways would occur early with increased mechanical loading of atrophied skeletal muscle and relate to concurrent damage of muscle fibers. Atrophy and slow-to-fast fiber transformation of rat soleus muscle was provoked by 14 days of hindlimb suspension (HS). Subsequent reloading of hindlimbs caused a fourfold increase in the percentage of muscle fibers, demonstrating endomysial tenascin-C staining. Five days after reloading, when 10% of the fibers were damaged, the normal muscle weight and slow-type fiber percentage were reestablished. Microarray analysis revealed major, biphasic patterns of gene expressional alterations with reloading that distinguish between treatments and gene ontologies. Transcript levels of factors involved in protein synthesis and certain proteasomal mRNAs were increased after 1 day of reloading and correlated to the percentage of fibers surrounded by tenascin-C. By contrast, levels of gene messages for fatty acid transporters, respiratory chain constituents, and voltage-gated cation channels were transiently reduced after 1 day of muscle loading and associated with the number of damaged fibers and the regain in muscle weight. This coregulation points toward important retooling of oxidative metabolism and the T- and SR-tubular systems with rebuilding of slow fibers. The observations demonstrate that early nuclear reprogramming with reloading of atrophic soleus muscle is coordinated and links to the processes involved in mechanical damage and regeneration of muscle fibers. 1000 Adrenal Medulla NCI60.44_LABEL48EXTRACT47SUB3 Source GEO sample is GSM134218 Last updated (according to GEO): Aug 06 2007 GM19128 brain, unknown: 00UO_e1_le1 1000 Hippocampus LT-Hematopoietic stem cell isolated by flow cytometry Source GEO sample is GSM149529 Last updated (according to GEO): Apr 27 2007 SpleenC57_222AFBB_091.txt 901 Autoimmune Diseases 1000 Lymphoma 606 582 in the brain hippocampus AcB55 #12256790b bladder Source GEO sample is GSM18629 Last updated (according to GEO): May 27 2005 Gene expression data from a placenta with chronic malaria Source GEO sample is GSM183610 Last updated (according to GEO): Apr 23 2007 1000 Hippocampus Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 24 h time point Source GEO sample is GSM159802 Last updated (according to GEO): Apr 23 2007 Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.49 Subject: 3076 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39064 Last updated (according to GEO): May 27 2005 Neoplasm 861 Cerebral cortex 861 cortex 27 33 AcB55 #12262264 GSE8870 91 from the bone marrow 72 brain, Left Temporal Parietal: Extract50_le1 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28733 Last updated (according to GEO): May 27 2005 amygdala long access to cocaine replicate 4 Parkinson Disease 1000 1000 Encephalitis 5 0 brain ileum (pool of 4 animals)_72h monoassociation with L.innocua(hly)_A_5555 Source GEO sample is GSM161584 Last updated (according to GEO): Apr 23 2007 Primary tumor 19 32 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132505 Last updated (according to GEO): Feb 26 2007 Dahl Salt Sensitive Rat Lung- Hypoxia, SU-5416, and Sorafenib rep2 Normal Source GEO sample is GSM175852 Last updated (according to GEO): Apr 09 2007 Autistic Disorder 877 of Parkinson's disease 450 471 brain 0 5 no additional Source GEO sample is GSM199052 Last updated (according to GEO): Jun 08 2007 Seminoma 1000 Organ 966 HDF-Skin 0 7 the blood 393 402 Brain 861 Endometrium/Ovary 10 Disease SN:1010390 Source GEO sample is GSM115374 Last updated (according to GEO): Jun 20 2006 1000 Leukemia, Myelocytic, Acute Brain 861 Male 68.4 yr after antibody enrichment scan 2 (U133B) bone_marrow_9 Source GEO sample is GSM80603 Last updated (according to GEO): Mar 31 2006 rat cortex Treatment, type=time_course, measurement=0.1 d Source GEO sample is GSM53200 Last updated (according to GEO): Jul 06 2005 hippocampus: Sample #3_e1_le1 1000 Liver cardiac 763 769 Prostatic Diseases 913 H9LMS00121513 91 from the bone marrow 72 Replicate3_Voxel A7 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=2 and B=0 (Acute rejection). Source GEO sample is GSM36436 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 901 Bone Marrow Breast Diseases 913 Osteoblasts 1000 Nasal Epithelium 901 Replicate2_Voxel E6 858 Mesodermal cell 1000 Hereditary Diseases 1000 Hippocampus Wild type inbred mice Source GEO sample is GSM82966 Last updated (according to GEO): Nov 10 2005 total RNA from biosource CC#34* Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92479 Last updated (according to GEO): Jan 13 2006 CO (Experiment shortNMDA: Run 19222) Treatment, type=time_course, measurement=0.0 m Source GEO sample is GSM96676 Last updated (according to GEO): Feb 14 2006 S11_Muscle_Insulin_30min gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134618 Last updated (according to GEO): Jul 09 2007 180 175 stroke Expression profiling of spinal cord section (T10) extracted from rats 7d following laminectomy (sham) Lot batch = Source GEO sample is GSM4438 Last updated (according to GEO): May 28 2005 Neurological diseases disrupt the quality of the lives of patients and often lead to their death prematurely. A common feature of most neurological diseases is the degeneration of neurons, which results from an inappropriate activation of apoptosis. Drugs that inhibit neuronal apoptosis could thus be candidates for therapeutic intervention in neurodegenerative disorders. We have identified (and recently reported) a chemical called GW5074 that inhibits apoptosis in a variety of cell culture paradigms of neuronal apoptosis. Additionally, we have found that GW5074 reduces neurodegeneration and improves behavioral outcome in a mouse model of Huntington's disease. Although GW5074 is a c-Raf inhibitor, we know very little about the molecular mechanisms underlying its neuroprotective action. Identifying genes that are regulated by GW5074 in neurons will shed insight into this issue. We believe that neuroprotection by GW5074 involves the regulation of several genes. Some of these genes are likely to be induced whereas the expression of other genes might be inhibited. The specific aim is to identify genes that are differentially expressed in neurons treated with GW5074. We believe that neuroprotection by GW5074 involves the regulation of several genes. Some of these genes are likely to be induced whereas the expression of other genes might be inhibited. Cultures of cerebellar granule neurons undergo apoptosis when switched from medium containing levated levels of potassium (high K+ or HK) to medium containing low potassium (LK). Although cell death begins at about 18 h, we have found that the by 6 h after LK treatment these neurons are irreversibly committed to cell death. We will treat cerebellar granule neuron cultures with LK medium (which induces them to undergo apoptosis) or with GW5074 (1 uM). We will extract RNA at two time-points after treatment: 3 h and 6 h. Analysis at the two different time-points will show us whether changes in expression of specific genes is transient or sustained or whether the changes occurs early or relatively late in the process. Neuronal cultures will be prepared from 1 week old Wistar rats. The cultures will be maintained in culture for 1 week before treatment. Following treatment the cells will be lysed and total RNA isolated. The RNA will be stored at -80oC and shipped to the microarray facility for analysis. The experiment will be done in triplicate. Thus, for each time-point (3 or 6h treatment) we will be hope to provide 3 sets of samples (each set coming from a different culture preparation and containing lysates from cells treated with LK or GW5074). Having samples from 3 independent cultures will mitigate any expression differences resulting from subtle variations in culture quality or in the preparation or quality of RNA.. Date GSE2872 Last Updated: Jul 06 2005 Contributers: S R D'Mello Includes GDS1837. Update date: Jun 09 2006. Dataset description GDS1837: Analysis of cultured cerebellar granule neurons in low potassium medium 3 and 6 hours following treatment with the c-Raf inhibitor GW5074. GW5074 blocks low potassium induced cell death. Results provide insight into the neuroprotective action of GW5074.. subthalamic_nucleus_8 none Source GEO sample is GSM244552 Last updated (according to GEO): Nov 23 2007 732 715 during metastasis 14 olanzapine 201 in the frontal cortex 221 Immature B cells cells sorted out of mouse bone marrow, sort no. 1 Source GEO sample is GSM611 Last updated (according to GEO): Mar 17 2006 366 354 encephalitis mild cognitive impairment - superior frontal gyrus 4 5 0 brain brain, cerebral cortex: Rat_03-14_NroLep_Lipska_e1_le1 Macrophage 14smi104 80 68 Control blood 23 0 SUMMARY Medulloblastoma Transitional epithelium 1000 Wild type inbred mice Source GEO sample is GSM82981 Last updated (according to GEO): Nov 10 2005 TEL-AML1-C40 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A GSE4329 861 Brain Immature B cells 9b none Source GEO sample is GSM149614 Last updated (according to GEO): Jan 03 2007 861 Heart 20 0 human caudate nucleus 13 7 cochlea gene expression data from ODC mouse skin samples Source GEO sample is GSM216670 Last updated (according to GEO): Aug 09 2007 1000 Pancreas 1175 1164 in 31 tumors Normal__Kidney_Norm_613NO on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 20 0 human caudate nucleus Probeset expression data from NA12751 growth 1 Source GEO sample is GSM201538 Last updated (according to GEO): Aug 08 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28816 Last updated (according to GEO): May 27 2005 1000 Spinal Cord Mouse_FGFR1_E12.5_hets_vs_hom_1 861 Hippocampus Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141300 Last updated (according to GEO): Oct 26 2006 mouse brain ipsilateral LPS.RU486, biological rep4 mouse brain contralateral LPS Source GEO sample is GSM149752 Last updated (according to GEO): Mar 15 2007 901 theca cell AA Treatment, type=remove Source GEO sample is GSM99505 Last updated (according to GEO): Apr 21 2006 I_U133Plus_36_CB FVB/NJ Cingulate Cortex C 913 Coronary heart disease testis 52 58 Epithelium 861 HapMap CEU_parent Female Source GEO sample is GSM159541 Last updated (according to GEO): Feb 01 2007 occipital regions 163 179 osteoblast 630 640 Ovary 1000 Brain 861 UET-13TR-EWS/ERG 48hr tet+ Brain 861 865 Disorder of artery Osteoblasts 1000 Normal Source GEO sample is GSM175898 Last updated (according to GEO): Apr 09 2007 from brain 21 30 10 weeks Source GEO sample is GSM147516 Last updated (according to GEO): Dec 01 2006 AD-361t1-A177-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 928 Hyperinsulinism 3AJZ02052108_Testi-GermCell CLL-65 Total RNA extracted from the forebrain of a Lh+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144410 Last updated (according to GEO): Nov 14 2006 Spleen 1000 1109 1090 to childhood asthma Epithelium 861 Pre-BI cells 10 of the liver 501 512 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114457 Last updated (according to GEO): Jun 16 2006 Stomach [JunctionChip 4 of 5] 1000 Cochlear structure Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228633 Last updated (according to GEO): Sep 11 2007 Whole Brain 73 83 Diet Induced Obese rat C6 861 Neoplasm 1000 Brain 861 Muscle 5 0 brain EWS-T4 on NHGRI-6.5k_b 1000 Adrenal Medulla S3_Muscle_Baseline_0min Recommended Affymetrix protocols were followed. Source GEO sample is GSM148469 Last updated (according to GEO): May 01 2007 Menstrual phase - Follicular Source GEO sample is GSM175766 Last updated (according to GEO): Apr 09 2007 Testis 1000 Dorsal Root Ganglia 10 Normal Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n120 Source GEO sample is GSM2032 Last updated (according to GEO): Nov 21 2005 n/a Source GEO sample is GSM177896 Last updated (according to GEO): Jun 11 2007 Cerebral cortex 861 addiction 132 141 Gene expression data from postmorten brain regions Source GEO sample is GSM146024 Last updated (according to GEO): Nov 20 2006 70 40 without coronary artery disease 147-96_Adeno Nrl ko samples were compared to wt at postnatal 2. Source GEO sample is GSM227454 Last updated (according to GEO): Sep 07 2007 Blood 1000 n/a Source GEO sample is GSM177978 Last updated (according to GEO): Jun 11 2007 Malignant neoplasm of stomach 901 Structure of blastomere 875 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-06/6974.gif Source GEO sample is GSM79963 Last updated (according to GEO): Sep 22 2006 VDXGUYU_4072 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs//23749.gif Source GEO sample is GSM66588 Last updated (according to GEO): Sep 22 2006 129 21-3-2 Muscle 861 Patau's syndrome NOS tibiae 115 120 tonsil_5 861 HIV Infections Cerebral cortex 861 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211387 Last updated (according to GEO): Jul 18 2007 119 96 in embryonic stem cells 913 Acute leukemia dorsal_root_ganglia_10 plasma cells 332 344 Brain 861 of the atrial 647 659 Stem cells 861 Obesity 1000 Lung tissue from C57BL/6 mice calorie restricted by 2/3 and sacrificed 4hrs after the onset of calorie restriction. Lot batch = Source GEO sample is GSM4028 Last updated (according to GEO): May 28 2005 Primary Neoplasm 1000 861 Cerebellum processed in batch 2 Source GEO sample is GSM90435 Last updated (according to GEO): Mar 20 2006 Cerebral cortex 861 1000 Synovial Membrane Lymphoblastoid Cell Line for Individual 8020.3 log phase none Source GEO sample is GSM123226 Last updated (according to GEO): Jul 26 2006 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD34 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD34 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36709 Last updated (according to GEO): May 27 2005 BXD38_M7SS02042214 27 CB A SVGR2 subclone 4-F6 GeneChip U133B f2#251 versus pool Mouse Brain tissue Liver 1000 14 hr Hela Double Thymidine 1000 Bone Marrow The epithelial cells 962 981 by spinal cord injury 538 558 5 0 brain Brain 1000 607 597 the rectum Blood 1000 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188821 Last updated (according to GEO): Jun 06 2007 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211259 Last updated (according to GEO): Jul 18 2007 vulva_9 Source GEO sample is GSM80899 Last updated (according to GEO): Mar 31 2006 MCF10A_Treated_#5 Gene expression data from postmorten brain regions Source GEO sample is GSM145284 Last updated (according to GEO): Nov 20 2006 GSE7084 861 Cerebral cortex 861 Cerebral cortex Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 10 hours after lights on. Original sample code = CM25A Source GEO sample is GSM227347 Last updated (according to GEO): Sep 10 2007 tongue_superior_part_w/_papillae_3 Gene expression data from epididymal fat tissues. Source GEO sample is GSM215582 Last updated (according to GEO): Aug 07 2007 901 frontal lobe 352 340 encephalitis Prostate 5 Disease 1000 Cerebral cortex Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151989 Last updated (according to GEO): Feb 06 2007 PGA-HMO-NonObese-1aUA-s2 Cy5-labeled cDNA was obtained from RNA sample reference, prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice. Keywords = wildtype mouse brain Source GEO sample is GSM34860 Last updated (according to GEO): Jun 19 2007 jzo021-rp1-v5-u74av2-met 861 frontal lobe NCI60.37_LABEL41EXTRACT40SUB3 Source GEO sample is GSM134178 Last updated (according to GEO): Aug 06 2007 f2#18 versus pool Mouse Brain tissue 24 0 human prostate PC3 tumors Laser capture lung cancer cells Source GEO sample is GSM190995 Last updated (according to GEO): May 25 2007 Transitional epithelium 1000 embryonic hearts 1064 1079 861 Blood Brain_PNET_6_PNET on Affymetrix GeneChip Human Full Length Array HuGeneFL Brain 1000 brain, hippocampus: C240-II_e1_le1 Herpes Simplex Infections 861 1000 Ischemia Primary Neoplasm 1000 C57BL/6 Benchmark Set for Early Cardiac Development 1000 Skeletal bone 6 hr Hela Double Thymidine, exp2 accumbens_8 27 0 cerebral cortex sprague 3914 Autistic Disorder 877 Bone structure of tibia 1000 1000 Cerebral cortex Leg 112 Day mdx rep 2 Gene expression data from the hippocampus of S1P2-knockout mouse Source GEO sample is GSM172963 Last updated (according to GEO): Mar 08 2007 865 Disorder of artery mouse brain contralateral saline.RU486, biological rep4 Ovarian_Tumor_Endometrioid_KU-OE-004 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs//7345.gif Source GEO sample is GSM79984 Last updated (according to GEO): Sep 22 2006 1000 Eye Disease Source GEO sample is GSM176091 Last updated (according to GEO): Apr 09 2007 TEL-AML1-#3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 728 716 ciliary body 21 0 Normal Caudate Nucleus 861 Spinal Cord Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28767 Last updated (according to GEO): May 27 2005 human cerebellum Source GEO sample is GSM87058 Last updated (according to GEO): Feb 08 2006 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp3326 Source GEO sample is GSM2119 Last updated (according to GEO): Nov 21 2005 Whole brain 0 10 H9LMS99102618 Standard Affymetrix Protocol Source GEO sample is GSM16486 Last updated (according to GEO): May 28 2005 20 0 human caudate nucleus Skeletal muscle structure 1000 HA96-61B Olfactory Epithelium 1000 1858 1835 against medulloblastoma 1000 Asthma brain, Right Parietal Lobe: Extract73_le2 plasma cells 332 344 Brain 1000 B6_SleepDep_ZT 6_3 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=1 (Non-acute rejection). Source GEO sample is GSM36442 Last updated (according to GEO): May 27 2005 n/a Source GEO sample is GSM178023 Last updated (according to GEO): Jun 11 2007 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=760650 LaserPower=2.211.28 Lot batch = LC17N120 Source GEO sample is GSM4836 Last updated (according to GEO): Nov 21 2005 Cortex_reserpine_treated_rep4 Osteoblasts 1000 15 0 human cerebellum to the viscera 483 497 Disorder of artery 865 Lung tissue from C57BL/6 mice that were always fed by 2/3 and sacrificed 12hrs after the onset of calorie-restriction in calorie-restricted mice. Lot batch = Source GEO sample is GSM4038 Last updated (according to GEO): May 28 2005 1000 Amygdaloid structure brain, forebrain: Sample16_e1_le1 infection 64 72 22 0 Mammary Gland @ Preg12 GM10847 Spinal Cord 1000 SNB-75 hgu95c Interatrial septum 865 861 Cerebral cortex Subthalamic Nucleus 8 Normal Bmi-1, hTERT, bone marrow cell Liver 1000 901 Caudate nucleus structure bone marrow-CD33Myeloid Source GEO sample is GSM18870 Last updated (according to GEO): Sep 25 2006 f2#168 versus pool Mouse Brain tissue 861 Cancer of Neck 913 Acute leukemia 153 136 severe infertility R462P00324 0 Human Cortex 11 Lymph node metastasis 19 40 HapMap CEU_parent Male Source GEO sample is GSM159555 Last updated (according to GEO): Feb 01 2007 861 Alzheimer's Disease PMN_LB_360min_Patient1 NCI60.38_LABEL42EXTRACT41SUB3 Source GEO sample is GSM134183 Last updated (according to GEO): Aug 06 2007 Adenocarcinoma 6 0 15 B2-9 on NCI-7.6k 861 Neostriatum 5 0 brain Testis [JunctionChip 3 of 5] Spleen vs Bombesin Treated B cell 240min (set1) medial prefrontal cortex long access to cocaine replicate 3 1000 Prostate 176 157 Analyzed spinal cord 117 112 Lipids 901 frontal lobe Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 2 - Pair 4 - LMN Source GEO sample is GSM49888 Last updated (according to GEO): Dec 20 2005 861 Immunoglobulins M7TW00121468 2023 2009 of the amygdala 861 Endometrium AD control Treatment, type=dissect Source GEO sample is GSM119622 Last updated (according to GEO): Jul 10 2006 Patient5D 91 from the bone marrow 72 f2#56 versus pool Mouse Brain tissue plasma cells 50 61 Spleen vs Prostaglandin E2 Treated B cell 30min (set1) na Source GEO sample is GSM181277 Last updated (according to GEO): Apr 10 2007 f2#107 versus pool Mouse Brain tissue Bone Marrow 1000 Cerebellum 861 hippocampi 102 111 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=740630 LaserPower=4.793.87 Lot batch = LC17N123 Source GEO sample is GSM4837 Last updated (according to GEO): Nov 21 2005 Brain 861 366 354 encephalitis Macrophage smi99 P21_cy3 861 Kidney Wild type inbred mice Source GEO sample is GSM82910 Last updated (according to GEO): Nov 10 2005 medulla_5 Source GEO sample is GSM80714 Last updated (according to GEO): Mar 31 2006 hindbrain 7 15 with mental retardation 241 263 Gene expression of modiolus of newborn rats_cultivation_hypoxia_repeat 1 inner ear 352 340 encephalitis Trigeminal ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until enough tissue was harvested to be pooled by genotype. Approximately 10-12 ganglia were pooled for a single analysis, which was extracted using the RNeasy system (Qiagen). Source GEO sample is GSM89141 Last updated (according to GEO): Dec 23 2005 Brain 50 55 from the Superior Frontal Gyrus 21 51 901 frontal lobe Brain_Rhab_7_AT/RT (Renal) on Affymetrix GeneChip Human Full Length Array HuGeneFL Timepoint 1r The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27036 Last updated (according to GEO): May 27 2005 midbrain_9 C103 on NCI-7.6k Brain 861 The epithelial cells 962 981 1000 Hippocampus Spleen 1000 Lymphoblastoid Cell Line for Individual 8153.4 log phase 1000 Cardiomyopathy, Alcoholic VDXRHU_1207 CNS-RM_Mod24h-2B-s2 nucleus accumbens_core sprague1 Obtained with a 14 gauge punch from chilled coronal brain slices (0.7-2.2 mm anterior to bregma; Paxinos and Watson, 1998; pool of 5 animals, 20 weeks old, male Sprague Dawley nucleus accumbens core file:R3JV01080107 Source GEO sample is GSM15199 Last updated (according to GEO): May 28 2005 Muscle Source GEO sample is GSM4308 Last updated (according to GEO): May 27 2005 brain 0 5 Testis 1000 Plasma 861 brain 0 5 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92377 Last updated (according to GEO): Jan 13 2006 The rearranged immunoglobulin 185 213 tibiae 115 120 Estrogen treated ipsilateral to stroke replicate E6IC-2a The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27025 Last updated (according to GEO): May 27 2005 Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 8597 blood H132 CN B 135 116 by CO2 asphyxiation 67 52 descending colon The sample is a part of a series describing gene expression changes during postnatal development of the small intestine Source GEO sample is GSM198842 Last updated (according to GEO): Jun 11 2007 Neoplasm 1000 1000 Cerebral cortex 5 0 brain 1000 frontal lobe Cerebral cortex 861 CNS-SpinalC-30mAdult-1C-s2 total prefrontal cortex RNA in female FVB/N mice (control) versus transgenic female mice overexpressing the human synaptic AChE Last Updated (by provider): May 29 2005 Contributers: Eran Meshorer Hermona Soreq Includes GDS891. Update date: Dec 28 2004. Dataset description GDS891: Gene expression profiles from prefrontal cortex of female FVB/N mice and female mice overexpressing human synaptic acetylcholinesterase (AChE).. 10 7 Left 1345 1336 of cancer 861 Brain Eye 1000 1037 of transitional epithelium 1012 Colon Cancer 5 16 5 0 Spleen 18 0 Menstruation blood 96 93 glia 10 weeks Source GEO sample is GSM147460 Last updated (according to GEO): Dec 01 2006 Spleen vs Lysophosphatidic Acid Treated B cell 30min (set1) Gene expression from Dendritic cells from human subject with pustule former phenotype infected with H. ducreyi. Source GEO sample is GSM128975 Last updated (according to GEO): Sep 13 2007 17 7 hippocampus of Parkinson's disease 450 471 474 470 brain Inbred congenic strain B6.C6.132.54/Vad was created using C57BL/6ByJ background and BALB/cJ donor strains. Flanking background markers at chr. 6: 75.9 Mb (rs4226008, NCBI Mouse Build 36 / dbSNP Build 126) and 122.3 Mb (rs3023093), and limiting donor markers at 81.9 Mb (rs4226024) and at 91.8 Mb (rs3712161) defined the introgressed region. We concluded the segment size must be between 9.9 Mb and 46.4 Mb. In a Quantitative Trait Gene identification study we compared brain (without cerebellum) gene expression between progenitors and congenics. Such comparisons can facilitate identification of cis-regulated genes and to establish genetic control of a complex phenotype whose expression is associated with the introgressed chromosome segment. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. Last Updated (by provider): Jun 27 2007 Contributers: Mariko Saito Csaba Vadasz 1000 Brain 861 Cerebral cortex embryonic hearts 1064 1079 Parkinson's model voxel H4 days nasal epithelium 1127 1148 861 Lymphoblastic Leukemia 20 0 human caudate nucleus 1000 Brain 1000 Brain 1000 jejunum 17 7 hippocampus spleen 214 220 n/a Source GEO sample is GSM177960 Last updated (according to GEO): Jun 11 2007 Gene expression data from a hippocampus of saline-injected mouse Source GEO sample is GSM147413 Last updated (according to GEO): Jan 03 2007 1000 Brain IFN_PBS_1 of somatomotor cortex 21 41 861 Gland structure 3ARS02080736f_DRG Branch 861 mod094_100nM-2 Basal Ganglia 1000 doxycycline, wt Source GEO sample is GSM213362 Last updated (according to GEO): Jul 26 2007 from the gut 1116 1127 Medulla Oblongata 861 starved 32 38 I_95Av2_2835_CB_1_GS 266 257 infection Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28723 Last updated (according to GEO): May 27 2005 Category: Serum-response Subcategory: Fibroblasts Scanning Software: unknown Software version: unknown Lot batch = 128 Source GEO sample is GSM1726 Last updated (according to GEO): Nov 21 2005 36 21 from whole brain 59 35 out of mouse bone marrow LEUK_SR on Affymetrix GeneChip Human Full Length Array HuGeneFL Endothelium 1000 3-day-denervated tibialis anterior muscles from runx1f/- control mice Treatment, type=add, description=runx1f/- Source GEO sample is GSM99421 Last updated (according to GEO): Mar 08 2006 1000 Hippocampus 14 NT C4 Treatment, type=add, description=10ng/mL Ciliary neurotrophiic factor, 4d Source GEO sample is GSM92502 Last updated (according to GEO): Jan 13 2006 n/a Source GEO sample is GSM178044 Last updated (according to GEO): Jun 11 2007 Biopsy of a colorectal adenoma from patient #32 Congenital Abnormality 853 outer medulla 31 43 Male 71.2 yr before antibody enrichment scan 1 (U133B) 1000 Brain Recurrent Carcinoma 875 5 0 brain striatum 34 42 Rostral #2 Gene expression was evaluated in the myocardium of male Wistar rats after a single sc administration of 0.5 mg of isoproterenol, a ?-adrenergic agonist that causes acute tachycardia with subsequent myocardial necrosis. Histology of the heart, clinical chemistry and hematology were evaluated at 9 time-points (0.5 hr to 14 d post-injection). Myocardial gene expression was evaluated at 4 time-points (1 hr to 3 d). Contraction bands and loss of cross striation were identified on phosphotungstic acid-hematoxylin-stained sections 0.5 hr post-dosing. Plasma troponin I elevation was detected at 0.5 hr, peaked at 3 hr, and returned to baseline values at 3 d post-dosing. Interleukin 6 (Il6) expression spiked at 1-3 hr and was followed by a short-lived time-dependant dysregulation of its downstream targets. Concurrently and consistent with the kinetics of the histologic findings, many pathways indicative of necrosis/apoptosis (p38 MAPK signaling, NF-kB signaling) and adaptation to hypertension (PPAR signaling) were over-represented at 3 hr. The 1 d and 3 d time-points indicated an adaptative response, with down-regulation of the fatty acid metabolism pathway, up-regulation of the fetal gene program, and superimposed inflammation and repair at 3 d. These results suggest early involvement of Il6 in isoproterenol-induced myocardial necrosis and emphasize the value of early time-points in transcriptomic studies Last Updated (by provider): Jun 01 2007 Contributers: Charu Kanwal Igor Mikaelian CNS-SpinalCsev-Adult-7d-4C-s2 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92348 Last updated (according to GEO): Jan 13 2006 of the atrial 647 659 Brain 1000 21 0 acute myeloid leukemia 861 Neoplasm Metastasis zhang-affy-mouse-175010 GSE6467 5 0 brain Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22572 Last updated (according to GEO): Sep 14 2005 of G protein? 285 297 26 0 Allergic contact dermatitis 462 458 iris 30 19 Solid tumor normal human skeletal muscle sample 2 DIV14 cortical neuron, control 2 861 Cerebral cortex Nervous system structure 901 Whole blood 0 10 Primary tumor 19 32 Primary Neoplasm 1000 PGA-MFD-MutantPD1-1aBv2-s2 Normal Source GEO sample is GSM176355 Last updated (according to GEO): Apr 09 2007 testis 52 58 GSE2392.1 none Source GEO sample is GSM239853 Last updated (according to GEO): Dec 07 2007 DMSO-control NG108 neuronal cells 7 mdx5cv quadriceps sample 1 Utricle structure 861 of somatomotor cortex 21 41 vehicle treatment, 24 hour time point, biological replicate 2 Brain 861 Head and neck cancer Source GEO sample is GSM155726 Last updated (according to GEO): Apr 24 2007 Normal Source GEO sample is GSM176145 Last updated (according to GEO): Apr 09 2007 Epithelium 865 **** Source GEO sample is GSM4322 Last updated (according to GEO): May 27 2005 from the femurs 95 109 3 0 Lung SWR/J Acute morphine treated, striatum, biological replicate 3 Source GEO sample is GSM187997 Last updated (according to GEO): Jun 14 2007 Subcutaeous isolated adipocytes, rep2 at the Human Brain 724 741 Autistic Disorder 1000 861 Brain plasma cells 332 344 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL4 for 60min Source GEO sample is GSM5631 Last updated (according to GEO): May 27 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-beta (IFN beta) for 240min Source GEO sample is GSM5599 Last updated (according to GEO): May 27 2005 Nasal Epithelium Inhalation Formaldehyde 07ppm 6h ID129 brain, unknown: R2A_e1_le2 861 Parkinson Disease 5 0 brain Small Intestine; Ileum Keywords = mouse gene expression database Source GEO sample is GSM29300 Last updated (according to GEO): May 27 2005 0 Frontal Cortex 13 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=700630 LaserPower=2.081.28 Lot batch = LC17N109 Source GEO sample is GSM4827 Last updated (according to GEO): Nov 21 2005 in bronchial epithelia 311 332 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211344 Last updated (according to GEO): Jul 18 2007 during acute measles 336 355 brain, Right Parietal Lobe: Extract71_le2 Gene expression data from retinas of two young SAMP10//Ta mice Source GEO sample is GSM143736 Last updated (according to GEO): Jan 24 2007 Cerebral cortex 861 7 Entorhinal Cortex 23 osteoblast 630 640 Medulla_Oblongata Source GEO sample is GSM18766 Last updated (according to GEO): Sep 25 2006 Brain 1000 1000 Dermatomyositis 11 0 mouse liver at the Human Brain 725 742 Migration Source GEO sample is GSM19105 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T10) extracted from rats 14d following mild injury Source GEO sample is GSM31307 Last updated (according to GEO): May 27 2005 Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM182004 Last updated (according to GEO): Apr 13 2007 Liver 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145984 Last updated (according to GEO): Nov 20 2006 PriG_5%O2_Expt3_Day2_rep1 112 98 from the kidney 2_hypothalamus_3hrs_sleep_#136 1000 Brain Temporal change in gene expression in the rat dentate gyrus following passive avoidance learning. 983 Structure of horn of uterus cerebellum 7 16 (cortex 19 25 Coronary heart disease 913 H9SGK99091502 7 0 prostate hippocampus rattus_norvegicus_strain iP animal_number 5 hrs nasal epithelium 1126 1146 Stria 861 861 Cerebral cortex Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 30min after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44492 Last updated (according to GEO): May 27 2005 663 mesenchymal stem cell 642 Primary tumor 19 32 1000 Tibialis anterior muscle structure Gene expression data from mouse colon Source GEO sample is GSM198113 Last updated (according to GEO): Aug 22 2007 335 325 The jejunum with autism spectrum disorder 37 65 Head and neck cancer Source GEO sample is GSM155674 Last updated (according to GEO): Apr 24 2007 A SIT D098 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108615 Last updated (according to GEO): Aug 22 2006 Breast 5 Disease Mucous Membrane 861 861 Cerebral cortex Expression profiling of spinal cord section (T10) extracted from rats 4h following mild injury Source GEO sample is GSM31334 Last updated (according to GEO): May 27 2005 MeHg intervention with PK11195 Liver 1000 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201808 Last updated (according to GEO): Jun 20 2007 days nasal epithelium 1126 1147 Gene expression data from postmorten brain regions Source GEO sample is GSM145772 Last updated (according to GEO): Nov 20 2006 human caudate nucleus Source GEO sample is GSM86823 Last updated (according to GEO): Feb 08 2006 This is replicate 2 of the 24 hour sample from passive avoidance trained rats. Source GEO sample is GSM17407 Last updated (according to GEO): Aug 22 2007 GC (HKG71N) B406 on Affymetrix GeneChip Human Full Length Array HuGeneFL Skeletal bone 861 165T low dose 12h, replicate 1 1000 Testis 1000 frontal lobe Gene expression profile of the cell line UB/OC-1 grown for 3 days under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1520 Last updated (according to GEO): May 27 2005 brain 0 5 Heart Atrium 1000 Atypical antipsychotic Clozapine has a superior antipsychotic and antimanic effects compared to other antisphicotics. Its widespread use was limited by the side effects of agranulocytosis, cardiomyopathy and metabolic anomalies such as weight gain, and diabetes. Very little is known about mechanisms by which Clozapine works. The aim of this experiment is to compare the chronic gene expression profile (i.e four weeks) of the atypical antipsychotic Clozapine to the typical antipsychotic drug Haloperidol using gene expression Microarray in order to understand the intercellular mechanism behind the therapeutic and the toxic effects of Clozapine. Last Updated (by provider): Dec 12 2006 Contributers: Mie A Rizig Hugh M Gurling PGA-HMO-MObese-4aUA-s2 PGA-Band_Sham_1w_7-m5 of a GIST 992 1000 CNS-SC_CtrB24h-1C-s2 ventral striatum wistar 4026 freehand block dissections, removed only cortex, individual animal, 10 weeks old, male Wistar ventral striatum file:p4026w Source GEO sample is GSM15191 Last updated (according to GEO): Oct 28 2005 entorhinal cortex layer II stellate island cells Source GEO sample is GSM107540 Last updated (according to GEO): May 01 2006 Retina 1000 H9LMS00092709 1st 6hr C-CA1 Normal Source GEO sample is GSM175823 Last updated (according to GEO): Apr 09 2007 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184748 Last updated (according to GEO): Apr 26 2007 Rat SCN Sample 9 (Technical replicate - 0 hr) Morula replication 2 Keywords = preimplantation Keywords = development Source GEO sample is GSM14688 Last updated (according to GEO): May 28 2005 in the endoplasmic reticulum 323 350 Normal human fetal cartilage from 18-22 weeks. Source GEO sample is GSM149647 Last updated (according to GEO): Jul 06 2007 Gene expression data from mouse colon Source GEO sample is GSM198107 Last updated (according to GEO): Aug 22 2007 Skeletal bone 861 861 Colon Dysregulation of Gene Expression in the 1-Methyl-4-Phenyl-1,2,3,6-Tetrahydropyridine-Lesioined Mouse Substantia Nigra 861 Cerebellum Epithelium 861 884 Vestibular ganglion Brain 861 Sample # 1530-1 Gene expression data from postmorten brain regions Source GEO sample is GSM145091 Last updated (according to GEO): Nov 20 2006 Breast 1 Disease 0 15 of coronary artery disease 317 342 GSE2873 5 0 brain Cerebellum_naive_ISS55_A 20 0 human caudate nucleus none Source GEO sample is GSM210347 Last updated (according to GEO): Jul 16 2007 861 Malignant Neoplasms ER-/LN+/Marks215 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Liver T2+ gr3 tumour Source GEO sample is GSM2506 Last updated (according to GEO): Mar 21 2006 HMVEC-L stimulated with LPS for 4 hours L04R2 272 259 from 6 brains 201 in the frontal cortex 221 0 Human Cortex 11 Utricle and 3 ampullae at E12.5, replicate1 H9RGV00102609 Heart failure 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with MIP3-alpha (Macrophage inflammatory protein-3) for 30min Source GEO sample is GSM5687 Last updated (according to GEO): May 27 2005 4h2 Motor neurons obtained from a wild type mouse by laser capture microdissection. Source GEO sample is GSM113718 Last updated (according to GEO): Jun 09 2006 Keywords = kidney 236 253 Low Freezing Source GEO sample is GSM92409 Last updated (according to GEO): Jan 13 2006 Duodenum [JunctionChip 3 of 5] To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132979 Last updated (according to GEO): Sep 12 2006 64 47 that whole ovaries 36 21 from mouse brain Blood Test (Blinded) Sample Source GEO sample is GSM130016 Last updated (according to GEO): Sep 18 2007 GM12801 Backskin_WT_P6_rep2 5 0 brain Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. 30min after sham surgery, a 7 mm disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44494 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145203 Last updated (according to GEO): Nov 20 2006 Cell Culture Exposure 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114243 Last updated (according to GEO): Jun 16 2006 Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics. Lymph node metastasis 19 40 Simple annotation: aging, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17542.gif Source GEO sample is GSM81561 Last updated (according to GEO): Sep 22 2006 Brain 861 ventral spinal cord 13 31 Primary Carcinoma 876 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169471 Last updated (according to GEO): Feb 21 2007 brain, cochlea: [3] Sample #3_le1 Brain 1000 DLCL-0049 861 Cerebral cortex Expression profiling of spinal cord section (T10) extracted from rats 7dh following severe injury Source GEO sample is GSM31391 Last updated (according to GEO): May 27 2005 Endometrium 8 Normal 861 Skeletal bone 5 0 brain 861 Acquired Immunodeficiency Syndrome 1BMH02082903_BM_CD105endothelial Cerebral cortex 861 Male 27.1 yr before antibody enrichment scan 1 (U133A) ALS model Source GEO sample is GSM75466 Last updated (according to GEO): Mar 06 2006 366 341 with systemic infections. 861 Neoplasm 492 475 in the PCOS oocyte Replicate1_Voxel G6 458 444 that histone H3 Wild type inbred mice Source GEO sample is GSM83042 Last updated (according to GEO): Nov 10 2005 ovarian tumor: serous Source GEO sample is GSM139458 Last updated (according to GEO): Apr 09 2007 1000 Left Spleen vs ELC Treated B cell 30min (set2) Leukemic fractions of ID28 AML patient have been hybridized. Source GEO sample is GSM103101 Last updated (according to GEO): Feb 26 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145996 Last updated (according to GEO): Nov 20 2006 1000 frontal lobe 12 0 ovarian tumor Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep7 114 101 brains quickly CAD_replicate88 7 frontal cortex 20 373 345 in the ventral tegmental area after infection 3144 3158 Endometrium/Ovary 16 Disease brain, unknown: 00PXR_e1_le1 Spleen vs IL4 Treated B cell 30min (set2) Liver 1000 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159953 Last updated (according to GEO): Feb 02 2007 1000 Heart T-47D hgu95a S1P2-KO-neocortex, biological rep7 (female) 587 577 such tumors Small cell carcinoma of lung 901 1000 Intestines, Small Mutant striatal cells Source GEO sample is GSM82448 Last updated (according to GEO): Jun 26 2007 176 to Haemophilus ducreyi 155 Cerebral cortex 861 Primary tumor 19 32 15 0 human cerebellum 1000 Spleen Anterior nares 1000 N30__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A NL-1884-A411-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Murine_NK_IL-15_24h_1 ALL-B-cell-8 on Affymetrix GeneChip Human Full Length Array HuGeneFL Brn3a Knockout TG e13.5 U74Bv2 1 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs//7271.gif Source GEO sample is GSM79719 Last updated (according to GEO): Sep 22 2006 12 4 of Kidney Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit. Source GEO sample is GSM199974 Last updated (according to GEO): Jul 09 2007 91 from the bone marrow 72 ER negative human primary breast tumor EA02014_41257_H133A_JA-248 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 5 day time point Source GEO sample is GSM159821 Last updated (according to GEO): Apr 23 2007 861 Blood Human lung tissue 55 71 GM18855 NMDA 30 7/8RC (Experiment NMDA1-Run 9136) Treatment, type=time_course, description=samples are treated for 10, 30 or 60 min with NMDA 1mM, the agonist is then washed out and the cells are harvested 24h later, measurement=30.0 m Source GEO sample is GSM96746 Last updated (according to GEO): Feb 14 2006 Gene expression profiling of facilitated L-LTP in VP16-CREB mice reveals that BDNF is critical for the maintenance of LTP and its synaptic capture. spinal cord 37 47 Utricle structure 861 cortex 7 12 Liver 0 4 heart failure 583 595 "Sample 22,>5 yr survival(106 months) age 45 erp yes" on vantveer-oligo GM12873 Expression profiling of spinal cord section (T9) extracted from rats 4h following moderate injury Source GEO sample is GSM31562 Last updated (according to GEO): May 27 2005 861 Ribosomal RNA GSE3651 Wild type inbred mice Source GEO sample is GSM82993 Last updated (according to GEO): Nov 10 2005 Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153775 Last updated (according to GEO): Jan 19 2007 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188724 Last updated (according to GEO): Jun 06 2007 Juvenile astrocytoma 1000 cardiac 746 752 1000 Lung D_U133Plus_17_DLPFC_R WSU1 outer medulla 31 43 CAD_replicate61 GSE2917 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27027 Last updated (according to GEO): May 27 2005 Epithelium of bronchus 983 Identification of activity-dependent gene expression profiles in cultured rat cortical neurons AML cDNA hybridization-ID04-L Epithelium of bronchus 983 7 cerebral cortex 21 FVB/NJ pituitary gland rep2 Gene expression data from epididymal fat tissues. Source GEO sample is GSM215586 Last updated (according to GEO): Aug 07 2007 Infection 1112 1121 RIIS/J_male_hypothalamus Source GEO sample is GSM184216 Last updated (according to GEO): Apr 26 2007 Diaphragm 14 Day mdx rep 1 Parkinson's disease sample x036 0 30 R6/1 wildtype, brain hemisphere Source GEO sample is GSM83873 Last updated (according to GEO): Apr 20 2007 Gene expression data from skeletal muscle at baseline Source GEO sample is GSM230450 Last updated (according to GEO): Sep 19 2007 Richard Almon-23-1133800609479 CBA/J_male_hypothalamus Source GEO sample is GSM184201 Last updated (according to GEO): Apr 26 2007 gfp pos. sorted cells from 3 disected e14.5 cortecies Treatment, type=wait Source GEO sample is GSM135770 Last updated (according to GEO): Sep 12 2006 Exp A, Animal #3, control (0mg/kg) CPF Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours Source GEO sample is GSM246130 Last updated (according to GEO): Dec 03 2007 primary hepatocytes, mouse, control condition Source GEO sample is GSM205896 Last updated (according to GEO): Jul 24 2007 outer medulla 31 43 Gene expression data from postmorten brain regions Source GEO sample is GSM145712 Last updated (according to GEO): Nov 20 2006 Lymphoblastoid Cell Line for Individual 8138.4 log phase 1000 Brain 626 615 PCOS oocytes HNC3055 Cerebellum 1000 17 7 hippocampus on the ventricles 598 614 Wild type inbred mice Source GEO sample is GSM82922 Last updated (according to GEO): Nov 10 2005 1000 Cerebral cortex Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184736 Last updated (according to GEO): Apr 26 2007 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the lv samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12329 Last updated (according to GEO): May 28 2005 0 Human Cortex 11 in mouse hearts 40 54 Esophagus 2 Normal 861 Colon Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles. PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity. Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence. To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips. Source GEO sample is GSM136519 Last updated (according to GEO): Jun 05 2007 Brain 861 Simple annotation: FNH, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7772.gif Source GEO sample is GSM79957 Last updated (according to GEO): Sep 22 2006 frontal lobe 1000 Normal Source GEO sample is GSM175836 Last updated (according to GEO): Apr 09 2007 1000 Brain 1000 Structure of locus ceruleus Brain 1000 Primary Neoplasm 1000 CC437 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114466 Last updated (according to GEO): Jun 16 2006 Richard Almon-10-1138200269680 comparison of olfactory-bulbectomized and sham-operated rats with depressive-like behaviour Source GEO sample is GSM247194 Last updated (according to GEO): Dec 11 2007 176 148 a Duchenne muscular dystrophy Medulla 861 CONTROL_2 of malignancy 326 338 729 718 of melanomas brain, unknown: Sample53_e1_le1 B64 on NCI-7.6k 1000 Spleen 60 45 of the Pituitary Blood Test (Blinded) Sample Source GEO sample is GSM129964 Last updated (according to GEO): Sep 18 2007 Two groups of 3 days old mice were treated with oil or retinoic acid. At day 4 one half of each group was treated with saline solution or dexametasone. Lungs were removed snap frozed for RNA extraction Source GEO sample is GSM4144 Last updated (according to GEO): May 27 2005 226 216 this cancer Brain 861 246 219 of parieto-occipital cortex Brain 1000 Structure of trigeminal ganglion 1000 Trachea 4 Normal olfactory epithelium 194 213 "Sample 85, BRCA1 mutation(10 months) age 30 erp no" on vantveer-oligo Rats 24h after injection with dose kainate. Treatment, type=time_course, description=KA animals are treated with kainate., measurement=24.0 h Source GEO sample is GSM32081 Last updated (according to GEO): May 27 2005 1000 Brain M7TW01010663 Pancreas at e12.5, Chip C, rep 2 to the nose 599 609 CNS-RM_Mod7d-2C-s2 MALME-3M hgu95c 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114472 Last updated (according to GEO): Jun 16 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145761 Last updated (according to GEO): Nov 20 2006 Nasal Epithelium Inhalation Formaldehyde 07ppm 5d ID139 GSE381 21h-Control replication 1 Keywords = preimplantation Keywords = development Source GEO sample is GSM14695 Last updated (according to GEO): May 28 2005 49 /demyelinating disease 70 DR6h(1) 861 Cerebral cortex total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with NGF (Nerve Growth Factor) for 30min Source GEO sample is GSM5698 Last updated (according to GEO): May 27 2005 861 Cerebral cortex Epithelial Cells 1000 Osteoblasts 1000 Mesenchymal stem cells 13 34 PMN_control_0min_Patient8 Type 1 Diabetes patient and the timepoint 1 month after diagnosis. Source GEO sample is GSM228614 Last updated (according to GEO): Sep 11 2007 Tonsil acute myeloid leukemia Source GEO sample is GSM227427 Last updated (according to GEO): Sep 12 2007 bc-ZT9-3 tTA 7288 /J mouse cingulate cortex 25 49 brain 0 5 n/a Source GEO sample is GSM178002 Last updated (according to GEO): Jun 11 2007 Infection 861 HCC (HBV+, HK53) Bipolar Disorder 1000 588 564 of the 16 prostate cancer 5 0 brain 5 0 blood 27 0 Leukemia Chronic Myelogenous 20 0 human caudate nucleus Gene expression data from postmorten brain regions Source GEO sample is GSM145954 Last updated (according to GEO): Nov 20 2006 1000 Coronary Arteriosclerosis 1000 Nose from the cerebellum 20 38 GSE4866 FVBN +Doxy 8337 Arteries 861 gene expression from allergen stimulated mouse lung Source GEO sample is GSM158134 Last updated (according to GEO): Jan 25 2007 NA12751 growth 3, replicate 4 Liver 1000 Cerebral cortical contusion in rat, 1 dpi, #2 Bone Marrow 1000 Proliferative endometrium from normal patient Source GEO sample is GSM150201 Last updated (according to GEO): Dec 14 2006 Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68036.gif Source GEO sample is GSM137410 Last updated (according to GEO): Sep 26 2006 129S6/SvEvTac bed nucleus of the stria terminalis rep2 (430 2.0 Array) Osteoblasts 1000 Date : 10/3/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 12 hrs post-injection Intervention : none Risk: estimated 20% increased risk for encephalopathy Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AG363 Source GEO sample is GSM12253 Last updated (according to GEO): May 28 2005 plasma cells 50 61 Cerebral cortex 1000 Blood Test (Blinded) Sample Source GEO sample is GSM129977 Last updated (according to GEO): Sep 18 2007 5 0 Uterus AT3-hTERT_1.5Gy_6h_C5_27019 thymocytes_DN3_1 stria terminalis 1000 Bone marrow, Mesenchymal stem cells: T4-1-101103_e1_le1 1000 Cochlear structure 1000 Prostate G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Source GEO sample is GSM9637 Last updated (according to GEO): May 28 2005 Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22570 Last updated (according to GEO): Sep 14 2005 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118339 Last updated (according to GEO): Jul 11 2006 CS 3147149A Skin; Fetal Skin Day 16 Keywords = mouse gene expression database Source GEO sample is GSM29436 Last updated (according to GEO): May 27 2005 PP243_unifected_Skin biopsy 5 0 Spleen Breast 3 Disease 0 15 276 260 in the rat retina Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 0948 blood Fibroblasts 1000 embryonic hearts 1064 1079 86 70 Fetal liver cells I_U133A_31_AnCg 330 324 uterus (No additional Information) Source GEO sample is GSM114424 Last updated (according to GEO): Jun 19 2006 66 50 Tongue epidermis Wild type inbred mice Source GEO sample is GSM82973 Last updated (according to GEO): Nov 10 2005 901 Caudate nucleus structure SN:Human Glioblastoma Biopsy 10514 1000 Spleen Diet induced changes in mouse liver mRNA profiles. One of 3 replicates of LDL receptor deficient mice maintained for 12 weeks on high fat Western style diet. Keywords = LDL receptor deficiency, high fat diet, atherosclerosis, liver Source GEO sample is GSM5410 Last updated (according to GEO): May 27 2005 mouse brain 478 489 84 69 by heart failure 751 731 of corneal epithelium Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9932.gif Source GEO sample is GSM79910 Last updated (according to GEO): Sep 22 2006 of mouse brain 9 23 1000 Prostate carcinoma tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44869 Last updated (according to GEO): May 27 2005 Muscle 1000 1000 Brain This is the mutant littermate at postnatal day 5 pooled 4 animals Lot batch = Source GEO sample is GSM4085 Last updated (according to GEO): May 28 2005 Expression profiling of somatomotor cortex extracted from rats at 4h following moderate injury Source GEO sample is GSM44450 Last updated (according to GEO): May 27 2005 Richard Almon-12-1133800609089 8 0 pituitary 121T 861 Cerebral cortex none Source GEO sample is GSM123204 Last updated (according to GEO): Jul 26 2006 Category: Tissue Rejection Subcategory: Kidney Wegners reccurence also in biopsy Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=790640 LaserPower=4.293.91 Lot batch = LC17N136 Source GEO sample is GSM4840 Last updated (according to GEO): Nov 21 2005 1000 Neuraxis nasal epithelial cells 28 49 861 Cerebellum Measles 861 754 749 (PNETs 0 Human Cortex 11 861 Brain MGMH030311039Btrachea 1000 Hippocampus Menstruation blood, HRF treatment, primary E6HRF 15 0 human cerebellum VDXRHU_1246 1000 Hippocampus in seminoma 28 38 NCI-H322 hgu95d TEL-AML1-C22 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1037 of transitional epithelium 1012 CNS-SpinalC-30mAdult-5B-s2 MF-35 13 0 G4 optic nerve adrenal_gland_cortex_4 Source GEO sample is GSM80608 Last updated (according to GEO): Mar 31 2006 Occipital lobe 861 Pituitary Gland 861 861 Muscle Cerebellum_nontransgenic control S46_10 months_replicate 2 928 Endometrium 8-cell embryo replication 4 Whole Brain 73 83 17 0 Trigeminal ganglia such as Post-Traumatic Stress Disorder 70 107 We have developed gene-targeted mice with deletion of Nkx2.5. Embryos were isolated at embryonic day 9.5 and the middle third containing the heart was run on Affymetrix Mu11kA and Mu11kB arrays. For more information about this model see http://cardiogenomics.med.harvard.edu/groups/proj1/pages/csx_home.html Last Updated (by provider): May 29 2005 Contributers: Martina Schinke Iuan Chen Seigo Izumo Lauren E Riggi Includes GDS49. Update date: Apr 04 2003. Dataset description GDS49: Use of E9.5 Csx/Nkx2.5 mutant embryos to identify downstream target genes and affected pathways of Nkx2.5 which has a function in cardiac differentiation.. Includes GDS50. Update date: Apr 08 2003. Dataset description GDS50: Use of E9.5 Csx/Nkx2.5 mutant embryos to identify downstream target genes and affected pathways of Nkx2.5 which has a function in cardiac differentiation.. Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12671.gif Source GEO sample is GSM79955 Last updated (according to GEO): Sep 22 2006 CNS-SCsev_InjB7d-1A-s2c Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188730 Last updated (according to GEO): Jun 06 2007 brain, cerebral cortex: Rat_02-130_TTX_Lipska_e1_le1 Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203964 Last updated (according to GEO): Aug 02 2007 human frontal cortex Source GEO sample is GSM87015 Last updated (according to GEO): Feb 08 2006 913 Coronary heart disease 29 0 cerebral cortex wistar ky 3912 Control 1 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:308, Count:32 Corner- Avg:38633, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:4.582736,SFGene:All Background:Avg:422.88,Stdev:4.58,Max:441.7,Min:411.8 Noise:Avg:8.65,Stdev:0.46,Max:9.9,Min:7.1 RawQ:12.76 Keywords = ALL Source GEO sample is GSM3428 Last updated (according to GEO): May 28 2005 5 0 brain C57L/J Basal Ganglia B Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68207 Last updated (according to GEO): Jul 07 2006 Lung 1000 hippocampal glutamatergic CA1 pyramidal neurons Source GEO sample is GSM35824 Last updated (according to GEO): May 27 2005 outer medulla 31 43 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225705 Last updated (according to GEO): Nov 05 2007 accumbens rattus_norvegicus_strain iP animal_number 1 70 40 without coronary artery disease 15 0 human cerebellum 214 192 in the small intestine 37 25 in leprosy to Gene expression data from postmorten brain regions Source GEO sample is GSM145337 Last updated (according to GEO): Nov 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145406 Last updated (according to GEO): Nov 20 2006 the blood 393 402 Deltoid Muscle 2 Normal nipple_cross-section_3 Source GEO sample is GSM80742 Last updated (according to GEO): Mar 31 2006 PMN_control_180min_Patient12 24 0 human prostate PC3 tumors LungP5_221AFBG_077b.txt To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at ?80C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at ?80°C before routine processing for GeneChip analysis. Source GEO sample is GSM28665 Last updated (according to GEO): Oct 28 2005 10 7 Left 200 in the frontal cortex 220 Stria 861 Spleen 0 5 brain, Left Temporal Lobe: Extract47_le2 1000 Spleen Amygdaloid structure 861 175 165 bone marrow Lymphoblastoid Cell Line for Individual 8157.3 log phase V5-P447 Gene expression data from postmorten brain regions Source GEO sample is GSM146074 Last updated (according to GEO): Nov 20 2006 normal human skeletal muscle sample 9 861 Cardiomyopathies Gene expression data from postmorten brain regions Source GEO sample is GSM145898 Last updated (according to GEO): Nov 20 2006 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13022.gif Source GEO sample is GSM76437 Last updated (according to GEO): Sep 22 2006 924 /2 cortex 932 1000 Retina C57L/J Cingulate Cortex B KT96_AR2/DT/IN PriG_5%O2_Expt3_Day5_rep1 Plasma 861 NA12044 1000 Liver autism 0 5 19 0 human frontal cortex 1000 Heart brain, Entorhinal Cortex: Sample10_e1_le1 29 6 (interventricular septum 1000 frontal lobe Cardiac-specific TNF-alpha transgenic mouse is an excellent model to study the pathologenesis of heart failure. Affytrix U74V2A was used to analyzed the gene expression profile of mice at the time point of compensated hypertrophy and dilated heart failure. Source GEO sample is GSM8988 Last updated (according to GEO): May 28 2005 Untreated,# 2 CNS-SC_InjB4h-4C-s2 875 Refractory Carcinoma Y HID D003 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108631 Last updated (according to GEO): Aug 22 2006 Lymphoblastoid Cell Line for Individual 8091.4 log phase Richard Almon-20-1138200270055 Ventral Tegmental Area 1000 Small cell carcinoma of lung 867 Whole neuroblastoma tumor_2216 1000 Impaired cognition Tumor__Breast_Adeno_92_I_078 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A M_U133Plus_113_HC in the heart 600 611 1000 Spleen Heart 861 A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism Source GEO sample is GSM5985 Last updated (according to GEO): Nov 21 2005 1000 Lung Disease Source GEO sample is GSM176405 Last updated (according to GEO): Apr 09 2007 Seminoma 1000 NCI60.42_LABEL46EXTRACT45SUB3 Source GEO sample is GSM134205 Last updated (according to GEO): Aug 06 2007 1000 Brain from ventral prostate 21 41 Communicable Diseases 1000 G9a-K165A_2 Spleen 1000 861 Cerebellum Cerebral cortex 901 861 Heart Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID52 ventral tegmental area long access to cocaine replicate 1 none Source GEO sample is GSM239926 Last updated (according to GEO): Dec 07 2007 cardiac 763 769 Gene expression data from a hippocampus from mouse injected 10 mg/kg nicotine Source GEO sample is GSM147426 Last updated (according to GEO): Jan 03 2007 This is the eighth replicate for the VTA neurons which were captured using LCM. Source GEO sample is GSM19341 Last updated (according to GEO): May 27 2005 Expression profiling of moderately injured raphe at 28d in rats Source GEO sample is GSM41595 Last updated (according to GEO): May 27 2005 Gene expression data from a placenta with chronic malaria Source GEO sample is GSM183612 Last updated (according to GEO): Apr 23 2007 Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203972 Last updated (according to GEO): Aug 02 2007 HC74 CN B None Source GEO sample is GSM214244 Last updated (according to GEO): Aug 01 2007 Blood 861 1000 Cardiomyopathy, Alcoholic 437_1 Gene expression data from postmorten brain regions Source GEO sample is GSM145077 Last updated (according to GEO): Nov 20 2006 Primary Carcinoma 876 basal- 22 27 KT1009_N AMM_0_0_Male8_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111852 Last updated (according to GEO): Nov 21 2006 Heart 861 Whole brain 0 10 ISR12-PERK-TM2 RNA from 2ug/ml tunicamycin treated PERK-/- cells. The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10895 Last updated (according to GEO): May 28 2005 Parkinson Disease 1000 861 Brain no additional Source GEO sample is GSM199191 Last updated (according to GEO): Jun 08 2007 ALLB-cell49 on Affymetrix GeneChip Human Full Length Array HuGeneFL 861 Cardiomyopathies VDXIGRU_171620 cortex 27 33 858 Mesodermal cell Cerebral cortex 1000 18 0 Human endometriosis Identification of gene expression profile in tolerizing murine cardiac allograft by costimulatory blockade. 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113906 Last updated (according to GEO): Jun 16 2006 no additional Source GEO sample is GSM199074 Last updated (according to GEO): Jun 08 2007 brain, hippocampus: CH7_e1_le1 Carcinoma of lung 884 Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging and comparing calorie restricted-fed 30-month-old to control-fed 30-month-old to investigate effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7457 Last updated (according to GEO): May 27 2005 The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76937 Last updated (according to GEO): Oct 11 2005 processed in batch 4 Source GEO sample is GSM90408 Last updated (according to GEO): Mar 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145549 Last updated (according to GEO): Nov 20 2006 rad001 12h, biological rep5 Neo6, no treatment 19 0 Head and neck cancer Retina [JunctionChip 1 of 5] Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:239, Count:32 Corner- Avg:38822, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:7.316926,SFGene:All Background:Avg:371.14,Stdev:5.69,Max:385.0,Min:359.1 Noise:Avg:10.15,Stdev:0.33,Max:11.2,Min:9.4 RawQ:12.76 Keywords = ALL Source GEO sample is GSM3492 Last updated (according to GEO): May 28 2005 knockin mouse cerebellum Treatment, type=time_course, measurement=11.0 weeks Source GEO sample is GSM53354 Last updated (according to GEO): Jul 06 2005 865 Disorder of artery LPS_pre_LPS_restimulation_rep_C Transplant Series 25 Left, Transplant # 3 cerebral cortex sprague 3916 Brain 861 25 7 Right Parietal Lobe none Source GEO sample is GSM239912 Last updated (according to GEO): Dec 07 2007 MGMH030312056Bbonemarrow 861 Acquired Immunodeficiency Syndrome during neurite outgrowth 28 51 brain, cerebral cortex: Rat_03-32_NroLep_Lipska_e1_le1 Medulla 1 Normal mouse brain 478 489 1000 Left AcB61 #12242847 outer medulla 31 43 NCI60.19_LABEL23EXTRACT22SUB3 Source GEO sample is GSM134089 Last updated (according to GEO): Aug 06 2007 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225653 Last updated (according to GEO): Aug 31 2007 Prostate 861 of mouse brain 9 23 Brain Stem 1000 Laser Capture Microdissection (LCM) to isolate tissue sections of the hippocampus area of Rasgrf1 knockout mice brains Source GEO sample is GSM209506 Last updated (according to GEO): Jul 12 2007 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225672 Last updated (according to GEO): Nov 02 2007 4wkA "17 hr Hela Double Thymidine, exp3" Heart Atrium 1000 normal lung 1074 Source GEO sample is GSM17289 Last updated (according to GEO): May 28 2005 072801 Mock 06.00 hr. T-Cell Plasma 861 Squamous cell carcinoma 884 mouse brain 478 489 359 in the frontal lobe 377 Bladder sample 1086-1 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114232 Last updated (according to GEO): Jun 16 2006 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11568 Last updated (according to GEO): May 28 2005 Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183412 Last updated (according to GEO): Apr 23 2007 Olfactory Epithelium 1000 Malignant Neoplasms 861 olfactory epithelium 194 213 7 cerebral cortex 21 Primary Neoplasm 1000 Cochlear nucleus structure 861 GBM: 6A33 Female 23.5 yr before antibody enrichment scan 1 (U133B) 861 Adipose tissue Most neuropharmacological agents and many drugs of abuse modulate the activity of heptahelical G-protein-coupled receptors. Although the effects of these ligands result from changes in cellular signaling, their neurobehavioral activity may not correlate with results of in vitro signal transduction assays. 5-Hydroxytryptamine 2A receptor (5-HT2AR) partial agonists that have similar pharmacological profiles differ in the behavioral responses they elicit. In vitro studies suggest that different agonists acting at the same receptor may establish distinct patterns of signal transduction. Testing this hypothesis in the brain requires a global signal transduction assay that is applicable in vivo. To distinguish the cellular effects of the different 5-HT2AR agonists, we developed an assay for global signal transduction on the basis of high throughput quantification of rapidly modulated transcripts. Study of the responses to agonists in human embryonic kidney 293 cells stably expressing 5-HT2ARs demonstrated that each agonist elicits a distinct transcriptome fingerprint. We therefore studied behavioral and cortical signal transduction responses in wild-type and 5-HT2AR null-mutant mice. The hallucinogenic chemicals (+/-)-2,5-dimethoxy-4-iodoamphetamine (DOI) and lysergic acid diethylamide (LSD) stimulated a head-twitch behavioral response that was not observed with the nonhallucinogenic lisuride hydrogen maleate (LHM) and was absent in receptor null-mutant mice. We also found that DOI, LSD, and LHM each induced distinct transcriptome fingerprints in somatosensory cortex that were absent in 5-HT2AR null-mutants. Moreover, DOI and LSD showed similarities in the transcriptome fingerprints obtained that were not observed with the behaviorally inactive drug LHM. Our results demonstrate that chemicals acting at the 5-HT2AR induce specific cellular response patterns in vivo that are reflected in unique changes in the somatosensory cortex transcriptome. B6 day 1, biological rep 2, tech rep 2 NoCAD_replicate5 Prostate 3 Disease C57BL/6 benchmark dataset: Embryonic day 15.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25175 Last updated (according to GEO): May 27 2005 Normal Pancreas HC68 CN B Voxel C1 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1400 Last updated (according to GEO): Nov 21 2005 G7 temporal retina 861 Cerebellum at the Human Brain 724 741 striatum rattus_norvegicus_strain iP animal_number 5 R722P00829 731 in skeletal muscle 713 Cerebellum 368 377 1M_120502 CT5-2 We report a genome-wide expression analysis of cultured rat cortical neurons treated with specific pharmacological agents, a model with alterations in neuronal activity. Using the microarray approach in combination with microelectrode array (MEA) technology, we ascertained out of approximately 27,000 genes 248 activity-dependent genes, which encompass a large number of members of distinct families, including synaptic vesicle proteins, ion channels, signal transduction molecules, synaptic growth regulators, and others. These genes were further confirmed to be Ca2+-sensitive, largely regulated by Ca2+ influx through N-methyl-D-aspartate (NMDA) receptors, and partly through L-type voltage-gated Ca2+ channels (VGCCs). In addition, the dynamics of gene expression cascades, specifically and temporally regulated, and the pools of those downstream genes, selectively responded to particular routes of Ca2+ entry, were also elucidated, as well as the functional consequences of candidate genes associated with synaptic plasticity. Last Updated (by provider): Nov 24 2006 Contributers: Guangxin Xiang S: Shock alone. Young male C57BL/6J mice were placed into the novel context 2 hours prior to receiving the training paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals remained in the training chamber for 1 hour after the last shock. RNA was extracted was extracted 4 hour after the last shock treatment. Source GEO sample is GSM4556 Last updated (according to GEO): May 27 2005 KO_sham_med_4 brain_DLPFC_bipolar B_mr781 Parkinson Disease 861 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211338 Last updated (according to GEO): Jul 18 2007 SNB-19_CL12002_CNS Osteoblasts 1000 in blood 16 23 NA Source GEO sample is GSM84314 Last updated (according to GEO): Dec 01 2005 1000 Cerebral cortex brain, hippocampus: LH5_e1_le1 901 Lung diseases CNS-SC_InjB24h-2C-s2 22 0 Normal epithelial cells (cortex 19 25 OA 5 in frontal cortex 69 85 Gene expression data from postmorten brain regions Source GEO sample is GSM144974 Last updated (according to GEO): Nov 20 2006 136 131 Aortae Male 73.5 yr after antibody enrichment scan 2 (U133A) 861 Epithelium 1000 Diabetes Mellitus, Insulin-Dependent Neoplasm 861 5 0 Spleen Macrophage 14smi028 1000 Mammary gland 44 10 from fresh prepared organ of Corti normal testis 54 66 Gene expression data from the right forebrain of C57BL mouse received Haloperidol oral treatment four weeks. Source GEO sample is GSM149808 Last updated (according to GEO): Dec 12 2006 CAD_replicate35 15 0 human cerebellum Gene expression profile of the cell line UB/OC-1 grown at 33C (undifferentiated, day 0) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1533 Last updated (according to GEO): May 27 2005 brain, cerebral cortex: Rat_02-48_VHL_Lipska_e1_le1 with myocardial infarction 272 297 861 Neoplasm Lymphoma Burkitt 50 65 Muscular Dystrophy, Duchenne 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28822 Last updated (according to GEO): May 27 2005 normal lung 2911 Source GEO sample is GSM17303 Last updated (according to GEO): May 28 2005 Category: Serum-response Subcategory: Fibroblasts Scanning Software: unknown Software version: unknown Lot batch = 412 Source GEO sample is GSM2162 Last updated (according to GEO): Nov 21 2005 eye 0 3 cy3:SHR treated w/ nifedipine and then washed out, biological rep 2g; cy5:pool of 6 WKY control rats Axon 861 Expression profiling of moderately injured raphe at 4h in rats Source GEO sample is GSM41616 Last updated (according to GEO): May 27 2005 brain 0 5 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD19 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD19 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36698 Last updated (according to GEO): May 27 2005 in somatosensory cortex 160 183 861 Nerve 852 843 /- retina Salivary Gland BD Normal Spleen vs Lysophosphatidic Acid Treated B cell 240min (set2) B227 immature DCs treated with anti- FcgRIIB antibody for 24 hrs Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120673 Last updated (according to GEO): May 14 2007 7 frontal cortex 20 lateral hypothalamus short access to cocaine replicate 3 Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM Source GEO sample is GSM207685 Last updated (according to GEO): Jul 09 2007 of coronary artery disease 317 342 ER negative human primary breast tumor EA02014_41282_H133A_JA-1555 H9LMS00092712 1000 Mammary gland total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Prostaglandin E2 for 60min Source GEO sample is GSM5734 Last updated (according to GEO): May 27 2005 CurrentSmoker 77 1000 Infection 5 0 Spleen 858 Prostatic Neoplasms GC (HKG29L) 1000 Brain Primary small cell lung carcinoma 2212 Source GEO sample is GSM17337 Last updated (according to GEO): May 28 2005 1066 1044 between prostate cancer Female 70.7 yr before antibody enrichment scan 1 (U133A) Gene expression data from human colon tumor tissue Source GEO sample is GSM173356 Last updated (according to GEO): Apr 20 2007 tongue_main_corpus_4 Source GEO sample is GSM80845 Last updated (according to GEO): Mar 31 2006 Lymphoblastoid Cell Line for Individual 8089.4 log phase HOP-92 hgu95c Gene expression data from postmorten brain regions Source GEO sample is GSM145181 Last updated (according to GEO): Nov 20 2006 Effect of dietary oils on hippocampus and liver gene expression CNS-SCsev_InjB24h-2C-s2 knockin mouse forebrain Treatment, type=time_course, measurement=11.0 weeks Source GEO sample is GSM53357 Last updated (according to GEO): Jul 06 2005 89 70 isolated theca cells R725P00941 Brain [JunctionChip 2 of 5] tTA 9310 brain, hindbrain and spinal cord: P0KO2_e1_le1 Mental Retardation 1000 brain 0 5 114 101 brains quickly Cardiac 523 530 T3 treatment for ind G 4 0 Heart osteoblast 627 637 nasal epithelial cells 28 49 1000 Primary carcinoma of the liver cells MGMH030311039Atrachea of meningiomas 1581 1594 Myometrium 46 Disease LDLR_HF_1 MCF7 hgu95a UBOC1 Exp A Day 9 (b) Olfactory Epithelium 1000 Fibroblasts 1000 Gonadectomized Dahl-Iwai Female HighSalt OuterMedulla rat6 gdahl_medullar_k_GX_6om_050702 Cerebellum 1000 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213477 Last updated (according to GEO): Jul 31 2007 861 Cholinergic Receptors (No additional information) Source GEO sample is GSM114391 Last updated (according to GEO): Jun 19 2006 23 11 of the kidney JMR-RatInj4h-3bA-s2 Ganglia, Spinal 923 Temporal Cortex Control (AD) 8 1000 Brain 861 Fissure Homozygous O377 mutant mouse line versus wildtype mice Source GEO sample is GSM86416 Last updated (according to GEO): Dec 08 2005 HNC2816 Leukemia, Lymphocytic, Chronic 1000 U87 glioblastoma cell, clone 3.3 (neo-resistant negative control) Keywords = bioinformatics Keywords = gene expression Keywords = cancer Keywords = platelet-derived growth factor Keywords = sterol regulatory element binding protein Keywords = glioblastoma multiformae Keywords = microarray Source GEO sample is GSM34583 Last updated (according to GEO): May 27 2005 Heart 1000 913 Spinal Injuries BL6:4-1 + 4-2 PAG 1000 Cochlear structure 41 29 Control blood mammary epithelial cells Source GEO sample is GSM5163 Last updated (according to GEO): May 27 2005 Donor 2 Time point 0 Infected with HIV-1, RF Lot batch = 11839152 Source GEO sample is GSM2608 Last updated (according to GEO): May 27 2005 MLL-#7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Medulla Oblongata 861 861 Intestines Primary Neoplasm 1000 B220hi sIgM+ Mature B cells sorted out of mouse bone marrow, sort no. 1_2 Source GEO sample is GSM623 Last updated (according to GEO): Mar 17 2006 eTat - Hu3hr - 2 SF-268 hgu95d 60 CN B in bronchial epithelia 311 332 7 0 prostate 14 days age control RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis. Source GEO sample is GSM10048 Last updated (according to GEO): May 28 2005 WKY rep2 335 325 The jejunum 67 52 descending colon Leukemia, Lymphocytic, Acute 901 none Source GEO sample is GSM244646 Last updated (according to GEO): Nov 23 2007 none Source GEO sample is GSM244583 Last updated (according to GEO): Nov 23 2007 the blood 393 402 7 0 prostate Spinal Cord 1000 7 0 prostate mouse brains 187 198 Neoplasm 1000 brain 0 5 1115 1102 cardiomyopathy SCG_sema3A_2h_rep1 Brain 1000 putamen_3 216 Ganglia 210 MGJZ030312065Bdorsalrootganglion PMN_control_180min_Patient1 human cerebellum Source GEO sample is GSM87131 Last updated (according to GEO): Feb 08 2006 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28747 Last updated (according to GEO): May 27 2005 Nrl ko samples were compared to wt at 2 months. Source GEO sample is GSM227465 Last updated (according to GEO): Sep 07 2007 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118344 Last updated (according to GEO): Jul 11 2006 38 26 on a histone- Cerebral cortex 861 Macrophage 14smi081 Large-scale analysis of the mouse transcriptome. Placenta from females with E18 embyros C57BL/6L, female, 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 322.71 Stdv: 17.06 Min: 297.98 Max: 355.16 Source GEO sample is GSM2973 Last updated (according to GEO): Mar 20 2006 Gut 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145033 Last updated (according to GEO): Nov 20 2006 cDNA probe amplified by Nugen kit Source GEO sample is GSM113691 Last updated (according to GEO): Jun 09 2006 Fbx15-null ES (rep2) umbilical cord_nobpd: 8C Superficial 1000 NL-1179-A408-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A D_U133A_9_nAcc with mental retardation 241 263 from colorectal adenoma 21 44 brain, frontal cortex: Sample60_e1_le1 dorsal_root_ganglia_10 Source GEO sample is GSM80630 Last updated (according to GEO): Mar 31 2006 /progenitor cells 414 430 875 Cerebellar Diseases Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153761 Last updated (according to GEO): Jan 19 2007 5 0 brain Levitiracetam frontal cortex 7 Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53460 Last updated (according to GEO): Jul 06 2005 52 37 without malaria UACC-62 hgu95b Brain 861 1000 jejunum HDMTX-10 Cochlear structure 1000 Chronic rejection of renal transplant 1000 H115 CB B Parkinson 0 8 Category: Lymphoma Classification Subcategory: Hematopoetic cell lines Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b026 Source GEO sample is GSM1985 Last updated (according to GEO): Nov 21 2005 Chromosomes 861 901 Heart failure Interatrial septum 865 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114460 Last updated (according to GEO): Jun 16 2006 14 0 Locus Coeruleus Coronary artery 901 MELAN_SKMEL28 on Affymetrix GeneChip Human Full Length Array HuGeneFL Nicotinic Receptors 1000 We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7. Source GEO sample is GSM200755 Last updated (according to GEO): Jul 12 2007 of mouse brain 9 23 Epithelium 861 Lung 1000 117 112 Lipids Hippocampus 1000 Femur 1000 pfc_1038_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Lymphoblastoid Cell Line for Individual 8163.5 log phase from liver 21 30 kidney 37 43 A HID I D008 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108592 Last updated (according to GEO): Aug 22 2006 Plasma 861 Plasma 861 Basal Cell 913 Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep2 Facial nerve nucleus 1000 Cockayne syndrome B cell Source GEO sample is GSM225381 Last updated (according to GEO): Sep 04 2007 D_95Av2_2835_AnCg_1_GS 3 min exposure to halothane prior to immediate perfusion with ice cold saline Keywords = Eckenhoff Keywords = anesthetics Source GEO sample is GSM11380 Last updated (according to GEO): May 28 2005 147 139 the heart 204 194 of retinal 15 7 hindbrain PGA_PA-N_291 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153437 Last updated (according to GEO): Jan 11 2007 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188773 Last updated (according to GEO): Jun 06 2007 EWS-T19 on NHGRI-6.5k_b Neoplasm 861 /tf Frontal Cortex A 10 29 913 Coronary heart disease 861 Blood Control VZ15 41 30 PCOS oocytes GBM: 6A35 #9 Lymphoblastoid Cell Line for Individual 8148.4 log phase 1000 Liver Myocardial Infarction 1000 41 29 Control blood Small cell carcinoma of lung 901 GSE4034 NCI60.55_LABEL59EXTRACT58SUB3 Source GEO sample is GSM134271 Last updated (according to GEO): Aug 06 2007 Week 2 - High Glucose Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141281 Last updated (according to GEO): Oct 26 2006 DLCL-0025 || lc4b059 D_U133A_76_HC 39 21 from mammary glands Cerebellum Source GEO sample is GSM53362 Last updated (according to GEO): Jul 06 2005 NCI60.23_LABEL27EXTRACT26SUB3 Source GEO sample is GSM134105 Last updated (according to GEO): Aug 06 2007 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 2 - Pair 3 - IML Source GEO sample is GSM49886 Last updated (according to GEO): Dec 20 2005 brain, frontal cortex: ADX AM LC b_e1_le1 Heart 861 350 341 (Carcinoma 3 0 skin liver 0 5 1000 Lung nic + nmda5 (Experiment Neuroprotection4- Run 14985) Treatment, type=timepoint, description=primary cortical neurons were treated for 18 h with nicotine 10uM ,NMDA 1mM was added for 30 min, both agonists were then washed out and the cells were harvested 24h later, measurement=24.0 h Source GEO sample is GSM96740 Last updated (according to GEO): Feb 14 2006 Normal Source GEO sample is GSM176370 Last updated (according to GEO): Apr 09 2007 GM18505 Exp A_3, 50mg/kg CPF 16-1 olfactory bulbs 3 22 1000 Brain 257 242 of uterine horns 9 of prefrontal cortex 28 of somatomotor cortex 21 41 Myocardial Infarction 1000 Infection 1000 Autistic Disorder 877 brain, cerebral cortex: NMDA 1_le1 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184739 Last updated (according to GEO): Apr 26 2007 1000 Optic Nerve 861 Stria Large-scale analysis of the mouse transcriptome. Cerebellum C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 251.51 Stdv: 10.45 Min: 237.31 Max: 274.78 Source GEO sample is GSM2912 Last updated (according to GEO): May 27 2005 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13155.gif Source GEO sample is GSM79723 Last updated (according to GEO): Sep 22 2006 1000 Cerebral cortex peripheral blood-CD56NKCells Source GEO sample is GSM18716 Last updated (according to GEO): Sep 25 2006 primary hepatocytes 0 19 RNA samples extracted from astrocytes cultured from wild type and Cx43 null neonatal mice were dye labeled and individually co-hybridized with a reference of labeled cDNAs pooled from a variety of tissues on eight gene arrays containing 8975 mouse DNA sequences. Lot batch = 4 Source GEO sample is GSM8892 Last updated (according to GEO): May 27 2005 1000 Cerebral cortex Lymphoblastoid Cell Line for Individual 8165.5 log phase 67 40 with coronary artery disease Dahl-Iwai Female LowSalt OuterMedulla rat105 dahl_medullar_105_1_OM_053001 MGMH030212057Aspinalcordlower prostate_gland_4 Source GEO sample is GSM80824 Last updated (according to GEO): Mar 31 2006 Primary Neoplasm 1000 brain, Medial Temporal Gyrus: Sample31_e1_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM145297 Last updated (according to GEO): Nov 20 2006 Frontal_Cerebrocortex_Vehicle_6hr_rep7 A VIS D067 PBMCs-Type 1 Diabetes-IDDM61_T1D_4MO 5 0 Spleen M_U133Plus_122_CB 0 cortex 5 blood, adrenal medulla: BG +/- replicate 2_e1_le1 984 973 in M+ tumors normal lung 1074 Source GEO sample is GSM17291 Last updated (according to GEO): May 28 2005 Paravertebral Muscle 5 Disease 0 29 Heart 861 Organ 966 Intestines, Small 901 Primary Neoplasm 1000 Cortex Treatment, type=pharmacogenomic_treatment, description=Chronic Immobilization Stress Source GEO sample is GSM53313 Last updated (according to GEO): Jul 06 2005 36 21 from whole brain NCI60.6_LABEL9EXTRACT8SUB3 Source GEO sample is GSM134024 Last updated (according to GEO): Aug 06 2007 Spinal Cord 861 Exp A, Animal #1, 10mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours Source GEO sample is GSM246136 Last updated (according to GEO): Dec 03 2007 amygdala_5 Source GEO sample is GSM80585 Last updated (according to GEO): Mar 31 2006 Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.43 Subject: 2846 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39036 Last updated (according to GEO): May 27 2005 olfactory bulb 257 270 901 Temporal Lobe This series represents 52 tissues hybridized across 5 different chip patterns. Probes were placed at every exon-exon junction in each transcript. Last Updated (by provider): May 29 2005 Contributers: Christopher D Armour Eric E Schadt Daniel D Shoemaker Patrick M Loerch Philip Garrett-Engele Jason M Johnson Roland Stoughton Ralph Santos Zhengyan Kan John Castle Includes GDS830. Update date: Nov 10 2004. Dataset description GDS830: Monitoring of mRNA splice variants for more than 10,000 multi-exon genes using arrays with oligonucleotide probes positioned at exon-exon junctions. mRNA from 52 tissues and cell lines examined. Results provide tissue distribution of splice variants and identify novel splice variants.. Includes GDS829. Update date: Nov 10 2004. Dataset description GDS829: Monitoring of mRNA splice variants for more than 10,000 multi-exon genes using arrays with oligonucleotide probes positioned at exon-exon junctions. mRNA from 52 tissues and cell lines examined. Results provide tissue distribution of splice variants and identify novel splice variants.. Includes GDS833. Update date: Nov 10 2004. Dataset description GDS833: Monitoring of mRNA splice variants for more than 10,000 multi-exon genes using arrays with oligonucleotide probes positioned at exon-exon junctions. mRNA from 52 tissues and cell lines examined. Results provide tissue distribution of splice variants and identify novel splice variants.. Includes GDS831. Update date: Nov 10 2004. Dataset description GDS831: Monitoring of mRNA splice variants for more than 10,000 multi-exon genes using arrays with oligonucleotide probes positioned at exon-exon junctions. mRNA from 52 tissues and cell lines examined. Results provide tissue distribution of splice variants and identify novel splice variants.. Includes GDS832. Update date: Nov 10 2004. Dataset description GDS832: Monitoring of mRNA splice variants for more than 10,000 multi-exon genes using arrays with oligonucleotide probes positioned at exon-exon junctions. mRNA from 52 tissues and cell lines examined. Results provide tissue distribution of splice variants and identify novel splice variants.. 76 65 from bronchi Untreated versus treated (bortezomib) breast cancer cells. Source GEO sample is GSM120350 Last updated (according to GEO): Jul 20 2006 3ARS02080772a_atrioventricular_node 0 Human Cortex 11 Characterization of weight loss and weight regain mechanisms after Roux-en-Y gastric bypass in rats B62 on NCI-7.6k M_U133A_6_AnCg 861 Thalamic structure Control, biological rep3 Gene expression data from a hippocampus from mouse injected 10 mg/kg nicotine Source GEO sample is GSM147424 Last updated (according to GEO): Jan 03 2007 bronchial epithelia 224 243 Wild type 8 wk old male C57BL/6J mouse hippocampus Source GEO sample is GSM107010 Last updated (according to GEO): Mar 05 2007 5 0 brain 19 0 human frontal cortex Gene expression data from postmorten brain regions Source GEO sample is GSM145018 Last updated (according to GEO): Nov 20 2006 no additional Source GEO sample is GSM199359 Last updated (according to GEO): Jun 08 2007 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD12 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD12 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36679 Last updated (according to GEO): May 27 2005 spleen 299 304 5 0 Spleen Expression profiling of spinal cord section (T9) extracted from rats 72h following moderate injury Source GEO sample is GSM31578 Last updated (according to GEO): May 27 2005 21 0 Mammary Gland @ Lac9 Endometrial Stromal Sarcoma 1000 1000 Skeletal muscle structure human cerebellum Source GEO sample is GSM87145 Last updated (according to GEO): Feb 08 2006 1000 Nervous system structure 31 21 spinal cord GBM Treatment, type=remove Source GEO sample is GSM99494 Last updated (according to GEO): Apr 21 2006 861 Brain thyroid_gland_3 19 0 human frontal cortex Cochlear nuclei pooled from 5 pups to generate one sample for one replicate hybridization out of 5 replicates. In this replicate, RNA underwent one round of linear amplification. Cohybridized with P21_cy5_3. Source GEO sample is GSM44975 Last updated (according to GEO): Jun 08 2005 Cerebral cortex 861 Brain 861 Spleen 1000 M_U133A_32_nAcc Laser captured visceral sensory neurons. Source GEO sample is GSM63693 Last updated (according to GEO): Dec 21 2005 Epithelial Cells 1000 Lmna H222P homozygous male 1 Spleen 1000 Lung; Adult Keywords = mouse gene expression database Source GEO sample is GSM29377 Last updated (according to GEO): May 27 2005 from progenitor satellite cells 36 66 H109 CN A 1000 Spleen 861 Cerebral cortex HapMap JPT Female Source GEO sample is GSM159656 Last updated (according to GEO): Feb 01 2007 1000 Prostate D_U133A_46_DLPFC 901 Caudate nucleus structure 913 Coronary heart disease M_U133A_32_AnCg tongue_main_corpus_3 Blood 1000 1000 Mammary Neoplasms Gene expression data from postmorten brain regions Source GEO sample is GSM145277 Last updated (according to GEO): Nov 20 2006 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24268.gif Source GEO sample is GSM66567 Last updated (according to GEO): Sep 22 2006 Expression profiling of somatomotor cortex extracted from rats at 4h following moderate injury Source GEO sample is GSM44454 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145904 Last updated (according to GEO): Nov 20 2006 0029_1349_H95A2_KF-113_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A hrs nasal epithelium 1126 1146 brain, Primary Visual Cortex: Sample73_e1_le1 861 Adenocarcinoma G42 neurons from cingulate cortex Source GEO sample is GSM63023 Last updated (according to GEO): Dec 01 2005 90-8_Infect_2 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132497 Last updated (according to GEO): Feb 26 2007 SN12C hgu95a Bronchopulmonary Dysplasia 1000 CLL-48 Brain 861 091214 OVR12 on Affymetrix GeneChip Human Full Length Array HuGeneFL VDXRHU_2587 Exaggerated neuroinflammation and sickness behavior in aged mice after activation of the peripheral innate immune system B220+c-kit+ Pre BIcells sorted out of mouse bone marrow, sort no. 3 Source GEO sample is GSM629 Last updated (according to GEO): Mar 17 2006 CNS-SC_CtrA30m-2A-s2 rat kidney at embryonic day 13, rep1 Structure of entorhinal cortex 1000 Starvation 916 Occipital Lobe 5 Normal Parkinson Disease 1000 4 0 Brain Expression profiling of moderately injured raphe at 3 months in rats Source GEO sample is GSM41605 Last updated (according to GEO): May 27 2005 39 24 of the human eye f2#153 versus pool Mouse Brain tissue Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225722 Last updated (according to GEO): Nov 02 2007 377 356 cognitive dysfunction Caudal 1000 brain, frontal cortex: Sample52_e1_le1 109 93 of heart failure 1000 DNA Damage n/a Source GEO sample is GSM178060 Last updated (according to GEO): Jun 11 2007 Oculomotor nucleus 1000 of somatomotor cortex 21 41 262 257 Spleen Carcinoma, Large Cell 888 Neoplasm 861 228 219 Hippocampi cerebellum Source GEO sample is GSM18918 Last updated (according to GEO): Sep 25 2006 Epithelium 861 5 0 brain spinal cord 0 11 Pressure-overload induced hypertrophy model. Mouse was sacrificed 1 week after aortic banding. Keywords = Cardiac hypertrophy Source GEO sample is GSM2243 Last updated (according to GEO): May 27 2005 35 0 Inflammatory myopathy specimen GEIM4 Expression profiling of somatomotor cortex extracted from rats at T0 naive Source GEO sample is GSM41684 Last updated (according to GEO): May 27 2005 Whole Brain 73 83 Liver 1000 NCI60.21_LABEL25EXTRACT24SUB3 Source GEO sample is GSM134095 Last updated (according to GEO): Aug 06 2007 Primary small cell lung carcinoma 3424 87 61 of parieto-occipital cortex mouse brains 187 198 Anterior interpositus nucleus-centered deep cerebellar nuclei were sampled using syringe needles Source GEO sample is GSM84981 Last updated (according to GEO): Mar 29 2006 Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation. Source GEO sample is GSM228470 Last updated (according to GEO): Sep 10 2007 Transitional epithelium 1000 M7TW00121829 Wild type inbred mice Source GEO sample is GSM83013 Last updated (according to GEO): Nov 10 2005 Healthy patient. Source GEO sample is GSM228581 Last updated (according to GEO): Sep 11 2007 cerebellum sprague 3901 Brain 861 1000 Heart failure Kidney YC-2B 861 Leukemia, Lymphocytic, Acute 1500 mg/kg X 6 hr Source GEO sample is GSM129833 Last updated (according to GEO): Sep 18 2007 thalamus_9 Source GEO sample is GSM80852 Last updated (according to GEO): Mar 31 2006 PGA-swim_10min_s995 0 9 Stem cells mdx TA sample 2 Blood 861 865 Disorder of artery olfactory epithelium 194 213 SCLC cell line MS-1 Source GEO sample is GSM17311 Last updated (according to GEO): May 28 2005 (cortex 19 25 in the brain 150 162 Probeset expression data from NA12751 growth 2, replicate 3 Source GEO sample is GSM195210 Last updated (according to GEO): Aug 08 2007 318 298 of ovarian follicles GM10845_technical_rep_2 8071_Lung did not develop PGD 1000 Skin Tumor__Lymphoma_Follicular_FSCC_S98_14359 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A f2#16 versus pool Mouse Brain tissue Individual array of a bladder cancer expression experiment. Source GEO sample is GSM180993 Last updated (according to GEO): Apr 12 2007 1000 Impaired cognition Heart 1000 Gene expression data from normal adrenal gland Source GEO sample is GSM211449 Last updated (according to GEO): Jul 18 2007 Spinal Cord 1000 5 0 Spleen ProstateCancer-2 on NHGRI-6.5k_c 43h-Control replication 3 Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231057 Last updated (according to GEO): Sep 26 2007 1000 Spleen Brain_Adult_Salineip_4hr_mouse3(YP3_#60) Neostriatum 1000 39 21 from mammary glands no additional Source GEO sample is GSM199050 Last updated (according to GEO): Jun 08 2007 072801 B7-2 01.00 hr. T-Cell 1000 Neoplasm Metastasis Prostate 861 to the nose 599 609 861 Cerebral cortex Aortic Aneurysm, Abdominal 1000 SN72h(1) 964 Neuroglia Parkinson Disease 1000 acute myeloid leukemia Source GEO sample is GSM227433 Last updated (according to GEO): Sep 12 2007 CNS-SC_InjA14d-3B-s2 Nasal Epithelium 865 1344 1322 by cervical dislocation between the LAD artery 266 287 Cerebral cortex 1000 Gene expression data from rat lungs exposed to Normoxia (room air). Source GEO sample is GSM184875 Last updated (according to GEO): Jun 14 2007 of coronary artery disease 317 342 24 0 Colorectal Adenocarcinoma Infection 1000 Ovarian_Tumor_Endometrioid_CHTN-OE-042 plasma cells 50 61 PBMCs-Type 1 Diabetes-IDDM48_T1D_New Melanoma 127 135 1000 Amygdaloid structure 1000 Leukemia, Myelocytic, Acute Cerebral cortex 1000 5 0 brain Utricle and 3 ampullae at E14, replicate1 1000 Lymphoma N4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A healthy subject Source GEO sample is GSM211112 Last updated (according to GEO): Sep 10 2007 Nose 1000 B_N4 on Affymetrix GeneChip Human Full Length Array HuGeneFL 861 Muscle 861 medulloblastoma 861 Myositis Carcinoma, Papillary 913 Donor A, prior to G-CSF Source GEO sample is GSM178549 Last updated (according to GEO): Aug 09 2007 861 Cerebral cortex from the cerebellum 20 38 861 Anterior Epithelium 861 861 Eye Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs//7301.gif Source GEO sample is GSM79709 Last updated (according to GEO): Sep 22 2006 brain 0 5 110 94 of heart failure 861 Cerebral cortex Analysis of gene expression in mammary epithelial cells transduced with either hTERT, empty LXSN vector or empty BABE vector.. Date GSE361 Last Updated: May 29 2005 Includes GDS337. Update date: May 21 2003. Dataset description GDS337: Effect of overexpression of the telomerase catalytic subunit (TERT) in mammary epithelial cells (HMEC). Findings imply that ectopic telomerase expression modulates growth-controlling genes and enhances cell proliferation.. 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114444 Last updated (according to GEO): Jun 16 2006 0 Human Cortex 11 ALL_19 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A osteoblast 627 637 injured cortex 69 82 hrs nasal epithelium 1126 1146 Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002. Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Part of the medium chain triacylglycerol oil in control diet was replaced with: 1.9% fish oil (providing 0.5 dietary wt% DHA and 1.0en%). Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily. Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France). Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h. After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hepatic gene expression analysis. From these 5 mice, livers were dissected according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancourt, France), which consisted of carefully dissecting out the liver, rinsing with 70% EtOH to remove adhering blood, trimming of adhering connective tissue with scissors, cutting into 100-150 mg subsections, freezing in liquid N2, and storing at -80°C until gene expression and lipid analysis. Hepatic lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5). Liver tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hepatic RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips. Source GEO sample is GSM2571 Last updated (according to GEO): Mar 17 2006 NA Source GEO sample is GSM198924 Last updated (according to GEO): Jun 07 2007 R590P01071 Gene expression data from the right forebrain of C57BL mouse received no treatment for four weeks. Source GEO sample is GSM149811 Last updated (according to GEO): Dec 12 2006 Ovary 1000 1000 Carcinoma of bladder forebrain 7 15 494 488 tumors 1000 Cerebral cortex 66 42 out of mouse bone marrow 26 16 of modiolus Plasma 861 GSE3497 glial cells 16 26 Subject code A39 1000 Spleen MO_control_180min_Patient7 processed in batch 3 Source GEO sample is GSM90438 Last updated (according to GEO): Mar 20 2006 hyperplasia 276 286 HapMap YRI_parent Female Source GEO sample is GSM159694 Last updated (according to GEO): Feb 01 2007 Brain 861 brain, cerebral cortex: Rat_02-143_TTX_Lipska_e1_le1 861 Colon Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68127 Last updated (according to GEO): Jul 07 2006 Nasal Epithelium Inhalation Formaldehyde 6ppm 6h ID287 Gene expression data from aldosterone-producing adenoma Source GEO sample is GSM211459 Last updated (according to GEO): Jul 18 2007 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b030 Source GEO sample is GSM1977 Last updated (according to GEO): Nov 21 2005 901 Caudate nucleus structure Prosencephalon 861 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181179 Last updated (according to GEO): Jul 12 2007 Epithelial Cells 1000 861 Hypothalamic structure 15 0 human cerebellum with Parkinson's disease 27 50 Disorder of artery 865 Neoplasm 1000 nmda 1h 9/06/02 (Experiment Neuroprotection3- Run 13276) Treatment, type=timepoint, description=primary cortical neurons were treated for 1 h with NMDA 1mM then were harvested, measurement=1.0 h Source GEO sample is GSM96708 Last updated (according to GEO): Feb 14 2006 Wild type voxel I2 bronchial epithelia 224 243 CC8 sample 2 To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132993 Last updated (according to GEO): Sep 12 2006 Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 7393 left_liver_lobe 38 21 from a hippocampus Pharyngeal Mucosa 3 Normal Brain of P10 Gja9 (+/-) C57Bl/6j mouse, replica H3 Two groups of 3 days old mice were treated with oil or retinoic acid. At day 4 one half of each group was treated with saline solution or dexametasone. Lungs were removed snap frozed for RNA extraction Source GEO sample is GSM4145 Last updated (according to GEO): May 27 2005 Squamous cell carcinoma 7 0 24 2.5 mg/kg 2CdA headfold at 3.0h Neoplasm 861 Coronary artery 901 NoCAD_replicate15 acute myeloid leukemia Source GEO sample is GSM227443 Last updated (according to GEO): Sep 12 2007 SCG explant cultured for 5 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246027 Last updated (according to GEO): Dec 03 2007 from a primary branch 21 41 Spleen vs Prostaglandin E2 Treated B cell 240min (set1) Expression profiling of spinal cord section (T8) extracted from rats 7d following severe injury Source GEO sample is GSM31501 Last updated (according to GEO): May 27 2005 n/a Source GEO sample is GSM177887 Last updated (according to GEO): Jun 11 2007 none Source GEO sample is GSM123196 Last updated (according to GEO): Jul 26 2006 861 Heart Diseases We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201770 Last updated (according to GEO): Jun 20 2007 PC 6Hr rat 3586 blood vs. 150mg/kg APAP 6Hr rat 3589 blood Gene expression data from postmorten brain regions Source GEO sample is GSM145061 Last updated (according to GEO): Nov 20 2006 861 Cerebral cortex human caudate nucleus Source GEO sample is GSM86888 Last updated (according to GEO): Feb 08 2006 Infection 861 Background: The prefrontal cortex is important in regulating sleep and mood. Diurnally regulated genes in the prefrontal cortex may be controlled by the circadian system, by the sleep-wake states, or by cellular metabolism or environmental responses. Bioinformatics analysis of these genes will provide insights into a wide-range of pathways that are involved in the pathophysiology of sleep disorders and psychiatric disorders with sleep disturbances. Results: We examined gene expression in the mouse prefrontal cortex at four time points during the 24-hour (12-hour light:12-hour dark) cycle by microarrays, and identified 3,890 transcripts corresponding to 2,927 genes with diurnally regulated expression patterns. We show that 16% of the genes identified in our study are orthologs of identified clock, clock controlled or sleep/wakefulness induced genes in the mouse liver and SCN, rat cortex and cerebellum, or Drosophila head. The diurnal expression patterns were confirmed in 16 out of 18 genes in an independent set of RNA samples. The diurnal genes fall into eight temporal categories with distinct functional attributes, as assessed by the Gene Ontology classification and by the analysis of enriched transcription factor binding sites. Conclusions: Our analysis demonstrates that ~10% of transcripts have diurnally regulated expression patterns in the mouse prefrontal cortex. Functional annotation of these genes will be important for the selection of candidate genes for behavioural mutants in the mouse and for genetic studies of disorders associated with anomalies in the sleep:wake cycle and circadian rhythms. Last Updated (by provider): Oct 30 2007 Contributers: Maja Bucan Kai Wang Sridhar Hannenhalli Shuzhang Yang Otto Valladares 1BMH02082907_PB_CD19BCells Trasnsformed Lymphocytes Bipolar Disorder Affected Twin Pair 1 (DCBD1.1)(TP5) B6_Control_ZT 12_2 P1.2A_KIDNEY_1 91 from the bone marrow 72 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:163, Count:32 Corner- Avg:30417, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:6.501025,SFGene:All Background:Avg:349.21,Stdev:5.59,Max:365.1,Min:336.9 Noise:Avg:8.08,Stdev:0.27,Max:8.9,Min:7.2 RawQ:11.68 Keywords = ALL Source GEO sample is GSM3388 Last updated (according to GEO): May 27 2005 D_U133A_62_DLPFC B220hi sIgM+ Mature B cells sorted out of mouse bone marrow, sort no. 9 Source GEO sample is GSM626 Last updated (according to GEO): May 27 2005 Wild type inbred mice Source GEO sample is GSM82923 Last updated (according to GEO): Nov 10 2005 228 211 in the cerebellum f2#312 versus pool Mouse Brain tissue 964 Body of uterus AJ 8-2-1 Kidney Haloperidol treated 12weeks AffyGC RMA rep6 3AJZ02022762_adrenal gland Mental Retardation 1000 861 Kidney Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184707 Last updated (according to GEO): Apr 26 2007 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92375 Last updated (according to GEO): Jan 13 2006 Leukemia, Myelocytic, Acute 1000 Standard affymetrix protocol Source GEO sample is GSM119712 Last updated (according to GEO): Jul 31 2007 brain, Right Temporal Parietal: Extract84_le2 occipital_lobe_2 contralateral Cortex 7 27 PBMCs-Type 1 Diabetes-IDDM55_T1D_New of the normal mucosa 7 26 spinal cord, ventral spinal cord: D28SDMN3_e1_le1 Heart Septal Defects, Atrial 1000 MO_control_0min_Patient2 Spleen BD Normal 1391 1378 in trisomy 21 human caudate nucleus Source GEO sample is GSM86802 Last updated (according to GEO): Feb 08 2006 Nasal Epithelium 901 25 0 3AJZ02022224_ spinal cord Leukemia, Myelocytic, Acute 1000 Normal Source GEO sample is GSM176298 Last updated (according to GEO): Apr 09 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145747 Last updated (according to GEO): Nov 20 2006 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225690 Last updated (according to GEO): Nov 05 2007 endometrium_9 Source GEO sample is GSM80673 Last updated (according to GEO): Mar 31 2006 JF1/Ms_male_hypothalamus Source GEO sample is GSM184206 Last updated (according to GEO): Apr 26 2007 1000 Spleen Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14354.gif Source GEO sample is GSM79623 Last updated (according to GEO): Sep 22 2006 1000 Lung Medulla Oblongata 861 14 0 Locus Coeruleus PGA_MI_ilv_48h_355 901 Coronary artery 453 434 The descending colon ovary 45 50 901 Caudate nucleus structure ES cell mutant, RNA 308 5 0 brain Sample was obtained from a 46 years old male subject with congestive heart failure. Good quality sample. Keywords = Congestive heart failure, eNOS, gene, dimethylarginine dimethylaminohydrolase Source GEO sample is GSM6549 Last updated (according to GEO): May 28 2005 "1 hr Hela Double Thymidine, exp3" brain 0 5 MuscleRegen-ctx1d-1LLAv2-s2 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213478 Last updated (according to GEO): Jul 31 2007 Lymphoblastoid Cell Line for Individual 8050.3 log phase eTat - Hu9hr - 2 861 Intestines putamen_2 Source GEO sample is GSM80570 Last updated (according to GEO): Mar 31 2006 12 0 ovarian tumor in hippocampus 18 32 Expression profiling of spinal cord section (T10) extracted from rats 0h following laminectomy (naïve) Lot batch = Source GEO sample is GSM4440 Last updated (according to GEO): Oct 28 2005 DNA Damage 1000 /J mouse periaqueductal gray 25 52 PHA, 01.00 hr. T-Cell, Repeat. Brain 1000 Laser capture lung cancer cells Source GEO sample is GSM191016 Last updated (according to GEO): May 25 2007 CNS-SpinalCsev-Adult-7d-3C-s2 091251 CAOV3 on Affymetrix GeneChip Human Full Length Array HuGeneFL S9_Muscle_Insulin_240min atrial septal defects 198 218 Gene expression data from the hippocampus of wild-type mouse Source GEO sample is GSM172956 Last updated (according to GEO): Mar 08 2007 I_U133A_56_Amy 1000 Muscle This dataset contains the gene expression profile of a CD11c high, CD4 positive splenic dendritic cell population. The cells were processed directly upon isolation. Global scaling was applied to Avg Difference intensity values. Keywords = mouse, dendritic cells, spleen Source GEO sample is GSM4697 Last updated (according to GEO): May 27 2005 861 Brain Expression profiling of spinal cord section (T9) extracted from rats 7d following severe injury Lot batch = Source GEO sample is GSM7594 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145990 Last updated (according to GEO): Nov 20 2006 Normal Source GEO sample is GSM176266 Last updated (according to GEO): Apr 09 2007 Tumor__Renal_Carcinoma_Carc_623TO on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Primary tumor 19 32 tissue-specific pattern of mRNA expression - Homo sapiens Abdominal aorta structure 865 brain, cerebral cortex: NMDA 9/06_le1 brain, Left frontal Lobe: Extract11_le2 1000 Brain f2#72 versus pool Mouse Brain tissue of human fibroblasts 44 63 PCA-54 on UMich-10k Whole Brain 62 72 Cerebral cortex 861 Gene targeting in mice has recently demonstrated that transcription factor KLF7 plays a critical role in neurite outgrowth and neuronal survival. Here we extended this genetic evidence by establishing the transcriptional profile of differentiating olfactory sensory neurons (OSNs) in Klf7(-/-) mice, and by identifying relevant genes that are directly regulated by KLF7. Functional clustering of DNA microarray data revealed that loss of KLF7 affects primarily the activity of genes involved in OSN differentiation, axonal growth, cytoskeletal dynamics, cell adhesion and synaptogenesis. Cell transfection experiments, on the other hand, demonstrated that the promoters of the genes encoding the OSN-specific OMP and the adhesion molecule L1 are both activated by KLF7 binding to CACCC motifs. Collectively, these results advance knowledge of transcriptional regulation of olfactory neurogenesis and KLF7 action. Mucous Membrane 861 brain, hippocampus: Hippocampus 9_le1 1000 Prostate Prosencephalon 1000 dorsal skin 11 21 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b059 Source GEO sample is GSM1974 Last updated (according to GEO): Nov 21 2005 40 21 from skeletal muscle 1000 Spleen Oj19: Hippocampus_21PT-AI_rep8 14 0 vantveer-breast from SVG-A glial cells 21 43 14 0 G6 ciliary body Plasma 861 HUMANCULTUREDADIPOCYTE Source GEO sample is GSM18975 Last updated (according to GEO): Sep 25 2006 Lymphoblastoid Cell Line for Individual 8043.4 log phase Gene expression data from postmorten brain regions Source GEO sample is GSM145252 Last updated (according to GEO): Nov 20 2006 901 Epithelial Cells gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134627 Last updated (according to GEO): Jul 09 2007 26T_Infect_2 861 Blood 1000 Coronary Arteriosclerosis of the stria terminalis 50 72 WT 1 VDXOXFU_320 from the olfactory epithelium tissue 172 208 N26__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 67 40 with coronary artery disease Utricle 0 6 We will separately dissect the maxillary and mandibular branches of the E10.5 first branchial arch from wild type, dlx2, dlx1/2 and Dlx5/6 mutants. The tissues wil be flash frozen within 1 min of removal.We have not performed the dissections yet so we dont know how much RNA will be get from each sample, but previous experience suggests that we will need ~10 branchial arches/experiment. Treatment, type=nucleic_acid_extraction, description=We anticipate using this method as it was recommended by TGEN for small amounts of tissue. Source GEO sample is GSM107881 Last updated (according to GEO): Jun 06 2006 Gene expression data from whole brain infected mouse, day 3 Source GEO sample is GSM189618 Last updated (according to GEO): May 16 2007 Heart 861 H9RGV00111001 in the brain 150 162 DLCL-0031 || lc8n108 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28463 Last updated (according to GEO): May 27 2005 861 Gland structure Bone structure of tibia 1000 ADH-1 ip saline ILI 24hrs post ILI sample A the ventricular 1095 1109 Cockayne syndrome B cell Source GEO sample is GSM226283 Last updated (according to GEO): Sep 04 2007 Calorie-related rapid onset of alveolar loss, regeneration, and changes in mouse lung gene expression. Neoplasm 861 CNS-SCsev_InjB24h-3C-s2 ovarian tumor: endometrioid Source GEO sample is GSM139419 Last updated (according to GEO): Apr 09 2007 1000 Coronary Arteriosclerosis 715 702 After the eyes total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Neuropeptide Y for 30min Source GEO sample is GSM5711 Last updated (according to GEO): May 27 2005 Neoplasm 861 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160324 Last updated (according to GEO): Feb 08 2007 1000 Prostate of 6 saccules 5 17 861 Cancer of Neck heart failure 583 595 no additional Source GEO sample is GSM199406 Last updated (according to GEO): Jun 08 2007 97 76 Normal Small Intestine Dahl-Iwai Female LowSalt Cortex rat103 dahl_cortexr_k_103c_072001 1000 Brain Blood 1000 frontal cortex wistar ky 3930 747 tumor cells 757 of isolated livers 1023 1040 Plasma 861 (1 utricle 11 20 Cerebral cortex 861 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225695 Last updated (according to GEO): Nov 05 2007 Keywords = Heart 505 521 928 Endometrium 5 0 Spleen Gene expression data from postmorten brain regions Source GEO sample is GSM145294 Last updated (according to GEO): Nov 20 2006 cerebral cortex 7 21 150 mg/kg X 24 hr Source GEO sample is GSM129863 Last updated (according to GEO): Sep 18 2007 NCI-H23 hgu95a 7 cerebral cortex 21 Secondary malignant neoplasm of lymph node 1000 10 0 Endometrium Gene expression data from whole brain infected mouse, day 6 Source GEO sample is GSM189655 Last updated (according to GEO): May 16 2007 Wild type P46 mouse visual cortex contralateral to monocular enucleation Source GEO sample is GSM97212 Last updated (according to GEO): Feb 17 2006 Osteoblasts 1000 861 Cardiomyopathies 200 in the frontal cortex 220 Category: Lymphoma Classification Subcategory: Chronic Lymphocytic Leukemia Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b046 Source GEO sample is GSM2002 Last updated (according to GEO): Nov 21 2005 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195248 Last updated (according to GEO): Sep 13 2007 CNS-SC_InjA30m-3B-s2 Nose 1000 Cerebellum 1000 Expression profiling of spinal cord section (T9) extracted from rats 14d following severe injury Source GEO sample is GSM31616 Last updated (according to GEO): May 27 2005 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12405.gif Source GEO sample is GSM79827 Last updated (according to GEO): Sep 22 2006 M_U133A_1_AnCg 1000 Coronary Arteriosclerosis Neoplasm 861 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs//23747.gif Source GEO sample is GSM66586 Last updated (according to GEO): Sep 22 2006 D2_Control_ZT 0_1 Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 5407 left_liver_lobe Transplant Series 42 , Transplant # 2 in the brain 150 162 4525 4520 liver /2 brain 1074 1082 HBL100_Untreated_0.1% aortic biopsy distensible Keywords = pulse wave velocity, arterial stiffness Source GEO sample is GSM6187 Last updated (according to GEO): May 27 2005 cerebellum wistar 3888 whole tissue, individual animal, 10 weeks old, male Wistar cerebellum file:p3888w Source GEO sample is GSM15131 Last updated (according to GEO): Oct 28 2005 nostrils 156 164 Liver 0 4 Plasma 861 high gestational age Source GEO sample is GSM213097 Last updated (according to GEO): Jul 25 2007 Parkinson Disease 1000 brain, cerebral cortex: 15001_e2_le1 Cerebral cortex 861 1000 Spleen from the forebrain 20 37 18 Trigeminal Ganglion 0 Gene expression data from postmorten brain regions Source GEO sample is GSM145115 Last updated (according to GEO): Nov 20 2006 of peripheral nervous system 73 100 1653 1648 livers Disease Source GEO sample is GSM176084 Last updated (according to GEO): Apr 09 2007 24 7 Right Frontal Lobe 5 0 brain Muscle; Smooth-Bladder_adult Keywords = mouse gene expression database Source GEO sample is GSM29406 Last updated (according to GEO): May 27 2005 332 322 hippocampus 861 Liver of cancer 25 33 Kidney 1000 osteoblast 627 637 NA12264 Aortic aneurysm without mention of rupture NOS 901 1000 Neurotoxicity Syndromes 1000 Microphthalmos Standard Affymetrix procedure Source GEO sample is GSM133006 Last updated (according to GEO): Aug 28 2007 Primary adenocarcinoma 0 21 98 86 of hippocampi Primary Neoplasm 1000 1000 Epithelial Cells Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5461.gif Source GEO sample is GSM93123 Last updated (according to GEO): Sep 22 2006 1076 1063 of an antibody 0 The prefrontal cortex 20 mouse brain 478 489 Subject code A34 1500 mg/kg X 6 hr Source GEO sample is GSM129837 Last updated (according to GEO): Sep 18 2007 Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. 4h after sham surgery, a 4 mm diameter disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44499 Last updated (according to GEO): May 27 2005 G5 ciliary body na Source GEO sample is GSM181255 Last updated (according to GEO): Apr 10 2007 114 101 brains quickly Nasal Epithelium Inhalation Formaldehyde 15ppm 6h ID341 Cerebral cortex 861 ERMS-T-TEST-22 on NHGRI-6.5k_b Parkinson Disease 1000 1000 Mitral Valve KM12_CL4017_Breast on Affymetrix GeneChip Human Full Length Array HuGeneFL total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with fMLP for 120min Source GEO sample is GSM5574 Last updated (according to GEO): May 27 2005 861 Acquired Immunodeficiency Syndrome NCI60.3_LABEL6EXTRACT5SUB3 Source GEO sample is GSM134005 Last updated (according to GEO): Aug 06 2007 Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 6 1000 Cornea 335 325 The jejunum 901 Caudate nucleus structure 1000 Cerebral cortex 5 0 brain 1000 hindbrain brain, cortex: 28dsham1_e1_le1 brain, Left frontal Lobe: Extract21_le2 Expression profiling of spinal cord section (T9) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM6666 Last updated (according to GEO): May 28 2005 1000 Coronary Arteriosclerosis Carcinoma, Large Cell 867 Heart 1000 SN:1010382 Source GEO sample is GSM115372 Last updated (according to GEO): Jun 20 2006 osteoblast 627 637 1000 Brain Large-scale analysis of the human transcriptome. Prostate Source: University of Virginia, see PMID 11507037 Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 135.45 Stdv: 6.23 Min: 120.79 Max: 144.47 Source GEO sample is GSM2864 Last updated (according to GEO): Mar 20 2006 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11095.gif Source GEO sample is GSM79808 Last updated (according to GEO): Sep 22 2006 HDMTX_MP-8 collagen 303 311 861 Brain X-ray irradiation (2 Gy). Source GEO sample is GSM203980 Last updated (according to GEO): Jun 25 2007 VDXKIU_2481 660 mesenchymal stem cell 639 experiment II LXSN replicate 1 1000 Decapitation 12 hr EE repl 2 Adenocarcinoma 6 CNS-RM_Ctr7d-2B-s2 leukemia, promyelocytic-HL-60 Source GEO sample is GSM18894 Last updated (according to GEO): Sep 25 2006 Total RNA from iPS clone was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations. Source GEO sample is GSM230264 Last updated (according to GEO): Nov 22 2007 1586 1573 schizophrenia Vector-veh-2 Tongue 1935 1922 out the liver Ganglia, Spinal 884 T-47D hgu95e Primary Neoplasm 1000 Muscle 861 f2#54 versus pool Mouse Brain tissue to the nose 599 609 Z1 juvenile biol repl 3 30 19 Solid tumor medulla_8 from the right forebrain 21 44 MCF7 Whole blood 0 10 858 Mesodermal cell none Source GEO sample is GSM244633 Last updated (according to GEO): Nov 23 2007 1578 1559 that fetal cartilage N-9_POST 673 659 by decapitation Gene expression profile of the cell line UB/OC-1 grown for 2 days under differentiating conditions (39C). This data set is a replica experiment of sample GSM1535. Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1546 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 Keywords = Infectious diseases 1133 1163 ileum 861 20 0 3AJZ02022870_ brain 338 333 brain 91 from the bone marrow 72 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:326, Count:32 Corner- Avg:31904, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:7.404772,SFGene:All Background:Avg:585.04,Stdev:47.68,Max:671.6,Min:469.8 Noise:Avg:12.17,Stdev:0.93,Max:15.1,Min:10.0 RawQ:15.78 Keywords = ALL Source GEO sample is GSM3418 Last updated (according to GEO): May 27 2005 Seminoma 1000 2 hr vehicle repl 1 1000 Skeletal muscle structure NA Source GEO sample is GSM198904 Last updated (according to GEO): Jun 07 2007 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160217 Last updated (according to GEO): Feb 08 2007 of the colon 28 39 1000 Retina ovarian tumor: endometrioid Source GEO sample is GSM139406 Last updated (according to GEO): Apr 09 2007 Liver 1000 NA Source GEO sample is GSM198897 Last updated (according to GEO): Jun 07 2007 Lymphoblastoid Cell Line for Individual 8172.4 log phase Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13406.gif Source GEO sample is GSM79725 Last updated (according to GEO): Sep 22 2006 1000 Brain Probeset expression data from NA12750 growth 1, replicate 3 Source GEO sample is GSM195193 Last updated (according to GEO): Aug 08 2007 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210417 Last updated (according to GEO): Jul 16 2007 A2780_cis_IC75_16h_2 P2B_KIDNEY_1 Cerebral cortex 901 C3H/HeJ bed nucleus of the stria terminalis rep2 (430 2.0 Array) Cardiomyopathies 861 m1-WT3 frontal lobe 1000 Brain 861 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68140 Last updated (according to GEO): Jul 07 2006 Bone Marrow 1000 NA12739 growth 1 Kidney 861 5 0 Brain 7 cerebral cortex 21 GM19138 Gap junctions and purinergic P2 receptors (P2Rs) can be regarded as belonging to a common functional unit, given that they are involved in the transmission of calcium signals between cells. We have previously shown that deletion of the Gja1 gene alters expression levels of numerous genes encoding proteins with diverse functions, including purinergic receptors (P2Rs), and have found that genes synergistically or antagonistically expressed in wild-type tissues are more prone to be similarly or oppositely regulated in Cx43-nulls. We have now explored the use of coordination analysis of gene expression as a strategy to identify interlinked genes encoding functionally related proteins and pull-downs to evaluate their interlinkage. Our findings indicate that, in brain and in cultured astrocytes, several of these coexpressed genes encode proteins that are components of P2R signal-transduction pathways and/or directly interact with these receptors, including the gap junction protein connexin43 (Cx43) and Cx45 as well as pannexins. It is proposed that coordination analysis of gene expression may provide a novel unbiased strategy for the identification of proteins belonging to supramolecular complexes. Diaphragm 14 Day mdx rep 2 AK_Control_ZT 12_1 Nasal Epithelium Inhalation Formaldehyde 0ppm 24h ID58 of fetal minamata disease 295 319 Pool of 10 (1 utricle and 3 ampullae) at E14 Source GEO sample is GSM182604 Last updated (according to GEO): Aug 14 2007 Nasal Epithelium 865 post infection 29 42 Prolymphocytic Leukemia 49 71 of the normal mucosa 7 26 human caudate nucleus Source GEO sample is GSM86910 Last updated (according to GEO): Feb 08 2006 Saline control-neocortex, biological rep1 jzo003-v5-u74av2-met 1000 Coronary Arteriosclerosis 1000 Cardiomyopathy, Alcoholic 928 Endometrium GM10831 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188716 Last updated (according to GEO): Jun 06 2007 252 239 neurofibromas Heart Source GEO sample is GSM18792 Last updated (according to GEO): Sep 25 2006 DBA 2:1-2 CA1 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b094 Source GEO sample is GSM2011 Last updated (according to GEO): Nov 21 2005 Normal Liver Gene expression data from postmorten brain regions Source GEO sample is GSM145901 Last updated (according to GEO): Nov 20 2006 with myocardial infarction 313 339 Aortic aneurysm without mention of rupture NOS 901 861 Uterus with some respiratory epithelium. 1039 1072 072801 100% CD28 beads 12.00 hr. T-Cell ileum 861 Recommended Affymetrix protocols were followed. Source GEO sample is GSM148472 Last updated (according to GEO): May 01 2007 Epithelium of bronchus 983 Nucleus Accumbends, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231029 Last updated (according to GEO): Sep 26 2007 SN:1030149 Source GEO sample is GSM115421 Last updated (according to GEO): Jun 20 2006 5 0 brain Ganglia, Spinal 923 Conjtissue3 Gene expression data from postmorten brain regions Source GEO sample is GSM145560 Last updated (according to GEO): Nov 20 2006 to the lamina propria 1530 1551 861 Brain Neoplasm Metastasis 1000 Malignant Neoplasms 1000 with experimental autoimmune encephalomyelitis 12 57 CNS-SC_Inj7d-1B-s2 15 7 brainstem WGACON-136 female us chip 58 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92343 Last updated (according to GEO): Jan 13 2006 HDMTX-20 sal-PVH3_1 Infection 1112 1121 M_U133A_84_DLPFC M-7-10-BO on UMich-10k Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM107993 Last updated (according to GEO): Jun 06 2006 Brain 861 Coronary artery 901 48 year old female Gene expression data from postmorten brain regions Source GEO sample is GSM145390 Last updated (according to GEO): Nov 20 2006 oocyte Source GEO sample is GSM18701 Last updated (according to GEO): May 27 2005 Blood 1000 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201249 Last updated (according to GEO): Jun 14 2007 Colorectal cancer patient SC14_vs_Pool VDXRHU_2039 Soleus muscle structure 861 861 Neoplasm Recurrent Squamous cell carcinoma 8 3AMH02082802_BM_CD71EarlyErythroid 3 0 Hair Gene expression data from postmorten brain regions Source GEO sample is GSM145930 Last updated (according to GEO): Nov 20 2006 607 597 the rectum ER negative human primary breast tumor EA02014_41275_H133A_JA-1568 1000 Spleen 1000 Rectum Gap junctions 0 12 136 131 Aortae 1000 Heart Two 90 minute exposures (3 hr recovery in between) to 0.8% halothane every day for 2.5 days, for a total of 5 exposures Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5111 Last updated (according to GEO): May 27 2005 865 Disorder of artery 8069_Lung did not develop PGD that fibroblasts 450 465 Site: University of California, Davis Cohort: Male/Female Control Set Diagnosis: Control pH: 6.49 Subject: 3076 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39061 Last updated (according to GEO): May 27 2005 M7TW00121388 Osteoblasts 1000 861 Brain Heart Atrium 1000 Gene expression data from brain of adult rats Source GEO sample is GSM101013 Last updated (according to GEO): Feb 20 2007 15_0002_Control_Day1_20 Parkinson Disease 861 861 Cerebral cortex SCG explant cultured for 48 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246068 Last updated (according to GEO): Dec 03 2007 110 FC BA9 B 31 21 spinal cord 16 6 (cerebellum R538P00541 in the brain 150 162 Liver Test (Blinded) Sample Source GEO sample is GSM130178 Last updated (according to GEO): Sep 18 2007 H9LMS99090506 Transcriptome of Ts1Cje and euploids cerebellum V5-P433 TGFBd8_12 861 Neoplasm 12 0 Normal Breast Medulla 3 Normal AD control Treatment, type=dissect Source GEO sample is GSM119639 Last updated (according to GEO): Jul 10 2006 20 0 human caudate nucleus Voxel J3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1457 Last updated (according to GEO): Nov 21 2005 Parkinson Disease 861 901 frontal lobe Brain 1000 Gene expression from Dendritic cells from human subject with resolver phenotype infected with H. ducreyi. Source GEO sample is GSM128971 Last updated (according to GEO): Sep 13 2007 1000 Prostate 1000 Structure of trigeminal ganglion 1000 Structure of parenchyma of lung Muscular Dystrophy, Duchenne 1000 10 7 Left 861 Gland structure none Source GEO sample is GSM239922 Last updated (according to GEO): Dec 07 2007 861 Mesentery brain, amygdala: Control-Cortex_e1_le2 Tumor__CNS_Glioblastoma_GlioB_4 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Cerebellum Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35379 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM176164 Last updated (according to GEO): Apr 09 2007 1000 Kidney brain, Left Parietal Lobe: Extract40_le2 Colorectal Cancer 1000 3 0 Lung 1000 Brain Liver Test (Blinded) Sample Source GEO sample is GSM130179 Last updated (according to GEO): Sep 18 2007 MuscleRegen-ctx6.5d-1RLAv2-s2 Primary tumor 19 32 T15__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A NeverSmoker 42 861 Occipital lobe 1000 Diabetes Mellitus GSE9630 MGJZ030211016Bkidney M7TW00122013 0 Human Cortex 11 861 Retina Acute myocardial infarction 1000 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68204 Last updated (according to GEO): Jul 07 2006 43 0 Chorionic mesoderm-derived mesenchymal cells bronchial epithelia 224 243 Axon 861 KT28_N Expression profiling of spinal cord section (T8) extracted from rats 4h following severe injury Source GEO sample is GSM31507 Last updated (according to GEO): May 27 2005 Normal__Peripheral_Blood_Mono_MONO5 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Hippocampus 5 Normal total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with BLC for 120min Source GEO sample is GSM5469 Last updated (according to GEO): May 27 2005 brain, Left frontal Lobe: Extract31_le2 Testis 861 Integumentary system 861 861 Cancer of Neck GSE397 Wild type inbred mice Source GEO sample is GSM82985 Last updated (according to GEO): Nov 10 2005 T-ALL-C10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A PGA_PA-D_348 A HID U D049 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108612 Last updated (according to GEO): Aug 22 2006 1000 Kidney G1E_30_B 26 15 endometrioid Occipital lobe 861 human cerebellum Source GEO sample is GSM87170 Last updated (according to GEO): Feb 08 2006 1000 Cerebellum Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell 120min (set2) 1000 Rhabdomyosarcoma to vascular signaling networks 963 993 no additional Source GEO sample is GSM199062 Last updated (according to GEO): Jun 08 2007 Colorectal Adenocarcinoma (SW480) [JunctionChip 4 of 5] Epithelial Cells 901 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15724 Last updated (according to GEO): May 28 2005 kidney 37 43 of caudal 93 101 Infected with PBS and euthanized 3 days post-infection Source GEO sample is GSM155205 Last updated (according to GEO): Aug 08 2007 salivary.gland.1 Spleen vs IL4 Treated B cell Transplant Series 36 , Transplant # 1 607 597 the rectum ALL_5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A "Sample 7,>5 yr survival(122 months) age 46 erp no" on vantveer-oligo of vascular networks 692 711 ovarian tumor: serous Source GEO sample is GSM139454 Last updated (according to GEO): Apr 09 2007 brain 0 5 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211261 Last updated (according to GEO): Jul 18 2007 249 225 of associated infertility 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113902 Last updated (according to GEO): Jun 16 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145161 Last updated (according to GEO): Nov 20 2006 spinal cord 832 843 330 324 uterus Donor 1 time point 24 hours Autologous control (uninfected) Source GEO sample is GSM2601 Last updated (according to GEO): May 27 2005 nc2 B Cells AntiCD40+Il4 30H 2 Activated coronary_artery_5 Source GEO sample is GSM80631 Last updated (according to GEO): Mar 31 2006 Infected with B. melitensis 16M and euthanized 3 days post-infection Source GEO sample is GSM155257 Last updated (according to GEO): Aug 08 2007 B6:4-4 striatum mouse brain ipsilateral LPS.RU486 Source GEO sample is GSM149782 Last updated (according to GEO): Mar 15 2007 PGA-MFD-CtrPD5-1aBv2-s2 Voxel F2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1423 Last updated (according to GEO): Nov 21 2005 morbidly obese 646 659 2038 2023 by decapitation 865 Disorder of artery 1000 Coronary Arteriosclerosis Tissue Source GEO sample is GSM67201 Last updated (according to GEO): Jan 19 2006 A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism Source GEO sample is GSM5980 Last updated (according to GEO): Nov 21 2005 of somatomotor cortex 21 41 352 347 brain Gene expression data from postmorten brain regions Source GEO sample is GSM145903 Last updated (according to GEO): Nov 20 2006 Prosencephalon 1000 MF-46 Towards a Systems Biology of Mouse Inner Ear Organogenesis: Gene Expression Pathways, Patterns and Network Analysis. Gene expressions affected by TNF alpha Source GEO sample is GSM189812 Last updated (according to GEO): May 21 2007 GSE484 Starvation 916 BACKGROUND: Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH) and microsatellite marker analysis for the detection of loss of heterozygosity (LOH). Currently, high throughput methods such as array comparative genomic hybridization (array CGH), single nucleotide polymorphism array (SNP array) and gene expression arrays are available to study genome-wide alterations. Integration of these 3 platforms allows detection of genomic alterations at high resolution and investigation of an association between copy number changes and expression. RESULTS: Genome-wide copy number and genotype analysis of 10 cervical cancer cell lines by array CGH and SNP array showed highly complex large-scale alterations. A comparison between array CGH and SNP array revealed that the overall concordance in detection of the same areas with copy number alterations (CNA) was above 90%. The use of SNP arrays demonstrated that about 75% of LOH events would not have been found by methods which screen for copy number changes, such as array CGH, since these were LOH events without CNA. Regions frequently targeted by CNA, as determined by array CGH, such as amplification of 5p and 20q, and loss of 8p were confirmed by fluorescent in situ hybridization (FISH). Genome-wide, we did not find a correlation between copy-number and gene expression. At chromosome arm 5p however, 22% of the genes were significantly upregulated in cell lines with amplifications as compared to cell lines without amplifications, as measured by gene expression arrays. For 3 genes, SKP2, ANKH and TRIO, expression differences were confirmed by quantitative real-time PCR (qRT-PCR). CONCLUSION: This study showed that copy number data retrieved from either array CGH or SNP array are comparable and that the integration of genome-wide LOH, copy number and gene expression is useful for the identification of gene specific targets that could be relevant for the development and progression in cervical cancer. Last Updated (by provider): Jul 30 2007 Contributers: Tom van Wezel Jan Oosting Gemma G Kenter Karoly Szuhai Ekaterina S Jordanova Jeroen Knijnenburg Arko Gorter Judith N Kloth Gert-Jan Fleuren Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11551 Last updated (according to GEO): May 28 2005 MOLT-4 hgu95b 3AJZ02061907_Hypothalamus TUMOR 23 0 7 ventral tegmental area 24 46 48 30 in HIV encephalitis Meningioma Reccurrent Grade 1 U133A Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108015 Last updated (according to GEO): Jun 06 2006 1000 Infection SN:Human Glioblastoma Biopsy 06573 N-8_PRE 861 Brain Blood Cells 906 AD control Treatment, type=dissect Source GEO sample is GSM119672 Last updated (according to GEO): Jul 10 2006 CAD_replicate84 Expression profiling of spinal cord section (T10) extracted from rats 30m following mild injury Source GEO sample is GSM31327 Last updated (according to GEO): May 27 2005 Gene expression data from a EFT cell line expressing EWS/E1AF Source GEO sample is GSM213311 Last updated (according to GEO): Jul 26 2007 The epithelial cells 962 981 800 788 PCOS oocytes brain 0 5 This is a wildtype littermate at postnatal day 1 pool of 5 animals Lot batch = Source GEO sample is GSM4049 Last updated (according to GEO): May 28 2005 Gene expression data from mouse brain infected with GNPs infected with retroviruses that express Cyclin D1 Source GEO sample is GSM148577 Last updated (according to GEO): Mar 14 2007 plasma cells 332 344 220 201 by CO2 asphyxiation Olfactory Epithelium 1000 Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. Moderate controlled cortical impact with pneumatic impactor, 6 m/s impact velocity and 1.5 mm deformation. 4h after surgery, a 4 mm diameter disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44465 Last updated (according to GEO): May 27 2005 Gene expression data from whole brain infected mouse, day 1 Source GEO sample is GSM189637 Last updated (according to GEO): May 16 2007 Primary tumor 19 32 Abdominal Aortic Aneurysm Male Pool I 1000 Coronary Arteriosclerosis brain, cortex: 7dsham2_e1_le1 brain, brainstem: cRNA-WT1 Tumors 91 96 1000 Glioblastoma Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16878.gif Source GEO sample is GSM81528 Last updated (according to GEO): Sep 22 2006 with multiple system atrophy 27 54 1BJZ02053108_CardiacMyocytes G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Keywords = Gata1, erythroid, mouse Source GEO sample is GSM9635 Last updated (according to GEO): May 28 2005 BPH-17 on NHGRI-6.5k_c 30minplus.2 cingulate cortex 901 of the normal mucosa 7 26 26 0 frontal cortex sprague 3935 Utricle structure 1000 7 frontal cortex 20 cervix_3 healthy control sample x198 GSE5810 Sample # 1663-1 Gene expression data from PD7 Foxo3 null ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203828 Last updated (according to GEO): Aug 02 2007 Brain 861 304 280 alcoholic cardiomyopathy Prefrontal Cortex Source GEO sample is GSM105459 Last updated (according to GEO): Apr 17 2006 1000 Brain 660 mesenchymal stem cell 639 human cerebellum Source GEO sample is GSM87076 Last updated (according to GEO): Feb 08 2006 Hypothalamus Source GEO sample is GSM18934 Last updated (according to GEO): Sep 25 2006 Postnatal day 3 corticospinal motor neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription. Source GEO sample is GSM37094 Last updated (according to GEO): May 27 2005 Experimental Autoimmune Encephalomyelitis 901 D_U133Plus_94_Amy pharyngeal_mucosa_1 Source GEO sample is GSM80750 Last updated (according to GEO): Mar 31 2006 21 0 acute myeloid leukemia A2780_cis_IC90_24h B4 1000 Hippocampus HDMTX-DX-15 d10.2 Expression profiling of spinal cord section (T8) extracted from rats 24h following severe injury Source GEO sample is GSM31466 Last updated (according to GEO): May 27 2005 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P21, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3224 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145734 Last updated (according to GEO): Nov 20 2006 W/type (triple treatment) 5267 AMM_0_0_Male7_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111851 Last updated (according to GEO): Nov 21 2006 cardiac 763 769 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132495 Last updated (according to GEO): Feb 26 2007 87 for Down syndrome 104 5 0 brain 888 Large-Cell Lymphomas normal liver 1518 1530 AD control Treatment, type=dissect Source GEO sample is GSM119683 Last updated (according to GEO): Jul 10 2006 Gene expression data Source GEO sample is GSM230354 Last updated (according to GEO): Sep 19 2007 Femur 1000 Skin 1 Normal A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke. White and grey matter in the distribution on the middle cerebral artery 6 hours after administration of the catalytic antioxidant AEOL 10150; third replicate; pooled mRNA from 6 brains. Source GEO sample is GSM2209 Last updated (according to GEO): May 27 2005 865 Ovarian Diseases GSE2005 19 0 Head and neck cancer 643 629 refractory AML Central gray substance of midbrain 1000 ovarian tumor: endometrioid Source GEO sample is GSM139410 Last updated (according to GEO): Apr 09 2007 tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44858 Last updated (according to GEO): May 27 2005 NA11881 901 Myeloid Leukemia Cerebral cortex 861 861 Brain none Source GEO sample is GSM244608 Last updated (according to GEO): Nov 23 2007 0 Human Cortex 11 from colorectal adenoma 21 44 in the brain 150 162 cerebral 0 7 GSE3211 1000 Epithelial Cells Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210411 Last updated (according to GEO): Jul 16 2007 Lymphoma Burkitt 50 65 1000 Thalamic structure 0 Frontal Cortex 13 R742P00670 WGACON-207 Gene expression data from postmorten brain regions Source GEO sample is GSM145096 Last updated (according to GEO): Nov 20 2006 fetal lung fibroblast #2 repeat, serum starved Analysis of target genes induced by the Amyloid Precursor Protein Intracellular Domain Source GEO sample is GSM93711 Last updated (according to GEO): Jan 25 2006 67 40 with coronary artery disease GSE934 VDXGUYU_4049 Tissue homogenate from cingulate cortex from G42 mouse (Ref. Pubmed:15509747 ). Source GEO sample is GSM64190 Last updated (according to GEO): Dec 01 2005 Hippocampus 861 Brain 861 I_U133A_87_AnCg Acetaminophen 6hr Rat 4101 blood vs. Acetaminophen 6hr Rat Pooled Control blood brain, amygdala: ADX AM A_e1_le1 38 21 from a hippocampus Gene expression data from colorectal adenoma. Source GEO sample is GSM215088 Last updated (according to GEO): Aug 02 2007 DLBC2 on Affymetrix GeneChip Human Full Length Array HuGeneFL Job's patient Source GEO sample is GSM211135 Last updated (according to GEO): Sep 10 2007 of Parkinson's disease 450 471 brain 0 5 V5-P480 I_U133A_104_CB 5 0 brain Untreated versus treated (bortezomib) breast cancer cells. Source GEO sample is GSM120347 Last updated (according to GEO): Jul 20 2006 118 FC BA9 B 1180 1168 in leg muscle Parkinson Disease 1000 human caudate nucleus Source GEO sample is GSM86873 Last updated (according to GEO): Feb 08 2006 Bicalutamide treated LNCaP cells not stimulated with DHT, biological replicate 1 Source GEO sample is GSM187374 Last updated (according to GEO): May 04 2007 1000 Neuraxis MF-25 913 Coronary heart disease seminoma specimen, pT1, patient age: 39y; W02 102 1000 Brain Stem To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28468 Last updated (according to GEO): May 27 2005 NA Source GEO sample is GSM109462 Last updated (according to GEO): May 22 2006 1000 Brain Mouse old heart w/ a- & g-tocopherol agT-Ht-5 Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for twelve weeks.. Source GEO sample is GSM148663 Last updated (according to GEO): Dec 12 2006 Wild type inbred mice Source GEO sample is GSM82903 Last updated (according to GEO): Nov 10 2005 Neoplasm 861 Synovium; normal Keywords = mouse gene expression database Source GEO sample is GSM29442 Last updated (according to GEO): May 27 2005 FVB/NJ amygdala rep2 N27__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Cerebral cortex 1000 HapMap CEU_parent Female Source GEO sample is GSM159522 Last updated (according to GEO): Feb 01 2007 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51119.gif Developmental Stage: E8.5 Source GEO sample is GSM229807 Last updated (according to GEO): Nov 06 2007 Squamous cell carcinoma 923 Expression profiling of laminectomized raphe at 4h in rats Source GEO sample is GSM41544 Last updated (according to GEO): May 27 2005 ALLSIL DMSO control 24h rep1 901 Mammary gland brain, cerebral cortex: PC15_e1_le1 CNS-SpinalCsev-Adult-28d-1A-s2 1000 Brain 7 0 Synovium Brain 1000 Exp C_1, 30mg/kg CPF outer medulla 31 43 Brain 861 S1P2-KO-hippocampus, biological rep8 (female) Richard Almon-33-1133800609760 Sex Specific Transciption in Human Hypothalamus between 7 male biological samples (2 technical replicates of each) and 5 female biological samples (2 technical replicates of 4 of these).. Date GSE1147 Last Updated: May 29 2005 Contributers: Mark Gerstein Petur Petersen Ian J Laurenzi Joel S Rozowsky Michael P Snyder Kaiyong Zon Weimin Zhong John L Rinn Includes GDS564. Update date: Apr 21 2004. Dataset description GDS564: Examination of sex specific transcription in hypothalamus using postmortem samples from individuals averaging 70 years of age.. Biopsy of a colorectal adenoma from patient #19 Organ 966 Dahl Salt Sensitive Rat Lung- Hypoxia with SU-5416 rep3 1000 Blind Vision no additional Source GEO sample is GSM199281 Last updated (according to GEO): Jun 08 2007 1000 Neuroectodermal Tumor, Primitive 30 0 Fetal Occipital cortex cocaine1 MDA134_Untreated_10% Parkinson Disease 861 Tumor__Renal_Carcinoma_5291 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Prosencephalon 1000 Prostate 861 rad001 9d, biological rep4 Wild type 8 wk old male FVB/NJ mouse periaqueductal gray Source GEO sample is GSM74995 Last updated (according to GEO): Feb 27 2007 1000 Liver 5 0 brain 861 Cardiomyopathies 861 Blood Plasma 861 of mouse brain 9 23 Expression profiling of laminectomized raphe at 28d in rats Source GEO sample is GSM41534 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145680 Last updated (according to GEO): Nov 20 2006 D_U133A_41_Amy Male 69.6 yr after antibody enrichment scan 2 (U133A) TEL-AML1-#13 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A GSE7155 861 Brain 361 335 hypertrophic cardiomyopathy This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12375 Last updated (according to GEO): May 28 2005 Bladder sample 1044-1 +_6314_batch1 on NHGRI-6.7k This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis. Stembase Experiment ID: E189 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189 SCGP Sample ID: S231 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_189 Short description: RNA isolated from first passage retinal sphere cells. Estimated purity: > 90% RNA concentration: > 30.0 ng Num cells for RNA prep: ~160,000 Sample volume: 5.0 ul Source GEO sample is GSM87194 Last updated (according to GEO): Jan 19 2006 861 Anterior Day 3_H_-LIF_Bchip CNS-SC_CtrA24h-2B-s2 GSE88 Gene expression data from brain of adult rats Source GEO sample is GSM101004 Last updated (according to GEO): Feb 20 2007 ileum 861 1000 Brain Comparison of SNc and VTA dopaminergic neurons. Greene-5P50NS038399-050001 Hyperdip>50-#1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A NA18576 361 335 hypertrophic cardiomyopathy Cerebral cortex 861 retina 5 10 mouse brains 187 198 TEL-AML1-C48 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Melanoma xenograft, MEA3_Sub_C (LeiFidler) CNS-RM_CtrT0-1B-s2 1000 Prostate human frontal cortex Source GEO sample is GSM86928 Last updated (according to GEO): Feb 08 2006 Normal Source GEO sample is GSM176317 Last updated (according to GEO): Apr 09 2007 Normal Source GEO sample is GSM176220 Last updated (according to GEO): Apr 09 2007 in blood 16 23 220-97_SCC by the liver 210 221 Gene expression data from brain hemispheres of experimentally naive male mice Source GEO sample is GSM172396 Last updated (according to GEO): Jun 27 2007 1790 HP48_21 Nervous system structure 901 Richard Almon-14-1133800609151 Gene expression data from 14B3 BMEL cells cultured under aggregate conditions. Source GEO sample is GSM160077 Last updated (according to GEO): Jul 11 2007 B_N3 on Affymetrix GeneChip Human Full Length Array HuGeneFL the heart 987 996 Gene expression data from postmorten brain regions Source GEO sample is GSM145711 Last updated (according to GEO): Nov 20 2006 Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92287 Last updated (according to GEO): Jan 13 2006 GSE7765 of tumor cells 1466 1480 olfactory epithelium SR-A mutant mouse 16 hpO Source GEO sample is GSM80209 Last updated (according to GEO): Oct 26 2005 in bronchial epithelia 311 332 Small cell carcinoma of lung 867 331 307 in central nervous system A2780_oxa_IC25_16h_1 LCCS sample 18 weeks 901 Bone Marrow liver_PPARa-knockout_control_5d_rep1 Dahl-Iwai Female HighSalt OuterMedulla rat106 dahl_medullar_106_1_OM_053001 Mouse Liver LRD Diet 5wk Control, biological replicate D seminoma specimen, pT2, patient age: 35y; W03 032 Testi_SeminiferousTubule Source GEO sample is GSM18989 Last updated (according to GEO): Sep 25 2006 1000 Spleen Macrophage 14smi100 Head and neck cancer Source GEO sample is GSM155696 Last updated (according to GEO): Apr 24 2007 1000 Left Gene expression data from a neocortex from mouse injected 10 mg/kg nicotine Source GEO sample is GSM147408 Last updated (according to GEO): Jan 03 2007 Muscular Dystrophy, Duchenne 1000 901 Mammary gland Neoplasm 1000 into one branch 883 898 Voxel G3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1434 Last updated (according to GEO): Nov 21 2005 Transcription profiling of human node-negative breast cancer samples to validate a VERIDEX 76 gene prognostic signature An important feature of human asthma and animal models of asthma is airway hyperresponsiveness. The symptoms of asthma are a narrowing of the airways caused by edema and the influx of inflammatory cells. The aim of this project is to determine the temporal relationship between gene expression and airway allergen challenge. 4 weeks old BALB/CJ mice were challenged on days 0,3,10 and 17 with PBS and ragweed pollen protein plus Alum. Last Updated (by provider): Aug 23 2005 Contributers: Marsha Wills-Karp Includes GDS42. Update date: Jun 27 2003. Dataset description GDS42: Analysis of allergic response to an immunogenic protein of ragweed pollen in lung. Determination of the temporal relationship between gene expression and airway allergen challenge.. Includes GDS58. Update date: Jun 27 2003. Dataset description GDS58: Analysis of allergic response to an immunogenic protein of ragweed pollen in lung. Determination of the temporal relationship between gene expression and airway allergen challenge.. Includes GDS56. Update date: Jun 27 2003. Dataset description GDS56: Analysis of allergic response to an immunogenic protein of ragweed pollen in lung. Determination of the temporal relationship between gene expression and airway allergen challenge.. Includes GDS14. Update date: Jun 27 2003. Dataset description GDS14: Analysis of allergic response to an immunogenic protein of ragweed pollen in lung. Determination of the temporal relationship between gene expression and airway allergen challenge.. Includes GDS60. Update date: Jun 27 2003. Dataset description GDS60: Analysis of allergic response to an immunogenic protein of ragweed pollen in lung. Determination of the temporal relationship between gene expression and airway allergen challenge.. Includes GDS13. Update date: Jun 27 2003. Dataset description GDS13: Analysis of allergic response to an immunogenic protein of ragweed pollen in lung. Determination of the temporal relationship between gene expression and airway allergen challenge.. 1000 Brain HepG2 0h 2 Control liver_4 Source GEO sample is GSM80739 Last updated (according to GEO): Mar 31 2006 DBA: 1-5 motor cortex to the nose 599 609 92 FC BA9 A normal testis 54 66 Hippocampus Source GEO sample is GSM53367 Last updated (according to GEO): Jul 06 2005 Plasma 861 Brain 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Leukotriene B4 (LTB4) for 60min Source GEO sample is GSM5678 Last updated (according to GEO): May 27 2005 Brain 1000 Communicable Diseases 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145551 Last updated (according to GEO): Nov 20 2006 ovarian tumor: endometrioid Source GEO sample is GSM139389 Last updated (according to GEO): Apr 09 2007 in B cell chronic lymphocytic leukemia 74 112 6 week mutant spinal cord rep 3 with Parkinson's disease 27 50 D_U133A_85_CB 411 394 in blood pressure AdipBrn022QAFBZ_048.txt GBM Treatment, type=remove Source GEO sample is GSM99525 Last updated (according to GEO): Apr 21 2006 Subcutaneous Tissue 913 901 Parietal Lobe 861 Muscle mouse hippocampus from COX-2 WT Source GEO sample is GSM121443 Last updated (according to GEO): Jan 31 2007 Gene expression data from human colon tumor tissue Source GEO sample is GSM173378 Last updated (according to GEO): Apr 20 2007 none Source GEO sample is GSM123225 Last updated (according to GEO): Jul 26 2006 1000 frontal lobe experiment I, hTERT, replicate 1 Lmna H222P heterozygous male 2 mouse brains 187 198 Whole Brain 62 72 CAD_replicate87 human cerebellum Source GEO sample is GSM87150 Last updated (according to GEO): Feb 08 2006 1000 Brain no additional Source GEO sample is GSM199024 Last updated (according to GEO): Jun 08 2007 NORMAL 5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A AML_8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Liver (SF33) of the colon 28 39 861 Cerebral cortex Brain 1000 1000 Encephalitis 3AJZ02022224_ spinal cord Whole blood 0 10 BC214A-AF 23 11 of the kidney spinal cord, ventral spinal cord: D60SODSPMN3_e1_le1 Olfactory Epithelium 1000 CNS-SC_InjA30m-1C-s2 Adipose tissue 884 Examining the effects of tTA expression in mouse hearts Source GEO sample is GSM15072 Last updated (according to GEO): May 28 2005 in bronchial epithelia 311 332 thigh fibroblast 0 15 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL4 for 120min Source GEO sample is GSM5639 Last updated (according to GEO): May 27 2005 skeletal muscle, tibialis anterior: Innervated MCK::cre 2_e1_le1 SN:Human Glioblastoma Biopsy 30150 Locus Coeruleus Source GEO sample is GSM107973 Last updated (according to GEO): Jun 06 2006 22 0 Mammary Gland @ Preg12 Plasma 861 adipose_tissue_omental_1 Hippocampus of schizophrenic, bipolar, and control subjects. Analyzed from CEL files. CD3 + CD28 beads + FK506 24.00 hr. T-cell Circadian Time Treatment, type=time_course, measurement=6.0 h Source GEO sample is GSM53329 Last updated (according to GEO): Jul 06 2005 0029_1429_H95A2_T97-017_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Replicate2_Voxel G9 CD3 beads 02.00 hr. T-Cell embryonic cortical neuron treated with NMDA Source GEO sample is GSM49557 Last updated (according to GEO): May 29 2005 Malignant Neoplasms 1000 861 leukemia gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134646 Last updated (according to GEO): Jul 09 2007 Fibroblasts 861 f2#63 versus pool Mouse Brain tissue Cerebral cortex 861 7 frontal cortex 20 human frontal cortex Source GEO sample is GSM87006 Last updated (according to GEO): Feb 08 2006 cerebellum wistar ky 3894 whole tissue, individual animal, 10 weeks old, male Wistar Kyoto cerebellum file:p3894w Source GEO sample is GSM15137 Last updated (according to GEO): Oct 28 2005 PGA_MI_ilv_1w_662 in the mammalian nervous system 110 141 of mouse brain 9 23 Whole Brain 73 83 from brain 21 30 Spleen 0 5 Blood 861 Analysis of prefrontal cortex from 3 biological replicates of C57BL/6J mice at four Zeitgeber Times (ZT 3, 9, 15, and 21). Source GEO sample is GSM240416 Last updated (according to GEO): Oct 30 2007 Gene expression data from human colon tumor tissue Source GEO sample is GSM173339 Last updated (according to GEO): Apr 20 2007 Normal human muscle Macrophage smi81 lateral hypothalamus long access to cocaine replicate 2 1000 Brain mouse cerebral cortex, cox-2 WT, rep3 n/a Source GEO sample is GSM178048 Last updated (according to GEO): Jun 11 2007 B_N5 on Affymetrix GeneChip Human Full Length Array HuGeneFL C57BL/6J hippocampus rep2 (430 2.0 Array) 1000 Spleen B6 2000-2 Kidney Plasma 861 no additional Source GEO sample is GSM199176 Last updated (according to GEO): Jun 08 2007 Tumor__Leukemia_AML_AML_(2,PK)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A MLL-#2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Small cell carcinoma of lung 867 92 80 of Alzheimer? in seminoma 28 38 D_U133A_98_DLPFC Bladder sample 112-10 GBM Treatment, type=remove Source GEO sample is GSM99594 Last updated (according to GEO): Apr 21 2006 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211415 Last updated (according to GEO): Jul 18 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28722 Last updated (according to GEO): May 27 2005 Muscle Source GEO sample is GSM4266 Last updated (according to GEO): May 27 2005 Primary Neoplasm 1000 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226045 Last updated (according to GEO): Nov 02 2007 51 29 in the developing brain Gene expression data from a EFT cell line expressing EWS/FLI1 typeI Source GEO sample is GSM213307 Last updated (according to GEO): Jul 26 2007 aml8-aml8_221_ab_hu68_abms on Affymetrix GeneChip Human Full Length Array HuGeneFL for the adenocarcinomas 619 641 861 Cardiomyopathies Structure of zygote 861 E8.0a_rep2 13 7 cochlea brain, frontal cortex: Sample51_e1_le1 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113961 Last updated (according to GEO): Jun 16 2006 left 35 38 1000 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145781 Last updated (according to GEO): Nov 20 2006 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225702 Last updated (according to GEO): Nov 05 2007 Gene expression data from human colon tumor tissue Source GEO sample is GSM173366 Last updated (according to GEO): Apr 20 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11538 Last updated (according to GEO): May 28 2005 Disorder of artery 865 861 Neoplasm brain, hippocampus: CON-CA3-22_e1_le1 brain, cortex: Sample8_e1_le1 901 Caudate nucleus structure Chronic Lymphocytic Leukemia 19 47 51 37 without malaria V5-P237 brain, amygdala: ADX PM A b_e1_le1 Heart failure 1000 NCI60.9_LABEL12EXTRACT11SUB3 Source GEO sample is GSM134039 Last updated (according to GEO): Aug 06 2007 HC102 CN A GSE1143 normal liver tissue Source GEO sample is GSM155961 Last updated (according to GEO): Jun 21 2007 1655 1643 after seizure Expression profiling of spinal cord section (T10) extracted from rats 4h following laminectomy (sham) Source GEO sample is GSM31287 Last updated (according to GEO): May 27 2005 PGA-Band_Sham_4h_1-m5 Gene expression data from postmorten brain regions Source GEO sample is GSM145681 Last updated (according to GEO): Nov 20 2006 U87 glioblastoma cell, parent Keywords = bioinformatics Keywords = gene expression Keywords = cancer Keywords = platelet-derived growth factor Keywords = sterol regulatory element binding protein Keywords = glioblastoma multiformae Keywords = microarray Source GEO sample is GSM34592 Last updated (according to GEO): May 27 2005 B_D2_SleepDep_ZT 6_1 B220+c-kit+ Pre BI cells sorted out of mouse bone marrow, sort no. 8 Source GEO sample is GSM630 Last updated (according to GEO): Mar 17 2006 Coronary heart disease 913 PGA-E12.5_2 Nose 1000 Alzheimer's Disease 861 660 mesenchymal stem cell 639 Ventral Tegmental Area 1000 875 Subcutaneous Tissue 2936 2918 anatomical location 30 CB A B209 on Affymetrix GeneChip Human Full Length Array HuGeneFL 861 Cerebellum 861 Brain human cerebellum Source GEO sample is GSM87089 Last updated (according to GEO): Feb 08 2006 CAD_replicate73 Primary Carcinoma 875 from colonic normal mucosa 21 47 of the colon 28 39 HapMap YRI_parent Male Source GEO sample is GSM159710 Last updated (according to GEO): Feb 01 2007 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2784 Source GEO sample is GSM2101 Last updated (according to GEO): Nov 21 2005 Central gray substance of midbrain 861 brain_DLPFC_bipolar C_mr701 osteoblast 627 637 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28746 Last updated (according to GEO): May 27 2005 861 Muscle HapMap CHB Female Source GEO sample is GSM159591 Last updated (according to GEO): Feb 01 2007 mouse brains 187 198 861 Blood cerebellum sprague 3897 bone marrow-CD105endothelia Source GEO sample is GSM18724 Last updated (according to GEO): Sep 25 2006 Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_4 months_replicate 4 1000 Hyperglycemia ProstateCancer-3 on NHGRI-6.5k_c Mouse old brain w/ a-tocopherol aT-Br-1 901 Hepatocyte We will separately dissect the maxillary and mandibular branches of the E10.5 first branchial arch from wild type, dlx2, dlx1/2 and Dlx5/6 mutants. The tissues wil be flash frozen within 1 min of removal.We have not performed the dissections yet so we dont know how much RNA will be get from each sample, but previous experience suggests that we will need ~10 branchial arches/experiment. Treatment, type=nucleic_acid_extraction, description=We anticipate using this method as it was recommended by TGEN for small amounts of tissue. Source GEO sample is GSM107885 Last updated (according to GEO): Jun 06 2006 Interatrial septum 865 19 0 Embryonal carcinoma at the Human Brain 734 751 Dahl-Iwai Male LowSalt OuterMedulla rat111 dahl_medullar_111_1_OM_053001 Gene expression profiling of hormone resistant prostate cancer brain, cerebral cortex: NMDA 30 2_le1 861 Brain 49 30 (predominantly valve Timepoint1 Disease Source GEO sample is GSM175804 Last updated (according to GEO): Apr 09 2007 from liver 21 30 WT_IL-6_400_rep2 H9RGV00102606 901 Caudate nucleus structure Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68350 Last updated (according to GEO): Jul 07 2006 59 CN A Hypothalamus of rats befrm (2d) heat acclimation and hypohydration (10% loss of b. wgt, water deprivation). RNA extraction was accomplished using Tri Reagent (Molecular Research Center Inc. Ohio, USA). The probes were labeled for 1 h by the reverse transcription of total RNA (3 µg) at 42°C in a primer mix (Clontech) containing [32P]dATP (Amersham Biosciences, Buckinghamshire, UK). The reaction was terminated by adding 0.1M EDTA and 1 mg/ml glycogen (Sigma).The unincorporated 32P-labeled nucleotides were removed by Nucleo-Spin extraction columns (Clontech). Source GEO sample is GSM62949 Last updated (according to GEO): Oct 28 2005 0029_1471_H95A2_T94-74_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A brain, SNc and VTA: SNc5_e1_le1 Neoplasm 861 1000 Kidney Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3334 Last updated (according to GEO): Mar 21 2006 between the LAD artery 266 287 Brain 1000 Mouse ileum with L.monocytogenes(delta-inlAB)_A_5551 Gene expression data from mouse primary visual cortex Source GEO sample is GSM101707 Last updated (according to GEO): Mar 27 2006 MGMH030228091Bembryoday10.5 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114416 Last updated (according to GEO): Jun 16 2006 10 Bone marrow 0 Nasal Epithelium Inhalation Formaldehyde 6ppm 24h ID289 R643P00803 GM12740 1000 Leukemia, Myelocytic, Acute Lmna H222P heterozygous male 5 Wild type 8 wk old male C57BL/6J mouse hippocampus Source GEO sample is GSM107009 Last updated (according to GEO): Mar 05 2007 PMN_control_180min_Patient10 1000 Communicable Diseases Post-transcriptional mechanisms play an important role in the control of gene expression. RNA-binding proteins are key players in the post-transcriptional control of many neural genes and they participate in multiple processes, from RNA splicing and mRNA transport to mRNA stability and translation. Our laboratory has developed the first mouse model overexpressing a RNA-binding protein, the ELAV-like protein HuD, in the CNS under the control of the CaMKinII alpha promoter. Initial behavioral characterization of the mice revealed that they had significant learning deficits together with abnormalities in prepulse inhibition (PPI). At the molecular level, we found that the expression of the growth-associated protein GAP-43, one of the targets of HuD, was increased in the hippocampus of HuD transgenic mice. To characterize these mice further and to evaluate the utility of these animals in understanding human diseases, we propose to use DNA microarray methods. To test our hypothesis we propose 2 specific aims: 1)To characterize the pattern of gene expression in the hippocampus of HuD overexpressor mice 2)To compare the pattern of gene expression in our mouse model with that in the hippocampus of rats prenatally exposed to alcohol (FAS model) and in post-mortem tissues of patients with schizophrenia Based on the behavioral and molecular properties of our HuD transgenic mice we hypothesize that these animals may be good models for the studying the basis of learning disabilities and of diseases that show deficits in PPI such as fetal alcohol syndrome and schizophrenia. All mice are in C57BL/6 background and are male approximately 60 days old. Initial studies were performed in animals that were not subjected to any experimental manipulation. Animals were bred and sacrificed according to our approved animal protocol. The brain was rapidly dissected on ice and we isolated the hippocampus, which has the highest expression of the transgene. After dissection both hippocampi were frozen in liquid nitrogen, pooled and stored at -80C until analysis. RNA samples were isolated using RNAeasy Qiagen columns. For our first experiment, we want to examine the pattern of gene expression in the hippocampus of 3 transgenic mice and 3 non-transgenic littermates. RNAs from the 6 hippocampi were of high quality as revealed by the integrity of the 28S and 18S rRNA. We will provide 6 samples containing 10 ug of RNA each in DEPC water at a concentration of about 0.5 ug/ul. Three of the samples (#1, #2 and # 3) are from transgenic mice and three from their non-transgenic littermates (#4, #5 and #6).. Date GSE2005 Last Updated: May 29 2005 Contributers: Nora I Perrone-Bizzozero Includes GDS1111. Update date: May 09 2005. Dataset description GDS1111: Analysis of hippocampus of 60 day old C57BL/6 males overexpressing the RNA binding protein HuD. HuD overexpressor mice exhibit learning deficits and abnormalities in prepulse inhibition.. 1000 Coronary Arteriosclerosis GC (HKG23T) Epithelium 861 91 from the bone marrow 72 Peripheral Nervous System 1000 Ventral tegmental area, male 10.5 week old c57bl/6J mouse, SUSCEPTIBLE group Source GEO sample is GSM224753 Last updated (according to GEO): Aug 31 2007 spleen 36 41 12hr post 10Gy IR 22 0 Mammary Gland @ Invo2 osteoblast 627 637 1000 Brain Cardiac 523 530 MuscleRegen-ctx7d-2LLAv2-s2 I_U133A_68_AnCg of coronary artery disease 317 342 861 Blood human frontal cortex Source GEO sample is GSM86978 Last updated (according to GEO): Feb 08 2006 Liver 1000 in bronchial epithelia 311 332 5 0 Spleen CAD_replicate79 Acetaminophen 6hr Rat 3763 blood vs. Acetaminophen 6hr Rat Pooled Control blood Post mortem human brain tissue comparison between HD patients and controls from 3 brain regions - cerebellum, frontal cortex [BA4, BA9] and caudate nucleus. Gene expression analysed using linear models from LIMMA package in Bioconductor suite. Last Updated (by provider): Feb 23 2006 Contributers: Aaron K Aragaki James M Olson Cathy Hartog Richard L Faull Anne B Young Mauro Delorenzi Peter A Holmans Sarah J Augood Francois Collin Gareth Hughes Charles Kooperberg Zane R Hollingsworth Thierry Sengstag Angela Hodges Lyn A Elliston Ruth Luthi-Carter Alexander Kuhn Doris Thu Andrew D Strand Beth Synek Nancy S Wexler Lesley Jones Darlene R Goldstein 5 0 Spleen the ventricular 1095 1109 Spinal Cord 1000 901 Mammary gland 335 325 The jejunum from the forebrain 20 37 HCC (HBV+, SF27) GSE1026 Expression profiling of spinal cord section (T10) extracted from rats 7d following laminectomy (sham) Lot batch = Source GEO sample is GSM6635 Last updated (according to GEO): May 28 2005 TAp63 alpha 24h induction s3 41 29 Control blood 1000 Endometrium plasma cells 50 61 Physiological genomics of human arteries: quantitative relationship between gene expression and arterial stiffness. VDXKIU_43C47 16 7 cerebellum Ny9: Hippocampus_5T-AI_rep5 152 132 in neural stem cells Muscle 645 650 Halothane 10 exposure-1 within endothelial cells 1298 1322 brain 0 5 48h +TGF-beta pulp tissue P46DR (dark reared) non-deprived visual cortex replicate 2 Substantia Nigra Reticulata 5 Normal no additional Source GEO sample is GSM199091 Last updated (according to GEO): Jun 08 2007 24 0 Substantia nigra PD rep16 Blood Test (Blinded) Sample Source GEO sample is GSM130025 Last updated (according to GEO): Sep 18 2007 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18170.gif Source GEO sample is GSM91492 Last updated (according to GEO): Sep 22 2006 Wild type P18 mouse visual cortex ipsilateral to monocular enucleation Source GEO sample is GSM97197 Last updated (according to GEO): Feb 17 2006 liver_wildtype_control_5d_pooled 129:24-4 pons Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132516 Last updated (according to GEO): Feb 26 2007 P18 non-deprived visual cortex replicate 5 1037 of transitional epithelium 1012 Blood Test (Blinded) Sample Source GEO sample is GSM129924 Last updated (according to GEO): Sep 18 2007 9 0 Blood Test 1000 Carcinoma Epilepsy 1000 MELAN_M14 on Affymetrix GeneChip Human Full Length Array HuGeneFL skin 48 51 WGACON-260 CNS-SMTC_Ctr7d-1B-s2 Expression profiling of somatomotor cortex extracted from rats at 3 months following moderate injury Source GEO sample is GSM41733 Last updated (according to GEO): May 27 2005 1000 Cerebral cortex CNS-SC_CtrB30m-2B-s2 prostate Source GEO sample is GSM203326 Last updated (according to GEO): Jun 21 2007 Urethra 2 Normal Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11515 Last updated (according to GEO): May 28 2005 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169480 Last updated (according to GEO): Feb 21 2007 Temporal neocortex mTLE 6 After 2 week acclimation to 12 hr/12 hr light/dark regimen, c57/Bl6 mice were subjected to a 36 hour period of constant darkness. Aortae were subsequently harvested at 4 hour intervals to 48 hours. Duplicate microarrays were hybridized with biotin-labeled probes derived from aorta tissue (6 pooled aortae/timepoint). Second chip data. Source GEO sample is GSM6102 Last updated (according to GEO): May 27 2005 n/a Source GEO sample is GSM177992 Last updated (according to GEO): Jun 11 2007 tonsil_3 Source GEO sample is GSM80886 Last updated (according to GEO): Mar 31 2006 Acetaminophen 24hr Rat 2330 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool cerebral cortex 7 21 TAp63 alpha 24h without induction s2 D_95Av2_2846_DLPFC_1_GS Parkinson Disease 1000 Lymphoblastoid Cell Line for Individual 8110.3 log phase Expression profiling of somatomotor cortex extracted from rats at 7d following moderate injury Lot batch = Source GEO sample is GSM44716 Last updated (according to GEO): May 29 2005 the blood 393 402 infection 409 418 861 Neoplasm Heart Septal Defects 884 1000 Brain 178-96_Adeno Putamen 5 Normal 5 0 Spleen 1037 of transitional epithelium 1012 CNS-SC_InjA14d-1C-s2 PGA_IGF1R-dnPI3K_1040 BALB-c mice were given intratracheal bleomycin (1.5U per kg). Lungs were harvested and frozen at 72h. Lot batch = Source GEO sample is GSM4157 Last updated (according to GEO): May 28 2005 khan-bluecell 2648 2640 28S rRNA Spleen vs Dimaprit Treated B cell 30min (set2) 7 0 Pancreas Spleen vs Bombesin Treated B cell 240min (set3) Serine Conjugated Surface 32 hours Levitiracetam hippocampus 6 Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53438 Last updated (according to GEO): Jul 06 2005 BTBR T+ tf-tf_male_hypothalamus /HeJ mouse periaqueductal gray 27 56 Hepatocyte 861 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153345 Last updated (according to GEO): Dec 27 2006 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour.This animal was sacrificed at 23 hours after lights on.Original sample code = CM35A Source GEO sample is GSM227324 Last updated (according to GEO): Sep 10 2007 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b007 Source GEO sample is GSM1964 Last updated (according to GEO): Nov 21 2005 PGA_MI_ilv_24h_363 Plasma 861 Subject code A51 19 0 Head and neck cancer striatum 31 39 brain 0 5 Sham 16 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107505 Last updated (according to GEO): May 01 2006 Primary Carcinoma 876 PGA-MPF-BALB-bleo-14d-1aAv2-s2 GC (HKG12T) brain, frontal cortex: Sample53_e1_le1 ER negative human primary breast tumor EA02014_41262_H133A_JA-1222 heart 1169 1173 966 Hippocampus Amygdala Source GEO sample is GSM107918 Last updated (according to GEO): Jun 06 2006 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47535 Last updated (according to GEO): May 29 2005 1000 Hippocampus brain, cerebral cortex: Rat_03-31_NroLep_Lipska_e1_le1 1000 Brain D_U133A_117_DLPFC Brain 1000 861 Stomach JejunTumorNew_0228AFCB_jtc.txt 361 335 hypertrophic cardiomyopathy Motor Neuron Disease 861 (1 utricle 11 20 966 Hippocampus spinal cord 0 11 human frontal cortex Source GEO sample is GSM86931 Last updated (according to GEO): Feb 08 2006 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19232 Last updated (according to GEO): May 27 2005 the heart 987 996 of the postmortem brains 674 698 861 Gland structure Normal Breast mouse brain 478 489 Epithelium of bronchus 983 Osteoblasts 1000 Normal Source GEO sample is GSM175830 Last updated (according to GEO): Apr 09 2007 26 0 cerebral cortex wistar 3903 brain, cortex: Sample10_e1_le1 outer medulla 31 43 of human airway epithelial cells 289 320 1000 Kidney n/a Source GEO sample is GSM178014 Last updated (according to GEO): Jun 11 2007 from brain 21 30 Expression profiling of spinal cord section (T10) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31283 Last updated (according to GEO): May 27 2005 861 Blood 861 Pancreas in the brain 150 162 228 219 Hippocampi liver, wild type mice, treatment with WY14643 for 6h Source GEO sample is GSM205769 Last updated (according to GEO): Jul 24 2007 Brain 861 dorsal_root_ganglia_1 861 Cerebellum of trisomy chromosome 21 33 56 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL10 for 120min Source GEO sample is GSM5644 Last updated (according to GEO): May 27 2005 Intraabdominal isolated adipocytes, rep3 Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35384 Last updated (according to GEO): May 27 2005 Mouse Liver AIN Diet 8hr 1mg/kg As Injection, biological replicate F Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228652 Last updated (according to GEO): Sep 11 2007 Spinal Cord 1000 outer medulla 31 43 human_hepatocytes_WY12h_pooled spinal cord 13 23 1000 Brain Skeletal bone 861 Exp B, Animal #1, 5mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 5mg/kg of CPF for 96 hours Source GEO sample is GSM246153 Last updated (according to GEO): Dec 03 2007 A61 NES 142Q TG2 F6/22 A61 NES Htt exon 1 142Q Mouse 8 months Cerebellum Male Source GEO sample is GSM73229 Last updated (according to GEO): Sep 06 2005 4 0 Brain Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181069 Last updated (according to GEO): Jul 12 2007 Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18220.gif Source GEO sample is GSM91540 Last updated (according to GEO): Sep 22 2006 1000 Cerebral cortex n/a Source GEO sample is GSM177905 Last updated (according to GEO): Jun 11 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28791 Last updated (according to GEO): May 27 2005 114 FC BA9 B 2500 mg/kg X 24 hr Source GEO sample is GSM129854 Last updated (according to GEO): Sep 18 2007 Levitiracetam brainstem 2 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53427 Last updated (according to GEO): Jul 06 2005 129S6/SvEvTac hypothalamus rep1 (430 2.0 Array) low gestational age Source GEO sample is GSM213091 Last updated (according to GEO): Jul 25 2007 zero_1 to the nose 599 609 120 FC BA9 A HUVEC isolate 9 rich media untreated Source GEO sample is GSM12924 Last updated (according to GEO): May 28 2005 AD control Treatment, type=dissect Source GEO sample is GSM119635 Last updated (according to GEO): Jul 10 2006 brain, Left frontal Lobe: Extract35_le1 5 0 brain Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184715 Last updated (according to GEO): Apr 26 2007 rat hippocampus Treatment, type=pharmacogenomic_treatment, description=Fed control diet Source GEO sample is GSM35871 Last updated (according to GEO): May 27 2005 D_U133A_6_nAcc Primary tumor 19 32 882 871 in cartilage Lymphoblastoid Cell Line for Individual 8061.4 log phase 1000 frontal lobe 89 68 with tricuspid valves Parkinson Disease 1000 4_cerebral_cortex_6hrs_sleep_deprivation_#49 966 Hippocampus HC102 CB B 913 Acute leukemia Gene expression data from postmorten brain regions Source GEO sample is GSM145668 Last updated (according to GEO): Nov 20 2006 CNS-SC_CtrA14d-1A-s2 Gene expression of modiolus of newborn rats inner ear Bone structure of tibia 1000 Trasnsformed Lymphocytes Unaffected Twin Pair 1(DCBD1.2)(TP6) VDXRHU_317 Caudal 1000 Plasma 861 Expression profiling of spinal cord section (T8) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM4453 Last updated (according to GEO): May 28 2005 861 Heart Expression profiling offers a potential high-throughput phenotype screen for mutant mouse embryonic stem (ES) cells. We have assessed the ability of expression arrays to distinguish among heterozygous mutant ES cell lines and to accurately reflect the normal function of the mutated genes. Two ES cell lines hemizygous for overlapping regions of mouse Chromosome (Chr) 5 differed substantially from the wildtype parental line and from each other. Expression differences included frequent downregulation of hemizygous genes and downstream effects on genes mapping to other chromosomes. Some genes were affected similarly in each deletion line, consistent with the overlap of the deletions. To determine whether such downstream effects reveal pathways impacted by a mutation, we examined ES cell lines heterozygous for mutations in either of two well-characterized genes. A heterozygous mutation in the gene encoding the cell cycle regulator, cyclin D kinase 4 ( Cdk4), affected expression of many genes involved in cell growth and proliferation. A heterozygous mutation in the ATP binding cassette transporter family A, member 1 ( Abca1) gene, altered genes associated with lipid homeostasis, the cytoskeleton, and vesicle trafficking. Heterozygous Abca1 mutation had similar effects in liver, indicating that ES cell expression profile reflects changes in fundamental processes relevant to mutant gene function in multiple cell types. 861 Carcinoma, Non-Small-Cell Lung CNS-SpinalC-conAdult-72h-1C-s2 Blood 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145811 Last updated (according to GEO): Nov 20 2006 24 skeletal muscle 10 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n037 Source GEO sample is GSM2065 Last updated (according to GEO): Nov 21 2005 plasma cells 50 61 GM07055 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 14 hours after lights on. Original RNA code = LC12A. Source GEO sample is GSM227397 Last updated (according to GEO): Sep 10 2007 Adenocarcinoma 861 NA12750 growth 3, replicate 1 /HeJ Hippocampus A 3 20 Liver 1000 1000 Heart Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188791 Last updated (according to GEO): Jun 06 2007 Collagen 1000 I_U133A_48_Amy 5 0 brain Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210407 Last updated (according to GEO): Jul 16 2007 GM12155 861 Ribosomal RNA Transitional epithelium 1000 24 0 Colorectal Adenocarcinoma heart failure 583 595 278 273 livers thyroid_gland_1 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10127.gif Source GEO sample is GSM79669 Last updated (according to GEO): Sep 22 2006 Primary Neoplasm 1000 Hippocamp22KAFAZ_003.txt thalamus_8 Source GEO sample is GSM80862 Last updated (according to GEO): Mar 31 2006 CNS-RM_Mod24h-1B-s2 22 0 Normal epithelial cells 913 Muscular Dystrophy, Duchenne 131 118 /soleus muscle 1000 Endometriosis, site unspecified brain 0 5 Disorder of artery 865 CS-B wt-rescued cell unirradiated replicate 2 U133A 3616 PC 24Hr (pool) vs. 150mg/kg APAP 24Hr rat 3617 blood A/J_male_hypothalamus Source GEO sample is GSM184190 Last updated (according to GEO): Apr 26 2007 nerve 0 5 Tumor__Colorectal_Adeno_95_I_057 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 861 Hepatocyte Parkinson Disease 1000 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27675.gif Source GEO sample is GSM66562 Last updated (according to GEO): Sep 22 2006 for nicotinic receptors 165 187 Simple annotation: Normal tissue, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3733.gif Source GEO sample is GSM76449 Last updated (according to GEO): Sep 22 2006 3696 3691 plasma 861 Blood 12 0 Normal Spleen /3T3 fibroblasts 295 310 Gene expression data from rat metanephric mesenchymes cultured for 5 days in the presence of the ANX fraction Source GEO sample is GSM126226 Last updated (according to GEO): Dec 08 2006 GM19159 1000 Brain brain 0 5 YFPH-Hippocampus-replicate1 Primary tumor 19 32 5 0 Spleen SmoothMuscle Source GEO sample is GSM18812 Last updated (according to GEO): Sep 25 2006 12 frontal Lobe 23 PGA-HMO-MObese-3aUA-s2 Expression profiling of spinal cord section (T9) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM1136 Last updated (according to GEO): May 28 2005 of gut neurospheres 39 57 75 46 with polycystic ovary syndrome Cultured_osteoblast-like_control_MC3T3-E1_cells_rep5 91 from the bone marrow 72 26 (entorhinal cortex 43 278 255 ischemic cardiomyopathy Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181057 Last updated (according to GEO): Jul 12 2007 38 21 from a hippocampus from colorectal adenoma 21 44 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156600 Last updated (according to GEO): Jan 22 2007 Expression profiling of spinal cord section (T8) extracted from rats 14d following mild injury Source GEO sample is GSM31430 Last updated (according to GEO): May 27 2005 Blood 1000 Exp 7 (-SB80) 43 0 Chorionic mesoderm-derived mesenchymal cells CNS-SpinalCsev-Adult-24h-3C-s2 bone marrow-CD71EarlyErythroid Source GEO sample is GSM18908 Last updated (according to GEO): Sep 25 2006 Carcinoma, Non-Small-Cell Lung 890 Diet induced changes in mouse liver mRNA profiles. One of 3 replicates of LDL receptor deficient mice maintained for 12 weeks on high fat Western style diet. Keywords = LDL receptor deficiency, high fat diet, atherosclerosis, liver Source GEO sample is GSM5411 Last updated (according to GEO): May 27 2005 This dataset contains the gene expression profile of a CD11c high, CD4 negative and CD8 negative ("Double Negative") splenic dendritic cell population. The cells were processed following 2 hour incubation in tissue culture medium at 37 C. Global scaling was applied to Avg Difference intensity values. Keywords = mouse, dendritic cells, spleen Source GEO sample is GSM4774 Last updated (according to GEO): May 27 2005 left hemi-diaphragm 27 45 Neoplasm 861 0029_1289_H95A2_KF-201_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A puroD is a clonal control(puromycin resistant) stable c17.2 neural stem cell line with similar proliferation rate as clone 48 and therefore both were matched for subsequent analysis. Source GEO sample is GSM82227 Last updated (according to GEO): Nov 07 2005 LungP1_022QAF6Z_077a.txt brain 0 5 sal-PVH_2 cerebral cortex wistar 3902 all cortical minus the frontal cortex, individual animal, 10 weeks old, male Wistar cerebral cortex file:p3902w Source GEO sample is GSM15144 Last updated (according to GEO): Oct 28 2005 GSE60 The most common congenital cardiac abnormalities 50 97 Spinal Cord Injuries 1000 CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of M?, rhM-CSF was added at 1000 U/ml on the same days. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5147 Last updated (according to GEO): Sep 08 2006 Plasma 861 Lymphoblastoid Cell Line for Individual 8201.3 log phase mouse hippocampus, cox-2 knockout, rep1 Bone Marrow 1000 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225732 Last updated (according to GEO): Nov 02 2007 901 Heart failure Parahippocampal Gyrus 913 Array representing the response of Human foreskin fibroblasts at 60min post HCMV infection Source GEO sample is GSM10372 Last updated (according to GEO): May 27 2005 Brain 1000 2295 2287 cerebella 5 0 Spleen Exp 3 (-TNFa) dnEgr (dominant negative Egr)/EGFP infected SH-SY5Y/TrkA cells: infection (at t=-18 hours), NGF treatment (at t=0 hours), harvest for total RNA extraction (at t=3 hours). Replicate 1 Treatment, type=add Source GEO sample is GSM53384 Last updated (according to GEO): Jul 06 2005 Primary tumor 19 32 23 11 of the kidney Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59855.gif Developmental Stage: E7.75 Source GEO sample is GSM229827 Last updated (according to GEO): Nov 06 2007 adenoma 861 ALL_14 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A D_U133Plus_93_HC ER+/LN+/Marks207 on Affymetrix GeneChip Human Full Length Array HuGeneFL spleen 36 41 1000 Brain osteoblast 627 637 GC (HKG64N) 338 333 brain Human prostate cancer cells in different conditions Source GEO sample is GSM13090 Last updated (according to GEO): May 28 2005 Primary Neoplasm 1000 Parkinson Disease 901 trigeminal_ganglia_10 Coronary Arteriosclerosis 1000 Melanoma xenograft, MEC1_Sub_B (LeiFidler) Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211317 Last updated (according to GEO): Jul 18 2007 Lymphoblastoid Cell Line for Individual 8193.4 log phase T43__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Congenital Abnormality 853 of the saphenous artery 117 139 human cerebellum Source GEO sample is GSM87157 Last updated (according to GEO): Feb 08 2006 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 3420 left_liver_lobe 983 Hair shaft structure Monocular deprivation left cortex, biological rep2 CHB MD-5 na Source GEO sample is GSM181292 Last updated (according to GEO): Apr 10 2007 of coronary artery disease 317 342 Lymphoblastoid Cell Line for Individual 8097.4 log phase CS 15h total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with 2-Methyl-thio-ATP for 120min Source GEO sample is GSM5426 Last updated (according to GEO): May 27 2005 AD brain 1892 1900 no additional Source GEO sample is GSM199043 Last updated (according to GEO): Jun 08 2007 none Source GEO sample is GSM239910 Last updated (according to GEO): Dec 07 2007 41 29 Control blood of the normal mucosa 7 26 Gene expression data from postmorten brain regions Source GEO sample is GSM145481 Last updated (according to GEO): Nov 20 2006 Heart failure 1000 1000 Structure of parenchyma of lung 3ARS02080773b_ciliary_ganglion 70 40 without coronary artery disease cy5:WKY treated w/ angtiotensin, biological rep 3r; cy3:pool of 6 WKY control rats Infection 1000 1000 Hypertrophic Cardiomyopathy 40 21 from dorsal pancreas Sample 106 on vantveer-oligo Melanoma xenograft, MED1_Sub_C (LeiFidler) from ventral prostate 21 41 Neoplasm 861 Spleen 1000 861 Heart Ta gr3 tumour Source GEO sample is GSM2522 Last updated (according to GEO): Mar 21 2006 901 Cerebral cortex no additional Source GEO sample is GSM199311 Last updated (according to GEO): Jun 08 2007 5 0 Muscle GSE128 large B-cell lymphoma 8 28 SN:1007067 Source GEO sample is GSM115360 Last updated (according to GEO): Jun 20 2006 osteoblast 627 637 Structure of horn of uterus 983 7 cerebral cortex 21 Average value of duplicate experiments of gut neurospheres (neurospheres of peripheral nervous system) of BMI-1 knockout mice (postnatal day 0). The cRNAs for hybridization were generated by two round RNA amplifications. Source GEO sample is GSM9244 Last updated (according to GEO): May 27 2005 861 Heart AD-120t1-A226-8 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Expression profiling of spinal cord section (T10) extracted from rats 14d following mild injury Source GEO sample is GSM31308 Last updated (according to GEO): May 27 2005 Malaria 1000 CNS-SpinalC-conAdult-14d-2B-s2 frontal cortex wistar 3921 861 Ovary aortic biopsy stiff Keywords = pulse wave velocity, arterial stiffness Source GEO sample is GSM6188 Last updated (according to GEO): May 27 2005 frontal cortex wistar ky 3929 healthy subject Source GEO sample is GSM211111 Last updated (according to GEO): Sep 10 2007 DRG Source GEO sample is GSM19010 Last updated (according to GEO): Sep 25 2006 cd8+Tcell Source GEO sample is GSM18675 Last updated (according to GEO): May 27 2005 Primary tumor 19 32 Coronary heart disease 913 surnSD_15, ZT6 Alzheimer's Disease 861 Spleen vs Terbutaline Treated B cell 60min (set3) Treated Source GEO sample is GSM176480 Last updated (according to GEO): Apr 09 2007 Transcriptional Profiling of the Transition from Normal Intestinal Epithelia to Adenomas and Carcinomas in the APC(Min/+) Mouse. Samples used in analysis: * GSM6191-GSM6196 (WT): Ilea epithelial cells from C57/BL6 wild-type samples * GSM6197-GSM6201 (Adenoma): Epithelial cells from crypts of adenomas of APC(Min/+) mice * GSM6202-GSM6206 (Carcinoma): Epithelial cells from crypts of carcinomas of APC(Min/+) mice Using a PixCell IIe instrument (Arcturus), ~30,000 laser firings per sample were used to collect cells of interest. RNA was extracted from captured cells by PicoPure (Arcturus) technique, followed by 2 rounds of RiboAmp amplification (Arcturus), with incorporation of biotinylated nucleotides (Enzo) in the IVT of round 2. All protocols were as per manufacturers instructions. 15ug of labeled cRNA from individual samples were hybridized to respective MG_U74Av2 chips (Affymetrix) and washed/stained using the standard EukGEWS2v4 protocol (Affymetrix). Chips were scanned and analyzed using MAS 5 (Affymetrix) and data scaled to TI=500. Pairwise comparisons using the Mann-Whitney test were performed in DMT 3 (Affymetrix), comparing: * WT vs Adenoma (n=6 x n=5; 83.3% concordance) * WT vs Carcinoma (n=5 x n=5; 84% concordance) * Adenoma vs Carcinoma (n=5 x n=5; 84% concordance) This resulted in the identification of differentially expressed transcripts. Fold changes were calculated from signal-log-ratios. Identified transcripts were clustered based on functional information which was publicly available at time of analysis, obtained through the NetAffx web portal (Affymetrix).. Date GSE422 Last Updated: Aug 29 2005 Contributers: Matthew W Feldman Linda S Gutierrez Nicholas F Paoni Francis J Castellino Victoria A Ploplis Includes GDS389. Update date: Sep 03 2003. Dataset description GDS389: Examination of transition from normal intestinal epithelia to adenomas and carcinomas in the multiple intestinal neoplasia adenomatous polyposis coli mutant mouse, APC(Min/+).. R6/1 18 week wildtype_15E8 26 15 endometrioid Hereditary Malignant Neoplasm 864 715 702 After the eyes Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188736 Last updated (according to GEO): Jun 06 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11344 Last updated (according to GEO): May 28 2005 cerebral cortex 7 21 1000 Brain AD-295t1-A105-3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A trigeminal_ganglia_9 Source GEO sample is GSM80906 Last updated (according to GEO): Mar 31 2006 of the atrial 647 659 brain 112 117 861 Salivary Glands 653 637 between leiomyoma RPMI-8226 hgu95c Lymphoblastoid Cell Line for Individual 8039.3 log phase Cerebral cortex 1000 Macrophage smi74 144 memory disorders 159 MO_control_180min_Patient14 whole blood_100416 072801 B7-2 02.00 hr. T-Cell Donor 1 time point 12 hours Autologous Control (uninfected) Source GEO sample is GSM2597 Last updated (according to GEO): May 27 2005 to the nose 599 609 19 0 Head and neck cancer Spleen vs 2-Methyl-thio-ATP Treated B cell 30min (set1) Muscle; Smooth - Bladder- day 1 postnatal male Keywords = mouse gene expression database Source GEO sample is GSM29404 Last updated (according to GEO): May 27 2005 Pituitary Gland 1000 from the right forebrain 21 44 Parkinson Disease 1000 f2#208 versus pool Mouse Brain tissue 1000 Spleen 10 Bone marrow 0 stria terminalis 1000 male us chip 37 Neoplasm 861 brain, Left frontal Lobe: ASTRO III 587_e1_le2 Heart Atrium 1000 MDA Mb231 + Cxcr4 2 Control Lung; Day 1 postnatal Keywords = mouse gene expression database Source GEO sample is GSM29378 Last updated (according to GEO): May 27 2005 NCI60.12_LABEL15EXTRACT14SUB3 Source GEO sample is GSM134054 Last updated (according to GEO): Aug 06 2007 Endometrium 0 10 Nose 1000 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201262 Last updated (according to GEO): Jun 14 2007 CNS-SMTC_Mod24h-3B-s2 861 Muscle 434 418 of the infection 20 0 Nicotine-hippocampus 1000 Brain Osteoblasts 1000 Expression profiling of spinal cord section (T8) extracted from rats 7d following severe injury Source GEO sample is GSM31493 Last updated (according to GEO): May 27 2005 DBA/2J Hippocampus B 5 0 brain Primary large cell carcinoma 1485 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with 2-Methyl-thio-ATP for 120min Source GEO sample is GSM5424 Last updated (according to GEO): May 27 2005 OVCAR-5 hgu95b 861 Asthma 1000 Spleen 1000 Cochlear structure healthy subject Source GEO sample is GSM211064 Last updated (according to GEO): Sep 10 2007 Alzheimer's Disease 861 S9_Muscle_Insulin_30min 1000 Amygdaloid structure zero_3 of underlying brain 171 190 901 Cerebral cortex Blood Test (Blinded) Sample Source GEO sample is GSM129981 Last updated (according to GEO): Sep 18 2007 C57/BL6 to C57/BL6 Source GEO sample is GSM8932 Last updated (according to GEO): May 28 2005 901 Caudate nucleus structure 901 Nervous system structure 901 Malignant neoplasm of prostate no additional Source GEO sample is GSM199409 Last updated (according to GEO): Jun 08 2007 TemporalLobe Source GEO sample is GSM18752 Last updated (according to GEO): Sep 25 2006 L_D2_Control_ZT 6_3 0 Frontal Cortex 13 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68252 Last updated (according to GEO): Jul 07 2006 GSE4180 Primary tumor 19 32 Skeletal bone 861 cirrhotic liver tissue from patients without HCC Source GEO sample is GSM155984 Last updated (according to GEO): Jun 21 2007 1000 Large Intestine Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92327 Last updated (according to GEO): Jan 13 2006 861 Neoplasm none Source GEO sample is GSM239839 Last updated (according to GEO): Dec 07 2007 CingulateCortex Source GEO sample is GSM18939 Last updated (according to GEO): Sep 25 2006 HCC (HBV+, SF35, 1) 861 Heart failure 12 frontal Lobe 23 Substantia nigra PD rep9 "23 hr Hela Double Thymidine, exp3" 861 Chromosomes none Source GEO sample is GSM239936 Last updated (according to GEO): Dec 07 2007 Spleen 0 5 RNA from Lymphoblastoid Cell Line from this individual Source GEO sample is GSM213296 Last updated (according to GEO): Jul 26 2007 PGA-swim_4w_n539 N46__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A FSCC13 on Affymetrix GeneChip Human Full Length Array HuGeneFL /HeJ pituitary gland rep1 3 27 23 11 of the kidney 11_0017_SepticShock_Day3_40 17 saline 21 0 acute myeloid leukemia 2532 HP24_31 Keywords = Infectious diseases 1069 1099 The epithelial cells 962 981 0029_1239_H95A2_KF0131_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 19 0 human frontal cortex brain, Left frontal Lobe: Extract5_le2 Brain_Aged_LPSip_4hr_mouse2 (OL2_#68) Epithelium of bronchus 983 5 0 brain liver 0 4 Gene expression changes and molecular pathways mediating activity-dependent plasticity in visual cortex. 51 39 with diabetes Although expression of some genes is known to change during neuronal activity or plasticity, the overall relationship of gene expression changes to memory or memory disorders is not well understood. Here, we combined extensive statistical microarray analyses with behavioral testing to comprehensively identify genes and pathways associated with aging and cognitive dysfunction. Aged rats were separated into cognitively unimpaired (AU) or impaired (AI) groups based on their Morris water maze performance relative to young-adult (Y) animals. Hippocampal gene expression was assessed in Y, AU, and AI on the fifth (last) day of maze training (5T) or 21 d posttraining (21PT) and in nontrained animals (eight groups total, one array per animal; n = 78 arrays). ANOVA and linear contrasts identified genes that differed from Y generally with aging (differed in both AU and AI) or selectively, with cognitive status (differed only in AI or AU). Altered pathways/processes were identified by overrepresentation analyses of changed genes. With general aging, there was downregulation of axonal growth, cytoskeletal assembly/transport, signaling, and lipogenic/uptake pathways, concomitant with upregulation in immune/inflammatory, lysosomal, lipid/protein degradation, cholesterol transport, transforming growth factor, and cAMP signaling pathways, primarily independent of training condition. Selectively, in AI, there was downregulation at 5T of immediate-early gene, Wnt (wingless integration site), insulin, and G-protein signaling, lipogenesis, and glucose utilization pathways, whereas Notch2 (oligodendrocyte development) and myelination pathways were upregulated, particularly at 21PT. In AU, receptor/signal transduction genes were upregulated, perhaps as compensatory responses. Immunohistochemistry confirmed and extended selected microarray results. Together, the findings suggest a new model, in which deficient neuroenergetics leads to downregulated neuronal signaling and increased glial activation, resulting in aging-related cognitive dysfunction. G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Source GEO sample is GSM9650 Last updated (according to GEO): May 28 2005 335 325 The jejunum Stem cells 1000 low gestational age Source GEO sample is GSM213118 Last updated (according to GEO): Jul 25 2007 302 295 seizures Levitiracetam frontal cortex 6 Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53459 Last updated (according to GEO): Jul 06 2005 Arteries 861 Gene expression data from aldosterone-producing adenoma Source GEO sample is GSM211456 Last updated (according to GEO): Jul 18 2007 Ileum [JunctionChip 5 of 5] accumbens_9 1000 Cerebellum prostate Source GEO sample is GSM203330 Last updated (according to GEO): Jun 21 2007 from the femurs 95 109 olfactory epithelium 194 213 brain, contralateral HC: Trizol Extraction31_le1 A series of chips with some repeated measurments. Each chip represents a pool of 4 collagen/chondroitin sulfate tissue engineering scaffold meshes seeded with 1 x 10^6 IMR-90 Human Fibroblasts. mRNA was isolated at 30 minutes, 1, 2, 4, 8, 12, 24, 48, and 72 hours after seeding. Last Updated (by provider): May 29 2005 Contributers: Catherine M Klapperich Carolyn R Bertozzi Includes GDS395. Update date: Oct 02 2003. Dataset description GDS395: Temporal gene expression analysis of fetal lung fibroblast cell line IMR-90 seeded onto collagen/chondroitin sulfate tissue engineering scaffold mesh material. Integration of genomic information with biomaterial engineering.. HTI-286, an analogue of hemiasterlin, interferes with microtubule dynamics and circumvents transport-based resistance to taxanes. In this study we evaluate the inhibitory effects of HTI-286 on human prostate cancer growth in vitro and in different in vivo models. The results show that HTI-286 is a potent inhibitor of proliferation and induced marked increases in apoptotic rates in all cell lines tested. Despite similar transcriptomic changes regarding cell death and cell cycle-regulating genes after exposure to HTI-286 or docetaxel, the gene array revealed distinct molecular signatures for both compounds. Last Updated (by provider): Jun 29 2007 Contributers: Susan L Ettinger Martin E Gleave Richard D Sowery Jenny Baybik Amina Zoubeidi Boris A Hadaschik Antonio Hurtado-Coll Michel Roberge 861 Neoplasm Metastasis Testis 1000 Total RNA extracted from the forebrain of a Tg+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144408 Last updated (according to GEO): Nov 14 2006 GSE4774 Brain 1000 Expression data from 59 human colon tumor tissue samples A HID U D045 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108611 Last updated (according to GEO): Aug 22 2006 660 mesenchymal stem cell 639 861 Cerebral cortex Structure of olfactory bulb 901 GSE9509 Gene expression data from postmorten brain regions Source GEO sample is GSM145590 Last updated (according to GEO): Nov 20 2006 of Parkinson's disease 450 471 HapMap YRI_parent Male Source GEO sample is GSM159681 Last updated (according to GEO): Feb 01 2007 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120694 Last updated (according to GEO): May 14 2007 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5152.gif Source GEO sample is GSM79926 Last updated (according to GEO): Sep 22 2006 CVB3_S-9h osteoblast 627 637 Wild type 8 wk old male DBA/2J mouse amygdala Source GEO sample is GSM74921 Last updated (according to GEO): Feb 27 2007 NHF3-hTERT_1.5Gy_24h_C5_21251 901 frontal lobe PBMCs-Type 1 Diabetes-IDDM48_T1D_1MO BXD42_M7SS02042217 Normal Source GEO sample is GSM175833 Last updated (according to GEO): Apr 09 2007 LOX IMVI hgu95b Effects of SOCS3 on transcriptional response of macrophages to IL-6. Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Replicate 1 after stimulation for 400 minutes with 10 ng/ml IL-6. Source GEO sample is GSM6074 Last updated (according to GEO): Mar 17 2006 Brain_MD_24_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL 5 0 brain SCG explant cultured for 2 hours in vitro Source GEO sample is GSM246046 Last updated (according to GEO): Dec 03 2007 1000 Uterus Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92325 Last updated (according to GEO): Jan 13 2006 VDXGUYU_4080 492 475 in the PCOS oocyte 5 0 brain Epithelium 861 861 Bone Marrow Ovary 861 (cortex 19 25 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195327 Last updated (according to GEO): Jun 04 2007 Pooled diaphragm RNA samples from five 8 wk old male C57BL10 mice Source GEO sample is GSM13564 Last updated (according to GEO): May 28 2005 861 Blood Mesenchymal Stem Cells 1000 GSE6628 861 Myopathy The genomic consequences of bursts of action potential firing induced by the treatment of cultured cortical neurons (9-11 DIV) with the GABAA receptor antagonist bicuculline (Bic, 50 ?M) and the potassium channel blocker 4-aminopyridine (4AP, 5 ?M). Source GEO sample is GSM144057 Last updated (according to GEO): Nov 24 2006 861 Malaria 1000 frontal lobe HC102 CN B Mesenchymal Stem Cells 1000 902 884 of medulloblastomas 36 21 from hippocampus NHF3-hTERT_S_C5_26555 with some respiratory epithelium. 1039 1072 ER negative human primary breast tumor EA02014_41300_H133A_JA-2025 no additional Source GEO sample is GSM199149 Last updated (according to GEO): Jun 08 2007 S46 WT5 F5/53 S46 wild type Mouse 10 months Cerebellum Female Source GEO sample is GSM73222 Last updated (according to GEO): Sep 06 2005 brain, contralateral HC: Trizol Extraction28_le1 MuscleRegen-ctx6d-2LLAv2-s2 mouse brains 187 198 906 Blood Cells Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181117 Last updated (according to GEO): Jul 12 2007 Menstrual phase - Follicular Source GEO sample is GSM175770 Last updated (according to GEO): Apr 09 2007 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15687 Last updated (according to GEO): May 28 2005 GBM Treatment, type=remove Source GEO sample is GSM99600 Last updated (according to GEO): Apr 21 2006 3AJZ02081478a_Superior_Cervical_Ganglion 132 121 among tumors HMEC control X HMEC+Interferon gamma 24hrs Lda1b 36 21 from whole brain Gene expression data from postmorten brain regions Source GEO sample is GSM145933 Last updated (according to GEO): Nov 20 2006 Laser captured visceral sensory neurons. Source GEO sample is GSM63662 Last updated (according to GEO): Dec 21 2005 f2#1 versus pool Mouse Brain tissue in the brain 248 259 Prostate 10 Disease 0 18 913 Coronary heart disease from the right forebrain 21 44 E2A-PBX1-#8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A GM18508 1000 Brain Injuries DRG005_c Epithelium of bronchus 983 861 Pancreas SN:Human Glioblastoma Biopsy 06527 1000 Skeletal muscle structure GSE4242 Gene expression data from postmorten brain regions Source GEO sample is GSM145142 Last updated (according to GEO): Nov 20 2006 Total RNA extracted from the forebrain of a Lh-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144386 Last updated (according to GEO): Nov 14 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145211 Last updated (according to GEO): Nov 20 2006 Saline ip saline ILI 4hrs post ILI sample B Control pool 3 (n=5) with acute measles 20 37 983 Endometrioid carcinoma ovary IGR-OV1 hgu95a HMVEC-L stimulated with LPS for 4 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114555 Last updated (according to GEO): Sep 20 2006 Expression profiling of somatomotor cortex extracted from rats at 4h following moderate injury Source GEO sample is GSM44441 Last updated (according to GEO): May 27 2005 Mouse Liver AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate C 861 Presynaptic Terminals 0029_1486_H95A2_T93-2_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 23 0 Substantia nigra PD rep8 Expression profiling of spinal cord section (T9) extracted from rats 4h following severe injury Lot batch = Source GEO sample is GSM7584 Last updated (according to GEO): May 28 2005 nasal epithelial cells 28 49 861 Cerebral cortex Ganglia, Spinal 923 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114248 Last updated (according to GEO): Jun 16 2006 from normal bone marrow 440 462 1000 Kidney 6874 on TGRI-6.5k between the two eyes 187 206 Lung Neuroendocrine Neoplasm 885 Mammary Gland @ Preg19, biological rep1 Ovary 1000 gene expression of 3 day LIF differentiated ESCs Source GEO sample is GSM181950 Last updated (according to GEO): Apr 12 2007 in fibroblasts 187 200 AD control Treatment, type=dissect Source GEO sample is GSM119684 Last updated (according to GEO): Jul 10 2006 GM18515 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc103 Source GEO sample is GSM1885 Last updated (according to GEO): Nov 21 2005 C3H/HeJ Amygdala F 861 Mammary gland Whole blood from a healthy control Source GEO sample is GSM153433 Last updated (according to GEO): Jan 11 2007 Osteoblasts 1000 24 14 (cerebellum Normal Source GEO sample is GSM175957 Last updated (according to GEO): Apr 09 2007 5 0 Spleen Lymphoblastic Leukemia 901 liver, wild type mice, treatment with WY14643 for 5d Source GEO sample is GSM205784 Last updated (according to GEO): Jul 24 2007 492 475 in the PCOS oocyte 901 Coronary artery bronchial epithelia 224 243 forebrain 7 15 1000 Cerebral cortex none Source GEO sample is GSM123189 Last updated (according to GEO): Jul 26 2006 Amygdala 3 Normal of mouse brain 9 23 olfactory epithelium 194 213 78 47 of the contused rat spinal cord SN:Human Glioblastoma Biopsy 12367 Brain 1000 Heart 1000 3AJZ02081482a_Appendix 0029_1237_H95A2_KF0125_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 3 hrs Pre-clamp sample 2 129 96 into mouse gastrocnemius muscle to NCI-H460 hgu95b 901 Ovarian adenocarcinoma 562 550 of the brain 913 frontal lobe C57BL/6 benchmark dataset: Embryonic day 15.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25176 Last updated (according to GEO): May 27 2005 of atrophied rat soleus muscle 47 76 913 Coronary heart disease 833 812 muscle-invasive tumors Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213467 Last updated (according to GEO): Jul 31 2007 BL6:4-3 -4-5 BNST DIV14 cortical neuron, control 1 Epithelium of bronchus 983 Brain 1000 Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. Moderate controlled cortical impact with pneumatic impactor, 6 m/s impact velocity and 1.5 mm deformation. 24h after surgery, a 4 mm diameter disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44463 Last updated (according to GEO): May 27 2005 4 0 Nasal Gene expression data from postmorten brain regions Source GEO sample is GSM144910 Last updated (according to GEO): Nov 20 2006 Infection 861 of the stria terminalis 56 78 1000 Lipids 1000 Hypothalamic structure 1000 Adipose tissue 1000 Hypothalamic structure Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hrs per day, 24 h time point Source GEO sample is GSM159747 Last updated (according to GEO): Apr 23 2007 DR72h(1) 468 459 the rectum EpiTl_022JACIP_114b.txt liver, wild-type mice, control conditions Source GEO sample is GSM205814 Last updated (according to GEO): Jul 24 2007 of the stria terminalis rep2 20 47 052201_HF_331FL normal 1103 1037 of transitional epithelium 1012 Colon 861 Epithelial Cells 901 R6/1 transgenic, brain hemisphere Source GEO sample is GSM83869 Last updated (according to GEO): Apr 20 2007 41 29 Control blood Skin 861 LDMTX_MP-DX-15 from rat mammary tumors 16 38 into the olfactory epithelium 193 221 C57L/J Basal Ganglia C medial prefrontal cortex short access to cocaine replicate 1 Brain 1000 I_U133A_6_CB 1500 mg/kg X 12 hr Source GEO sample is GSM129887 Last updated (according to GEO): Sep 18 2007 of caudal 93 101 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15727 Last updated (according to GEO): May 28 2005 861 Fibroblasts Breast 861 NSCLC_NCIH332M on Affymetrix GeneChip Human Full Length Array HuGeneFL GM10860_technical_rep_2 of mouse brain 9 23 Pregnant females fed with maltose dextrin, PF03 (Pair Fed) corresponds to replicate 3 Transplant Series 34 , Transplant # 4 9 0 Blood Test 861 Cerebral cortex "Sample 50, <5 yr survival(15 months) age 39 erp yes" on vantveer-oligo 1321 1299 by cervical dislocation COLO 205 hgu95e Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs//7277.gif Source GEO sample is GSM79731 Last updated (according to GEO): Sep 22 2006 By using high-density oligonucleotide arrays, we profiled gene expression in reward-related brain regions of rats that developed escalated cocaine intake after extended access to cocaine (6 h per day). Rats allowed restricted daily access to cocaine (only 1 h) that displayed a stable level of cocaine intake and cocaine naive rats were used for controls. Four analysis methods were compared: Affymetrix microarray suite 4 and microarray suite 5, which use perfect-match-minus-mismatch models, and dchip and rma, which use perfect-match-only models to generate expression values. Results were validated by RT-PCR in individual animals from an independent replication of the experiment. A small number of genes was associated with escalated cocaine intake (ESC genes). Unexpectedly, of the brain regions examined [prefrontal cortex, nucleus accumbens, septum, lateral hypothalamus (LH), amygdala, and ventral tegmental area], the LH was the most transcriptionally responsive in escalation of cocaine intake. Most of the ESC genes identified are also expressed during synaptogenesis and synaptic plasticity and include genes that code for several presynaptic and postsynaptic proteins involved in neurotransmission. These results suggest that LH intrinsic circuitry undergoes a structural reorganization during escalation of cocaine use. This remodeling of LH circuitry could contribute to the chronic deficit in reward function that has been hypothesized to drive the transition to drug addiction. Results also support the value of using multiple analysis strategies to identify the most robust changes in gene expression and to compensate for the biases that affect each strategy. Gene expression data from colonic normal mucosa. Source GEO sample is GSM215077 Last updated (according to GEO): Aug 02 2007 mouse brain 478 489 861 Blood R591P01072 Mitochondria 1000 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181176 Last updated (according to GEO): Jul 12 2007 Normal Source GEO sample is GSM176020 Last updated (according to GEO): Apr 09 2007 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs//27682.gif Source GEO sample is GSM66573 Last updated (according to GEO): Sep 22 2006 861 Nerve Median eminence of hypothalamus 1000 cingulate cortex 861 N45__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A hc2 1000 Obesity 1000 Pancreas Osteoblasts 1000 3T3-L1 Preads A on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A Cell membrane 1000 Spleen vs Terbutaline Treated B cell 120min (set1) Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11334 Last updated (according to GEO): May 28 2005 Anterior nares 1000 uterus Source GEO sample is GSM18621 Last updated (according to GEO): May 27 2005 Expression data with no treatment Source GEO sample is GSM230903 Last updated (according to GEO): Sep 20 2007 none Source GEO sample is GSM123258 Last updated (according to GEO): Jul 26 2006 913 Coronary heart disease Blood 1000 Sample was obtained from a 46 years old male subject with congestive heart failure. Good quality sample. Keywords = Congestive heart failure, eNOS, gene, dimethylarginine dimethylaminohydrolase Source GEO sample is GSM6551 Last updated (according to GEO): May 28 2005 n/a Source GEO sample is GSM178033 Last updated (according to GEO): Jun 11 2007 Parkinson Disease 1000 1000 Hippocampus 1000 Hippocampus Plasma 861 cellular proliferation 1075 1097 861 Cornea Disease Source GEO sample is GSM176438 Last updated (according to GEO): Apr 09 2007 B195 DCs treated with inflammatory cytokines for 24 hrs myocardial infarction 383 403 PGA-MAH-HeJO3-1bAv2-s1 1000 Brain 231 227 liver Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181111 Last updated (according to GEO): Jul 12 2007 of the nasal olfactory epithelium 380 412 Eye 1000 Gene expression profile of the cell line UB/OC-1 grown for 5 days under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1538 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145870 Last updated (according to GEO): Nov 20 2006 mouse brain ipsilateral saline.RU486, biological rep1 Epithelium 865 Parkinson's disease sample x007 D_U133Plus_107_nAcc KPeterson-NonMet-2+box2-2G110-s2 8073_Lung did not develop PGD Ldn3 Succinate semialdehyde dehydrogenase (SSADH) deficiency is a rare autosomal recessive disorder effecting approximately 350 people around the world. Patients suffering from SSADH deficiency experience language acquisition failure, memory deficiencies, autism, increased aggressive behaviors, and seizures. There is a chemical buildup of both gamma-aminobutyric acid (GABA) and gamma-hydroxybutyric acid (GHB) in the neurological system of these patients. The Aldh5a1-/- knock out mouse model of SSADH deficiency shows the same chemical imbalances as the human disease, with additional fatal tonic-clonic seizures at three weeks of age. The elucidation of seizure causing pathways will facilitate treatment of seizure phenotypes in diseases with related epilepsy. Gene expression patterns within the hippocampus, cerebellum, and cortex of SSADH deficient mice (Aldh5a1-/- mice) will be compared to wild type mice at a time point immediately prior to fatal seizures. We hypothesis that the SSADH deficient mice experience a dysfunction of glutamate/GABA/ glutamine neurotransmitter cycle linked to astroglial metabolism and/or uptake of neuronally-released glutamate. The increased levels of GHB and GABA lead to down regulation of GABA-B-Receptor leading to seizures. The SSADH deficient phenotype may also be caused by ongoing oxidative damage and the pathological role of succinic semialdehyde. SSADH deficient mice (Aldh5a1-/- knock out) exhibit fatal seizures around three weeks of age. Mutant and wild type mice will be sacrificed between 17 and 19 days of life, and brain sections will be extracted and frozen (using a standard protocol). Hippocampus, cerebellum, and cortex from three mutant mice and three wild type mice will individually be expression profiled on the Affymetrix platform, giving a total of eighteen arrays. Comparative analysis will then be carried out, evaluating the transcript differences between mutant and wild type mice in each brain region.. Date GSE2866 Last Updated: Jun 08 2006 Contributers: E A Donarum Includes GDS1745. Update date: Jun 08 2006. Dataset description GDS1745: Analysis of brain hippocampi, cerebella, and cortices of succinate semialdehyde dehydrogenase (SSADH)-deficient mutants at 3 weeks of age, when fatal seizures occur. Results indicate that SSADH deficiency results in the dysregulation of genes involved in myelin structure and compaction.. Blood Test (Blinded) Sample Source GEO sample is GSM130043 Last updated (according to GEO): Sep 18 2007 988 980 cerebella 91 from the bone marrow 72 brain 0 5 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=2 and B=1 (Acute rejection). One of two samples from the same patient, different visits Source GEO sample is GSM36438 Last updated (according to GEO): May 27 2005 G1 Lens Sum102_2 228 219 Hippocampi Tumor__Leukemia_ALL-T_ALL_(17638)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Plasma 861 KT31_N no additional Source GEO sample is GSM199346 Last updated (according to GEO): Jun 08 2007 1000 Intestines, Small Mucous Membrane 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145084 Last updated (according to GEO): Nov 20 2006 AD control Treatment, type=dissect Source GEO sample is GSM119669 Last updated (according to GEO): Jul 10 2006 PMN_control_0min_Patient16 19 0 Head and neck cancer 19 0 Kainate-hippocampus Brain 861 brain, ipsi HC: Trizol Extraction20_le1 861 Mammary gland G1E_3_C 1000 Neuraxis liver 184 189 89 72 Normal Bone Marrow hippocampus wistar ky 3956 Cochlea at E12, replicate1 Tumor__Leukemia_ALL-B_ALL_(19183)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Adenocarcinoma 861 placebo 12h, biological rep2 861 Thymus Gland Autistic Disorder 1000 TEL-AML1-C31 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Hippocampus 1989 15 month Old 8 uterine horns 411 425 1000 ovarian neoplasm Whole ganglioneuroma tumor_1250 f2#304 versus pool Mouse Brain tissue Infection 1000 GM10838 Rat frontal cortex RNA - VH TTX Experiment Source GEO sample is GSM92313 Last updated (according to GEO): Jan 13 2006 Myocardium 861 Gene expression data from mouse primary visual cortex Source GEO sample is GSM101723 Last updated (according to GEO): Jun 15 2006 BC107B-BE Immature B cells 8 MOLT-4 hgu95d Gene expression data from a neocortex of saline-injected mouse Source GEO sample is GSM147398 Last updated (according to GEO): Jan 03 2007 Untreated versus treated (bortezomib) breast cancer cells. Source GEO sample is GSM120356 Last updated (according to GEO): Jul 20 2006 contralateral Cortex 7 27 861 Ganglia 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201295 Last updated (according to GEO): Jun 14 2007 861 Cerebral cortex hc1 with some respiratory epithelium. 1039 1072 HMVEC-L stimulated without LPS for 4 hours c04R3 in the mammalian nervous system 110 141 3 0 Hair in blood 16 23 Wild-type-hippocampus, biological rep1 (male) Infection 1000 Blood 861 plasma cells 332 344 Retina 1000 Epithelium 861 Heart 1000 of the lung 47 58 865 Ovarian Diseases DLCL-0036;OCT Adenocarcinoma 9 Hypertension, Pulmonary 1000 days nasal epithelium 1127 1148 Muscle; Smooth-Bladder_adult Keywords = mouse gene expression database Source GEO sample is GSM29407 Last updated (according to GEO): May 27 2005 f2#343 versus pool Mouse Brain tissue 1037 of transitional epithelium 1012 861 Lung 1000 Prostate Acetaminophen 24hr Rat 7404 blood vs. Acetaminophen 24hr Rat Pooled Control blood Mouse brain region gene expression (430 2.0 Array) Head and neck cancer Source GEO sample is GSM155721 Last updated (according to GEO): Apr 24 2007 brain 0 5 AD control Treatment, type=dissect Source GEO sample is GSM119665 Last updated (according to GEO): Jul 10 2006 901 frontal lobe H85 CN A 84 69 by heart failure G30 neurons from cingulate cortex Source GEO sample is GSM63025 Last updated (according to GEO): Dec 01 2005 Normal__Uterus_UT_8 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 154 147 in lung 0 Human Cortex 11 HC73 CN B Plasma 861 Spleen 1000 4 0 Colon This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis. Stembase Experiment ID: E189 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189 SCGP Sample ID: S238 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_196 Short description: RNA isolated from primary retinal sphere cells. Estimated purity: > 90% Num cells for RNA prep: ~600,000 Sample volume: 5.0 ul Source GEO sample is GSM87199 Last updated (according to GEO): Jan 19 2006 AD-212t1-A145-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 41 28 in mouse brain 1000 Heart failure Heart Septal Defects 884 Gene expression data from the neocortex of S1P3-knockout mouse Source GEO sample is GSM172949 Last updated (according to GEO): Mar 08 2007 861 Chromosomes 1000 Immune system 6 month spinal cord rep 2 na Source GEO sample is GSM181266 Last updated (according to GEO): Apr 10 2007 913 Coronary heart disease the blood 393 402 Untreated Control 12weeks AffyGC RMA rep3 Blood 1000 brain, Medial Temporal Gyrus: Sample33_e1_le1 Carcinoma, Non-Small-Cell Lung 890 949 938 in the skin Biopsy of the normal mucosa of the colon from patient #32 Gene expression data from postmorten brain regions Source GEO sample is GSM145249 Last updated (according to GEO): Nov 20 2006 1000 Kidney Brain 861 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n125 Source GEO sample is GSM2039 Last updated (according to GEO): Nov 21 2005 Diaphragm 7 Day control rep 1 Arteries 861 0029_1457_H95A2_T97-281_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from postmorten brain regions Source GEO sample is GSM146064 Last updated (according to GEO): Nov 20 2006 Infection 861 Analysis of prefrontal cortex from 3 biological replicates of C57BL/6J mice at four Zeitgeber Times (ZT 3, 9, 15, and 21). Source GEO sample is GSM240423 Last updated (according to GEO): Oct 30 2007 ovary 45 50 spinal_cord_8 1000 Skeletal muscle structure B41 on NCI-7.6k retina 5 10 Endometrium/Ovary-Disease 9 brain, amygdala: Control-Cortex_e1_le1 Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Meningioma Primary Grade 2. Source GEO sample is GSM108038 Last updated (according to GEO): Jun 06 2006 Communicable Diseases 861 MuscleRegen-ctx5d-2RLAv2-s2 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10952.gif Source GEO sample is GSM76444 Last updated (according to GEO): Sep 22 2006 n/a Source GEO sample is GSM177894 Last updated (according to GEO): Jun 11 2007 Lymphoblastoid Cell Line for Individual 8192.3 log phase Gut neurospheres 32 47 Gene expression data from postmorten brain regions Source GEO sample is GSM144983 Last updated (according to GEO): Nov 20 2006 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188725 Last updated (according to GEO): Jun 06 2007 DBA whole brain 4B Spleen vs Interferon-beta (IFN beta) Treated B cell 60min (set3) of parieto-occipital cortex 223 250 Skin 861 861 Neoplasm of human fibroblasts 44 63 Primary carcinoma of the liver cells 1000 3616 PC 24Hr (pool) vs. 2500mg/kg APAP 24Hr rat 3629 blood Malignant Neoplasms 1000 14 days, repeat 3 Heart Septal Defects 884 Gene expression data from human colon tumor tissue Source GEO sample is GSM173344 Last updated (according to GEO): Apr 20 2007 GSE59 861 Patau's syndrome NOS 861 Cardiomyopathies C1 on NCI-7.6k Menstrual phase - Follicular Source GEO sample is GSM175773 Last updated (according to GEO): Apr 09 2007 Primary Neoplasm 1000 /tf Hippocampus A 10 26 Spleen vs BLC Treated B cell 60min (set3) ILS/ISS Cerebellum Comparison Affy430 M7TW01010685 Plasma 861 861 frontal lobe Abdominal aorta 0 14 oral_mucosa_3 Gene expression data from postmorten brain regions Source GEO sample is GSM145780 Last updated (according to GEO): Nov 20 2006 NA07034 Blood Test (Blinded) Sample Source GEO sample is GSM130015 Last updated (according to GEO): Sep 18 2007 1000 Brain 1000 Cerebral cortex D_U133Plus_124_DLPFC 1000 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM144935 Last updated (according to GEO): Nov 20 2006 Tonsil Memory B || lc4b050 Spleen vs IL4 Treated B cell 60min (set2) outer medulla 31 43 91 from the bone marrow 72 of somatomotor cortex 21 41 NCI60.37_LABEL41EXTRACT40SUB3 Source GEO sample is GSM134175 Last updated (according to GEO): Aug 06 2007 U937 Prosencephalon 861 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188750 Last updated (according to GEO): Jun 06 2007 O377 homozygotes brains 13 Ogle-5P01NS037520-05 brain, cortex: 7dexp3_e1_le1 n/a Source GEO sample is GSM178050 Last updated (according to GEO): Jun 11 2007 Analysis of target genes induced by the Amyloid Precursor Protein Intracellular Domain Gene expression data from postmorten brain regions Source GEO sample is GSM145496 Last updated (according to GEO): Nov 20 2006 1656 1635 in the diabetic kidney Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. All patients were considered sporadic cases on the basis that no clinical antecedents of familial adenomatous polyposis were reported, and those that met the clinical criteria for hereditary non-polyposis colon cancer (Amsterdam criteria) were excluded. Source GEO sample is GSM112305 Last updated (according to GEO): Jun 06 2006 Brain 861 Cardiac 523 530 Spleen 255 260 Synovial Membrane 6 Normal 861 Cerebral cortex myometrium_8 Replicate1_Voxel E10 1000 Primary carcinoma of the liver cells Spleen vs 2-Methyl-thio-ATP Treated B cell 60min (set1) Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM Source GEO sample is GSM207688 Last updated (according to GEO): Jul 09 2007 Abdominal aortic aneurysm 0 24 Brain 861 brain, cerebral cortex: Total RNA extraction_le1 261183 1000 Optic Disk Primary Neoplasm 1000 Brain 861 of whole nodose ganglia 88 110 Control 5 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10143.gif Source GEO sample is GSM79629 Last updated (according to GEO): Sep 22 2006 8M_122002 5 0 brain 861 Cerebral cortex 901 Coronary artery Left hemidiaphragm 884 Wild type 8 wk old male 129S6/SvEvTac mouse periaqueductal gray Source GEO sample is GSM74985 Last updated (according to GEO): Feb 27 2007 NCI60.23_LABEL27EXTRACT26SUB3 Source GEO sample is GSM134109 Last updated (according to GEO): Aug 06 2007 T19__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A of muscle 596 605 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156716 Last updated (according to GEO): Jan 22 2007 Group 2 PEITC treated, pool #EP 14 vs. reference pool 4 0 Brain osteoblast 627 637 Antipsychotic drugs are classified as typical and atypical based on extrapyramidal effects. However, since the frontal cortex is one of the most important regions for antipsychotic actions, this study attempted to classify antipsychotic drugs based on gene expression in the frontal cortex. Chlorpromazine and thioridazine were selected as typical antipsychotics, and olanzapine and quetiapine as atypical antipsychotics. Since these drugs have similar chemical structures, the effect of the basic structure on gene expression can be eliminated. Cluster analysis of microarray experiments separated 4-drug-administered mice into chlorpromazine-quetiapine and thioridazine-olanzapine groups. This classification scheme is different from that which is based on criteria currently used to group the typical and atypical drugs and suggests that antipsychotic drugs can be further separated into multiple groups. Nervous System; Day 2 postnatal whole brain Keywords = mouse gene expression database Source GEO sample is GSM29415 Last updated (according to GEO): May 27 2005 Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID325 GIN (Gad1 inhibitory ref. (pubmed id:10777798) ) neurons from hippocampus Source GEO sample is GSM63017 Last updated (according to GEO): Dec 01 2005 271 258 from 6 brains 16 7 Cerebellum 27 CB B Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183417 Last updated (according to GEO): Apr 23 2007 2N-5-MGU74B 981 953 in the endoplasmic reticulum trachea_4 Source GEO sample is GSM80890 Last updated (according to GEO): Mar 31 2006 Primary Carcinoma 875 Normal_2222 12 4 of Kidney that fibroblasts 448 463 Spinal Cord 1000 861 Cardiomyopathies DNA Damage 1000 of the mouse brain 76 93 p63 mutations have been associated with several human hereditary disorders characterized by ectodermal dysplasia such as EEC (ectrodactyly, ectodermal dysplasia, clefting) syndrome, ADULT (acro, dermato, ungual, lacrimal, tooth) syndrome and AEC (ankyloblepharon, ectodermal dysplasia, clefting) syndrome (also called Hay-Wells syndrome). The location and functional effects of the mutations that underlie these syndromes reveal a striking genotype-phenotype correlation. Unlike EEC and ADULT that result from missense mutations in the DNA-binding domain of p63, AEC is solely caused by missense mutations in the SAM domain of p63. In this paper we report a study on the TAp63alpha isoform, the first to be expressed during development of the embryonic epithelia, and on its naturally occurring Q540L mutant derived from an AEC patient. To assess the effects of the Q540L mutation, we generated stable cell lines expressing TAp63alpha wt, DeltaNp63alpha or the TAp63alpha-Q540L mutant protein and used them to systematically compare the cell growth regulatory activity of the mutant and wt p63 proteins and to generate, by microarray analysis, a comprehensive profile of differential gene expression. We found that the Q540L substitution impairs the transcriptional activity of TAp63alpha and causes misregulation of genes involved in the control of cell growth and epidermal differentiation. Transcription factor GATA-1 is required for erythropoiesis, yet its full actions are unknown. We performed transcriptome analysis of G1E-ER4 cells, a GATA-1-null erythroblast line that undergoes synchronous erythroid maturation when GATA-1 activity is restored. We interrogated more than 9000 transcripts at 6 time points representing the transition from late burst forming unit-erythroid (BFU-E) to basophilic erythroblast stages. Our findings illuminate several new aspects of GATA-1 function. First, the large number of genes responding quickly to restoration of GATA-1 extends the repertoire of its potential targets. Second, many transcripts were rapidly down-regulated, highlighting the importance of GATA-1 in gene repression. Third, up-regulation of some known GATA-1 targets was delayed, suggesting that auxiliary factors are required. For example, induction of the direct GATA-1 target gene beta major globin was late and, surprisingly, required new protein synthesis. In contrast, the gene encoding Fog1, which cooperates with GATA-1 in beta globin transcription, was rapidly induced independently of protein synthesis. Guided by bioinformatic analysis, we demonstrated that selected regions of the Fog1 gene exhibit enhancer activity and in vivo occupancy by GATA-1. These findings define a regulatory loop for beta globin expression and, more generally, demonstrate how transcriptome analysis can be used to generate testable hypotheses regarding transcriptional networks. Hippocampus VC mice on Dox 28 24 Heart MGJZ030212055Bepidermis Whole Brain 73 83 21 0 acute myeloid leukemia brain, hippocampus: KA-6h-P15-I_e1_le1 Gene expression data from liver Source GEO sample is GSM243387 Last updated (according to GEO): Nov 16 2007 46 15 of diffuse large B-cell lymphoma Brain 861 NCI60.12_LABEL15EXTRACT14SUB3 Source GEO sample is GSM134051 Last updated (according to GEO): Aug 06 2007 Comparison of conventional and germ-free gastrointestinal tract 861 Blood 23 14 from lungs Heart 1000 central nervous systems 460 482 278 255 ischemic cardiomyopathy Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11263 Last updated (according to GEO): May 28 2005 1000 Brain 861 Brain Infection 1000 Donor 2 Time point 0 Autologous Control (uninfected) Lot batch = 11839152 Source GEO sample is GSM2607 Last updated (according to GEO): May 27 2005 Measles virus continues to cause morbidity and mortality despite the existence of a safe and efficacious vaccine. Measles is associated with induction of both a long-lived protective immune response and immunosuppression. To gain insight into immunological changes during measles, we examined gene expression in blood mononuclear cells during acute measles and convalescence compared to uninfected control children. There were 13 significantly up-regulated and 206 down-regulated genes. Up-regulated genes included the immune regulatory molecules interleukin (IL)-1beta, CIAS-1, tumor necrosis factor-alpha, PDE4B, PTGS2, IL-8, CXCL2, CCL4, ICAM-1, CD83, GOS-2, IER3 (IEX-1) and TNFAIP3 (A20). Plasma levels of IL-1beta and IL-8 were elevated during measles. Down-regulated genes mainly involved three gene ontology biological processes: transcription, signal transduction and the immune response and included IL-16 and cell surface receptors IL-4R, IL-6R, IL-7R, IL-27RA, CCR2 and CCR7. Most mRNAs had not returned to control values 1 month after discharge, consistent with prolonged immune response abnormalities during measles. M7TW00121355 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=690650 LaserPower=2.161.29 Lot batch = LC17N039 Source GEO sample is GSM4792 Last updated (according to GEO): Nov 21 2005 POU-domain factor Brn3a regulates both distinct and common programs of gene expression in the spinal and trigeminal sensory ganglia. Wild type inbred mice Source GEO sample is GSM83011 Last updated (according to GEO): Nov 10 2005 16 6 (transverse biopsy sample obtained from a male Duchenne Muscular Dystrophy patient(unknown age) Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15841 Last updated (according to GEO): Sep 08 2006 of coronary artery disease 258 284 Total RNA from iPS clone was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations. Source GEO sample is GSM239964 Last updated (according to GEO): Nov 22 2007 Investigation into murine dermal burn wound. Mouse thermal injury induced, and skin excised at 0 hours, 2 hours, 3 days and 14 days post-injury.. Date GSE460 Last Updated: Jun 15 2005 Contributers: David W Mozingo Robert J Feezor Lyle L Moldawer Heather N Paddock Juan C Varela Gregory S Schultz Henry V Baker Includes GDS353. Update date: Jun 23 2003. Dataset description GDS353: Investigation into dermal burn wound healing. Thermal dermal injury induced. Skin excised at 0 hours, 2 hours, 3 days and 14 days post-injury.. Primary tumor 19 32 cy5:SHR treated w/ nifedipine, biological rep 1r; cy3:pool of 6 WKY control rats Substantia Nigra MML Sample2 RMA, MAS 5, dChip 1000 Neurologic Manifestations Motor neurons from the spinal cord of wildtype mice Treatment, type=linear_amplification, description=T7-based RNA amplification Source GEO sample is GSM113704 Last updated (according to GEO): Jun 09 2006 Gastrointestinal Stromal Tumors 1000 719 693 in the posterior pituitary Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15737 Last updated (according to GEO): May 28 2005 Mesenchymal Stem Cells 1000 nasal epithelial cells 28 49 Heart 1000 tTA +Doxy 7399 31 11 bone marrow cell UET9 B307 on Affymetrix GeneChip Human Full Length Array HuGeneFL processed in batch 5 Source GEO sample is GSM90416 Last updated (according to GEO): Mar 20 2006 1000 Prostate CNS-SpinalC-conAdult-4h-1A-s2 C57BL/6J hypothalamus rep1 brain, contralateral Cortex: Trizol Extraction43_le1 Ventral tegmental area, male 10.5 week old c57bl/6J mouse, NON-DEFEATED control Source GEO sample is GSM224746 Last updated (according to GEO): Aug 31 2007 1000 Hippocampus Blood Test (Blinded) Sample Source GEO sample is GSM129952 Last updated (according to GEO): Sep 18 2007 Cell source of DN2_1, DN3_1, and DN4_1 are identical. Cell source of DN2_2, DN3_2, and DN4_2 are identical. Cell source of DN2_3, DN3_3, and DN4_3 are identical. Cell source of DN2_4, DN3_4, and DN4_4 are identical. Each cell sorce was derived from four mice. Source GEO sample is GSM188612 Last updated (according to GEO): May 16 2007 in muscle 1132 1141 olfactory epithelium wild type mouse 48 hpO Source GEO sample is GSM80195 Last updated (according to GEO): Oct 26 2005 43 0 Chorionic mesoderm-derived mesenchymal cells 861 Cochlear structure 433 424 of cancers 1000 Brain C57BL/6 benchmark dataset: Embryonic day 11.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25154 Last updated (according to GEO): May 27 2005 Whole Brain 62 72 PR(LL) Cecum 1000 Cerebellum 1000 nostrils 156 164 Medulla 861 Naive (control) #2 in some fibres 1827 1840 1000 Schizophrenia NA12751 growth 1, replicate 4 1209 1202 decorin Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132517 Last updated (according to GEO): Feb 26 2007 56 32 out of mouse bone marrow in embryonic superior cervical ganglia 853 890 Zoghbi-5R01NS027699-14 Epithelium 861 Dorsal Root Ganglia 2 Normal A critical and difficult part of studying cancer with DNA microarrays is data interpretation. Besides the need for data analysis algorithms, integration of additional information about genes might be useful. We performed genome-wide expression profiling of 36 types of normal human tissues and identified 2503 tissue-specific genes. We then systematically studied the expression of these genes in cancers by reanalyzing a large collection of published DNA microarray datasets. We observed that the expression level of liver-specific genes in hepatocellular carcinoma (HCC) correlates with the clinically defined degree of tumor differentiation. Through unsupervised clustering of tissue-specific genes differentially expressed in tumors, we extracted expression patterns that are characteristic of individual cell types, uncovering differences in cell lineage among tumor subtypes. We were able to detect the expression signature of hepatoctyes in HCC, neuron cells in medulloblastoma, glia cells in glioma, basal and luminal epithelial cells in breast tumors, and various cell types in lung cancer samples. We also demonstrated that tissue-specific expression signatures are useful in locating the origin of metastatic tumors. Our study shows that integration of each gene's breadth of expression (BOE) in normal tissues is important for biological interpretation of the expression profiles of cancers in terms of tumor differentiation, cell lineage, and metastasis. Testis 861 574 557 of hair follicles 1BJZ02052308_Islet the tumour 1027 1037 lymph_nodes_4 Source GEO sample is GSM80738 Last updated (according to GEO): Mar 31 2006 plasma cells 332 344 Brn3a Knockout DRG e13.5 430A v2.0 replicate Standard Affymetrix Protocol Source GEO sample is GSM16490 Last updated (according to GEO): May 28 2005 Coronary heart disease 913 Lungs 153 157 Septum Source GEO sample is GSM107905 Last updated (according to GEO): Jun 06 2006 Cell source of DN2_1, DN3_1, and DN4_1 are identical. Cell source of DN2_2, DN3_2, and DN4_2 are identical. Cell source of DN2_3, DN3_3, and DN4_3 are identical. Cell source of DN2_4, DN3_4, and DN4_4 are identical. Each cell sorce was derived from four mice. Source GEO sample is GSM188613 Last updated (according to GEO): May 16 2007 Skeletal bone 861 Whole Brain 73 83 19 0 Head and neck cancer 649 641 in liver Primary adenocarcinoma Source GEO sample is GSM16561 Last updated (according to GEO): May 28 2005 low gestational age Source GEO sample is GSM213117 Last updated (according to GEO): Jul 25 2007 Liver 1000 330 324 uterus the blood 393 402 DLBC32 on Affymetrix GeneChip Human Full Length Array HuGeneFL /3T3 fibroblasts 295 310 frontal lobe 1000 Brain 861 Mental Retardation 1000 human caudate nucleus Source GEO sample is GSM86880 Last updated (according to GEO): Feb 08 2006 Sample is skeletal muscle from nonobese patient undergoing elective abdominal surgery Source GEO sample is GSM3992 Last updated (according to GEO): May 28 2005 Expression profiling of spinal cord section (T8) extracted from rats 0h following laminectomy (naive) Source GEO sample is GSM31417 Last updated (according to GEO): May 27 2005 outer medulla 31 43 This study aims at giving an insight on gene expression in CCAM. Last Updated (by provider): May 05 2006 Contributers: Agnes Paquet Sam Hawgood Amy Wagner from mouse colon 21 36 Donor B, post G-CSF PGA-HMO-NonObese-4aUA-s2 M1 juvenile biol repl 3 HC71 CB B pfc_1010_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 95 FC BA9 B Coronary Arteriosclerosis 1000 Muscle 861 GSE8970 Mek exp1 NMDA Total RNA from brain sample of wild type mice at P0. Treatment, type=purify, measurement=0.0 years Source GEO sample is GSM113679 Last updated (according to GEO): Jun 09 2006 5 0 brain brain 0 5 861 Immunoglobulins HapMap JPT Male Source GEO sample is GSM159651 Last updated (according to GEO): Feb 01 2007 in renal cell carcinoma 34 56 966 Hippocampus of visceral metastases 1057 1078 R625P00906 plasma cells 332 344 1000 Cerebellum with mental retardation 241 263 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3304 Last updated (according to GEO): Mar 21 2006 Laser capture lung cancer cells Source GEO sample is GSM191047 Last updated (according to GEO): May 25 2007 00291127H95A2-T010585v2p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A D_U133A_49_nAcc none Source GEO sample is GSM239933 Last updated (according to GEO): Dec 07 2007 1197 1183 of chromosome 6 spinal cord smaples 1477 1495 19 0 human frontal cortex Primary small cell lung carcinoma 2229 Source GEO sample is GSM17338 Last updated (according to GEO): May 28 2005 EOM 56 Day mdx rep 2 117 112 Lipids 861 Pituitary Gland, Posterior in the cerebellum 29 45 MCF10A_Treated_#3 n/a Source GEO sample is GSM178008 Last updated (according to GEO): Jun 11 2007 1000 Liver IDC130 on harvard-12k 19 0 human frontal cortex brain 0 5 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195358 Last updated (according to GEO): Jun 04 2007 Voxel H3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1442 Last updated (according to GEO): Nov 21 2005 Epithelium of bronchus 983 40 21 from skeletal muscle 80 68 Control blood Epithelium 861 standard Affymetrix protocol, MAS 5.0 Source GEO sample is GSM9128 Last updated (according to GEO): May 28 2005 901 Spinal Cord Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19193 Last updated (according to GEO): May 27 2005 bc-ZT21-2 34 16 in aortic aneurysms 25 0 Bipolar affective disorder 5 0 brain lateral motoneurons (LMN) 20 12 Temporal Lobe 24 Abdominal aortic aneurysm 0 24 Cerebral cortex 1000 21 0 acute myeloid leukemia DMN-NF1Hippo15d-1dAv2-s2 CNS-SC_CtrA30m-2B-s2 861 Brain 64 47 that whole ovaries SW-620_CL4009_Colon on Affymetrix GeneChip Human Full Length Array HuGeneFL 197 176 with coxsackievirus B3 Pressure-overload induced hypertrophy model. Mouse was sacrificed 1 week after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2260 Last updated (according to GEO): May 27 2005 Lymph Node [JunctionChip 5 of 5] Posterior root of spinal nerve 861 H117 CB B This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195260 Last updated (according to GEO): Sep 13 2007 Tumor__Lymphoma_Large_B-Cell_L_B_CELL_S93_04233_Y on Affymetrix GeneChip Human 35K SubA Array Hu35k-A placenta-0491-uninflamed-infected-rep1 Expression profiling of spinal cord section (T10) extracted from rats 14d following severe injury Source GEO sample is GSM31347 Last updated (according to GEO): May 27 2005 no additional Source GEO sample is GSM199079 Last updated (according to GEO): Jun 08 2007 1000 Malignant Neoplasms amygdala rattus_norvegicus_strain iP animal_number 3 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68333 Last updated (according to GEO): Jul 07 2006 Leukemic fractions of ID60 AML patient have been hybridized. Source GEO sample is GSM154053 Last updated (according to GEO): Feb 26 2007 SN:1022996;Fetal Cartilage, biological rep1 control (unstimulated) cells, biological rep1 Substantia Nigra Pars Compacta 2 Disease ISR11 114 cortex 120 DLBC52 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Hippocampus brain 0 5 the heart 987 996 Alzheimer's Disease 861 10463 on TGRI-6.5k AT2-hTERT_basal_C5_53962 28 13 from spinal cord no additional Source GEO sample is GSM199088 Last updated (according to GEO): Jun 08 2007 67 40 with coronary artery disease Blood Test (Blinded) Sample Source GEO sample is GSM129954 Last updated (according to GEO): Sep 18 2007 Brain 1000 Category: Cell-line Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc128 Source GEO sample is GSM1865 Last updated (according to GEO): Nov 21 2005 Nasal Epithelium Inhalation Formaldehyde 0ppm 24h ID56 Hypothalamic structure 861 Brain 861 7 cerebral cortex 21 Cerebral cortex 1000 1000 Hypothalamic structure 1000 Epithelial Cells Gene expression data from postmorten brain regions Source GEO sample is GSM145628 Last updated (according to GEO): Nov 20 2006 HapMap CEU_parent Female Source GEO sample is GSM159517 Last updated (according to GEO): Feb 01 2007 GBM Treatment, type=remove Source GEO sample is GSM99564 Last updated (according to GEO): Apr 21 2006 861 Bone Marrow Entorhinal Cortex 7 23 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15753 Last updated (according to GEO): May 28 2005 Measles 861 Trisomy 21 sample 3 (cerebrum) H131 CB B CNS-SpinalCmod-Adult-28d-5B-s2 Temporal Cortex Alzheimer's disease 4 861 Cerebral cortex collagen 302 310 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 5 day time point Source GEO sample is GSM159737 Last updated (according to GEO): Apr 23 2007 CNS-SCsev_InjA7d-4C-s2 1000 ovarian neoplasm Spinal Cord 1000 Liver 1000 YFPH-Amygdala-replicate1 ER-/LN-/Nevins48 on Affymetrix GeneChip Human Full Length Array HuGeneFL UET-13TR-EWS/FLI1 72hr Heart 1000 1000 Tibialis anterior muscle structure 901 frontal lobe Stria 861 Parkinson Disease 861 plasma cells 50 61 861 Pituitary Gland to the nose 599 609 1000 Fibroblasts This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12341 Last updated (according to GEO): May 28 2005 Brain 1000 Replicate1_Voxel F10 brain, cochlea: [16] Sample #16_le1 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28698 Last updated (according to GEO): May 27 2005 Tumor__Colorectal_Adeno_mCRT2_(9752) on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 14 0 globus_pallidus 50 41 mouse lung 913 Coronary heart disease plasma cells 50 61 no additional Source GEO sample is GSM199326 Last updated (according to GEO): Jun 08 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145296 Last updated (according to GEO): Nov 20 2006 1000 Substantia nigra structure 06_0006_SepticShock_Day3_84 Wild type inbred mice Source GEO sample is GSM83018 Last updated (according to GEO): Nov 10 2005 heart 171 176 Category: Lymphoma Classification Subcategory: Hematopoetic cell lines Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b042 Source GEO sample is GSM2015 Last updated (according to GEO): Nov 21 2005 that prion infection 973 992 861 Cerebral cortex Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28729 Last updated (according to GEO): May 27 2005 Infection 1000 Infection 861 Fvbn +Doxy 8341 with Alzheimer's disease 27 50 Infection 1000 mouse brains 187 198 17 7 hippocampus HDMTX_MP-DX-7 Gonadectomized Dahl-Iwai Male HighSalt Cortex rat11 gdahl_cortexr_k_GX_11c_051702 Cerebral cortex 861 Blood Test (Blinded) Sample Source GEO sample is GSM130038 Last updated (according to GEO): Sep 18 2007 This dataset contains the gene expression profile of a CD11c high, CD8 positive splenic dendritic cell population. The cells were processed directly after isolation. Global scaling was applied to Avg Difference intensity values. Keywords = mouse, dendritic cells, spleen Source GEO sample is GSM4709 Last updated (according to GEO): May 27 2005 728 719 in kidney Epithelial Cells 1000 Primary Carcinoma 875 CurrentSmoker 111 to psychosis 673 685 5 0 Spleen H Fed Rep 2 Autistic Disorder 877 Anterior interpositus nucleus-centered deep cerebellar nuclei were sampled using syringe needles Source GEO sample is GSM84984 Last updated (according to GEO): Mar 29 2006 Epithelium 861 1000 jejunum 5 0 Tonsil M_U133A_33_AnCg Lymphoblastoid Cell Line for Individual 8060.4 log phase olfactory epithelium 194 213 52 year old male Pooled EDL RNA samples from five 8 wk old male mdx mice Source GEO sample is GSM13670 Last updated (according to GEO): May 28 2005 vestibular_nuclei_superior_6 The peroxisome proliferator-activated receptor alpha (PPAR?) is a fatty acid-activated transcription factor that governs a variety of biological processes. Little is known about the role of PPAR? in the small intestine. Since this organ is frequently exposed to high levels of PPAR? ligands via the diet, we set out to characterize the function of PPAR? in small intestine using functional genomics experiments and bioinformatics tools. PPAR? was expressed at high levels in both human and murine small intestine. Detailed analyses showed that PPAR? was expressed highest in villus cells of proximal jejunum. Microarray analyses of total tissue samples revealed, that in addition to genes involved in fatty acid and triacylglycerol metabolism, transcription factors and enzymes connected to sterol and bile acid metabolism, including FXR and SREBP1, were specifically induced. In contrast, genes involved in cell cycle and differentiation, apoptosis, and host defense were repressed by PPAR? activation. Additional analyses showed that intestinal PPAR? dependent gene regulation occurred in villus cells. Functional implications of array results were corroborated by morphometric data. The repression of genes involved in proliferation and apoptosis was accompanied by a 22% increase in villus height, and a 34% increase in villus area of wild-type animals treated with WY14643. This is the first report providing a comprehensive overview of processes under control of PPAR? in the small intestine. We show that PPAR? is an important transcriptional regulator in small intestine, which may be of importance for the development of novel foods and therapies for obesity and inflammatory bowel diseases. Last Updated (by provider): Jun 28 2007 Contributers: Heleen M van den Bosch Sander Kersten Meike Bunger Jolanda van der Meijde Michael Muller Guido J Hooiveld Posterior root of spinal nerve 901 1000 Brain Epididymis [JunctionChip 2 of 5] Gene Expression Analysis of Endometrium Reveals Progesterone Resistance and Candidate Susceptibility Genes in Women with Endometriosis. Unfertilized egg replication 1 0 29 CS-B cell UVC-irradiated (12hour) replicate 3 U133A 1000 Infection 27 7 Medial Temporal Gyrus Cerebral cortex 861 Fasted Mouse 2 na Source GEO sample is GSM181289 Last updated (according to GEO): Apr 10 2007 91 from the bone marrow 72 861 Cerebellum 320 291 of human oral epithelial cells Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11299 Last updated (according to GEO): May 28 2005 Muscle Source GEO sample is GSM4275 Last updated (according to GEO): May 27 2005 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11583 Last updated (according to GEO): May 28 2005 tourt-affy-mouse-243760 Bone Marrow 1000 into hepatocytes 628 643 SN:Human Glioblastoma Biopsy 12386 NCI60.43_LABEL47EXTRACT46SUB3 Source GEO sample is GSM134211 Last updated (according to GEO): Aug 06 2007 mouse brain 478 489 1000 Cerebral cortex UACC903, 48h treatment with 5 AzadC 861 Cerebellum Gene expression data from postmorten brain regions Source GEO sample is GSM145785 Last updated (according to GEO): Nov 20 2006 Simple annotation: Cell-cycle, Mitotic selection Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16451.gif Source GEO sample is GSM79708 Last updated (according to GEO): Sep 22 2006 1000 Rectum Brain 1000 91 from the bone marrow 72 The epithelial cells 962 981 100121 1000 Left 861 Chondrocytes none Source GEO sample is GSM149560 Last updated (according to GEO): Jan 03 2007 Category: Lymphoma Classification Subcategory: Follicular Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n015 Source GEO sample is GSM2027 Last updated (according to GEO): Nov 21 2005 5 0 brain 0.5 mg/kg/ml Isoproterenol treatment, 24 hour time point, biological rep 2 The epithelial cells 962 981 868 850 of medulloblastoma 5 0 brain Breast 861 PGA_MI_nilv_1w_662 Spinal Cord 1000 ER-/LN+/Nevins99 on Affymetrix GeneChip Human Full Length Array HuGeneFL with mental retardation 241 263 Physiologic cardiac hypertrophy 287 260 at the longitudinal fissure 14 7 amygdala mild cognitive impairment - hippocampus 2 Primary tumor 19 32 BTBR T+ tf/tf Cingulate Cortex B D_U133A_29_nAcc Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225745 Last updated (according to GEO): Nov 02 2007 Testis 861 starved 34 40 278 255 ischemic cardiomyopathy Our study seeks to identify genes differentially expressed between uterine leiomyomas and normal myometrial tissue. This series consists of samples derived from normal myometrium and uterine leiomyomas obtained from fibroid afflicted patients.Total RNA was extracted from samples, converted to biotin-labeled cRNA, hybridized to oligonucleotide arrays, and followed by model based expression analysis. In order to select differentially expressed genes of interest, dChip model-based expression analysis was employed. Significant genes were identified, utilizing the dChip software, as having an average fold change of > +1.5 or < -1.5 between leiomyoma and normal myometrium and p < 0.05. Under these conditions the 226 genes in the following list were identified.. Date GSE593 Last Updated: May 29 2005 Contributers: Dawn B Milliken Ryan R Davis Jeffrey P Gregg Paul J Hoffman Includes GDS484. Update date: Dec 01 2003. Dataset description GDS484: Comparison of normal myometrium and uterine leiomyomas obtained from fibroid afflicted patients.. TEL-AML1-C8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 4010 blood Adenocarcinoma 5 /3T3 fibroblasts 295 310 NB69 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92351 Last updated (according to GEO): Jan 13 2006 The limit fold change model: a practical approach for selecting differentially expressed genes from microarray data. Plasma 861 Richard Almon-28-1133800609620 brain, hippocampus: C72-III_e1_le1 Trigeminal Ganglion Source GEO sample is GSM53322 Last updated (according to GEO): Jul 06 2005 218 214 liver Gene expression data from postmorten brain regions Source GEO sample is GSM145112 Last updated (according to GEO): Nov 20 2006 1000 Gastrocnemius muscle structure 0 Huntington's disease 19 406 395 whose hearts rotenone 2 weeks C Treatment, type=time_course, measurement=2.0 weeks Source GEO sample is GSM107860 Last updated (according to GEO): Jun 06 2006 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28738 Last updated (according to GEO): May 27 2005 1000 Spinal Cord 7 cortex 12 Frontal Cortex Source GEO sample is GSM107938 Last updated (according to GEO): Jun 06 2006 Parkinson's disease sample x178 0 30 Treated Source GEO sample is GSM176461 Last updated (according to GEO): Apr 09 2007 166 156 of retinal 1000 Prostate Parkinson's disease sample x200 0 30 GBM Treatment, type=remove Source GEO sample is GSM99462 Last updated (according to GEO): Apr 21 2006 861 Cerebellum Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210405 Last updated (according to GEO): Jul 16 2007 Simple annotation: Metastatic tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5185.gif Source GEO sample is GSM79821 Last updated (according to GEO): Sep 22 2006 PriG_5%O2_Expt2_Day2_rep1 1000 frontal lobe CNS-SC_CtrAT0-2A-s2 Parkinson's disease sample x204 861 Brain 40 21 from skeletal muscle Expression profile of genes in mouse brain Source GEO sample is GSM21053 Last updated (according to GEO): May 27 2005 3AMH02030704_Prostate from whole tumor 21 36 T-ALL-R1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A healthy subject Source GEO sample is GSM211059 Last updated (according to GEO): Sep 10 2007 966 Hippocampus VDXKIU_16G1 861 hair 1000 Infection biopsy sample obtained from 36-year-old female individual Keywords = gene expression profile of normal human skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15831 Last updated (according to GEO): May 28 2005 1000 Muscle E2A-PBX1-C10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A UterViEs_022YACHS_112b.txt in the brain 150 162 Chronic Lymphocytic Leukemia 19 47 Normal Source GEO sample is GSM175979 Last updated (according to GEO): Apr 09 2007 Expression profiling of spinal cord section (T8) extracted from rats 14d following mild injury Source GEO sample is GSM31420 Last updated (according to GEO): May 27 2005 Resistance Exercise Reverses Aging in Human Skeletal Muscle Leukemia, Lymphocytic, Chronic 1000 brain 0 5 1000 Adenocarcinoma of large intestine brain, cortex: norm3_e1_le2 Occipital lobe 861 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 24 h time point Source GEO sample is GSM159803 Last updated (according to GEO): Apr 23 2007 P46 deprived visual cortex replicate 3 Gene expression data from postmorten brain regions Source GEO sample is GSM145742 Last updated (according to GEO): Nov 20 2006 Nasal Epithelium 865 Effect of left ventricular assist device support on congestive heart failure patients 861 Substantia nigra structure Pressure-overload induced hypertrophy model. Mouse was sacrificed 4 hours after aortic banding. Keywords = Cardiac hypertrophy Source GEO sample is GSM2235 Last updated (according to GEO): May 27 2005 NCI60.31_LABEL35EXTRACT34SUB3 Source GEO sample is GSM134145 Last updated (according to GEO): Aug 06 2007 Expression profiling of spinal cord section (T10) extracted from rats 24h following severe injury Source GEO sample is GSM31357 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM176014 Last updated (according to GEO): Apr 09 2007 in the mammalian nervous system 110 141 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68179 Last updated (according to GEO): Jul 07 2006 mouse hippocampus from COX-1 Knockout Source GEO sample is GSM121439 Last updated (according to GEO): Jan 31 2007 Balb/c day 6, biological rep 2, tech rep 2 olfactory epithelium 194 213 wild-type mouse cerebellum Treatment, type=time_course, measurement=4.0 weeks Source GEO sample is GSM53344 Last updated (according to GEO): Jul 06 2005 Standard Affymetrix Protocol Source GEO sample is GSM15864 Last updated (according to GEO): May 28 2005 Affymetrix protocol Source GEO sample is GSM213817 Last updated (according to GEO): Aug 02 2007 9 0 Blood Test BRCA2_s1816 on NHGRI-6.5k Macrophage 14smi021 NA19152 HCC (HBV+, HK3) Trauma 1000 Cerebral cortex 1000 11 0 Normal Ovary Heart 861 NG108 rat neuronal cell culture exposed to 0.25% DMSO (control) for two hours. 10 µg total RNA hybridized per chip. RNA STAT 60 used to extract RNA. Standard Affymetrix chip scaling factors used. No other data transformation. Source GEO sample is GSM1656 Last updated (according to GEO): Oct 28 2005 36 21 from whole brain of muscle 928 936 Fibroblasts 861 Control rats 240h after injection with PBS Treatment, type=time_course, description=Control animals are treated with PBS, measurement=240.0 h Source GEO sample is GSM32092 Last updated (according to GEO): May 27 2005 9 0 Blood Test CHIPEXP_NAME: 230_2_050531tpj_38h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Isoproterenol TREAT_TOX_MECHANISM1: Heart_Cardiotoxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0.5 SAMPLING_TIME: 3 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197615 Last updated (according to GEO): Jun 01 2007 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs//23748.gif Source GEO sample is GSM66587 Last updated (according to GEO): Sep 22 2006 The paraventricular hypothalamic nucleus (PVH) is a key site for integrating neuroendocrine, autonomic, and behavioral adjustments to diverse homeostatic challenges, including "physiological" (e.g., infection or hemorrhage) and "emotional" [e.g., restraint (RST) or footshock] stresses. Both types of challenges ultimately converge to activate common response systems represented in PVH, including the hypothalamo-pituitary-adrenal axis and the sympathoadrenal system. Oligonucleotide microarrays (U74A; Affymetrix, Santa Clara, CA) were used to compare and contrast gene expression profiles in the PVH elicited at 1 and 3 hr after acute exposure to representative physiological [intraperitoneal injection of 10 microg lipopolysaccharide (LPS)] and emotional (30 min RST) stressors. In general, the two challenges recruited relatively few genes in common, with the degree of overlap varying across functional classes of genes. The greatest degree of commonality was seen among signaling molecules and neuropeptides, whereas transcription factors upregulated by RST and LPS were largely distinct. Unexpectedly, RST induced a number of immune-related molecules, which were not regulated by LPS. Hybridization histochemical analyses localized a subset of responsive transcripts to the PVH and/or immediately adjoining regions. Immunerelated molecules in particular distributed broadly to vascular and other barrier-associated cell types. These global transcriptional profiles inform the search for early (transcription factors) and late (target genes) mechanisms in the modulation of PVH, and generalized CNS, responses to categorically distinct stressors. M_U133Plus_116_AnCg hippocampus_1 brain, brainstem: LB1_e1_le1 HCC (HBV+, HK37) brain 0 5 spleen 338 343 F4_1, mouse, FVB, control (non-infected), 4 day time matched control_rep 1 of infected skin 33 48 1000 Hippocampus Brain 1000 Blood 1000 in the mammalian nervous system 110 141 AD control Treatment, type=dissect Source GEO sample is GSM119648 Last updated (according to GEO): Jul 10 2006 brain, cerebral cortex: Co4_le1 Brain 861 884 Cervix carcinoma M_U133A_114_nAcc 2920 2912 28S rRNA 1000 Left at the Human Brain 744 761 /3T3 fibroblasts 743 759 Cerebral cortex 861 brain, amygdala: Stress-Amygdala_e1_le3 861 Cerebral cortex 861 Malignant Neoplasms 211 in the posterior pituitary 185 Sprague-Dawley Male HighSalt OuterMedulla rat712 sd_medullar_k_712r_om_070302 DLBC38 on Affymetrix GeneChip Human Full Length Array HuGeneFL in primary human breast tumors 242 272 B10.PL mice with experimental autoimmune encephalomyelitis (MS model) were treated with either placebo or 200 ng 1,25(OH)2D3. Six hours later, the spinal cords were harvested and mRNA extracted for analysis. Naive mice served as controls. Keywords = Experimental autoimmune encephalomyelitis Keywords = multiple sclerosis Keywords = 1 Keywords = 25(OH)2D3 Source GEO sample is GSM13054 Last updated (according to GEO): May 28 2005 days nasal epithelium 1126 1147 Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35386 Last updated (according to GEO): May 27 2005 Prosencephalon 861 liver 0 5 Stem cells 913 I_U133A_118_AnCg Dissection of E16.5 cortex for RNA extraction. Cortex Hemispheres of E16.5 mice were divided into the medial (R1), dorsal (R2), ventral (R3), lateral (R4), and occipital regions (R5). Preparation of RNA and Synthesis of cDNA. Poly A+ RNA was obtained through twice column procedures with oligo dT cellulose column (New England Biolabs, Beverly, MA) and was used for synthesis of cDNA. 1ug of polyA+ RNA was converted into double-stranded cDNA by reverse transcription using ReverTra Ace (ToYoBo, Japan) with oligo dT(24) primers containing the T7 RNA polymerase promotor sequence (Amersham Pharmacia Biotech, Japan). The integrity of RNA was confirmed by agarose electrophoresis and RNA contents were analyzed by measuring the optical density at 260 nm. Target preparation and array processing. The following procedures including preparation of cRNA targets, hybridization, washing, staining, and scanning were performed as described in the Expression Analysis Technical Manual (Affymetrix, CA). Briefly, biotin-labeled antisense cRNA targets were synthesized in in vitro transcription reaction system (IVT) using cDNA as template (ENZO BioArrayTM HighYieldTM RNA Transcription Labeling kit with T7 RNA polymerase, Enzo, NY). The cRNA targets were size-fragmented to 35-200 bp in a buffer containing potassium and magnesium acetate at 94°C for 35 minutes and were used for hybridization as cRNA targets. The hybridization cocktail [containing 10 ug of target cRNA, control oligo BS (Affymetrix), and Eukaryotic Hybridization controls (Affymetrix)] was hybridized with a mouse U74A array at 42°C for 16 hours in GeneChip Hybridization Oven 640. Washing and staining were performed after hybridization under the fluidics station protocol, EuGE-WS2, on GeneChip Fluidics Station 400. Then, we scanned the array twice on HP GeneArrayTM scanner. Experiments were repeated twice with independent dissection. Data analysis. To quantify the expression level of a transcript, the average difference value (Adv) was calculated from the intensities against the probe cells using the global methods of normalization by Microarray Suite ver. 4.0 (Affymetrix). Source GEO sample is GSM14601 Last updated (according to GEO): Oct 28 2005 Epithelium of bronchus 983 Primary large cell carcinoma 745 861 Blood Expression profiling of somatomotor cortex extracted from rats at 3 months following moderate injury Source GEO sample is GSM41727 Last updated (according to GEO): May 27 2005 PC 12Hr rat 4126 blood vs. 1500mg/kg APAP 12Hr rat 4134 blood Brain 1000 Epithelium of bronchus 983 Week 7 - High Glucose plasma cells 332 344 7 0 prostate 861 Acquired Immunodeficiency Syndrome Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7702.gif Source GEO sample is GSM79985 Last updated (according to GEO): Sep 22 2006 Carcinoma 861 1000 Cardiomyopathy, Alcoholic D_U133A_41_DLPFC Skeletal bone 861 at the Human Brain 745 762 Timed pregnant C57Bl6 mice were exposed to ethanol during gestational day 15 to day 18 and ethanol exposed fetuses were delivered by cessarian section on gestational day 19. Alcohol exposed fetuses were compared to control timed pregnant mice and to pair fed controls (animals fed with maltose dextrose) Source GEO sample is GSM116851 Last updated (according to GEO): Jul 03 2006 human cerebellum Source GEO sample is GSM87100 Last updated (according to GEO): Feb 08 2006 skmuscle-TEST-9 on NHGRI-6.5k_b Suprachiasmatic Nucleus after 30-min Light pulse rep3 Nasal Epithelium Inhalation Formaldehyde 0ppm 8d ID64 Hypothalamic structure 861 no additional Source GEO sample is GSM199256 Last updated (according to GEO): Jun 08 2007 Nothing in line. Source GEO sample is GSM154222 Last updated (according to GEO): Jul 05 2007 1000 Encephalitis plasma cells 50 61 Cerebral cortex 1000 Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age.. Date GSE30 Last Updated: May 29 2005 Contributers: Simon Yee Alex Ossadtchi Richard M Leahy Vanessa M Brown Arshad H Khan Desmond J Smith William P Melega Simon R Cherry Includes GDS22. Update date: Mar 22 2004. Dataset description GDS22: Generation of a three-dimensional brain gene expression patterns for both normal brain and a pharmacological model of Parkinson's disease. Networks of anatomically coregulated genes defined.. none Source GEO sample is GSM123201 Last updated (according to GEO): Jul 26 2006 Primary small cell lung carcinoma 8526 0 37 901 Brain Injuries Anterior nares 1000 32 0 Normal bronchial epithelial cell 1000 frontal lobe folatedeficientAs10ppm3 Heart 861 brain, frontal cortex: pADX PM DR b_e1_le1 861 Chromosomes Lymphoblastic Leukemia 901 CNS-SMTC_CtrT0-2C-s2 cerebral cortex 7 21 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM119696 Last updated (according to GEO): Jul 11 2006 NoCAD_replicate26 from the right forebrain 21 44 901 Hepatocyte Brain 1000 1000 lymph nodes CNS-SMTC_Mod28d-1C-s2 n/a Source GEO sample is GSM177981 Last updated (according to GEO): Jun 11 2007 Plasma 861 7 cerebral cortex 21 Liver (HBV+, HK36) na Source GEO sample is GSM181281 Last updated (according to GEO): Apr 10 2007 1000 ovarian neoplasm Occipital lobe 861 Richard Almon-30-1138200270367 FC 79h 1000 Adenocarcinoma of large intestine 9 0 Blood Test Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16924.gif Source GEO sample is GSM91603 Last updated (according to GEO): Sep 22 2006 19 0 Head and neck cancer none Source GEO sample is GSM244610 Last updated (according to GEO): Nov 23 2007 Mid secretory endometrium from patient with endometriosis Source GEO sample is GSM150212 Last updated (according to GEO): Dec 14 2006 Heart 1000 hippocampus 7 17 Large-scale analysis of the human transcriptome. Promyelocytic leukemia Source: ATCC Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 182.44 Stdv: 8.00 Min: 165.67 Max: 192.85 Source GEO sample is GSM2892 Last updated (according to GEO): Mar 20 2006 Bladder sample 968_1 Primary Neoplasm 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM146006 Last updated (according to GEO): Nov 20 2006 Ovarian_Tumor_Endometrioid_CHTN-OE-061 brain 0 5 1BJZ02022227_fetalbrain The epithelial cells 962 981 Expression profiling of moderately injured raphe at 24h in rats Source GEO sample is GSM41586 Last updated (according to GEO): May 27 2005 1000 Brain 1037 of transitional epithelium 1012 EOM 28 Day Control rep 2 1000 Coronary Arteriosclerosis 901 Cerebral cortex no additional Source GEO sample is GSM199083 Last updated (according to GEO): Jun 08 2007 whole blood_100247 901 Nervous system structure of the stria terminalis rep2 19 46 Autistic Disorder 877 Tumor__Renal_Carcinoma_92_I_126 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Heart 1000 BRCA1_s1822 on NHGRI-6.5k corticosterone_treated_rep7 (06SE464) 789 772 in the hippocampus in cigulate cortex 26 43 Whole Brain 62 72 none Source GEO sample is GSM149511 Last updated (according to GEO): Jan 03 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145730 Last updated (according to GEO): Nov 20 2006 1000 Nervous system structure metastasis 598 607 Lymphoblastoid Cell Line for Individual 8165.4 log phase Gene expression data from postmorten brain regions Source GEO sample is GSM144955 Last updated (according to GEO): Nov 20 2006 jzo017-rp1-v5-u74av2-met 1541 1521 of corneal epithelium Parkinson Disease 861 167T organs 28 33 861 Cerebral cortex Oculomotor nucleus 901 This is replicate 1 of the 2 hour sample from passive avoidance trained rats. Source GEO sample is GSM17398 Last updated (according to GEO): Aug 22 2007 Tumor__Prostate_Adeno_LocalCaP10T on Affymetrix GeneChip Human 35K SubA Array Hu35k-A hypothalamus 0 11 Heart failure sample 2 Expression profiling of somatomotor cortex extracted from rats at 4h following sham surgery Source GEO sample is GSM41662 Last updated (according to GEO): May 27 2005 Bipolar Disorder 1000 ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes_A_5543 Source GEO sample is GSM161223 Last updated (according to GEO): Apr 23 2007 MCF7 pre-treated for 1h with cycloheximide, treated with E2 for 24h Source GEO sample is GSM213319 Last updated (according to GEO): Jul 26 2007 861 Cerebral cortex Alzheimer's Disease 1000 NCI60.54_LABEL58EXTRACT57SUB3 Source GEO sample is GSM134265 Last updated (according to GEO): Aug 06 2007 Gene expression data of primary and secondary glioblastoma subgroups. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Nov 01 2006 Contributers: Allen Day Paul S Mischel Linda M Liau William A Freije Ederlyn Q Dia Timothy F Cloughesy Yohan Lee Cho-Lea Tso Ally Perlina Zugen Chen Stanley F Nelson Barry Merriman Koji Yoshimoto 23 0 skeletal muscle sprague1 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 1 hour after the last shock treatment. Source GEO sample is GSM4525 Last updated (according to GEO): May 27 2005 406 395 whose hearts 69 47 Secondary Glioblastomas Primary Carcinoma 876 brain_control_sampleid_mr284 1000 Cerebral cortex NCI60.33_LABEL37EXTRACT36SUB3 Source GEO sample is GSM134156 Last updated (according to GEO): Aug 06 2007 myocardial infarction 383 403 ipsi Cortex 7 17 ipsi Cortex 7 17 brain, Left frontal Lobe: Extract9_le1 Blood Test (Blinded) Sample Source GEO sample is GSM129937 Last updated (according to GEO): Sep 18 2007 none Source GEO sample is GSM239953 Last updated (according to GEO): Dec 07 2007 rat hippocampus Treatment, type=time_course, measurement=6.0 h Source GEO sample is GSM32130 Last updated (according to GEO): May 27 2005 Parkinson Disease 1000 Control rats 72h after injection with PBS Treatment, type=time_course, description=Control animals are treated with PBS, measurement=72.0 h Source GEO sample is GSM32089 Last updated (according to GEO): May 27 2005 GBM Treatment, type=remove Source GEO sample is GSM99560 Last updated (according to GEO): Apr 21 2006 Voxel E1 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1414 Last updated (according to GEO): Nov 21 2005 from colonic normal mucosa 21 47 861 Cerebellum corticosterone_treated_rep2 (06SE456) D1_TP-24_C Occipital lobe 861 HapMap YRI_parent Female Source GEO sample is GSM159706 Last updated (according to GEO): Feb 01 2007 2920 2912 28S rRNA Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181141 Last updated (according to GEO): Jul 12 2007 Septum Source GEO sample is GSM107947 Last updated (according to GEO): Jun 06 2006 +_7667_batch2 on NHGRI-6.7k Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection). One of two samples from the same patient, different visits Source GEO sample is GSM36449 Last updated (according to GEO): May 27 2005 50 41 mouse lung to metastasis 1415 1427 mouse cerebral cortex, cox-2 WT, rep2 Acetaminophen 24hr Rat 8002 blood vs. Acetaminophen 24hr Rat Pooled Control blood Control male 5 39 21 from mammary glands Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68226 Last updated (according to GEO): Jul 07 2006 CNS-SC_CtrBT0-2C-s2 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16659.gif Source GEO sample is GSM81570 Last updated (according to GEO): Sep 22 2006 M_U133A_76_nAcc Richard Almon-1-1133800608698 M7TW00121889 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213485 Last updated (according to GEO): Jul 31 2007 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211388 Last updated (according to GEO): Jul 18 2007 Glioblastoma is the most common and aggressive primary brain cancer. Recent isolation and characterization of brain tumor-initiating cells supports the concept that transformed neural stem cells may seed glioblastoma. We previously identified a wide array of mesenchymal tissue transcripts overexpressed in a broad set of primary glioblastoma (de novo) tumors but not in secondary glioblastoma (derived from lower-grade) tumors, low-grade astrocytomas, or normal brain tissues. Here, we extend this observation and show that a subset of primary glioblastoma tumors and their derived tumor lines express cellular and molecular markers that are associated with mesenchymal stem cells (MSC) and that glioblastoma cell cultures can be induced to differentiate into multiple mesenchymal lineage-like cell types. These findings suggest either that a subset of primary glioblastomas derive from transformed stem cells containing MSC-like properties and retain partial phenotypic aspects of a MSC nature in tumors or that glioblastomas activate a series of genes that result in mesenchymal properties of the cancer cells to effect sustained tumor growth and malignant progression. HC61 FC BA4 B Brain 861 Sham Day 5,# 1 Primary adenocarcinoma Source GEO sample is GSM16564 Last updated (according to GEO): May 28 2005 7 0 prostate B_D2_Control_ZT 6_3 to the cerebellum 1859 1875 standard Affymetrix protocol, MAS 5.0 Source GEO sample is GSM9135 Last updated (according to GEO): May 28 2005 Cerebral cortex 861 272 257 dermatomyositis west-breast 0 10 Samp10 Retina Old Sample 1 8M_120502 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CGS for 240min Source GEO sample is GSM5519 Last updated (according to GEO): May 27 2005 in the cerebellum 29 45 1000 Brain Injuries 1000 Solid tumor FVB/NJ hippocampus rep1 (430 2.0 Array) Colorectal cancer patient SC18_vs_Pool 861 Cerebral cortex scalp fibroblast 0 15 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210375 Last updated (according to GEO): Jul 16 2007 with acute measles 20 37 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11445 Last updated (according to GEO): May 28 2005 861 Blood nostrils 156 164 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7554.gif Source GEO sample is GSM79951 Last updated (according to GEO): Sep 22 2006 Liver 1000 skeletal_muscle_5 Spleen vs Prostaglandin E2 Treated B cell 120min (set2) Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68266 Last updated (according to GEO): Jul 07 2006 861 Encephalitis 1000 Muscle 1000 Communicable Diseases Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18896.gif Source GEO sample is GSM84127 Last updated (according to GEO): Sep 22 2006 to the nose 599 609 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201290 Last updated (according to GEO): Jun 14 2007 Standard affymetrix protocol Source GEO sample is GSM119495 Last updated (according to GEO): Jul 31 2007 913 Coronary heart disease The most common congenital cardiac abnormalities 50 97 Colonic mucous membrane 913 Two 90 minute exposures (3 hr recovery in between) to 0.8% halothane every day for 2.5 days, for a total of 5 exposures Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5112 Last updated (according to GEO): May 27 2005 liver 0 5 hippocampus_7 861 Oocytes 861 Cerebellum Bone Marrow 1000 Brain Injuries 901 1000 hindbrain C57BL/6J CHR, Rep2 healthy subject Source GEO sample is GSM211055 Last updated (according to GEO): Sep 10 2007 Olfactory Epithelium 1000 OVCAR-4 hgu95d Myocardium 861 26 15 endometrioid I_U133A_15_AnCg 861 Epithelial Cells Myometrium 23 Disease +_6629_batch1 on NHGRI-6.7k 901 Parietal Lobe Unique gene expression profiles of human macrophages and dendritic cells to phylogenetically distinct parasites. WGACON-232 the spinal cords 144 159 C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 1hr after experimental mice received their last shock treatment. Source GEO sample is GSM4501 Last updated (according to GEO): May 27 2005 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134642 Last updated (according to GEO): Jul 09 2007 2972 2966 spleens Healthy donor SN_45_vs_Pool 1000 Liver 861 Blood 070302_HF_331MB Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184671 Last updated (according to GEO): Apr 26 2007 MGMH030212061Bbrownfat 91 from the bone marrow 72 Feeder-independent ES cell line was grown using standard culture conditions. RNA was isolated using RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol. Data were normalized by AffyMetrix MAS5.0 using defaults. Keywords = embryonic stem cholesterol transport Source GEO sample is GSM9276 Last updated (according to GEO): May 27 2005 neurological disease control sample x132 Replicate2_Voxel C10 hTERT transduced mammary epithelial cells Source GEO sample is GSM5169 Last updated (according to GEO): May 27 2005 NA12750 growth 1 Ovarian_Tumor_Serous_CHTN-OS-044 the heart 987 996 from ventral prostate 21 41 17 7 hippocampus 7 0 prostate of the postmortem brains 654 678 861 Neoplasm Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 6 hours after lights on. Original RNA code = LC41A. Source GEO sample is GSM227394 Last updated (according to GEO): Sep 10 2007 Heart Ventricle 1000 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120660 Last updated (according to GEO): May 14 2007 Bipolar affective disorder is a severe psychiatric disorder with a strong genetic component but unknown pathophysiology. We used microarray technology to determine the expression of approximately 22,000 mRNA transcripts in post-mortem tissue from two brain regions in patients with bipolar disorder and matched healthy controls. Dorsolateral prefrontal cortex tissue from a cohort of 70 subjects and orbitofrontal cortex tissue from a separate cohort of 30 subjects was investigated. The final analysis included 30 bipolar and 31 control subjects for the dorsolateral prefrontal cortex and 10 bipolar and 11 control subjects for the orbitofrontal cortex. Differences between disease and control groups were identified using a rigorous statistical analysis with correction for confounding variables and multiple testing. In the orbitofrontal cortex, 393 differentially expressed transcripts were identified by microarray analysis and a representative subset was validated by quantitative real-time PCR. Pathway analysis revealed significant upregulation of genes involved in G-protein coupled receptor signalling and response to stimulus (in particular the immune response), while genes relating to the ubiquitin cycle and intracellular transport showed coordinated downregulation in bipolar disorder. Additionally, several genes involved in synaptic function were significantly downregulated in bipolar disorder. No significant changes in gene expression were observed in the dorsolateral prefrontal cortex using microarray analysis or quantitative real-time PCR. Our findings implicate the orbitofrontal cortex as a region prominently involved in bipolar disorder and indicate that diverse processes are affected. Overall, our results suggest that dysregulation of the ubiquitin pathway and synaptic function may be central to the disease process. 786-0 hgu95b none Source GEO sample is GSM149625 Last updated (according to GEO): Jan 03 2007 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:393, Count:32 Corner- Avg:35118, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:4.876832,SFGene:All Background:Avg:539.48,Stdev:6.19,Max:562.3,Min:520.1 Noise:Avg:10.84,Stdev:0.32,Max:11.7,Min:9.6 RawQ:14.98 Keywords = ALL Source GEO sample is GSM3398 Last updated (according to GEO): May 27 2005 2500 mg/kg X 24 hr Source GEO sample is GSM129855 Last updated (according to GEO): Sep 18 2007 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120681 Last updated (according to GEO): May 14 2007 1000 Brain 320 306 Keywords = HIV Mouse Liver AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate E DRG014_c 1000 Brain Motor neurons from the spinal cord of SOD1 mutant mice Treatment, type=linear_amplification, description=T7-based RNA amplification Source GEO sample is GSM113705 Last updated (according to GEO): Jun 09 2006 mild cognitive impairment - posterior cingulate cortex 4 cortex rattus_norvegicus_strain iP animal_number 3 CNS-SpinalC-conAdult-72h-1B-s2 Skin 5 Normal 1 22 0 Mammary Gland @ Preg19 Cells were either prestimulated (1_X) or not (0_X) for 18h with 100 ng/ml LPS. Media was exchanged and after 2h rest, cells either restimulated (X_1) or not (X_0) with again 100 ng/ml LPS. This resulted in 4 experimental conditions: 0_0, 0_1, 1_0 and 1_1. There were 3 biological replicates done, resulting in 12 arrays altogether. Source GEO sample is GSM213694 Last updated (according to GEO): Aug 01 2007 P2B_KIDNEY_3 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 2 hour after the last shock treatment. Source GEO sample is GSM4526 Last updated (according to GEO): May 27 2005 Authors: **** Source GEO sample is GSM6687 Last updated (according to GEO): Jul 21 2006 906 Blood Cells brain 0 5 Lymphoblastoid Cell Line for Individual 8007.4 log phase brain 0 5 Baclofen treated 1 Epithelium 861 Osteoblasts 1000 56 37 with chronic malaria BALB-RAG_OVA Replicate 1 Leukemia Lymphoblastic (MOLT-4) [JunctionChip 2 of 5] brain, Left Temporal Lobe: Extract46_le2 corpus_callosum_8 S1P2-KO-neocortex, biological rep3 (male) 1000 ovarian neoplasm CNS-RM_Mod14d-1C-s2 Infection 1176 1185 Epithelium 861 To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132973 Last updated (according to GEO): Sep 12 2006 Voxel G2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1431 Last updated (according to GEO): Nov 21 2005 lung 191 195 Parkinson's disease sample x189 0 30 no additional Source GEO sample is GSM199140 Last updated (according to GEO): Jun 08 2007 861 Intestines Leg 28 Day mdx rep 1 7 frontal cortex 20 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b008 Source GEO sample is GSM1954 Last updated (according to GEO): Nov 21 2005 Tumor__Breast_Adeno_94_I_159 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Left 1000 Decapitation HCC (HBV+, HK86) prostate Source GEO sample is GSM203393 Last updated (according to GEO): Jun 21 2007 Osteoblasts 1000 Central gray substance of midbrain 861 Dorsal Raphe Source GEO sample is GSM107925 Last updated (according to GEO): Jun 06 2006 Frontal cortex 254 267 Mouse Kidney Female 1 (technical replicate) Hyperdip>50-C41 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002. Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Part of the medium chain triacylglycerol oil in control diet was replaced with: 1.9% fish oil (providing 0.5 dietary wt% DHA and 1.0en%). Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily. Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France). Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h. After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hippocampal gene expression analysis. From these same 5 mice, the hippocampus was dissected from the mice according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancour, France) rinsed as described for livers, cut into 17-50 mg subsections, and frozen as described for livers. Hippocampal lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5). Hippocampal tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hippocampal RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips. Source GEO sample is GSM2563 Last updated (according to GEO): Mar 17 2006 Spinal Cord Injuries 1000 D_U133Plus_121_nAcc Normal Source GEO sample is GSM176101 Last updated (according to GEO): Apr 09 2007 brain 0 5 24 7 Right Frontal Lobe Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92337 Last updated (according to GEO): Jan 13 2006 Brain 884 15_360plus3 11 Bone marrow 0 861 Alzheimer's Disease Kidney 861 Paravertebral Muscle 11 Disease 0 30 G7 nasal retina 861 Brain Gene expression data from UET-13TR-EWS/ERG cells incubated in the presence of tetracycline for 48 hours Source GEO sample is GSM214929 Last updated (according to GEO): Aug 02 2007 mod095_1uM-2 1000 Asthma osteoblast 630 640 1000 Brain Normal Source GEO sample is GSM175982 Last updated (according to GEO): Apr 09 2007 by the liver 210 221 V5-P091 no additional Source GEO sample is GSM199303 Last updated (according to GEO): Jun 08 2007 1000 Coronary Arteriosclerosis of the colon 28 39 861 Cardiomyopathies 5 0 brain 12 frontal Lobe 23 Gene expression data from postmorten brain regions Source GEO sample is GSM145043 Last updated (according to GEO): Nov 20 2006 Endometrium 1000 Cerebellum 861 PGC-1a null (PGC-1a-/- ) and wild-type (PGC-1a+/+) mice were obtained by breeding heterozygous (PGC-1a+/-) founder mice as described (Leone et al., 2005). Source GEO sample is GSM135217 Last updated (according to GEO): Oct 05 2006 660 mesenchymal stem cell 639 MLL-#6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A the blood 393 402 D_95Av2_2835_CB_1_GS Schizophrenia 1000 3ARS02080773a_ciliary_ganglion M_U133A_78_AnCg of the tumors 838 850 Gene expression data from B6xBALB F2 mouse lung Source GEO sample is GSM133476 Last updated (according to GEO): Apr 05 2007 Formaldehyde, an important industrial chemical, is used for multiple commercial purposes throughout the industrialized world. This simple, one carbon aldehyde is a natural metabolite formed in cells throughput the body. However, it is also a rodent nasal carcinogen, when inhaled by rats every day for two-years at irritant concentrations. High tumor incidences occur at concentration of 10 ppm and above; no tumors are observed at concentrations below 6.0 ppm. The US Environmental Protection Agency (US EPA) is now (2007) conducting a risk assessment to try to evaluate possible cancer risks for much lower levels of human exposure. Sensitive methods are needed to evaluate tissue responses below those concentrations that are clearly irritant or carcinogenic. This microarray study was undertaken to evaluate the mode of action for nasal responses to inhaled formaldehyde in Fisher 344 rats over a range of exposure concentrations. The range of concentrations used spanned those at which virtually no tissue responses were observed (0.7 ppm) to those that represent the highest concentration in the cancer studies (15 ppm) that produced nasal tumors in half the exposed group of rats. The study identified doses at which there were no statistically significant changes in gene expression; intermediate doses with changes in a small number of genes not easily grouped by function; and then concentrations where changes were consistent with irritation and cell stress responses. Last Updated (by provider): Apr 26 2007 Contributers: Russell S Thomas Harvey J Clewell Longlong Yang Melvin E Andersen Edilberto Bermudez Linda J Pluta Pancreas at e14.5, Chip C, rep 1 Large-scale analysis of the human transcriptome. Brain, thalamus Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 114.50 Stdv: 4.21 Min: 105.65 Max: 118.77 Source GEO sample is GSM2881 Last updated (according to GEO): Mar 20 2006 Whole brain 0 10 114 101 brains quickly /NJ mouse periaqueductal gray 27 55 prostate Source GEO sample is GSM203325 Last updated (according to GEO): Jun 21 2007 669 stem cells 660 GC (HKG16T) intestine_PPARa-knockout_control_rep3 Probeset expression data from NA12751 growth 1, replicate 4 Source GEO sample is GSM195206 Last updated (according to GEO): Aug 08 2007 1st 1hr C-DG 861 Cerebral cortex 901 Coronary artery healthy subject Source GEO sample is GSM211142 Last updated (according to GEO): Sep 10 2007 Adenocarcinoma 1000 to the nose 599 609 prostate Source GEO sample is GSM203290 Last updated (according to GEO): Jun 21 2007 Cerebral cortex 861 12 0 ovarian tumor CNS-SpinalC-conAdult-7d-2C-s2 Gene expression data from a neocortex of saline-injected mouse Source GEO sample is GSM147400 Last updated (according to GEO): Jan 03 2007 human caudate nucleus Source GEO sample is GSM86804 Last updated (according to GEO): Feb 08 2006 CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of DC, recombinant human (rh) IL-4 and rhGMCSF were added to the culture at 50 ng/ml on days 1, 3, and 5 of culture. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5132 Last updated (according to GEO): Mar 21 2006 2_cerebral_cortex_6hrs_sleep_#61 1000 Hippocampus Cardiac-specific TNF-alpha transgenic mouse is an excellent model to study the pathologenesis of heart failure. Affytrix U74V2A was used to analyzed the gene expression profile of mice at the time point of compensated hypertrophy and dilated heart failure Source GEO sample is GSM8982 Last updated (according to GEO): May 28 2005 no additional Source GEO sample is GSM199162 Last updated (according to GEO): Jun 08 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145384 Last updated (according to GEO): Nov 20 2006 ChWK4 DBA/2J hypothalamus rep2 (430 2.0 Array) mouse brains 187 198 453 434 The descending colon M_U133A_52_AnCg_redo 1000 Rectum PMN_LB_360min_Patient4 We analyzed gene expression patterns in human gastric cancers by using cDNA microarrays representing approximately equal 30,300 genes. Expression of PLA2G2A, a gene previously implicated as a modifier of the Apc(Min/+) (multiple intestinal neoplasia 1) mutant phenotype in the mouse, was significantly correlated with patient survival. We confirmed this observation in an independent set of patient samples by using quantitative RT-PCR. Beyond its potential diagnostic and prognostic significance, this result suggests the intriguing possibility that the activity of PLA2G2A may suppress progression or metastasis of human gastric cancer. Backskin_DN-CLIM_P14_rep3 1000 Amygdaloid structure CNS-RM_Mod7d-4B-s2 Disease Source GEO sample is GSM175813 Last updated (according to GEO): Apr 09 2007 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132528 Last updated (according to GEO): Feb 26 2007 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120704 Last updated (according to GEO): May 14 2007 Macrophage 14smi094 861 Brain Lymphoblastoid Cell Line for Individual 8175.3 log phase HTI-286 in docetaxel-refractory prostate cancer (Biological Replicate 1) Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210379 Last updated (according to GEO): Jul 16 2007 1 of 3 replicates in treatment group Source GEO sample is GSM206025 Last updated (according to GEO): Jun 29 2007 bc-ZT3-3 Spinal Cord 1000 1000 Cerebral cortex Wild type inbred mice Source GEO sample is GSM82969 Last updated (according to GEO): Nov 10 2005 Tumor__Uterus_Adeno_3663 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A of mouse brain 9 23 Muscle Source GEO sample is GSM4273 Last updated (according to GEO): May 27 2005 brain, ipsi Cortex: Trizol Extraction34_le1 5 0 Spleen of mouse brain 9 23 PGA-swim_1w_s1023 338 333 brain plasma cells 50 61 608 569 of the posterior pituitary neural lobe B6_Control_ZT 0_1 861 Heart Bladder sample 1352-1 1000 Brain Tosini-1R01NS043459-01A1 Gene expression data from postmorten brain regions Source GEO sample is GSM145177 Last updated (according to GEO): Nov 20 2006 40 21 from dorsal pancreas Squamous cell carcinoma 923 1000 Tricuspid valve structure Whole Brain 73 83 Central gray substance of midbrain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145056 Last updated (according to GEO): Nov 20 2006 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141299 Last updated (according to GEO): Oct 26 2006 f2#45 versus pool Mouse Brain tissue Primary typical carcinoid 8512 Brain 1000 hippocampus: Sample #4_e1_le1 D_U133Plus_111_CB brain, cortex: Sample17_e1_le1 Aldosterone-producing adenoma (APA12) 1000 ovarian neoplasm 865 Disorder of artery Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26118.gif Source GEO sample is GSM81538 Last updated (according to GEO): Sep 22 2006 Expression profiling of naive raphe (T0) in rats Source GEO sample is GSM41556 Last updated (according to GEO): May 27 2005 24 0 Proliferative endometrium testis 52 58 M_U133A_17_AnCg Muscle 861 B260 on Affymetrix GeneChip Human Full Length Array HuGeneFL human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195321 Last updated (according to GEO): Jun 04 2007 1000 Heart 861 Cerebral cortex 95 75 Normal Salivary Gland Diet induced changes in mouse liver mRNA profiles. One of 3 replicates of C57BL/6 mice maintained for 12 weeks on low fat diet. Keywords = LDL receptor deficiency, high fat diet, atherosclerosis, liver Source GEO sample is GSM5407 Last updated (according to GEO): May 27 2005 861 Cerebral cortex Nasal; Olfactory Epithelium Keywords = mouse gene expression database Source GEO sample is GSM29409 Last updated (according to GEO): May 27 2005 CNS-SMTC_Ctr24h-2B-s2 "38 hr Hela Double Thymidine, exp3" Kidney (fetal) [JunctionChip 3 of 5] 1000 ovarian neoplasm total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lipopolysaccharide (LPS) for 240min Source GEO sample is GSM5670 Last updated (according to GEO): May 27 2005 brain, cerebellum: Tg+/+_Crb2_e1_le1 Brain 861 Leukemia, Lymphocytic, Chronic 884 1000 Heart failure Blood Test (Blinded) Sample Source GEO sample is GSM129945 Last updated (according to GEO): Sep 18 2007 160 141 longitudinal studies We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201784 Last updated (according to GEO): Jun 20 2007 254 238 of neural retinas Kidney CR-4B Nasal Epithelium 901 Cortex_Control_rep3 (06SE457) 101 86 of the amygdalae Transitional epithelium 1000 226 212 lacrimal, tooth Brain 861 Transplant Series 34 , Transplant # 3 861 Cerebral cortex in mouse hearts 40 54 861 Brain Adenoma 19 26 amygdala_1 Source GEO sample is GSM80565 Last updated (according to GEO): Mar 31 2006 of coronary artery disease 258 284 Paravertebral Muscle 4 Disease 0 29 3ARS0207253IA_PLACENTA 1000 Prostate n/a Source GEO sample is GSM178080 Last updated (according to GEO): Jun 11 2007 brain, ipsi Cortex: Trizol Extraction40_le1 Lymphoblastoid Cell Line for Individual 8080.5 log phase The epithelial cells 962 981 23 0 Substantia nigra PD rep3 EWS-C2 on NHGRI-6.5k_b 1000 Heart 5 0 brain of seminoma 1138 1149 861 Cardiomyopathies Gene expression regulated by DACH1-1 HapMap CHB Female Source GEO sample is GSM159575 Last updated (according to GEO): Feb 01 2007 Kidney 861 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs//13412.gif Source GEO sample is GSM79640 Last updated (according to GEO): Sep 22 2006 Osteoblasts 1000 Liver 1000 Mucous Membrane 861 osteoblast 627 637 3AJZ02052114_TestiSeminiferousTubule 1000 Stem cells 1006 997 in glioma Neoplasm 861 Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002. Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Part of the medium chain triacylglycerol oil in control diet was replaced with: 1.1% fungal oil and 1.9% fish oil. Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily. Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France). Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h. After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hepatic gene expression analysis. From these 5 mice, livers were dissected according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancourt, France), which consisted of carefully dissecting out the liver, rinsing with 70% EtOH to remove adhering blood, trimming of adhering connective tissue with scissors, cutting into 100-150 mg subsections, freezing in liquid N2, and storing at -80°C until gene expression and lipid analysis. Hepatic lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5). Liver tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hepatic RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips. Source GEO sample is GSM2574 Last updated (according to GEO): Mar 17 2006 Skeletal muscle biopsy was obtained before a two-hours of hyperinsulinaemic (40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172123 Last updated (according to GEO): Feb 28 2007 5 0 brain RNA isolated from fetal cerebrum Keywords = trisomy Keywords = brain Keywords = Down syndrome Source GEO sample is GSM22510 Last updated (according to GEO): May 27 2005 861 Cerebellum Wild type 8 wk old male DBA/2J mouse pituitary gland Source GEO sample is GSM75005 Last updated (according to GEO): Feb 27 2007 Normal Source GEO sample is GSM176273 Last updated (according to GEO): Apr 09 2007 861 Heart Diseases Transplant Series 13 , Transplant # 2 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215079 Last updated (according to GEO): Aug 02 2007 1384 1377 (myosin in livers 1540 1548 Control frontal cortex 5 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53471 Last updated (according to GEO): Jul 06 2005 This mouse is transgenic for constitutively active PI3k. caPI3K transgenic animals have hearts 20% larger than those of wild type littermates. These arrays were scanned at a PMT of 10%. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/pi3k_home.html Keywords = cardiac, pi3k, hypertrophy Source GEO sample is GSM8521 Last updated (according to GEO): May 27 2005 brain 0 5 C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P28 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25143 Last updated (according to GEO): May 27 2005 whole blood_101060 Colon Carcinoma 1000 7 frontal cortex 20 Cerebellum_naive_ISS55_B MuscleRegen-ctx8d-1RLAv2-s2 91 from the bone marrow 72 Spleen 0 5 41 29 Control blood brain, forebrain: Sample11_e1_le1 M_U133A_20_nAcc Squamous cell carcinoma 5 41 29 Control blood Gene expression data from hippocampus of one young SAMP8/Ta mouse Source GEO sample is GSM143754 Last updated (according to GEO): Jan 24 2007 B6 day 6, biological rep 1, tech rep 2 41 29 Control blood 36 8 in the developing spinal cord 1000 Nervous system structure Endometrium/Ovary 17 Disease 3AMH02022205_Brain Amygdala amygdala wistar 3723 861 Neoplasm Gene expression data from aneurismal tissues obtained from patients with tricuspid valves. Source GEO sample is GSM116794 Last updated (according to GEO): Jun 28 2006 Whole Brain 73 83 Expression profiling of spinal cord section (T9) extracted from rats 7d following severe injury Lot batch = Source GEO sample is GSM7596 Last updated (according to GEO): May 28 2005 Neoplasm 861 Normal Source GEO sample is GSM176047 Last updated (according to GEO): Apr 09 2007 cornea Sprague1 whole tissue, pool of 5 animals, 16 weeks old, male Sprague Dawley cornea file:R3RS01112801 Source GEO sample is GSM15237 Last updated (according to GEO): May 28 2005 XX19_InX Mouse old brain C30-Br-2 Replicate2_Voxel G2 Replicate2_Voxel F10 1000 Brain Stem Expression profiling of moderately injured raphe at 3 months in rats Source GEO sample is GSM41607 Last updated (according to GEO): May 27 2005 liver, PPARa-null mice, treatment with WY14643 for 6h Source GEO sample is GSM205779 Last updated (according to GEO): Jul 24 2007 NA Source GEO sample is GSM84324 Last updated (according to GEO): Dec 01 2005 Gene expression data from brain of adult rats Source GEO sample is GSM101054 Last updated (according to GEO): Feb 20 2007 at the Human Brain 744 761 bladder_T2-4_pool-3 Skeletal muscle structure 1000 861 Liver 5 0 Spleen Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242047 Last updated (according to GEO): Dec 04 2007 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/9631.gif Source GEO sample is GSM79881 Last updated (according to GEO): Sep 22 2006 KOPTK1 DMSO control 24h rep2 1000 Liver osteoblast 627 637 Integumentary system 1000 CNS-SpinalCsev-Adult-28d-1C-s2 867 Large-Cell Lymphomas Accumbens P9 Normal Brain 1000 Occipital region 983 Parkinson's disease sample x124 0 30 Lmna H222P homozygous male 4 Disorder of artery 865 NCI60.50_LABEL54EXTRACT53SUB3 Source GEO sample is GSM134245 Last updated (according to GEO): Aug 06 2007 ER negative human primary breast tumor EA02014_41270_H133A_JA-1501 Saccule structure 1000 67 40 with coronary artery disease with Parkinson's disease 27 50 8 uterine horns 421 435 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. 4h after sham surgery, a 7 mm disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44529 Last updated (according to GEO): May 27 2005 TestiIntersitial Source GEO sample is GSM18988 Last updated (according to GEO): Sep 25 2006 olfactory epithelium SR-A mutant mouse 2 hpO Source GEO sample is GSM80201 Last updated (according to GEO): Oct 26 2005 bladder 113 119 NA12751 growth 3, replicate 3 626 615 PCOS oocytes none Source GEO sample is GSM244605 Last updated (according to GEO): Nov 23 2007 Primary large cell lung carcinoma 1531 Source GEO sample is GSM18309 Last updated (according to GEO): May 27 2005 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Tumor necrosis factor-alpha labeled with Cy5- time course with repeats. Date GSE401 Last Updated: May 29 2005 Contributers: Sun Young Lee Sangdun Choi Yun Anna Cao Angela Alexander Joella Grossoehme Robert Hsueh Mi Sook Chang Jong-Woo Kim Rebecca Hart Zhen Yan Includes GDS322. Update date: Nov 18 2003. Dataset description GDS322: Temporal analysis of effects induced by 6 nM tumor necrosis factor-alpha in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. Amyotrophic Lateral Sclerosis 1000 Richard Almon-47-1138200270852 0 Human Cortex 11 outer medulla 31 43 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12530.gif Source GEO sample is GSM79986 Last updated (according to GEO): Sep 22 2006 D_U133A_50_DLPFC Sprague-Dawley Male LowSalt OuterMedulla rat707 sd_medullar_k_707r_om_070302 human cerebellum Source GEO sample is GSM87168 Last updated (according to GEO): Feb 08 2006 1000 Brain 48 19 of systemic autoimmune disease 1000 Epilepsy GSE6686 brain, hindbrain and spinal cord: P0KO1_e1_le1 from the forebrain 20 37 Epithelial Cells 901 Ganglia, Spinal 884 cardiac 763 769 Brain 861 Normal epithelial cells were removed by dissection and digestion from bronchi of donor long tissue from normal subject. Source GEO sample is GSM3917 Last updated (according to GEO): May 27 2005 Heart Atrium 1000 Squamous cell carcinoma 875 embryo day 10.5 Source GEO sample is GSM18631 Last updated (according to GEO): May 27 2005 41 29 Control blood 29 0 Adrenal cortex [JunctionChip 1 17 7 hippocampus Cochlear nucleus structure 901 1000 Kidney Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68144 Last updated (according to GEO): Jul 07 2006 Gene expression data from colorectal adenoma. Source GEO sample is GSM215110 Last updated (according to GEO): Aug 02 2007 240 218 of cognitive impairment CNS-SpinalC-4hAdult-3A-s2 Transcriptional reprogramming during reloading of atrophied rat soleus muscle Astrocytoma 861 Expression profiling of naive raphe (T0) in rats Source GEO sample is GSM41559 Last updated (according to GEO): May 27 2005 GSE9744 901 Intestines, Small G30-CingulateCortex replicate2 mouse brain ipsilateral LPS.RU486 Source GEO sample is GSM149783 Last updated (according to GEO): Mar 15 2007 Posterior root of spinal nerve 901 striatum_Hdh4Q80_8S 61 50 Spleen C57BL 1175 1164 in 31 tumors 19 0 human frontal cortex 861 Cerebral cortex Retinal Degeneration 901 A HID U D005 259_2 NCI60.9_LABEL12EXTRACT11SUB3 Source GEO sample is GSM134038 Last updated (according to GEO): Aug 06 2007 amygdala 25 33 Spinal Cord 901 HOP-62 hgu95d none Source GEO sample is GSM123237 Last updated (according to GEO): Jul 26 2006 DLBC51 on Affymetrix GeneChip Human Full Length Array HuGeneFL CNS-SC_CtrA4h-1A-s2 Sham 13 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107497 Last updated (according to GEO): May 01 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145247 Last updated (according to GEO): Nov 20 2006 Normal human tissue:Normal Testis Keywords = Human, Normal Tissue, Normal Testis Source GEO sample is GSM44701 Last updated (according to GEO): May 27 2005 Timepoint4r 1000 Spleen Neoplasm 861 from the right forebrain 21 44 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201285 Last updated (according to GEO): Jun 14 2007 15 0 human cerebellum CurrentSmoker 91 Nose 1000 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68288 Last updated (according to GEO): Jul 07 2006 M7TW01013109 77 66 Normal Colon /2J mouse cingulate cortex 27 52 none Source GEO sample is GSM123257 Last updated (according to GEO): Jul 26 2006 Luminal breast tumor cell line ZR75-1 Keywords = Agilent microarray, Expression analysis, EGFR, Breast cancer growth Source GEO sample is GSM29514 Last updated (according to GEO): Dec 13 2006 Primary tumor 19 32 no additional Source GEO sample is GSM199425 Last updated (according to GEO): Jun 08 2007 C57BL/6J pituitary gland rep1 (430 2.0 Array) total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withSLC (Secondary lymphoid-organ chemokine) for 30min Source GEO sample is GSM5768 Last updated (according to GEO): May 27 2005 Mice sacrificed after swimming twice a day for 2.5 days. Keywords = exercise induced hypertrophy Source GEO sample is GSM2348 Last updated (according to GEO): May 27 2005 861 Brain A/J periaqueductal gray rep2 Mesenchymal Stem Cells 1000 27 17 (cerebellum PGA-lv_8w_329 17 7 hippocampus 1000 Left Leg 23 Day mdx rep 3 of a colorectal adenoma 7 29 brain, frontal cortex: Sham AM LC_e1_le1 Cerebral cortex 861 913 Coronary heart disease 10 weeks Source GEO sample is GSM147509 Last updated (according to GEO): Dec 01 2006 184-96_Adeno 861 Cerebral cortex 46 8 in docetaxel-refractory prostate cancer Standard Affymetrix procedure Source GEO sample is GSM133011 Last updated (according to GEO): Aug 28 2007 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc52 Source GEO sample is GSM1859 Last updated (according to GEO): Nov 21 2005 BPHF 1598 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Motor neurons from the spinal cord of wildtype mice Treatment, type=linear_amplification, description=T7-based RNA amplification Source GEO sample is GSM113702 Last updated (according to GEO): Jun 09 2006 901 Temporal Lobe 57 39 with endometriosis Dopamine Receptor 1000 Infection 1113 1122 We analyzed the lumbar spinal cord tract of transplanted nmd mice (n=3), untransplanted nmd mice (n=3) and wild-type mice (n=3) (all mice are of male gender). The latter groups underwent surgical procedure with vehicle. The surgical procedure and spinal cord-derived neural stem cell transplantation (intratechal injection) were done at P1 and the animals were sacrificed at 6 weeks of age. Source GEO sample is GSM67524 Last updated (according to GEO): Dec 21 2005 1000 Rectum 9 0 Metastasis Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation. Source GEO sample is GSM228473 Last updated (according to GEO): Sep 10 2007 kidney 37 43 1000 Rectum low gestational age Source GEO sample is GSM213112 Last updated (according to GEO): Jul 25 2007 861 Alzheimer's Disease Epithelium 861 ND011 GM10851 1000 Left 1000 Skeletal muscle structure PMN_control_180min_Patient17 NoCAD_replicate21 Cerebral cortex 861 901 frontal lobe atrioventricular_node Source GEO sample is GSM19007 Last updated (according to GEO): Sep 25 2006 The relationships between profiles of global gene expression and DNA damage checkpoint functions were studied in cells from patients with ataxia telangiectasia (AT). Three telomerase-expressing AT fibroblast lines displayed the expected hypersensitivity to ionizing radiation (IR) and defects in DNA damage checkpoints. Profiles of global gene expression in AT cells were determined at 2, 6 and 24 h after treatment with 1.5 Gy IR or sham-treatment, and were compared to those previously recognized in normal human fibroblasts. Under basal conditions 160 genes or ESTs were differentially expressed in AT and normal fibroblasts, and these were associated by gene ontology with insulin-like growth factor binding and regulation of cell growth. Upon DNA damage, 1091 gene mRNAs were changed in at least two of the three AT cell lines. When compared with the 1811 genes changed in normal human fibroblasts after the same treatment, 715 were found in both AT and normal fibroblasts, including most genes categorized by gene ontology into cell cycle, cell growth and DNA damage response pathways. However, the IR-induced changes in these 715 genes in AT cells usually were delayed or attenuated in comparison to normal cells. The reduced change in DNA-damage-response genes and the attenuated repression of cell-cycle-regulated genes may account for the defects in cell cycle checkpoint function in AT cells. The observation of attenuated and not ablated checkpoint responses in AT cells supports a hypothesis that the ATM- and rad3-related checkpoint kinase ATR also responds to IR-induced DNA damage and complements ATM signaling. Last Updated (by provider): Feb 08 2007 Contributers: Jeff Chou Tong Zhou William Kaufmann 32 F arm fibroblast LS10, asynchronous 861 Colon NA19137 1373 neurological disease 1393 1000 Hippocampus 1000 Neuraxis in seminoma 28 38 Primary Neoplasm 1000 Brain 861 17 6 (hippocampus SN:1010397 Source GEO sample is GSM115380 Last updated (according to GEO): Jun 20 2006 20 0 human caudate nucleus Brain 1000 Congenital Abnormality 853 66 42 out of mouse bone marrow 861 Parkinson Disease Brain 861 Plasma 861 1135 1118 leg muscle groups mouse brains 187 198 913 Acute leukemia AD control Treatment, type=dissect Source GEO sample is GSM119637 Last updated (according to GEO): Jul 10 2006 Large cell neuroendocrine carcinoma 901 days nasal epithelium 1127 1148 Mouse young brain C5-Br-5 1000 Carcinoma, Embryonal Hippocampus Source GEO sample is GSM107961 Last updated (according to GEO): Jun 06 2006 experiment II, hTERT, replicate 2 1000 Brain /HeJ mouse cingulate cortex 27 53 Medulla 861 861 Cerebral cortex human frontal cortex Source GEO sample is GSM87048 Last updated (according to GEO): Feb 08 2006 Organ 861 Barcode: 251316210241 Source GEO sample is GSM159378 Last updated (according to GEO): Jul 17 2007 from mouse colon 21 36 Brain 1000 70 50 Skeletal muscle C57BL 13 0 Normal Stomach Cerebral cortex 861 T05__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Nervous system structure 861 Colon 861 Liver 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201234 Last updated (according to GEO): Jun 14 2007 no additional Source GEO sample is GSM199212 Last updated (according to GEO): Jun 08 2007 Cerebral cortex 861 LOX IMVI hgu95e Gene expression data from brain of adult rats Source GEO sample is GSM101034 Last updated (according to GEO): Feb 20 2007 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13427.gif Source GEO sample is GSM79665 Last updated (according to GEO): Sep 22 2006 511 479 of APC-related colorectal cancer Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18597.gif Source GEO sample is GSM66577 Last updated (according to GEO): Sep 22 2006 long access to cocaine, nucleus accumbens, 6 hrs/day access to cocaine Source GEO sample is GSM93822 Last updated (according to GEO): Jan 26 2006 Cannabinoid receptor double knockout mice (Cnr1 -/- /Cnr2 -/-) in CHS model total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CGS for 120min Source GEO sample is GSM5515 Last updated (according to GEO): May 27 2005 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156605 Last updated (according to GEO): Jan 22 2007 Performed by UCI Microarray Facility. Source GEO sample is GSM203587 Last updated (according to GEO): Jun 22 2007 wt mouse number 3 Source GEO sample is GSM186668 Last updated (according to GEO): Jun 11 2007 Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21271.gif Source GEO sample is GSM91558 Last updated (according to GEO): Sep 22 2006 Gene expression data from a neocortex from mouse injected 10 mg/kg nicotine Source GEO sample is GSM147412 Last updated (according to GEO): Jan 03 2007 861 Cerebral cortex hrs nasal epithelium 1127 1147 1000 Muscle We will separately dissect the maxillary and mandibular branches of the E10.5 first branchial arch from wild type, dlx2, dlx1/2 and Dlx5/6 mutants. The tissues wil be flash frozen within 1 min of removal.We have not performed the dissections yet so we dont know how much RNA will be get from each sample, but previous experience suggests that we will need ~10 branchial arches/experiment. Treatment, type=nucleic_acid_extraction, description=We anticipate using this method as it was recommended by TGEN for small amounts of tissue. Source GEO sample is GSM107891 Last updated (according to GEO): Jun 06 2006 ColonDistal0220AFAR_071.txt Mucous Membrane 861 Richard Almon-39-1138200270633 15 0 human cerebellum 15 7 hindbrain 1824 1809 of brain injury Acetaminophen 3hr Rat 6161 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool This mouse is transgenic for dominant-negative forms of PI3k. dnPI3K transgenic animals have hearts that are 17% smaller than those of wild type littermates. These arrays were scanned at a PMT of 10%. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/pi3k_home.html Keywords = cardiac, pi3k, hypertrophy Source GEO sample is GSM8523 Last updated (according to GEO): May 27 2005 Pulmonary Emphysema 1000 57 39 with endometriosis Primary Neoplasm 1000 Olfactory Epithelium 1000 /3T3 fibroblasts 478 493 Expression profiling of spinal cord section (T9) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM4421 Last updated (according to GEO): May 28 2005 Whole Brain 62 72 of cancers 378 387 of bladder cancer 126 142 Plasma 861 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:343, Count:32 Corner- Avg:35802, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:6.656495,SFGene:All Background:Avg:490.51,Stdev:6.18,Max:507.2,Min:477.7 Noise:Avg:9.41,Stdev:0.30,Max:10.4,Min:8.5 RawQ:14.06 Keywords = ALL Source GEO sample is GSM3411 Last updated (according to GEO): May 28 2005 Two 90 minute exposures (3 hr recovery in between) to 0.8% halothane every day for 5 days, for a total of 10 exposures Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5110 Last updated (according to GEO): Mar 17 2006 TUMOR 29 0 7 1000 Spleen 861 Blood 1000 Prostate Expression profiling of spinal cord section (T9) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31252 Last updated (according to GEO): May 27 2005 5 0 brain B220hi sIgM+ Mature B cells sorted out of mouse bone marrow, sort no. 11 Source GEO sample is GSM648 Last updated (according to GEO): Mar 20 2006 "Sample 45, <5 yr survival(13 months) age 37 erp yes" on vantveer-oligo OlfactoryBulb Source GEO sample is GSM18860 Last updated (according to GEO): Sep 25 2006 858 Prostatic Neoplasms none Source GEO sample is GSM149524 Last updated (according to GEO): Jan 03 2007 Neoplasm 861 98 of cortex 106 Brain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145010 Last updated (according to GEO): Nov 20 2006 5 0 brain Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16251.gif Source GEO sample is GSM91514 Last updated (according to GEO): Sep 22 2006 of regenerating Dorsal Root Ganglia 21 55 trigeminal Source GEO sample is GSM18609 Last updated (according to GEO): May 27 2005 human caudate nucleus Source GEO sample is GSM86813 Last updated (according to GEO): Feb 08 2006 C57BL/6J Cingulate Cortex C Kainate-hippocampus, biological rep1 tongue_superior_part_w/_papillae_2 Source GEO sample is GSM80883 Last updated (according to GEO): Mar 31 2006 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68221 Last updated (according to GEO): Jul 07 2006 1000 Brain 338 333 brain Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 5 day time point Source GEO sample is GSM159769 Last updated (according to GEO): Apr 23 2007 no doxycycline, wt Source GEO sample is GSM213390 Last updated (according to GEO): Jul 26 2007 Untreated versus treated (bortezomib), untranformed MCF10A and Transformed (see Adler et al, Nature Gen. 2006) Source GEO sample is GSM120220 Last updated (according to GEO): Jul 20 2006 Subject code A3 Liver 1000 ovarian tumor: clear cell Source GEO sample is GSM139382 Last updated (according to GEO): Apr 09 2007 Leukemia, Lymphocytic, Chronic 1000 Parkinson Disease 861 Brain 861 12 0 ovarian tumor Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17077.gif Source GEO sample is GSM91589 Last updated (according to GEO): Sep 22 2006 Mice sacrificed at 12 weeks of age. Can be used as a control for the 3 and 4 week swim mice Keywords = exercise induced hypertrophy Source GEO sample is GSM2363 Last updated (according to GEO): May 27 2005 Mouse Liver AIN Diet 8hr 1mg/kg Dex Injection, biological replicate C stria terminalis 901 mRNA was isolated after 1 hour of incubation from IMR-90 cells seeded onto a collagen/chondroitin sulfate tissue engineering scaffold mesh material. Cells were seeded at a density of 1 x 10^6 cells/ mesh, and this chip represents a pooling of cells from 4 meshes. Keywords = tissue engineering mesh, collagen, chondroitin sulfate, biomaterials design Source GEO sample is GSM6043 Last updated (according to GEO): May 27 2005 Parkinson Disease 1000 corticosterone_treated_rep6 (06SE463) Squamous cell carcinoma 853 492 475 in the PCOS oocyte NA06985 Ventral Tegmental Area 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-gamma (IFN gamma) for 30min Source GEO sample is GSM5602 Last updated (according to GEO): May 27 2005 BALB-c mice were given intratracheal bleomycin (1.5U per kg). Lungs were harvested and frozen at 72h. Lot batch = Source GEO sample is GSM4151 Last updated (according to GEO): May 28 2005 CH2118 of a resistance artery 191 212 B6:19-8 cortex Normal Source GEO sample is GSM176133 Last updated (according to GEO): Apr 09 2007 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198657 Last updated (according to GEO): Jun 06 2007 NCI60.58_LABEL62EXTRACT61SUB3 Source GEO sample is GSM134288 Last updated (according to GEO): Aug 06 2007 211 204 tumours 17 7 hippocampus 861 Hippocampus Liver 0 4 The epithelial cells 962 981 DCN_U7_B Nasal Epithelium 901 1000 Hippocampus Universal Mouse Reference RNA Source GEO sample is GSM93429 Last updated (according to GEO): Jan 23 2006 786-0 hgu95e 861 Liver Cortex from rats with cerebral cortical contusion 4 day post injury, injured cortex (ipsilateral side) -uninjured cortex (contralateral side) were hybridised onto a 6240 cDNA probe microarray. Expression ratios were calculated using injured/un-injured cortex Source GEO sample is GSM76236 Last updated (according to GEO): Sep 29 2005 22 19 left Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231055 Last updated (according to GEO): Sep 26 2007 Gene expression data from epididymal fat tissues. Source GEO sample is GSM215579 Last updated (according to GEO): Aug 07 2007 Amino acid conjugated surfaces and controls at 6 and 32 hours. Date GSE1000 Last Updated: May 29 2005 Contributers: Catherine M Klapperich Carolyn R Bertozzi Jie Song Includes GDS562. Update date: Apr 21 2004. Dataset description GDS562: Evaluation of osteosarcoma TE85 cell tissue culture on a variety of amino acid conjugated surfaces at 6 and 32 hours. Study holds potential applications for bone tissue engineering.. thymus Source GEO sample is GSM18669 Last updated (according to GEO): May 27 2005 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9769.gif Source GEO sample is GSM76451 Last updated (according to GEO): Sep 22 2006 Liver 1000 SN:Human Glioblastoma Biopsy 30147 1000 Spleen at the Human Brain 746 763 1000 Amygdaloid structure Subject code A16 brain 112 117 Skeletal bone 861 19 0 human frontal cortex male C57BL6, double amplification Source GEO sample is GSM5418 Last updated (according to GEO): Mar 17 2006 91 from the bone marrow 72 91 from the bone marrow 72 5 0 brain 1000 Left 14 0 Locus Coeruleus Seminoma 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145401 Last updated (according to GEO): Nov 20 2006 Squamous epithelial cell 861 human cerebellum Source GEO sample is GSM87067 Last updated (according to GEO): Feb 08 2006 Nervous system structure 901 Cerebral cortex 861 HNC012 DCIS210 on harvard-12k GC (HKG76T) ovary 197 201 IRTGFBd8_23 devellis-5U24NS043562-02 5 0 Spleen Expression profiling of spinal cord section (T8) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM6636 Last updated (according to GEO): May 28 2005 Brains 714 719 Thymus [JunctionChip 5 of 5] foreskin fibroblast #1, asynchronous brain_control_sampleid_mr951 359 342 with breast tumors Wild type 3 Thymus, Whole thymus: Amplified mRNA_le1 Cerebral cortex 861 Osteoblasts 1000 L_D2_SleepDep_ZT 6_1 1000 Cerebellum brain, Entorhinal Cortex: 98-18 normal_e1_le1 C3H/HeJ pituitary gland rep1 194 Raphe magnus 183 861 Alzheimer's Disease 861 Cerebral cortex CNS-SpinalCsev-Adult-14d-2C-s2 91 80 from bronchi 1000 Brain Control hippocampus 4 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53450 Last updated (according to GEO): Jul 06 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145768 Last updated (according to GEO): Nov 20 2006 Expression profiling of spinal cord section (T9) extracted from rats 7d following moderate injury Source GEO sample is GSM31584 Last updated (according to GEO): May 27 2005 mouse brains 187 198 brain, cortex: 3dexp4_e1_le1 Anterior nares 1000 Amyotrophic lateral sclerosis (ALS) spares the ocular motor system. In this study, we tested the hypothesis that the oculomotor neurons are intrinsically protected in ALS. Using high-density cDNA microarrays, we examined the transcriptome of oculomotor nuclei and spinal cords in mice expressing a human mutant SOD1, the SOD1(G93A) ALS model, at 6 and 10 weeks of age. Comparison of gene expression profiles of these pre-symptomatic SOD1(G93A) mice showed a shift to a proapoptotic state in spinal cords, while the opposite was true in oculomotor nuclei. Seventeen members of the A, B, C and D Hox clusters increased in oculomotor nuclei from 6 to 10 weeks of age; 15 were downregulated in spinal cord. Although only the first 4 classes of a given Hox cluster (e.g., Hoxa1-4) are normally expressed in the developing hindbrain, we found differential expression of mostly the latter classes in both oculomotor nuclei and spinal cords. Also, semaphorin 3B was expressed at 28-fold greater levels in oculomotor nuclei and 61-fold less in spinal cords in 10-week old SOD1(G93A) mice compared to 6-week old mice. Semaphorins 3A and 3E were also differentially regulated. Comparison of gene expression profiles of control SOD1 mice of 6 and 10 weeks of age did not show these changes. Based on these results, we rejected our hypothesis and conclude that the oculomotor nuclei actively adapt to the ALS-inducing mutation. Supported by NEI and ALSA. Last Updated (by provider): Oct 28 2005 Contributers: Francisco H Andrade Colleen A McMullen Includes GDS1716. Update date: May 05 2006. Dataset description GDS1716: Analysis of oculomotor motor neurons (OMNs) of SOD1-G93A transgenic model of amyotrophic lateral sclerosis (ALS) at 6 and 10 weeks of age. ALS spares the ocular neurons suggesting they are intrinsically protected against ALS. Results instead suggest OMNs actively adapt to the ALS-inducing mutation.. oocyte Source GEO sample is GSM18700 Last updated (according to GEO): May 27 2005 861 Skeletal bone Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 13 hours after lights on. Original RNA code = LC11A. Source GEO sample is GSM227378 Last updated (according to GEO): Sep 10 2007 861 Femur prostate Source GEO sample is GSM203391 Last updated (according to GEO): Jun 21 2007 Fibroblasts 861 NA12248 1000 Kidney Parkinson Disease 861 f2#33 versus pool Mouse Brain tissue Spleen 1000 1633 for retinal diseases 1652 Cerebral cortex 861 Wild type inbred mice Source GEO sample is GSM83022 Last updated (according to GEO): Nov 10 2005 Stem cells 1000 Plasma 861 861 Cardiomyopathies 1000 Skeletal muscle structure of lower leg with Alzheimer's disease 27 50 brain, cortex: Sample11_e1_le1 most pertinently the striatum 1131 1160 starved 143 149 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184819 Last updated (according to GEO): Apr 26 2007 small intestine wild type mice, treated with WY14,643 for 5 days. The WY14.643 was present in the diet at 0.1% w/w. Source GEO sample is GSM124311 Last updated (according to GEO): Jun 28 2007 Sample6, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53257 Last updated (according to GEO): Jul 06 2005 brain, cerebral cortex: Rat_03-61_NroLep_Lipska_e1_le1 Ld3 Exp A, Animal #1, 50mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 50mg/kg of CPF for 96 hours Source GEO sample is GSM246141 Last updated (according to GEO): Dec 03 2007 NeverSmoker 78 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P21, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3223 Last updated (according to GEO): May 28 2005 Transitional epithelium 1000 861 Heart 10 7 Left HMEC S1 day 5 sample 2 pineal sprague1 whole tissue, pool of 5 animals, 10 weeks old, male Sprague Dawley pineal file:R3JBH02100401 Source GEO sample is GSM15193 Last updated (according to GEO): May 28 2005 Parkinson Disease 861 Carcinoma, Large Cell 867 Mice sacrificed after swimming twice a day for 3 weeks. Keywords = exercise induced hypertrophy Source GEO sample is GSM2356 Last updated (according to GEO): May 27 2005 myocardial infarction 383 403 200 184 such as epilepsy Amplified RNA from lungs of ovalbumen sensitized and challenged C3H 4 mouse vs. pool of amplified RNA from lungs of control C3H mice. Source GEO sample is GSM6741 Last updated (according to GEO): Nov 21 2005 Adenoma (SF25) 1000 Spinal Cord 1000 Descending colon B330 on Affymetrix GeneChip Human Full Length Array HuGeneFL from whole tumor 21 36 619 600 of proximal jejunum Epithelial Cells 901 of secondary brain damage 194 219 Differential gene expression in anatomical compartments of the human eye. Leukemia Promyelocytic (HL-60) [JunctionChip 4 of 5] 46 8 in docetaxel-refractory prostate cancer We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201773 Last updated (according to GEO): Jun 20 2007 BPD bronchopulmonary dysplasia 83 113 SAMR1 Hippocampus Young Sample 2 861 frontal lobe Infection 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with 2-Methyl-thio-ATP for 240min Source GEO sample is GSM5437 Last updated (according to GEO): May 27 2005 1000 Hippocampus Ta gr2 tumour Source GEO sample is GSM2521 Last updated (according to GEO): May 27 2005 9 0 rat kidney spinal cord 37 47 UBOC1 Exp A Day 14 (a) ACTH treated rep2 Spleen 0 5 LDMTX_MP-12 Contusion - 35 Day Epicenter Rep2 91 from the bone marrow 72 Brain 1000 853 Malignant Neoplasms 1000 Alzheimer's Disease Breast 861 Ovarian_Tumor_Endometrioid_CHTN-OE-023 CNS-RM_Mod7d-3B-s2 Sprague-Dawley Female HighSalt OuterMedulla rat704 sd_medullar_k_704r_om_070302 Expression profiling of spinal cord section (T9) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31253 Last updated (according to GEO): May 27 2005 38 21 of medulloblastoma HT29 hgu95c Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225689 Last updated (according to GEO): Nov 05 2007 7 cerebral cortex 21 40 29 from kidneys from progenitor satellite cells 36 66 KT1001d_CAN Gene expression data from postmorten brain regions Source GEO sample is GSM145564 Last updated (according to GEO): Nov 20 2006 Disease Source GEO sample is GSM176044 Last updated (according to GEO): Apr 09 2007 Chronic Lymphocytic Leukemia 19 47 2nd 2hr C-CA1 Abdominal aorta collected during autopsy within 24 hours post mortem Source GEO sample is GSM170564 Last updated (according to GEO): Jul 26 2007 cy5:SHR control, biological rep 1r; cy3:pool of 6 WKY control rats Plasma 861 15 0 human cerebellum 1037 of transitional epithelium 1012 Lung 861 Acetaminophen 24hr Rat 2344 blood vs. Acetaminophen 24hr Rat Pooled Control blood Oat cell carcinoma 867 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211311 Last updated (according to GEO): Jul 18 2007 ESE_N_664 901 Nervous system structure /6J mouse periaqueductal gray 29 57 Abdomen 861 Ion channel splice array data from cerebellum brain tissue samples collected from control (non Alzheimer's disease) subjects. Last Updated (by provider): Jan 22 2007 Contributers: David B Goldstein Erin L Heinzen Liver Test (Blinded) Sample Source GEO sample is GSM130121 Last updated (according to GEO): Sep 18 2007 n/a Source GEO sample is GSM177997 Last updated (according to GEO): Jun 11 2007 Basal- 0 5 PLACENTA Source GEO sample is GSM18808 Last updated (according to GEO): Sep 25 2006 To understand the commitment of the genome to nervous system differentiation and function, we sought to compare nervous system gene expression to that of a wide variety of other tissues by gene expression database construction and mining. Gene expression profiles of 10 different adult nervous tissues were compared with that of 72 other tissues. Using ANOVA, we identified 1,361 genes whose expression was higher in the nervous system than other organs and, separately, 600 genes whose expression was at least threefold higher in one or more regions of the nervous system compared with their median expression across all organs. Of the 600 genes, 381 overlapped with the 1,361-gene list. Limited in situ gene expression analysis confirmed that identified genes did represent nervous system-enriched gene expression, and we therefore sought to evaluate the validity and significance of these top-ranked nervous system genes using known gene literature and gene ontology categorization criteria. Diverse functional categories were present in the 381 genes, including genes involved in intracellular signaling, cytoskeleton structure and function, enzymes, RNA metabolism and transcription, membrane proteins, as well as cell differentiation, death, proliferation, and division. We searched existing public sites and identified 110 known genes related to mental retardation, neurological disease, and neurodegeneration. Twenty-one of the 381 genes were within the 110-gene list, compared with a random expectation of 5. This suggests that the 381 genes provide a candidate set for further analyses in neurological and psychiatric disease studies and that as a field, we are as yet, far from a large-scale understanding of the genes that are critical for nervous system structure and function. Together, our data indicate the power of profiling an individual biologic system in a multisystem context to gain insight into the genomic basis of its structure and function. Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202674 Last updated (according to GEO): Jun 20 2007 GSE3087 PCA-45 on UMich-10k Lymphoblastoid Cell Line for Individual 8116.4 log phase GSE400 Neoplasm 861 Breast 861 584 558 from articular chondrocytes Dark rearing, biological rep1 CHB DR-1 of mouse brain 9 23 D11 0h Media Spinal Cord 5 Normal 1000 Brain Neoplasm 861 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160209 Last updated (according to GEO): Feb 08 2007 Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics. 901 frontal lobe of 2182 tumor 50 62 Brain 1000 5 0 brain CNS-SC_InjA24h-4C-s2 Lipids 1000 Temporal Cortex Control (mTLE) 8 no additional Source GEO sample is GSM199280 Last updated (according to GEO): Jun 08 2007 1000 Obesity 861 Muscle Cerebral cortex 861 A2780_control_2h Multiple Myeloma 861 861 Infection Replicate1_Voxel F9 Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep4 Cerebral cortex 1000 Lymphoblastoid Cell Line for Individual 8081.3 log phase N3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Blood Test (Blinded) Sample Source GEO sample is GSM130029 Last updated (according to GEO): Sep 18 2007 40 16 in human optic nerve head MGMH030401094Apreoptic GM12156 G42-LGN replicate3 Skeletal bone 861 41 29 Control blood Organ 966 Tongue Superior With Papillae 3 Normal 15 0 human cerebellum in blood 16 23 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114413 Last updated (according to GEO): Jun 16 2006 Communicable Diseases 901 Gene expression data from male mice. Source GEO sample is GSM115536 Last updated (according to GEO): Jun 13 2007 1000 Aorta C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 1hr after experimental mice received their last shock treatment. Source GEO sample is GSM4510 Last updated (according to GEO): May 27 2005 to lymph node metastasis 612 635 Spleen vs Bombesin Treated B cell 120min (set2) Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132555 Last updated (according to GEO): Feb 26 2007 Medulla Oblongata 861 To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18428 Last updated (according to GEO): May 27 2005 Cerebral cortex 1000 to psychosis 673 685 CNS-SMTC_Ctr3mo-1C-s2 861 Cancer of Neck PBMCs-Type 2 Diabetes-T2D_8_New total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells cultured for 120min Source GEO sample is GSM5846 Last updated (according to GEO): May 27 2005 Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells 861 Ribosomal RNA 7 cerebral cortex 21 858 Mesodermal cell 19 0 Head and neck cancer ER negative human primary breast tumor EA02014_41291_H133A_JA-1939 Islet Source GEO sample is GSM18820 Last updated (according to GEO): Sep 25 2006 Expression data with no treatment Source GEO sample is GSM230907 Last updated (according to GEO): Sep 20 2007 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16369.gif Source GEO sample is GSM91533 Last updated (according to GEO): Sep 22 2006 Epithelium 861 Neoplasm Metastasis 1000 DIF 2, chip MOE430A 1478 1471 cancers Gene expression data from retinas of two young SAMP8/Ta mice Source GEO sample is GSM143740 Last updated (according to GEO): Jan 24 2007 Primary tumor 19 32 BAL_45b_A2B0 Early secretory endometrium from patient with endometriosis Source GEO sample is GSM150204 Last updated (according to GEO): Dec 14 2006 Spleen vs Neuropeptide Y Treated B cell 120min (set3) SCLC cell line SBC-3 Source GEO sample is GSM17313 Last updated (according to GEO): May 28 2005 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228616 Last updated (according to GEO): Sep 11 2007 D2_Control_ZT 6_2 n/a Source GEO sample is GSM177929 Last updated (according to GEO): Jun 11 2007 Euploid sample 4 (cerebrum) bone marrow-CD34 Source GEO sample is GSM18886 Last updated (according to GEO): Sep 25 2006 Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM Source GEO sample is GSM207679 Last updated (according to GEO): Jul 09 2007 post HCMV infection 17 35 Control gray matter 3 Heart 1000 Nrl ko samples were compared to wt at postnatal 10. Source GEO sample is GSM227461 Last updated (according to GEO): Sep 07 2007 of coronary artery disease 258 284 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114228 Last updated (according to GEO): Jun 16 2006 HapMap JPT Female Source GEO sample is GSM159620 Last updated (according to GEO): Feb 01 2007 GSE3791.2 trigeminal_ganglia_4 Source GEO sample is GSM80878 Last updated (according to GEO): Mar 31 2006 1000 Pulmonary alveolar structure Untreated versus treated (bortezomib), untranformed MCF10A and Transformed (see Adler et al, Nature Gen. 2006) Source GEO sample is GSM120277 Last updated (according to GEO): Jul 20 2006 Neostriatum 1000 cerebral cortex 7 21 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11490 Last updated (according to GEO): May 28 2005 with autism spectrum disorder 37 65 no_pre_no_restimulation_rep_C Average value of triplicate experiments of brain neurospheres of WT (wild type) mice (postnatal day 0). The cRNAs for hybridization were generated by one round RNA amplification. Source GEO sample is GSM9243 Last updated (according to GEO): May 27 2005 CNS-SC_InjA4h-1B-s2 861 Muscle cerebral_cortex_2 Source GEO sample is GSM80651 Last updated (according to GEO): Mar 31 2006 Skeletal bone 861 Plasma 861 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b059 Source GEO sample is GSM2012 Last updated (according to GEO): Nov 21 2005 M_U133A_3_AnCg Day 1_H_+RA_Achip Kidney CR-5B Spleen 1000 UBOC1 Exp A Day 7 (a) 1000 Rectum 15 0 human cerebellum 901 Caudate nucleus structure 1000 Amygdaloid structure 197 176 with coxsackievirus B3 Gene expression data from postmorten brain regions Source GEO sample is GSM145581 Last updated (according to GEO): Nov 20 2006 6 0 Mammary GM10851_technical_rep_2 Neoplasm 861 cortex 1674 1679 OVCAR-3 hgu95b ovarian tumor: serous Source GEO sample is GSM139444 Last updated (according to GEO): Apr 09 2007 "Sample 46, <5 yr survival(42 months) age 44 erp no" on vantveer-oligo of mouse brain 9 23 091261 Pool2(3tissues) on Affymetrix GeneChip Human Full Length Array HuGeneFL Expression profiling of spinal cord section (T9) extracted from rats 7d following severe injury Lot batch = Source GEO sample is GSM7598 Last updated (according to GEO): May 28 2005 CNS-SpinalCsev-Adult-14d-3C-s2 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68141 Last updated (according to GEO): Jul 07 2006 1000 pars nervosa of hypophysis khatua-astrocytoma 861 Ganglia 1000 Pancreas Gene expression data from postmorten brain regions Source GEO sample is GSM144897 Last updated (according to GEO): Nov 20 2006 Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 2431 blood Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8406.gif Source GEO sample is GSM76417 Last updated (according to GEO): Sep 22 2006 Normal Source GEO sample is GSM176243 Last updated (according to GEO): Apr 09 2007 861 Basal Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18930.gif Source GEO sample is GSM84135 Last updated (according to GEO): Sep 22 2006 NA18624 1000 Brain Neonatal (P0) whole brain mRNA from 40,XX female C57BL/6J x C3H/Paf Source GEO sample is GSM27459 Last updated (according to GEO): May 27 2005 Neoplasm 861 58 17 heterogeneous intracranial glial neoplasms Cervix carcinoma 1000 Female 24.4 yr after antibody enrichment scan 2 (U133A) ventral spinal cord 13 31 Callosal Neurons P3 2 KM12 hgu95a 20 0 human caudate nucleus brain, hippocampus: Ctr-24h-P15-III_e1_le1 5 0 Spleen Epithelium 861 S462_Mock_2 Job's patient Source GEO sample is GSM211036 Last updated (according to GEO): Sep 10 2007 Neoplasm 861 1000 Hypertrophic Cardiomyopathy Liver Test (Blinded) Sample Source GEO sample is GSM130072 Last updated (according to GEO): Sep 18 2007 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68242 Last updated (according to GEO): Jul 07 2006 from liver 21 30 brain, ipsi HC: Trizol Extraction24_le1 We investigated the molecular basis of progressive diabetic renal injury in db/db mice by profiling kidney gene expression. Using high-density microarrays, we identified 482 RNA transcripts differentially expressed in 8-wk db/db vs. nondiabetic db/m kidneys, a time characterized by hyperglycemia but by little renal histopathology. By 16 wk significant mesangial expansion had developed. Sixteen-week db/db kidneys differentially expressed 639 RNA transcripts. Diabetic kidneys specifically expressed several genes normally found in adipocytes, including adipocyte differentiation-regulated protein (ADRP; or adipophilin in humans). ADRP mRNA was specifically upregulated 5.4-fold in 16-wk db/db kidneys. This finding was confirmed at the protein level by Western blotting, and immunohistochemistry localized ADRP diffusely to tubular epithelium throughout the cortex. ADRP is a perilipin family protein that forms lipid storage vesicles and controls triglyceride utilization; we showed that accumulation of lipid storage droplets correlated with the magnitude and localization of ADRP in db/db kidneys. Other genes involved in lipid transport, oxidation, and storage were differentially regulated in db/db kidneys, and peroxisome proliferator-activated receptor-alpha (PPAR alpha) has been shown to regulate their expression in adipocytes. In our experiments, PPAR alpha mRNA was elevated in db/db diabetic kidneys, and PPAR alpha protein was upregulated in glomeruli, cortical tubules, and renal arterial vessels of db/db mice. In conclusion, these studies furnish new RNA-based data for mechanistic investigation into renal injury in the diabetic kidney and identify a switch of kidney phenotype in favor of lipid accumulation in diabetic kidney. NCI60.13_LABEL16EXTRACT15SUB3 Source GEO sample is GSM134058 Last updated (according to GEO): Aug 06 2007 Temporal Lobe 3 Normal 40 21 from dorsal pancreas Acetaminophen 3hr Rat 0613 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 23.75 hours after lights on. Original RNA code = LC54A. Source GEO sample is GSM227382 Last updated (according to GEO): Sep 10 2007 UET-13TR-EWS/ERG 24hr 1640 1628 in the retina total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Insulin-like growth factor 1 for 240min Source GEO sample is GSM5624 Last updated (according to GEO): May 27 2005 mRNA was isolated after 48 hours of incubation from IMR-90 cells seeded onto a collagen/chondroitin sulfate tissue engineering scaffold mesh material. Cells were seeded at a density of 1 x 10^6 cells/ mesh, and this chip represents a pooling of cells from 4 meshes. Keywords = tissue engineering mesh, collagen, chondroitin sulfate, biomaterials design Source GEO sample is GSM6055 Last updated (according to GEO): May 27 2005 861 Liver brain, brainstem: CB7_e1_le1 brain, hippocampus: KA-240h-P15-II_e1_le1 lateral hypothalamus 25 45 861 Cochlear structure 19 0 Head and neck cancer substantia_nigra_2 Source GEO sample is GSM80831 Last updated (according to GEO): Mar 31 2006 Gene expression data from UET-13TR-EWS/FLI1 cells incubated in the absence of tetracycline for 48 hours Source GEO sample is GSM214919 Last updated (according to GEO): Aug 02 2007 infection 410 419 1000 Muscle 7 cerebral cortex 21 innervated tibialis anterior muscles from runx1f/- control mice Treatment, type=add, description=runx1f/- Source GEO sample is GSM99429 Last updated (according to GEO): Mar 08 2006 MCF10A_Treated_#6 Cerebellum 1000 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211304 Last updated (according to GEO): Jul 18 2007 G7 cornea The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160218 Last updated (according to GEO): Feb 08 2007 trachea_2 Source GEO sample is GSM80887 Last updated (according to GEO): Mar 31 2006 Expression profiling of spinal cord section (T9) extracted from rats 7d following laminectomy (sham) Lot batch = Source GEO sample is GSM1336 Last updated (according to GEO): May 28 2005 days nasal epithelium 1126 1147 DLCL-0002 HMEC X HMEC+Interferon alpha 24hrs IGF1 and IGF1 receptors (IGF1R) are present in the adult heart and have been shown to be essential for myocardial performance. Insulin-like growth factor 1 (IGF1) is produced in numerous tissues particularly by the liver in response to growth hormone stimulation and is an important factor in the regulation of post-natal growth and development. We have generated and characterized transgenic mice over-expressing the IGF1R. We crossed IGF1R transgenic mice with dominant negative (dn)PI3K (p110) and with constitutively active (ca)PI3K(p110) transgenic mice. Expression profiling was performed on the ventricles of IGF1R, IGF1R-caPI3K, IGF1R-dnPI3K, caPI3K, dnPI3K transgenic female mice at 3 months of age. Non-transgenic littermates were used as controls. Keywords = insulin growth factor, IGF, cardiac, hypertrophy Source GEO sample is GSM18364 Last updated (according to GEO): May 27 2005 Simple annotation: RNA coimmunoprecipitation, development Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/9244.gif Source GEO sample is GSM78469 Last updated (according to GEO): Sep 22 2006 361 335 hypertrophic cardiomyopathy 1000 Spleen of regenerating Dorsal Root Ganglia 21 55 Pool Eu_P15_hyb2 15 7 brainstem Expression profiling of spinal cord section (T8) extracted from rats 24h following severe injury Source GEO sample is GSM31469 Last updated (according to GEO): May 27 2005 a7 Heart Atrium 1000 Fibroblasts 861 26 11 /Ovary-Disease 3 MCF7 human breast cancer cells treated with DMSO and used as a control in a 2 platform, three replicate experiment Source GEO sample is GSM188020 Last updated (according to GEO): May 11 2007 17 0 Multiple sclerosis CNS-SCsev_InjB4h-4A-s2 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc106 Source GEO sample is GSM1889 Last updated (according to GEO): Nov 21 2005 86 70 Fetal liver cells 1000 Retina Kidney 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145940 Last updated (according to GEO): Nov 20 2006 CNS-SCsev_InjA24h-4B-s2 olfactory epithelium 194 213 Cells were either prestimulated (1_X) or not (0_X) for 18h with 100 ng/ml LPS. Media was exchanged and after 2h rest, cells either restimulated (X_1) or not (X_0) with again 100 ng/ml LPS. This resulted in 4 experimental conditions: 0_0, 0_1, 1_0 and 1_1. There were 3 biological replicates done, resulting in 12 arrays altogether. Source GEO sample is GSM213699 Last updated (according to GEO): Aug 01 2007 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120688 Last updated (according to GEO): May 14 2007 JejuPrxTumor2022JAFBY_jtc.txt Brain 861 Background. Nuclear factor I-A (NFI-A), a phylogenetically conserved transcription/replication protein, plays a crucial role in mouse brain development. Previous studies showed that disruption of the Nfia gene in mice leads to perinatal lethality, corpus callosum agenesis, and hydrocephalus. Results. To identify potential NFI-A target genes involved in the observed tissue malformations, we analyzed gene expression in brains from NFI-A-deficient and wild-type littermate control mice at the mRNA level using oligonucleotide microarrays. In young postnatal animals (P16), 356 genes were detected as differentially regulated, whereas at the late embryonic stage (E18), only 5 dysregulated genes were found. An in silico analysis identified phylogenetically conserved NFI binding sites in at least 70 of the differentially regulated genes. Moreover, assignment of gene function showed that marker genes for immature neural cells and neural precursors were expressed at elevated levels in young postnatal NFI-A mutants. By contrast, marker genes for differentiated neural cells were down-regulated at this stage. In particular, genes relevant for oligodendrocyte differentiation were affected. Conclusions. Our results suggest that a delay in early postnatal development, especially oligodendrocyte maturation, is exhibited by NFI-A knock-out mice, and at least partly accounts for their phenotype. The identification of potential NFI-A target genes by our study should both help to elucidate NFI-A-dependent transcriptional pathways and contribute to a better understanding of this period of brain formation, especially with regard to the function of NFI-A. Material and method Animals NFI-A-deficient mice were bred and maintained as described [20]. Animals were sacrificed by CO2 at embryonic stage E18.5 (E18) or postnatal day 16 (P16). Brains were dissected and snap frozen in liquid nitrogen. The respective KO and WT animals used for analysis at E18 and P16 were littermates. Only male mice were used. All of the animals were F1 hybrids of C57Bl/6 and 129S6 animals. Within these matings, males had a B6 and females had a 129S6 background. In a large scale test, 38.5% of the offspring survive until P30 using this kind of mating. In purebred B6, we observed 0% survival at P1 (R.M.G., unpublished observations). All animal use was performed under the approved protocol BCH05082N (RMG) of the University at Buffalo Institutional Animal Care and Use Committee in the UB Laboratory Animal Facility, an AAALAC licensed facility. RNA preparation Total RNA was extracted from the entire brain of NF-I-A-deficient and wild-type control mice (n=3 each) using TRIzol (Invitrogen) according to the manufacturer?s instructions. Further purification of RNA was performed with the RNeasy Mini Kit (Qiagen). Total RNA concentration was determined using a spectrophotometer at 260 nm and 280 nm wavelength. To check RNA integrity, total RNA was separated in a 1% agarose gel containing formaldehyde, and the intensity ratio of 28S and 18S ribosomal RNA bands was assessed after ethidium bromide staining. Microarray hybridization and signal detection Procedures for cDNA synthesis, labeling and hybridization were carried out according to the manufacturer's protocol (Affymetrix). All experiments were performed using Affymetrix mouse genome Genechip U74A version 2. Briefly, 15mg of total RNA were used for first strand cDNA synthesis with an HPLC-purified T7-(dT)24 primer. Synthesis of biotin-labeled cRNA was carried out using the ENZO RNA transcript labeling kit (Affymetrix). For hybridization, 15 µg of fragmented cRNA were incubated with the chip in 200 µl of hybridization solution in Hybridization Oven 640 (Affymetrix) at 45oC for 16 hours. Genechips were washed and stained with streptavidin-phycoerythrin using the microfluidic workstation? (Affymetrix) and scanned with a laser scanner (Agilent Technologies). Microarray quantification and statistical analysis Quality controls were performed using Affymetrix Microarray Suite 5.0 (MAS 5.0) software. Data and statistical analysis and data visualization were performed with GeneSpring? (Agilent Technologies). Expression values were extracted from the CEL file, and imported to GeneSpring using Robust Multi-array Average (RMA) for further analysis [24]. Two criteria were used to select for significant changes in gene expression. First, probe sets with less than 1.2 fold change comparing the KO to WT (control) were removed in order to reduce the number of genes undergoing statistical analysis. Second, genes were then tested statistically for significant changes in all three wild-type or NFI-A-deficient samples, using Student's t-test. Finally, genes were grouped based on their biological function using Affymetrix NetAffx, and NCBI Locuslink. Last Updated (by provider): Jan 22 2007 Contributers: Thomas Streichert Melitta Schachner Yongwee Wong Thomas Tilling Richard M Gronostajski We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201806 Last updated (according to GEO): Jun 20 2007 GBM Treatment, type=remove Source GEO sample is GSM99483 Last updated (according to GEO): Apr 21 2006 5 0 brain 7 0 Pancreas 861 Cerebellum 1000 Retina Nasal Epithelium 901 5 0 brain Gene expression evidence for remodeling of lateral hypothalamic circuitry in cocaine addiction 901 frontal lobe Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD28 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD28 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36715 Last updated (according to GEO): May 27 2005 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11232 Last updated (according to GEO): May 28 2005 1000 Cerebrovascular accident ALL-B-cell-21 on Affymetrix GeneChip Human Full Length Array HuGeneFL Brain 1000 129:4-3 + 4-4 PAG ER negative human primary breast tumor EA02014_41265_H133A_JA-1069 Tumor__Pancreas_Adeno_Pan_6T on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19223 Last updated (according to GEO): May 27 2005 1000 Brain brain, hippocampus: C72-I_e1_le1 The epithelial cells 962 981 7 cerebral cortex 21 Untreated cells. Source GEO sample is GSM203990 Last updated (according to GEO): Jun 25 2007 "27 hr Hela Double Thymidine, exp3" Normal__Whole_Brain_BRAIN_1 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Normal Source GEO sample is GSM176114 Last updated (according to GEO): Apr 09 2007 Brain 861 1000 Brain 861 Cardiomyopathies 89 68 with tricuspid valves Gene expression data from postmorten brain regions Source GEO sample is GSM145826 Last updated (according to GEO): Nov 20 2006 1000 ovarian neoplasm advanced HCC Source GEO sample is GSM155985 Last updated (according to GEO): Jun 21 2007 Immune; Lymph Node_Comprlete Freunds Adjuvant stimulated Keywords = mouse gene expression database Source GEO sample is GSM29350 Last updated (according to GEO): May 27 2005 Lymphoblastoid Cell Line for Individual 8122.4 log phase plasma cells 332 344 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151970 Last updated (according to GEO): Feb 06 2007 Non-inner ear tissues pooled from E9.5 to E10.5, replicate1 Brain 861 of coronary artery disease 258 284 4 0 Liver 41 29 Control blood Heart 1000 Epithelial Cells 1000 1000 Neuraxis 1000 Heart failure CLL-58 lung.2 at the Human Brain 743 760 Head and neck cancer Source GEO sample is GSM155656 Last updated (according to GEO): Apr 24 2007 NCI60.33_LABEL37EXTRACT36SUB3 Source GEO sample is GSM134159 Last updated (according to GEO): Aug 06 2007 861 Brain skeletal_muscle_3 1 on NHGRI-13.8k Timepoint 2r Simple annotation: RNA coimmunoprecipitation, development Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8804.gif Source GEO sample is GSM78459 Last updated (according to GEO): Sep 22 2006 CNS-SC_CtrA14d-2B-s2 853 Structure of blastomere Parkinson Disease 1000 861 Cerebral cortex Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Source GEO sample is GSM15949 Last updated (according to GEO): May 28 2005 Skeletal bone 861 brain, cerebral cortex: CO2_le1 Primary tumor 19 32 I-8_POST Mouse Kidney Female 2 Gene expression data from postmorten brain regions Source GEO sample is GSM145790 Last updated (according to GEO): Nov 20 2006 spleen 301 306 CNS-SpinalCmod-Adult-24h-2A-s2 1000 Nose Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50636.gif Developmental Stage: E6.5 Source GEO sample is GSM229814 Last updated (according to GEO): Nov 06 2007 8 0 Intestine Parkinson 0 8 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153372 Last updated (according to GEO): Dec 27 2006 the ventricular 1095 1109 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n093 Source GEO sample is GSM2075 Last updated (according to GEO): Nov 21 2005 in bronchial epithelia 311 332 P14CN1 in blood 16 23 19 0 Head and neck cancer human cerebellum Source GEO sample is GSM87182 Last updated (according to GEO): Feb 08 2006 D_U133A_30_Amy Mislabeled (was labeled Heart (interventricular septum)) [JunctionChip 2 of 5] 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14968 Last updated (according to GEO): Oct 28 2005 861 Cerebral cortex Spleen 1000 41 29 Control blood brain, cerebellum: RNA#17_le1 928 Hyperinsulinism Category: Cell-line Subcategory: Reproducibility Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp3307 Source GEO sample is GSM2137 Last updated (according to GEO): Nov 21 2005 1000 Left Neoplasm 861 nerve, HumanSuralNerve: Human Schwann cell RNA extracts 351 Passage 3_le1 Brain 861 7110_Lung did not develop PGD rat hippocampus Treatment, type=time_course, measurement=24.0 h Source GEO sample is GSM32138 Last updated (according to GEO): May 27 2005 5 0 Muscle 1000 Prostate Control 2 Benign Neoplasm 1000 Endothelial Cells 1000 Lymphoblastoid Cell Line for Individual 8132.3 log phase N-4_POST 1000 Brain Parkinson Disease 861 297 293 uteri Neoplasm 861 none Source GEO sample is GSM239859 Last updated (according to GEO): Dec 07 2007 B6_Control_ZT 6_1 TNFTG-40w-f-2 SN:1007086 Source GEO sample is GSM115367 Last updated (according to GEO): Jun 20 2006 Parkinson Disease 861 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68116 Last updated (according to GEO): Jul 07 2006 28 week Pre Natal Human lung tissue Source GEO sample is GSM107824 Last updated (according to GEO): May 04 2006 Simple annotation: Lymph node metastasis, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3953.gif Source GEO sample is GSM76453 Last updated (according to GEO): Sep 22 2006 25 0 Bipolar affective disorder 42 minus the frontal cortex 66 Gene expression data from postmorten brain regions Source GEO sample is GSM145414 Last updated (according to GEO): Nov 20 2006 plasma cells 50 61 total RNA derived from a leprosy lesion Source GEO sample is GSM6770 Last updated (according to GEO): May 27 2005 Human retinal sphere RNA-1, chip HG-U133B Medulla Oblongata 861 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113954 Last updated (according to GEO): Jun 16 2006 Universal Mouse Reference RNA Source GEO sample is GSM93434 Last updated (according to GEO): Jan 23 2006 skin 80 83 Small cell carcinoma of lung 867 B52 on NCI-7.6k Transplant Series 13 , Transplant # 3 CNS-RM_Ctr24h-2C-s2 1000 frontal lobe of the postmortem brains 675 699 129P3/J Saline treated, striatum, biological replicate 3 Source GEO sample is GSM187967 Last updated (according to GEO): Jun 14 2007 278 255 ischemic cardiomyopathy cocaine naive, lateral hypothalamus, 0 hrs/day access to cocaine Source GEO sample is GSM93837 Last updated (according to GEO): Jan 26 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM144973 Last updated (according to GEO): Nov 20 2006 73 68 livers The epithelial cells 962 981 60 45 of the Pituitary Lung 861 Ovary 1000 Cerebral cortex 1000 453 434 The descending colon Prostate [JunctionChip 4 of 5] Lymphoblastoid Cell Line for Individual 8064.3 log phase Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=780640 LaserPower=2.221.29 Lot batch = LC17N046 Source GEO sample is GSM4795 Last updated (according to GEO): Nov 21 2005 Duchenne muscular dystrophy 0 26 B220+CD25+sIg- Small Pre BII cells sorted out of mouse bone marrow, sort no. 3 Source GEO sample is GSM661 Last updated (according to GEO): Mar 20 2006 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181173 Last updated (according to GEO): Jul 12 2007 861 Cerebral cortex A study of differential gene expression in the hippocampus of CV mice (C57Bl x VM/Dk) inoculated with ME7 scrapie to determine the molecular events that accompany the scrapie-associated hippocampal neuropathology. Analysis was performed at 170 days post infection, a timepoint that coincides with severe hippocampal neuronal loss. Fibroblasts 861 5 0 Kidney CNS-SC_InjB4h-4dA-s2 Pressure-overload induced hypertrophy model. Mouse was sacrificed 4 hours after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2253 Last updated (according to GEO): May 27 2005 Skeletal bone 861 913 Coronary heart disease Fertilized egg replication 3 Keywords = preimplantation Keywords = development Source GEO sample is GSM14665 Last updated (according to GEO): May 28 2005 285_1 91 from the bone marrow 72 Cerebral cortex 1000 after infection 650 665 Heart Ventricle 1000 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153329 Last updated (according to GEO): Dec 27 2006 Gene expression changes in anti-FcgRIIb treated DCs and monocytes CNS-SpinalCmod-Adult-4h-4A-s2 7 Entorhinal Cortex 23 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2847 Source GEO sample is GSM2089 Last updated (according to GEO): Nov 21 2005 901 Caudate nucleus structure 901 Bone Marrow Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184737 Last updated (according to GEO): Apr 26 2007 861 Cerebral cortex 430A2_1945_60_control_neuropath_midbrain Source GEO sample is GSM242689 Last updated (according to GEO): Nov 15 2007 Nasal Epithelium 901 861 Cerebral cortex /NJ Frontal Cortex A 3 22 HCC (Fibrolamellar, SF13) Mesenchymal Stem Cells 1000 1000 Brain Performed by UCI Microarray Facility. Source GEO sample is GSM203200 Last updated (according to GEO): Jun 22 2007 FVB/NJ bed nucleus of the stria terminalis rep1 Probeset expression data from NA12744 growth 1 Source GEO sample is GSM201529 Last updated (according to GEO): Aug 08 2007 spinal cord 0 11 239 233 Retinas 1000 Brain 1_hypothalamus_12hrs_sleep_#18 HC55 FC BA4 B Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13125.gif Source GEO sample is GSM79637 Last updated (according to GEO): Sep 22 2006 Heart Septal Defects, Atrial 1000 853 Structure of blastomere Category: Cell-line Subcategory: Breast This experiment was an out file converted from rana. The original files were not provided to load this experiment in Oracle. Category and Subcategories were made by curators. Scanning Software: unknown Software version: unknown Lot batch = dtp3685 Source GEO sample is GSM2151 Last updated (according to GEO): Nov 21 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145596 Last updated (according to GEO): Nov 20 2006 Carcinoma 861 f2#253 versus pool Mouse Brain tissue 1000 Brain 132 with Turner syndrome 151 Gene expression data from postmorten brain regions Source GEO sample is GSM145029 Last updated (according to GEO): Nov 20 2006 28 CB B G1E_0_C 861 Neoplasm 861 Infertility Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213504 Last updated (according to GEO): Jul 31 2007 M_U133Plus_94_nAcc Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11270 Last updated (according to GEO): May 28 2005 Liver 1000 621-5 861 Brain placebo 48h, biological rep5 with some respiratory epithelium. 1039 1072 21 0 Rat vestibular ganglia HapMap CHB Female Source GEO sample is GSM159601 Last updated (according to GEO): Feb 01 2007 901 Spinal Cord WT 3 hip_1049_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Cochlea_WT_9mo_4 normal testis 54 66 Transcriptome analysis in rat Kidney; Adult Keywords = mouse gene expression database Source GEO sample is GSM29358 Last updated (according to GEO): May 27 2005 Fertilized egg replication 2 0 27 Exp 6 (-SB80) vagina_9 Source GEO sample is GSM80903 Last updated (according to GEO): Mar 31 2006 Prosencephalon 1000 adenoma 1000 861 Communicable Diseases Primary small cell lung carcinoma 2942 Source GEO sample is GSM17342 Last updated (according to GEO): May 28 2005 1000 frontal lobe 12 0 ovarian tumor 913 Dermatitis, Atopic 20 0 human caudate nucleus Gene expression data from postmorten brain regions Source GEO sample is GSM145738 Last updated (according to GEO): Nov 20 2006 none Source GEO sample is GSM239880 Last updated (according to GEO): Dec 07 2007 M_U133A_22_nAcc SN:1012368 Source GEO sample is GSM115407 Last updated (according to GEO): Jun 20 2006 of the postmortem brains 675 699 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28473 Last updated (according to GEO): May 27 2005 17 0 Trigeminal ganglia 43h-AM replication 3 Keywords = preimplantation Keywords = development Source GEO sample is GSM14712 Last updated (according to GEO): May 28 2005 1145 1134 of the brain 5 0 brain Plasma 861 Brain 1000 ALL_7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A SK-MEL-28 hgu95e Control rat 5 ventral tegmental area Source GEO sample is GSM32166 Last updated (according to GEO): May 27 2005 Brain 1000 human cerebellum Source GEO sample is GSM87086 Last updated (according to GEO): Feb 08 2006 healthy subject Source GEO sample is GSM211141 Last updated (according to GEO): Sep 10 2007 bronchial epithelia 224 243 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27738.gif Source GEO sample is GSM66571 Last updated (according to GEO): Sep 22 2006 Lymphatic Metastasis 877 218 214 liver singh-prostate osteoblast 627 637 Blood T cells;Adult Naive CD4+ I+P Stimulated in fibroblasts 1222 1236 Communicable Diseases 1000 Kidney 1000 GBM Treatment, type=remove Source GEO sample is GSM99541 Last updated (according to GEO): Apr 21 2006 KT12b_AR2/DT/IN Gene expression data from postmorten brain regions Source GEO sample is GSM145637 Last updated (according to GEO): Nov 20 2006 kidney 37 43 74 52 for prostate malignancy Infection 861 Heart Septal Defects 884 M_U133A_32_HC Gene expression data from postmorten brain regions Source GEO sample is GSM145962 Last updated (according to GEO): Nov 20 2006 M_U133A_47_DLPFC cerebellum 7 16 92 38 of nicotinic acetylcholine receptor subunit mutant mice Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 23 hours after lights on. Original RNA code = LC17A. Source GEO sample is GSM227370 Last updated (according to GEO): Sep 10 2007 SN:1006527 Source GEO sample is GSM115347 Last updated (according to GEO): Jun 20 2006 Lymphoblastoid Cell Line for Individual 8111.3 log phase AD-163t1-A203-8 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 901 Coronary artery Skeletal muscle structure 1000 Medulla Oblongata 861 amygdala wistar 3722 whole tissue, individual animal, 10 weeks old, male Wistar amygdala file:p3720w Source GEO sample is GSM15121 Last updated (according to GEO): Oct 28 2005 Normal Source GEO sample is GSM176173 Last updated (according to GEO): Apr 09 2007 5 0 brain total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with NGF (Nerve Growth Factor) for 120min Source GEO sample is GSM5705 Last updated (according to GEO): May 27 2005 BALB-c mice were given intratracheal bleomycin (1.5U per kg). Lungs were frozen at 24hr 72hr 10d 14d Lot batch = Source GEO sample is GSM4149 Last updated (according to GEO): May 28 2005 healthy subject Source GEO sample is GSM211033 Last updated (according to GEO): Sep 10 2007 Kidney 1000 MGMH030312016Akidney mouse brain contralateral LPS.RU486, biological rep4 corticosterone_treated_rep5 (06SE462) plasma cells 50 61 Brain 1000 2737 tumor cells 2747 988 980 cerebella brain, Right Temporal Parietal: Extract83_le1 Heart 1000 12 0 Blood B cells 861 Bladder Communicable Diseases 1000 with myocardial infarction 312 338 D_U133A_40_DLPFC NA18973 KT25b_AR2 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225961 Last updated (according to GEO): Nov 02 2007 into generalized convulsive seizures 188 223 Prostate 17 Disease Thymus Gland 1000 1000 Cerebral cortex brain 0 5 78 66 Control blood 5 0 brain 861 Cardiomyopathies GSE343 Gene expression data from liver Source GEO sample is GSM243384 Last updated (according to GEO): Nov 16 2007 1164 1158 histone 3519 3502 denervated muscles Vulva 3 Normal 32 16 of organ of Corti Large-scale analysis of the human transcriptome. CD34+THY+ hematopoietic stem cells, GCSF-treated patients Source: Internal GNF, mail mcooke@gnf.org Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 134.39 Stdv: 6.08 Min: 119.69 Max: 144.12 Source GEO sample is GSM2840 Last updated (according to GEO): Mar 20 2006 Brain 1000 PAX sample 10 1000 Brain Large cell neuroendocrine carcinoma 901 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15720 Last updated (according to GEO): May 28 2005 CUTLL1 DMSO control 24h rep2 861 Carcinoma periaqueductal gray 130 149 brain, Superior Frontal Gyrus: Sample57_e1_le1 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26624.gif Source GEO sample is GSM81549 Last updated (according to GEO): Sep 22 2006 Lymphoblastoid Cell Line for Individual 8172.5 log phase CAD_replicate62 of the colon 28 39 901 Malignant neoplasm of prostate BrnD2_0227ACHJ.txt Normal Source GEO sample is GSM176433 Last updated (according to GEO): Apr 09 2007 Heart failure 1000 frontal_lobe_5 B220Low sIgM+ immature B cells sorted out of mouse bone marrow, sort no. 11 Source GEO sample is GSM638 Last updated (according to GEO): May 27 2005 olfactory epithelium 194 213 1000 Hair follicle structure 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114470 Last updated (according to GEO): Jun 16 2006 861 Branch Parkinson 0 8 HDMTX-DX-12 none Source GEO sample is GSM123246 Last updated (according to GEO): Jul 26 2006 6 0 Cancers Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68223 Last updated (according to GEO): Jul 07 2006 H9RGV99031201 Brain 1000 Control frontal cortex 6 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53472 Last updated (according to GEO): Jul 06 2005 brain, unknown: C2A_e1_le1 Aorta 1000 Bone Marrow 1000 901 Caudate nucleus structure It has been shown that dexamethasone (Dex) impairs the normal lung septation that occurs in the early postnatal period. Treatment with retinoic acid (ATRA) abrogates the effects of Dex. To understand the molecular basis for the Dex indiced inhibition of the formation of the alveoli and the ability of ATRA to prevent the inhibition of septation, gene expression was analyzed in 4-day old mice treated with diluent (control), Dex-treated and ATRA+Dex-treated.. Date GSE484 Last Updated: Aug 24 2005 Contributers: Linda Clerch Includes GDS250. Update date: Jun 27 2003. Dataset description GDS250: Analysis of how dexamethasone (DEX) inhibits normal lung septation and alveoli formation, and mechanism by which retinoic acid (ATRA) protects against DEX. Three day old mice treated with ATRA or control. On day 4, half of each group administered DEX.. PHG-LTM-1bAv2-s2 Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell 30min (set3) 20 0 human caudate nucleus 7 0 Prostate GBM Treatment, type=remove Source GEO sample is GSM99468 Last updated (according to GEO): Apr 21 2006 1000 Brain NCI60.27_LABEL31EXTRACT30SUB3 Source GEO sample is GSM134127 Last updated (according to GEO): Aug 06 2007 Bone Marrow 1000 1000 Adrenal Medulla Muscle Source GEO sample is GSM4289 Last updated (according to GEO): May 27 2005 513 500 in leg muscle throughout the lung 132 150 Cerebral cortex 861 "Sample 31,>5 yr survival(153 months) age 52 erp yes" on vantveer-oligo Pancreas [JunctionChip 5 of 5] Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28784 Last updated (according to GEO): May 27 2005 C57/BL6 to C57/BL6 Balb/c to C57/BL6 Balb/c to C57/BL6 with anti CD80/86 mAb Identificaton of gene expression profile in tolerizing murine cardiac allograft by co-stimulatory blockade. The induction of specific tolerance would be the ultimate achievement in transplant immunology, but the precise mechanisms of immunological tolerance remain largely unknown. Here, we investigated global gene expression analysis in tolerizing murine cardiac allografts by means of oligonucleotide microarrays. Tolerance induction was achieved in cardiac allografts from BALB/c to C57BL/6 mice by daily intraperitoneal injection of anti-CD80 and CD86 mAbs. Comparative analysis revealed 64 genes to be induced more extensively in the tolerizing than in the syngeneic isografts, and 16 genes than in the rejecting allografts. Two genes were specifically upregulated in the tolerizing allografts. In the tolerizing allografts there were induced marked expressions of a number of genes for proinflammatory factors, including interferon-gamma inducible cytokines and chemokines, as well as apoptosis-related genes which were also upregulated in the rejecting allografts. Moreover, these gene expression patterns continued to be upregulated more than 70 days post transplant. These results provide evidence that immunological tolerance can be induced and maintained in the presence of prominent proinflammatory gene expression in vivo.. Date GSE582 Last Updated: Jun 15 2005 Contributers: M Sata K Naruse T Kodama T Hamakubo S Ihara H Aburatani T Kohro A Saiura H Yagita Y Sugawara C Mataki T Yamaguchi A Izumi T Sakihama M Makuuchi Y Matsui T Minami Includes GDS437. Update date: Nov 26 2003. Dataset description GDS437: Examination of immunologic tolerance induction achieved in cardiac allografts from BALB/c to C57BL/6 mice by daily intraperitoneal injection of anti-CD80 and anti-CD86 monoclonal antibodies (mAbs).. 5 0 brain Ganglia, Spinal 923 ATCC number CRL-1502 Source GEO sample is GSM6812 Last updated (according to GEO): May 27 2005 1000 Coronary Arteriosclerosis Cerebral cortex 1000 M_U133A_75_HC 352 347 brain 1000 Schizophrenia brain, Right Cerebellum: Extract53_le2 brain_OFC_bipolar B_mr384 26 15 endometrioid 16 0 Mitochondrial DNA Alzheimer's Disease 1000 1000 Left Arteries 861 NCI60.33_LABEL37EXTRACT36SUB3 Source GEO sample is GSM134155 Last updated (according to GEO): Aug 06 2007 Myocardial Infarction 1000 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201278 Last updated (according to GEO): Jun 14 2007 Spleen 0 5 1000 Hypertrophic Cardiomyopathy 1000 Ischemia VDXGUYU_4062 Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 72h. Lot batch = Source GEO sample is GSM1255 Last updated (according to GEO): May 28 2005 Ovary 1000 V5-P084 1684 1673 in glaucoma Astrocytoma 861 861 Cerebral cortex Fibroblasts 1000 no additional Source GEO sample is GSM199389 Last updated (according to GEO): Jun 08 2007 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15751 Last updated (according to GEO): May 28 2005 Normal Source GEO sample is GSM175878 Last updated (according to GEO): Apr 09 2007 NG108 rat neuronal cell culture exposed to 0.25% DMSO (control) for two hours. 10 µg total RNA hybridized per chip. RNA STAT 60 used to extract RNA. Standard Affymetrix chip scaling factors used. No other data transformation. Source GEO sample is GSM1655 Last updated (according to GEO): Oct 28 2005 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12360 Last updated (according to GEO): May 28 2005 healthy subject Source GEO sample is GSM211013 Last updated (according to GEO): Sep 10 2007 Nasal Epithelium 865 17 7 hippocampus mouse brain 478 489 1100 1087 heart failure Heart Septal Defects, Atrial 1000 1000 Structure of parenchyma of lung Sham infected HIGK cells, biological rep1 Parkinson's disease sample x188 0 30 brain 0 5 starved 41 47 none Source GEO sample is GSM210321 Last updated (according to GEO): Jul 16 2007 Neoplasm 861 gene expression of 3 day LIF differentiated ESCs Source GEO sample is GSM181951 Last updated (according to GEO): Apr 12 2007 E10.5 craniofacial tissue, first branchial arch: WT_MNA-1_e1_le1 Parietal Lobe 1 Normal Gene expression data from postmorten brain regions Source GEO sample is GSM144939 Last updated (according to GEO): Nov 20 2006 Brain 861 brain 0 5 Brain 861 Liver Test (Blinded) Sample Source GEO sample is GSM130130 Last updated (according to GEO): Sep 18 2007 Muscle Source GEO sample is GSM4281 Last updated (according to GEO): May 27 2005 nostrils 156 164 Cerebral cortex 861 Heart 1000 brain, Left Parietal Lobe: Extract41_le1 Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35376 Last updated (according to GEO): May 27 2005 1000 Hippocampus 983 Breast Carcinoma Brain 861 901 Temporal Lobe 861 Heart failure of mouse brain 9 23 861 Neoplasm Myocardial Infarction 1000 HepG2 0h 1 Control Plasma 861 2 hrs Post-clamp sample 5 36 21 from whole brain Acetaminophen 24hr Rat 0685 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool Interatrial septum 865 858 Mesodermal cell A/OVX/P4/6h/UTX 129/SvImJ WT 28 22 starved CCAT Full Length Rep A1 Spleen 0 5 Spleen vs Untreated B cell Time 0 (set27) Tissue homogenate from cingulate cortex from G42 mouse (Ref. Pubmed:15509747 ). Source GEO sample is GSM64191 Last updated (according to GEO): Dec 01 2005 ISR2 Parkinson Disease 861 of the stria terminalis rep1 16 43 brain, hippocampus: Sample19_e1_le1 Blood Test (Blinded) Sample Source GEO sample is GSM130001 Last updated (according to GEO): Sep 18 2007 Lymphoblastoid Cell Line for Individual 8171.4 log phase Acetaminophen (APAP) Rat Blood Test Gene Expression Data Set 135 99 in peripheral blood mononuclear cells Brain_Adult_LPSip_4hr_mouse3 (YL3_#66) Gene expression data from older female during 1 week of inadequate protein intake Source GEO sample is GSM209822 Last updated (according to GEO): Jul 11 2007 22 hr Hela Double Thymidine, exp2 WGACON-105 in human abdominal aortic aneurysms 81 116 Collagen 1000 (SCLC 367 371 Neoplasm 861 total RNA from biosource CC#3S Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92471 Last updated (according to GEO): Jan 13 2006 Ovary Primary tumor 19 32 Brain 861 tongue_superior_part_w/_papillae_1 Source GEO sample is GSM80882 Last updated (according to GEO): Mar 31 2006 primary lung adenocarcinomas 774 801 Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242069 Last updated (according to GEO): Dec 04 2007 brain, cerebral cortex: Rat_03-19_NroLep_Lipska_e1_le1 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12970.gif Source GEO sample is GSM79796 Last updated (according to GEO): Sep 22 2006 Muscular Dystrophies 861 1000 Endometriosis, site unspecified 861 Intestines D1_TP-0_C 7 0 prostate M_U133A_111_DLPFC ATCC number CRL-1502 Source GEO sample is GSM6802 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145374 Last updated (according to GEO): Nov 20 2006 923 Congestive heart failure 1000 Hippocampus of mouse brain 9 23 no additional Source GEO sample is GSM199252 Last updated (according to GEO): Jun 08 2007 of the postmortem brains 675 699 the ventricular 1095 1109 human cerebellum Source GEO sample is GSM87133 Last updated (according to GEO): Feb 08 2006 861 Brain Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13135.gif Source GEO sample is GSM79655 Last updated (according to GEO): Sep 22 2006 cortex rattus_norvegicus_strain iP animal_number 5 from nose 98 106 MGMH030312028Bskeletalmuscle Infection 1000 Heart 861 858 Mesodermal cell Human skeletal muscle 0 20 f2#42 versus pool Mouse Brain tissue 1000 Heart failure Gene expression data from mouse brain infected with GNPs infected with retroviruses that express Cyclin D1 Source GEO sample is GSM148582 Last updated (according to GEO): Mar 14 2007 HUVECs (human umbilical cord vein endothelial cells) are treated with the angiogenic factors VEGF-A (vascular endothelial growth factor-A) and PlGF (placental growth factor) in low or high serum media.. Date GSE837 Last Updated: May 29 2005 Includes GDS495. Update date: Mar 01 2004. Dataset description GDS495: Temporal analysis of human umbilical cord vein endothelial cell (HUVEC) isolates treated with angiogenic factors vascular endothelial growth factor-A (VEGF-A) and placental growth factor (PlGF) in low or high serum media.. Expression profile of genes in mouse brain Source GEO sample is GSM21040 Last updated (according to GEO): May 27 2005 brain, retina: 3 Retina at ZT 12_e1_le1 nostrils 156 164 Aorta 1000 T2+ gr3 tumour Source GEO sample is GSM2538 Last updated (according to GEO): Mar 21 2006 AKR/J Basal Ganglia F Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15725 Last updated (according to GEO): May 28 2005 brain 0 5 Tenascin 1000 1000 Prostate collagen 302 310 5 0 brain lung_1 Source GEO sample is GSM80710 Last updated (according to GEO): Mar 31 2006 Mouse Ovary 1 Y HID D077 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108636 Last updated (according to GEO): Aug 22 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with BLC for 60min Source GEO sample is GSM5467 Last updated (according to GEO): May 27 2005 ko mouse number 2 Source GEO sample is GSM187134 Last updated (according to GEO): Jun 11 2007 5 0 brain Oat cell carcinoma 867 Saccule at E14.5, replicate2 1933 tumor cells 1943 from nose 102 110 OVCAR-5_CL6003_OVARIAN RST-PVH_2 91 from the bone marrow 72 Affymetrix GeneChip® Mouse Genome 430 2.0 Array Source GEO sample is GSM197118 Last updated (according to GEO): May 31 2007 Compare the brain transcriptomes of Gja9 (-/-) and Gja9 (+/-) mice with that of wildtype mice to detect transcriptomic alterationss induced by total or partial ablation of Gja9 Source GEO sample is GSM146907 Last updated (according to GEO): Nov 29 2006 Hypothalamic structure 861 32h-Control replication 2 Sample 5 Treatment, type=add, description=low potassium Source GEO sample is GSM53248 Last updated (according to GEO): Jul 06 2005 of somatomotor cortex 21 41 Immature B cells 11 A HID I D056 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108600 Last updated (according to GEO): Aug 22 2006 olfactory epithelium 194 213 Tumor__Pancreas_Adeno_Pan_4T on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene expression data from postmorten brain regions Source GEO sample is GSM144919 Last updated (according to GEO): Nov 20 2006 320 306 Keywords = HIV Gene expression data from the right forebrain of C57BL mouse received Haloperidol oral treatment for twelve weeks. Source GEO sample is GSM148667 Last updated (according to GEO): Dec 12 2006 M_95A_3023_CB_0_GS NO_KIDNEY_6 for hereditary non-polyposis colon cancer 340 380 CAD_replicate45 with some respiratory epithelium. 1039 1072 Expression profiling of spinal cord section (T8) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM6638 Last updated (according to GEO): May 28 2005 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22185.gif Source GEO sample is GSM78458 Last updated (according to GEO): Sep 22 2006 Neoplasm Metastasis 1000 none Source GEO sample is GSM210290 Last updated (according to GEO): Jul 16 2007 Frontal Lobe 9 Normal BALB/cByJ_male_hypothalamus Source GEO sample is GSM184192 Last updated (according to GEO): Apr 26 2007 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3297 Last updated (according to GEO): Mar 21 2006 Gene expression data from the right forebrain of C57BL mouse received Haloperidol oral treatment for four weeks. Source GEO sample is GSM149810 Last updated (according to GEO): Dec 12 2006 fatal seizures 221 234 CNS-SC_Inj7d-4B-s2 Gene expression data from postmorten brain regions Source GEO sample is GSM145649 Last updated (according to GEO): Nov 20 2006 HA01-57B 861 Blood 9 0 Blood Test AML54 on Affymetrix GeneChip Human Full Length Array HuGeneFL Alk shRNA, biological rep2 NoCAD_replicate22 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213506 Last updated (according to GEO): Jul 31 2007 Prostate 7 Disease 0 17 NA18612 Liver 0 4 Replicate2_Voxel A3 111 of liver cells 124 17 7 hippocampus Gene expression data from postmorten brain regions Source GEO sample is GSM145683 Last updated (according to GEO): Nov 20 2006 G42 neurons from cingulate cortex Source GEO sample is GSM63022 Last updated (according to GEO): Dec 01 2005 5.0 mg/kg MeHg exposure Primary tumor 19 32 kidney 37 43 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120664 Last updated (according to GEO): May 14 2007 861 Brain brain_DLPFC_bipolar B_mr426 1000 Brain Myometrium 52 Disease of several solid tumors 51 74 pars nervosa of hypophysis 1000 81 68 Normal Trachea none Source GEO sample is GSM239902 Last updated (according to GEO): Dec 07 2007 1000 Neuraxis 1000 Globus Pallidus Whole ganglioneuroblastoma tumor_1589 Microarray analysis of NL and PCOS oocytes (NL4) Disease Source GEO sample is GSM176087 Last updated (according to GEO): Apr 09 2007 DLBC13 on Affymetrix GeneChip Human Full Length Array HuGeneFL Dynamics of global gene expression changes during mouse preimplantation development. endometrium_10 stria terminalis 901 Anterior nares 1000 VDXGUYU_4054 heart failure 583 595 of mouse brain 9 23 1100 1077 of Medulloblastoma - 8 - 1000 Brain None Source GEO sample is GSM214248 Last updated (according to GEO): Aug 01 2007 1000 Amyotrophic Lateral Sclerosis HeLa sample 1 Human Sural Nerve Schwann Cell Donor 317 Passage 1 Treatment, type=add, description=growth factors heregulin and forskolin added Source GEO sample is GSM92233 Last updated (according to GEO): Jan 13 2006 ISS/ILS_cerebellum_naive_435 1000 Hippocampus Acute leukemia 913 329 306 valvular cardiomyopathy 861 Mammary gland Primary tumor 19 32 Embryonal carcinoma, NCR-G1, adherent Mammary Gland @ Preg17, biological rep3 Human papillomaviruses (HPV) are associated with nearly all cervical cancers, 20% to 30% of head and neck cancers (HNC), and other cancers. Because HNCs also arise in HPV-negative patients, this type of cancer provides unique opportunities to define similarities and differences of HPV-positive versus HPV-negative cancers arising in the same tissue. Here, we describe genome-wide expression profiling of 84 HNCs, cervical cancers, and site-matched normal epithelial samples in which we used laser capture microdissection to enrich samples for tumor-derived versus normal epithelial cells. This analysis revealed that HPV(+) HNCs and cervical cancers differed in their patterns of gene expression yet shared many changes compared with HPV(-) HNCs. Some of these shared changes were predicted, but many others were not. Notably, HPV(+) HNCs and cervical cancers were found to be up-regulated in their expression of a distinct and larger subset of cell cycle genes than that observed in HPV(-) HNC. Moreover, HPV(+) cancers overexpressed testis-specific genes that are normally expressed only in meiotic cells. Many, although not all, of the hallmark differences between HPV(+) HNC and HPV(-) HNC were a direct consequence of HPV and in particular the viral E6 and E7 oncogenes. This included a novel association of HPV oncogenes with testis-specific gene expression. These findings in primary human tumors provide novel biomarkers for early detection of HPV(+) and HPV(-) cancers, and emphasize the potential value of targeting E6 and E7 function, alone or combined with radiation and/or traditional chemotherapy, in the treatment of HPV(+) cancers. [Cancer Res 2007;67(10):4605-19]. Ovarian Diseases 877 Expression data from experimental murine asthma brain, Right Frontal Parietal: Extract66_le2 Heart failure 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145861 Last updated (according to GEO): Nov 20 2006 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:208, Count:32 Corner- Avg:35505, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:11.218446,SFGene:All Background:Avg:425.32,Stdev:14.65,Max:488.3,Min:396.6 Noise:Avg:9.75,Stdev:1.22,Max:14.7,Min:7.3 RawQ:13.05 Keywords = ALL Source GEO sample is GSM3416 Last updated (according to GEO): May 28 2005 1000 Brain brain, cerebral cortex: NMDA 1mM 1HOUR_le1 1000 Endometrium Temporal neocortex mTLE 7 25 7 Right Temporal Lobe brain, amygdala: pADX PM A b_e1_le1 15 0 human cerebellum Tumor__Leukemia_ALL-B_ALL_(28373)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Balb/c day 0, biological rep 4, tech rep 2 bronchial epithelia 224 243 ci_NY78 1000 Epilepsy brain_control_sampleid_mr276 f2#264 versus pool Mouse Brain tissue heart 1169 1173 Gene expression profiling predicts clinical outcome of breast cancer. NCI60.59_LABEL123EXTRACT61SUB3 Source GEO sample is GSM134289 Last updated (according to GEO): Aug 06 2007 human frontal cortex Source GEO sample is GSM86954 Last updated (according to GEO): Feb 08 2006 129/SvImJ Amygdala B placenta-0502-uninflamed-uninfected-rep1 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225734 Last updated (according to GEO): Nov 02 2007 Blood 7 11 23 0 mammary epithelial cells Neoplasm 861 861 Neurofibromatoses Epithelial Cells 1000 SCLC cell line SBC-5 Source GEO sample is GSM17314 Last updated (according to GEO): May 28 2005 30 month oculomotor nucleus rep 3 Tongue SG Normal AO Treatment, type=remove Source GEO sample is GSM99516 Last updated (according to GEO): Apr 21 2006 607 597 the rectum Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16598.gif Source GEO sample is GSM91572 Last updated (according to GEO): Sep 22 2006 PBMCs-Type 1 Diabetes-IDDM59_T1D_4MO NMDA 30 7/8 (Experiment NMDA1-Run 9136) Treatment, type=time_course, description=samples are treated for 10, 30 or 60 min with NMDA 1mM, the agonist is then washed out and the cells are harvested 24h later, measurement=30.0 m Source GEO sample is GSM96745 Last updated (according to GEO): Feb 14 2006 331 307 in central nervous system Femur 1000 Liver 1000 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9971.gif Source GEO sample is GSM79824 Last updated (according to GEO): Sep 22 2006 Skeletal bone 861 901 Mammary gland 1000 Skeletal muscle structure 12 frontal Lobe 23 AD-170t1-A251-10 ** on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Cerebral cortex 7 0 Lymphoma Spleen vs Sphingosine-1-phosphate Treated B cell 60min (set3) Whole blood from a patient with progressive supranuclear palsy Source GEO sample is GSM153447 Last updated (according to GEO): Jan 11 2007 Brain 861 Plasma 861 Neoplasm 861 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181052 Last updated (according to GEO): Jul 12 2007 brain, Right Frontal Parietal: Extract65_le1 43 0 Chorionic mesoderm-derived mesenchymal cells Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203959 Last updated (according to GEO): Aug 02 2007 Prostate 861 Gene expression data from liver Source GEO sample is GSM243402 Last updated (according to GEO): Nov 16 2007 Liver 1000 Amyotrophic Lateral Sclerosis 1000 H129 CB B 97 76 Normal Pituitary Gland Fibroblasts 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145860 Last updated (according to GEO): Nov 20 2006 1000 Hypothalamic structure n/a Source GEO sample is GSM177885 Last updated (according to GEO): Jun 11 2007 75 54 of the human skeleton Amyotrophic lateral sclerosis 0 28 GSE8717 with myocardial infarction 272 297 Osteoblasts 1000 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225920 Last updated (according to GEO): Nov 02 2007 0 Human Cortex 11 from spleens 340 351 cerebellum 7 16 cy3:WKY treated w/ angtiotensin, biological rep 5g; cy5:pool of 6 WKY control rats 1933 tumor cells 1943 cerebral cortex 7 21 amygdala 24 32 brain_DLPFC_bipolar C_mr404 HTI-286 in docetaxel-refractory prostate cancer Source GEO sample is GSM206167 Last updated (according to GEO): Jun 29 2007 1000 Benign prostatic hypertrophy 901 Bone Marrow Muscle_adequate protein_male_rep2 1000 Spleen Disease Source GEO sample is GSM175791 Last updated (according to GEO): Apr 09 2007 Melanoma xenograft, MEA3_Sub_A (LeiFidler) Nervous system structure 901 plasma cells 50 61 EWS-T1 on NHGRI-6.5k_b Communicable Diseases 861 M_U133A_66_AnCg 868 850 of medulloblastoma Hippocampus 1000 1321 1319 rod 861 Spinal Cord forebrain 7 15 91 from the bone marrow 72 Kidney 1000 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM119704 Last updated (according to GEO): Jul 11 2006 cortex from B6 mice at ZT21 rep2 Source GEO sample is GSM160462 Last updated (according to GEO): Feb 05 2007 Massively Parallel Signature Sequencing (MPSS), a recently developed high-throughput transcription profiling technology, has the ability to profile almost every transcript in a sample without requiring prior knowledge of the sequence of the transcribed genes. As is the case with DNA microarrays, effective data analysis depends crucially on understanding how noise affects measurements. We analyze the sources of noise in MPSS and present a quantitative model describing the variability between replicate MPSS assays. We use this model to construct statistical hypotheses that test whether an observed change in gene expression in a pair-wise comparison is significant. This analysis is then extended to the determination of the significance of changes in expression levels measured over the course of a time series of measurements. We apply these analytic techniques to the study of a time series of MPSS gene expression measurements on LPS-stimulated macrophages. To evaluate our statistical significance metrics, we compare our results with published data on macrophage activation measured by using Affymetrix GeneChips. 901 Mammary Neoplasms IM-6_POST 10 week control OMN rep 1 1000 Lung 0 Human Cortex 11 Keywords = muscle 124 141 gene expression from allergen stimulated mouse lung Source GEO sample is GSM158147 Last updated (according to GEO): Jan 25 2007 91 65 of anovulatory infertility Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188819 Last updated (according to GEO): Jun 06 2007 Eye 1000 Essential Tremor 1000 PGA-MurLungRag-pbs-72h-1aBv2-s2 Expression profiling of spinal cord section (T8) extracted from rats 30m following laminectomy (sham) Source GEO sample is GSM31407 Last updated (according to GEO): May 27 2005 Cerebral cortex 1000 1000 melanoma hydroxyacyl-CoA dehydrogenase 376 404 with mental retardation 241 263 C3H 8-3.1 Spleen 861 Blood Central gray substance of midbrain 861 118 94 in acute myeloid leukemia Brain 861 1000 Malignant Neoplasms rat cortex Treatment, type=time_course, measurement=14.0 d Source GEO sample is GSM53227 Last updated (according to GEO): Jul 06 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145741 Last updated (according to GEO): Nov 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145892 Last updated (according to GEO): Nov 20 2006 861 Pancreas Nasal Epithelium 865 17 7 hippocampus Expression profiling of spinal cord section (T8) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM6637 Last updated (according to GEO): May 28 2005 brain, Posterior Singulate: Sample51_e1_le1 Epithelium 861 SAMR1 Retina Old Sample 1 Muscle 1000 1000 Brain of lytic infection 128 145 normal liver tissue Source GEO sample is GSM155928 Last updated (according to GEO): Jun 21 2007 NFIA P16WT2 Transitional epithelium 1000 861 Ribosomal RNA osteoblast 630 640 DBA/2J ACU, Rep3 83 54 of Duchenne muscular dystrophy Cerebral cortex 861 Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18215.gif Source GEO sample is GSM91520 Last updated (according to GEO): Sep 22 2006 Cochlea 0 6 1000 Myositis 3792 0a 79 CB A 7 cerebral cortex 21 gene expression data from melanoma xenografts following ILI with melphalan Source GEO sample is GSM213637 Last updated (according to GEO): Jul 27 2007 normal lung 1502 Source GEO sample is GSM17299 Last updated (according to GEO): May 28 2005 207 199 infection Expression profiling of spinal cord section (T9) extracted from rats 24h following severe injury Lot batch = Source GEO sample is GSM7566 Last updated (according to GEO): May 28 2005 adenoma 861 microdissected oocytes 902 923 Tonsil [JunctionChip 5 of 5] Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184745 Last updated (according to GEO): Apr 26 2007 0 Human Cortex 11 Gene expression data from postmorten brain regions Source GEO sample is GSM145908 Last updated (according to GEO): Nov 20 2006 G5 lens mouse brains 187 198 NA19092 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28807 Last updated (according to GEO): May 27 2005 starved 143 149 plasma cells 332 344 WGACON-243 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 1 - Pair 3 - LMN Source GEO sample is GSM49881 Last updated (according to GEO): Dec 20 2005 119 FC BA9 A GSE3253 Nasal Epithelium 865 Uterus [JunctionChip 1 of 5] 861 Cerebral cortex Human Hypothalamus Female 1 36 0 Control rat 3 ventral tegmental area Mental Retardation 1000 ALL B-cell48 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Brain dorsal_root_ganglia_9 Source GEO sample is GSM80649 Last updated (according to GEO): Mar 31 2006 Hereditary Malignant Neoplasm 876 861 Blood brain, cerebral cortex: Sham16_e1_le1 1000 Spleen brain, cerebral cortex: PC19_e1_le1 913 Coronary heart disease 266 257 infection NCI60.7_LABEL10EXTRACT9SUB3 Source GEO sample is GSM134026 Last updated (according to GEO): Aug 06 2007 86 FC BA9 B CNS-SMTC_Ctr24h-2A-s2 D_U133A_68_nAcc of parieto-occipital cortex 223 250 Bone structure of tibia 1000 Malignant Neoplasms 861 Brain 861 Gene expression data from a neocortex from mouse injected 15 mg/kg kainate Source GEO sample is GSM147403 Last updated (according to GEO): Jan 03 2007 11 Bone marrow 0 Expression profiling of somatomotor cortex extracted from rats at 28d following sham surgery Source GEO sample is GSM41646 Last updated (according to GEO): May 27 2005 kidney 37 43 CNS-SCsev_InjB14d-1B-s2 861 Breast 110 94 of heart failure brain, hippocampus: PR-DG-8_e1_le1 Communicable Diseases 1000 Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 0685 left_liver_lobe of somatomotor cortex 21 41 Stem cells 901 Disease Source GEO sample is GSM175930 Last updated (according to GEO): Apr 09 2007 Obesity 1000 1000 Spleen C57BL-6J_male_hypothalamus D01 0h Media cerebellum 7 16 MALME-3M hgu95e Cerebral cortex 861 958 Heart failure Untreated versus treated (bortezomib), untranformed MCF10A and Transformed (see Adler et al, Nature Gen. 2006) Source GEO sample is GSM120223 Last updated (according to GEO): Jul 20 2006 557 541 to normal oocytes This dataset contains the gene expression profile of a CD11c high, CD4 positive splenic dendritic cell population. The cells were processed directly after isolation. Global scaling was applied to Avg Difference intensity values. Keywords = mouse, dendritic cells, spleen Source GEO sample is GSM4708 Last updated (according to GEO): May 27 2005 brain, Superior Frontal Gyrus: Sample56_e1_le1 1791 1786 livers of Parkinson's disease 450 471 DCIS133 on harvard-12k CNS-SC_CtrA24h-1A-s2 Liver 0 4 4R-3 1/29 (Experiment 4Rlong: Run 19283) Treatment, type=timepoint, description=Primary cortical neurons were treated for 18h with a new non competitive antagonist for nicotinic receptors (4R 2uM), the antagonist was then washed out and the cells were harvested 24h later, measurement=24.0 h Source GEO sample is GSM96741 Last updated (according to GEO): Feb 14 2006 virtaneva-aml8 bc-ZT15-2 Standard Affymetrix procedure Source GEO sample is GSM132966 Last updated (according to GEO): Aug 28 2007 human caudate nucleus Source GEO sample is GSM86839 Last updated (according to GEO): Feb 08 2006 GC (HKG44N) Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225935 Last updated (according to GEO): Nov 02 2007 The paraventricular hypothalamic nucleus (PVH) is a key site for integrating neuroendocrine, autonomic, and behavioral adjustments to diverse homeostatic challenges, including "physiological" (e.g., infection or hemorrhage) and "emotional" [e.g., restraint (RST) or footshock] stresses. Both types of challenges ultimately converge to activate common response systems represented in PVH, including the hypothalamo-pituitary-adrenal axis and the sympathoadrenal system. Oligonucleotide microarrays (U74A; Affymetrix, Santa Clara, CA) were used to compare and contrast gene expression profiles in the PVH elicited at 1 and 3 hr after acute exposure to representative physiological [intraperitoneal injection of 10 microg lipopolysaccharide (LPS)] and emotional (30 min RST) stressors. In general, the two challenges recruited relatively few genes in common, with the degree of overlap varying across functional classes of genes. The greatest degree of commonality was seen among signaling molecules and neuropeptides, whereas transcription factors upregulated by RST and LPS were largely distinct. Unexpectedly, RST induced a number of immune-related molecules, which were not regulated by LPS. Hybridization histochemical analyses localized a subset of responsive transcripts to the PVH and/or immediately adjoining regions. Immunerelated molecules in particular distributed broadly to vascular and other barrier-associated cell types. These global transcriptional profiles inform the search for early (transcription factors) and late (target genes) mechanisms in the modulation of PVH, and generalized CNS, responses to categorically distinct stressors.. Date GSE367 Last Updated: Jun 15 2005 Contributers: P E Sawchenko T M Reyes Includes GDS324. Update date: Jul 03 2003. Dataset description GDS324: Analysis of gene expression profiles in the paraventricular nucleus of the hypothalamus in male C57BL6. Mice subjected to either bacterial lipopolysaccharide (LPS) challenge, restraint stress or a saline control for 1 or 3 hours.. Investigation into murine dermal burn wound. Mouse thermal injury induced, and skin excised at different times post-injury. Source GEO sample is GSM7487 Last updated (according to GEO): May 27 2005 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92349 Last updated (according to GEO): Jan 13 2006 Large cell neuroendocrine carcinoma 901 90 FC BA9 A Date : 10/29/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 24 hrs post-injection Intervention : none Risk: estimated 20% increased risk for encephalopathy Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AF625 Source GEO sample is GSM12256 Last updated (according to GEO): May 28 2005 Primary Carcinoma 876 Average value of duplicate experiments of gut neurospheres (neurospheres of peripheral nervous system) of WT (wild type) mice (postnatal day 0). The cRNAs for hybridization were generated by two round RNA amplifications. Source GEO sample is GSM9245 Last updated (according to GEO): May 27 2005 Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242043 Last updated (according to GEO): Dec 04 2007 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7709.gif Source GEO sample is GSM79784 Last updated (according to GEO): Sep 22 2006 Myocardium 861 Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14350.gif Source GEO sample is GSM79733 Last updated (according to GEO): Sep 22 2006 GSE3583 Expression profiling of moderately injured raphe at 4h in rats Source GEO sample is GSM41617 Last updated (according to GEO): May 27 2005 Myometrium 53 Disease 1000 Uterus V5-P604 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 12.25 hours after lights on. Original sample code = CM46A Source GEO sample is GSM227333 Last updated (according to GEO): Sep 10 2007 Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16370.gif Source GEO sample is GSM91545 Last updated (according to GEO): Sep 22 2006 P7_cy3_2 M1 biol repl 3 0029_1249_H95A2_KF0134_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Medulla Oblongata 861 Brain Stem 1000 E10.5 craniofacial tissue, first branchial arch: 5_6_MNA-2_e1_le1 brain, cerebellum: Tg-/-_Crb1_e1_le1 CNS-SpinalC-ConAdult-24h-2A-s2b 31 0 Familial combined hyperlipidemia Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188755 Last updated (according to GEO): Jun 06 2007 1000 Left Brain_Rhab_1_AT/RT (Brain) on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Axon Lymphoblastoid Cell Line for Individual 8016.3 log phase 182 153 to the central nervous system 1000 Adipose tissue R6/1 22 week wildtype_C835 Whole blood 0 10 SN:1006484 Source GEO sample is GSM115342 Last updated (according to GEO): Jun 20 2006 Parkinson Disease 1000 Sample17, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53268 Last updated (according to GEO): Jul 06 2005 Gain-of-function mutations in NOTCH1 are common in T-cell lymphoblastic leukemias making this receptor a promising target for drugs such as gamma-secretase inhibitors, which block a proteolytic cleavage required for NOTCH1 activation. However, the enthusiasm for these therapies has been tempered by tumor resistance and the paucity of information on the oncogenic programs regulated by oncogenic NOTCH1. Here we show that NOTCH1 regulates PTEN expression and the activity of the PI3K-AKT signaling pathway in normal and leukemic T cells. Notch signaling and the PI3K-AKT pathway synergize in vivo in a Drosophila model of Notch-induced tumorigenesis, and mutational loss of PTEN is associated with increased glycolysis and resistance to NOTCH1 inhibition in human T-ALL. These findings identify the transcriptional regulation of PTEN and the control of cellular metabolism as key elements of the oncogenic program activated by NOTCH1 and provide the basis for the design of new therapeutic strategies for T-ALL. Last Updated (by provider): Sep 05 2006 Contributers: Jean Buteau Sherrie L Perkins Govind Bhagat Teresa Palomero Maria Dominguez Maria Cortina Giuseppe Basso Adolfo A Ferrando Kelly Barnes MariaLuisa Sulis Esther Caparros Maria Ciofani Ramon Parsons JuanCarlos Zúñiga-Pflücker Archana Mishra Pedro J Real Kristy Brown TAp63 alpha Q540L 24h without induction s3 GM18506 Melanoma xenograft, MA1_Sub_A (LeiATCC) total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Dimaprit for 30min Source GEO sample is GSM5532 Last updated (according to GEO): May 27 2005 ovarian tumor: serous Source GEO sample is GSM139474 Last updated (according to GEO): Apr 09 2007 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225698 Last updated (according to GEO): Nov 05 2007 67 40 with coronary artery disease Gene expression data from human colon tumor tissue Source GEO sample is GSM173376 Last updated (according to GEO): Apr 20 2007 Seminoma 1000 brain 0 5 Colon 861 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181232 Last updated (according to GEO): Jul 12 2007 Changes in PBMC Gene Expression During Acute Measles Sensitized on days 0 and 3 with ragweed pollen protein and alum, challenged intratrecheally on days 10 and 17 with ragweed pollen protein and sacrificed after 72h. Lot batch = Source GEO sample is GSM1277 Last updated (according to GEO): May 28 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68122 Last updated (according to GEO): Jul 07 2006 Healthy donor SN_10_vs_Pool of underlying brain 171 190 Brain 1000 Endometrium/Ovary 4 Disease Host Susceptibility to H. ducreyi Infection is Associated with Unique Transcript Profiles in Tissue and Dendritic Cells Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n014 Source GEO sample is GSM2061 Last updated (according to GEO): Nov 21 2005 901 Epithelial Cells Neoplasm 1000 1000 Cerebellum brain, Right Frontal Lobe: Extract63_le1 NCI60.30_LABEL34EXTRACT33SUB3 Source GEO sample is GSM134141 Last updated (according to GEO): Aug 06 2007 0 cortex 5 3ARS02080776b_skin 1560 1547 breast cancers 861 Cerebral cortex Brain 1000 5 0 brain 1000 Spleen mouse brain 478 489 Anterior nares 1000 Bladder tumour stage classification NoCAD_replicate6 126 118 to bregma 861 Oocytes Mouse Testis 1 (technical replicate) 5 0 brain Central gray substance of midbrain 861 Nose 1000 Brown Adipose Tissue Keywords = mouse gene expression database Source GEO sample is GSM29327 Last updated (according to GEO): May 27 2005 gene expression data from ODC mouse skin samples Source GEO sample is GSM216660 Last updated (according to GEO): Aug 09 2007 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211422 Last updated (according to GEO): Jul 18 2007 Carcinoma, Large Cell 867 Expression profiling of moderately injured raphe at 14d in rats Source GEO sample is GSM41563 Last updated (according to GEO): May 27 2005 Spleen 1000 1000 Eye HCC (HBV+, HK54) bronchial epithelia 224 243 brain, cerebral cortex: NMDA10 7/8RC_le1 Femur 1000 cerebral_cortex_8 Fibroblasts 1000 54h-AM replication 3 Keywords = preimplantation Keywords = development Source GEO sample is GSM14715 Last updated (according to GEO): May 28 2005 Pool of five normal Trabecular Meshwork cultured cells treated with EtOH for ten days ages 30-66-73-76 and 86 (named tc1) Source GEO sample is GSM7623 Last updated (according to GEO): May 28 2005 861 anatomic valve 1000 Brain Mouse ileum 0 10 in seminoma 28 38 119 96 in embryonic stem cells occipital_lobe_4 Liver 1000 Brain 861 heart failure 583 595 Lymphoblastoid Cell Line for Individual 8124.5 log phase Ganglia 861 3082 Pulmonary Hypertension 3061 24 skeletal muscle 10 Head and neck cancer Source GEO sample is GSM155647 Last updated (according to GEO): Apr 24 2007 with myocardial infarction 313 339 Expression profiling of spinal cord section (T9) extracted from rats 28d following moderate injury Source GEO sample is GSM31546 Last updated (according to GEO): May 27 2005 725 713 in the brain "32 hr Hela Double Thymidine, exp3" IDC169 on harvard-12k Chronic leukemia NOS 913 Donor E, pre G-CSF Plasma 861 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113903 Last updated (according to GEO): Jun 16 2006 Epithelium of bronchus 983 in blood 16 23 from liver 21 30 pancreas Source GEO sample is GSM18703 Last updated (according to GEO): May 27 2005 Parkinson's model voxel G2 861 Cerebral cortex rat hippocampus Treatment, type=time_course, measurement=24.0 h Source GEO sample is GSM32136 Last updated (according to GEO): May 27 2005 brain, cerebral cortex: Sham7_e1_le1 none Source GEO sample is GSM149628 Last updated (according to GEO): Jan 03 2007 MP-DX-8 7 0 prostate an adenovirus 57 69 Normal__Prostate_95_I_255 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Normal__Colon_CR_6 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A G5 temp retina Female mice used were SvJ/129, 10-16 weeks of age, with both copies of the Hoxa-10 gene (GenBank # NM_008263) present (wildtype). These mice were littermates of Hoxa-10-/- mice used in parallel experiments. 14 days after ovariectomy, mice were injected subcutaneously with progesterone dissolved in sesame oil (Sigma; 0.2mg/0.1mL/mouse), followed by sacrifice and removal of uterine horns at 6 hours after injection. 8 uterine horns from 4 mice were pooled to form one sample. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix. Source GEO sample is GSM3043 Last updated (according to GEO): May 27 2005 1000 Atherosclerosis 1000 Neoplasm Metastasis 1000 Brain 861 Blood subthalamic_nucleus_10 Source GEO sample is GSM80854 Last updated (according to GEO): Mar 31 2006 Lung diseases 861 Expression profiling of spinal cord section (T8) extracted from rats 7d following laminectomy (sham) Lot batch = Source GEO sample is GSM4431 Last updated (according to GEO): May 28 2005 ALL-B-cell-27 on Affymetrix GeneChip Human Full Length Array HuGeneFL Parkinson Disease 1000 Caudate P6 Normal Liver Test (Blinded) Sample Source GEO sample is GSM130062 Last updated (according to GEO): Sep 18 2007 Gene expression data from the right forebrain of C57BL mouse received no treatment for twelve weeks. Source GEO sample is GSM148680 Last updated (according to GEO): Dec 12 2006 15 7 hindbrain for human cancer 27 42 cardiac 763 769 304 280 alcoholic cardiomyopathy brain, cerebral cortex: Rat_02-54_VHL_Lipska_e1_le1 114 101 brains quickly Gonadectomized Dahl-Iwai Female LowSalt OuterMedulla rat2 gdahl_medullar_k_GX_2om_050702 Liver Test (Blinded) Sample Source GEO sample is GSM130063 Last updated (according to GEO): Sep 18 2007 PCA132_localized prostate cancer 0 31 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195251 Last updated (according to GEO): Sep 13 2007 Cerebral cortex 1000 of the atrial 647 659 brain 0 5 rat hippocampus Treatment, type=time_course, measurement=240.0 h Source GEO sample is GSM32151 Last updated (according to GEO): May 27 2005 Category: Lymphoma Classification Subcategory: Hematopoetic cell lines Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n086 Source GEO sample is GSM2071 Last updated (according to GEO): Nov 21 2005 f2#4 versus pool Mouse Brain tissue 1000 Brain Stem Parkinson's disease is a prevalent neurodegenerative disorder for which there is no cure. The cause of PD symptoms is loss of dopamine neurons in the midbrain, but it is not known why these neurons die. Pesticide exposure is epidemiologically associated with PD, and administration of the organic pesticide rotenone to rats recapitulates most of the behavioral, neurochemical, and neuropathological findings in PD, including specific death of dopamine neurons. We have developed an in vitro model of rotenone toxicity using a dopaminergic cell line (SK-N-MC neuroblastoma cells) that mimics many of the cellular changes seen with in vivo rotenone toxicity and with PD, such as alpha-synuclein aggregation and oxidative damage. We are currently using this simple model to explore mechanisms of dopaminergic neurodegeneration, with our ultimate goal being the discovery of novel mechanisms for dopaminergic neuroprotection in PD. We will examine gene expression profiles of cultured SK-N-MC cells at several time points during rotenone exposure to determine pathways involved in rotenone toxicity and dopaminergic degeneration. We will compare these profiles to baseline profiles of rodent dopaminergic neurons that we have already obtained, as well as to profiles of dopamine neurons from rotenone-treated rats that we will obtain in the near future. We will also compare these data to published results from SN neurons from human PD patients. This technique will not only help us to detect gene expression changes relevant to dopaminergic neurodegeneration in PD, but it will allow us to determine if the SK-N-MC system can be reliably used to screen for neuroprotective therapies for PD. We anticipate that SK-N-MC cells will show a relevant subset of the gene changes seen in dopamine neurons in vivo and that this will guide us in the sorts of mechanisms and drugs that can be screened in this system. Chronic exposure to low levels of rotenone causes changes in gene expression in SK-N-MC cells that sensitize the cells to toxic insults. We also hypothesize that there are several compensatory protective pathways that are stimulated by chronic rotenone, although these pathways are ultimately ineffective at preventing damage. We anticipate that gene expression profiling of rotenone-treated cells over time will suggest several novel strategies for neuroprotective intervention. SK-N-MC cells will be grown in three different media: media only, vehicle (EtOH), and rotenone (5 nM). All current experimental evidence in our lab indicates that vehicle-treated cells are indistinguishable from media-only cells. Rotenone-treated cellls have a stereotypical response in culture. At one week, the only noticed change is an increase in alph-synuclein aggregation. At two weeks, evidence of increased oxidative stress appears (increased protein carbonyls and lipid peroxidation). At four weeks, the cells are markedly sensitized to oxidative challenge with H2O2. Therefore, we will examine gene expression at baseline, and during 1, 2, and 4 weeks of rotenone treatment. Three experiments will be performed, each lasting 4 weeks. For each experiment, three separate dishes of vehicle-treated, and rotenone-treated cells will be harvested at 1, 2, and 4 weeks (18 independent samples). Untreated, media-only cells will be harvested after 1 week in vitro to serve as baseline cells. Total RNA will be isolated. An equal amount of RNA from one dish per experiment per group will be used to compose the final samples. Therefore, each independent sample will consist of RNA from 3 separate experiments. This will allow us to take advantage of a pooling strategy, yet not sacrifice technical and biological replication. 21 samples will be sent to the Consortium. Three will be from untreated cells. Nine will be vehicle-treated at 1, 2, and 4 weeks (3 each). Nine will be rotenone-treated at 1, 2 , and 4 weeks (3 each). Each sample will be labeled and hybridized to one Affymetrix Human Genome U133 Plus 2.0 Gene Chip. With assistance of the consortium, we will analyze the data using the Signifiance Analysis of Microarrays (SAM) program and self-organizing map algorithms. Last Updated (by provider): Jun 06 2006 Contributers: James G Greene Bone marrow [JunctionChip 3 of 5] HapMap CHB Female Source GEO sample is GSM159602 Last updated (according to GEO): Feb 01 2007 Agranulocytosis 1000 I_95Av2_3023_DLPFC_0_GS 21 0 acute myeloid leukemia 1000 Cochlear structure 1000 Atherosclerosis Gene expression data from postmorten brain regions Source GEO sample is GSM145108 Last updated (according to GEO): Nov 20 2006 M_U133A_48_nAcc 1000 Brain Injuries ALL B-cell 40 on Affymetrix GeneChip Human Full Length Array HuGeneFL NCI60.29_LABEL33EXTRACT32SUB3 Source GEO sample is GSM134135 Last updated (according to GEO): Aug 06 2007 901 Caudate nucleus structure starved 39 45 Liver 1000 Muscular Dystrophy, Duchenne 875 brainThalamus Source GEO sample is GSM18776 Last updated (according to GEO): Sep 25 2006 Nose 1000 M7TW00121476 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184822 Last updated (according to GEO): Apr 26 2007 We used cDNA microarrays to explore the variation in expression of approximately 8,000 unique genes among the 60 cell lines used in the National Cancer Institute's screen for anti-cancer drugs. Classification of the cell lines based solely on the observed patterns of gene expression revealed a correspondence to the ostensible origins of the tumors from which the cell lines were derived. The consistent relationship between the gene expression patterns and the tissue of origin allowed us to recognize outliers whose previous classification appeared incorrect. Specific features of the gene expression patterns appeared to be related to physiological properties of the cell lines, such as their doubling time in culture, drug metabolism or the interferon response. Comparison of gene expression patterns in the cell lines to those observed in normal breast tissue or in breast tumor specimens revealed features of the expression patterns in the tumors that had recognizable counterparts in specific cell lines, reflecting the tumor, stromal and inflammatory components of the tumor tissue. These results provided a novel molecular characterization of this important group of human cell lines and their relationships to tumors in vivo. This study is described more fully in Ross DT et al.(2000) Nat Genet 24:227-35 Last Updated (by provider): May 29 2005 Contributers: D Botstein U Scherf M Waltham P O Brown T G Myers S S Jeffrey J N Weinstein D Shalon D Lashkari D T Ross A Pergamenschikov C M Perou U Eisen V Iyer P Spellman J C Lee C Rees M van de Rijn Includes GDS89. Update date: Apr 08 2003. Dataset description GDS89: Analysis of cell lines used in the National Cancer Institute's screen for anti-cancer drugs. Gene expression is linked to phenotypic properties and drug sensitivity profiles of the cell lines.. Includes GDS88. Update date: Apr 08 2003. Dataset description GDS88: Analysis of cell lines used in the National Cancer Institute's screen for anti-cancer drugs. Gene expression is linked to phenotypic properties and drug sensitivity profiles of the cell lines.. [Switched to use 10k_merged by Gemma] how the liver 645 657 Backskin_WT_P14_rep2 Epithelium of bronchus 983 NL-2562-A413-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Primary Neoplasm 1000 Sample 105 on vantveer-oligo Large-scale analysis of the human transcriptome. Whole brain Source: Research Genetics, http://www.resgen.com/products/DLmRNA.php3 Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 116.33 Stdv: 5.23 Min: 102.93 Max: 122.67 Source GEO sample is GSM2837 Last updated (according to GEO): Mar 10 2006 none Source GEO sample is GSM244623 Last updated (according to GEO): Nov 23 2007 thymocytes_DN3_4 Brain 861 Tissue Source GEO sample is GSM67258 Last updated (according to GEO): Jan 19 2006 Mek exp1 PD98059 Stomach 1000 Osteoblasts 1000 /6J pituitary gland rep1 5 28 The epithelial cells 962 981 91 from the bone marrow 72 Mouse ileum with L.innocua(inlA)_A_5557 1000 ovarian neoplasm Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228637 Last updated (according to GEO): Sep 11 2007 Squamous cell carcinoma 853 7 0 prostate from colonic normal mucosa 21 47 366 354 encephalitis spleen 36 41 Brain 861 1000 Hippocampus 861 Cochlear structure 68 52 of breast cancer tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44876 Last updated (according to GEO): May 27 2005 1000 Liver Motor neurons from the spinal cord of wildtype mice Treatment, type=linear_amplification, description=T7-based RNA amplification Source GEO sample is GSM113703 Last updated (according to GEO): Jun 09 2006 861 Hormones Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3321 Last updated (according to GEO): Mar 21 2006 brain, Left frontal Lobe: Extract33_le1 Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit. Source GEO sample is GSM200591 Last updated (according to GEO): Jul 09 2007 Teeth 1500 mg/kg X 6 hr Source GEO sample is GSM129839 Last updated (according to GEO): Sep 18 2007 Myopathy 875 23 8 bone marrow cell Liver 1000 Sample # 1041-1 Cochlear nuclei pooled from 5 pups to generate one sample for one replicate hybridization out of 5. For this replicate RNA underwent one round of linear amplification. Cohybridized with P7_cy3_3. Source GEO sample is GSM44986 Last updated (according to GEO): Jun 08 2005 liver 0 5 CNS-SpinalCsev-Adult-24h-1A-s2 0 Human Cortex 11 Muscular Dystrophies 901 NCI60.1_LABEL124EXTRACT63SUB3 Source GEO sample is GSM133996 Last updated (according to GEO): Aug 06 2007 MSE_D_540 D_U133A_47_HC 1000 Cerebral cortex 865 Disorder of artery cardiac 746 752 21 adrenal medulla 7 Voxel G2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1432 Last updated (according to GEO): Nov 21 2005 Ovarian_Tumor_Serous_CHTN-OS-020 1000 Spleen Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=750670 LaserPower=2.121.28 Lot batch = LC17N118 Source GEO sample is GSM4833 Last updated (according to GEO): Nov 21 2005 40 21 from skeletal muscle Olfactory Epithelium 1000 Localized Malignant Neoplasm 853 67 40 with coronary artery disease Ta gr2 tumour Source GEO sample is GSM2489 Last updated (according to GEO): May 27 2005 Male; Epididymis-head Keywords = mouse gene expression database Source GEO sample is GSM29393 Last updated (according to GEO): May 27 2005 Gene expression data from whole brain infected mouse, day 6 Source GEO sample is GSM189652 Last updated (according to GEO): May 16 2007 121 98 of contused spinal cords Primary tumor 19 32 PGA-MCR-CR-72h-1aAv2-s1 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5825 Last updated (according to GEO): May 27 2005 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15689 Last updated (according to GEO): May 28 2005 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184669 Last updated (according to GEO): Apr 26 2007 Testis 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145359 Last updated (according to GEO): Nov 20 2006 922 903 in developing brain 1000 Hypothalamic structure Cerebral cortex 1000 NCI60.47_LABEL51EXTRACT50SUB3 Source GEO sample is GSM134231 Last updated (according to GEO): Aug 06 2007 Acetaminophen 24hr Rat 4678 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool Brain 1000 osteoblast 630 640 228 219 Hippocampi Medial #2 Arteries 861 aml8-aml8_965_ab_hu68_abms on Affymetrix GeneChip Human Full Length Array HuGeneFL Endometrium/Ovary 1 Disease D_U133Plus_83_CB GSE6904 Barcode: 251316210236 Source GEO sample is GSM159376 Last updated (according to GEO): Jul 17 2007 Brain 861 Brain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM146048 Last updated (according to GEO): Nov 20 2006 Central gray substance of midbrain 861 1000 Brain Tongue Main Corpus 4 Normal brain 0 5 10 0 whole brain Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit. Source GEO sample is GSM200586 Last updated (according to GEO): Jul 09 2007 1000 Spleen CAD_replicate97 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153485 Last updated (according to GEO): Jan 11 2007 Whole brain 773 783 5 0 brain Spinal Cord NCI60.2_LABEL125EXTRACT64SUB3 Source GEO sample is GSM134001 Last updated (according to GEO): Aug 06 2007 1hr time point after 10 Gy of IR exposure Source GEO sample is GSM10972 Last updated (according to GEO): May 28 2005 in a resistance artery 16 37 DLCL-0017 || lc4b031 gene expression data from ODC mouse skin samples Source GEO sample is GSM216654 Last updated (according to GEO): Aug 09 2007 861 Blood The epithelial cells 962 981 Gene expression data from dorsal pancreas at e15.5, MG-U74A version2 Source GEO sample is GSM199449 Last updated (according to GEO): Jun 08 2007 in the mammalian nervous system 110 141 of the heart 842 854 11 0 Hypothalamus Expression profiling of somatomotor cortex extracted from rats at 7d following moderate injury Source GEO sample is GSM48635 Last updated (according to GEO): May 29 2005 Central gray substance of midbrain 861 861 Neoplasm mouse brains 187 198 0 Human Cortex 11 NA19101 JMR-MurInj24h-2cAv2-s2 Acetaminophen 6hr Rat 0089 blood vs. Acetaminophen 6hr Rat Pooled Control blood dhanasekaran-prstate 1000 Heart failure 861 Cerebellum BC305B-AF 11_0037_Control_Day1_25 Stem cells 1000 Synapses 928 Natural gene expression variation in the HapMap CEU and YRI samples Fibroid_2540B HTI-286 in docetaxel-refractory prostate cancer_docet (Dye flip2) 430A2_1945_63_control_neuropath_medulla Source GEO sample is GSM242690 Last updated (according to GEO): Nov 15 2007 Brain 861 AD-313t1-A268-10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Prostate 861 The purpose of this study is to discover genes that might increase aqueous humor outflow when human ciliary muscle or human trabecular meshwork cells are treated with the prostaglandin analogues latanoprost free acid or prostaglandin F2alpha. Five tissue donors were pooled on each chip.. Date GSE492 Last Updated: Jul 27 2006 Contributers: Paul Russell Includes GDS359. Update date: Apr 14 2004. Dataset description GDS359: Glaucoma study investigating molecular basis of increase in aqueous humor outflow when human ciliary muscle or human trabecular meshwork cells are treated with prostaglandin analogs latanoprost free acid or prostaglandin F2alpha.. 1000 Infection endometrium_10 Source GEO sample is GSM80674 Last updated (according to GEO): Mar 31 2006 brain 0 5 Skeletal muscle biopsy was obtained after a 3-hour hyperinsulinemic (infusion rate 40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172158 Last updated (according to GEO): Feb 28 2007 of coronary artery disease 258 284 Brain 861 Zeitgeber Time Treatment, type=time_course, measurement=6.0 h Source GEO sample is GSM53333 Last updated (according to GEO): Jul 06 2005 Voxel B4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1397 Last updated (according to GEO): Nov 21 2005 Sensitized on days 0 and 3 with ragweed pollen protein and alum, challenged intratrecheally on days 10 and 17 with ragweed pollen protein and sacrificed after 72h. Lot batch = Source GEO sample is GSM1268 Last updated (according to GEO): May 28 2005 Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7475 Last updated (according to GEO): May 27 2005 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P7, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3186 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145442 Last updated (according to GEO): Nov 20 2006 468 459 the rectum Expression profiling of spinal cord section (T9) extracted from rats 48h following laminectomy (sham) Source GEO sample is GSM31268 Last updated (according to GEO): May 27 2005 5 0 brain Large-scale analysis of the mouse transcriptome. Large intestine, cecum C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 248.85 Stdv: 9.03 Min: 234.66 Max: 265.94 Source GEO sample is GSM2931 Last updated (according to GEO): Mar 20 2006 E2A-PBX1-C3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A BC118B-BE Disease Source GEO sample is GSM176400 Last updated (according to GEO): Apr 09 2007 Whole Brain 62 72 Pool of 12 otic vesicles at E9.5 Source GEO sample is GSM182566 Last updated (according to GEO): Aug 14 2007 brain, cerebral cortex: Rat_03-37_NroLep_Lipska_e1_le1 LOX IMVI hgu95d Heart 1000 embryonic cortical neuron treated with NMDA and PD98059 Source GEO sample is GSM49561 Last updated (according to GEO): May 29 2005 Conversion MLL_12 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Migration Source GEO sample is GSM19099 Last updated (according to GEO): May 27 2005 Osteoblasts 1000 901 Nervous system structure Heart Ventricle 2 Normal Standard Affymetrix Protocol Keywords = microarray Keywords = muscle Source GEO sample is GSM15849 Last updated (according to GEO): May 28 2005 861 Heart Wild type P46 mouse visual cortex ipsilateral to monocular enucleation Source GEO sample is GSM97215 Last updated (according to GEO): Feb 17 2006 Compare the transcriptomes of Cx43 null and Cx43 siRNA treated cortical astrocytes with the transcriptome of the wildtype cortical astrocytes Source GEO sample is GSM200855 Last updated (according to GEO): Jun 19 2007 Posterior root of spinal nerve 861 M_U133A_22_DLPFC_R n/a Source GEO sample is GSM177958 Last updated (according to GEO): Jun 11 2007 861 Acquired Immunodeficiency Syndrome Keywords = kidney 236 253 Medulla 861 RR216_infected_DC Effects of TGF-?1 on expression profile of human pulp and odontoblasts 861 Cerebellum Entorhinal Cortex 7 23 bone_marrow_2 Parkinson Disease 1000 Wild type P24 mouse visual cortex contralateral to monocular enucleation Source GEO sample is GSM97204 Last updated (according to GEO): Feb 17 2006 Adipocytes 0 9 Homozygous O377 mutant mouse line versus wildtype mice Source GEO sample is GSM86412 Last updated (according to GEO): Dec 08 2005 Adenocarcinoma 1000 ER negative human primary breast tumor EA02014_41260_H133A_JA-941 861 Blood Uninfected Source GEO sample is GSM34386 Last updated (according to GEO): Oct 16 2006 SN:Human Glioblastoma Biopsy 10396 Marfan Syndrome 1000 861 Blood 331 307 in central nervous system Plasma 861 Cerebral cortex 901 nostrils 156 164 861 Aortic aneurysm without mention of rupture NOS 10 weeks Source GEO sample is GSM147517 Last updated (according to GEO): Dec 01 2006 The epithelial cells 962 981 1000 Cerebellum CS-B cell UVC-irradiated (2hour) replicate 2 U133B plasma cells 50 61 Cerebral cortex 861 861 Testis Large-scale analysis of the human transcriptome. Dorsal root ganglia Source: Analytical Biological Services; http://www.absbioreagents.com Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 155.22 Stdv: 8.99 Min: 133.06 Max: 168.20 Source GEO sample is GSM2888 Last updated (according to GEO): Mar 20 2006 no additional Source GEO sample is GSM199236 Last updated (according to GEO): Jun 08 2007 3463 3451 hippocampus 3 12 0 ovarian tumor (a resistance artery 141 160 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181072 Last updated (according to GEO): Jul 12 2007 GSE370 CS-B cell unirradiated replicate 1 U133A Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92334 Last updated (according to GEO): Jan 13 2006 901 Caudate nucleus structure Coronary artery 901 324 318 cardiac BALB/cByJ Cingulate Cortex C WGACON-118 Cerebral cortex 861 human frontal cortex Source GEO sample is GSM86977 Last updated (according to GEO): Feb 08 2006 CNS-SCsev_InjA14d-1C-s2 Myocardial Infarction 1000 Brain 1000 Cockayne syndrome B wt-rescued cell Source GEO sample is GSM226616 Last updated (according to GEO): Sep 04 2007 19 0 human frontal cortex C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 4hr after experimental mice received their last shock treatment. Source GEO sample is GSM4499 Last updated (according to GEO): May 27 2005 tibiae 115 120 Mc2: Hippocampus_5T-Y_rep3 Hippocampus 861 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3286 Last updated (according to GEO): Mar 21 2006 HNC2910 861 Blood PCA132_localized prostate cancer and benign prostate hyperplasia labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156694 Last updated (according to GEO): Jan 22 2007 PGA-E18.5_3 1000 Brain 91 from the bone marrow 72 CNS-RM_Ctr14d-1B-s2 Blood B cells;memory CD27+ Corticotectal Neurons P14 1 Bone Marrow 1000 1466 1456 metastasis RNA from Lymphoblastoid Cell Line from this individual Source GEO sample is GSM213294 Last updated (according to GEO): Jul 26 2007 Primary Neoplasm 1000 Levitiracetam hippocampus 1 Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53433 Last updated (according to GEO): Jul 06 2005 Whole neuroblastoma tumor_2237 5 0 Muscle CNS-SpinalCmod-Adult-72h-1C-s2 Subject code A36 +_test-4_batch5 on NHGRI-6.7k 200 in the frontal cortex 220 CurrentSmoker 115 119 96 in embryonic stem cells 1000 Cochlear structure **** Source GEO sample is GSM4263 Last updated (according to GEO): May 27 2005 Pituitary Gland 861 skeletal muscle Source GEO sample is GSM18681 Last updated (according to GEO): May 27 2005 Neoplasm 861 T62__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hrs per day, 24 h time point Source GEO sample is GSM159744 Last updated (according to GEO): Apr 23 2007 861 Blood skeletal muscle, tibialis anterior: Denervated 3-day Control 1_e1_le1 GM11882 from liver 21 30 Spleen 0 5 Normal__Breast_93_I_184 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Exp B_4, control (0mg/kg) CPF Primary Neoplasm 1000 Coronary artery 901 of the brain 1283 1295 normal liver tissue Source GEO sample is GSM155926 Last updated (according to GEO): Jun 21 2007 Standard Affymetrix Protocol Source GEO sample is GSM15858 Last updated (according to GEO): May 28 2005 901 Coronary artery Huntington's disease: Gene expression changes caused by Hdh CAG mutation or 3-nitropropionic acid in striatal cells DBA/2J bed nucleus of the stria terminalis rep1 Untreated cells. Source GEO sample is GSM203992 Last updated (according to GEO): Jun 25 2007 Breast 861 1000 Mammary Neoplasms 1000 Brain Intestines, Small 1000 small intestine sprague1 whole tissue, individual animal, 10 weeks old, male Sprague Dawley small intestine file:R3JW02103001 Source GEO sample is GSM15201 Last updated (according to GEO): May 28 2005 Rat SCN Sample 1 (Exp 1 - 0 hr) GSE8621 from the spinal cord 14 33 Parkinson Disease 861 5 0 Spleen 239 233 Retinas Sph 3, chip MOE430A 3_cerebral_cortex_3hrs_sleep_deprivation_#45 861 Substantia nigra structure GM12762 901 Caudate nucleus structure HMVEC-L stimulated with LPS for 4 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114554 Last updated (according to GEO): Sep 20 2006 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152014 Last updated (according to GEO): Feb 06 2007 Cerebral cortex 1000 in visceral afferents 1518 1538 Myocardial Infarction 1000 H128 CN A embryonic cortical neuron treated with CSS Source GEO sample is GSM49618 Last updated (according to GEO): May 29 2005 MO_control_0min_Patient7 Nasal Epithelium 901 5 0 brain 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113911 Last updated (according to GEO): Jun 16 2006 Normal Source GEO sample is GSM176417 Last updated (according to GEO): Apr 09 2007 Communicable Diseases 861 136 122 from the kidney 72 47 in murine small intestine substantia_nigra_10 Gene expression data from hippocampus of one old SAMR1TA mouse Source GEO sample is GSM143758 Last updated (according to GEO): Jan 24 2007 EpiHd_022CACIO_114a.txt 3AJZ02072570_HUMANCULTUREDADIPOCYTE Primary tumor 19 32 24 skeletal muscle 10 Blastocyst replication 4 PANC-1 x SR21 #2 Cerebral cortex 1000 11 0 Hypothalamus Heart 861 716 695 by comparing the basal 15 7 hindbrain MCF7D-repro brain, hippocampus: Ctr-24h-P15-I_e1_le1 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Anti-IgM for 240min Source GEO sample is GSM5449 Last updated (according to GEO): May 27 2005 schizophrenia. 308 322 1000 jejunum 1000 Descending colon Fibroblasts 1000 Alzheimer's Disease 1000 Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S25_3 months_replicate 3 Parkinson Disease 861 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114462 Last updated (according to GEO): Jun 16 2006 Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153764 Last updated (according to GEO): Jan 19 2007 na Source GEO sample is GSM181258 Last updated (according to GEO): Apr 10 2007 1000 frontal lobe 1000 Spleen 1000 ovarian neoplasm Whole Brain 62 72 10 0 whole brain 861 Heart E9.0_rep1 C6fast2 wtPrE serumfree 2 5 0 Spleen /SvEvTac mouse pituitary gland 29 58 long access to cocaine, amygdala, 6 hrs/day access to cocaine Source GEO sample is GSM93835 Last updated (according to GEO): Jan 26 2006 in bronchial epithelia 311 332 Lymphoblastoid Cell Line for Individual 8131.5 log phase CNS-SMTC_Mod7d-3B-s2 hrs nasal epithelium 1126 1146 tonsil_2 ALLT-cell67 on Affymetrix GeneChip Human Full Length Array HuGeneFL GSE7819 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13101.gif Source GEO sample is GSM79932 Last updated (according to GEO): Sep 22 2006 Large Pre-BII cells 1 DCIS65 on harvard-12k adenoma 1000 Olfactory Epithelium 1000 Expression data from adult laboratory mouse brain hemispheres 5 0 brain Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151974 Last updated (according to GEO): Feb 06 2007 19 0 Head and neck cancer Thalamus Subthalamic Nucleus 4 Normal Expression profiling of somatomotor cortex extracted from rats at 4h following moderate injury Source GEO sample is GSM44451 Last updated (according to GEO): May 27 2005 Chronic Lymphocytic Leukemia 19 47 to the nose 599 609 human cerebellum Source GEO sample is GSM87078 Last updated (according to GEO): Feb 08 2006 healthy subject Source GEO sample is GSM211139 Last updated (according to GEO): Sep 10 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145410 Last updated (according to GEO): Nov 20 2006 3rd 6hr C-CA1 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11475 Last updated (according to GEO): May 28 2005 MGMH030312023Bovary in the brain 150 162 861 Brain 875 Cerebellar Diseases plasma cells 50 61 Voxel A1 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1126 Last updated (according to GEO): Nov 21 2005 Blood 861 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225951 Last updated (according to GEO): Nov 02 2007 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226159 Last updated (according to GEO): Nov 02 2007 f2#330 versus pool Mouse Brain tissue nasal epithelial cells 28 49 Normal human fetal cartilage from 18-22 weeks. Source GEO sample is GSM149652 Last updated (according to GEO): Jul 06 2007 Brain 1000 15 0 skeletal muscle Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152010 Last updated (according to GEO): Feb 06 2007 1000 Rectum seminoma specimen, pT2, pN1, patient age: 43y; W00 120 Tonsil [JunctionChip 2 of 5] GM07034 Nasal Epithelium Inhalation Formaldehyde 6ppm 8d ID301 21 0 cerebellum wistar 3886 whole blood_100409 Parkinson Disease 861 onto a collagen 71 85 PBMCs-Type 1 Diabetes-IDDM16_T1D_New brain, cerebral cortex: Control 8/23_le1 1000 Cartilage pfc_1030_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 966 Hippocampus PGA-MCR-ctr-12h-1bAv2-s1 NORMAL 7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 2_cerebral_cortex_3hrs_sleep_deprivation_#42 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225364 Last updated (according to GEO): Aug 31 2007 SN:1022991;Fetal Cartilage, biological rep1 5 0 Spleen Alzheimer's Disease 1000 cerebral cortex 7 21 FSCC12 on Affymetrix GeneChip Human Full Length Array HuGeneFL 091224 OVR19 on Affymetrix GeneChip Human Full Length Array HuGeneFL cy3:SHR treated w/ nifedipine, biological rep 5g; cy5:pool of 6 WKY control rats Prosencephalon 861 Skeletal bone 861 I_U133A_98_Amy Expression profiling of spinal cord section (T10) extracted from rats 4h following mild injury Source GEO sample is GSM31332 Last updated (according to GEO): May 27 2005 brain_OFC_control C_mr169 CC600 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156700 Last updated (according to GEO): Jan 22 2007 Replicate1_Voxel E8 IOBA5 Normal__Whole_Brain_BRAIN_2 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Structure of superior cervical ganglion 861 Blood Gene expression data from postmorten brain regions Source GEO sample is GSM145920 Last updated (according to GEO): Nov 20 2006 Gene expression data from a placenta without malaria, but with histological evidence of a past infection Source GEO sample is GSM183620 Last updated (according to GEO): Apr 23 2007 Macrophage smi47 Hippocampus Source GEO sample is GSM107964 Last updated (according to GEO): Jun 06 2006 Neoplasm 861 NCI60.20_LABEL24EXTRACT23SUB3 Source GEO sample is GSM134094 Last updated (according to GEO): Aug 06 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM146084 Last updated (according to GEO): Nov 20 2006 Total RNA extracted from the forebrain of a Tg+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144409 Last updated (according to GEO): Nov 14 2006 skeletal muscle, tibialis anterior: Innvervated Control 3_e1_le1 Prosencephalon 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145145 Last updated (according to GEO): Nov 20 2006 7 0 prostate 861 Epithelial Cells Malignant Neoplasms 1000 421 412 infection Male C57BL/6 mice (20-25 g) were anesthetized with isoflurane/oxygen. Moderate controlled cortical impact with pneumatic impactor, 6 m/s impact velocity and 1.5 mm deformation. 24h after surgery, a 4 mm diameter disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44503 Last updated (according to GEO): May 27 2005 "8 hr Hela Double Thymidine, exp3" 1000 Rectum 901 Caudate nucleus structure Testis 1000 bronchial epithelia 224 243 Gene expression data from postmorten brain regions Source GEO sample is GSM145829 Last updated (according to GEO): Nov 20 2006 in the mammalian nervous system 110 141 5_hypothalamus_6hrs_sleep_#157 Rb-/-PrE serumfree 1 91 from the bone marrow 72 Heart Ventricle 1000 1000 Brain 5 0 testis SWR/J ACU, Rep2 ADH-1 ip LPAM ILI 48hrs post ILI Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26625.gif Source GEO sample is GSM81550 Last updated (according to GEO): Sep 22 2006 38 an autoimmune disorder 59 VDXKIU_205 Ganglia, Spinal 923 Liver Test (Blinded) Sample Source GEO sample is GSM130197 Last updated (according to GEO): Sep 18 2007 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181213 Last updated (according to GEO): Jul 12 2007 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198655 Last updated (according to GEO): Jun 06 2007 861 Cerebellum 901 Coronary artery plasma cells 332 344 12 0 ovarian tumor plasma cells 50 61 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b055 Source GEO sample is GSM1999 Last updated (according to GEO): Nov 21 2005 6hr post 3Gy IR 923 Ganglia, Spinal CNS-RM_Mod7d-4A-s2 Spleen vs Tumor necrosis factor-alpha Treated B cell 120min (set3) AML cDNA hybridization-ID36-L 36 21 from whole brain PC 19 Treatment, type=incubate, description=Hypoxic preconditioning Source GEO sample is GSM107503 Last updated (according to GEO): May 01 2006 Epithelium of bronchus 983 collagen 301 309 luo-prostate Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 2360 blood cortex 7 12 17 7 hippocampus 1000 Integumentary system 21 0 acute myeloid leukemia Approximately 10 pairs of the most anterior dorsal root ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until sufficient tissue was harvested to be pooled by genotype. Ganglia from 5 embryos were pooled for a single analysis and RNA extracted using the RNeasy system (Qiagen). Source GEO sample is GSM132431 Last updated (according to GEO): Aug 30 2006 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:366, Count:32 Corner- Avg:40249, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:4.871372,SFGene:All Background:Avg:575.57,Stdev:36.37,Max:645.9,Min:509.4 Noise:Avg:10.66,Stdev:0.59,Max:12.9,Min:9.2 RawQ:15.10 Keywords = ALL Source GEO sample is GSM3402 Last updated (according to GEO): May 27 2005 Brain 861 C3H-HeJ mice were exposed to ozone. Lungs were removed-frozen in liquid nitrogen-RNA extraction. Lot batch = Source GEO sample is GSM4015 Last updated (according to GEO): May 28 2005 n/a Source GEO sample is GSM177904 Last updated (according to GEO): Jun 11 2007 Epithelium 861 Lymphoblastoid Cell Line for Individual 8166.4 log phase e_NY16 To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132982 Last updated (according to GEO): Sep 12 2006 Plasma 861 Exp A, Animal #4, 10mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours Source GEO sample is GSM246139 Last updated (according to GEO): Dec 03 2007 22 19 left NeverSmoker 38 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hour time point Source GEO sample is GSM159806 Last updated (according to GEO): Apr 23 2007 HapMap YRI_parent Female Source GEO sample is GSM159671 Last updated (according to GEO): Feb 01 2007 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 6 hours after lights on. Original RNA code = LC5A. Source GEO sample is GSM227383 Last updated (according to GEO): Sep 10 2007 861 Blood Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211340 Last updated (according to GEO): Jul 18 2007 Adult occipital cortex cocaine2 brain 0 5 V5-P303 Bone marrow macrophages were cultured from 16 week old apoE-deficient F2 mice from an AKRxDBA/2 intercross Gene expression profiling was performed using Affy 430v2 arrays, and 1967 informative SNP markers were genotyped for each mouse Supplementary file of SNP data attached below from ParAllele 5K mouse linkage panel Last Updated (by provider): Jul 18 2007 Contributers: Jonathan D Smith Jeffrey M Bhasin 861 Brain 7 0 prostate D_U133A_35_nAcc SWR/J Acute morphine treated, striatum, biological replicate 1 Source GEO sample is GSM187995 Last updated (according to GEO): Jun 14 2007 1000 hindbrain 1008 996 to M0 tumors Parkinson's model voxel A3 1000 Structure of locus ceruleus Heart Ventricle 1000 Date 3/26/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : headfold Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 2.5 mg/kg Time : 3.0 hrs post-injection Intervention : none Risk: benchmark dose modeled for 5% increased risk of microphthalmia Conditional biomarker: post-injection interval prior to p53 protein induction Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 16-20 headfolds pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = embryo Keywords = microphthalmia Lot batch = AN961 Source GEO sample is GSM12068 Last updated (according to GEO): May 28 2005 Wild type inbred mice Source GEO sample is GSM82930 Last updated (according to GEO): Nov 10 2005 1000 frontal lobe Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183413 Last updated (according to GEO): Apr 23 2007 1000 Muscle in the brain 150 162 861 Ovary CD3 beads 48.00 hr. T-Cell 225 209 of microphthalmia 901 Structure of trigeminal ganglion hippocampal glutamatergic CA1 pyramidal neurons Source GEO sample is GSM35812 Last updated (according to GEO): May 27 2005 861 Epithelial Cells O377 homozygotes brains 7 Acetaminophen 24hr Rat 1457 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool M_U133Plus_78_HC Ventral tegmental area 28 50 10_0020_SepticShock_Day3_58 12 0 ovarian tumor f2#147 versus pool Mouse Brain tissue for liver 26 35 forebrain 7 15 hippocampal glutamatergic CA1 pyramidal neurons Source GEO sample is GSM35832 Last updated (according to GEO): May 27 2005 913 Coronary heart disease 861 Gland structure 1173 1156 in prostate cancer Acetaminophen 3hr Rat 2652 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool UACC-62 hgu95c NCI-H23_CL1001__NSCLC Richard Almon-41-1133800610057 861 Cerebral cortex SN12C hgu95c Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 19 day time point Source GEO sample is GSM159814 Last updated (according to GEO): Apr 23 2007 cerebellum_9 Cochlea 0 6 none Source GEO sample is GSM246005 Last updated (according to GEO): Dec 03 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CGS for 60min Source GEO sample is GSM5512 Last updated (according to GEO): May 27 2005 2 hrs Pre-clamp sample 6 NMDA60 (Experiment shortNMDA: Run 19222) Treatment, type=time_course, description=primary cortical neurons were treated with 1 mM NMDA for increasing periods of time (10 to 360 min)., measurement=60.0 m Source GEO sample is GSM96764 Last updated (according to GEO): Feb 14 2006 Gene expression data from brain of adult rats Source GEO sample is GSM101051 Last updated (according to GEO): Feb 20 2007 1000 Solid tumor Cerebral cortex 1000 kidney Source GEO sample is GSM18796 Last updated (according to GEO): Sep 25 2006 of cancer 25 33 from ventral prostate 21 41 Control 8/30/02 (Experiment Neuroprotection3-Run 13276) Treatment, type=timepoint, measurement=0.0 h Source GEO sample is GSM96667 Last updated (according to GEO): Feb 14 2006 f2#349 versus pool Mouse Brain tissue 861 Mammary gland Brain 1000 10 0 Endometrium Huntington's disease 0 19 S462_Infect_2 medial motoneurons (MMN) 21 Ptdsr-/- fibroblast_rep7 of microphthalmia 174 190 with mental retardation 241 263 Muscle Source GEO sample is GSM4264 Last updated (according to GEO): May 27 2005 Wild type inbred mice Source GEO sample is GSM82934 Last updated (according to GEO): Nov 10 2005 O377 homozygotes brains_1 Parkinson Disease 1000 Trigeminal Ganglia 1 Normal 17 7 hippocampus 23 11 of the kidney 983 Cell Adhesion Molecules C57L/J Hippocampus A 972 Structure of middle temporal gyrus brain, contralateral Cortex: Trizol Extraction47_le1 Monocular deprivation left cortex, biological rep1 CHB MD-4 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide Source GEO sample is GSM225347 Last updated (according to GEO): Aug 31 2007 Brain (fetal) [JunctionChip 2 of 5] Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132553 Last updated (according to GEO): Feb 26 2007 Contribution of Nuclear and Extranuclear PolyQ to Neurological Phenotypes in Mouse Models of Huntington?s Disease D_U133Plus_109_CB 4 0 Brain S462_Mock_3 Liver 1000 NCI60.1_LABEL124EXTRACT63SUB3 Source GEO sample is GSM133997 Last updated (according to GEO): Aug 06 2007 Ventral Tegmental Area 1000 Simple annotation: Cell-cycle, Mitotic selection Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16435.gif Source GEO sample is GSM79650 Last updated (according to GEO): Sep 22 2006 PE_N_M169 Ptdsr-/- fibroblast_rep12 Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles. PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity. Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence. To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips. Source GEO sample is GSM136533 Last updated (according to GEO): Jun 05 2007 huang-breast GC (HKG30T) none Source GEO sample is GSM210294 Last updated (according to GEO): Jul 16 2007 901 frontal lobe on dystrophin 38 50 Mesenchymal stem cells 13 34 GM06993 1000 Mammary Neoplasms total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withSLC (Secondary lymphoid-organ chemokine) for 120min Source GEO sample is GSM5773 Last updated (according to GEO): May 27 2005 Caudal 1000 ALL-B-cell-22 on Affymetrix GeneChip Human Full Length Array HuGeneFL 861 Communicable Diseases Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203993 Last updated (according to GEO): Aug 02 2007 Wild type 8 wk old male FVB/NJ mouse hypothalamus Source GEO sample is GSM74981 Last updated (according to GEO): Feb 27 2007 861 Blood L_B6_SleepDep_ZT 6_3 Gene expression data from postmorten brain regions Source GEO sample is GSM145676 Last updated (according to GEO): Nov 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM144986 Last updated (according to GEO): Nov 20 2006 CNS-SC_CtrB24h-2C-s2 NO_KIDNEY_2 13 7 cochlea Communicable Diseases 1000 Dendritic Cells, Exposed to Brugia malayi (50) - Repeat #2 913 Coronary heart disease (CLL 70 73 1000 Spinal Cord 913 Coronary heart disease V5-P379 Comparison of control wild-type and Rb-/- prostate epithelial cell lines under untreated and serum-free conditions. Date GSE934 Last Updated: Jul 20 2005 Contributers: Michael T McCabe Mark L Day Includes GDS575. Update date: May 06 2004. Dataset description GDS575: Comparison of retinoblastoma-deficient (Rb-/-) and control wild type prostate epithelial cell lines maintained in RPMI-1640 medium supplemented with 5% fetal bovine serum, or without serum for 48 hours.. Coronary Arteriosclerosis 1000 M_95A_2978_AnCg_0_GS MDA Mb231 6h + 75 nM Cxcl12 3 Treated D_U133A_6_HC Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_10 months_replicate 1 901 Caudate nucleus structure 7116_Lung developed PGD from rat lungs 21 34 1000 Bone Marrow Liver Test (Blinded) Sample Source GEO sample is GSM130137 Last updated (according to GEO): Sep 18 2007 I_U133A_77_AnCg in the brain 150 162 C57BL/6J ACU, Rep3 Ovary 1000 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188771 Last updated (according to GEO): Jun 06 2007 brain, cerebellum: RNA#2S_le1 20 0 Nicotine-hippocampus Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184809 Last updated (according to GEO): Apr 26 2007 913 Coronary heart disease Primary tumor 19 32 (ventral tegmental area 788 810 861 Colon Cerebral cortex 861 884 Structure of horn of uterus 5 0 brain Gene expression data from postmorten brain regions Source GEO sample is GSM146056 Last updated (according to GEO): Nov 20 2006 WGACON-82 FVB/NJ hippocampus rep2 (430 2.0 Array) Spleen vs ELC Treated B cell 120min (set1) Arteries 861 1000 jejunum Epithelium of bronchus 983 from the cerebellum 20 38 in blood mononuclear cells 309 334 to the nose 599 609 SN12C hgu95d 861 Brain human caudate nucleus Source GEO sample is GSM86787 Last updated (according to GEO): Feb 08 2006 TNF-alpha, 12.00 hr. T-cell. C3H-HeOuJ mice exposed to ozone for 72hrs- lungs were removed-frozen in liquid nitrogen-RNA extraction. Lot batch = Source GEO sample is GSM4019 Last updated (according to GEO): May 28 2005 D_U133Plus_77_CB Nasal Epithelium 865 861 Cerebellum HDMTX_MP-DX-6 Date : 6/11/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 1.25 mg/kg Time : 3 hrs post-injection Intervention : none Risk: subNOAEL (no increased risk for malformations) Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AO027 Source GEO sample is GSM12237 Last updated (according to GEO): May 28 2005 Spleen vs fMLP Treated B cell 240min (set3) Wild type 8 wk old male DBA/2J mouse hypothalamus Source GEO sample is GSM74979 Last updated (according to GEO): Feb 27 2007 of multiple common adult malignancies 312 348 861 Cerebellum Whole Brain 62 72 GC (HKG26N) Metabotropic gamma-aminobutyric acid receptors (GABA(B)Rs) play a critical role in inhibitory synaptic transmission in the hippocampus. However, little is known about a possible long-term effect requiring transcriptional changes. Here, using microarray technology and RT-PCR of RNA from cultured rat embryonic hippocampal neurones, we report the profile of genes that are up- or downregulated by activation of GABA(B)Rs by baclofen but are not changed by baclofen in the presence of the GABA(B)R antagonist CGP-55845A. Our data show, for the first time, regulation of transcription of defined mRNAs after specific GABA(B) receptor activation. The identified genes can be grouped into those encoding signal transduction, endocytosis/trafficking, and structural classes of proteins. For example, butyrylcholinesterase, brain-derived neurotrophic factor, and COPS5 (Jab1) genes were upregulated, whereas Rab8 interacting protein and Rho GTPase-activating protein 4 were downregulated. These results provide important baseline genomic data for future studies aimed at investigating the long-term effects of GABA(B)R activation in neurones such as their roles in neuronal growth, pathway formation and stabilization, and synaptic plasticity. 1000 Heart Seminoma 1000 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P21, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3238 Last updated (according to GEO): May 28 2005 861 Neoplasm brain, brainstem: LB5_e1_le1 861 Carcinoma Gene expression data from SVG-A glial cells. Source GEO sample is GSM189710 Last updated (according to GEO): May 16 2007 Fibroblasts 1000 Acetaminophen 24hr Rat 0572 blood vs. Acetaminophen 24hr Rat Pooled Control blood Wild type P104 mouse visual cortex contralateral to monocular enucleation Source GEO sample is GSM97220 Last updated (according to GEO): Feb 17 2006 861 Cerebellum Basal- 0 5 1000 Infection Wild type inbred mice Source GEO sample is GSM83040 Last updated (according to GEO): Nov 10 2005 at the Human Brain 724 741 osteoblast 627 637 We will separately dissect the maxillary and mandibular branches of the E10.5 first branchial arch from wild type, dlx2, dlx1/2 and Dlx5/6 mutants. The tissues wil be flash frozen within 1 min of removal.We have not performed the dissections yet so we dont know how much RNA will be get from each sample, but previous experience suggests that we will need ~10 branchial arches/experiment. Treatment, type=nucleic_acid_extraction, description=We anticipate using this method as it was recommended by TGEN for small amounts of tissue. Source GEO sample is GSM107893 Last updated (according to GEO): Jun 06 2006 CNS-SCsev_InjB4h-4B-s2 5 0 brain Transplant Series 34 , Transplant # 5 1000 Communicable Diseases 1000 hindbrain Hypothalamic structure 1000 Gene expression data from liver Source GEO sample is GSM243375 Last updated (according to GEO): Nov 16 2007 Neoplasm 861 Neoplasm Metastasis 1000 Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit. Source GEO sample is GSM200588 Last updated (according to GEO): Jul 09 2007 SON 3d dehydrated Source GEO sample is GSM69862 Last updated (according to GEO): Dec 02 2005 607 594 in endometrium 1023 1003 progressive hair loss Barcode: 251316210242 Source GEO sample is GSM159383 Last updated (according to GEO): Jul 17 2007 NA18637 pfc_1058_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 13 0 Brain Amygdala 861 Colon 697 680 in contact allergy M_95Av2_2846_DLPFC_1_GS (cortex 19 25 5 0 brain Simple annotation: Cell-line, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2872.gif Source GEO sample is GSM79876 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM144925 Last updated (according to GEO): Nov 20 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-gamma (IFN gamma) for 30min Source GEO sample is GSM5604 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145554 Last updated (according to GEO): Nov 20 2006 Replicate1_Voxel A6 4 0 HEART Nose 1000 adenocarcinoma 3240 0 18 Job's patient Source GEO sample is GSM211027 Last updated (according to GEO): Sep 10 2007 Cerebellum_nontransgenic control S46_3.5 months_replicate 2 Disease Source GEO sample is GSM176240 Last updated (according to GEO): Apr 09 2007 M_U133A_102_HC 5 0 brain Ganglia 861 GSE6433 Mental Retardation 1000 1000 Coronary Arteriosclerosis Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181978 Last updated (according to GEO): Apr 13 2007 D_U133Plus_70_CB 2nd 1hr C-DG 129P3/J CHR, Rep3 68 64 Lungs 1000 ovarian neoplasm hip_1063_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A PGA_MI_nilv_24h_361 by plasma cells 950 964 for pulmonary vascular 1227 1248 70 40 without coronary artery disease 304 280 alcoholic cardiomyopathy Bone Marrow 1000 Hippocampus 861 861 Brain of parieto-occipital cortex 223 250 861 Neoplasm 0 Cortex 5 HC72 FC BA4 A GSE936 17 7 hippocampus Large-scale analysis of the mouse transcriptome. Bladder C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 447.07 Stdv: 22.40 Min: 408.35 Max: 493.15 Source GEO sample is GSM2947 Last updated (according to GEO): May 27 2005 of somatomotor cortex 21 41 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68319 Last updated (according to GEO): Jul 07 2006 Category: Lymphoma Classification Subcategory: Hematopoetic cell lines Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc5b003 Source GEO sample is GSM1957 Last updated (according to GEO): Nov 21 2005 1000 Hippocampus prostate 0 7 spinal cords 921 933 CNS-SpinalC-conAdult-14d-1C-s2 Arteries 861 Fluid-percussion head injury 86 113 CNS-SMTC_Mod24h-3C-s2 Myocardial Infarction 1000 Neoplasm 861 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b050 Source GEO sample is GSM1961 Last updated (according to GEO): Nov 21 2005 861 Colon hypothalamus_1 Source GEO sample is GSM80690 Last updated (according to GEO): Mar 31 2006 20 0 human caudate nucleus 5 0 Tongue Nose 1000 Type 1 Diabetes patient and the timepoint 1 month after diagnosis. Source GEO sample is GSM228623 Last updated (according to GEO): Sep 11 2007 in neural stem cells 721 741 19 0 human frontal cortex from liver 21 30 Spleen 1000 901 frontal lobe with some respiratory epithelium. 1039 1072 GSE8146 1514 from epithelial cells 1534 861 Epithelium 901 Structure of extensor digitorum muscle of hand Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc53 Source GEO sample is GSM1904 Last updated (according to GEO): Nov 21 2005 Abdominal aortic aneurysm obtained from surgery to correct. Source GEO sample is GSM170567 Last updated (according to GEO): Jul 26 2007 Neostriatum 1000 NAT-23 on UMich-10k HCC (HBV+, SF1, 2) 17 7 hippocampus MGJZ030228092Bvomeralnasalorgan(VMO) NCI60.16_LABEL20EXTRACT19SUB3 Source GEO sample is GSM134071 Last updated (according to GEO): Aug 06 2007 Chronic Lymphocytic Leukemia 19 47 Dioxin treated MCF7 breast cancer cells [HG-U133A] Exp 1 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181137 Last updated (according to GEO): Jul 12 2007 Epithelium 861 gene expression data from ODC mouse skin samples Source GEO sample is GSM216656 Last updated (according to GEO): Aug 09 2007 Neoplasm 861 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201794 Last updated (according to GEO): Jun 20 2007 12 0 ovarian tumor EOM 14 Day COntrol rep 3 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18938.gif Source GEO sample is GSM84141 Last updated (according to GEO): Sep 22 2006 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195356 Last updated (according to GEO): Jun 04 2007 rat cortex Treatment, type=time_course, measurement=3.0 d Source GEO sample is GSM53211 Last updated (according to GEO): Jul 06 2005 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211406 Last updated (according to GEO): Jul 18 2007 I_U133Plus_122_Amy 1000 Muscle from somatosensory cortex 12 36 Changes in mouse liver mRNA profiles following intra-peritoneal cytokine injection. One of 2 replicates of Interferon-gamma-/- mice, injected with phosphate-buffered saline, and killed after 4h. Source GEO sample is GSM5954 Last updated (according to GEO): May 27 2005 Medulla Oblongata 861 Macrophages, Exposed to Leishmania major - Repeat #1 abd skin fibroblast (1.4AF), serum starved Myocardium 861 Coronary artery 901 mouse brain 478 489 Parkinson Disease 1000 329 306 valvular cardiomyopathy serotonin 1372 1380 none Source GEO sample is GSM239875 Last updated (according to GEO): Dec 07 2007 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17029.gif Source GEO sample is GSM81534 Last updated (according to GEO): Sep 22 2006 304 280 alcoholic cardiomyopathy cirrhotic liver tissue Source GEO sample is GSM155923 Last updated (according to GEO): Jun 21 2007 Ok4: Hippocampus_NT-A_rep9 Skeletal bone 861 Parkinson's disease sample x118 G9a-WT_2 Mouse_E13.5_Front_Middle_Back_17 Ts1Cje-3-MGU74B Nasal Epithelium Inhalation Formaldehyde 0ppm 8d ID67 Nose 1000 1000 Solid tumor Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68269 Last updated (according to GEO): Jul 07 2006 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9931.gif Source GEO sample is GSM79909 Last updated (according to GEO): Sep 22 2006 AD-337t1-A224-8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A brain, cerebral cortex: 14988_e2_le1 JMR-RatSham4h-3aA-s2 Nasal Epithelium Inhalation Formaldehyde 2ppm 24h ID213 861 Cerebral cortex 913 Coronary heart disease plus_1440_3 858 Mesodermal cell Macrophage 14smi026 tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44903 Last updated (according to GEO): May 27 2005 861 Cerebral cortex none Source GEO sample is GSM239885 Last updated (according to GEO): Dec 07 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11559 Last updated (according to GEO): May 28 2005 435_2 AML-29 on Affymetrix GeneChip Human Full Length Array HuGeneFL 861 Cerebral cortex Retina [JunctionChip 5 of 5] EGFP infected SH-SY5Y/TrkA cells: infection (at t=-18 hours), NGF treatment (at t=0 hours), harvest for total RNA extraction (at t=3 hours). Replicate 2 Treatment, type=add Source GEO sample is GSM53385 Last updated (according to GEO): Jul 06 2005 1000 Temporal Lobe SCG explant cultured for 12 hours in vitro Source GEO sample is GSM246048 Last updated (according to GEO): Dec 03 2007 f2#324 versus pool Mouse Brain tissue CNS-SpinalCsev-Adult-7d-3A-s2 Epithelium of bronchus 983 brain, cerebral cortex: Control 4_le1 4 0 Heart Occipital #1 plasma cells 332 344 901 Coronary artery CNS-RM_Ctr7d-1C-s2 The nose 94 101 Gene expression data from mammary glands of lactating mice Source GEO sample is GSM202690 Last updated (according to GEO): Jun 20 2007 Samples taken from spinal cord of naive animal above injury level Source GEO sample is GSM4432 Last updated (according to GEO): May 27 2005 mouse hippocampus, cox-1 knockout, rep1 Sham 15 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107499 Last updated (according to GEO): May 01 2006 HTI-286 in docetaxel-refractory prostate cancer Source GEO sample is GSM206169 Last updated (according to GEO): Jun 29 2007 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM80005 Last updated (according to GEO): Oct 26 2005 Cerebellar astrocyte chip 1. CHIP ID 10489 Source GEO sample is GSM130362 Last updated (according to GEO): Mar 14 2007 in dystrophic muscle 1426 1446 Expression profiling of somatomotor cortex extracted from rats at 24h following sham surgery Source GEO sample is GSM41642 Last updated (according to GEO): May 27 2005 Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174505 Last updated (according to GEO): Mar 14 2007 25 0 frontal cortex wistar 3924 hippocampus_5 861 Pancreas Neoplasm 861 1000 Leukemia, Myelocytic, Acute Parkinson Disease 1000 Expression profiling of somatomotor cortex extracted from rats at 4h following moderate injury Source GEO sample is GSM44452 Last updated (according to GEO): May 27 2005 ovarian tumor: endometrioid Source GEO sample is GSM139397 Last updated (according to GEO): Apr 09 2007 endothelial cells 1142 1158 Human prostate cancer cells in different conditions Source GEO sample is GSM13088 Last updated (according to GEO): May 28 2005 901 Coronary artery 5 0 brain KT1002_N Cerebral cortex 861 CNS-SC_InjA7d-4A-s2 Prosencephalon 1000 Gonadectomized Dahl-Iwai Male HighSalt OuterMedulla rat12 gdahl_medullar_k_GX_12om_rh_051402 f2#247 versus pool Mouse Brain tissue Spinal Injuries 853 A HID I D050 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108596 Last updated (according to GEO): Aug 22 2006 Lymphoblastoid Cell Line for Individual 8050.4 log phase Spleen vs Dimaprit Treated B cell 30min (set1) 249 225 of Fetal Minimata Disease GTP-Binding Proteins 1000 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201266 Last updated (according to GEO): Jun 14 2007 Primary Carcinoma 876 M_U133A_117_nAcc 861 Blood no additional Source GEO sample is GSM199245 Last updated (according to GEO): Jun 08 2007 B464 on Affymetrix GeneChip Human Full Length Array HuGeneFL H118 CN A M_U133Plus_16_DLPFC ER+/LN+/Nevins40 on Affymetrix GeneChip Human Full Length Array HuGeneFL 691 670 in the maxillay branch medulla_9 Source GEO sample is GSM80723 Last updated (according to GEO): Mar 31 2006 mod093_10nM-2 staunton-nci60 7 frontal cortex 20 PGA-MCR-ctr-0h-1aAv2-s1 1000 Mammary Neoplasms Spleen vs Tumor necrosis factor-alpha Treated B cell 60min (set1) Heart 1000 with some respiratory epithelium. 1039 1072 Frontal_Cerebrocortex_Vehicle_6hr_rep9 Gene expression data from postmorten brain regions Source GEO sample is GSM145340 Last updated (according to GEO): Nov 20 2006 Cerebral cortex 1000 46 8 in docetaxel-refractory prostate cancer ventral striatum sprague 3963 freehand block dissections, removed only cortex, individual animal, 10 weeks old, male Sprague Dawley ventral striatum file:p3963w Source GEO sample is GSM15185 Last updated (according to GEO): Oct 28 2005 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM79053 Last updated (according to GEO): Oct 24 2005 Lymphoblastoid Cell Line for Individual 8111.5 log phase Communicable Diseases 861 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181149 Last updated (according to GEO): Jul 12 2007 Transplant Series 17 , Transplant # 5 Trigeminal Ganglion Source GEO sample is GSM53323 Last updated (according to GEO): Jul 06 2005 5 0 Spleen Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19214 Last updated (according to GEO): May 27 2005 cd4+Tcell Source GEO sample is GSM18673 Last updated (according to GEO): May 27 2005 983 Systemic infection RNA was obtained from vastus lateralis muscle biopsies from 4 healthy men, 22-31 years old. RNA was pooled before cDNA synthesis. Analysis done with Affymetrix Microarray Suite 5.0 software. Source GEO sample is GSM2395 Last updated (according to GEO): May 27 2005 1000 Brain 126 123 (ALS tumor 203 207 R7N 7 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210400 Last updated (according to GEO): Jul 16 2007 1000 Temporal Lobe 105 87 of atherosclerosis Study the transcriptomic effects of the shear stress on cultured osteoblast-like MC3T3 cells Source GEO sample is GSM201201 Last updated (according to GEO): Jun 19 2007 CNS-SC_InjB24h-1C-s2 of 7 saccules 5 17 AdipBrn022QAFC0_048.txt Penis 4 Normal 1000 medulloblastoma Mutations in presenilins (PS) 1 and 2 are the major cause of familial Alzheimer's disease. Conditional double knock-out mice lacking both presenilins in the postnatal forebrain (PS cDKO mice) exhibit memory and synaptic plasticity impairments followed by progressive neurodegeneration in the cerebral cortex. Here we further investigate the molecular events that may underlie the observed phenotypes and identify additional neuropathological markers in the PS cDKO brain. Enzyme-linked immunosorbent assay analysis showed reduced levels of the toxic beta-amyloid (Abeta) peptides in the cerebral cortex of PS cDKO mice. Interestingly, the reduction in Abeta40 and Abeta42 peptides is similar in PS1 conditional knock-out and PS cDKO mice. We further examined the gene expression profile by oligonucleotide microarrays in the PS cDKO cerebral cortex and found that a high number of genes are differentially expressed, most notably a group of up-regulated inflammatory genes. Quantitative real-time reverse transcription PCR and Western analyses confirmed the elevated levels of glial fibrillary acidic protein, complement component C1q, and cathepsin S, up-regulation of which has been associated with inflammatory responses in various neurodegenerative processes. Immunohistochemical analysis revealed that the increase in complement component C1q is confined to the hippocampal formation, whereas glial fibrillary acidic protein and cathepsin S are up-regulated throughout the entire neocortex and hippocampus. In addition, strong microglial activation occurs in the hippocampus and the deeper cortical layers of PS cDKO mice. These results indicate that the memory impairment and neurodegeneration in PS cDKO mice are not caused by Abeta accumulation and that loss of PS function leads to differential up-regulation of inflammatory markers in the cerebral cortex. Epithelium 861 The nasal epithelium is an important target site for chemically-induced toxicity and carcinogenicity. Human epidemiological investigations and experimental laboratory animal studies show that the nasal olfactory epithelium is selectively damaged by inhalation exposure to several chemicals, including vinyl acetate and hydrogen sulfide. The reason for the relative sensitivity of the nasal olfactory epithelium is not known. To better understand and predict the response of the nasal epithelium to inhaled xenobiotics, gene expression profiles from na?ve male and female Sprague-Dawley rats were constructed. Epithelial cells were manually collected from the nasal septum, naso- and maxillo-turbinates, and ethmoid turbinates of 9 male and 9 female rats. Gene expression analysis was performed using the Affymetrix Rat Genome 430 2.0 microarray. Gene ontology enrichment analysis identified several functional categories including xenobiotic metabolism, cell cycle, apoptosis, and ion channel/transport with significantly different expression between tissue types. Surprisingly, there were few gender differences in gene expression. This baseline data will contribute to our understanding of the normal physiology and selectivity of the nasal epithelial cells? response to inhaled environmental toxicants. Last Updated (by provider): Nov 21 2006 Contributers: David C Dorman Todd J Page Elizabeth S Roberts Russell S Thomas Anna M Bonner Nicole V Soucy brain, cerebellum: KCb4w#2_e1_le1 GM19138_technical_rep_1 early HCC Source GEO sample is GSM155939 Last updated (according to GEO): Jun 21 2007 Laser capture lung cancer cells Source GEO sample is GSM191042 Last updated (according to GEO): May 25 2007 861 Dorsum of tongue 901 Epithelial Cells Neoplasm 861 CLL-16 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184729 Last updated (according to GEO): Apr 26 2007 Normal Cerebellum HOXB4 const_w/o TMX, 1hour, biological rep2 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 2 - Pair 1 - MMN Source GEO sample is GSM49872 Last updated (according to GEO): Dec 20 2005 in the distal colon 491 509 Skeletal Muscle 2 Normal 872 Blood Cells Wild type 8 wk old male C57BL/6J mouse pituitary gland Source GEO sample is GSM75001 Last updated (according to GEO): Feb 27 2007 MK 2hr S-CA1 15 7 brainstem 1056 1036 of retinal structure 5 0 brain BALB/cByJ Hippocampus C G3 Macula 35 29 in lung NL-279n1-A98-3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Spleen 270 275 Primary small cell lung carcinoma 2760 0 37 Parkinson's disease sample x110 0 30 none Source GEO sample is GSM123214 Last updated (according to GEO): Jul 26 2006 2869 tumor cells 2880 Validation of lung metastasis signature (LMS) and its association with risk of developing lung metastasis and with primary tumor size. Last Updated (by provider): May 14 2007 Contributers: Andy Minn John Foekens Yixin Wang Joan Massague G8 Retina Epithelial Cells 901 no additional Source GEO sample is GSM199194 Last updated (according to GEO): Jun 08 2007 cocaine naive,medial prefrontal cortex, 0 hrs/day access to cocaine Source GEO sample is GSM93869 Last updated (according to GEO): Jan 26 2006 R6/1 27 week transgenic_2C4C 31 20 Whole thymus HapMap YRI_parent Male Source GEO sample is GSM159670 Last updated (according to GEO): Feb 01 2007 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198650 Last updated (according to GEO): Jun 06 2007 Stria 861 913 Coronary heart disease midbrain_5 Source GEO sample is GSM80703 Last updated (according to GEO): Mar 31 2006 entorhinal cortex layer II stellate island cells Source GEO sample is GSM107536 Last updated (according to GEO): May 01 2006 Date : 8/23/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 12 hrs post-injection Intervention : none Risk: estimated 20% increased risk for encephalopathy Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AF604 Source GEO sample is GSM12252 Last updated (according to GEO): May 28 2005 D_U133A_66_nAcc peripheral blood-CD14Monocytes Source GEO sample is GSM18712 Last updated (according to GEO): Sep 25 2006 intermediolateral column motoneurons (IML) 11 skeletal muscle sprague2 whole tissue, individual animal, 10 weeks old, male Sprague Dawley skeletal muscle file:R3JW02103004 Source GEO sample is GSM15204 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145567 Last updated (according to GEO): Nov 20 2006 Localized Malignant Neoplasm 853 1000 Brain DBA 1-1 Thymus cortex 27 33 1000 Brain Heart 1000 Fibroblasts 861 861 Ventral Tegmental Area Epithelial Cells 901 Liver 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145921 Last updated (according to GEO): Nov 20 2006 1000 Malignant Glioma cerebellum 7 16 C2C12_2.5_hr Neoplasm 861 1000 Neoplasm total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CpG-oligodeoxynucleotide for 30min Source GEO sample is GSM5521 Last updated (according to GEO): May 27 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68178 Last updated (according to GEO): Jul 07 2006 heart Source GEO sample is GSM18679 Last updated (according to GEO): May 27 2005 3616 PC 24Hr (pool) vs. 150mg/kg APAP 24Hr rat 3619 blood an inherited neurodegenerative disease 29 66 17 7 hippocampus 7117_Lung did not develop PGD One third to one half of all infants born before the 28th wek of gestation develop BPD bronchopulmonary dysplasia. Our objective is to evaluate the feasibility of using expression profiling in umbilical cord tissue to discover molecular signatures for developmental staging and for risk of BPD. Last Updated (by provider): Jul 25 2007 Contributers: Isaac Kohane Jennifer Cohen Bone structure of tibia 1000 Bone Marrow 1000 Replicate2_Voxel E2 Blood 861 1000 Brain Epithelium of bronchus 983 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188822 Last updated (according to GEO): Jun 06 2007 brain, brainstem: LB6_e1_le1 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68189 Last updated (according to GEO): Jul 07 2006 0 Human Cortex 11 5 0 brain aml8-aml8_294_ab_hu68_abms on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Brain Liver (SF9) Normal Source GEO sample is GSM176325 Last updated (according to GEO): Apr 09 2007 hippocampal glutamatergic CA3 pyramidal neurons Source GEO sample is GSM35800 Last updated (according to GEO): May 27 2005 Heart; tg - hyperdynamic Keywords = mouse gene expression database Source GEO sample is GSM29347 Last updated (according to GEO): May 27 2005 Array representing the response of Human foreskin fibroblasts at 48h post HCMV infection Source GEO sample is GSM10358 Last updated (according to GEO): May 27 2005 Interatrial septum 865 brain, Left frontal Lobe: ASTRO III 587_e1_le1 Uterus_6wk_FVB Wt Coronary Arteriosclerosis 1000 tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44896 Last updated (according to GEO): May 27 2005 Tumor__Renal_Carcinoma_5382 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A brain_Down_syndrome_sampleid_jg1734 brain, hippocampus: PH7_e1_le1 Hippocampus 861 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228642 Last updated (according to GEO): Sep 11 2007 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:215, Count:32 Corner- Avg:35328, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:11.352031,SFGene:All Background:Avg:320.18,Stdev:5.90,Max:336.6,Min:306.8 Noise:Avg:7.65,Stdev:0.20,Max:8.2,Min:6.7 RawQ:11.39 Keywords = ALL Source GEO sample is GSM3462 Last updated (according to GEO): May 28 2005 hrs nasal epithelium 1126 1146 CVB3_V-5h Gene expression data from postmorten brain regions Source GEO sample is GSM145201 Last updated (according to GEO): Nov 20 2006 Gene Expression data from the suprachiasmatic nucleus of an animal euthanized 1.5 hours after lights off. Source GEO sample is GSM159292 Last updated (according to GEO): Oct 31 2007 SCG explant cultured for 65 hours in vitro Source GEO sample is GSM246063 Last updated (according to GEO): Dec 03 2007 861 Blood Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141326 Last updated (according to GEO): Oct 26 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145988 Last updated (according to GEO): Nov 20 2006 1500 mg/kg X 6 hr Source GEO sample is GSM129841 Last updated (according to GEO): Sep 18 2007 M_U133Plus_36_nAcc Isolated adipocytes from intraabdominal adipose issue Source GEO sample is GSM210985 Last updated (according to GEO): Jul 17 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145841 Last updated (according to GEO): Nov 20 2006 brain, Left frontal Lobe: Extract23_le1 Spleen vs Sphingosine-1-phosphate Treated B cell 240min (set1) Primary small cell lung carcinoma 3170 Source GEO sample is GSM17344 Last updated (according to GEO): May 28 2005 40 21 from the hippocampus total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5824 Last updated (according to GEO): May 27 2005 Pool of total RNA from 2 euploid cerebella at P30 postnatal stage Keywords = Down syndrome Keywords = Chromosome 21 Keywords = Transcriptome Keywords = Microarray Keywords = Brain Keywords = Cerebellum Keywords = Development Source GEO sample is GSM27477 Last updated (according to GEO): May 27 2005 the heart 987 996 Structure of hemidiaphragm 861 tongue_main_corpus_1 71 CB B Brown Adipose Tissue Keywords = mouse gene expression database Source GEO sample is GSM29328 Last updated (according to GEO): May 27 2005 UET-13TR-EWS/ERG72hr tet+ Prefrontal Cortex Source GEO sample is GSM105470 Last updated (according to GEO): Apr 17 2006 Parkinson Disease 1000 MGJZ030207041Buterus Seminoma 1000 within adipose tissue 1526 1547 1100 1077 of Medulloblastoma - 8 - Expression profiling of spinal cord section (T10) extracted from rats 4h following severe injury Source GEO sample is GSM31376 Last updated (according to GEO): May 27 2005 Neocortical and hippocampal gene expression in kainate- and nicotine-injected juvenile mice Amygdaloid structure 1000 861 Blood n/a Source GEO sample is GSM178020 Last updated (according to GEO): Jun 11 2007 Spleen 0 5 Hippocampus 861 SN:1010408 Source GEO sample is GSM115390 Last updated (according to GEO): Jun 20 2006 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11218 Last updated (according to GEO): May 28 2005 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the lv samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12326 Last updated (according to GEO): May 28 2005 861 Colon from brain 21 30 1000 Heart failure KO_IL-6_0_rep3 healthy control sample x027 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16658.gif Source GEO sample is GSM81569 Last updated (according to GEO): Sep 22 2006 cerebral cortex 0 14 with myocardial infarction 313 339 Neoplasm 861 NCI60.2_LABEL125EXTRACT64SUB3 Source GEO sample is GSM134000 Last updated (according to GEO): Aug 06 2007 whole blood_100354 Brain 861 861 Lung Endometrium 0 10 Central gray substance of midbrain 861 MP-5 T-ALL-C4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A PGA-MCR-ctr-12h-1aAv2-s1 L_AK_Control_ZT 6_2 26 15 endometrioid 91 from the bone marrow 72 Hippocampus Source GEO sample is GSM107920 Last updated (according to GEO): Jun 06 2006 861 Carcinoma 1000 Spinal Cord Parkinson's model voxel I4 Gene expression data from postmorten brain regions Source GEO sample is GSM145429 Last updated (according to GEO): Nov 20 2006 1000 Cerebral cortex adenoma 861 brain 0 5 Lung Neuroendocrine Neoplasm 983 cerebellum wistar ky 3894 PGA_MI_ilv_8w_326 901 Coronary artery Muscle 861 nic + nmda1 (Experiment Neuroprotection4- Run 21823) Treatment, type=timepoint, description=Same sample used for Experiment Neuroprotection4-Run 14985, samples were rerun due to oven failure, measurement=0.0 h Source GEO sample is GSM96698 Last updated (according to GEO): Feb 14 2006 Tumor tissue heterogeneity is a well known feature of several solid tumors. Neuroblastic Tumors (NTs) is a group of paediatric cancers with a great tissue heterogeneity. Most of NTs are composed of undifferentiated, poorly differentiated or differentiating neuroblastic (Nb) cells with very few or absent Schwannian stromal (SS) cells: these tumors are grouped as Neuroblastoma (Schwannian stroma-poor). The remaining NTs are composed of abundant SS cells and classified as Ganglioneuroblastoma (Schwannian stroma-rich) intermixed or nodular and Ganglioneuroma. The importance to understand Nb and SS gene signatures in NTs, is to clarify the complex network mechanism of tumor growth and progression. In order to identify the Nb and SS cells gene signatures, we analyzed the gene expression profiling of 19 cases of neuroblastic tumors: 10 stroma poor (NTs-SP) and 9 stroma rich (NTs-SR), by high density oligonucleotide microarrays. Moreover, the analysis was performed in parallel on both whole and laser microdissected tumor samples: from 4 of 19 cases, was isolated different areas all composed of pure cellular populations. We performed genome wide expression analysis by using Affymetrix technology and we used two different approaches for data analysis: SAM (Significance Analysis of Microarrays) and a method based on Game Theory (GT), to identify genes differently expressed in SS and Nb cells. Differently from the SAM method, the analysis based on GT (Moretti et al. (2006)) gives the advantage of selecting relevant genes not only according to the expression profile of each single gene, but considering also gene interaction. Last Updated (by provider): Apr 16 2007 Contributers: Domenico Albino Stefano Moretti (cortex 19 25 Brain 861 Malignant neoplasm of liver 901 Primary large cell lung carcinoma 745 0 36 Brain 861 park_1151_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A at the Human Brain 724 741 1000 Intestines, Small brain, hippocampus: PR-CA3-9_e1_le1 brain, cerebral cortex: Rat_03-24_NroLep_Lipska_e1_le1 Fibroblasts 861 Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep3 75 65 Normal Lung 14 7 amygdala M_U133Plus_116_HC brain, amygdala: Amygdala 12_le1 HC83 CN B brain, forebrain: Sample10_e1_le1 21 0 Mammary Gland @ Preg7 2500 mg/kg X 24 hr Source GEO sample is GSM129858 Last updated (according to GEO): Sep 18 2007 Primary tumor 19 32 medulla_10 Source GEO sample is GSM80724 Last updated (according to GEO): Mar 31 2006 Osteoblasts 1000 Gene Expression Comparison of First Passage vs. Primary Human and Mouse Retinal Sphere Cells - Mus musculus Arteries 861 b6 brain, hindbrain and spinal cord: P5KO3_e1_le1 861 Liver I_U133A_29_AnCg 983 Muscle Nasal Epithelium Inhalation Formaldehyde 0ppm 19d ID75 Congenital Abnormality 853 1000 Left brain_DLPFC_bipolar B_mr867 5 0 brain CAD_replicate13 spinal cord rep 3 16 32 861 Medulla 3_hypothalamus_12hrs_sleep_#111 10_0020_SepticShock_Day1_57 0 Human Cortex 11 1000 Brain none Source GEO sample is GSM244558 Last updated (according to GEO): Nov 23 2007 "Sample 44,>5 yr survival(62 months) age 53 erp no" on vantveer-oligo CNS-RM_Mod4h-1B-s2 858 Mesodermal cell Ovary_Normal_UM-NO-5 Lymphoblastoid Cell Line for Individual 8043.3 log phase 10 0 hippocampus 901 Coronary artery Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=720590 LaserPower=2.041.31 Lot batch = LC17N027 Source GEO sample is GSM4779 Last updated (according to GEO): Nov 21 2005 361 335 hypertrophic cardiomyopathy Liver 1000 928 Hyperinsulinism GM12761 861 Bladder Brain 861 AKR/J Cingulate Cortex D 211 190 with coxsackievirus B3 0 Epithelial cells 15 1BMH02083004_PB_CD14Monocytes male MhmBN chip 27 91 from the bone marrow 72 CNS-SC_Inj24h-1C-s2 HDMTX-12 Epithelium of bronchus 983 in the aged cortex 640 658 Heart 1000 Brain 1000 Skeletal bone 861 Ovary 1000 To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at ?80C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at ?80°C before routine processing for GeneChip analysis. Source GEO sample is GSM28660 Last updated (according to GEO): Oct 28 2005 Richard Almon-41-1138200270696 Abdomen 861 901 Coronary artery 1100 1077 of Medulloblastoma - 8 - Blood Test (Blinded) Sample Source GEO sample is GSM129942 Last updated (according to GEO): Sep 18 2007 Nasal Epithelium 901 Ganglia 1000 SN:Human Glioblastoma Biopsy 07091 GSE5961 adenoma 861 12 The prefrontal cortex 32 C57BL/6J Olfactory Bulb C Normal Source GEO sample is GSM176137 Last updated (according to GEO): Apr 09 2007 Infection 861 Heart 861 14 days hindlimb suspended RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis. Source GEO sample is GSM10056 Last updated (according to GEO): May 28 2005 78 66 Control blood Spleen 1000 of the brain 233 245 Gene expression data from postmorten brain regions Source GEO sample is GSM145132 Last updated (according to GEO): Nov 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145882 Last updated (according to GEO): Nov 20 2006 Skeletal bone 861 B6C3Fe-SpinalC-1moM-1aAv2-s2 AML_17 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A from the sarcolemma 146 164 advanced HCC Source GEO sample is GSM155942 Last updated (according to GEO): Jun 21 2007 Large-scale analysis of the human transcriptome. Prostate cancer Source: University of Virginia, see PMID 11507037 Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 185.65 Stdv: 7.90 Min: 171.05 Max: 197.40 Source GEO sample is GSM2863 Last updated (according to GEO): May 27 2005 1000 Structure of corneal epithelium R589P01070 GC (HKG39T) Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68206 Last updated (according to GEO): Jul 07 2006 e_B13 LDMTX_MP-10 Tumor__Prostate_Adeno_LocalCaP1T on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 928 Endometrium Dorsal Root Ganglia 9 Normal entorhinal cortex layer II stellate island cells Source GEO sample is GSM107523 Last updated (according to GEO): May 01 2006 plasma cells 332 344 We evaluated cutaneous contact hypersensitivity (CHS) in Cnr1-/-/Cnr2-/- animals using the obligate contact allergen 2,4-dinitrofluorobenzene (DNFB), which generates a specific cutaneous T-cell mediated allergic response upon repeated allergen contact. Allergic contact dermatitis affects about 5% of men and 11% of women in industrialized countries and is one of the leading causes for occupational diseases. In an animal model for cutaneous contact hypersensitivity we show that mice lacking both known cannabinoid receptors display exacerbated allergic inflammation. In contrast, fatty acid amide hydrolase deficient mice, which have increased levels of the endocannabinoid anandamide, displayed reduced allergic responses in the skin. Cannabinoid receptor antagonists exacerbated whereas receptor agonists attenuated allergic inflammation. These results demonstrate a protective role of the endocannabinoid system in contact allergy in the skin, and suggest a novel target for therapeutic intervention. Last Updated (by provider): Jun 11 2007 Contributers: Andreas Zimmer Evelyn Gaffal Thomas Tüting Lihua Wang-Eckhardt Meliha Karsak Sensitized on days 0 and 3 with ragweed pollen protein and alum, challenged intratrecheally on days 10 and 17 with ragweed pollen protein and sacrificed after 72h. Lot batch = Source GEO sample is GSM1274 Last updated (according to GEO): May 28 2005 days nasal epithelium 1126 1147 Muscle 861 CNS-SCsev_InjB4h-2A-s2 Salivary Gland [JunctionChip 1 of 5] D_U133Plus_110_HC P46 non-deprived visual cortex replicate 1 Cells isolated from whole bone marrow Source GEO sample is GSM149534 Last updated (according to GEO): Apr 27 2007 from ventral prostate 21 41 Spleen vs CpG-oligodeoxynucleotide Treated B cell 60min (set2) Infection 1000 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b018 Source GEO sample is GSM1994 Last updated (according to GEO): Nov 21 2005 in the mammalian nervous system 110 141 1046 1030 during infection plasma cells 332 344 olfactory epithelium 194 213 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114227 Last updated (according to GEO): Jun 16 2006 Brain 861 Neoplasm 861 1000 Prostate NHF1-hTERT_G2_C3_16168 16 7 cerebellum 32h-AM replication 1 Keywords = preimplantation Keywords = development Source GEO sample is GSM14707 Last updated (according to GEO): May 28 2005 Mouse Kidney Female 2 (technical replicate) Monocular deprivation right cortex, biological rep1 CHC MD-3 Normal__Pancreas_Pan13N on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Control Mouse 4 Transitional epithelium 1000 Wildtype cocaine, biological replicate 3 HC66 CN A Liver 1000 CA99-43A none Source GEO sample is GSM161910 Last updated (according to GEO): Feb 16 2007 1000 Neoplasm Laser captured visceral sensory neurons. Source GEO sample is GSM63663 Last updated (according to GEO): Dec 21 2005 Brain 1000 861 Cochlear structure Vestibular organ 0 15 Hypothalamus Source GEO sample is GSM107907 Last updated (according to GEO): Jun 06 2006 Recommended Affymetrix protocols were followed. Source GEO sample is GSM148471 Last updated (according to GEO): May 01 2007 of the lamina propria 1628 1648 Nasal Epithelium 865 in murine small intestine 76 100 healthy subject Source GEO sample is GSM211070 Last updated (according to GEO): Sep 10 2007 Neoplasm 861 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184783 Last updated (according to GEO): Apr 26 2007 Nose 1000 HTI-286 in docetaxel-refractory prostate cancer Source GEO sample is GSM206100 Last updated (according to GEO): Jun 29 2007 25 7 Right Temporal Lobe 136 131 Aortae normal lung 1050 Source GEO sample is GSM17288 Last updated (according to GEO): May 28 2005 Primary tumor 19 32 brain, cerebral cortex: Sham6_e1_le1 Normal Source GEO sample is GSM176390 Last updated (according to GEO): Apr 09 2007 transplanted nmd spinal cord 818 845 Wild type P18 mouse visual cortex ipsilateral to monocular enucleation Source GEO sample is GSM97199 Last updated (according to GEO): Feb 17 2006 days nasal epithelium 1126 1147 corpus_callosum_9 Source GEO sample is GSM80646 Last updated (according to GEO): Mar 31 2006 seminoma specimen, pT2, patient age: 46y; W03 017 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211256 Last updated (according to GEO): Jul 18 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114449 Last updated (according to GEO): Jun 16 2006 NA18635 61 50 Spleen C57BL Stem cells 901 X-ray irradiation (2 Gy) and TGFB added. Source GEO sample is GSM203981 Last updated (according to GEO): Jun 25 2007 NCI60.38_LABEL42EXTRACT41SUB3 Source GEO sample is GSM134182 Last updated (according to GEO): Aug 06 2007 with some respiratory epithelium. 1039 1072 Heart [JunctionChip 4 of 5] Neoplasm 1000 Neoplasm 861 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 1 hour after lights on. Original sample code = CM38A Source GEO sample is GSM227330 Last updated (according to GEO): Sep 10 2007 MuscleRegen-con8wk-1RLAv2-s2 Leukemic fractions of ID70 AML patient have been hybridized. Source GEO sample is GSM154055 Last updated (according to GEO): Feb 26 2007 Sample 3 at Time 3 Source GEO sample is GSM113093 Last updated (according to GEO): Jun 06 2006 P2B_KIDNEY_12 cortex 7 12 Metastasis is the deadliest phase of cancer progression. Experimental models using immunodeficient mice have been used to gain insights into the mechanisms of metastasis. We report here the identification of a ?metastasis aggressiveness gene expression signature? derived using human melanoma cells selected based on their metastatic potentials in a xenotransplant metastasis model. Comparison with expression data from human melanoma patients shows that this metastasis gene signature correlates with the aggressiveness of melanoma metastases in human patients. Many genes encoding secreted and membrane proteins are included in the signature, suggesting the importance of tumor-microenvironment interactions during metastasis. Last Updated (by provider): Jun 04 2007 Contributers: R O Hynes K Ross Y Hoshida Lei Xu S Ramaswamy A Subramanian Steven S Shen JP Brunet S N Wagner J P Mesirov Squamous cell carcinoma 3 0 24 Brain 861 O377 homozygotes brains_3 30 (orbitofrontal cortex 50 861 Labyrinth GM12717 Sample39, Post Injury 24 hours Treatment, type=wait Source GEO sample is GSM53290 Last updated (according to GEO): Jul 06 2005 Hypothalamus of rats before and during subjection to long term (30d) heat acclimation and hypohydration (10% loss of b. wgt, water deprivation). RNA extraction was accomplished using Tri Reagent (Molecular Research Center Inc. Ohio, USA). The probes were labeled for 1 h by the reverse transcription of total RNA (3 µg) at 42°C in a primer mix (Clontech) containing [32P]dATP (Amersham Biosciences, Buckinghamshire, UK). The reaction was terminated by adding 0.1M EDTA and 1 mg/ml glycogen (Sigma).The unincorporated 32P-labeled nucleotides were removed by Nucleo-Spin extraction columns (Clontech). Source GEO sample is GSM63225 Last updated (according to GEO): Oct 28 2005 Prostate 861 7 cerebral cortex 21 brain 0 5 19 0 human frontal cortex Probeset expression data from NA12751 growth 2, replicate 5 Source GEO sample is GSM195212 Last updated (according to GEO): Aug 08 2007 84 69 by heart failure 901 frontal lobe 1000 Spleen I_U133Plus_116_Amy Thalamus Subthalamic Nucleus 1 Disease 1000 Brain Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13430.gif Source GEO sample is GSM79686 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145378 Last updated (according to GEO): Nov 20 2006 AK_SleepDep_ZT 6_3 HDMTX-3 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with MIP3-alpha labeled with Cy5- time course with repeats. Date GSE391 Last Updated: May 29 2005 Contributers: Joella Grossoehme Yun Anna Cao Sangdun Choi Angela Alexander Mi Sook Chang Zhen Yan Rebecca Hart Jong-Woo Kim Robert Hsueh Sun Young Lee Includes GDS312. Update date: Nov 18 2003. Dataset description GDS312: Temporal analysis of effects induced by 120 nM macrophage inflammatory protein-3 in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. Cerebellum_nontransgenic control A39_8 months_replicate 2 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188809 Last updated (according to GEO): Jun 06 2007 Skin 1000 B371 on Affymetrix GeneChip Human Full Length Array HuGeneFL Locus Coeruleus Source GEO sample is GSM107933 Last updated (according to GEO): Jun 06 2006 Fibroblasts 1000 9 of prefrontal cortex 28 1000 Communicable Diseases Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour.This animal was sacrificed at 2 hours after lights on.Original sample code = CM3A Source GEO sample is GSM227325 Last updated (according to GEO): Sep 10 2007 Replicate3_Voxel F4 1000 Tibialis anterior muscle structure 1000 Retina Richard Almon-35-1133800609839 2007 1993 adhering blood Plasma 861 861 Cerebral cortex HapMap CEU_parent Female Source GEO sample is GSM159554 Last updated (according to GEO): Feb 01 2007 Nasal Epithelium 1000 1000 Brain CNS_SF268 on Affymetrix GeneChip Human Full Length Array HuGeneFL f2#239 versus pool Mouse Brain tissue 257 237 cognitive impairment Dorsal Raphe Source GEO sample is GSM107926 Last updated (according to GEO): Jun 06 2006 20 0 human caudate nucleus 5 0 brain CAKI-1 hgu95b 386 0b Granulosa cell of ovary 923 1968 1958 for livers The goal of these experiments was to identify the genes that are regulated by CCAT, a novel transcription factor derived from the C-terminus of CaV1.2. Neuro2A neuroblastoma cells were transfected with the last 503 AA of CaV1.2 which is full length CCAT (CCAT FL) or with the last 280 AA of CaV1.2, a form of CCAT that lacks the transcriptional activation domain (CCAT DTA). The mRNA from either CCAT FL or CCAT DTA expressing cells was hybridized to Agilent mouse genome microarrays along with mRNA from untransfected neuro2A cells. The microarray data was subsequently analyzed with the Rossetta Luminator gene expression data analysis system. Subsequent investigation revealed that CCAT DTA can still activate transcription albeit at much lower levels than CCAT FL. Source GEO sample is GSM95645 Last updated (according to GEO): Feb 07 2006 12 hr EE repl 1 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181123 Last updated (according to GEO): Jul 12 2007 CAD_replicate106 6 week mutant OMN rep 1 63 50 Prostate C57BL Nervous system structure 901 22 7 bone marrow cell Cartilage plays a fundamental role in the development of the human skeleton. Early in embryogenesis, mesenchymal cells condense and differentiate to chondrocytes to shape the early skeleton. Subsequently, the cartilage anlagen differentiate to form the growth plates, which are responsible for linear bone growth, and the articular chondrocytes, which facilitate joint function. However, despite the multiplicity of roles of cartilage during human fetal life, surprisingly little is known about its transcriptome. To address this, a whole genome microarray expression profile was generated using RNA isolated from 18-22 week human distal femur fetal cartilage and compared with a database of control normal human tissues aggregated at UCLA, termed CELSIUS. From the wealth of data, 161 cartilage-selective genes were identified, defined as genes significantly expressed in cartilage with low expression and little variation across a panel of 34 non-cartilage tissues. Among these 161 genes were cartilage-specific genes such as collagen genes and 25 genes which have been associated with skeletal phenotypes in humans and/or mice. Many of the other cartilage-selective genes do not have established roles in cartilage or are novel, unannotated genes. Quantitative RT-PCR confirmed the unique pattern of gene expression observed by microarray analysis. Defining the gene expression pattern for cartilage has identified new genes that may contribute to human skeletogenesis as well as provided further candidate genes for skeletal dysplasias. The data suggest that fetal cartilage is a complex and transcriptionally active tissue and demonstrate that the set of genes selectively expressed in the tissue has been greatly underestimated. Last Updated (by provider): Jul 06 2007 Contributers: Zachery A Cohn Deborah Krakow Daniel H Cohn Allen Day Vincent A Funari Stanley F Nelson Zugen Chen Expression profiling of spinal cord section (T10) extracted from rats 14d following severe injury Source GEO sample is GSM31344 Last updated (according to GEO): May 27 2005 1000 Spleen brain_OFC_control C_mr96 Hypothalamic structure 861 Normal_1801 23 11 of the kidney 861 Neoplasm Brain 1000 cerebral cortex sprague 3914 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 5 day time point Source GEO sample is GSM159735 Last updated (according to GEO): Apr 23 2007 129 JD2:1-4 Dentate Gyrus Normal Source GEO sample is GSM176381 Last updated (according to GEO): Apr 09 2007 Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_3 months_replicate 2 KT99_CAN/AR3 5 0 brain 12 Down syndrome 0 DBA/2J Chronic morphine treated, striatum, biological replicate 3 Source GEO sample is GSM187991 Last updated (according to GEO): Jun 14 2007 7 0 prostate Pituitary Gland 861 Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92281 Last updated (according to GEO): Jan 13 2006 Gene expression data from whole tumor Source GEO sample is GSM182293 Last updated (according to GEO): Apr 16 2007 861 Ovary 17 7 hippocampus A HID B D011 Spinal cord tissue from wildtype mice Treatment, type=linear_amplification, description=T7-based RNA amplification Source GEO sample is GSM113697 Last updated (according to GEO): Jun 09 2006 In this dose series pregnant CD-1 (outbred) dams were exposed to the 2-chloro analogue of 2'-deoxyadenosine (a metabolic toxin) on 8 d.p.c. Test doses were developed from a teratological series for 2CdA-induced microphthalmia using BMDS modeling software from the US EPA. Benchmark doses for microarray analysis were: 5.0 mg/kg (25% risk), 2.5 mg/kg (5% risk), 1.25 mg/kg (NOAEL), and 0.625 mg/kg (subNOAEL). All measurements were on RNA from the embryo proper at 3.0h post-treatment.. Date GSE1068 Last Updated: May 29 2005 Contributers: Jeffrey H Charlap Kimberly R Nemeth Amar V Singh Thomas B Knudsen Includes GDS630. Update date: Jul 13 2004. Dataset description GDS630: Dose response analysis of ocular teratogen 2-chloro-2'deoxyadenosine (2CdA) exposure and induction of microphthalmia (small eye syndrome). Pregnant 8 days post coitum CD-1 dams exposed to 5, 2.5, 1.25 or 0.625 mg/kg 2CdA, and embryos examined at 3 hours.. 10 7 Left gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134643 Last updated (according to GEO): Jul 09 2007 Coronary artery 901 Expression profiling of spinal cord section (T10) extracted from rats 14d following mild injury Source GEO sample is GSM31315 Last updated (according to GEO): May 27 2005 lg_NY23 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181178 Last updated (according to GEO): Jul 12 2007 DNA Damage 1000 Brain 861 Nasal Epithelium 865 Gene expression data from postmorten brain regions Source GEO sample is GSM144884 Last updated (according to GEO): Nov 20 2006 861 Blood CNS-SpinalC-conAdult-24h-1C-s2 7125_Lung did not develop PGD Spleen vs Leukotriene B4 (LTB4)Treated B cell 240min (set2) Brain 861 left 35 38 mouse hippocampus, cox-2 heterozygous, rep3 Small cell carcinoma of lung 867 25 17 (cerebrum SQ-SQ20t1-A366-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 352 340 encephalitis Bronchial epithelial cell line Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181120 Last updated (according to GEO): Jul 12 2007 METH 3 large intestine sprague2 whole tissue, individual animal, 10 weeks old, male Sprague Dawley large intestine file:R3JW02103014 Source GEO sample is GSM15212 Last updated (according to GEO): May 28 2005 C57BL/6J hippocampus rep1 (430 2.0 Array) 1000 Skeletal muscle structure at the Human Brain 744 761 1000 Plasma I_U133A_13_Amy Category: Serum-response Subcategory: Fibroblasts Scanning Software: unknown Software version: unknown Lot batch = 407 Source GEO sample is GSM2159 Last updated (according to GEO): Nov 21 2005 TUMOR 31 0 7 mouse brain ipsilateral LPS Source GEO sample is GSM149770 Last updated (according to GEO): Mar 15 2007 14 0 globus_pallidus 56 37 with chronic malaria Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211232 Last updated (according to GEO): Jul 18 2007 Autistic Disorder 877 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202686 Last updated (according to GEO): Jun 20 2007 793 781 in the brains 1000 jejunum Tumor__Uterus_Adeno_4840 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Pregnant females fed with maltose dextrin, PF04 (Pair Fed) corresponds to replicate 4 CNS-SCmod_InjB24h-1A-s2 19 0 human frontal cortex Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 5389 left_liver_lobe Mek exp2 control Skeletal bone 861 1000 Brain tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44892 Last updated (according to GEO): May 27 2005 SCCH196 SQ-SQ14t1-A365-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Brain 861 Temporal Lobe 2 Normal Bipolar Disorder 1000 plasma cells 332 344 Prostate 861 1BJZ02041227_salivarygland Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 9 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10949 Last updated (according to GEO): May 27 2005 Brain 861 VDXKIU_15D7 T10__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A pooled RNA of the kidney of 36 day old rats Source GEO sample is GSM86655 Last updated (according to GEO): Jun 12 2006 861 Cardiomyopathies Alzheimer's Disease 861 plasma cells 50 61 13 0 Nervous System Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210423 Last updated (according to GEO): Jul 16 2007 1000 Hippocampus Subthalamic Nucleus 6 Normal none Source GEO sample is GSM244627 Last updated (according to GEO): Nov 23 2007 Brain_MGlio_3_Malignant Glioma on Affymetrix GeneChip Human Full Length Array HuGeneFL Parkinson's disease sample x115 0 30 A/J Cerebellum F 861 Cerebellum Primary tumor 19 32 27 0 Leukemia Chronic Myelogenous 1000 Cerebral cortex GBM Treatment, type=remove Source GEO sample is GSM99477 Last updated (according to GEO): Apr 21 2006 Occipital lobe 861 M_U133Plus_117_HC Spleen vs 2-Methyl-thio-ATP Treated B cell 240min (set1) C49 on NCI-7.6k 20 0 human caudate nucleus 3AJZ02022105_ leukemia, chronic Myelogenous K-562 Communicable Diseases 1000 GC (HKG81T) Expression profiling of spinal cord section (T8) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM6646 Last updated (according to GEO): May 28 2005 Jejunum [JunctionChip 2 of 5] Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_3 months_replicate 4 Normal human tissue:Normal Thyroid Keywords = Human, Normal Tissue, Normal Thyroid Source GEO sample is GSM44685 Last updated (according to GEO): May 27 2005 861 Salivary Glands Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11449 Last updated (according to GEO): May 28 2005 Thalamic Diseases 862 C57BL/6J SAL, Rep2 of a colorectal adenoma 7 29 Plasma 861 Primary Neoplasm 1000 A HID U D053 brain, cerebellum: WCb4w#1_e1_le1 Primary tumor 19 32 subthalamic_nucleus_3 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 6071 left_liver_lobe 1517 1497 of adhesion molecules D2_Control_ZT 18_2 in the brain 150 162 Striatal sample from a 12-month-old Hdh4/Q80 mouse. Source GEO sample is GSM238693 Last updated (according to GEO): Oct 19 2007 I_U133A_17_AnCg Communicable Diseases 861 Heart Septal Defects 884 1000 Rectum CLL-67 PP164_infected_DC AT1-hTERT_1.5Gy_6h_C5_21712 1000 Amygdaloid structure 1000 Liver Cirrhosis low gestational age Source GEO sample is GSM213119 Last updated (according to GEO): Jul 25 2007 861 Malignant Neoplasms SN7d(3) Epithelial Cells 901 of 1589 tumor 24 36 PGA_MI_nilv_8w_326 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=680640 LaserPower=1.951.32 Lot batch = LC17N024 Source GEO sample is GSM4776 Last updated (according to GEO): Nov 21 2005 WGACON-84 1000 Coronary Arteriosclerosis CNS-SC_Inj24h-1B-s2c PMN_LB_360min_Patient17 brain, brainstem: CB2_e1_le1 Brain 1000 Brain 1000 DMN-CtrHippo15d-1bAv2-s2 Heart 861 1000 Brain plasma cells 50 61 ipsi Cortex 7 17 27 17 (cerebellum mRNA was isolated after 24 hours of incubation from IMR-90 cells seeded onto a collagen/chondroitin sulfate tissue engineering scaffold mesh material. Cells were seeded at a density of 1 x 10^6 cells/ mesh, and this chip represents a pooling of cells from 4 meshes. Keywords = tissue engineering mesh, collagen, chondroitin sulfate, biomaterials design Source GEO sample is GSM6048 Last updated (according to GEO): May 27 2005 Neocortical astrocyte 3 The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76955 Last updated (according to GEO): Oct 11 2005 Blood Test (Blinded) Sample Source GEO sample is GSM129985 Last updated (according to GEO): Sep 18 2007 B6 day 6, biological rep 2, tech rep 1 Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for twelve weeks. Source GEO sample is GSM148664 Last updated (according to GEO): Dec 12 2006 primary tumor growth 691 710 239 233 Retinas D_U133A_35_Amy Expression profile of genes in mouse brain Source GEO sample is GSM21048 Last updated (according to GEO): May 27 2005 Study of in vitro granulocyte differentiation Source GEO sample is GSM137472 Last updated (according to GEO): Jun 06 2007 Gene expression data from a hippocampus from mouse injected 15 mg/kg kainate Source GEO sample is GSM147423 Last updated (according to GEO): Jan 03 2007 727 721 spleens Untreated versus treated (bortezomib) breast cancer cells. Source GEO sample is GSM120352 Last updated (according to GEO): Jul 20 2006 861 Cardiomyopathies 901 Heart failure 5 0 brain Spinal Cord 1000 C57 whole brain 1B Cortex_reserpine_treated_rep2 nostrils 156 164 plasma cells 50 61 10 Bone marrow 0 R7N 5 Epithelium of bronchus 983 of regenerating Dorsal Root Ganglia 21 55 Wild type inbred mice Source GEO sample is GSM82914 Last updated (according to GEO): Nov 10 2005 with multiple myeloma 1834 1855 Prostate 861 Head and neck cancer Source GEO sample is GSM155650 Last updated (according to GEO): Apr 24 2007 Temporal Cortex Alzheimer's disease 10 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with 2-Methyl-thio-ATP for 30min Source GEO sample is GSM5420 Last updated (according to GEO): May 27 2005 61 41 from postmortem brain 861 Malignant neoplasm of prostate Infection 1000 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P18, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3220 Last updated (according to GEO): May 28 2005 SF-268_CL12014_CNS on Affymetrix GeneChip Human Full Length Array HuGeneFL Lymphoblastoid Cell Line for Individual 8103.4 log phase Spleen 1000 Menstrual phase - Follicular Source GEO sample is GSM175785 Last updated (according to GEO): Apr 09 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM144907 Last updated (according to GEO): Nov 20 2006 Amygdaloid structure 1000 5 0 Muscle A catalytic antioxidant (AEOL 10150) atenuates expression of inflammatory genes in stroke. White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by 6 hours of reperfusion; first replicate; pooled mRNA from 6 brains. Source GEO sample is GSM2213 Last updated (according to GEO): May 27 2005 blood 0 5 966 Hippocampus NG010_b Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92291 Last updated (according to GEO): Jan 13 2006 Large-scale analysis of the mouse transcriptome. Eye C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 267.25 Stdv: 8.85 Min: 253.99 Max: 280.72 Source GEO sample is GSM2944 Last updated (according to GEO): Mar 20 2006 M_U133Plus_112_nAcc Cerebral cortex 861 Lymphoblastoid Cell Line for Individual 8107.3 log phase GC (HKG9T) Temporal Lobe 8 Normal whole blood_101025 Communicable Diseases 901 Ny13: Hippocampus_5T-AU_rep8 Gene expression data from aneurismal tissues obtained from patients with bicuspid valves. Source GEO sample is GSM116792 Last updated (according to GEO): Jun 28 2006 Bladder sample 1117-1 Tumors 91 96 B363 on Affymetrix GeneChip Human Full Length Array HuGeneFL Affymetrix protocol Source GEO sample is GSM213807 Last updated (according to GEO): Aug 02 2007 Osteoblasts 1000 Seizures 1000 Dystrophin 1000 E2A-PBX1-2M#1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from whole brain infected mouse, day 3 Source GEO sample is GSM189649 Last updated (according to GEO): May 16 2007 jzo033-rp1-v5_u74av2-met 1000 Spleen 861 Retina 7 frontal cortex 20 Heart 1000 CD3 beads 24.00 hr. T-Cell Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11584 Last updated (according to GEO): May 28 2005 660 mesenchymal stem cell 639 901 Heart Diseases 1000 Liver Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132539 Last updated (according to GEO): Feb 26 2007 Testis 1000 mouse brains 187 198 PBMCs-Type 1 Diabetes-IDDM42_T1D_1MO 490_9d Gene expression data of substantia nigra from postmortem brain of normal controls Source GEO sample is GSM184361 Last updated (according to GEO): May 29 2007 Muscle 1000 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211353 Last updated (according to GEO): Jul 18 2007 M_U133A_31_DLPFC_R Pooled quad RNA samples from five 8 wk old male mdx5cv mice Source GEO sample is GSM13728 Last updated (according to GEO): May 28 2005 Femur 1000 Myocardial Infarction 1000 1000 Maxilla Biopsy of a colorectal adenoma from patient #12 S25 NLS 142Q TG1 F4/23 S25 NLS Htt exon 1 142Q Mouse 3 months Cerebellum Male Source GEO sample is GSM73203 Last updated (according to GEO): Sep 06 2005 Recommended Affymetrix protocols were followed. Source GEO sample is GSM148473 Last updated (according to GEO): May 01 2007 GC (HKG69N) 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201255 Last updated (according to GEO): Jun 14 2007 an infantile autosomal-recessive motor neuron disease 69 121 none Source GEO sample is GSM149609 Last updated (according to GEO): Jan 03 2007 1000 Brain 849 804 metastatic, hormone-refractory prostate cancer ProstateCancer-15 on NHGRI-6.5k_c "Sample 53, <5 yr survival(3 months) age 28 erp no" on vantveer-oligo Osteoblasts 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145388 Last updated (according to GEO): Nov 20 2006 long access to cocaine, amygdala, 6 hrs/day access to cocaine Source GEO sample is GSM93833 Last updated (according to GEO): Jan 26 2006 Substantia nigra normal rep1 Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92298 Last updated (according to GEO): Jan 13 2006 plasma cells 332 344 660 mesenchymal stem cell 639 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118351 Last updated (according to GEO): Jul 11 2006 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy, pathological hypertrophy, rat, heart failure, cardiomyopathy Source GEO sample is GSM12310 Last updated (according to GEO): May 28 2005 Arteries 861 frontal cortex wistar 3660 901 frontal lobe The nose 94 101 endothelial cells sprague1 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11574 Last updated (according to GEO): May 28 2005 AT2-hTERT_1.5Gy_2h_C5_26744 Large Pre-BII cells 10b Localized Carcinoma 853 861 HIV Infections V5-P575 Arteries 861 1000 Decapitation Gene Profiling of Endometrium Reveals Progesterone Resistance and Candidate Genetic Loci in Women with Endometriosis Olfactory Epithelium 1000 Gene expression data from skeletal muscle following 240 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230446 Last updated (according to GEO): Sep 19 2007 Hereditary Malignant Neoplasm 876 304 280 alcoholic cardiomyopathy Carcinoma, Large Cell 867 1000 Skeletal muscle structure 966 Hippocampus Normal Source GEO sample is GSM175845 Last updated (according to GEO): Apr 09 2007 gastric carcinomas 1064 1082 100109 of brain cortex 25 39 Spleen vs Interferon-gamma (IFN gamma) Treated B cell 60min (set3) Liver Test (Blinded) Sample Source GEO sample is GSM130195 Last updated (according to GEO): Sep 18 2007 1000 Heart Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs//17159.gif Source GEO sample is GSM91495 Last updated (according to GEO): Sep 22 2006 Lymph node metastasis 19 40 Expression profiling of spinal cord section (T9) extracted from rats 4h following moderate injury Source GEO sample is GSM31558 Last updated (according to GEO): May 27 2005 Spleen vs IL4 Treated B cell 30min (set1) 330 324 uterus none Source GEO sample is GSM149519 Last updated (according to GEO): Jan 03 2007 114 cortex 120 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114242 Last updated (according to GEO): Jun 16 2006 1000 Tibialis anterior muscle structure 1000 frontal lobe 38 10 from cultured organ of Corti NA18959 Brain 861 This sample was obtained from a 37 years old female heart failure subjects. Good quality sample. Keywords = Congestive heart failure, eNOS, gene, dimethylarginine dimethylaminohydrolase Source GEO sample is GSM6542 Last updated (according to GEO): May 28 2005 Exp 6 (+SB80) left 35 38 861 Brain SN:1007081 Source GEO sample is GSM115362 Last updated (according to GEO): Jun 20 2006 The Huntington's disease (HD) CAG repeat, encoding a polymorphic glutamine tract in huntingtin, is inversely correlated with cellular energy level, with alleles over approximately 37 repeats leading to the loss of striatal neurons. This early HD neuronal specificity can be modeled by respiratory chain inhibitor 3-nitropropionic acid (3-NP) and, like 3-NP, mutant huntingtin has been proposed to directly influence the mitochondrion, via interaction or decreased PGC-1alpha expression. We have tested this hypothesis by comparing the gene expression changes due to mutant huntingtin accurately expressed in STHdh(Q111/Q111) cells with the changes produced by 3-NP treatment of wild-type striatal cells. In general, the HD mutation did not mimic 3-NP, although both produced a state of energy collapse that was mildly alleviated by the PGC-1alpha-coregulated nuclear respiratory factor 1 (Nrf-1). Moreover, unlike 3-NP, the HD CAG repeat did not significantly alter mitochondrial pathways in STHdh(Q111/Q111) cells, despite decreased Ppargc1a expression. Instead, the HD mutation enriched for processes linked to huntingtin normal function and Nf-kappaB signaling. Thus, rather than a direct impact on the mitochondrion, the polyglutamine tract may modulate some aspect of huntingtin's activity in extra-mitochondrial energy metabolism. Elucidation of this HD CAG-dependent pathway would spur efforts to achieve energy-based therapeutics in HD. Ganglia, Spinal 923 basal ganglia Source GEO sample is GSM38974 Last updated (according to GEO): May 27 2005 1000 Hippocampus Hypertensive disease 861 Expression profiling of moderately injured raphe at 14d in rats Source GEO sample is GSM41572 Last updated (according to GEO): May 27 2005 from whole tumor 21 36 Gene expression data from postmorten brain regions Source GEO sample is GSM145407 Last updated (according to GEO): Nov 20 2006 of the colon 28 39 CAD_replicate49 ALL-B-cell-5 on Affymetrix GeneChip Human Full Length Array HuGeneFL tongue epidermis; dorsal tongue surface Source GEO sample is GSM18646 Last updated (according to GEO): May 27 2005 to each tumor 540 552 Endometrium-Normal 8 01_0024_SepticShock_Day3_117 Gene expression data from postmorten brain regions Source GEO sample is GSM145935 Last updated (according to GEO): Nov 20 2006 hrs nasal epithelium 1126 1146 (No additional Information) Source GEO sample is GSM114428 Last updated (according to GEO): Jun 19 2006 low-grade dysplastic liver tissue Source GEO sample is GSM155972 Last updated (according to GEO): Jun 21 2007 Vector-R-30pM brain 0 5 Rats 240h after injection with dose kainate. Treatment, type=time_course, description=KA animals are treated with kainate., measurement=240.0 h Source GEO sample is GSM32096 Last updated (according to GEO): May 27 2005 0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point, biological rep 5 of somatomotor cortex 21 41 Epithelial Cells 901 Endothelial Cells 1000 1008 997 in Ta tumors o Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181931 Last updated (according to GEO): Apr 13 2007 Expression profiling of moderately injured raphe at 24h in rats Source GEO sample is GSM41581 Last updated (according to GEO): May 27 2005 Ovary 3 Normal Myocytes, Cardiac 966 Brain 1000 Keywords = Heart 505 521 0029_1476_H95A2_T95-74_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Brain 861 199-97_Adeno_c 983 Pervasive Development Disorders Brain 861 1000 Brain Epithelium of bronchus 983 861 Cardiomyopathies 53 30 (interventricular septum autism 0 5 Parkinson's model voxel E3 78 66 Control blood large cell lung carcinoma 4222 0 29 I_U133A_102_AnCg Cerebral cortex 861 901 Nervous system structure 1591 1574 such as infection 901 frontal lobe 1000 Solid tumor 91 from the bone marrow 72 166 161 spleen Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11507 Last updated (according to GEO): May 28 2005 14 0 Small Intestine hTERT transduced mammary epithelial cells Source GEO sample is GSM5166 Last updated (according to GEO): May 27 2005 Epithelial Cells 1000 Standard Affymetrix Protocol Source GEO sample is GSM16475 Last updated (according to GEO): May 28 2005 23 0 3AJZ02022105_ leukemia Gene expression data from postmorten brain regions Source GEO sample is GSM145109 Last updated (according to GEO): Nov 20 2006 Normal Source GEO sample is GSM175990 Last updated (according to GEO): Apr 09 2007 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy, pathological hypertrophy, rat, heart failure, cardiomyopathy Source GEO sample is GSM12313 Last updated (according to GEO): May 28 2005 Cells captured via Arcturus LCM system, amplified (RiboAmp, 2 rounds) and labeled (Enzo) for hybridizaton to Affymetrix MG_U74Av2 arrays, using manufacturers protocols in each step. Source GEO sample is GSM6196 Last updated (according to GEO): Mar 17 2006 The epithelial cells 962 981 1000 Basal Ganglia I_U133A_112_CB gene expression of 1 day RA differentiated ESCs Source GEO sample is GSM181964 Last updated (according to GEO): Apr 12 2007 NA12006 GSE375 Replicate2_Voxel A4 CNS-SpinalC-conAdult-48h-2C-s2 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181100 Last updated (according to GEO): Jul 12 2007 HMVEC-L stimulated without LPS for 8 hours c08R2 I_U133Plus_110_AnCg Gene expression data from postmorten brain regions Source GEO sample is GSM145695 Last updated (according to GEO): Nov 20 2006 1000 Structure of locus ceruleus Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 6034 blood Malignant Neoplasms 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145126 Last updated (according to GEO): Nov 20 2006 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-06/6919.gif Source GEO sample is GSM79818 Last updated (according to GEO): Sep 22 2006 nerve, HumanSuralNerve: Human Schwann cell RNA extracts 329 Passage 1_le1 Sample details: We analysed changes in gene expression in the dorsal telencephalon of forebrain-specific FGFR1 mutant mice. Gene expression was compared between the dorsal telencephalons of single E12.5 embryos of two genotypes: FGFR1 heterozygous (HET1,3,8) and homozygous mutants (HOM2,4,7) that were both heterozygous for the FoxG1 transcription factor, as Cre recombinase expression is driven off the endogenous FoxG1 locus in these animals (Hebert, J. M., Lin, M., Partanen, J., Rossant, J. and McConnell, S. K. (2003b). FGF signaling through FGFR1 is required for olfactory bulb morphogenesis. Development 130, 1101-11. & Hebert, J. M. and McConnell, S. K. (2000). Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures. Dev Biol 222, 296-306. Source GEO sample is GSM62848 Last updated (according to GEO): Aug 26 2005 liver, PPARa-null mice, treatment with WY14643 for 5d Source GEO sample is GSM205803 Last updated (according to GEO): Jul 24 2007 1000 Iris Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202681 Last updated (according to GEO): Jun 20 2007 This dataset contains the gene expression profile of a CD11c high, CD4 positive splenic dendritic cell population. The cells were processed directly after isolation. Global scaling was applied to Avg Difference intensity values. Keywords = mouse, dendritic cells, spleen Source GEO sample is GSM4707 Last updated (according to GEO): May 27 2005 901 Caudate nucleus structure total RNA derived from a leprosy lesion Source GEO sample is GSM6775 Last updated (according to GEO): May 27 2005 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198652 Last updated (according to GEO): Jun 06 2007 76 CB A 12 frontal Lobe 23 657 645 how the liver Keywords = kidney 149 166 Epithelium 865 Tumor__CNS_Medulloblastoma_M42_A10 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1217 1207 The tumours Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16876.gif Source GEO sample is GSM81525 Last updated (according to GEO): Sep 22 2006 Whole blood 0 10 Cerebral cortex 861 43 0 Chorionic mesoderm-derived mesenchymal cells olfactory epithelium SR-A mutant mouse 8 hpO Source GEO sample is GSM80206 Last updated (according to GEO): Oct 26 2005 TUMOR 13 A on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A on the mitochondrion 1199 1219 332 315 of medulloblastoma Spleen vs Leukotriene B4 (LTB4)Treated B cell 60min (set2) Gene expression data from postmorten brain regions Source GEO sample is GSM145866 Last updated (according to GEO): Nov 20 2006 cardiac 763 769 outer medulla 31 43 large intestine sprague1 rat hippocampus Treatment, type=time_course, measurement=1.0 h Source GEO sample is GSM32123 Last updated (according to GEO): May 27 2005 NA12750 growth 2, replicate 4 Gene expression data from postmorten brain regions Source GEO sample is GSM144950 Last updated (according to GEO): Nov 20 2006 from colonic normal mucosa 21 47 ES cell line, RNA 70 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the lv samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12334 Last updated (according to GEO): May 28 2005 1667 1657 for obesity Expression profiling of spinal cord section (T9) extracted from rats 7d following severe injury Lot batch = Source GEO sample is GSM7599 Last updated (according to GEO): May 28 2005 total RNA extracted from one ApoE-/- mouse infected wtih a control adenovirus expressing GFP Source GEO sample is GSM157859 Last updated (according to GEO): Jan 25 2007 NG073_a Lymphoblastoid Cell Line for Individual 8007.3 log phase DCIS152 on harvard-12k Lymphoblastoid Cell Line for Individual 8210.3 log phase Effects of SOCS3 on transcriptional response of macrophages to IL-6. Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Replicate 3 unstimulated. Source GEO sample is GSM6086 Last updated (according to GEO): Mar 17 2006 Ganglia 861 Spleen vs CD27 Treated B cell 240min (set1) total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Dimaprit for 240min Source GEO sample is GSM5542 Last updated (according to GEO): May 27 2005 Whole blood from a healthy control Source GEO sample is GSM153497 Last updated (according to GEO): Jan 11 2007 Total RNA extracted from the forebrain of a stg-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144384 Last updated (according to GEO): Nov 14 2006 standard Affymetrix protocol, MAS 5.0 Source GEO sample is GSM9132 Last updated (according to GEO): May 28 2005 Neoplasm 861 Control total RNA was pooled from the kidney of five normal BALB/c mice. Total RNA was extracted from the kidney of BALB/c mice injected with anti-GBM antibody for 7 day. Source GEO sample is GSM15080 Last updated (according to GEO): May 28 2005 Tissue transferred into RNAlater within 30 minutes of removal, and frozen at -20C Source GEO sample is GSM9094 Last updated (according to GEO): May 28 2005 Serum 0 861 Heart Untreated versus treated (bortezomib), untranformed MCF10A and Transformed (see Adler et al, Nature Gen. 2006) Source GEO sample is GSM120279 Last updated (according to GEO): Jul 20 2006 91 from the bone marrow 72 Spleen vs CGS Treated B cell 120min (set2) Nervous System; Striatum Keywords = mouse gene expression database Source GEO sample is GSM29428 Last updated (according to GEO): May 27 2005 The epithelial cells 962 981 Brn3a Knockout TG e13.5 U74Av2 2 brain 0 5 Cerebellum 2 Normal plasma cells 332 344 GBM Treatment, type=remove Source GEO sample is GSM99458 Last updated (according to GEO): Apr 21 2006 spleen 36 41 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68254 Last updated (according to GEO): Jul 07 2006 NoCAD_replicate19 osteoblast 630 640 224 206 Embryonic forebrain I_U133A_67_CB Duchenne muscular dystrophy 0 26 861 Hormones NCI60.19_LABEL23EXTRACT22SUB3 Source GEO sample is GSM134086 Last updated (according to GEO): Aug 06 2007 f2#91 versus pool Mouse Brain tissue M_U133Plus_123_nAcc Medulla 9 Normal cirrhotic liver tissue Source GEO sample is GSM155968 Last updated (according to GEO): Jun 21 2007 GSE3621 atrial septal defects 198 218 Mesenchymal Stem Cells 1000 Cerebellum 1000 a_NY34 Richard Almon-49-1133800610260 Disease Source GEO sample is GSM175913 Last updated (according to GEO): Apr 09 2007 15 0 human cerebellum Epithelial Cells 1000 11 0 Glioblastoma The nose 94 101 52 37 Alzheimer's mice of coronary artery disease 258 284 Kidney 1000 the blood 393 402 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226150 Last updated (according to GEO): Nov 02 2007 1000 Substantia nigra structure M4 biol repl 3 HC66 FC BA4 B I_U133A_7_Amy amygdala rattus_norvegicus_strain iNP animal_number 10 brain 0 5 Mature B cells 1b Replicate2_Voxel C5 5 0 brain Whole blood 0 10 thigh fibroblast (1.5F) serum starved 91 from the bone marrow 72 none Source GEO sample is GSM210335 Last updated (according to GEO): Jul 16 2007 prostate Source GEO sample is GSM203310 Last updated (according to GEO): Jun 21 2007 Gastrointestinal Stromal Tumors 1000 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201243 Last updated (according to GEO): Jun 14 2007 Brain 1000 Cardiac 523 530 GSE1994 with some respiratory epithelium. 1039 1072 Healthy donor SN61_vs_Pool TUMOR 12 0 7 Gene expression data from postmorten brain regions Source GEO sample is GSM145031 Last updated (according to GEO): Nov 20 2006 Mouse ileum with B.thetaiotaomicron_B_5560 D_U133Plus_73_Amy Expression profiling of somatomotor cortex extracted from rats at 7d following sham surgery Source GEO sample is GSM41670 Last updated (according to GEO): May 27 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CGS for 60min Source GEO sample is GSM5513 Last updated (according to GEO): May 27 2005 861 Cardiomyopathies Gene expression data from postmorten brain regions Source GEO sample is GSM144969 Last updated (according to GEO): Nov 20 2006 M_U133A_51_HC Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3874 Last updated (according to GEO): May 27 2005 1000 Brain ACHN hgu95c Brain 1000 24 0 human prostate PC3 tumors Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15561.gif Source GEO sample is GSM84147 Last updated (according to GEO): Sep 22 2006 wild-type mouse cerebellum Treatment, type=time_course, measurement=4.0 weeks Source GEO sample is GSM53346 Last updated (according to GEO): Jul 06 2005 865 Disorder of artery 861 Cancer of Neck 9 of prefrontal cortex 28 1st 6hr C+S-DG Identification of amyotrophic lateral sclerosis (ALS) associated genes. Post mortem spinal cord grey matter from sporadic and familial ALS patients compared with controls.. Date GSE833 Last Updated: Jun 28 2005 Contributers: Steven R Gullans Robert H Brown Fernando Dangond Includes GDS412. Update date: Nov 24 2003. Dataset description GDS412: Identification of amyotrophic lateral sclerosis (ALS) associated genes. Post mortem spinal cord grey matter from sporadic and familial ALS patients compared with controls. Attempt to identify mechanisms by which ALS destroys motor neurons.. 865 Disorder of artery Olfactory Epithelium 901 brain, cerebellum: RNA#41_le1 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68287 Last updated (according to GEO): Jul 07 2006 medulla_8 Source GEO sample is GSM80722 Last updated (according to GEO): Mar 31 2006 Muscle Weakness 1000 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with fMLP labeled with Cy5- time course with repeats. Date GSE381 Last Updated: May 29 2005 Contributers: Zhen Yan Yun Anna Cao Rebecca Hart Sangdun Choi Angela Alexander Mi Sook Chang Robert Hsueh Joella Grossoehme Jong-Woo Kim Sun Young Lee Includes GDS302. Update date: Nov 18 2003. Dataset description GDS302: Temporal analysis of effects induced by 0.1 mM formyl-Met-Leu-Phe in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. 19 0 human frontal cortex Epithelial Cells 901 Hyperdip>50-C32 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A no additional Source GEO sample is GSM199224 Last updated (according to GEO): Jun 08 2007 in the adult heart 44 61 Seminoma 1000 S1_Muscle_Insulin_30min 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114213 Last updated (according to GEO): Jun 16 2006 from the femurs 95 109 brain, hippocampus: CON-DG-26_e1_le1 Structure of entorhinal cortex 1000 Donor 2 Time point 24 hours Autologous Control (uninfected) Source GEO sample is GSM2611 Last updated (according to GEO): May 27 2005 pM category 884 RNA of Kidney was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 biological replicates were analyzed. Keywords = db/m mice Keywords = kidney Source GEO sample is GSM9924 Last updated (according to GEO): May 27 2005 Nasal Epithelium 865 861 Blood Chronic constriction injury in cholecystokinin b receptor (Cckbr)-deficient mice 1000 Hereditary Diseases 901 frontal lobe Whole blood 0 10 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188761 Last updated (according to GEO): Jun 06 2007 To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at ?80C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at ?80°C before routine processing for GeneChip analysis. Source GEO sample is GSM28663 Last updated (according to GEO): Oct 28 2005 Saline ip LPAM ILI 24hrs post ILI sample B 134 105 in the preimplantation uterus Molecular pathways involved in neuronal degeneration of polyglutamine mouse models Skeletal bone 861 M_U133Plus_101_HC CNS-SC_InjA4h-4B-s2 Hyperdip>50-#12 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Cells were either prestimulated (1_X) or not (0_X) for 18h with 100 ng/ml LPS. Media was exchanged and after 2h rest, cells either restimulated (X_1) or not (X_0) with again 100 ng/ml LPS. This resulted in 4 experimental conditions: 0_0, 0_1, 1_0 and 1_1. There were 3 biological replicates done, resulting in 12 arrays altogether. Source GEO sample is GSM213700 Last updated (according to GEO): Aug 01 2007 cy3:SHR control, biological rep 5g; cy5:pool of 6 WKY control rats Whole blood from a healthy control Source GEO sample is GSM153451 Last updated (according to GEO): Jan 11 2007 human frontal cortex Source GEO sample is GSM87032 Last updated (according to GEO): Feb 08 2006 Gene expression in brain following stroke Cochlea 0 6 65 50 Small intestine Tumor__Lymphoma_Follicular_FSCC_S98_10416 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Communicable Diseases 861 5 0 brain Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68281 Last updated (according to GEO): Jul 07 2006 21 0 Normal Pituitary Gland none Source GEO sample is GSM210330 Last updated (according to GEO): Jul 16 2007 1000 Brain 10 0 Whole Brain Rat frontal cortex RNA - VH TTX Experiment Source GEO sample is GSM92318 Last updated (according to GEO): Jan 13 2006 Gene Signature for Aggression of Melanoma Metastases - Melanoma Metastasis (LeiATCC) Gene expression data from skeletal muscle at baseline Source GEO sample is GSM230459 Last updated (according to GEO): Sep 19 2007 onto a collagen 72 86 M_95A_2672_CB_0_GS 4 0 Brain Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225918 Last updated (according to GEO): Nov 02 2007 Fibroblasts 38 48 processed in batch 2 Source GEO sample is GSM90441 Last updated (according to GEO): Mar 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145627 Last updated (according to GEO): Nov 20 2006 Retina 1000 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68194 Last updated (according to GEO): Jul 07 2006 Donor 3 Time point 12 hours post infection with HIV-1, RF Source GEO sample is GSM2620 Last updated (according to GEO): May 27 2005 44 26 of Cerebral Malaria NIA-NEUROARRAY_DH1 21 7 adrenal medulla This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12380 Last updated (according to GEO): May 28 2005 HapMap YRI_parent Male Source GEO sample is GSM159688 Last updated (according to GEO): Feb 01 2007 CNS-SC_CtrA7d-1A-s2 Skeletal bone 861 Sample Type: cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 15 ppm, 6 h time point Source GEO sample is GSM159770 Last updated (according to GEO): Apr 23 2007 subthalamic_nucleus_5 Source GEO sample is GSM80846 Last updated (according to GEO): Mar 31 2006 brain, hippocampus: Ctr-1h-P15-III_e1_le1 761 746 Upon DNA damage 1000 Skeletal muscle structure H117 FC BA4 A Heart Ventricle 1000 4535 4527 hepatoma 1000 Brain Hypothalamus 151 163 RENAL_TK10 on Affymetrix GeneChip Human Full Length Array HuGeneFL Liver 1000 liver_PPARa-knockout_WY14643_5d_pooled 972 Structure of middle temporal gyrus to the nose 599 609 Marfan Syndrome 1000 Mesenchymal Stem Cells 1000 861 Iris M-7-9-BO on UMich-10k s6 Acetaminophen 3hr Rat 5557 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool Sample was obtained from a 64 years old male subject with congestive heart failure. Good quality sample. Keywords = Congestive heart failure, eNOS, gene, dimethylarginine dimethylaminohydrolase Source GEO sample is GSM6547 Last updated (according to GEO): May 28 2005 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160322 Last updated (according to GEO): Feb 08 2007 mouse brain 478 489 brain, hippocampus: KA1-III_e1_le1 861 Cerebral cortex Day 16 Mouse #91 - 1st replicate Diaphragm 14 Day control rep 1 1000 Glioblastoma G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Keywords = Gata1, erythroid, mouse Source GEO sample is GSM9604 Last updated (according to GEO): May 28 2005 mouse brain ipsilateral LPS.Dmso, biological rep4 with myocardial infarction 313 339 Study of in vitro granulocyte differentiation Source GEO sample is GSM137480 Last updated (according to GEO): Jun 06 2007 SCG explant cultured for 65 hours in vitro Source GEO sample is GSM246037 Last updated (according to GEO): Dec 03 2007 Transitional epithelium 1000 Locus Coeruleus Source GEO sample is GSM107935 Last updated (according to GEO): Jun 06 2006 GC (HKG22T) 1000 Brain Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226155 Last updated (according to GEO): Nov 02 2007 Chromosomes 861 Epithelium 861 Neoplasm 861 CVB3_V-9h Muscle_adequate protein_female_rep6 1000 Spinal Cord Gender-specific gene expression in post-mortem human brain: localization to sex chromosomes. 10_0004_SepticShock_Day1_73 3-day-denervated tibialis anterior muscles from runx1f/- control mice Treatment, type=add, description=5-day-denervated tibialis anterior muscles from runx1f/- control mice Source GEO sample is GSM99423 Last updated (according to GEO): Mar 08 2006 Simple annotation: Chronic Lymphocytic Leukemia, Fludarabine chemotherapy Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2985.gif Source GEO sample is GSM72218 Last updated (according to GEO): Sep 22 2006 2500mg/kg APAP 12Hr rat 4138 blood vs. PC 12Hr rat 4126 blood human cerebellum Source GEO sample is GSM87181 Last updated (according to GEO): Feb 08 2006 Structure of olfactory bulb 861 ParietalLobe Source GEO sample is GSM18924 Last updated (according to GEO): Sep 25 2006 toe fibroblast repeat, serum starved Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11325 Last updated (according to GEO): May 28 2005 Pressure-overload induced hypertrophy model. Mouse was sacrificed 1 hour after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2250 Last updated (according to GEO): May 27 2005 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159761 Last updated (according to GEO): Apr 23 2007 GSE483 Nose 1000 Kidney 861 The temporal program of gene expression during a model physiological response of human cells, the response of fibroblasts to serum, was explored with a complementary DNA microarray representing about 8600 different human genes. Genes could be clustered in groups on the basis of their temporal patterns of expression in this program. Many features of the transcriptional program appeared to be related to the physiology of wound repair suggesting that fibroblasts play a larger and richer role in this complex multicellular response than had previously been appreciated. This study is described more fully in Iyer VR, et al. 1999. Science 283:83-7 Note: 4 samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: GSM2166, GSM2169, GSM2163, GSM2168, Last Updated (by provider): May 29 2005 Contributers: G Schuler T Moore M S Boguski J M Trent J Hudson D Botstein P O Brown M B Eisen D T Ross J C Lee V R Iyer L M Staudt D Lashkari D Shalon Includes GDS85. Update date: Mar 22 2004. Dataset description GDS85: Temporal transcriptional program of primary fibroblasts in response to serum. Samples taken at various time points up to 24 hours.. Includes GDS86. Update date: Apr 08 2003. Dataset description GDS86: Analysis of a temporal transcriptional program in the response of primary fibroblast cultures to serum. Samples taken at 15 minutes and 2 hours.. [Switched to use 10k_merged by Gemma] M7TW01010673 5 0 brain CNS-RM_Mod28d-3A-s2 861 Histones 1000 Hypertrophic Cardiomyopathy total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Bombesin labeled with Cy5- time course with repeats. Date GSE374 Last Updated: May 29 2005 Contributers: Yun Anna Cao Angela Alexander Jong-Woo Kim Sangdun Choi Rebecca Hart Robert Hsueh Joella Grossoehme Sun Young Lee Mi Sook Chang Zhen Yan Includes GDS295. Update date: Nov 18 2003. Dataset description GDS295: Temporal analysis of effects induced by 1 uM bombesin in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. 9 0 Blood Test Plasma 861 Skeletal bone 861 1000 Cerebellum Gene expression data from postmorten brain regions Source GEO sample is GSM145380 Last updated (according to GEO): Nov 20 2006 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92369 Last updated (according to GEO): Jan 13 2006 86 65 with HIV encephalitis high gestational age Source GEO sample is GSM213076 Last updated (according to GEO): Jul 25 2007 Hyperdip>50-C3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A NA Source GEO sample is GSM198892 Last updated (according to GEO): Jun 07 2007 861 Neoplasm Astrocytoma 861 329 306 valvular cardiomyopathy Bladder sample 1008-1 Spleen vs CD40 Treated B cell 120min (set2) Spleen 1000 1000 Communicable Diseases R493P00433 861 Muscle Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181984 Last updated (according to GEO): Apr 13 2007 913 Coronary heart disease Gut 1000 Whole blood 0 10 1000 Decapitation Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 1045 left_liver_lobe I_U133A_90_Amy Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213505 Last updated (according to GEO): Jul 31 2007 of 11 saccules 5 18 1000 Brain 1000 Cerebral cortex Heart 1000 245 218 of parieto-occipital cortex Nose 1000 861 Blood 20 0 human caudate nucleus Autistic Disorder 877 267 251 to the brainstem Spinal cord injury causes secondary biochemical changes leading to neuronal cell death. To clarify the molecular basis of this delayed injury, we subjected rats to spinal cord injury and identified gene expression patterns by high-density oligonucleotide arrays (8,800 genes studied) at 30 minutes, 4 hours, 24 hours, or 7 days after injury (total of 26 U34A profiles). Detailed analyses were limited to 4,300 genes consistently expressed above background. Temporal clustering showed rapid expression of immediate early genes (30 minutes), followed by genes associated with inflammation, oxidative stress, DNA damage, and cell cycle (4 and 24 hours). Functional clustering showed a novel pattern of cell cycle mRNAs at 4 and 24 hours after trauma. Quantitative reverse transcription polymerase chain reaction verified mRNA changes in this group, which included gadd45a, c-myc, cyclin D1 and cdk4, pcna, cyclin G, Rb, and E2F5. Changes in their protein products were quantified by Western blot, and cell-specific expression was determined by immunocytochemistry. Cell cycle proteins showed an increased expression 24 hours after injury and were, in part, colocalized in neurons showing morphological evidence of apoptosis. These findings suggest that cell cycle-related genes, induced after spinal cord injury, are involved in neuronal damage and subsequent cell death. Whole blood 0 10 D_U133Plus_97_HC Mouse Liver AIN Diet 8hr 1mg/kg As Injection, biological replicate B none Source GEO sample is GSM210297 Last updated (according to GEO): Jul 16 2007 89 68 with tricuspid valves Primary Neoplasm 1000 Untreated LNCaP cells stimulated with DHT, biological replicate 3 Source GEO sample is GSM187373 Last updated (according to GEO): May 04 2007 in the brain 150 162 DRG019_a brain 0 5 861 Bladder Gene expression data from postmorten brain regions Source GEO sample is GSM145054 Last updated (according to GEO): Nov 20 2006 ER+/LN+/Marks208 on Affymetrix GeneChip Human Full Length Array HuGeneFL /tf Amygdala A 10 23 none Source GEO sample is GSM244533 Last updated (according to GEO): Nov 23 2007 PGA-MurLungRag-pbs-72h-1bCv2-s2 CH1813 #6 (isolate C rich media VEGF-A 24hours) Central gray substance of midbrain 861 M_95A_2672_DLPFC_0_GS Plasma 861 1000 Retina in bronchial epithelia 311 332 91 from the bone marrow 72 Blood Test (Blinded) Sample Source GEO sample is GSM130023 Last updated (according to GEO): Sep 18 2007 NA Source GEO sample is GSM84337 Last updated (according to GEO): Dec 01 2005 in cigulate cortex 26 43 Cerebral cortex 861 858 Prostatic Neoplasms Transient phosphorylation of the alpha-subunit of translation initiation factor 2 (eIF2alpha) represses translation and activates select gene expression under diverse stressful conditions. Defects in the eIF2alpha phosphorylation-dependent integrated stress response impair resistance to accumulation of malfolded proteins in the endoplasmic reticulum (ER stress), to oxidative stress and to nutrient deprivations. To study the hypothesized protective role of eIF2alpha phosphorylation in isolation of parallel stress signaling pathways, we fused the kinase domain of pancreatic endoplasmic reticulum kinase (PERK), an ER stress-inducible eIF2alpha kinase that is normally activated by dimerization, to a protein module that binds a small dimerizer molecule. The activity of this artificial eIF2alpha kinase, Fv2E-PERK, is subordinate to the dimerizer and is uncoupled from upstream stress signaling. Fv2E-PERK activation enhanced the expression of numerous stress-induced genes and protected cells from the lethal effects of oxidants, peroxynitrite donors and ER stress. Our findings indicate that eIF2alpha phosphorylation can initiate signaling in a cytoprotective gene expression pathway independently of other parallel stress-induced signals and that activation of this pathway can single-handedly promote a stress-resistant preconditioned state. 1000 Cartilage 1717 1709 amygdala PBMCs-Type 2 Diabetes-T2D_6_New 1000 Retina KO_sham_mid_2 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211381 Last updated (according to GEO): Jul 18 2007 brain, contralateral Cortex: Trizol Extraction9_le1 Primary Neoplasm 1000 Cerebral cortex 861 heart 1169 1173 spinal cord 13 23 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211238 Last updated (according to GEO): Jul 18 2007 865 Disorder of artery Spleen vs Leukotriene B4 (LTB4)Treated B cell 120min (set1) Lymphoblastoid Cell Line for Individual 8083.5 log phase tibiae 115 120 Primary large cell carcinoma 3387 0 32 Control3 ERMS-T-TEST-24 on NHGRI-6.5k_b To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18480 Last updated (according to GEO): May 27 2005 healthy control sample x201 52 42 in melanoma AA Treatment, type=remove Source GEO sample is GSM99503 Last updated (according to GEO): Apr 21 2006 1000 Descending colon Mid secretory endometrium from patient with endometriosis Source GEO sample is GSM150219 Last updated (according to GEO): Dec 14 2006 Leukemic fractions of ID44 AML patient have been hybridized. Source GEO sample is GSM103106 Last updated (according to GEO): Feb 26 2007 HapMap YRI_parent Male Source GEO sample is GSM159712 Last updated (according to GEO): Feb 01 2007 1000 Neuroglia 21 0 acute myeloid leukemia 1000 Cerebral cortex at the Human Brain 724 741 PBMCs-Type 1 Diabetes-IDDM5_T1D_New Meningioma Primary Grade 1 Source GEO sample is GSM108023 Last updated (according to GEO): Jun 06 2006 Cerebral cortex 861 (heart 1235 1241 ExpressionLevel:GXN-00534 on Affymetrix GeneChip Mouse Expression Array 430A and Mouse Genome 430A 2.0 Array of infected skin 33 48 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11280 Last updated (according to GEO): May 28 2005 cerebellum_3 Source GEO sample is GSM80618 Last updated (according to GEO): Mar 31 2006 Lymphoblastoid Cell Line for Individual 8037.4 log phase 1000 Prostate human cerebellum Source GEO sample is GSM87186 Last updated (according to GEO): Feb 08 2006 CHIPEXP_NAME: 230_2_050531tpj_7h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Vehicle_Control TREAT_TOX_MECHANISM1: Liver_Non_Toxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0 SAMPLING_TIME: 3 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197612 Last updated (according to GEO): Jun 01 2007 7wkC 1000 Muscle 858 Prostatic Neoplasms 983 Cervix carcinoma FL-12;CD19+ of 13 saccules 5 18 Subcutaneous Fat 913 T56__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A biopsy sample obtained from a 3.5-year-old male Duchenne Muscular Dystrophy patient Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15837 Last updated (according to GEO): Sep 08 2006 biopsy sample obtained from a male Duchenne Muscular Dystrophy patient(age: unknown) Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15842 Last updated (according to GEO): Sep 08 2006 70 40 without coronary artery disease adrenal_gland_cortex_3 070302_HF_301VC kidney 37 43 1000 Substantia nigra structure NCI60.42_LABEL46EXTRACT45SUB3 Source GEO sample is GSM134201 Last updated (according to GEO): Aug 06 2007 The epithelial cells 962 981 901 Myeloid Leukemia 861 Brain Gene expression regulation of transporters and phase I/II metabolic enzymes in murine small intestine during fasting Carcinoma, Non-Small-Cell Lung 861 forebrain 1893 1901 861 Cancer of Neck Neoplasm 861 CNS-SC_InjB14d-1C-s2 Blood 1000 plasma cells 50 61 861 Brain 6 stomach 0 Connexin43 null neonatal mouse brain1 (K43-1) 901 Caudate nucleus structure Human Hypothalamus Female 5 CNS-SC_CtrA24h-1C-s2 1406 1387 to hyperinsulinemia Standard Affymetrix Protocol Keywords = microarray Keywords = muscle Source GEO sample is GSM15935 Last updated (according to GEO): May 28 2005 Sample Type: cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde instilation exposure, vehicle control, single exposure, 6 h time point Source GEO sample is GSM159790 Last updated (according to GEO): Apr 23 2007 C57BL/6J bed nucleus of the stria terminalis rep1 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156162 Last updated (according to GEO): Jan 22 2007 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27031 Last updated (according to GEO): May 27 2005 7 cerebral cortex 21 Lung 861 f2#2 versus pool Mouse Brain tissue 861 Brain 1000 Spleen from nose 96 104 Spleen vs IL10 Treated B cell 60min (set1) Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225652 Last updated (according to GEO): Nov 02 2007 N42__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Hyperdip>50-C7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A adenoma 861 cardiac 746 752 Coronary Arteriosclerosis 1000 vomeral nasal organ Source GEO sample is GSM18652 Last updated (according to GEO): May 27 2005 Heart 861 WGACON-142 Control1 MGJZ030312082Acd8+Tcell GBM: 70P Category: Cell-line Subcategory: Breast MDA-MB-231 isolate obtained from NCI60 cell line set Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc73 Source GEO sample is GSM1883 Last updated (according to GEO): Nov 21 2005 AD-111T2-A8-1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 30 19 Solid tumor 1000 Left 1000 Hypothalamic structure 861 Asthma Wild type inbred mice Source GEO sample is GSM82956 Last updated (according to GEO): Nov 10 2005 3_cerebral_cortex_6hrs_sleep_#62 847 throughout the cortex 868 AD-119t3-A195-8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A #8 (isolate 9 low serum media VEGF-A 4hours) 9 0 Blood Test Dissection of E16.5 cortex for RNA extraction. Cortex Hemispheres of E16.5 mice were divided into the medial (R1), dorsal (R2), ventral (R3), lateral (R4), and occipital regions (R5). Preparation of RNA and Synthesis of cDNA. Poly A+ RNA was obtained through twice column procedures with oligo dT cellulose column (New England Biolabs, Beverly, MA) and was used for synthesis of cDNA. 1ug of polyA+ RNA was converted into double-stranded cDNA by reverse transcription using ReverTra Ace (ToYoBo, Japan) with oligo dT(24) primers containing the T7 RNA polymerase promotor sequence (Amersham Pharmacia Biotech, Japan). The integrity of RNA was confirmed by agarose electrophoresis and RNA contents were analyzed by measuring the optical density at 260 nm. Target preparation and array processing. The following procedures including preparation of cRNA targets, hybridization, washing, staining, and scanning were performed as described in the Expression Analysis Technical Manual (Affymetrix, CA). Briefly, biotin-labeled antisense cRNA targets were synthesized in in vitro transcription reaction system (IVT) using cDNA as template (ENZO BioArrayTM HighYieldTM RNA Transcription Labeling kit with T7 RNA polymerase, Enzo, NY). The cRNA targets were size-fragmented to 35-200 bp in a buffer containing potassium and magnesium acetate at 94°C for 35 minutes and were used for hybridization as cRNA targets. The hybridization cocktail [containing 10 ug of target cRNA, control oligo BS (Affymetrix), and Eukaryotic Hybridization controls (Affymetrix)] was hybridized with a mouse U74A array at 42°C for 16 hours in GeneChip Hybridization Oven 640. Washing and staining were performed after hybridization under the fluidics station protocol, EuGE-WS2, on GeneChip Fluidics Station 400. Then, we scanned the array twice on HP GeneArrayTM scanner. Experiments were repeated twice with independent dissection. Data analysis. To quantify the expression level of a transcript, the average difference value (Adv) was calculated from the intensities against the probe cells using the global methods of normalization by Microarray Suite ver. 4.0 (Affymetrix). Source GEO sample is GSM14598 Last updated (according to GEO): Oct 28 2005 Olfactory Epithelium 1000 Olfactory Epithelium 1000 1000 Intestines, Small Large-scale analysis of the human transcriptome. Ovary, stroma-enriched Source: CHTN, see PMID 11158614 Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 133.93 Stdv: 5.74 Min: 122.53 Max: 142.72 Source GEO sample is GSM2869 Last updated (according to GEO): Mar 20 2006 1000 lymph nodes Wild type 8 wk old male A/J mouse periaqueductal gray Source GEO sample is GSM107032 Last updated (according to GEO): Mar 05 2007 861 Cerebral cortex SQ-4172-A326-5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 26 15 endometrioid Against Breast Cancer 57 77 6 month oculomotor nucleus rep 1 Bone Marrow 1000 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 30 minutes following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10951 Last updated (according to GEO): May 27 2005 D12 12h TLR2/1L no additional Source GEO sample is GSM199243 Last updated (according to GEO): Jun 08 2007 The peroxisome proliferator-activated receptor alpha is a fatty acid-activated transcription factor that governs a variety of biological processes. Little is known about the role of PPARalpha in the small intestine. Since this organ is frequently exposed to high levels of PPARalpha ligands via the diet, we set out to characterize the function of PPARalpha in small intestine using functional genomics experiments and bioinformatics tools. PPARalpha was expressed at high levels in both human and murine small intestine. Detailed analyses showed that PPARalpha was expressed highest in villus cells of proximal jejunum. Microarray analyses of total tissue samples revealed, that in addition to genes involved in fatty acid and triacylglycerol metabolism, transcription factors and enzymes connected to sterol and bile acid metabolism, including FXR and SREBP1, were specifically induced. In contrast, genes involved in cell cycle and differentiation, apoptosis, and host defense were repressed by PPARalpha activation. Additional analyses showed that intestinal PPARalpha dependent gene regulation occurred in villus cells. Functional implications of array results were corroborated by morphometric data. The repression of genes involved in proliferation and apoptosis was accompanied by a 22% increase in villus height, and a 34% increase in villus area of wild-type animals treated with WY14643. This is the first report providing a comprehensive overview of processes under control of PPARalpha in the small intestine. We show that PPARalpha is an important transcriptional regulator in small intestine, which may be of importance for the development of novel foods and therapies for obesity and inflammatory bowel diseases. Key words: microarray, small intestine, peroxisome proliferators-activated receptor alpha, gene expression, crypt-villus axis. Spleen vs ELC Treated B cell 30min (set1) BTBR T+ tf/J_female_hypothalamus Source GEO sample is GSM138566 Last updated (according to GEO): Apr 18 2007 Tonsil 5 Normal C57 whole brain 4 Medulla Oblongata 861 eye 0 3 nasal epithelial cells 28 49 N-4_PRE cortex 7 12 893 873 /extracellular matrix 1 of 3 replicates in treatment group Source GEO sample is GSM206023 Last updated (according to GEO): Jun 29 2007 Acetaminophen 6hr Rat 5407 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool brain, adrenal medulla: 1C_e1_le1 861 Brain olfactory epithelium 194 213 Lymphoblastoid Cell Line for Individual 8201.4 log phase 43 0 Chorionic mesoderm-derived mesenchymal cells biopsy sample obtained from 4-year-old female individual Keywords = gene expression profile of normal human skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15828 Last updated (according to GEO): May 28 2005 1000 Eye C57BL/6J bed nucleus of the stria terminalis rep1 (430 2.0 Array) PGA-HBE-NormRV18h-1aA-S2 cerebral_cortex_1 Source GEO sample is GSM80650 Last updated (according to GEO): Mar 31 2006 ES cell line was grown on irradiated MEF feeders using standard culture conditions. Feeders were then depleted and ES cells plated on gelatin for ~2 days. RNA was isolated using Trizol/RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol. Data were normalized by AffyMetrix MAS5.0 using defaults. Keywords = embryonic stem cholesterol transport Source GEO sample is GSM9274 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM175926 Last updated (according to GEO): Apr 09 2007 Pool Eu_P30_hyb2 1000 Infection Exp B_1, control (0mg/kg) CPF 1000 Infection 26 16 of modiolus lateral hypothalamus 24 44 Gene expression data from postmorten brain regions Source GEO sample is GSM145534 Last updated (according to GEO): Nov 20 2006 861 Longitudinal Plasma 861 B404 on Affymetrix GeneChip Human Full Length Array HuGeneFL Brain 861 317 293 of fetal minamata disease Exp B, Animal #1, 0.5mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 0.5mg/kg of CPF for 96 hours Source GEO sample is GSM246149 Last updated (according to GEO): Dec 03 2007 861 Colon bronchial epithelia 224 243 Cerebral cortex 1000 Brain 861 30 19 Solid tumor 1000 Intestines, Small Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181119 Last updated (according to GEO): Jul 12 2007 901 Myeloid Leukemia MF-41 3rd 2hr C-DG (cortex 19 25 AD-267t1-A91-3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Spleen 1000 Starvation 916 Macrophage 14smi031 Cerebral cortex 861 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with TGF-beta (transforming growth factor-beta) for 120min Source GEO sample is GSM5797 Last updated (according to GEO): May 27 2005 Bone Marrow 1000 Chronic leukemia NOS 913 1000 Neuraxis This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques P. Tremblay (jacques-p.tremblay@crchul.ulaval.ca; 2705 boulevard Laurier) for analysis. Stembase Experiment ID: E205 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205 SCGP Sample ID: S270 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205#SAMPLE_247 Short description: Cells from sphere were incubated in a differentiation medium. They differentiated into neurons after 7 days in culture. Analysis requested: mouse genechips RNA concentration: 0.689 ug/uL Sample volume: 15 uL total Source GEO sample is GSM93613 Last updated (according to GEO): Jan 23 2006 861 Colon 1000 Brain Acetaminophen 3hr Rat 7515 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool 406 395 whose hearts Epithelium 861 to UVC-induced DNA damage 211 235 liver, PPARa-null mice, treatment with WY14643 for 5d Source GEO sample is GSM205798 Last updated (according to GEO): Jul 24 2007 Tumor__CNS_Medulloblastoma_M22_A50 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Prostate 861 Brain 1000 ER+/LN-/Nevins22 on Affymetrix GeneChip Human Full Length Array HuGeneFL Primary Neoplasm 1000 prostate Source GEO sample is GSM203273 Last updated (according to GEO): Jun 21 2007 PGA-E12.5_1A Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 5889 left_liver_lobe NCI60.32_LABEL36EXTRACT35SUB3 Source GEO sample is GSM134154 Last updated (according to GEO): Aug 06 2007 861 Neuroglia Expression profiling of somatomotor cortex extracted from rats at 28d following moderate injury Source GEO sample is GSM41717 Last updated (according to GEO): May 27 2005 Lung 1000 on the ventricles 598 614 1000 ovarian neoplasm RPMI-8226 hgu95d Liver (fetal) [JunctionChip 3 of 5] 53 22 Undifferentiated bone tumor GST6 858 Prostatic Neoplasms f2#261 versus pool Mouse Brain tissue none Source GEO sample is GSM149522 Last updated (according to GEO): Jan 03 2007 Disorder of artery 865 spinal cord 37 47 5 0 brain Lymphoblastoid Cell Line for Individual 8093.4 log phase Communicable Diseases 861 RNA isolated from post-mortem tissues Source GEO sample is GSM6833 Last updated (according to GEO): May 28 2005 Heart 1000 11 0 Normal ovary Leg 14 Day Control rep 1 f2#359 versus pool Mouse Brain tissue M_U133A_61_DLPFC human caudate nucleus Source GEO sample is GSM86899 Last updated (according to GEO): Feb 08 2006 861 Cardiomyopathies D_U133A_80_CB thyroid_gland_3 Source GEO sample is GSM80866 Last updated (according to GEO): Mar 31 2006 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114229 Last updated (according to GEO): Jun 16 2006 Brain 861 SAMR1 Retina Young Sample 2 mefloquine-treated NG108 neuronal cells 8 EAE, 1,25(OH)2D3-treated #7 GSE5545 Meningioma Primary Grade 1 Source GEO sample is GSM108022 Last updated (according to GEO): Jun 06 2006 I_U133A_9_AnCg 1BJZ02081478b_Superior_Cervical_Ganglion Temporal profiling in muscle regeneration. nasal epithelial cells 28 49 Renal carcinoma 902 Kidney CR-2B Type 1 Diabetes patient and the timepoint 4 months after diagnosis. Source GEO sample is GSM228636 Last updated (according to GEO): Sep 11 2007 Infection 1000 Neoplasm 861 WGACON-180 Keywords = Heart 505 521 mouse brains 187 198 Macrophage smi116 Myocardial Infarction 1000 1000 Kidney of the small intestine 97 118 Gene expression from Dendritic cells from human subject with resolver phenotype uninfected. Source GEO sample is GSM128967 Last updated (according to GEO): Sep 13 2007 Brain 861 Cells captured via Arcturus LCM system, amplified (RiboAmp, 2 rounds) and labeled (Enzo) for hybridizaton to Affymetrix MG_U74Av2 arrays, using manufacturers protocols in each step. Source GEO sample is GSM6203 Last updated (according to GEO): Mar 17 2006 Gene expression data from whole brain infected mouse, day 3 Source GEO sample is GSM189646 Last updated (according to GEO): May 16 2007 GSE8597 between superficial 307 325 brain, cerebral cortex: Rat_03-51_NroLep_Lipska_e1_le1 Resistance exercise reverses aging in human skeletal muscle. 11 0 Fetal brains PMN_LB_180min_Patient18 1000 Amygdaloid structure Tacrine 2.7mg/kg/day from 5 weeks Moclobemide 10mg/kg/day Creatine 1%w/v added to wet mash Lot batch = 5213 Source GEO sample is GSM13361 Last updated (according to GEO): May 28 2005 heart failure 583 595 Pooled TA RNA samples from five 8 wk old male C57BL10 mice Source GEO sample is GSM13745 Last updated (according to GEO): May 28 2005 prostate Source GEO sample is GSM203343 Last updated (according to GEO): Jun 21 2007 PP149_infected_DC H9LMS99080701 129/SvImJ Frontal Cortex B n/a Source GEO sample is GSM177933 Last updated (according to GEO): Jun 11 2007 Central gray substance of midbrain 861 Nose 1000 1783 CP24_23 1000 Brain with Job's syndrome 439 457 1000 Decapitation Brain 1000 NMDA 1h (Experiment NMDA2-Run 9600) Treatment, type=time_course, description=samples are treated for 10, 30 or 60 min with NMDA 1mM, the agonist is then washed out and the cells are harvested 24h later, measurement=60.0 m Source GEO sample is GSM96762 Last updated (according to GEO): Feb 14 2006 Fibroblasts 861 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188798 Last updated (according to GEO): Jun 06 2007 AML_22 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A I_U133A_65_AnCg 21 0 Mammary Gland @ Preg1 Liver Test (Blinded) Sample Source GEO sample is GSM130095 Last updated (according to GEO): Sep 18 2007 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213480 Last updated (according to GEO): Jul 31 2007 gene expression from allergen stimulated mouse lung Source GEO sample is GSM158138 Last updated (according to GEO): Jan 25 2007 Tissue fiber 1000 of the postmortem brains 674 698 of human breast cancer 332 354 cDNAs were generated from 5ug of total RNA per sample by reverse transcription (RT) for two hours at 42oC using the 3DNA SubmicroTM Oligo Expression Array Detection Kit (Genisphere, Hatfield, PA) and Superscript II (Invitrogen, Carlsbad, CA). For each microarray chip two consecutive hybridizations were performed with cDNAs and the fluorescent probes following the manufacture?s specifications. Briefly, in the first hybridization reaction the solution containing the mixture of cDNAs obtained from control and treated cells was loaded onto the CAG Human 19K array and incubated overnight at 55oC in a hybridization chamber (Genemachines, San Carlos, CA). The human 19K array (www.cag.icph.org/microarray_facility.htm) contains 60-mer oligonucleotides (Compugen, San Jose, CA) representing 18,861 human genes spotted onto poly-l-lysine coated glass microscope slides. In the second hybridization reaction Cy3 (green) and Cy5 (red) fluorescent probes were used to label the cDNAs from control and PGJ2-treated cells, respectively. The second hybridization was carried out for 3 hours at 65oC in the hybridization chambers. The arrays were scanned using an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) with laser intensities adjusted to bring the brightest spot just below saturation and the data extracted with the Axon GenePix Pro software. Source GEO sample is GSM98765 Last updated (according to GEO): May 31 2006 Stem cells 901 1000 Caudate nucleus structure 59-96_SCC Mammary Gland @ Preg12, biological rep1 in the mammalian nervous system 110 141 cy3:WKY control, biological rep 6g; cy5:pool of 6 WKY control rats 129S1/SvImJ_female_hypothalamus CAD_replicate48 Nasal Epithelium 865 Heart 1000 15 0 human cerebellum VDXGUYU_4067 PGA-Csx_het_8b-m4 Utricle structure 861 none Source GEO sample is GSM149541 Last updated (according to GEO): Jan 03 2007 M_U133A_5_HC Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13414.gif Source GEO sample is GSM79643 Last updated (according to GEO): Sep 22 2006 HCC (HBV+, HK20) Pressure-overload induced hypertrophy model. Mouse was sacrificed 1 hour after aortic banding. Keywords = Cardiac hypertrophy Source GEO sample is GSM2231 Last updated (according to GEO): May 27 2005 in the cerebellum 29 45 Transplant Series 25 Right, Transplant # 3 Gene expression data from brain of adult rats Source GEO sample is GSM101017 Last updated (according to GEO): Feb 20 2007 Haloperidol treated 4weeks AffyGC RMA rep2 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47527 Last updated (according to GEO): May 29 2005 Biopsy of the normal mucosa of the colon from patient #7 Normal Source GEO sample is GSM175952 Last updated (according to GEO): Apr 09 2007 Total RNA extracted from the cerebellum of a Lh-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144396 Last updated (according to GEO): Nov 14 2006 Large cell neuroendocrine carcinoma 901 858 Prostatic Neoplasms Lymphoblastic Leukemia 1000 Parkinson Disease 861 Muscular Dystrophies 901 Total RNA from brain sample of wild type mice at P0 Treatment, type=purify, measurement=0.0 years Source GEO sample is GSM113681 Last updated (according to GEO): Jun 09 2006 Gene expression data from whole brain infected mouse, day 1 Source GEO sample is GSM189636 Last updated (according to GEO): May 16 2007 Kidney 861 Determination of gene expression changes in extraocular muscle of mdx (dystrophin-deficient) mice at postnatal ages 14, 28, 56, and 112 days. 3 independent replicates/age/strain. Data form part of publications: Human Molecular Genetics 12:1813-1821, 2003 and FASEB Journal 17: 893-895, 2003 (on-line full article available at http://www.fasebj.org/cgi/doi/10.1096/fj.02-0810fje).. Date GSE1008 Last Updated: May 29 2005 Contributers: John D Porter Includes GDS614. Update date: Jul 08 2004. Dataset description GDS614: Analysis of extraocular muscle (EOM) from dystrophin-deficient mdx mice, a Duchenne muscular dystrophy (DMD) model. Postnatal ages 14, 28, 56, and 112 days examined. EOM is unaffected in DMD, so results provide insight into mdx EOM protective mechanisms.. starved 41 47 HMEC X BC21 315 291 of fetal minamata disease CNS-SpinalC-30mAdult-4A-s2 Sum102 in the mouse colon 266 283 5 0 brain Gene expression data from postmorten brain regions Source GEO sample is GSM145190 Last updated (according to GEO): Nov 20 2006 entorhinal cortex layer II stellate island cells Source GEO sample is GSM107539 Last updated (according to GEO): May 01 2006 I_U133A_42_Amy WGACON-210 Epithelium 861 1967 1957 for livers PGA-Band_1w_5-m5 1000 Polycystic Ovary Syndrome Neuraxis 1000 Successful regeneration of injured neurons requires a complex molecular response that involves the expression, modification and transport of large numbers of proteins. The neuronal proteins responsible for the initiation of regenerative neurite outgrowth are largely unknown. Dorsal root ganglion (DRG) neurons display robust and successful regeneration following lesion of their peripheral neurite, whereas outgrowth of central neurites is weak and does not lead to functional recovery. We have utilized this differential response to gain insight in the early transcriptional events associated with successful regeneration. Surprisingly, our study shows that peripheral and central nerve crushes elicit very distinct transcriptional activation, revealing a large set of novel genes that are differentially regulated within the first 24 hours after the lesion. A large number of known regeneration associated genes were retrieved in our study, and, in addition, hundreds of novel genes possibly involved in the transcriptional regulatory network underlying successful regeneration. Please refer to Stam et al., Eur. J. Neurosci 25:3629 (2007). Last Updated (by provider): Jul 09 2007 Contributers: Yi Zhang Mathisca C de Gunst August B Smit Floor J Stam Nicola J Armstrong Joost Verhaagen CNS-SMTC_Ctr3mo-2A-s2 (cortex 19 25 the blood 393 402 519 508 of the brain at the Human Brain 743 760 AT3-hTERT_1.5Gy_2h_C5_27045 24 0 human prostate PC3 tumors human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195331 Last updated (according to GEO): Jun 04 2007 861 Occipital lobe The mammalian forebrain is a tissue of stunning complexity comprised of numerous regions each containing many distinct cell types that differ in their intrinsic and synaptic physiology, morphology and connectivity. These differences are likely conferred by differential gene expression, but the extent and nature of cell type specific gene expression is largely unknown. Here, we carried out microarray analysis of twelve major classes of fluorescently labelled neurons within the forebrain and provide the first comprehensive view of gene expression differences. The results demonstrate a profound molecular heterogeneity among neuronal subtypes, represented disproportionately by gene paralogs, and begin to reveal the genetic programs underlying the fundamental divisions between neuronal classes including that between glutamatergic and GABAergic neurons. Last Updated (by provider): Jan 09 2006 Contributers: Chris M Hempel Sacha B Nelson Ken Sugino Includes GDS1522. Update date: Jun 05 2006. Dataset description GDS1522: Analysis of 12 distinct neuronal subpopulations from 5 regions of the adult forebrain. Results identify highly heterogeneous expression profiles that likely underlie the fundamental differences observed between neuronal classes and between glutamatergic and GABAergic neurons within a given class.. Burden-2R01NS036193-06A1 Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. A/J periaqueductal gray rep1 402 386 to chromosome 21 CNS-SC_CtrA7d-1C-s2 p53 +/-, 0 hour, replicate b Source GEO sample is GSM2551 Last updated (according to GEO): May 27 2005 CNS-SpinalCmod-Adult-28d-1A-s2 Cytoskeleton 1000 Infection 1000 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27026 Last updated (according to GEO): May 27 2005 Acetaminophen 6hr Rat 9709 blood vs. Acetaminophen 6hr Rat Pooled Control blood Chronic leukemia NOS 913 no additional Source GEO sample is GSM199341 Last updated (according to GEO): Jun 08 2007 onto a collagen 71 85 lateral hypothalamus 25 45 861 Brain in the SCA7 retinal degeneration 35 67 139 adenocarcinomas 280 298 91 from the bone marrow 72 Meningioma Recurrent Grade 1 Treatment, type=harvest, description=There is no treatment. Tumors were flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108019 Last updated (according to GEO): Jun 06 2006 Ganglia, Spinal 923 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188858 Last updated (according to GEO): Jun 06 2007 1000 Spleen 1000 Brain 42 30 Control blood Ta gr2 tumour Source GEO sample is GSM2500 Last updated (according to GEO): May 27 2005 Macrophage 14smi019 Epithelium 861 brain, cerebral cortex: 4R 2 (4/22)_le1 913 Acute leukemia Adipose tissue 901 Spleen 0 5 Cerebral cortex 861 Cochlear nuclei 0 14 This SuperSeries is composed of the following subset Series: GSE1654: Circadian Profiling of the Transcriptome in Immortalized Rat SCN Cells (3 biological replicates) GSE1673: Circadian Profiling of the Transcriptome in Immortalized Rat SCN Cells: Comparison to Long-Evans Rat SCN Last Updated (by provider): Feb 07 2006 Includes GDS1629. Update date: Aug 25 2006. Dataset description GDS1629: Analysis of suprachiasmatic nucleus (SCN) immortalized cell line SCN2.2 at 6 hour intervals over 2 circadian cycles. The master clock responsible for the regulation of circadian rhythms in the body is located in the SCN. Results indicate that SCN2.2 retains intrinsic rhythm-generating properties.. 861 Neoplasm cerebellum Source GEO sample is GSM18607 Last updated (according to GEO): May 27 2005 H9RGV00102611 Ventral tegmental area, male 10.5 week old c57bl/6J mouse, SUSCEPTIBLE group Source GEO sample is GSM224741 Last updated (according to GEO): Aug 31 2007 CNS-SC_InjB24h-2B-s2 CNS-SMTC_Mod3mo-3C-s2 WKY rep3 Expression profiling of spinal cord section (T8) extracted from rats 24h following laminectomy (sham) Lot batch = Source GEO sample is GSM6625 Last updated (according to GEO): May 28 2005 861 Ovary Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7435.gif Source GEO sample is GSM79835 Last updated (according to GEO): Sep 22 2006 1000 Spleen Richard Almon-4-1133800608823 Biopsy of a colorectal adenoma from patient #22 Cerebral cortex 1000 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3526.gif Source GEO sample is GSM93138 Last updated (according to GEO): Sep 22 2006 Prostatic Diseases 913 901 Coronary artery Colonic mucous membrane 913 human frontal cortex Source GEO sample is GSM87028 Last updated (according to GEO): Feb 08 2006 Brain_MGlio_1_Malignant Glioma on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Lung 41 29 Control blood ADH-1 ip saline ILI 4hrs post ILI sample A Whole blood from a healthy control Source GEO sample is GSM153429 Last updated (according to GEO): Jan 11 2007 HapMap JPT Female Source GEO sample is GSM159646 Last updated (according to GEO): Feb 01 2007 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 2 hour after the last shock treatment. Source GEO sample is GSM4521 Last updated (according to GEO): May 27 2005 bronchial epithelia 224 243 Skeletal bone 861 91 from the bone marrow 72 brain 0 5 WGACON-277 Epithelium of bronchus 983 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD38 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD38 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36685 Last updated (according to GEO): May 27 2005 from the olfactory epithelium tissue 171 207 MSS-Spa1-2moF-1aAv2-s2 Voxel J1 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1454 Last updated (according to GEO): Nov 21 2005 330 324 uterus 913 Acute leukemia Time point at 14h post HCMV infection Nervous System; Spinal Cord Keywords = mouse gene expression database Source GEO sample is GSM29426 Last updated (according to GEO): May 27 2005 Diaphragm 28 Day mdx rep 2 Brain 1000 5 0 brain H9LMS00112901 Macrophage smi67 875 Acute leukemia HRPC122_hormone resistant prostate cancer late stage 1789 CP48_23 1000 Kidney 74 55 of hyperinsulinaemic Plasma 861 MDA-MB-231 cells was transfected with pIND-DACH1 and EGRE5-VgRxR, and selected by Zeocin and G418. Keywords = DACH1 Keywords = gene expression Source GEO sample is GSM11079 Last updated (according to GEO): May 28 2005 Transitional epithelium 1000 Liver 1000 191 181 of ischemia prefrontal cortex sprague2 whole tissue, pool of 5 animals, 20 weeks old, male Sprague Dawley prefrontal cortex file:R3MH02052402 Source GEO sample is GSM15230 Last updated (according to GEO): May 28 2005 43 0 Chorionic mesoderm-derived mesenchymal cells T265_Mock_3 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11478.gif Source GEO sample is GSM79867 Last updated (according to GEO): Sep 22 2006 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225739 Last updated (according to GEO): Nov 02 2007 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12370 Last updated (according to GEO): May 28 2005 Localized Carcinoma 853 MLL_16 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A T-ALL-C12 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A nostrils 156 164 Expression profiling of spinal cord section (T10) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31275 Last updated (according to GEO): May 27 2005 brain, cerebellum: KCx4w#3_e1_le1 1000 Pancreas brain, unknown: Sample63_e1_le1 in Dendrites 75 86 Osteoblasts 1000 B6Midbrain(1)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B Myocytes, Cardiac 1000 D14 12h Media 901 Heart failure Hippocampus Source GEO sample is GSM107922 Last updated (according to GEO): Jun 06 2006 Cell Culture: Hippocampal cells from E18 rat embryos were plated at a density of 500,000 cells per 60 mm poly-L-lysine (1mg/ml; Sigma) coated dish. Cultures were maintained at 37 C in 5% CO2 humidified incubator and used for experiments at 21 day in vitro (DIV). Control and experimental group cultures were incubated with 10 micro M TTX for 15 min followed by addition of 100 micro M baclofen or vehicle. Total RNA preparation: Each experimental group was compared as replicates of three. For each replicate cultured hippocampal neurones were harvested after 2 hours incubation +/- baclofen and total RNA was isolated using RNeasy Mini kit (Qiagen, UK) according to the manufacturer's protocol. Microarray Target Labelling and Hybridisation: Targets for cDNA microarrays were generated using 5 micro g of total RNA in a standard reverse transcription (RT) reaction. RNA was annealed, in 16 micro l water, with 1 micro g of 24-mer poly(dT) primer (Invitrogen, UK), by heating at 65oC for 10 min and cooling on ice for 2 min. The RT reaction was performed by adding 8 micro l of 5X first strand RT buffer (Life technologies, MD), 4 micro l of 20mM dNTPs minus dCTP (Pharmacia, UK), 4 micro l of 0.1M DTT, 40U of RNAse OUT (Life Technologies, MD), 6 micro l of 3000 Ci/mmol 33P-dCTP (ICN Biomedicals, UK) to the RNA/primer mixture to a final volume of 40 micro l. Two micro l (400 U) of Superscript II reverse transcriptase (Life Technologies, MD) was then added and the sample incubated for 30 min at 42oC followed by additional 2 micro l of Superscript II reverse transcriptase and another 30 min incubation. The reaction was stopped by addition of 5 micro l 0.5 M EDTA. Samples were incubated at 65oC for 30 min after addition of 10 micro l of 0.1M NaOH to hydrolyse and remove RNA. Samples were pH neutralized with 45 micro l 0.5M Tris, pH 8.0 and purified using Bio-Rad 6 purification columns (BioRad, UK). The NIA NeuroArray consists of 1152 cDNAs printed on nylon membrane in duplicate. The arrays were hybridised with alpha-33P-dCTP labelled cDNA probes overnight at 50oC in 4ml of hybridisation solution. Hybridised arrays were rinsed in 50ml of 2XSSC and 1%SDS twice at 55oC followed by two washes in 2X SSC and 1% SDS at 55oC for 15 min each. The microarrays were exposed to phosphorimager screens for 1-3 days. The screens were then scanned with Molecular Dynamics STORM PhosphorImager (Sunnyvale, CA) at 25 micro m resolution. Source GEO sample is GSM28534 Last updated (according to GEO): May 27 2005 GC (HKG25T) Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15712 Last updated (according to GEO): May 28 2005 no additional Source GEO sample is GSM199304 Last updated (according to GEO): Jun 08 2007 715 703 in the retina Osteoblasts 1000 Blood Test (Blinded) Sample Source GEO sample is GSM129921 Last updated (according to GEO): Sep 18 2007 /J Basal Ganglia A 3 20 Heart 861 1000 Solid tumor 861 Cerebellum Gene expression data from postmorten brain regions Source GEO sample is GSM145635 Last updated (according to GEO): Nov 20 2006 Normal__Kidney_Norm_622NO on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Thalamic structure 129:22-2 midbrain-thalamus Gut 861 Donor 2 Time point 48 hours post infection with HIV-1, RF Source GEO sample is GSM2614 Last updated (according to GEO): May 27 2005 Liver Test (Blinded) Sample Source GEO sample is GSM130119 Last updated (according to GEO): Sep 18 2007 1000 Neoplasm Gene expression data from rat metanephric mesenchymes cultured for 4 days in the presence of NGAL Source GEO sample is GSM126211 Last updated (according to GEO): Dec 08 2006 Heart Ventricle 1000 865 Disorder of artery Striatal sample from a 12-month-old wild-type mouse. Source GEO sample is GSM238688 Last updated (according to GEO): Oct 19 2007 uterus Source GEO sample is GSM18620 Last updated (according to GEO): May 27 2005 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b057 Source GEO sample is GSM1998 Last updated (according to GEO): Nov 21 2005 Caudal 1000 bronchial epithelia 224 243 SNU387 cells human cerebellum Source GEO sample is GSM87120 Last updated (according to GEO): Feb 08 2006 575-1 from colonic normal mucosa 21 47 NA Source GEO sample is GSM198925 Last updated (according to GEO): Jun 07 2007 Normal__Prostate_PR_2 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A mammary epithelial cells transduced with empty LXSN vector Source GEO sample is GSM5162 Last updated (according to GEO): May 27 2005 901 Bone Marrow 91 from the bone marrow 72 HMVEC-L stimulated with LPS for 24 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114560 Last updated (according to GEO): Sep 20 2006 HCT-116_CL4003_Colon on Affymetrix GeneChip Human Full Length Array HuGeneFL Affymetrix RGU34A 6HC 861 Brain rotenone 1 week A Treatment, type=time_course, measurement=1.0 weeks Source GEO sample is GSM107853 Last updated (according to GEO): Jun 06 2006 o Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181934 Last updated (according to GEO): Apr 13 2007 19 0 human frontal cortex Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188759 Last updated (according to GEO): Jun 06 2007 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201300 Last updated (according to GEO): Jun 14 2007 31 0 Cerebellum Alzheimer's disease 4 1000 Obesity 861 Longitudinal NA18981 Macrophage 14smi065 Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 8194 left_liver_lobe 1000 Kidney thyroid_gland_2 37 0 3AMH02030601_Colorectal Adenocarcinoma Myocardium 861 Liver Test (Blinded) Sample Source GEO sample is GSM130113 Last updated (according to GEO): Sep 18 2007 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156615 Last updated (according to GEO): Jan 22 2007 Craniocerebral Trauma 861 plasma cells 50 61 Heart 1000 of myocardial infarction 12 35 Compare the brain transcriptomes of Gja9 (-/-) and Gja9 (+/-) mice with that of wildtype mice to detect transcriptomic alterationss induced by total or partial ablation of Gja9 Source GEO sample is GSM146908 Last updated (according to GEO): Nov 29 2006 Primary Carcinoma 876 1206 1184 by cervical dislocation 674 653 extra-cellular matrix outer medulla 31 43 Blood 1000 1000 Spleen Spleen 1000 Epithelium 861 with some respiratory epithelium. 1039 1072 GSE8586 24 skeletal muscle 10 46 8 in docetaxel-refractory prostate cancer DBA whole brain 1B 60 50 Ovary C57BL Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7982.gif Source GEO sample is GSM76448 Last updated (according to GEO): Sep 22 2006 RNA of Kidney was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 biological replicates were analyzed. Keywords = db/m mice Keywords = kidney Source GEO sample is GSM9926 Last updated (according to GEO): May 27 2005 30 0 Adrenal medulla [JunctionChip 4 Liver 1000 V5-P393 227 223 Brain GM11992 short access to cocaine ,medial prefrontal cortex, 1 hr/day access to cocaine Source GEO sample is GSM93871 Last updated (according to GEO): Jan 26 2006 Cerebral cortex 1000 Endometrium 9 Normal Keywords = Infectious diseases 1133 1163 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188796 Last updated (according to GEO): Jun 06 2007 Brain 861 cerebral cortex sprague 3917 all cortical minus the frontal cortex, individual animal, 10 weeks old, male Sprague Dawley cerebral cortex file:p3917w Source GEO sample is GSM15154 Last updated (according to GEO): Oct 28 2005 136 131 Aortae CVB3-infected HeLa cells (multiple time points) Huntington Disease 861 of the postmortem brains 674 698 Total RNA extracted from the cerebellum of a Tg+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144416 Last updated (according to GEO): Nov 14 2006 858 Mesodermal cell with mental retardation 241 263 Expression profiling of spinal cord section (T10) extracted from rats 28d following severe injury Source GEO sample is GSM31367 Last updated (according to GEO): May 27 2005 brain 0 5 1000 Hippocampus The sample is a part of a series describing gene expression changes during postnatal development of the small intestine Source GEO sample is GSM198881 Last updated (according to GEO): Jun 11 2007 Mental Retardation 1000 NA12056 C57BLKS/J_male_hypothalamus Source GEO sample is GSM184198 Last updated (according to GEO): Apr 26 2007 plasma cells 332 344 for liver 26 35 tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44873 Last updated (according to GEO): May 27 2005 M_U133Plus_110_CB Anterior nares 1000 Structure of olfactory bulb 901 Sample represents the Neurointermediate lobe of the Pituitary from 5 dehydrated animals (3 Days) Source GEO sample is GSM69785 Last updated (according to GEO): Dec 15 2005 Prostate carcinoma 1000 Changes in gene expression profiles in developing B cells of murine bone marrow. 0 Human Cortex 11 5 0 brain Gene expression data from postmorten brain regions Source GEO sample is GSM145130 Last updated (according to GEO): Nov 20 2006 1000 Caudate nucleus structure Effects of cigarette smoke on the human airway epithelial cell transcriptome. Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 0893 blood Spinal Cord 901 861 Neoplasm H9LMS00111004 of the heart 842 854 I_U133A_106_AnCg I_95Av2_2835_AnCg_1_GS Bone structure of tibia 1000 17 7 hippocampus nmda1 (Experiment Neuroprotection4- Run 21823) Treatment, type=timepoint, description=Same sample used for Experiment Neuroprotection4-Run 14985, samples were rerun due to oven failure, measurement=0.0 h Source GEO sample is GSM96693 Last updated (according to GEO): Feb 14 2006 Skeletal bone 861 24 7 Right Frontal Lobe Pituitary Gland 861 mid back fibroblast (1.3F), asynch Hs578t 10 0 fetal brain Normal Source GEO sample is GSM176423 Last updated (according to GEO): Apr 09 2007 PBMCs-Type 1 Diabetes-IDDM34_T1D_New -uninjured cortex 103 119 Midbrain 8 Normal Cerebral cortex 861 Nasal Epithelium 865 Y HID D078 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108637 Last updated (according to GEO): Aug 22 2006 12 0 ovarian tumor LDMTX_MP-DX-13 bc-ZT9-1 861 Retina 1000 Ovary cortex Source GEO sample is GSM38980 Last updated (according to GEO): May 27 2005 1000 Communicable Diseases Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:273, Count:32 Corner- Avg:37090, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:5.683659,SFGene:All Background:Avg:409.43,Stdev:11.84,Max:460.3,Min:388.3 Noise:Avg:8.85,Stdev:0.62,Max:11.7,Min:7.9 RawQ:12.28 Keywords = ALL Source GEO sample is GSM3389 Last updated (according to GEO): May 27 2005 861 Blood R433P00224 hippocampus wistar ky 3956 whole tissue, individual animal, 10 weeks old, male Wistar Kyoto hippocampus file:p3956w Source GEO sample is GSM15178 Last updated (according to GEO): Oct 28 2005 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:387, Count:32 Corner- Avg:36935, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:4.951684,SFGene:All Background:Avg:493.24,Stdev:7.44,Max:514.6,Min:480.1 Noise:Avg:11.19,Stdev:0.52,Max:12.8,Min:9.4 RawQ:14.58 Keywords = ALL Source GEO sample is GSM3438 Last updated (according to GEO): May 28 2005 with some respiratory epithelium. 1039 1072 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/9474.gif Source GEO sample is GSM79849 Last updated (according to GEO): Sep 22 2006 Epithelium of bronchus 983 1307 1290 in skeletal muscle hind Source GEO sample is GSM67220 Last updated (according to GEO): Jan 19 2006 88 68 with bicuspid valves of somatomotor cortex 21 41 16 7 cerebellum 0029_1340_H95A2_KF-069_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A human ciliary muscle 94 113 Blood 861 Expression profiling of spinal cord section (T9) extracted from rats 7d following moderate injury Source GEO sample is GSM31593 Last updated (according to GEO): May 27 2005 Brain 1000 Gelsolin 1000 Exp A_1, 50mg/kg CPF ColonProx_022XAC3F_070.txt 901 Parkinson Disease Primary tumor 19 32 80 68 Control blood 39 21 of substantia nigra CNS-SC_InjB7d-2B-s2 Alzheimer's Disease 861 10 0 Endometrium 23 3 /BnJmale_hypothalamus AML cDNA hybridization-ID05-L 5 0 brain Gene expression data for comparing calorie restricted-fed 30-month-old to control-fed 30-month-old for investigating effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7455 Last updated (according to GEO): May 27 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL4 for 240min Source GEO sample is GSM5641 Last updated (according to GEO): May 27 2005 brain, hippocampus: Ctr-240h-P15-I_e1_le1 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188708 Last updated (according to GEO): Jun 06 2007 216 200 of neural retinas GSE6864 Infection 1176 1185 PGC-1a null (PGC-1a-/- ) and wild-type (PGC-1a+/+) mice were obtained by breeding heterozygous (PGC-1a+/-) founder mice as described (Leone et al., 2005). Source GEO sample is GSM135225 Last updated (according to GEO): Oct 05 2006 5 0 brain Ovarian_Tumor_ClearCell_KU-OC-005 cerebellum wistar 3885 Femur 1000 HMEC S1 day 7 sample 2 Ptdsr-/- fibroblast_rep9 5 0 brain 5 0 brain RR203_uninfected_DC Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc126 Source GEO sample is GSM1908 Last updated (according to GEO): Nov 21 2005 Primary tumor 19 32 Diaphragm 56 Day control rep 2 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15389.gif Source GEO sample is GSM84161 Last updated (according to GEO): Sep 22 2006 7 0 prostate 1000 ovarian neoplasm GBM Treatment, type=remove Source GEO sample is GSM99486 Last updated (according to GEO): Apr 21 2006 1000 Left PGA-MFD-CtrPD5-1aAv2-s2 7 frontal cortex 20 SCG acutely dissected from embryos Source GEO sample is GSM246044 Last updated (according to GEO): Dec 03 2007 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Dimaprit labeled with Cy5- time course with repeats. Date GSE379 Last Updated: May 29 2005 Contributers: Yun Anna Cao Joella Grossoehme Angela Alexander Sangdun Choi Mi Sook Chang Rebecca Hart Sun Young Lee Jong-Woo Kim Robert Hsueh Zhen Yan Includes GDS300. Update date: Nov 18 2003. Dataset description GDS300: Temporal analysis of effects induced by 10 uM dimaprit in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. AD-210t1-A144-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3320 Last updated (according to GEO): Mar 21 2006 Baseline comparison of global gene expression in ILS and ISS cerebellum to find differences in the naive state. Source GEO sample is GSM69570 Last updated (according to GEO): Oct 28 2005 395 383 of carcinomas 901 Basal Ganglia 861 Adipose tissue Head and neck cancer Source GEO sample is GSM155654 Last updated (according to GEO): Apr 24 2007 12 frontal Lobe 23 Gene expression data from NICM NYHA III-IV CHF patients Source GEO sample is GSM231008 Last updated (according to GEO): Sep 21 2007 Expression profile of genes in mouse brain Source GEO sample is GSM21063 Last updated (according to GEO): May 27 2005 SN12C_CL9008__RENAL Stem cells 901 1000 Brain Ta gr2 tumour Source GEO sample is GSM2533 Last updated (according to GEO): Mar 21 2006 in metastasis 1452 1464 7 frontal cortex 20 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188689 Last updated (according to GEO): Jun 06 2007 Gene expression data from rat metanephric mesenchymes cultured for 1 day in the presence of NGAL Source GEO sample is GSM126205 Last updated (according to GEO): Dec 08 2006 of the atrial 647 659 in blood 16 23 brain, unknown: Sample44_e1_le1 Ovarian_Tumor_Endometrioid_CHTN-OE-029 striatum 24 32 5 0 Asthma Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108005 Last updated (according to GEO): Jun 06 2006 861 Cerebral cortex Central gray substance of midbrain 861 Gene expression data from mouse colon Source GEO sample is GSM198119 Last updated (according to GEO): Aug 22 2007 myometrium_3 Source GEO sample is GSM80727 Last updated (according to GEO): Mar 31 2006 Macrophage smi79 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 18 hours after lights on. Original sample code = CM50A Source GEO sample is GSM227322 Last updated (according to GEO): Sep 10 2007 for basal- 1515 1524 Liver 1000 brain 0 5 861 frontal lobe 1000 Liver Gene expression data from postmorten brain regions Source GEO sample is GSM145361 Last updated (according to GEO): Nov 20 2006 PGA-MFD-MutantPD1-2aCv2-s2 1000 Brain none Source GEO sample is GSM210314 Last updated (according to GEO): Jul 16 2007 Jejunum 2 [JunctionChip 2 of 5] 861 Colon 2nd 1hr C+S-DG Expression profiling of spinal cord section (T8) extracted from rats 14d following severe injury Source GEO sample is GSM31457 Last updated (according to GEO): May 27 2005 of the postmortem brains 674 698 KidP2_022UAFAL_107.txt Structure of parenchyma of lung 1000 1000 Brain of the heart 842 854 Parkinson 0 8 Brain 861 1000 Dementia 901 Heart Diseases Normal Source GEO sample is GSM176205 Last updated (according to GEO): Apr 09 2007 Olfactory Epithelium 1000 Disease Source GEO sample is GSM176109 Last updated (according to GEO): Apr 09 2007 Disease Source GEO sample is GSM176314 Last updated (according to GEO): Apr 09 2007 brain, cerebral cortex: NMDA 1mM 10'_le1 7 0 prostate 61 of Down syndrome 46 1000 Brain 1586 1576 Five brains 78 66 Control blood 5 0 brain Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9868.gif Source GEO sample is GSM79921 Last updated (according to GEO): Sep 22 2006 861 Malignant Neoplasms 129:4-1 + 4-2 PAG of regenerating Dorsal Root Ganglia 21 55 861 Pancreas nostrils 156 164 Gene expression data from postmorten brain regions Source GEO sample is GSM145499 Last updated (according to GEO): Nov 20 2006 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132490 Last updated (according to GEO): Feb 26 2007 901 Mammary gland Gene expression data from postmorten brain regions Source GEO sample is GSM145557 Last updated (according to GEO): Nov 20 2006 Entorhinal Cortex 7 23 1000 Cerebellum 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113976 Last updated (according to GEO): Jun 16 2006 GSE9443 ER-/LN-/Nevins26 on Affymetrix GeneChip Human Full Length Array HuGeneFL 78 73 rectum 36 21 from whole brain from brain 21 30 (parietal cortex 1046 1061 The sample is a part of a series describing gene expression changes during postnatal development of the small intestine Source GEO sample is GSM198878 Last updated (according to GEO): Jun 11 2007 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10007.gif Source GEO sample is GSM79816 Last updated (according to GEO): Sep 22 2006 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225678 Last updated (according to GEO): Nov 02 2007 Donor D, after G-CSF Source GEO sample is GSM178557 Last updated (according to GEO): Aug 09 2007 no additional Source GEO sample is GSM199242 Last updated (according to GEO): Jun 08 2007 In innate immune responses, activation of Toll-like receptors (TLRs) triggers direct antimicrobial activity against intracellular bacteria, which in murine, but not human, monocytes and macrophages is mediated principally by nitric oxide. We report here that TLR activation of human macrophages up-regulated expression of the vitamin D receptor and the vitamin D-1-hydroxylase genes, leading to induction of the antimicrobial peptide cathelicidin and killing of intracellular Mycobacterium tuberculosis. We also observed that sera from African-American individuals, known to have increased susceptibility to tuberculosis, had low 25-hydroxyvitamin D and were inefficient in supporting cathelicidin messenger RNA induction. These data support a link between TLRs and vitamin D-mediated innate immunity and suggest that differences in ability of human populations to produce vitamin D may contribute to susceptibility to microbial infection. Last Updated (by provider): Aug 31 2007 Contributers: Belinda H Tan Stephan R Krutzik Robert L Modlin Huiying Li Philip T Liu brain, cerebral cortex: Nico + NMDA 8/30_le1 brain, cerebral cortex: Rat_03-08_NroLep_Lipska_e1_le1 GRP sample 3 of somatomotor cortex 21 41 total RNA derived from a leprosy lesion Source GEO sample is GSM6773 Last updated (according to GEO): May 27 2005 Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging and comparing calorie restricted-fed 30-month-old to control-fed 30-month-old to investigate effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7466 Last updated (according to GEO): May 27 2005 Synovial Membrane 8 Disease Large-scale analysis of the human transcriptome. Leukemia lymphoblastic, MOLT-4 Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 359.81 Stdv: 15.09 Min: 334.81 Max: 383.57 Source GEO sample is GSM2878 Last updated (according to GEO): Mar 20 2006 To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18482 Last updated (according to GEO): May 27 2005 Spleen 1000 HUVEC isolate 36 low serum media control for #12 Source GEO sample is GSM12904 Last updated (according to GEO): May 28 2005 ovarian tumor: mucinous Source GEO sample is GSM139425 Last updated (according to GEO): Apr 09 2007 Coronary heart disease 913 Parkinson's disease sample x103 0 30 Blood 861 V5-P270 B_B6_Control_ZT 6_2 1000 Familial cancer of breast Blood 1000 mouse cerebral cortex, cox-1 WT, rep2 41 30 PCOS oocytes Acetaminophen 3hr Rat 2730 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool mouse cerebral cortex 0 21 1000 frontal lobe Gene expression data from postmorten brain regions Source GEO sample is GSM145986 Last updated (according to GEO): Nov 20 2006 Abdominal aortic aneurysm obtained from surgery to correct. Source GEO sample is GSM170566 Last updated (according to GEO): Jul 26 2007 skeletal Source GEO sample is GSM67249 Last updated (according to GEO): Jan 19 2006 30 19 Solid tumor cDNAs were generated from 5ug of total RNA per sample by reverse transcription (RT) for two hours at 42oC using the 3DNA SubmicroTM Oligo Expression Array Detection Kit (Genisphere, Hatfield, PA) and Superscript II (Invitrogen, Carlsbad, CA). For each microarray chip two consecutive hybridizations were performed with cDNAs and the fluorescent probes following the manufacture?s specifications. Briefly, in the first hybridization reaction the solution containing the mixture of cDNAs obtained from control and treated cells was loaded onto the CAG Human 19K array and incubated overnight at 55oC in a hybridization chamber (Genemachines, San Carlos, CA). The human 19K array (www.cag.icph.org/microarray_facility.htm) contains 60-mer oligonucleotides (Compugen, San Jose, CA) representing 18,861 human genes spotted onto poly-l-lysine coated glass microscope slides. In the second hybridization reaction Cy3 (green) and Cy5 (red) fluorescent probes were used to label the cDNAs from control and PGJ2-treated cells, respectively. The second hybridization was carried out for 3 hours at 65oC in the hybridization chambers. The arrays were scanned using an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) with laser intensities adjusted to bring the brightest spot just below saturation and the data extracted with the Axon GenePix Pro software. Source GEO sample is GSM98759 Last updated (according to GEO): May 31 2006 in fibroblasts 1222 1236 1000 Brain Epithelium 861 Brain 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145763 Last updated (according to GEO): Nov 20 2006 129/SvImJ Cingulate Cortex B 6hr post 10Gy IR 861 Cerebral cortex Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs//27676.gif Source GEO sample is GSM66563 Last updated (according to GEO): Sep 22 2006 Skeletal bone 1000 ovary 45 50 Coronary artery 901 Nrl ko P10 replicate 2 30 19 Solid tumor NA19098 Skeletal muscle structure 1000 Adipose tissue 884 hrs nasal epithelium 1126 1146 Muscle 861 AEOL 10150 control #1 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13091.gif Source GEO sample is GSM76419 Last updated (according to GEO): Sep 22 2006 Affymetrix GeneChip® Mouse Genome 430 2.0 Array Source GEO sample is GSM197115 Last updated (according to GEO): May 31 2007 Bicalutamide_2 14 7 amygdala 861 Colon 861 Cancer of Neck CLL-65? T2+ gr 3 tumour Source GEO sample is GSM2512 Last updated (according to GEO): May 27 2005 M7TW00121824 Expression profiling of spinal cord section (T10) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM6658 Last updated (according to GEO): May 28 2005 Brain 861 TS13 sample 3 (cerebrum) 1000 Hippocampus Nrl ko samples were compared to wt at postnatal 10. Source GEO sample is GSM227463 Last updated (according to GEO): Sep 07 2007 7 0 prostate Egr1/Egr3 double knockout #3 Source GEO sample is GSM107469 Last updated (according to GEO): May 01 2006 human peripheral blood derived monocytes, 2 hour LPS stimulation, biological rep3 Wild type 8 wk old male C57BL/6J mouse amygdala Source GEO sample is GSM74917 Last updated (according to GEO): Feb 27 2007 458 447 of the liver from the cerebellum 20 38 307 292 during infection Adipose tissue 884 Gene expression data from PD3 Foxo3 Null ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203851 Last updated (according to GEO): Aug 02 2007 4 0 Brain A/J pituitary gland rep1 brain, hippocampus: KA-24h-P15-III_e1_le1 Heart failure_LVAD_2 between the LAD artery 266 287 161-96_Adeno Large Intestine; Proximal Colon Keywords = mouse gene expression database Source GEO sample is GSM29305 Last updated (according to GEO): May 27 2005 1000 Brain N2_d6 #1(16012165010072) 1000 Brain Liver 1000 in normal testis 659 675 1172 1159 of carcinomas 304 280 alcoholic cardiomyopathy 1000 Heart failure 144 114 from a single adult spinal cord Liver 1000 DCIS191 on harvard-12k 0 Lung tissue 10 Gene expression data from postmorten brain regions Source GEO sample is GSM144962 Last updated (according to GEO): Nov 20 2006 kidney 176 182 CD3 + CD28 beads + FK506 12.00 hr. T-cell 100213 5 0 brain DMN-NF1Hippo10d-1aAv2-s2 "Sample 42,>5 yr survival(66 months) age 54 erp yes" on vantveer-oligo metanephric mesenchyme, NGAL, 7 days, biological rep1 Ovary 1000 Liver 1000 GC (HKG36N) vagina_9 1000 ovarian neoplasm from rat lungs 21 34 Lipopolysaccharide-induced Changes in Gene Expression in Human Lung Microvascular Endothelial Cells over Time C57BL-6J were given intratracheal bleomycin (1.5U per kg). Lungs were harvested and frozen at 14d. Lot batch = Source GEO sample is GSM4160 Last updated (according to GEO): May 28 2005 SCG_control_24h_rep2 Cy3-labeled cDNA from brains of neonatal C57BL/6j wildtype mice was compared to Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice. Keywords = wildtype mouse brain Source GEO sample is GSM34855 Last updated (according to GEO): Jun 19 2007 861 Amygdaloid structure Osteoblasts 1000 1000 Retina Liver 0 4 Cerebral cortex 861 Dendritic Cells, Exposed to Leishmania major - Repeat #2 brain, Right Temporal Parietal: Extract85_le1 36 21 from mouse brain HapMap CHB Male Source GEO sample is GSM159612 Last updated (according to GEO): Feb 01 2007 1000 Spleen 913 Acute leukemia C85 on NCI-7.6k Simple annotation: Drug_treatment, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10258.gif Source GEO sample is GSM78478 Last updated (according to GEO): Sep 22 2006 N-6_POST 901 Mammary gland M_U133A_7_AnCg Pancreas at e15.5, Chip B, rep 1 Blood B cells Colonic mucous membrane 913 1000 Neoplasm 861 Retina of mouse brain 9 23 1000 Brain Tumor__Leukemia_ALL-B_ALL_(19769)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A of parieto-occipital cortex 117 143 861 Blood Gene expression data from postmorten brain regions Source GEO sample is GSM145217 Last updated (according to GEO): Nov 20 2006 Coronary artery 901 AT3-hTERT_1.5Gy_24h_C5_27021 62 38 out of mouse bone marrow 1000 Amygdaloid structure Matrigel culture, 9A1, rep 2 201 174 at the longitudinal fissure D_U133A_31_HC 41 36 spleen mouse liver, RNA B6999A Sprague-Dawley Male LowSalt OuterMedulla rat709 sd_medullar_k_709r_om_070302 Spinal Injuries 913 Epithelial Cells 1000 405_1 atrial septal defects 198 218 Tonsil Source GEO sample is GSM18742 Last updated (according to GEO): Sep 25 2006 Ky6: Hippocampus_21PT-Y_rep5 "32h Thy-Noc, Exp4" 861 Medulla forebrain 7 15 JMR-MurInj24h-3cAv2-s2 blood 0 5 HapMap YRI_parent Female Source GEO sample is GSM159673 Last updated (according to GEO): Feb 01 2007 heart failure 583 595 frontal cortex wistar ky 3928 0 cortex 5 R467P00436 Cerebral cortex 861 main olfactory epithelium 0 24 Expression profiling of spinal cord section (T9) extracted from rats 7d following laminectomy (sham) Lot batch = Source GEO sample is GSM6676 Last updated (according to GEO): May 28 2005 1h -TGF-beta odontoblasts Chromosomes 861 1000 Structure of dentate gyrus Spleen vs fMLP Treated B cell 30min (set1) Gene expression data from older female during 1 week of inadequate protein intake Source GEO sample is GSM209824 Last updated (according to GEO): Jul 11 2007 in the spinal cord 1014 1032 Disorder of artery 865 Disease Source GEO sample is GSM176444 Last updated (according to GEO): Apr 09 2007 Heart Atrium 1000 Molecular profiles of inflammatory myopathies. Cerebral cortex 1000 Normal Source GEO sample is GSM176183 Last updated (according to GEO): Apr 09 2007 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.4 Subject: 2978 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39043 Last updated (according to GEO): May 27 2005 10 Bone marrow 0 1000 Amygdaloid structure 861 Cerebral cortex 1000 Prostate 26 15 endometrioid 1026 1011 on chromosome 9 861 Cerebral cortex no additional Source GEO sample is GSM199392 Last updated (according to GEO): Jun 08 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114406 Last updated (according to GEO): Jun 16 2006 2053 2024 of inflammatory renal disease Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210381 Last updated (according to GEO): Jul 16 2007 doxycycline, mutant Source GEO sample is GSM213365 Last updated (according to GEO): Jul 26 2007 4 0 Colon StomMucos_0229AFBC_064.txt Wild type replicate #3 Source GEO sample is GSM107466 Last updated (according to GEO): May 01 2006 Neocortical astrocyte 1 Ganglia, Spinal 923 Dorsal Root Ganglia 1 Normal Brain 1000 Disorder of artery 865 1000 Liver 228 219 Hippocampi 15 0 human cerebellum Expression profiling of somatomotor cortex extracted from rats at 3 months following moderate injury Source GEO sample is GSM41729 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T10) extracted from rats 14d following mild injury Source GEO sample is GSM31303 Last updated (according to GEO): May 27 2005 335 325 The jejunum cortex 7 12 R723P00881 The nose 94 101 Large-scale analysis of the mouse transcriptome. Uterus C57BL/6L, female, 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 272.79 Stdv: 45.66 Min: 201.48 Max: 334.55 Source GEO sample is GSM2962 Last updated (according to GEO): May 27 2005 Hyperdip>50-#2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Heart Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3332 Last updated (according to GEO): Mar 21 2006 Liver 0 4 Liver Test (Blinded) Sample Source GEO sample is GSM130199 Last updated (according to GEO): Sep 18 2007 PGC-1a null (PGC-1a-/- ) and wild-type (PGC-1a+/+) mice were obtained by breeding heterozygous (PGC-1a+/-) founder mice as described (Leone et al., 2005). Source GEO sample is GSM135221 Last updated (according to GEO): Oct 05 2006 HapMap CHB Male Source GEO sample is GSM159608 Last updated (according to GEO): Feb 01 2007 35 CB B 861 Cardiomyopathies Two groups of 3 days old mice were treated with oil or retinoic acid. At day 4 one half of each group was treated with saline solution or dexametasone. Lungs were removed snap frozed for RNA extraction Source GEO sample is GSM4141 Last updated (according to GEO): May 27 2005 5 0 brain 861 Cerebral cortex Olfactory Epithelium 1000 Timecourse of TLR2/1 stimulated human dendritic cells with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225867 Last updated (according to GEO): Aug 31 2007 plasma cells 332 344 A YOKE D027 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108624 Last updated (according to GEO): Aug 22 2006 1000 frontal lobe TS21 sample 2 (astrocyte) Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9890.gif Source GEO sample is GSM79804 Last updated (according to GEO): Sep 22 2006 239 233 Retinas Gene expression data from postmorten brain regions Source GEO sample is GSM145309 Last updated (according to GEO): Nov 20 2006 861 Colon Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188844 Last updated (according to GEO): Jun 06 2007 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225709 Last updated (according to GEO): Nov 05 2007 36 hr Hela Double Thymidine, exp2 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181199 Last updated (according to GEO): Jul 12 2007 901 Coronary artery GBM: 34A33 brain, cerebral cortex: NMDA 369 4_le1 86 71 from femur C57BL 861 Cancer of Neck Temporal gene expression profiling of dystrophin-deficient (mdx) mouse diaphragm identifies conserved and muscle group-specific mechanisms in the pathogenesis of muscular dystrophy. 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114182 Last updated (according to GEO): Jun 16 2006 151 to genetic disorders 170 CNS-SpinalC-conAdult-T0-2A-s2 skin 48 51 SCG_control_2h_rep2 901 Nervous system structure 1000 Neoplasms, Embryonal Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 2486 blood Saccule at E13, replicate1 Spleen 1000 of 6 saccules 5 17 Prosencephalon 861 Expression profiling of spinal cord section (T9) extracted from rats 12h following moderate injury Source GEO sample is GSM31522 Last updated (according to GEO): May 27 2005 10 0 whole brain human caudate nucleus Source GEO sample is GSM86872 Last updated (according to GEO): Feb 08 2006 Femur 1000 mouse brains 187 198 1000 Hypothalamic structure HC82 CN A 861 Oocytes Exp 2 Time point 7 Lb16: Hippocampus_5T-AU_rep3 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells cultured for 30min Source GEO sample is GSM5838 Last updated (according to GEO): May 27 2005 2821 2803 in skeletal muscle 1000 Heart failure NOS exp2 NMDA GM12006 Normal Source GEO sample is GSM175906 Last updated (according to GEO): Apr 09 2007 861 Prostate Primary typical carcinoid 7787 Source GEO sample is GSM17325 Last updated (according to GEO): May 28 2005 913 Coronary heart disease 1000 Muscle peripheral blood-CD19BCells Source GEO sample is GSM18881 Last updated (according to GEO): Sep 25 2006 5 0 brain Mouse ileum with L.innocua(inlA)_B_5558 Mouse ileum 0 10 Parkinson's disease sample x123 875 Subcutaneous Tissue in the brain 150 162 T49__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 928 Endometrium Prostate 861 Cerebellum Alzheimer's disease 8 none Source GEO sample is GSM244587 Last updated (according to GEO): Nov 23 2007 umbilical cord_nobpd: 3C Normal Source GEO sample is GSM176427 Last updated (according to GEO): Apr 09 2007 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM79047 Last updated (according to GEO): Oct 24 2005 Heart 861 861 Integumentary system Untreated Control 12weeks AffyGC RMA rep7 the blood 393 402 Primary Neoplasm 1000 Colon 861 Spleen 1000 1000 Brain that CLL 500 507 In an ongoing translational research program involving microarray-based expression profiles in pediatric septic shock, we have now conducted longitudinal studies focused on the temporal expression profiles of canonical signaling pathways and gene networks. Genome-level expression profiles were generated from whole blood-derived RNA samples of children with septic shock (n = 30 individual patients) corresponding to days 1 and 3 of admission to the pediatric intensive care unit. Based on sequential statistical and expression filters, day 1 and day 3 of septic shock were characterized by differential regulation of 2,142 and 2,504 gene probes, respectively, relative to normal control patients. Venn analysis demonstrated 239 unique genes in the day 1 data set, 598 unique genes in the day 3 data set, and 1,906 genes common to both data sets. Analyses targeted toward derivation of biological function from these data sets demonstrated time-dependent, differential regulation of genes involved in multiple canonical signaling pathways and gene networks primarily related to immunity and inflammation. Notably, multiple and distinct gene networks involving T cell- and MHC antigen-related biological processes were persistently downregulated from day 1 to day 3. Further analyses demonstrated large scale and persistent downregulation of genes corresponding to functional annotations related to zinc homeostasis. These data represent the largest reported cohort of patients with septic shock, which has undergone longitudinal genome-level expression profiling. The data further advance our genome-level understanding of pediatric septic shock and support novel hypotheses that can be readily tested at both the experimental and translational levels. Last Updated (by provider): Jun 14 2007 in blood 16 23 Brain_MD_6_Medulloblastoma_Classic_D on Affymetrix GeneChip Human Full Length Array HuGeneFL with mental retardation 241 263 Whole blood 0 10 brain, left frontal temporal lobe: Extract36_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM145059 Last updated (according to GEO): Nov 20 2006 to the nose 599 609 Disease Source GEO sample is GSM176362 Last updated (according to GEO): Apr 09 2007 503 497 organs olanzapine-treated mouse brain 91 from the bone marrow 72 Amygdala Treatment, type=pharmacogenomic_treatment, description=Handled (no stress) control Source GEO sample is GSM53306 Last updated (according to GEO): Jul 06 2005 Gene expression data from a neocortex from mouse injected 15 mg/kg kainate Source GEO sample is GSM147402 Last updated (according to GEO): Jan 03 2007 Brain 861 K-562 hgu95c 901 Coronary artery 1000 Heart M_95A_3023_Cg_0_GS 8 CN A Neoplasm 1000 Biopsy of a colorectal adenoma from patient #30 10 7 Left E10.5 craniofacial tissue, first branchial arch: WT_MXA2-1_e1_le1 Gene expression data from mammary glands of involuting mice Source GEO sample is GSM202704 Last updated (according to GEO): Jun 20 2007 from colorectal adenoma 21 44 4 0 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145613 Last updated (according to GEO): Nov 20 2006 943 924 of transgenic hearts Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 6954 blood Myocardium 861 mRNA was isolated after 2 hours of incubation from IMR-90 cells seeded onto a collagen/chondroitin sulfate tissue engineering scaffold mesh material. Cells were seeded at a density of 1 x 10^6 cells/ mesh, and this chip represents a pooling of cells from 4 meshes. Keywords = tissue engineering mesh, collagen, chondroitin sulfate, biomaterials design Source GEO sample is GSM6051 Last updated (according to GEO): May 27 2005 from ventral prostate 21 41 116 FC BA9 B post Infection 29 42 Brain 1000 Adenocarcinoma 861 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour.This animal was sacrificed at 4 hours after lights on.Original sample code = CM4A Source GEO sample is GSM227335 Last updated (according to GEO): Sep 10 2007 long access to cocaine, nucleus accumbens, 6 hrs/day access to cocaine Source GEO sample is GSM93824 Last updated (according to GEO): Jan 26 2006 Hippocampus Source GEO sample is GSM107924 Last updated (according to GEO): Jun 06 2006 Spleen vs BAFF Treated B cell 60min (set1) in murine small intestine 76 100 GSE7208 Aortic aneurysm without mention of rupture NOS 901 430A2_1945_38_KO_sham_midbrain Source GEO sample is GSM242685 Last updated (according to GEO): Nov 15 2007 Putamen P9 Normal 59 50 Lung C57BL Biopsy of a colorectal adenoma from patient #6 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151980 Last updated (according to GEO): Feb 06 2007 Brain_MD_10_Medulloblastoma_Classic _D on Affymetrix GeneChip Human Full Length Array HuGeneFL skeletal.muscle.3 9 of prefrontal cortex 28 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188831 Last updated (according to GEO): Jun 06 2007 To evaluate gene expression in human peripheral blood derived monocytes over the course of an LPS stimulation time-series. Last Updated (by provider): Aug 15 2006 Contributers: Jared C Roach 3073 HP6_42 Colon 861 Human muscle cultures were prepared from progenitor satellite cells isolated from a muscle biopsy of a 16-donor subject through an explant-reexplant technique (5). Biopsies were obtained with informed consent and approval of the Human Use Committee of the Hospital Vall d?Hebrón, Barcelona. A batch of cells isolated after 1 explant and 4 consecutive subcultures at dilution (1:3) were induced to differentiate for 15 days and then weekly monitored for the stated parameters. Growth medium was DMEM:MEM-199 3:1, supplemented with 10 % fetal bovine serum (FBS), 10 µg/ml insulin, 2 mM glutamine, 25 ng/ml fibroblast growth factor (FGF) and 10 ng/ml epidermal growth factor (EGF). Differentiating medium had the same composition except FGF and EGF. Cultures were kept at 37ºC in a humidified 5% CO2 atmosphere. Source GEO sample is GSM19156 Last updated (according to GEO): Oct 28 2005 13 7 cochlea 1103 1092 /db kidneys 7 frontal cortex 20 861 Brain 61 50 Thymus C57BL 1000 Endometriosis, site unspecified Tumor__Uterus_Adeno_4203 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Neuraxis Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211297 Last updated (according to GEO): Jul 18 2007 human frontal cortex Source GEO sample is GSM86972 Last updated (according to GEO): Feb 08 2006 901 Heart Diseases TEL-AML1-C25 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A N31__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Two groups of 3 days old mice were treated with oil or retinoic acid. At day 4 one half of each group was treated with saline solution or dexametasone. Lungs were removed snap frozed for RNA extraction Source GEO sample is GSM4142 Last updated (according to GEO): May 27 2005 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159956 Last updated (according to GEO): Feb 01 2007 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169502 Last updated (according to GEO): Feb 21 2007 Stem cells 913 1000 Integumentary system /J Cerebellum A 3 17 Gene expression data from postmorten brain regions Source GEO sample is GSM145915 Last updated (according to GEO): Nov 20 2006 brain 0 5 Occipital lobe 861 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9926.gif Source GEO sample is GSM79891 Last updated (according to GEO): Sep 22 2006 "Sample 51, <5 yr survival(59 months) age 41 erp yes" on vantveer-oligo AD-304t1-A240-8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 983 Cell Adhesion Molecules Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8739.gif Source GEO sample is GSM76433 Last updated (according to GEO): Sep 22 2006 Medulla 861 Mucous Membrane 861 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68293 Last updated (according to GEO): Jul 07 2006 liver, wild type mice, control conditions Source GEO sample is GSM205816 Last updated (according to GEO): Jul 24 2007 Brain 1000 861 Colon Brain 861 Skin 1000 901 Coronary artery 320 291 of human oral epithelial cells The most common congenital cardiac abnormalities 50 97 Untreated versus treated (bortezomib), untranformed MCF10A and Transformed (see Adler et al, Nature Gen. 2006) Source GEO sample is GSM120227 Last updated (according to GEO): Jul 20 2006 FVB/NJ pituitary gland rep1 starved 30 36 of 1919 tumor 50 62 Spinal Cord 1000 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 3 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10947 Last updated (according to GEO): May 27 2005 HBEC Source GEO sample is GSM18815 Last updated (according to GEO): Sep 25 2006 11 0 Hypothalamus Whole blood 0 10 313-99PT_Adeno Brain 861 in the mouse visual system 176 202 NoCAD_replicate30 913 frontal lobe Delineation of prognostic biomarkers in prostate cancer. affy original enzo kit processing Source GEO sample is GSM120463 Last updated (according to GEO): Jul 17 2006 Retina 1000 of caudal 93 101 Disorder of artery 865 Biopsy of the normal mucosa of the colon from patient #15 36 21 from whole brain femurs 2781 2787 Disorder of artery 865 Patient5F 0 Human Cortex 11 Nothing in line. Source GEO sample is GSM154218 Last updated (according to GEO): Jul 05 2007 Plasma 861 spinal cord 21 31 SW-620 hgu95a 1000 Endometriosis, site unspecified plasma cells 332 344 Arteries 861 brain, frontal cortex: ADX AM DR b_e1_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM145688 Last updated (according to GEO): Nov 20 2006 high gestational age Source GEO sample is GSM213099 Last updated (according to GEO): Jul 25 2007 GBM Treatment, type=remove Source GEO sample is GSM99537 Last updated (according to GEO): Apr 21 2006 Date : 4/29/2002 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 4.5 hrs post-injection Intervention : 4.0 mg/kg PK11195 co-administered Risk: anticipated remediation to <10% malformations Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots Keywords = methylmercury Keywords = PK11195 Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = SC906 Source GEO sample is GSM12263 Last updated (according to GEO): May 28 2005 861 Neoplasm Neoplasm 861 CAD_replicate90 Brain 861 14 0 Small Intestine D_U133Plus_59_Amy cy5:WKY control, biological rep 4r; cy3:pool of 6 WKY control rats Expression profiling of spinal cord section (T9) extracted from rats 7d following severe injury Lot batch = Source GEO sample is GSM7597 Last updated (according to GEO): May 28 2005 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184693 Last updated (according to GEO): Apr 26 2007 Laser captured visceral sensory neurons. Source GEO sample is GSM63656 Last updated (according to GEO): Dec 21 2005 Epithelium 861 Fibroblasts 861 63 50 Amygdala C57BL 1000 Endometrium R6 3 Large-scale analysis of the mouse transcriptome. Lymph node, mesenteric C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 281.71 Stdv: 13.46 Min: 260.68 Max: 305.19 Source GEO sample is GSM2939 Last updated (according to GEO): Mar 20 2006 861 Adrenal Cortex Primary Neoplasm 1000 H9LMS00111506 Expression Proflies of Human Normal tissues 1000 Cerebrovascular accident Spleen 0 5 of Parkinson's disease 450 471 Sample20, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53271 Last updated (according to GEO): Jul 06 2005 liver 0 5 Whole Brain 62 72 Gene expression data from postmorten brain regions Source GEO sample is GSM145354 Last updated (according to GEO): Nov 20 2006 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195257 Last updated (according to GEO): Sep 13 2007 neurological disease control sample x166 MP-DX-6 Brain 861 Malignant neoplasm of ovary 901 Control Source GEO sample is GSM175961 Last updated (according to GEO): Apr 09 2007 Cerebral cortex 901 861 Hypothalamic structure plasma cells 50 61 CNS-RM_Mod7d-1C-s2 This experiment set contains the complete set of raw data for Whitfield et al. (2002)Mol.Biol.Cell. HeLa S3 cells were synchronized by three different methods (double thymidine block, thymidine-nocodazole block or mitotic shake-off)in five independent time courses. mRNA from the first and second double thymidine block experiments were converted to cDNA by standard methods using an oligo-dT/random hexamer mix and hybridized to 24K arrays; mRNA from the third double thymidine and thymidine-nocodazole block experiments were converted to cDNA using olido-dT alone and hybridized to 43K arrays; total RNA from the mitotic shake-off experiment was first amplified using a modified eberwine protocol, aRNA converted to cDNA by reverse transcription with random hexamer and hybridized to 43K arrays. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Last Updated (by provider): Oct 21 2005 Contributers: Janos Demeter Michael Whitfield [Switched to use SH-WHIT by Gemma] OCI Ly10 brain, hippocampus: CH6_e1_le1 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-gamma (IFN gamma) for 120min Source GEO sample is GSM5608 Last updated (according to GEO): May 27 2005 brain, Entorhinal Cortex: Arcturus PicoPure_le1 CAD_replicate89 63 59 /Neck pfc_1020_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Expression profiling of somatomotor cortex extracted from rats at 14d following moderate injury Source GEO sample is GSM41697 Last updated (according to GEO): May 27 2005 Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep4 861 Blood R685P01201 Primary tumor 19 32 861 Kidney Abdominal aorta structure 865 10 7 Left 9 0 Blood Test cerebellum wistar 3886 whole tissue, individual animal, 10 weeks old, male Wistar cerebellum file:p3886w Source GEO sample is GSM15129 Last updated (according to GEO): Oct 28 2005 Traumatic brain injury (TBI) induces a complex cascade of molecular and physiological effects. This study proposes to investigate the gene expression profile in cortex and hippocampus over early time points, following two different injury severities. These results will complement prior knowledge of both metabolic and neuroplastic changes after TBI, as well as serve as a starting point to investigate additional gene families whose expression is altered after TBI. To characterize the profile of gene expression following a diffuse traumatic brain injury of varying severity in adult rats. Distinct patterns of gene expression following traumatic brain injury will occur in a time- and injury-dependent fashion. In particular, changes in expression of enzymes involved in energy metabolism and neuroplasticity will be detected. Adult rats will be subjected to mild and severe lateral fluid percussion injury OR sham surgery without injury. At various post-injury timepoints (0.5, 4 and 24 hours), animals will be sacrificed, brain regions (parietal cortex and hippocampus, ipsilateral and contralateral to injury) will be dissected and RNA isolated. RNA will be used to synthesize cRNA probes for microarray hybridization. RNA from 2 matched animals will be pooled onto a single chip (U34A rat, Affymetrix). Comparisons will be made between sham and injured animals, with brain region, injury severity, and post-injury time point as the experimental variables.. Date GSE2871 Last Updated: Jul 06 2005 Contributers: C C Giza Includes GDS1795. Update date: Jun 09 2006. Dataset description GDS1795: Analysis of cortices and hippocampi of animals 4 and 24 hours after mild or severe traumatic brain injury (TBI). TBI induced by lateral fluid percussion. Gene expression in tissues ipsi- and contralateral to the injury examined.. 1000 frontal lobe Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160715 Last updated (according to GEO): Sep 24 2007 C57BL/6J CHR, Rep3 1056 1049 muscles with autism spectrum disorder 37 65 UterViEs_0226ACII_112b.txt frontal lobe 1000 E7.75_rep2 Gene expression data from hippocampus of one old SAMP10//Ta mouse Source GEO sample is GSM143748 Last updated (according to GEO): Jan 24 2007 Temporal neocortex mTLE 10 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152004 Last updated (according to GEO): Feb 06 2007 Cerebral cortex 861 Heart 1000 Bone Marrow 1000 Total RNA from fresh prepared OC, pool from 12 cochleas (=6 animals); used as control. Source GEO sample is GSM124561 Last updated (according to GEO): Aug 04 2006 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215060 Last updated (according to GEO): Aug 02 2007 Unsusceptible Group, Nucleus accumbens, Biological Replicate 2 Epithelium 861 (cortex 19 25 Hippocampus 861 861 Blood in Huntington's disease 265 287 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14973 Last updated (according to GEO): Oct 28 2005 n/a Source GEO sample is GSM177996 Last updated (according to GEO): Jun 11 2007 Macrophage 14smi052 In current clinical practice, histology-based grading of diffuse infiltrative gliomas is the best predictor of patient survival time. Yet histology provides little insight into the underlying biology of gliomas and is limited in its ability to identify and guide new molecularly targeted therapies. We have performed large-scale gene expression analysis using the Affymetrix HG U133 oligonucleotide arrays on 85 diffuse infiltrating gliomas of all histologic types to assess whether a gene expression-based, histology-independent classifier is predictive of survival and to determine whether gene expression signatures provide insight into the biology of gliomas. We found that gene expression-based grouping of tumors is a more powerful survival predictor than histologic grade or age. The poor prognosis samples could be grouped into three different poor prognosis groups, each with distinct molecular signatures. We further describe a list of 44 genes whose expression patterns reliably classify gliomas into previously unrecognized biological and prognostic groups: these genes are outstanding candidates for use in histology-independent classification of high-grade gliomas. The ability of the large scale and 44 gene set expression signatures to group tumors into strong survival groups was validated with an additional external and independent data set from another institution composed of 50 additional gliomas. This demonstrates that large-scale gene expression analysis and subset analysis of gliomas reveals unrecognized heterogeneity of tumors and is efficient at selecting prognosis-related gene expression differences which are able to be applied across institutions. M_U133A_97_AnCg freshly dissected metanephric mesenchyme, biological rep2 Malignant neoplasm of breast 1000 9 of prefrontal cortex 28 Gene expression data from 14B3 BMEL cells cultured under Matrigel conditions. Source GEO sample is GSM160081 Last updated (according to GEO): Jul 11 2007 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68328 Last updated (according to GEO): Jul 07 2006 Skeletal bone 861 Microdissected area # 2 of 1919 tumor 1st 2hr C-DG Muscle 645 650 2.5 mg/kg 2CdA embryo at 3.0h adrenal gland Source GEO sample is GSM18627 Last updated (according to GEO): May 27 2005 9 0 Blood Test 366 354 encephalitis 1000 Amygdaloid structure The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169477 Last updated (according to GEO): Feb 21 2007 36 21 from whole brain AD-122t3-A197-8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 7 frontal cortex 20 Myocardium 861 Peripheral Nervous System 1000 901 Coronary artery Spleen 0 5 HMEC X BC17 129P3/J ACU, Rep3 L_B6_SleepDep_ZT 6_1 861 Prostate 660 mesenchymal stem cell 639 HC80 CN A Brain 1000 gene expression from allergen stimulated mouse lung Source GEO sample is GSM158140 Last updated (according to GEO): Jan 25 2007 hind.brain.1 Transcription profiling involves H3 methyltransferase G9a-deleted MEFs reconstituted with empty vector (delta), wild type FLAG-G9a (WT), FLAG-G9a K165A (K165A) or FLAG-G9a H1093K catalytic mutant (H1093K). Source GEO sample is GSM197747 Last updated (according to GEO): Jul 16 2007 DLCL-0040 Blood 861 f2#150 versus pool Mouse Brain tissue NoCAD_replicate3 T60__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A GSE8096 861 Cerebellum Spleen vs Prostaglandin E2 Treated B cell 120min (set3) Skeletal muscle biopsy was obtained before a 3-hour hyperinsulinemic (infusion rate 40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172163 Last updated (according to GEO): Feb 28 2007 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13433.gif Source GEO sample is GSM79692 Last updated (according to GEO): Sep 22 2006 Mid secretory endometrium from normal patient Source GEO sample is GSM150225 Last updated (according to GEO): Dec 14 2006 Occipital lobe 861 Blood 1000 Brain 861 Expression profiling of spinal cord section (T8) extracted from rats 4h following severe injury Source GEO sample is GSM31483 Last updated (according to GEO): May 27 2005 91 from the bone marrow 72 plasma cells 50 61 Trauma 1000 5 0 Muscle cortex 27 33 1000 Structure of postcentral gyrus Carcinoma, Large Cell 867 Mesenchymal Stem Cells 1000 Ewing, Cancer 1000 Primary carcinoma of the liver cells Acetaminophen 6hr Rat 1045 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool H124 FC BA4 B Whole blood from a patient with multiple system atrophy Source GEO sample is GSM153472 Last updated (according to GEO): Jan 11 2007 78 66 Control blood Peripheral Nerves 851 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 9 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10950 Last updated (according to GEO): May 27 2005 Myometrium 34 Disease The most common congenital cardiac abnormalities 50 97 Plasma 861 CVB3_S-1h DMN-NF1Hippo10d-2aAv2-s2 24 skeletal muscle 10 Skeletal bone 861 24 0 human prostate PC3 tumors Serum 0.5 Cerebellum 1000 the ventricular 1095 1109 cerebral cortex 7 21 Distinctive molecular profiles of high-grade and low-grade gliomas based on oligonucleotide microarray analysis. The most common congenital cardiac abnormalities 50 97 Sun177_BAV13 group 3_hypothalamus_6hrs_sleep_deprivation_#127 Bone Marrow 1000 M_U133A_62_nAcc brain_DLPFC_bipolar B_mr553 Brain 861 Proliferative endometrium from normal patient Source GEO sample is GSM150197 Last updated (according to GEO): Dec 14 2006 in hepatocellular carcinoma 31 58 Tissue Source GEO sample is GSM67203 Last updated (according to GEO): Jan 19 2006 Expression profile of genes in mouse brain Source GEO sample is GSM21050 Last updated (according to GEO): May 27 2005 1000 Coronary Arteriosclerosis 861 Substantia nigra structure Brain 1000 brain, Left frontal Lobe: Extract6_le1 928 Hyperinsulinism 1000 Solid tumor Spleen 1000 1100 1087 heart failure 111 102 infection GM10839 in the hippocampus 645 662 Nose 1000 adipose tissue 0 13 prostate Source GEO sample is GSM203401 Last updated (according to GEO): Jun 21 2007 861 Aortic Aneurysm 7 cerebral cortex 21 Parkinson's disease sample x032 Skin 1000 Heart Atrium 1000 12 Down syndrome 25 252 239 MCA parenchyma 17 on NHGRI-13.8k of central neurites 430 448 36 21 from whole brain Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27668.gif Source GEO sample is GSM66576 Last updated (according to GEO): Sep 22 2006 small intestine PPARalpha knockout mice, control diet. Source GEO sample is GSM124315 Last updated (according to GEO): Jun 28 2007 861 Cerebral cortex Brain 1000 A YOKE D063 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108626 Last updated (according to GEO): Aug 22 2006 BXD 1_M7SS02080615 kidney 37 43 Brain 1000 865 Disorder of artery septum no access to cocaine replicate 1 EMT initiation in MCF10A cells subjected to ionizing radiation and treatment with transforming growth factor beta-1. Cerebral cortex 861 861 Blood SN:Human Glioblastoma Biopsy 10399 f2#331 versus pool Mouse Brain tissue 15 0 human cerebellum lymphnode; mesenteric Source GEO sample is GSM18616 Last updated (according to GEO): May 27 2005 861 Retina Osteoblasts 1000 Intestines, Small 1000 124 112 basal ganglia 901 frontal lobe 8 brown fat 0 C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 1hr after experimental mice received their last shock treatment. Source GEO sample is GSM4497 Last updated (according to GEO): May 27 2005 7 0 prostate 2hr S-DG 72 CB B 1000 Spleen 1000 Colon from liver 21 30 PGA-MurLungRag-pbs-72h-1aCv2-s2 1BJZ02081482a_Appendix Mesenchymal Stem Cells 1000 861 Cerebral cortex /3T3 fibroblasts 743 759 901 frontal lobe 861 Chondrocytes osteoblast 627 637 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:262, Count:32 Corner- Avg:29837, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:6.318184,SFGene:All Background:Avg:496.31,Stdev:11.28,Max:524.2,Min:464.0 Noise:Avg:9.36,Stdev:0.32,Max:10.6,Min:8.4 RawQ:13.92 Keywords = ALL Source GEO sample is GSM3397 Last updated (according to GEO): May 27 2005 20 0 Normal Salivary Gland The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27019 Last updated (according to GEO): May 27 2005 1000 jejunum 1000 Hippocampus D_95Av2_1905_DLPFC_1_GS Thyroid [JunctionChip 4 of 5] 5 0 brain Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589?595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164?169.) Source GEO sample is GSM159478 Last updated (according to GEO): Jun 21 2007 M7TW00121387 901 Stem cells Heart Septal Defects 884 1000 Neuraxis plasma cells 332 344 cocaine naive, ventral tegmental area 0 37 Skin 2 Disease 0 13 338 333 brain Standard Affymetrix Protocol Source GEO sample is GSM15851 Last updated (according to GEO): May 28 2005 AJ 1-2 Heart that fibroblasts 926 941 AD-302t3-A238-8 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from postmorten brain regions Source GEO sample is GSM145620 Last updated (according to GEO): Nov 20 2006 Expression profiling of spinal cord section (T10) extracted from rats 4h following laminectomy (sham) Source GEO sample is GSM31289 Last updated (according to GEO): May 27 2005 1000 Brain MOLT3 DMSO control 24h rep1 861 Endometriosis, site unspecified C57_HF_1 Total RNA from cultured organ of Corti, pool from 12 cochleas; used as control for hypoxia. Source GEO sample is GSM124567 Last updated (according to GEO): Aug 04 2006 Infection 1000 Nasal Epithelium 901 of the postmortem brains 676 700 no additional Source GEO sample is GSM199321 Last updated (according to GEO): Jun 08 2007 Parkinson Disease 861 CS-B wt-rescued cell UVC-irradiated (2hour) replicate 3 U133B Estrogen treated ipsilateral to stroke E6IC-1a amygdala no access to cocaine replicate 3 Dahl-Iwai Male HighSalt Cortex rat114 dahl_cortexr_k_114c_072001 11_0020_Control_Day1_37 1000 Prostate to muscle 2251 2259 Cochlear structure 1000 Gene expression data from biopsy of PBS treated skin of subject with resolver phenotype. (control) Source GEO sample is GSM128955 Last updated (according to GEO): Sep 13 2007 small intestine PPARalpha knockout mice, control diet. Source GEO sample is GSM124316 Last updated (according to GEO): Jun 28 2007 **** Source GEO sample is GSM4282 Last updated (according to GEO): May 27 2005 861 Heart kidney 37 43 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155060 Last updated (according to GEO): Jun 04 2007 Parkinson Disease 861 Hippocampus 1000 Y VIS D066 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108650 Last updated (according to GEO): Aug 22 2006 Heart 1000 Standard Affymetrix Protocol Source GEO sample is GSM16494 Last updated (according to GEO): May 28 2005 brain, cerebral cortex: Sham11_e1_le1 Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22575 Last updated (according to GEO): May 27 2005 NCI60.39_LABEL43EXTRACT42SUB3 Source GEO sample is GSM134186 Last updated (according to GEO): Aug 06 2007 Testis 1000 Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed for 24 h to hydrostatic pressure (HP24), pressure experiment # 3 (PE3). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11413 Last updated (according to GEO): Dec 15 2006 P7_3 The etiology of the central nervous system (CNS) alterations after human immunodeficiency virus (HIV) infection, such as dementia and encephalitis, remains unknown. We have used microarray analysis in a monkey model of neuroAIDS to identify 98 genes, many previously unrecognized in lentiviral CNS pathogenesis, whose expression is significantly up-regulated in the frontal lobe of simian immunodeficiency virus-infected brains. Further, through immunohistochemical illumination, distinct classes of genes were found whose protein products localized to infiltrating macrophages, endothelial cells and resident glia, such as CD163, Glut5, and ISG15. In addition we found proteins induced in cortical neurons (ie, cyclin D3, tissue transglutaminase, 1-antichymotrypsin, and STAT1), which have not previously been described as participating in simian immunodeficiency virus or HIV-related CNS pathology. This molecular phenotyping in the infected brains revealed pathways promoting entry of macrophages into the brain and their subsequent detrimental effects on neurons. These data support the hypothesis that in HIV-induced CNS disease products of activated macrophages and astrocytes lead to CNS dysfunction by directly damaging neurons, as well as by induction of altered gene and protein expression profiles in neurons themselves which are deleterious to their function. Last Updated (by provider): Jun 29 2005 Contributers: Eleanor Roberts Debbie D Watry Howard S Fox Steven J Henriksen Lisa J Madden Michael A Taffe Steven R Head Michelle A Zandonatti human cerebellum Source GEO sample is GSM87122 Last updated (according to GEO): Feb 08 2006 12h mitotic selection Gene expression data from postmorten brain regions Source GEO sample is GSM145519 Last updated (according to GEO): Nov 20 2006 A YOKE D061 Basal 1000 Normal Source GEO sample is GSM176369 Last updated (according to GEO): Apr 09 2007 I_U133A_71_AnCg 144 109 Keywords = congenital heart disease Liver 1000 Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_3 months_replicate 1 between the LAD artery 266 287 Infection 1000 Primary Neoplasm 1000 nostrils 156 164 Neuraxis 1000 1000 Liver C57BL/6 benchmark dataset: Embryonic day 14.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25169 Last updated (according to GEO): May 27 2005 1000 Structure of locus ceruleus 5 0 brain Cell Culture Exposure (1MAC Halo1) Wild-type 8 months old, male Source GEO sample is GSM154352 Last updated (according to GEO): Jan 09 2007 Nicotinic Receptors 1000 Tolerizing allografts 7 days No.2 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184787 Last updated (according to GEO): Apr 26 2007 1BJZ02051716_Tonsil of uterine horns 365 380 BC110B-BE Spleen [JunctionChip 1 of 5] 14 0 Normal Prostate 1000 Spleen 901 frontal lobe plasma cells 50 61 ipsi Cortex 7 17 Fibroblasts 1000 of Parkinson? 89 101 Leprosy presents as a clinical and immunological spectrum of disease. With the use of gene expression profiling, we observed that a distinction in gene expression correlates with and accurately classifies the clinical form of the disease. Genes belonging to the leukocyte immunoglobulin-like receptor (LIR) family were significantly up-regulated in lesions of lepromatous patients suffering from the disseminated form of the infection. In functional studies, LIR-7 suppressed innate host defense mechanisms by shifting monocyte production from interleukin-12 toward interleukin-10 and by blocking antimicrobial activity triggered by Toll-like receptors. Gene expression profiles may be useful in defining clinical forms of disease and providing insights into the regulation of immune responses to pathogens. 40 21 from skeletal muscle 861 Cerebellum 861 Gland structure 861 Fissure 1000 Cerebral cortex brain 0 5 sensorimotor cortex 200 218 C57BL/6 benchmark dataset: Embryonic day 13.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25164 Last updated (according to GEO): May 27 2005 in the mammalian nervous system 110 141 Mq2: Hippocampus_NT-A_rep3 Blood 1000 Sample represents the Paraventricular nucleus from 5 control animals Source GEO sample is GSM69476 Last updated (according to GEO): Dec 16 2005 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210389 Last updated (according to GEO): Jul 16 2007 67 40 with coronary artery disease 2CdA: PK11195 intervention at 4.5h Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188693 Last updated (according to GEO): Jun 06 2007 MDA-MB-231/ATCC hgu95b Cerebral cortex 861 Lymphoblastoid Cell Line for Individual 8177.5 log phase Macrophage 14smi086 the spinal cords 144 159 861 Skeletal bone CLL-46 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188784 Last updated (according to GEO): Jun 06 2007 Standard Affymetrix Protocol Source GEO sample is GSM15862 Last updated (according to GEO): May 28 2005 1000 Prostatic Neoplasms Wild type 8 wk old male C3H/HeJ mouse amygdala Source GEO sample is GSM74919 Last updated (according to GEO): Feb 27 2007 861 ovarian neoplasm NoCAD_replicate1 MGJZ030211018Bliver no additional Source GEO sample is GSM199258 Last updated (according to GEO): Jun 08 2007 Prefrontal Cortex Source GEO sample is GSM105455 Last updated (according to GEO): Apr 17 2006 XX1_Paf HUVEC isolate 8 rich media plGF 24hours cf. #21 Source GEO sample is GSM12915 Last updated (according to GEO): May 28 2005 SCG_control_40h_rep2 Prefrontal Cortex 0 16 Mid secretory endometrium from normal patient Source GEO sample is GSM150227 Last updated (according to GEO): Dec 14 2006 The nose 94 101 NHE1 null mutation brain stem-diencephalon-1 Subthalamic Nucleus 10 Normal Tumor__Bladder_TCC_B_0008 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 10 Bone marrow 0 1000 Hippocampus Isograft 7 days No.2 Bone Marrow 1000 Brain 861 Brain 861 Expression profiling of spinal cord section (T9) extracted from rats 24h following severe injury Lot batch = Source GEO sample is GSM7572 Last updated (according to GEO): May 28 2005 88 63 of non-Hodgkin's lymphoma from subcutaeous adipose tissue 20 50 Study of in vitro granulocyte differentiation Source GEO sample is GSM137468 Last updated (according to GEO): Jun 06 2007 1324 1303 that cognitive decline 15 0 human cerebellum 5 0 brain This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195254 Last updated (according to GEO): Sep 13 2007 brain, contralateral HC: Trizol Extraction30_le1 Hyperaldosteronism 861 Gene expression data Source GEO sample is GSM183175 Last updated (according to GEO): Jul 30 2007 CNS-SMTC_Mod7d-1A-s2b DMSO-control NG108 neuronal cells 2 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211345 Last updated (according to GEO): Jul 18 2007 1000 Heart failure f2#83 versus pool Mouse Brain tissue of Parkinson's disease 450 471 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211359 Last updated (according to GEO): Jul 18 2007 861 Cerebral cortex H9LMS00110803 T-ALL-C9 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 5 0 brain Lymphoblastoid Cell Line for Individual 8139.3 log phase frontal_lobe_3 306-99_Adeno Heart 1000 Brain 861 RNA isolated from fetal heart (predominantly valve and canal regions) Keywords = trisomy Keywords = heart Keywords = Down syndrome Source GEO sample is GSM22612 Last updated (according to GEO): May 27 2005 Disease Source GEO sample is GSM175796 Last updated (according to GEO): Apr 09 2007 Phagocytosis of apoptotic cells is fundamental to animal development, immune function and cellular homeostasis. The phosphatidylserine receptor (Ptdsr) on phagocytes has been implicated in the recognition and engulfment of apoptotic cells and in anti-inflammatory signaling. Ptdsr is essential for the development and differentiation of multiple organs during embryogenesis. Ptdsr may thus have a novel, unexpected developmental function as an important differentiation-promoting gene. Moreover, Ptdsr is not required for apoptotic cell clearance by macrophages but seems to be necessary for the regulation of macrophage cytokine responses. Last Updated (by provider): Feb 05 2007 Contributers: Johannes Beckers Jens Böse Andreas Lengeling Marion Horsch with some respiratory epithelium. 1039 1072 Neurodegenerative Disorders 1000 Infection 1000 Rat SCN Sample 8 (Exp 1 - 42 hr) /3T3 fibroblasts 478 493 IsletCell Source GEO sample is GSM18980 Last updated (according to GEO): Sep 25 2006 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19261 Last updated (according to GEO): May 27 2005 861 Mammary gland Urine 1000 10 hr Hela Double Thymidine, exp2 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 2 hours after lights on. Original RNA code = LC39A. Source GEO sample is GSM227390 Last updated (according to GEO): Sep 10 2007 Brain 861 "Sample 25,>5 yr survival(161 months) age 45 erp yes" on vantveer-oligo P2A_KIDNEY_4 Schizophrenia 1000 Brain 861 H9RGV00102607 PGA_MI_ilv_48h_354 Epithelium 861 9 0 Blood Test 861 Cerebral cortex left 35 38 5 0 Spleen 50 41 mouse lung cardiac 746 752 SN:1010398 Source GEO sample is GSM115381 Last updated (according to GEO): Jun 20 2006 cervix_10 858 Prostatic Neoplasms /3T3 fibroblasts 478 493 Parkinson Disease 861 eye, retina: 1 Retina at ZT 12_e1_le1 Job's Syndrome 1000 myocardial infarction 383 403 Substantia nigra PD rep4 Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep3 I_U133A_35_Amy Muscle 1000 seminoma specimen, pT2, patient age: 28y; W03 012 globus_pallidus Source GEO sample is GSM18754 Last updated (according to GEO): Sep 25 2006 5 0 brain 861 Cerebral cortex 861 Blood Contralateral 5 ISR9-PERK-UT1, RNA from untreated PERK-/- cells; The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules. Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10892 Last updated (according to GEO): May 27 2005 of somatomotor cortex 21 41 Keywords = Heart 505 521 580 endothelial cells 596 Brn3a Wildtype TG e13.5 U74Bv2 1 468 459 the rectum medulla_4 Source GEO sample is GSM80713 Last updated (according to GEO): Mar 31 2006 Ileal profiles from gnotobiotic mice mono-associated with Listeria species or B. thetaiotaomicron. Samples were derived from 72h colonizations of Fabpi-hEcad transgenic B6 mice fed a standard-chow polysaccharide rich (PR) diet. Last Updated (by provider): Apr 23 2007 Contributers: Marc Lecuit Pascale Cossart Jeffrey I Gordon Justin L Sonnenburg Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10009.gif Source GEO sample is GSM79820 Last updated (according to GEO): Sep 22 2006 Large-scale analysis of the human transcriptome. Umbilical vein endothelial cells Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 116.40 Stdv: 4.29 Min: 107.11 Max: 124.51 Source GEO sample is GSM2903 Last updated (according to GEO): Mar 20 2006 high gestational age Source GEO sample is GSM213093 Last updated (according to GEO): Jul 25 2007 to the nose 599 609 Brain_PNET_5_PNET on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Spleen This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195301 Last updated (according to GEO): Sep 13 2007 AK_SleepDep_ZT 12_3 901 Spinal Cord Brain 861 901 Contact Dermatitis of G protein? 285 297 Pressure-overload induced hypertrophy model. Mouse was sacrificed 48 hours after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2258 Last updated (according to GEO): May 27 2005 Richard Almon-8-1133800608948 861 Neoplasm S3_PBS_2 3AJZ02081483a_Trigeminal_Ganglion Autistic Disorder 877 Diaphragm 23 Day mdx rep 1 thalamus_1 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11516 Last updated (according to GEO): May 28 2005 plasma cells 50 61 1000 Uterine Fibroids 9 0 Blood Test pull-downSD_6, ZT6 Parkinson Disease 861 A2780_oxa_IC90_pre_2 embryo_U0126-treated_at_day2.5_rep1 Nasal Epithelium 865 to the nose 599 609 Expression profiling of spinal cord section (T10) extracted from rats 30min following laminectomy (sham) Source GEO sample is GSM31282 Last updated (according to GEO): May 27 2005 umbilical cord_nobpd: 7D Mouse ileum 0 10 Primary large cell neuroendocrine carcinoma 571 0 46 Epithelial Cells 1000 19 0 human frontal cortex JMR-RatSham24hf-2aA-s2 Alcohol abuse 1000 brain, hippocampus: C1-I_e1_le1 1000 Liver TEL-AML1-C46 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Aldosterone-producing adenoma (APA6) 5 0 Spleen 61 44 in the endometrium Skin 861 Gene expression data from SVGR2 glial cells. Source GEO sample is GSM189711 Last updated (according to GEO): May 16 2007 f2#255 versus pool Mouse Brain tissue Brain_nAChRbeta4SubunitDeficent_MiceNob4398 Chromosomes 861 1000 Brain Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.13 Subject: 1871 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39024 Last updated (according to GEO): May 27 2005 Infection 1176 1185 VDXIGRU_255160 861 Myositis total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withTerbutaline for 240min Source GEO sample is GSM5789 Last updated (according to GEO): May 27 2005 861 Encephalitis Bronchus 4 Normal Bladder sample 876-5 901 Caudate nucleus structure 1000 Brain 1000 Liver Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological diseases. We have reconstructed 2-dimensional images of gene expression for 20,000 genes in a coronal slice of the mouse brain at the level of the striatum by using microarrays in combination with voxelation at a resolution of 1 mm3. Good reliability of the microarray results were confirmed using multiple replicates, subsequent quantitative RT-PCR voxelation, mass spectrometry voxelation and publicly available in situ hybridization data. Known and novel genes were identified with expression patterns localized to defined substructures within the brain. In addition, genes with unexpected patterns were identified and cluster analysis identified a set of genes with a gradient of dorsal/ventral expression not restricted to known anatomical boundaries. The genome-scale maps of gene expression obtained using voxelation will be a valuable tool for the neuroscience community. Key words: Voxelation, gene expression, microarrays, mouse brain, genome. Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3330 Last updated (according to GEO): Mar 21 2006 84 69 by heart failure Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9928.gif Source GEO sample is GSM79894 Last updated (according to GEO): Sep 22 2006 1000 Prostate Mesenchymal Stem Cells 1000 Gene expression data from DAOY cells stably expressing Alk shRNA Source GEO sample is GSM182015 Last updated (according to GEO): Apr 23 2007 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181076 Last updated (according to GEO): Jul 12 2007 mouse brain ipsilateral control, biological rep5 /6J periaqueductal gray rep2 5 32 861 Cerebral cortex Fibroblasts 861 brain, Right Temporal Lobe: Extract79_le1 1000 Brain Heart 1000 accumbens rattus_norvegicus_strain iNP animal_number 8 4R 2 (Experiment 4R18h: Run 19869) Treatment, type=timepoint, description=Primary cortical neurons were treated for 18h with a new non competitive antagonist for nicotinic receptors (4R 2uM), and then the cells were harvested, measurement=18.0 h Source GEO sample is GSM96731 Last updated (according to GEO): Feb 14 2006 of parieto-occipital cortex 223 250 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184696 Last updated (according to GEO): Apr 26 2007 cerebellum wistar 3888 Endometrium-Normal 1 1000 Substantia nigra structure SK-MEL-5_CL10007_Melanoma on Affymetrix GeneChip Human Full Length Array HuGeneFL Spleen vs Neuropeptide Y Treated B cell 240min (set2) from colorectal adenoma 21 44 SQ-2921-A322-5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 4535 4527 hepatoma Bone Marrow 1000 859 849 in synaptic Brain 861 RR200_uninfected_DC Skeletal bone 861 7 cerebral cortex 21 brain, adrenal medulla: Sample#B2 (Ctrl Pt2)_e1_le1 Wild type inbred mice Source GEO sample is GSM82898 Last updated (according to GEO): Nov 10 2005 Nasal Epithelium 901 freshly dissected metanephric mesenchyme, biological rep1 Muscle 1000 453 434 The descending colon Blood 1000 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213487 Last updated (according to GEO): Jul 31 2007 36 31 stroke /2J mouse cingulate cortex 27 52 Macrophage smi123 901 Coronary artery "Sample 98, BRCA1 mutation(57 months) age 32 erp no" on vantveer-oligo Brain 861 mouse brain 478 489 3 Retina 15 22 Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 5421 blood Neoplasm 861 testis 52 58 15 0 human cerebellum 15 0 human cerebellum Posterior root of spinal nerve 901 Probeset expression data from NA12750 growth 2, replicate 5 Source GEO sample is GSM195199 Last updated (according to GEO): Aug 08 2007 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19638.gif Source GEO sample is GSM91539 Last updated (according to GEO): Sep 22 2006 HapMap YRI_parent Female Source GEO sample is GSM159682 Last updated (according to GEO): Feb 01 2007 861 Skeletal bone 861 Neoplasm Expression profiling of spinal cord section (T10) extracted from rats 4h following mild injury Source GEO sample is GSM31336 Last updated (according to GEO): May 27 2005 Nrl ko samples were compared to wt at postnatal 2. Source GEO sample is GSM227455 Last updated (according to GEO): Sep 07 2007 none Source GEO sample is GSM149567 Last updated (according to GEO): Jan 03 2007 FVB/NJ hippocampus rep1 Nervous system structure 901 pituitary_gland_3 Source GEO sample is GSM80818 Last updated (according to GEO): Mar 31 2006 1000 Brain C57BL/6 benchmark dataset: Embryonic day 18.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25180 Last updated (according to GEO): May 27 2005 Obesity 861 Brain_MD_4_Medulloblastoma_Classic_D on Affymetrix GeneChip Human Full Length Array HuGeneFL high dose 6h, replicate 1 tTA 7310 Parkinson 0 8 1950 1933 of muscle atrophy in seminoma 28 38 CNS-SCsev_InjA24h-3C-s2 Disorder of artery 865 M_U133Plus_110_AnCg Replicate2_Voxel G8 Blood 861 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-gamma (IFN gamma) for 60min Source GEO sample is GSM5607 Last updated (according to GEO): May 27 2005 AO Treatment, type=remove Source GEO sample is GSM99510 Last updated (according to GEO): Apr 21 2006 858 Mesodermal cell PBMCs-Type 1 Diabetes-IDDM38_T1D_New MK 2hr S-DG in bronchial epithelia 311 332 human caudate nucleus Source GEO sample is GSM86922 Last updated (according to GEO): Feb 08 2006 HC81 CB B 3 0 Pons Axon 1000 in the brain 150 162 brain 0 5 Primary tumor 19 32 DRG_control_12h_rep1 Putamen 3 Normal Normal Source GEO sample is GSM176398 Last updated (according to GEO): Apr 09 2007 Parkinson Disease 861 Cell Culture Exposure (3MAC Halo3) 861 Neoplasm 753 742 optic nerve tibiae 115 120 rat hippocampus Treatment, type=time_course, measurement=72.0 h Source GEO sample is GSM32141 Last updated (according to GEO): May 27 2005 Coronary heart disease 913 biopsy sample obtained from 58-year-old female individual Keywords = gene expression profile of normal human skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15830 Last updated (according to GEO): May 28 2005 Olfactory Epithelium 861 heart 1169 1173 5 0 Muscle G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Source GEO sample is GSM9645 Last updated (according to GEO): May 28 2005 D_U133A_4_DLPFC Gene expression data from biopsy of infected skin of subject with pustule former phenotype. Source GEO sample is GSM128965 Last updated (according to GEO): Sep 13 2007 Amygdaloid structure 1000 of a colorectal adenoma 7 29 to chronic psychiatric illness 1695 1725 660 mesenchymal stem cell 639 a devastating neurodegenerative disorder 28 67 Brain 1000 from mouse colon 21 36 f2#358 versus pool Mouse Brain tissue Replicate2_Voxel G3 post infection 29 42 adipose_tissue_subcutaneous_5 Nasal Epithelium 901 Expression profiling of spinal cord section (T8) extracted from rats 4h following mild injury Source GEO sample is GSM31447 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 Liver (SF8) AD control Treatment, type=dissect Source GEO sample is GSM119677 Last updated (according to GEO): Jul 10 2006 9 0 Blood Test PGA_MI_ilv_1w_670 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b019 Source GEO sample is GSM1995 Last updated (according to GEO): Nov 21 2005 RNA from Lymphoblastoid Cell Line from this individual Source GEO sample is GSM213303 Last updated (according to GEO): Jul 26 2007 Tumor__Breast_Adeno_94_I_155 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Brain artery 234 239 DLCL-0051 Brain 861 277 271 Retinas 100338 no additional Source GEO sample is GSM199101 Last updated (according to GEO): Jun 08 2007 heart 1169 1173 Sample is skeletal muscle from obese patient undergoing elective abdominal surgery Source GEO sample is GSM4001 Last updated (according to GEO): May 28 2005 Early secretory endometrium from patient with endometriosis Source GEO sample is GSM150202 Last updated (according to GEO): Dec 14 2006 901 frontal lobe 352 340 encephalitis Infection 1176 1185 ER+/LN-/Nevins39 on Affymetrix GeneChip Human Full Length Array HuGeneFL Bone Marrow 1000 GBM Treatment, type=remove Source GEO sample is GSM99569 Last updated (according to GEO): Apr 21 2006 1000 frontal lobe 861 Muscle T47__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A no additional Source GEO sample is GSM199039 Last updated (according to GEO): Jun 08 2007 MO_control_180min_Patient8 Olfactory Epithelium 1000 Primary tumor 19 32 KHG-HG-5Av2-s2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35382 Last updated (according to GEO): May 27 2005 22-oct-2002-BrainFsubB-ab150 Cerebral cortex 1000 myocardial infarction 383 403 Liver 2 Normal Melanoma xenograft, MEC1_Sub_C (LeiFidler) Haloperidol treated 12weeks AffyGC RMA rep9 4 0 Colon B10.PL mice with experimental autoimmune encephalomyelitis (MS model) were treated with either placebo or 200 ng 1,25(OH)2D3. Six hours later, the spinal cords were harvested and mRNA extracted for analysis. Naive mice served as controls. Keywords = Experimental autoimmune encephalomyelitis Keywords = multiple sclerosis Keywords = 1 Keywords = 25(OH)2D3 Source GEO sample is GSM13055 Last updated (according to GEO): May 28 2005 of hindbrain 1513 1524 1592 1564 of medulloblastoma metastasis days nasal epithelium 1127 1148 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b027 Source GEO sample is GSM1979 Last updated (according to GEO): Nov 21 2005 kidney 37 43 Lymphoblastoid Cell Line for Individual 8137.3 log phase 1000 Rectum 12 0 ovarian tumor na Source GEO sample is GSM181260 Last updated (according to GEO): Apr 10 2007 E8.5b_rep2 Gene expression patterns were determined from five brain regions (bed nucleus of the stria terminalis, hippocampus, hypothalamus, periaqueductal gray, and pituitary gland) in six mouse strains (129S6/SvEvTac, A/J, C57BL/6J, C3H/HeJ, DBA/2J, and FVB/NJ). At least two replicate samples per brain region/strain were analyzed using Affymetrix Mouse Genome 430 2.0 arrays. Last Updated (by provider): Mar 05 2007 Contributers: Iiris Hovatta David J Lockhart Carrolee Barlow short access to cocaine, nucleus accumbens, 1 hr/day access to cocaine Source GEO sample is GSM93818 Last updated (according to GEO): Jan 26 2006 Haloperidol treated 12weeks AffyGC RMA rep5 in the mammalian nervous system 110 141 DNA-4HRS 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114251 Last updated (according to GEO): Jun 16 2006 Knockout 3 months old, male Source GEO sample is GSM154337 Last updated (according to GEO): Jan 09 2007 Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7468 Last updated (according to GEO): May 27 2005 1000 Muscle CNS-SMTC_Mod4h-4B-s2 spinal cord 1528 1539 **** Source GEO sample is GSM4279 Last updated (according to GEO): May 27 2005 with some respiratory epithelium. 1039 1072 olfactory epithelium 194 213 1000 Cerebral cortex 269811CE_4 TNFTG-3w-f-1 Primary large cell neuroendocrine carcinoma 5883 Brain Amygdala Source GEO sample is GSM18769 Last updated (according to GEO): Sep 25 2006 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 0186 left_liver_lobe Large-scale analysis of the mouse transcriptome. prostate C57BL/6L, male, 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 269.71 Stdv: 12.29 Min: 252.68 Max: 290.32 Source GEO sample is GSM2943 Last updated (according to GEO): Mar 20 2006 Macrophage smi82 861 Hippocampus R6 1 Chromosomes 861 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153376 Last updated (according to GEO): Dec 27 2006 Muscle 861 medulla_9 from hippocampus 57 72 Parkinson Disease 861 BRCA1_s1996 on NHGRI-6.5k 24 0 human prostate PC3 tumors the synaptic 1452 1463 CD28 beads 01.00 hr. T-Cell M_U133A_50_DLPFC 7 0 prostate ER-/LN-/Nevins25 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Spinal Cord HCT-15 hgu95e **** Source GEO sample is GSM4314 Last updated (according to GEO): May 27 2005 Myometrium 45 Disease nerve 0 5 5 0 brain Spleen vs SDF1 alpha (Stromal cell derived factor-1) Treated B cell This is replicate 2 of the 12 hour sample from passive avoidance trained rats. Source GEO sample is GSM17405 Last updated (according to GEO): Aug 22 2007 Paravertebral Muscle 7 Disease Simple annotation: Normal tissue, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3507.gif Source GEO sample is GSM76431 Last updated (according to GEO): Sep 22 2006 MP(BT) Cerebral Cortex 8 Normal 1000 Decapitation Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188772 Last updated (according to GEO): Jun 06 2007 1000 Retina 10 7 left Utricle 0 6 858 Prostatic Neoplasms brain, Superior Frontal Gyrus: Sample58_e1_le1 rat hippocampus Treatment, type=time_course, measurement=24.0 h Source GEO sample is GSM32139 Last updated (according to GEO): May 27 2005 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15693 Last updated (according to GEO): May 28 2005 Primary tumor 19 32 Hyperdip>50-C1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 15 0 The hypothalamus Nose 1000 sandberg-mousebrain Transcriptional reprogramming during reloading of atrophied rat soleus muscle. 1000 Hippocampus Occipital lobe 861 Gene expression data of substantia nigra from postmortem brain of normal controls Source GEO sample is GSM184356 Last updated (according to GEO): May 29 2007 DBA/2J pituitary gland rep1 PBMCs-Type 1 Diabetes-IDDM46_T1D_4MO D_U133A_91_nAcc Whole Brain 62 72 861 Cerebral cortex prostate Source GEO sample is GSM203315 Last updated (according to GEO): Jun 21 2007 24 7 Right Frontal Lobe Tonsil [JunctionChip 3 of 5] brain_DLPFC_bipolar C_mr544 Autistic Disorder 877 prostate 101 109 Hypothalamus RYGB-Fail Repl2 406 395 whose hearts Cerebral cortex 861 Coronary artery 901 39 21 of substantia nigra stomach_pyloric_1 23 11 of the kidney Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11501 Last updated (according to GEO): May 28 2005 ventral_tegmental_area_5 Neoplasm 861 861 Blood Bone Marrow 1000 Date : 3/10/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 3.0 hrs post-injection Intervention : none Risk: estimated 20% increased risk for encephalopathy Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AE194 Source GEO sample is GSM12246 Last updated (according to GEO): May 28 2005 plasma cells 50 61 Bone Marrow 1000 1000 Brain Macrophage smi89 no additional Source GEO sample is GSM199319 Last updated (according to GEO): Jun 08 2007 Lung 1000 Liver (HBV+, HK3) Prostate [JunctionChip 5 of 5] nasal epithelial cells 28 49 Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation. Source GEO sample is GSM228476 Last updated (according to GEO): Sep 10 2007 CVB3_VU-9h-2 Leukemia, Myelocytic, Acute 1000 FVBN +Doxy 8340 Infection 1000 in seminoma 28 38 1000 Pancreas Changes in mouse liver mRNA profiles following intraperitoneal cytokine injection. One of 2 replicates of albumin-cre(+) Socs3(-/fl) mice, injected with interleukin-6, and killed after 4h. Source GEO sample is GSM5956 Last updated (according to GEO): May 27 2005 1000 Lens, Crystalline the infection 46 58 brain, cerebellum: WCb4w#3_e1_le1 Clozapine treated 12weeks AffyGC RMA rep3 FSCC2 on Affymetrix GeneChip Human Full Length Array HuGeneFL Brain trauma is a major cause of morbidity and mortality, both in adult and pediatric populations. Much of the functional deficit derives from delayed cell death resulting from induction of neurotoxic factors that overwhelm endogenous neuroprotective responses. To identify the potential molecular mechanisms underlying such delayed responses, we compared gene expression patterns using high-density oligonucleotide arrays at 4, 8, 24, and 72 h after moderate levels of lateral fluid percussion-induced brain injury in rats and lateral controlled cortical impact injury in mice (a total of 47 profiles). Expression of 82 genes in 12 functional categories was significantly changed in both species after trauma. The largest number of gene expression changes were found in the functional groups related to inflammation (17%), transcription regulation (16%), and cell adhesion/extracellular matrix (15%). Fifty percent of genes similarly altered across models had not been previously implicated in traumatic brain injury. Of particular interest were expression changes in genes linked to neurodegeneration, such as ATF3 and lysosomal membrane glycoprotein 2, and to neuroprotection including lipocortin 1, calponin 3, gelsolin, Id-1, and p45 NF-E2. Gene expression profiling across species and models may help identify candidate molecular pathways induced by brain injury, some of which may provide novel targets for therapeutic intervention. 861 Spinal Cord of coronary artery disease 317 342 Oat cell carcinoma 867 Primary Neoplasm 1000 liver_wildtype_control_5d_rep3 B6_SleepDep_ZT 18_3 3AMH02030706_Liver Lymphoblastoid Cell Line for Individual 8073.3 log phase The nose 94 101 Forebrain 229 237 1000 Maxilla 901 Heart failure 1749 1731 in diabetic kidney Gene expression data from postmorten brain regions Source GEO sample is GSM144998 Last updated (according to GEO): Nov 20 2006 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.31 Lot batch = lc8n134 Source GEO sample is GSM2060 Last updated (according to GEO): Nov 21 2005 H9LMS00110802 Spleen vs IL10 Treated B cell 23 14 from lungs Saccule structure 861 nostrils 156 164 Fibroblasts 861 S8_Muscle_Insulin_30min mouse hippocampus 0 17 Individual array of a bladder cancer expression experiment. Source GEO sample is GSM181001 Last updated (according to GEO): Apr 12 2007 Total RNA extracted from the cerebellum of a Lh+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144402 Last updated (according to GEO): Nov 14 2006 072801 100% CD28 beads 06.00 hr. T-Cell SCG explant cultured for 65 hours in vitro Source GEO sample is GSM246051 Last updated (according to GEO): Dec 03 2007 NCI60.31_LABEL35EXTRACT34SUB3 Source GEO sample is GSM134149 Last updated (according to GEO): Aug 06 2007 56 47 hippocampi Ovary_PD7_Foxo3 Null_Replica 2 5_cerebral_cortex_3hrs_sleep_deprivation_#67 Gene expression data from skeletal muscle following 30 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230445 Last updated (according to GEO): Sep 19 2007 1000 Acquired Immunodeficiency Syndrome Ganglia, Spinal 884 olfactory.bulb.3 Nervous system structure 901 M_U133A_30_DLPFC_R Gene expression data from postmorten brain regions Source GEO sample is GSM145402 Last updated (according to GEO): Nov 20 2006 Gene expression data from rat lungs exposed to FiO2 of ~9.5% and SU-5416 (hypoxia-SU-5416). Source GEO sample is GSM201487 Last updated (according to GEO): Jun 14 2007 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 19 day time point Source GEO sample is GSM159755 Last updated (according to GEO): Apr 23 2007 blood, Blood: 2153_0103_le1 olfactory bulb Source GEO sample is GSM18604 Last updated (according to GEO): May 27 2005 to muscle 77 85 861 Brain Epithelium 861 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195280 Last updated (according to GEO): Sep 13 2007 Transitional epithelial cell 861 H9LMS99072808 HUVEC isolate 22 low serum media VEGF-A 4hours cf. #9 Source GEO sample is GSM12903 Last updated (according to GEO): May 28 2005 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213488 Last updated (according to GEO): Jul 31 2007 12 0 ovarian tumor 20 0 Inflammatory myopathy Cerebral cortex 1000 Simple annotation: Drug_treatment, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8961.gif Source GEO sample is GSM78476 Last updated (according to GEO): Sep 22 2006 Epithelial Cells 901 WT_IL-6_100_rep2 861 Cerebellum Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3318 Last updated (according to GEO): Mar 21 2006 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10145.gif Source GEO sample is GSM79630 Last updated (according to GEO): Sep 22 2006 T-ALL-R2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113920 Last updated (according to GEO): Jun 16 2006 Ganglia, Spinal 923 Skeletal bone 861 40 17 mammary epithelial cells Day 1_M_-LIF_Achip Parkinson's model voxel H3 plasma cells 50 61 D_U133A_90_CB 13 0 Bladder cancer Richard Almon-22-1138200270133 brain 0 5 Locus Coeruleus Source GEO sample is GSM107975 Last updated (according to GEO): Jun 06 2006 Healthy patient. Source GEO sample is GSM228575 Last updated (according to GEO): Sep 11 2007 spleen 214 220 TUMOR 17 0 7 AK_SleepDep_ZT 0_2 Biopsy of the normal mucosa of the colon from patient #1 COID-COID10t1-A347-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 129 122 jejunum cardiac 763 769 C57BL-6J were given intratracheal saline control. Lungs were harvested and frozen at 14d. Lot batch = Source GEO sample is GSM4166 Last updated (according to GEO): May 28 2005 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114190 Last updated (according to GEO): Jun 16 2006 861 Brain Phobia, Social 1000 1000 Brain GSE9118 Cortex 0 5 Malignant neoplasm of breast 1000 C8161, 48h treatment with 5 AzadC Blood 1000 68 64 Lungs 1000 Structure of atrioventricular node 36 21 from whole brain Spinal Cord 1000 337 324 muscle atrophy Conventional Rectum 1 Luminal breast tumor cell line SKBR3 Keywords = Agilent microarray, Expression analysis, EGFR, Breast cancer growth Source GEO sample is GSM29517 Last updated (according to GEO): Dec 13 2006 of Huntington? 90 103 Fetal occipital cortex cocaine4 Brain 861 488 467 that the immune system Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28719 Last updated (according to GEO): May 27 2005 Male 68.4 yr before antibody enrichment scan 1 (U133A) 14 NT C4 Treatment, type=add, description=10ng/mL Ciliary neurotrophiic factor, 4d Source GEO sample is GSM92490 Last updated (according to GEO): Jan 13 2006 Muscular Dystrophy, Duchenne 913 PCA33_localized prostate cancer 0 30 861 Lung by the liver 210 221 Acetaminophen 3hr Rat 1049 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool 981 963 normal fibroblasts Nose 1000 Congenital Abnormality 853 1000 frontal lobe Cerebral cortex 861 Neoplasm 861 SNB-19 hgu95c Gene expression data from mouse primary visual cortex Source GEO sample is GSM101701 Last updated (according to GEO): Mar 27 2006 Hippocampus 1000 Spleen vs Untreated B cell Time 0 (set23) Lymphoblastoid Cell Line for Individual 8165.3 log phase mouse cerebral cortex 0 20 with Alzheimer's disease 27 50 861 Carcinoma Medulla Oblongata 861 41 29 Control blood brain 0 5 Mammary Gland @ Preg7, biological rep3 861 Cerebellum Primary Neoplasm 1000 1000 Mammary gland park_1146_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A the blood 393 402 1000 Brain Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 1457 left_liver_lobe H9LMS00102607 861 Cerebral cortex G42-Homogenate-CingulateCortex replicate2 Muscle 645 650 86 82 Lungs We build a model for the molecular and cellular events underlying phenotypic discordance in glycine receptor defects (beta subunit). Some mice progress and die, while their littermates recover and get better, despite the same mutation on an inbred genetic background. We find evidence for glycine neurotransmitter toxicity and loss of glycinergic interneurons early in the disease, but some mice are able to keep things going until they can over-express homomeric alpha1 channels, whereupon they recover. In the mice progressing towards lethality, neurotransmitter toxicity too quickly extends to GABAergic interneurons and motorneurons, and they lose their window of time to upregulate the alpha1 glycine receptor, and they crash and burn. Importantly, human patients with glycine receptor defects typically show a resolution of their phenotype with age, and we propose that the same remodeling events are occuring in human patients. Source GEO sample is GSM31000 Last updated (according to GEO): May 27 2005 Sample details: Three pools of rostral (R1-3), three pools of middle (M1-3), and three pools of caudal (C1-3) E13.5 MF1 neocortex were collected from 4 embryos. All possible 18 comparisons were carried out. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. Source GEO sample is GSM62835 Last updated (according to GEO): Aug 26 2005 none Source GEO sample is GSM241959 Last updated (according to GEO): Nov 29 2007 CD3 + CD28 beads 00.00 hr. T-Cell spinal cord, ventral spinal cord: D60SODSP1_e1_le1 1000 Retina Non-inner ear tissue at E9, replicate1 CNS-SC_InjA24h-1A-s2 myometrium_7 Source GEO sample is GSM80717 Last updated (according to GEO): Mar 31 2006 Macrophages, Baseline - Repeat #1 D_U133Plus_126_nAcc Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15008.gif Source GEO sample is GSM91602 Last updated (according to GEO): Sep 22 2006 Euploid sample 2 (astrocyte) 1000 Cerebellum Proteoglycan 1000 CHIPEXP_NAME: 230_2_050531tpj_5h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Vehicle_Control TREAT_TOX_MECHANISM1: Liver_Non_Toxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0 SAMPLING_TIME: 1 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197605 Last updated (according to GEO): Jun 01 2007 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=780620 LaserPower=4.483.8 Lot batch = LC17N126 Source GEO sample is GSM4838 Last updated (according to GEO): Nov 21 2005 left 35 38 Cerebral cortex 861 1000 Brain MELAN_SKMEL2 on Affymetrix GeneChip Human Full Length Array HuGeneFL whole blood_100476 Ovary 1000 1000 Brain 454 of neurodegenerative diseases 483 (cortex 19 25 amygdala rattus_norvegicus_strain iNP animal_number 12 84 69 by heart failure Leukemia, Myelocytic, Acute 861 Occipital lobe 983 Endometrium-Normal 10 1000 Hypothalamic structure Mouse Ovary 2 (technical replicate) Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11597 Last updated (according to GEO): May 28 2005 1000 medulloblastoma with myocardial infarction 313 339 41 29 Control blood 1000 Brain Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211254 Last updated (according to GEO): Jul 18 2007 22 19 left DMN-CtrHippo10d-2bAv2-s2 brain_healthy_control_sampleid_jg1745 70 40 without coronary artery disease BCR-ABL-#8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Skin 1000 3857 3845 hypothalamus 1000 Brain 34 16 of stria vascularis SCG explant cultured for 2 hours in vitro Source GEO sample is GSM246020 Last updated (according to GEO): Dec 03 2007 Primary typical carcinoid 3313 seizures 296 304 MSS-Ctr12moF-1bAv2-s2 puroB replicate 1 Gene expression data from whole brain infected mouse, day 6 Source GEO sample is GSM189621 Last updated (according to GEO): May 16 2007 brain, Entorhinal Cortex: Sample5_e1_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM146054 Last updated (according to GEO): Nov 20 2006 Brain 861 Brain 1000 R7E 4 091246 SKOV8 on Affymetrix GeneChip Human Full Length Array HuGeneFL KM12 hgu95c WGACON-120 A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37ºC in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the experimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained constant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic measurements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Last Updated (by provider): Oct 28 2005 Contributers: J Kelleher R Raab M Wong G Stephanopoulos Includes GDS284. Update date: May 13 2004. Dataset description GDS284: Temporal analysis of the effect of glutamine concentration on hepatoma cell line, Hepa1-6. Experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while control flasks remained constant at 4 mM.. Eye 1000 Ovum 861 Heart failure 1000 post-traumatic stress disorder 158 188 21 6 (caudate nucleus Muscle 861 nasal epithelial cells 28 49 PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls. All samples were normalized with quantile normalization and summarized using RMA. Source GEO sample is GSM135572 Last updated (according to GEO): Dec 19 2006 Gastrointestinal stromal tumors 0 30 663 mesenchymal stem cell 642 Mental Retardation 1000 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92324 Last updated (according to GEO): Jan 13 2006 Striatal sample from a 12-month-old wild-type mouse. Source GEO sample is GSM238690 Last updated (according to GEO): Oct 19 2007 Breast Tumor 16 X NCI reference I_U133Plus_16_CB Skeletal muscle structure 1000 with acute measles 20 37 olfactory epithelium wild type mouse 0 h Source GEO sample is GSM78345 Last updated (according to GEO): Oct 26 2005 Brain (caudate nucleus) [JunctionChip 4 of 5] skin 48 51 Job's patient Source GEO sample is GSM211106 Last updated (according to GEO): Sep 10 2007 Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells. TEL-AML1-#9 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Expression profiling of spinal cord section (T8) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM4444 Last updated (according to GEO): May 28 2005 Nervous system structure 901 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10397.gif Source GEO sample is GSM79879 Last updated (according to GEO): Sep 22 2006 no additional Source GEO sample is GSM199059 Last updated (according to GEO): Jun 08 2007 in genetic diseases werefound 1280 1308 TemporalLobe Source GEO sample is GSM18911 Last updated (according to GEO): Sep 25 2006 with mental retardation 241 263 Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles. PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity. Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence. To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips Source GEO sample is GSM136511 Last updated (according to GEO): Jun 05 2007 Normal Source GEO sample is GSM176210 Last updated (according to GEO): Apr 09 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145731 Last updated (according to GEO): Nov 20 2006 Saccule structure 861 7120_Lung did not develop PGD Control 9/06/02 (Experiment Neuroprotection3-Run 13276) Treatment, type=timepoint, measurement=0.0 h Source GEO sample is GSM96668 Last updated (according to GEO): Feb 14 2006 Primary large cell neuroendocrine carcinoma 2144 0 47 Colo205 x SR21 40 21 from skeletal muscle 13 on NHGRI-13.8k The goal of the research proposed herein is to identify (i) gene products that allow identification of specific precursor populations in vivo and (ii) genetic programs that regulate the generation of lineaege-restricted precursor (LRP) cells from neuroepithelial stem cells (NSC). As these cells play a major role in development and tissue repair, this effort will enhance both basic and clinically relevant research. Note: Funding for this micro-array analysis was granted through NINDS as supplement 3R01NS042820-02S1. Our ability to generate essentially unlimited numbers of purified rodent NSCs, thier restricted decendants leading the generation of macroglia - and also to control the generation of each of these cell types from its immediate ancestor - provides us with a unique system for studying the multi-step nature of differentiation. Using defined conditions, samples will be isolated from each type of purified cell population. Expression profiles will be compared to reveal cell type specific markers and regulatory factors. The generation of differentiated cell types from neuroepithelial stem cells appears to require progression through a sequence of lineaege-restricted intermediate cell stages. In the case of at least one of the pathways involved in oliigodendrocyte generation, it now appears that all of the stages of this sequence have been defined and all of the intermediate cells have been isolated (as detailed in the Noble, M. et al. (2004) Dev. Biol. 265, 33-52). Studies in vitro, and consequent to cell transplantation, have enabled us to gain an increasingly detailed understanding of the differentiation potential of these cells. The microarray analysis proposed herein will provide the specific markers that will enable the LRP cells to be unambiguously identified in vivo, thereby setting the stage to develop a detailed mapping of the role of these cells during development. RNA will be isolated from purified cell populations. All populations will initially be derived from spinal cord. Preparation of purified populations of each of these cell types has been described in multiple of our previous publications (Mayer, M. et al. (1994) Development 120, 142-153; Mayer-Pröschel, M. et al. (1997) Neuron 19, 773-785; Rao, M. and Mayer-Pröschel, M. (1997) Dev. Biology 188, 48-63). Total RNA from purified cell cultures will be extracted in a two step process. RNA will first be extracted by dounce homogenization in phenol/guanidine isothiocyonate solution (Trizol, Invitrogen, California) followed by isopropanol precipitation. Contaminating traces of DNA and protein will then be removed by silica-based affinity chromatography and Dnase treatment (NucleoSpin RNA Purification system, Clontech, California). Depending on the cell type, 5x105 cells will typically yield 5-15µg of high quality RNA (OD260/280=2.1 at pH7.5). In order to determine purity and molecular weight distribution, samples will be routinely tested on a Agilent Bioanalyzer. cDNA will be generated from total RNA and then be submitted to one round of amplification and labeling using the messageAmp system (Ambion). Probes are then hybridized to the Affymerix Rat 230 (A/B or 2.0) GeneChip expression array. Array data will be processed using the Micro Array Suite 5.0 (MAS, Affymetrix). Cel files containing normalized, relative expression data for all genes tested will be used for downstream statistical analysis. Last Updated (by provider): Jan 13 2006 Contributers: Christoph Proschel GM19221 VDXKIU_279C61 Primary carcinoma of the liver cells 1000 f2#243 versus pool Mouse Brain tissue Nervous system structure 861 of a colorectal adenoma 7 29 of uterine horns 365 380 D_U133A_33_HC Autistic Disorder 877 Pituitary Gland 1000 Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 4145 blood Cerebral cortex 861 Hypothalamus RYGB-Success Repl3 Adenocarcinoma 861 1000 frontal lobe healthy subject Source GEO sample is GSM211121 Last updated (according to GEO): Sep 10 2007 no additional Source GEO sample is GSM199163 Last updated (according to GEO): Jun 08 2007 N55__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A CNS-SC_InjA4h-1C-s2 19 0 Head and neck cancer of the postmortem brains 676 700 18 0 Menstruation blood embryo_U0126-treated_at_day2.5_rep2 5 0 brain pfc_1007_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Primary Neoplasm 1000 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210376 Last updated (according to GEO): Jul 16 2007 placebo 48h, biological rep1 LOX IMVI hgu95a ICM pool 2 (n=2) Spleen 1000 Bone Marrow 1000 brain, brainstem: D60SODFNMN3_e1_le1 Expression data from mouse liver Sample40, Post Injury 24 hours Treatment, type=wait Source GEO sample is GSM53291 Last updated (according to GEO): Jul 06 2005 861 Breast Normal__Lung_LU_1 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A from ventral prostate 21 41 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28825 Last updated (according to GEO): May 27 2005 salivary gland Source GEO sample is GSM18693 Last updated (according to GEO): May 27 2005 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28474 Last updated (according to GEO): May 27 2005 Supranuclear Palsy, Progressive 1000 Large cell carcinoma of lung 937 Caudal 1000 Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 24h. Lot batch = Source GEO sample is GSM1232 Last updated (according to GEO): May 28 2005 11 on NHGRI-13.8k 70 40 without coronary artery disease 1037 of transitional epithelium 1012 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195345 Last updated (according to GEO): Jun 04 2007 Adipose Tissue 4 Normal Brain 1000 HUVEC isolate 55 rich media control for #4 Source GEO sample is GSM12896 Last updated (according to GEO): May 28 2005 Neoplasm Metastasis 1000 966 Organ Spleen vs BLC Treated B cell 120min (set1) Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 5 day time point Source GEO sample is GSM159725 Last updated (according to GEO): Apr 23 2007 67 52 descending colon 1 of 3 replicates in treatment group Source GEO sample is GSM206036 Last updated (according to GEO): Jun 29 2007 Normal Source GEO sample is GSM176167 Last updated (according to GEO): Apr 09 2007 brain, Superior Frontal Gyrus: Sample53_e1_le1 861 HIV Infections Cochlear nucleus structure 1000 In the classical form of ?1antitrypsin deficiency a mutant protein accumulates in a polymerized form in the ER of liver cells causing liver damage and carcinogenesis by a gain-of-toxic function mechanism. Recent studies have indicated that the accumulation of mutant ?1antitrypsin Z in the ER specifically activates the autophagic response but not the unfolded protein response and that autophagy plays a critical role in disposal of insoluble ?1antitrypsin Z. In this study, we used genomic analysis of the liver in a novel transgenic mouse model with inducible expression to screen for changes in gene expression that would potentially define how the liver responds to accumulation of this mutant protein. Last Updated (by provider): Jul 26 2007 Contributers: Karoly Mirnics Michael Ewing Tunda Hidvegi Liver Test (Blinded) Sample Source GEO sample is GSM130139 Last updated (according to GEO): Sep 18 2007 884 Spinal Cord Injuries Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Globin reduction was performed according to the Affymetrix technical note. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183405 Last updated (according to GEO): Apr 23 2007 Epithelium 861 Bone structure of tibia 1000 Sample 118 on vantveer-oligo 0 cortex 5 umbilical cord_nobpd: 2A tumor suppressor gene inactivation 191 224 861 Retina in the mammalian nervous system 110 141 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.43 Subject: 2846 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39033 Last updated (according to GEO): May 27 2005 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD9 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD9 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36700 Last updated (according to GEO): May 27 2005 for liver 26 35 Wild type inbred mice Source GEO sample is GSM82938 Last updated (according to GEO): Nov 10 2005 963 of Parkinson's disease 985 Primary tumor 19 32 plasma cells 332 344 Hippocampus 1000 10 0 hippocampus femur 6 10 Primary tumor 19 32 ventral spinal cord 13 31 Hyperdip>50-C13 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Tumor__Melanoma_96_I_166 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene expression data from male mice. Source GEO sample is GSM115533 Last updated (according to GEO): Jun 13 2007 Parkinson's model voxel C2 1000 Lung Major Depressive Disorder 120 144 3AJZ02052323_FETALTHYROID Neoplasm 861 NSCLC_NCI-H226_CL1013 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Hypertrophic Cardiomyopathy hindbrain 1000 Alzheimer's Disease 1000 MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120661 Last updated (according to GEO): May 14 2007 Kidney 1000 1000 Bone Marrow NA Source GEO sample is GSM84329 Last updated (according to GEO): Dec 01 2005 PriG_Expt2_Day0_rep2 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells cultured for 240min Source GEO sample is GSM5849 Last updated (according to GEO): May 27 2005 WGACON-55 Cerebral cortex 901 VDXRHU_1959 Leukemia, Myelocytic, Acute 1000 1183 1175 in tumors 901 Caudate nucleus structure Brain_MD_36_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL in dendrites 96 108 CN407 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188824 Last updated (according to GEO): Jun 06 2007 DMN-CtrHippo18d-1dAv2-s2 skin 80 83 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68303 Last updated (according to GEO): Jul 07 2006 Osteoblasts 1000 Sex Chromosomes 1000 adrenalgland Source GEO sample is GSM18788 Last updated (according to GEO): Sep 25 2006 brain, Right Temporal Lobe: Extract76_le2 1000 Neurofibromatosis 1 Exp 2 Time point 4 123 98 extensor digitorum longus 861 Brain ES cell line was grown on irradiated MEF feeders using standard culture conditions. Feeders were then depleted and ES cells plated on gelatin for ~2 days. RNA was isolated using Trizol/RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol. Data were normalized by AffyMetrix MAS5.0 using defaults. Keywords = embryonic stem cholesterol transport Source GEO sample is GSM9270 Last updated (according to GEO): May 27 2005 Gene expression data from colorectal adenoma. Source GEO sample is GSM215094 Last updated (according to GEO): Aug 02 2007 KHG-HG-1Av2-s2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Liver Test (Blinded) Sample Source GEO sample is GSM130201 Last updated (according to GEO): Sep 18 2007 "2 hr Hela Double Thymidine, exp3" 1143 1132 of epilepsy 1000 Retina Leprosy lesion gene expression 1000 Spleen Biopsy of a colorectal adenoma from patient #2 Trigeminal ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until enough tissue was harvested to be pooled by genotype. Approximately 10-12 ganglia were pooled for a single analysis, which was extracted using the RNeasy system (Qiagen). Source GEO sample is GSM89136 Last updated (according to GEO): Dec 23 2005 Replicate3_Voxel A8 Lung 1000 1000 Malignant Neoplasms nostrils 156 164 BALB-c mice were given intratracheal bleomycin (1.5U per kg). Lungs were frozen at 24hr 72hr 10d 14d Lot batch = Source GEO sample is GSM4150 Last updated (according to GEO): May 28 2005 1715 1700 by decapitation Rat SCN Sample 15 (Technical replicate - 36 hr) 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114214 Last updated (according to GEO): Jun 16 2006 129:26-2 spinal cord Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 24 h to ambient pressure (CP24) and harvested with cells exposed for 24 h to hydrostatic pressure, pressure experiment # 1 (PE1). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11394 Last updated (according to GEO): Dec 15 2006 715 702 After the eyes Bone Marrow 1000 Muscle 861 Cerebral cortex 861 Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153777 Last updated (according to GEO): Jan 19 2007 melanoma 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Neuropeptide Y for 30min Source GEO sample is GSM5709 Last updated (according to GEO): May 27 2005 P7 cochlear nuclei 0 17 KPeterson-Met-13G110-s2 Affymetrix protocol Source GEO sample is GSM213821 Last updated (according to GEO): Aug 02 2007 brain, amygdala: Stress-Cortex_e1_le1 Nasal Epithelium Inhalation Formaldehyde 07ppm 8d ID144 3x24 hr vehicle repl 2 Transitional epithelium 1000 I_U133A_77_Amy WGACON-108 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21035.gif Source GEO sample is GSM91496 Last updated (according to GEO): Sep 22 2006 1000 Cerebrovascular accident 1000 Spleen Benign prostatic hypertrophy 1000 CO_sham_mid_1 1BMH02082912_PB_BDCA4DendriticCells none Source GEO sample is GSM123230 Last updated (according to GEO): Jul 26 2006 Normal Source GEO sample is GSM176241 Last updated (according to GEO): Apr 09 2007 121 114 synaptic Primary Neoplasm 1000 Epithelial Cells 1000 placenta-0482-uninflamed-past-rep1 861 Colon Large cell neuroendocrine carcinoma 901 Macrophage 14smi010 LT-Hematopoietic stem cell isolated by flow cytometry Source GEO sample is GSM149537 Last updated (according to GEO): Apr 27 2007 NA18594 S8_Muscle_Baseline_0min Tumor__Lymphoma_Large_B-Cell_L_B_CELL_S98_12453_R on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 24 7 Right Frontal Lobe P1_KIDNEY_1 Ovarian_Tumor_Endometrioid_CHTN-OE-059 901 frontal lobe R6/1 wildtype, brain hemisphere Source GEO sample is GSM83871 Last updated (according to GEO): Apr 20 2007 Operator Name: Sample Type: Sample Description: Comments: Reagents: Reagent Lot: Algorithm: Statistical Corner+ Avg:404, Count:32 Corner- Avg:39671, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:4.818338,SFGene:All Background:Avg:542.73,Stdev:10.40,Max:572.5,Min:520.5 Noise:Avg:14.47,Stdev:1.34,Max:19.9,Min:12.3 RawQ:15.60 Keywords = ALL Source GEO sample is GSM3463 Last updated (according to GEO): May 28 2005 50 43 jejunum 1000 hindbrain 901 Heart failure Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28762 Last updated (according to GEO): May 27 2005 14 days hindlimb suspended, 1 day reloaded RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis. Source GEO sample is GSM10062 Last updated (according to GEO): May 28 2005 Hypothalamic structure 1000 5 0 brain rat hippocampus Treatment, type=pharmacogenomic_treatment, description=Fed isocaloric diet Source GEO sample is GSM35875 Last updated (according to GEO): May 27 2005 1000 Tricuspid valve structure brain, hippocampus: PR-CA1-A25_e1_le1 from ventral prostate 21 41 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132510 Last updated (according to GEO): Feb 26 2007 Abdominal aorta 0 14 p53 -/-, 0 hour, replicate a Keywords = colon cancer, p53, expression Source GEO sample is GSM2546 Last updated (according to GEO): May 27 2005 Prosencephalon 861 of a colorectal adenoma 7 29 861 Cardiomyopathies C42 on NCI-7.6k Cerebellum 1000 1000 Left Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22581 Last updated (according to GEO): May 27 2005 Replicate3_Voxel D3 1000 Cafe-au-Lait Spots Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15734 Last updated (according to GEO): May 28 2005 in blood 16 23 Normal Source GEO sample is GSM175892 Last updated (according to GEO): Apr 09 2007 39 21 from mammary glands Spleen 1000 total spinal cord from a wild type mouse. Source GEO sample is GSM113716 Last updated (according to GEO): Jun 09 2006 861 Lung Skeletal bone 861 Gene expression data from mouse colon Source GEO sample is GSM198108 Last updated (according to GEO): Aug 22 2007 I_U133A_76_Amy Epithelial Cells 1000 human frontal cortex Source GEO sample is GSM86966 Last updated (according to GEO): Feb 08 2006 1000 Adrenal Medulla 15 0 human cerebellum Amygdala Source GEO sample is GSM107955 Last updated (according to GEO): Jun 06 2006 A/OVX/P4/9h/UTX 129/SvImJ WT occipital_lobe_10 Source GEO sample is GSM80756 Last updated (according to GEO): Mar 31 2006 na Source GEO sample is GSM181259 Last updated (according to GEO): Apr 10 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11606 Last updated (according to GEO): May 28 2005 Occipital lobe 861 Nasal Epithelium 865 Macrophage smi51 884 Malignant neoplasm of cervix uteri 292 280 neuroblastoma Insulin-like growth factor 1 (IGF1) was considered a potential candidate for the treatment of heart failure. However, some animal studies and clinical trials have questioned whether elevating IGF1 chronically is beneficial. Secondary effects of increased serum IGF1 levels on other tissues may explain these unfavorable results. The aim of the current study was to examine the role of IGF1 in cardiac myocytes in the absence of secondary effects, and to elucidate downstream signaling pathways and transcriptional regulatory effects of the IGF1 receptor (IGF1R). Transgenic mice overexpressing IGF1R in the heart displayed cardiac hypertrophy, which was the result of an increase in myocyte size, and there was no evidence of histopathology. IGF1R transgenics also displayed enhanced systolic function at 3 months of age, and this was maintained at 12-16 months of age. The phosphoinositide 3-kinase (PI3K)-Akt-p70S6K1 pathway was significantly activated in hearts from IGF1R transgenics. Cardiac hypertrophy induced by overexpression of IGF1R was completely blocked by a dominant negative PI3K(p110alpha) mutant, suggesting IGF1R promotes compensated cardiac hypertrophy in a PI3K(p110alpha)-dependent manner. This study suggests that targeting the cardiac IGF1R-PI3K(p110alpha) pathway could be a potential therapeutic strategy for the treatment of heart failure. 1000 Descending colon Gene expression data from postmorten brain regions Source GEO sample is GSM145818 Last updated (according to GEO): Nov 20 2006 TEL-AML1-C36 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A a1 VDXRHU_302 High Density Lipoproteins 1000 brain, hippocampus: Ctr-1h-P15-I_e1_le1 M_U133Plus_120_nAcc 861 Brain Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma. Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153340 Last updated (according to GEO): Dec 27 2006 901 Coronary artery Agenesis of corpus callosum 1000 Gene expression data from liver Source GEO sample is GSM243380 Last updated (according to GEO): Nov 16 2007 Donor A, post G-CSF prostate Source GEO sample is GSM203379 Last updated (according to GEO): Jun 21 2007 This sample was obtained from a 42 years old female with congestive heart failure at 89 days after left ventricular assist device support. High quality sample. Keywords = Congestive heart failure, left ventricular assist device, eNOS, gene, dimethylarginine dimethylaminohydrolase Source GEO sample is GSM6541 Last updated (according to GEO): May 28 2005 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:306, Count:32 Corner- Avg:34655, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:6.310359,SFGene:All Background:Avg:579.31,Stdev:20.01,Max:616.0,Min:535.1 Noise:Avg:14.79,Stdev:0.63,Max:16.8,Min:12.9 RawQ:17.41 Keywords = ALL Source GEO sample is GSM3439 Last updated (according to GEO): May 27 2005 CNS-RM_Mod3mo-4A-s2 healthy control sample x062 B220+CD25+sIg- Small Pre BII cells sorted out of mouse bone marrow, sort no. 1 Source GEO sample is GSM659 Last updated (according to GEO): Mar 20 2006 brain, Right Frontal Lobe: Extract56_le1 Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160705 Last updated (according to GEO): Sep 24 2007 Disease Source GEO sample is GSM176248 Last updated (according to GEO): Apr 09 2007 pfc_1013_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Bic/4AP 2h pulse Anterior nares 1000 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48014.gif Developmental Stage: E6.5 Source GEO sample is GSM229819 Last updated (according to GEO): Nov 06 2007 Gene expression changes in fetuses exposed to ethanol in utero 1000 Hypertrophic Cardiomyopathy 1000 Malignant neoplasm of breast Spleen 1000 PBMCs-Healthy-HIDDM2_Healthy mdx EDL sample 2 of somatomotor cortex 21 41 in muscle 897 905 midbrain_6 858 Mesodermal cell Blood 1000 46 8 in docetaxel-refractory prostate cancer GC (HKG57L) 14 0 Normal Pancreas 861 Cerebellum 1000 Spleen Gene expression data from postmorten brain regions Source GEO sample is GSM145189 Last updated (according to GEO): Nov 20 2006 660 mesenchymal stem cell 639 1000 Left Measles 1000 SNU449 cells 221 202 by CO2 asphyxiation Plasma 861 low gestational age Source GEO sample is GSM213088 Last updated (according to GEO): Jul 25 2007 Metastatic Carcinoma 902 with autism spectrum disorder 37 65 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210365 Last updated (according to GEO): Jul 16 2007 Gene expression data from rat metanephric mesenchymes cultured for 4 days in the presence of NGAL Source GEO sample is GSM126212 Last updated (according to GEO): Dec 08 2006 Comparison of RNA levels in the neocortex of normal mice versus synaptically silent munc18-1 null mutants. Source GEO sample is GSM84366 Last updated (according to GEO): Aug 01 2006 HMEC-C Confluent Gene expression profile of the cell line UB/OC-1 grown for 2 days under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1519 Last updated (according to GEO): May 27 2005 Heart Septal Defects 884 Spleen 0 5 Ovary 1000 of motor axons 1151 1164 Thyroid Gland 1 Normal none Source GEO sample is GSM244563 Last updated (according to GEO): Nov 23 2007 Wild type inbred mice Source GEO sample is GSM82952 Last updated (according to GEO): Nov 10 2005 984 966 from hyperglycemia with Alzheimer's disease 27 50 long access to cocaine, nucleus accumbens, 6 hrs/day access to cocaine Source GEO sample is GSM93823 Last updated (according to GEO): Jan 26 2006 Parietal Lobe 3 Normal 431 426 tumors 42 of ciliary epithelium 22 Expression profiling of spinal cord section (T9) extracted from rats 0 following laminectomy (naïve) Source GEO sample is GSM31511 Last updated (according to GEO): Oct 28 2005 Lymphoblastoid Cell Line for Individual 8167.3 log phase in hippocampus 698 711 861 Acquired Immunodeficiency Syndrome Expression profiling of spinal cord section (T10) extracted from rats 0h following laminectomy (naïve) Lot batch = Source GEO sample is GSM4441 Last updated (according to GEO): Oct 28 2005 1000 Amygdaloid structure 1000 Spleen Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211374 Last updated (according to GEO): Jul 18 2007 Gastrin-CCK double Knockout replicate 1 20 0 Mammary Gland @ Lac2 12 0 ovarian tumor from epididymal fat tissues 21 48 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8438.gif Source GEO sample is GSM76404 Last updated (according to GEO): Sep 22 2006 brain, amygdala: pADX AM A b_e1_le1 861 Heart Diseases Primary tumor 19 32 testis 52 58 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225661 Last updated (according to GEO): Aug 31 2007 Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 0246 blood 861 Fissure Primary tumor 19 32 Nervous system structure 901 Bone marrow cell (commercial item), primary 861 Malaria bladder_control_pool-1 M_U133A_10_nAcc Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92357 Last updated (according to GEO): Jan 13 2006 Gene expression regulated by DACH1-2 n/a Source GEO sample is GSM178039 Last updated (according to GEO): Jun 11 2007 AcB55 #12256568b 3ARS02080777a_subthalamic_nucleus amyotrophic lateral sclerosis preferentially 229 272 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213486 Last updated (according to GEO): Jul 31 2007 The nose 94 101 OBX Day 1,# 1 in bipolar disorder 31 49 Lymphoblastoid Cell Line for Individual 8044.3 log phase Kidney YC-5A Lymphoblastoid Cell Line for Individual 8090.4 log phase 4 0 Brain Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162148 Last updated (according to GEO): Jun 12 2007 Simple annotation: Reference verification, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10004.gif Source GEO sample is GSM78455 Last updated (according to GEO): Sep 22 2006 Brain_Wild-type_MiceNoLT345 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211234 Last updated (according to GEO): Jul 18 2007 861 Blood Mouse Testis 3 (technical replicate) Plasma 861 liver_PPARa-knockout_WY14643_5d_rep1 1000 Brain Primary Neoplasm 1000 CVB3_S-0h Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188720 Last updated (according to GEO): Jun 06 2007 Compare the transcriptomes of Cx43 null and Cx43 siRNA treated cortical astrocytes with the transcriptome of the wildtype cortical astrocytes Source GEO sample is GSM200844 Last updated (according to GEO): Jun 19 2007 Standard Affymetrix Protocol Source GEO sample is GSM16471 Last updated (according to GEO): May 28 2005 1000 Neoplasm Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231050 Last updated (according to GEO): Sep 26 2007 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153364 Last updated (according to GEO): Dec 27 2006 I_U133Plus_123_Amy 10 7 Left 1000 Prostate whole brain from nicotinic acetylcholine receptor beta4 subunit null mutant mouse Source GEO sample is GSM120581 Last updated (according to GEO): Sep 22 2006 1000 Cerebral cortex Gene expression data from postmorten brain regions Source GEO sample is GSM146041 Last updated (according to GEO): Nov 20 2006 PGA-MurLungRag-pbs-24h-1bBv2-s2 861 Communicable Diseases retina Source GEO sample is GSM18614 Last updated (according to GEO): May 27 2005 in B Cell Chronic Lymphocytic Leukemia 74 111 141 106 Keywords = Congestive heart failure Tumor__Colorectal_Adeno_0001c026_CC on Affymetrix GeneChip Human 35K SubA Array Hu35k-A from brain 14 23 CNS-SC_CtrA7d-2B-s2 of the stria terminalis rep1 19 46 plasma cells 332 344 from colorectal adenoma 21 44 861 Blood advanced HCC Source GEO sample is GSM155938 Last updated (according to GEO): Jun 21 2007 Subject code A46 Normal Source GEO sample is GSM176372 Last updated (according to GEO): Apr 09 2007 acute myeloid leukemia Source GEO sample is GSM227436 Last updated (according to GEO): Sep 12 2007 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226168 Last updated (according to GEO): Nov 05 2007 Animals were sacrificed and organs were rapidly frozen in liquid nitrogen, and subsequently stored at <ETH>80oC. Tissues were mechanically homogenized with a polytron and total cellular RNA was extracted using a commercially available reagent (TMTRIzol; Invitrogen). The poly-(A)+ fraction of the RNA was isolated by chromatography with oligo d(T) cellulose beads. For cDNA labeling, either 25 mg of total RNA or 2.5 mg of poly-(A) RNA was converted into cDNA using reverse transcriptase (RT; Super Script II, Invitrogen) and alternatively Cy5 or Cy3-labeled dCTP (1mM, Perkin Elmer-Cetus/NEN, Boston) in a reaction mixture containing 1.5 mL oligo (dT) (100pmol/ mL), 3 mL dNTP-dCTP (6.67mM each), 1 mL dCTP (2mM), 4 mL DTT (100mM), 8 mL 5 X RT Buffer (Invitrogen, California). The reactions were carried out at 42¼C for 3 hrs, after which the RNA was degraded by the addition of 0.5 mL RNase A (1 mg/mL) and 1.5 mL RNaseH 5 units/mL). Labeled cDNA was separated from unincorporated nucleotides (Qiagen column) and further concentrated by evaporation under vacuum. The arrays were pre-hybridized for 1-2hrs with DIGEasy hybridization buffer (Roche) containing 10ug/ml denatured salmon sperm DNA, and 10ug/ml yeast tRNA. The Cy5 and Cy3 labelled cDNAs were combined and hybridized in the same medium and incubated with the arrays for 16-18hrs at 37Co. Finally, the arrays were washed 3 x 10 mins in 0.1 x SSC (20 X SSC is 3M sodium chloride, 0.3 M sodium citrate, pH 7.0), 0.1%SDS at 50Co, and 4 x 3min in 0.1 x SSC at room temperature, and dried by centrifugation. Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray fluorescent scanner and image intensity data were extracted and analyzed with QuantArray 3.0 analysis software. Quantification data was imported in GeneSpring (Silicon Genetics). The import format was modified to maintain information relevant to user-contributed flagging as well as QC parameter furnished by the array manufacturer. Dye swap and Intensity-based normalization (Lowess) were performed using the default settings. Keywords = spleen Keywords = malaria Source GEO sample is GSM11007 Last updated (according to GEO): Oct 28 2005 Primary tumor 19 32 plasma cells 50 61 RNA from three stroke patients was pooled. Source GEO sample is GSM239105 Last updated (according to GEO): Oct 29 2007 Primary Neoplasm 1000 mouse hippocampus from COX-1 WT Source GEO sample is GSM121436 Last updated (according to GEO): Jan 31 2007 from epididymal fat tissues 21 48 Arteries 861 861 Cerebral cortex 5 0 Spleen Communicable Diseases 1000 hippocampus rattus_norvegicus_strain iNP animal_number 7 Communicable Diseases 1000 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181184 Last updated (according to GEO): Jul 12 2007 6,18,30 month oculomotor nucleus and spinal cord Source GEO sample is GSM74345 Last updated (according to GEO): Sep 16 2005 5.0 mg/kg MeHg forebrain at 3.0h AR-R-90pM Macrophage 14smi027 C3H/HeJ Cingulate Cortex F Blood Test (Blinded) Sample Source GEO sample is GSM129936 Last updated (according to GEO): Sep 18 2007 Posterior root of spinal nerve 861 NCI60.14_LABEL18EXTRACT17SUB3 Source GEO sample is GSM134061 Last updated (according to GEO): Aug 06 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM144904 Last updated (according to GEO): Nov 20 2006 Blood 861 142 129 other cancers Primary typical carcinoid 791 Autistic Disorder 877 29 0 H14A Human Embryonic Stem cell Amygdaloid structure 1000 The nose 94 101 Epithelium of bronchus 983 brain 0 5 Lung carcinoma (A549) [JunctionChip 4 of 5] plasma cells 332 344 in mammary epithelial cells growing 103 137 Skeletal bone 861 861 Cerebral cortex Liver (HBV+, HK27) 1000 Prostate Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188813 Last updated (according to GEO): Jun 06 2007 Epithelium of bronchus 983 brain 0 5 10 7 Left 2CdA-induced microphthalmia 5 0 brain 861 Cerebral cortex Gene expression data from older male during 1 week of inadequate protein intake Source GEO sample is GSM209820 Last updated (according to GEO): Jul 11 2007 Gene expression data from skeletal muscle following 30 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230457 Last updated (according to GEO): Sep 19 2007 Expression profiling of laminectomized raphe at 7d in rats Source GEO sample is GSM41550 Last updated (according to GEO): May 27 2005 Aortic Aneurysm, Abdominal 1000 901 Autoimmune Diseases D_U133A_79_DLPFC Acute myeloid leukemia (AML) is a heterogeneous group of diseases. Normal cytogenetics (CN) constitutes the single largest group, while trisomy 8 (+8) as a sole abnormality is the most frequent trisomy. How trisomy contributes to tumorigenesis is unknown. We used oligonucleotide-based DNA microarrays to study global gene expression in AML+8 patients with +8 as the sole chromosomal abnormality and AML-CN patients. CD34(+) cells purified from normal bone marrow (BM) were also analyzed as a representative heterogeneous population of stem and progenitor cells. Expression patterns of AML patients were clearly distinct from those of CD34(+) cells of normal individuals. We show that AML+8 blasts overexpress genes on chromosome 8, estimated at 32% on average, suggesting gene-dosage effects underlying AML+8. Systematic analysis by cellular function indicated up-regulation of genes involved in cell adhesion in both groups of AML compared with CD34(+) blasts from normal individuals. Perhaps most interestingly, apoptosis-regulating genes were significantly down-regulated in AML+8 compared with AML-CN. We conclude that the clinical and cytogenetic heterogeneity of AML is due to fundamental biological differences. Transitional epithelium 1000 I_U133A_63_CB Ovary 1000 Prosencephalon 1000 H118 FC BA4 A mouse hippocampus from COX-2 knockout Source GEO sample is GSM121446 Last updated (according to GEO): Jan 31 2007 Disease Source GEO sample is GSM176307 Last updated (according to GEO): Apr 09 2007 Heart 861 corpus_callosum_2 Source GEO sample is GSM80621 Last updated (according to GEO): Mar 31 2006 no additional Source GEO sample is GSM199104 Last updated (according to GEO): Jun 08 2007 VIIIcDG_Signal on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B 1000 Decapitation 166 156 of retinal none Source GEO sample is GSM149562 Last updated (according to GEO): Jan 03 2007 145 134 liver damage Cells were either prestimulated (1_X) or not (0_X) for 18h with 100 ng/ml LPS. Media was exchanged and after 2h rest, cells either restimulated (X_1) or not (X_0) with again 100 ng/ml LPS. This resulted in 4 experimental conditions: 0_0, 0_1, 1_0 and 1_1. There were 3 biological replicates done, resulting in 12 arrays altogether. Source GEO sample is GSM213703 Last updated (according to GEO): Aug 01 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lysophosphatidic Acid for 30min Source GEO sample is GSM5651 Last updated (according to GEO): May 27 2005 Category: Cell-line Subcategory: HMEC Scanning Software: unknown Software version: unknown Lot batch = 0088-5k Source GEO sample is GSM1938 Last updated (according to GEO): Nov 21 2005 1000 Cerebral cortex Olfactory Epithelium 1000 Spinal Cord 1000 Replicate3_Voxel E11 Spleen 0 5 N60__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A in blood 16 23 I_U133A_47_CB kidney_medulla_2 Acetaminophen 24hr Rat 1580 blood vs. Acetaminophen 24hr Rat Pooled Control blood The nose 94 101 Kidney 1000 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160329 Last updated (according to GEO): Feb 08 2007 Category: Cell-line Subcategory: HMEC Scanning Software: unknown Software version: unknown Lot batch = 0174-5k Source GEO sample is GSM1948 Last updated (according to GEO): Nov 21 2005 ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes_D_5550 Source GEO sample is GSM161571 Last updated (according to GEO): Apr 23 2007 1000 Cerebral cortex Leukemia, Lymphocytic, Chronic 1000 24 14 (cerebellum D09 0h Media Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Globin reduction was performed according to the Affymetrix technical note. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183399 Last updated (according to GEO): Apr 23 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145630 Last updated (according to GEO): Nov 20 2006 with Alzheimer's disease 27 50 I_U133Plus_94_Amy 8072_Lung did not develop PGD 861 Cerebral cortex 37 17 with isotype antibody 875 Cerebellar Diseases SiHa sample 1 between the LAD artery 266 287 Normal Source GEO sample is GSM176129 Last updated (according to GEO): Apr 09 2007 Leukemic fractions of ID07 AML patient have been hybridized. Source GEO sample is GSM103097 Last updated (according to GEO): Feb 26 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Tumor necrosis factor-alpha for 240min Source GEO sample is GSM5809 Last updated (according to GEO): May 27 2005 HBL100_Treated Breast Tumor 2 X NCI reference of the normal mucosa 7 26 brain, cortex: 14dsham2_e1_le1 1000 Cardiomyopathy, Alcoholic 7 Entorhinal Cortex 23 Esophagus 4 Normal 7 cerebral cortex 21 GSE5107 "Sample 58, <5 yr survival(13 months) age 38 erp yes" on vantveer-oligo M_U133A_28_AnCg labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156159 Last updated (according to GEO): Jan 22 2007 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211361 Last updated (according to GEO): Jul 18 2007 Trasnsformed Lymphocytes Unaffected Twin Pair 3 (DCBD3.2)(TP10) 865 Disorder of artery brain, cochlea: [7] Sample #7_le1 Expression profiling of spinal cord section (T8) extracted from rats 24h following laminectomy (sham) Source GEO sample is GSM31401 Last updated (according to GEO): May 27 2005 Comprehensive description of the transcriptome of neurointermediate lobe in euhydrated and dehydrated rat Gene expression data from hippocampus of one young SAMR1TA mouse Source GEO sample is GSM143760 Last updated (according to GEO): Jan 24 2007 1000 Structure of ciliary ganglion rat model organism with depression left untreated or treated with reserpine Source GEO sample is GSM247187 Last updated (according to GEO): Dec 11 2007 Revealing the mechanisms for neuronal somatic diversification remains a central challenge for understanding individual differences in brain organization and function. Here we show that an engineered human LINE-1 (for long interspersed nuclear element-1; also known as L1) element can retrotranspose in neuronal precursors derived from rat hippocampus neural stem cells. The resulting retrotransposition events can alter the expression of neuronal genes, which, in turn, can influence neuronal cell fate in vitro. We further show that retrotransposition of a human L1 in transgenic mice results in neuronal somatic mosaicism. The molecular mechanism of action is probably mediated through Sox2, because a decrease in Sox2 expression during the early stages of neuronal differentiation is correlated with increases in both L1 transcription and retrotransposition. Our data therefore indicate that neuronal genomes might not be static, but some might be mosaic because of de novo L1 retrotransposition events. Wild type inbred mice Source GEO sample is GSM82951 Last updated (according to GEO): Nov 10 2005 Gene expression data from embryos released from the U0126-induced arrest at day 3.5. Source GEO sample is GSM176491 Last updated (according to GEO): Mar 19 2007 IR2Gyd8_22 10 0 Whole Brain Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213496 Last updated (according to GEO): Jul 31 2007 breast cancers 75 89 Blood Test (Blinded) Sample Source GEO sample is GSM129998 Last updated (according to GEO): Sep 18 2007 7 cerebral cortex 21 gfp neg. sorted cells from 3 disected e14.5 cortecies Treatment, type=wait Source GEO sample is GSM135774 Last updated (according to GEO): Sep 12 2006 UET-13TR-EWS/ERG 72hr High Freezing Source GEO sample is GSM92427 Last updated (according to GEO): Jan 13 2006 7 0 prostate MuscleRegen-ctx4d-8LLA-s2 Blood 1000 CNS-SpinalCmod-Adult-72h-4A-s2 Voxel D3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1409 Last updated (according to GEO): Nov 21 2005 861 Cerebral cortex Cerebellum 1000 12 Temporal Lobe 24 Autistic Disorder 877 121 FC BA9 B 861 Cerebral cortex Expression profiling of somatomotor cortex extracted from rats at 7d following moderate injury Source GEO sample is GSM48639 Last updated (according to GEO): May 29 2005 U87 glioblastoma cell, clone 3.3 neo resistant negative control Keywords = bioinformatics Keywords = gene expression Keywords = cancer Keywords = platelet-derived growth factor Keywords = sterol regulatory element binding protein Keywords = glioblastoma multiformae Keywords = microarray Source GEO sample is GSM34585 Last updated (according to GEO): May 27 2005 Standard Affymetrix Protocol Source GEO sample is GSM16501 Last updated (according to GEO): May 28 2005 10 7 Left 352 340 encephalitis Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11578 Last updated (according to GEO): May 28 2005 Ganglia 1000 Male Sprague-Dawley rats (400Ã?±25 g) were anesthetized with sodium pentobarbital. 8h after sham surgery, a 7 mm disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling Source GEO sample is GSM44467 Last updated (according to GEO): Oct 28 2005 GM10860 Glyoxalase 1 and glutathione reductase 1 regulate anxiety in mice. 91 from the bone marrow 72 Brain (fetal) [JunctionChip 3 of 5] Category: Cell-line Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc54 Source GEO sample is GSM1912 Last updated (according to GEO): Nov 21 2005 plasma cells 50 61 14 7 amygdala Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132489 Last updated (according to GEO): Feb 26 2007 861 Cerebral cortex 5 0 brain ileum 861 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Leukotriene B4 (LTB4) for 30min Source GEO sample is GSM5674 Last updated (according to GEO): May 27 2005 293 of skeletal muscle 276 30 0 Skeletal Muscle [JunctionChip 5 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with ELC for 120min Source GEO sample is GSM5551 Last updated (according to GEO): May 27 2005 861 Blood 195 181 the Huntington? The epithelial cells 962 981 1000 Lipids HRPC269_hormone resistant prostate cancer early stage Estrogen receptors (ERs), which mediate the proliferative action of estrogens in breast cancer cells, are ligand-dependent transcription factors that regulate expression of their primary target genes through several mechanisms. In addition to direct binding to cognate DNA sequences, ERs can be recruited to DNA through other transcription factors (tethering), or affect gene transcription through modulation of signaling cascades by non-genomic mechanisms of action. To better characterize the mechanisms of gene regulation by estrogens, we have identified more than 700 putative primary and more than 1500 putative secondary target genes of estradiol in MCF7 cells through microarray analysis performed in the presence or absence of the translation inhibitor cycloheximide. Last Updated (by provider): Jul 26 2007 Contributers: David Laperrière John H White Julie Deschênes Véronique Bourdeau Sylvie Mader 4 0 Heart Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19482.gif Source GEO sample is GSM91506 Last updated (according to GEO): Sep 22 2006 281 256 for Parkinson's Disease to spinal cord 0 11 with Parkinson's disease 27 50 brain 0 5 Euploid sample 1 (cerebellum) Immune system 1000 861 Cerebral cortex Coronary Arteriosclerosis 1000 DLCL-0037 || lc4b036 spinal_cord_9 Hypothalamus RYGB- 0 17 Neoplasm 861 SN:Human Glioblastoma Biopsy 06725 Lymphoblastoid Cell Line for Individual 8033.4 log phase 204 194 of retinal Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation. Source GEO sample is GSM228477 Last updated (according to GEO): Sep 10 2007 PGA-MurLungRag-rwp-72h-1bA-s2 30 19 Solid tumor FBooth-MDX-1Av2-s2 mouse cerebral cortex 0 21 MeHg-induced encephalopathy 1000 medulloblastoma The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169496 Last updated (according to GEO): Feb 21 2007 Job's patient Source GEO sample is GSM211119 Last updated (according to GEO): Sep 10 2007 Large-scale analysis of the human transcriptome. Prostate cancer Source: University of Virginia, see PMID 11507037 Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 114.93 Stdv: 3.44 Min: 109.69 Max: 119.51 Source GEO sample is GSM2860 Last updated (according to GEO): Mar 20 2006 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68264 Last updated (according to GEO): Jul 07 2006 6 0 Cancers To date, there is little information on early molecular events in the development of N-nitrosomethylbenzylamine (NMBA) induced esophageal tumorigenesis and of the effects of chemopreventive agents on these events. In this study, we identified genes in rat esophagus that were differentially expressed in response to short?term NMBA-treatment and modulated by co-treatment with phenethylisothiocyanate (PEITC). Rats were fed AIN-76A diet or AIN-76A diet containing PEITC for three weeks. During the third week of dietary treatment, they were administered three s.c. doses of NMBA (0.5 mg/kg b.w.). Rats were sacrificed 24 h after the last treatment, esophagi excised and processed for histological grading, microarray and real-time PCR analysis. Our histopathological data showed that treatment of rats with PEITC had protective effect on NMBA-induced preneoplastic lesions in the rat esophagus. We identified 2261 genes that were differentially expressed in the NMBA-treated vs. control esophagi and 1936 genes in the NMBA+PEITC- vs. NMBA-treated esophagi. The intersection of these two sets resulted in the identification of 1323 genes in NMBA-treated esophagus that were modulated by PEITC to near-normal levels of expression. The measured changes in the expression levels of 10 selected genes were validated using real-time PCR. Principle components analysis (PCA) was applied to all twelve microarrays in the study, which suggested that in terms of global gene expression, PEITC treatment had a genome-wide modulating effect on NMBA-induced gene expression. Samples obtained from animals treated with PEITC alone or co-treated with NMBA were more similar to controls than they were to NMBA treatment alone. Last Updated (by provider): Jul 17 2007 Contributers: Alan A Dombkowski Ronald Nines Daniela Cukovic Rashmeet K Reen Laura A Kresty Gary D Stoner Sridevi Salagrama Jennifer M Mele spinal cord, ventral spinal cord: D28WTMN3_e1_le1 HCC (HBV+, HK67, T2) 299 295 liver 1000 Decapitation null Source GEO sample is GSM227362 Last updated (according to GEO): Sep 10 2007 P24 non-deprived visual cortex replicate 4 CNS-SCsev_InjB4h-3B-s2 collagen 303 311 861 Cerebral cortex Central gray substance of midbrain 861 Replicate3_Voxel E10 from SVG-A glial cells 21 43 Brain 861 715 705 from livers R457P00303 567 548 the descending colon seminoma specimen, pT2, patient age: 30y; W03 036 GM19094 Lymphoblastoid Cell Line for Individual 8021.4 log phase Gene expression data from human prostate tissue with 90 percent tumor content Source GEO sample is GSM119302 Last updated (according to GEO): Feb 23 2007 Primary tumor 19 32 1000 Infection T-ALL-C18 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Cerebral cortex 861 Skeletal bone 861 "42 hr Hela Double Thymidine, exp3" Brain (thalamus) [JunctionChip 4 of 5] Brain 861 1000 Cerebral cortex Ciliary muscle structure 901 Normal Source GEO sample is GSM176353 Last updated (according to GEO): Apr 09 2007 PMN_LB_180min_Patient14 spinal cord 0 11 Dopamine Receptor 1000 25 0 frontal cortex wistar 3659 Brain 50 55 Blood 1000 Anterior nares 1000 5 0 Muscle 101109 130 122 in uterus 331 307 in central nervous system 1000 Retina Spinal cord tissue from wildtype mice Treatment, type=linear_amplification, description=T7-based RNA amplification Source GEO sample is GSM113698 Last updated (according to GEO): Jun 09 2006 46 8 in docetaxel-refractory prostate cancer Gene expression profile of the cell line UB/OC-1 grown for 1 day under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1518 Last updated (according to GEO): May 27 2005 AD 2hr C-CA1 from ventral prostate 21 41 normal lung 1112 Source GEO sample is GSM17292 Last updated (according to GEO): May 28 2005 901 Autoimmune Diseases Hippocampus 861 Acetaminophen 3hr Rat 4623 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool HapMap YRI_parent Female Source GEO sample is GSM159698 Last updated (according to GEO): Feb 01 2007 Disease Source GEO sample is GSM176309 Last updated (according to GEO): Apr 09 2007 1000 Coronary Arteriosclerosis 861 Cerebral cortex Primary Neoplasm 1000 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201302 Last updated (according to GEO): Jun 14 2007 Gene expression data from colorectal adenoma. Source GEO sample is GSM215085 Last updated (according to GEO): Aug 02 2007 1000 Brain GC (HKG10L) JMR-RatInj21d-1bA-s2 subthalamic_nucleus Source GEO sample is GSM18937 Last updated (according to GEO): Sep 25 2006 - Source GEO sample is GSM162899 Last updated (according to GEO): Aug 28 2007 3 hrs Post-clamp sample 1 1000 Coronary Arteriosclerosis Testis 1000 trauma 2006 2011 Brain 1000 Colon (descending) [JunctionChip 1 of 5] plasma cells 50 61 SCG explant cultured for 12 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246054 Last updated (according to GEO): Dec 03 2007 to cardiovascular disease 265 289 321 of Down syndrome. 304 none Source GEO sample is GSM244591 Last updated (according to GEO): Nov 23 2007 in the periimplantation uterus 921 951 Nose 1000 VDXGUYU_4033 Neoplasm 861 brain, Left Parietal Occipital: Extract43_le1 metanephric mesenchyme, ANX, 4 days, biological rep2 pyramidal cells 227 241 861 Substantia nigra structure 1000 Cartilage D_U133Plus_121_HC 1000 Aorta Gene expression data from B6xBALB F2 mouse lung Source GEO sample is GSM133469 Last updated (according to GEO): Apr 05 2007 We have used commercially available oligonucleotide arrays to measure the relative expression levels of >10,000 genes and ESTs. Recent evidence suggested certain advantages of performing such expression experiments on two or more different platforms of oligonucleotide arrays. Here we have used two oligonucleotide platforms, MG U74Av2.0 arrays from Affymetrix and CodeLink UniSet1 from GE Healthcare, to assess whole brain gene expression patterns in naive C57BL/6 and DBA/2J mice. C57BL/6J (n = 5) and DBA/2J (n = 4) male mice, 25-30 g body weight, were obtained from Jackson Laboratories. Animals were group-housed and quickly sacrificed by CO2 exposure according to a protocol approved by the UCHSC IACUC. Brains were rapidly removed and stored at -80oC until use. Whole brain was homogenized in lysis buffer using a Polytron, and total RNA was isolated using the RNeasy Midi Kit (Qiagen) following the protocol supplied by the manufacturer. An additional clean-up of total RNA was carried out using the RNeasy Mini Kit (Qiagen). Using the protocol supplied by the manufacturer, double-stranded cDNA was synthesized from the total RNA (4 ug of total RNA from an individual mouse brain was used for each array) and was used to obtain biotin-labeled cRNA by an in vitro transcription reaction. Biotin-labeled cRNA was recovered using the RNeasy kit. Biotin-labeled cRNA from each mouse was then fragmented and hybridized with two separate (duplicate) CodeLink BioArrays. The average of the gene expression intensity values for each probe set from these technical replicates was used for data analysis. The BioArrays were subsequently stained for 30 min with Cy5-Streptavidin and washed prior to scanning. For MG U74Av2 arrays,double-stranded cDNA was synthesized from 5 ug of total RNA, using the protocol supplied by the manufacturer, and used to obtain biotin-labeled cRNA by an in vitro transcription reaction. Biotin-labeled cRNA was then fragmented and the quality of the fragmented cRNA was assessed using Test2 chips prior to hybridization with the Affymetrix arrays. Hybridization of the cRNA with the Affymetrix arrays was carried out according to the manufacturer's protocol. The arrays were stained with streptavidin-phycoerythrin conjugate and scanned by a GeneArray scanner. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Jun 29 2005 Contributers: Sanjiv V Bhave Boris Tabakoff Natalie Lassen Vasilis Vasiliou Richard A Deitrich Paula L Hoffman Operator Name: Sample Type: Sample Description: Comments: Reagents: Reagent Lot: Algorithm: Statistical Corner+ Avg:378, Count:32 Corner- Avg:32046, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:8.905122,SFGene:All Background:Avg:591.35,Stdev:17.35,Max:645.6,Min:568.9 Noise:Avg:13.72,Stdev:0.52,Max:15.2,Min:12.2 RawQ:17.88 Keywords = ALL Source GEO sample is GSM3481 Last updated (according to GEO): May 27 2005 Timed pregnant C57Bl6 mice were exposed to ethanol during a critical period, gestational day 15 to 18, of cerebral cortical development to identify gene expression changes in the cerebral cortex of developing fetus due to this ethanol exposure Last Updated (by provider): Jul 03 2006 Contributers: Leena Kumar Rajesh C Miranda 901 Heart failure 1000 Retina M14 hgu95b 1000 Liver Euploid sample 2 (heart) Large-scale analysis of the human transcriptome. Trachea Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 105.12 Stdv: 3.59 Min: 98.45 Max: 110.41 Source GEO sample is GSM2873 Last updated (according to GEO): Mar 20 2006 C57/BL6 to C57/BL6 Source GEO sample is GSM8933 Last updated (according to GEO): May 28 2005 Blood 861 Proliferative endometrium from normal patient Source GEO sample is GSM150196 Last updated (according to GEO): Dec 14 2006 Expression profiling of spinal cord section (T9) extracted from rats 24h following severe injury Lot batch = Source GEO sample is GSM7574 Last updated (according to GEO): May 28 2005 67 40 with coronary artery disease no additional Source GEO sample is GSM199273 Last updated (according to GEO): Jun 08 2007 Ganglia, Spinal 923 861 Brain Neocortical astrocyte chip 1. CHIP ID 10486 Source GEO sample is GSM128874 Last updated (according to GEO): Mar 14 2007 Donor D, post G-CSF schizophrenia 559 572 1000 Brain Job's patient Source GEO sample is GSM211118 Last updated (according to GEO): Sep 10 2007 Spinal Cord 1000 plasma cells 332 344 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201298 Last updated (according to GEO): Jun 14 2007 Bone marrow cell, primary Yub10F D_U133A_21_HC Occipital Lobe 2 Normal 104 85 in breast carcinoma 115 FC BA9 A 1000 Kidney spinal cord 37 47 1000 Heart occipital_lobe_5 Source GEO sample is GSM80754 Last updated (according to GEO): Mar 31 2006 brain 0 5 RNA from Lymphoblastoid Cell Line from this individual Source GEO sample is GSM213300 Last updated (according to GEO): Jul 26 2007 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68260 Last updated (according to GEO): Jul 07 2006 660 mesenchymal stem cell 639 1000 Retina tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44868 Last updated (according to GEO): May 27 2005 10 0 Spinal Cord 901 Coronary artery Creatine-treated, biological rep1 D_U133A_32_HC ventral striatum wistar 3958 861 Cerebral cortex Bladder sample 930_1 Vulva 8 Normal 1000 Amygdaloid structure Subject code A43 1000 Retina Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14600.gif Source GEO sample is GSM91614 Last updated (according to GEO): Sep 22 2006 Cochlea at E13.5, replicate2 264 253 of chromatin Primary small cell lung carcinoma 3424 0 37 vestibular_nuclei_superior_9 Brain 861 5 0 Spleen We have previously shown that pluripotent stem cells are induced from mouse fibroblasts by retroviral introduction of Oct3/4, Sox2, c-Myc and Klf4, and subsequent selection for Fbx15 expression. These iPS (induced pluripotent stem) cells are similar to embryonic stem (ES) cells in morphology, proliferation and teratoma formation. Fbx15-iPS cells, however, are different in gene expression and DNA methylation patterns and fail to produce adult chimeras. Here we show that selection for Nanog results in germ-line competent iPS cells, with more ES cell-like gene expression and DNA methylation patterns. The four transgenes were strongly silenced. We obtained adult chimeras from seven Nanog-iPS clones, with one clone transmitted through the germ-line to the next generation. Approximately 20% of the offspring developed tumors, where c-Myc transgene was reactivated. Thus iPS cells competent for germ-line chimeras can be obtained from fibroblasts, but retroviral introduction of c-Myc should be avoided for clinical application. Last Updated (by provider): May 18 2007 Contributers: Keisuke Okita Shinya Yamanaka Tomoko Ichisaka Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 3 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10964 Last updated (according to GEO): May 27 2005 with bacterial infections 1758 1782 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228587 Last updated (according to GEO): Sep 11 2007 WGACON-71 Neoplasm 861 BXD 16_M7SS02080614 861 Pituitary Gland 861 Cardiomyopathies Richard Almon-17-1138200269946 5 0 brain in the hippocampus 40 57 122 for Down syndrome 105 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159975 Last updated (according to GEO): Feb 01 2007 Temporal Cortex Alzheimer's disease 9 brain, cerebellum: RNA#5S_le1 cells stimulated with lipoprotein prep 2, biological rep1 Muscle Cells 861 Spleen 0 5 GSE2868 very advanced HCC Source GEO sample is GSM155943 Last updated (according to GEO): Jun 21 2007 BrnD2_0220ACHI.txt "Sample 38,>5 yr survival(88 months) age 52 erp yes" on vantveer-oligo Neostriatum 1000 12 0 ovarian tumor NA12751 growth 2 1000 Descending colon Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160722 Last updated (according to GEO): Sep 24 2007 testis 52 58 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27043 Last updated (according to GEO): May 27 2005 865 Disorder of artery Hereditary Malignant Neoplasm 876 Pancreas Keywords = mouse gene expression database Source GEO sample is GSM39103 Last updated (according to GEO): May 27 2005 Nasal Epithelium Inhalation Formaldehyde 2ppm 24h ID212 913 Coronary heart disease Critical aspects of the biology and molecular basis for prostate malignancy remain poorly understood. To reveal fundamental differences between benign and malignant growth of prostate cells, we performed gene expression profiling of primary human prostate cancer and benign prostatic hyperplasia (BPH) using cDNA microarrays consisting of 6500 human genes. Frozen prostate specimens were processed to facilitate extraction of RNA from regions of tissue enriched in either benign or malignant epithelial cell growth within a given specimen. Gene expression in each of the 16 prostate cancer and nine BPH specimens was compared with a common reference to generate normalized measures for each gene across all of the samples. Using an analysis of complete pairwise comparisons of expression profiles among all of the samples, we observed clearly discernable patterns of overall gene expression that differentiated prostate cancer from BPH. Further analysis of the data identified 210 genes with statistically significant differences in expression between prostate cancer and BPH. These genes include many not recognized previously as differentially expressed in prostate cancer and BPH, including hepsin, which codes for a transmembrane serine protease. This study reveals for the first time that significant and widespread differences in gene expression patterns exist between benign and malignant growth of the prostate gland. Gene expression analysis of prostate tissues should help to disclose the molecular mechanisms underlying prostate malignant growth and identify molecular markers for diagnostic, prognostic, and therapeutic use. 2011 2001 for livers lateral motoneurons (LMN) 1 913 CA1 field 1000 Autistic Disorder 861 Cardiomyopathies Brain 861 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21761.gif Source GEO sample is GSM93135 Last updated (according to GEO): Sep 22 2006 Plasma 861 Brain 1000 E6.5_rep2 1000 Pancreas 17 7 hippocampus Primary typical carcinoid 7787 of 7 saccules 5 17 tibiae 115 120 1000 ovarian neoplasm 861 Cerebral cortex 25 0 frontal cortex wistar 3921 of coronary artery disease 258 284 rat kidney at embryonic day 13, rep2 Cells captured via Arcturus LCM system, amplified (RiboAmp, 2 rounds) and labeled (Enzo) for hybridizaton to Affymetrix MG_U74Av2 arrays, using manufacturers protocols in each step. Source GEO sample is GSM6191 Last updated (according to GEO): May 27 2005 Whole Brain 73 83 CAD_replicate31 1000 Liver neurological disease control sample x116 OBX Day 5,# 2 0029_1473_H95A2_T95-28_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Trauma 1000 1509 1500 of gliomas H115 CN A Z4 juvenile biol repl 1 LungE165_022NAFBE_078.txt GSE7390 for hereditary non-polyposis colon cancer 340 380 HUVEC isolate 22 low serum media VEGF-A 24hours cf. #15 Source GEO sample is GSM12909 Last updated (according to GEO): May 28 2005 9 DNA damage 0 Parietal Lobe 1000 Nodose Ganglion 1000 PGA-Band_1w_1-m5 Fibroblasts 861 6 0 Mammary Spleen 0 5 Gene expression data from liver Source GEO sample is GSM243362 Last updated (according to GEO): Nov 16 2007 Myocardial Infarction 1000 Spleen 1000 high gestational age Source GEO sample is GSM213121 Last updated (according to GEO): Jul 25 2007 BCR-ABL-C1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A lung 141 145 "Sample 27,>5 yr survival(62 months) age 45 erp yes" on vantveer-oligo frontal lobe 901 ALL-T-cell-6 on Affymetrix GeneChip Human Full Length Array HuGeneFL f2#144 versus pool Mouse Brain tissue Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed 24 h to hydrostatic pressure (HP24), pressure experiment # 1 (PE1). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11402 Last updated (according to GEO): Dec 15 2006 927 902 in the trigeminal ganglion 861 Cerebellum Fibroblasts 1000 1000 Cerebellum Normal human tissue:Normal Kidney Keywords = Human, Normal Tissue, Normal Kidney Source GEO sample is GSM44675 Last updated (according to GEO): May 27 2005 1BMH02022104_thyroid Lymphoblastoid Cell Line for Individual 8118.5 log phase TEL-AML1-C55 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145810 Last updated (according to GEO): Nov 20 2006 Blood 1000 Femur 1000 HT29 hgu95b Wild type 8 wk old male FVB/NJ mouse periaqueductal gray Source GEO sample is GSM107039 Last updated (according to GEO): Mar 05 2007 TEL-AML1-C53 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 100104 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152016 Last updated (according to GEO): Feb 06 2007 1000 Descending colon 0 Rett syndrome 12 HC69 CB B 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201230 Last updated (according to GEO): Jun 14 2007 3AMH02082315_PB_CD14Monocytes striatum 32 40 861 Cerebral cortex days nasal epithelium 1127 1148 Neoplasm 861 Liver Test (Blinded) Sample Source GEO sample is GSM130175 Last updated (according to GEO): Sep 18 2007 of mouse brain 9 23 Whole Brain 73 83 Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP), exposed 6 h more to ambient pressure (CP6) and harvested with cells exposed for 6 h to hydrostatic pressure, pressure experiment # 3 (PE3). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11385 Last updated (according to GEO): Dec 15 2006 Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160706 Last updated (according to GEO): Sep 24 2007 Structure of entorhinal cortex 1000 CNS-SMTC_Mod14d-2A-s2 NCI60.20_LABEL24EXTRACT23SUB3 Source GEO sample is GSM134093 Last updated (according to GEO): Aug 06 2007 917 913 (ADCs 41 29 Control blood 16 7 cerebellum D_U133A_2_nAcc 861 Heart Diseases Spinal Cord 1000 GSE4411 CNS-SC_Inj14d-2A-s2x Wild type 8 wk old male C57BL/6J mouse amygdala Source GEO sample is GSM74918 Last updated (according to GEO): Feb 27 2007 719 in the posterior pituitary 693 Simple annotation: FNH, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7774.gif Source GEO sample is GSM79961 Last updated (according to GEO): Sep 22 2006 Kidney 861 brain, Left Temporal Lobe: Extract48_le1 Kidney 861 254 238 of neural retinas Cerebral cortex 861 Duchenne muscular dystrophy (DMD) patient?s skeletal muscle sample 8 Little is known about the global transcriptional program underlying granulocytic (G) commitment, differentiation and maturation. Using DNA microarrays and Q-RT-PCR, we examined the transcriptional profile of G differentiation of human CD34-positive hematopoietic stem and progenitor cells cultured with interleukin-3, interleukin-6 granulocyte colony stimulating factor and stem cell factor. The goal this study was to identify genes involved in the various facets of G differentiation including commitment, expansion, differentiation and functional capacity. Last Updated (by provider): Jun 06 2007 Contributers: William M Miller Huang Li Ting Eleftherios T Papoutsakis CNS-SpinalC-conAdult-48h-1C-s2 177 with primary, untreated non-small cell lung cancer 128 D_U133A_27_DLPFC NCI60.26_LABEL30EXTRACT29SUB3 Source GEO sample is GSM134124 Last updated (according to GEO): Aug 06 2007 NCI60.52_LABEL56EXTRACT55SUB3 Source GEO sample is GSM134256 Last updated (according to GEO): Aug 06 2007 Normal__Lung_LU_3 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A PMN_LB_360min_Patient7 1000 Leukemia, Myelocytic, Acute N58__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 901 Caudate nucleus structure /J Olfactory Bulb A 4 22 Plasma 861 none Source GEO sample is GSM244530 Last updated (according to GEO): Nov 23 2007 41 29 Control blood 71 cortex 77 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120667 Last updated (according to GEO): May 14 2007 none Source GEO sample is GSM149576 Last updated (according to GEO): Jan 03 2007 1000 Intestines, Small Breast Carcinoma 1000 adenocarcinoma 314 328 Malignant Neoplasms 861 072801 Time Zero Z3 T-Cell in brain 950 957 RNA from muscle biopsy specimen Source GEO sample is GSM3717 Last updated (according to GEO): May 27 2005 N-3_PRE 2nd 4hr C+S-CA1 T Cells AntiCD3 30h 1 Activated PGA-HMO-Obese-2aUA-s2 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. 30min after sham surgery, a 7 mm disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44509 Last updated (according to GEO): May 27 2005 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13146.gif Source GEO sample is GSM79685 Last updated (according to GEO): Sep 22 2006 1BJZ02022636_testis 1000 Hippocampus 0 Human Cortex 11 1000 hair Heart 1000 mouse brain ipsilateral saline.RU486, biological rep2 D_U133Plus_118_HC none Source GEO sample is GSM210296 Last updated (according to GEO): Jul 16 2007 Olfactory Epithelium 1000 Skeletal bone 861 Spleen 1000 901 Nervous system structure 861 Blood 2784 2776 28S rRNA Integrated stress response Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141324 Last updated (according to GEO): Oct 26 2006 B240 MOnocytes treated with anti-FcgRIIB antibody for 24 hrs Central gray substance of midbrain 861 10 0 fetal liver GPX-000046 Heart 1000 GBM: 40L Trasnsformed Lymphocytes Bipolar Disorder Affected Twin Pair 2 (DCBD2.1)(TP7) DuodTumor022YAFBV_dtb.txt Expression profiling of spinal cord section (T10) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM4460 Last updated (according to GEO): May 28 2005 9 0 Blood Test Myocardial Infarction 1000 NG108 rat neuronal cell culture exposed to 4400 ng/ml mefloquine (treated) for two hours. 10 µg total RNA hybridized per chip. RNA STAT 60 used to extract RNA. Standard Affymetrix chip scaling factors used. No other data transformation. Source GEO sample is GSM1666 Last updated (according to GEO): Oct 28 2005 retina 5 10 Conjtissue4 BPH138_benign prostate hyperplasia 0 33 15 0 human cerebellum 1BMH02082908_PB_CD19BCells 40 21 from dorsal pancreas this sample is from a 16-week-old male mdx mice gastrocnemius muscle Source GEO sample is GSM4379 Last updated (according to GEO): May 28 2005 5 0 brain 901 frontal lobe Parkinson 0 8 12 0 ovarian tumor 861 Hereditary Diseases 6 0 Bladder The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169488 Last updated (according to GEO): Feb 21 2007 Pooled EDL RNA samples from five 8 wk old male C57BL10 mice Source GEO sample is GSM13672 Last updated (according to GEO): May 28 2005 JMR-RatInj24hf-3aA-s2 bronchial epithelia 224 243 861 Cerebral cortex 865 Disorder of artery P21CN2 Gene expression data from liver Source GEO sample is GSM243369 Last updated (according to GEO): Nov 16 2007 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/9655.gif Source GEO sample is GSM79928 Last updated (according to GEO): Sep 22 2006 Coronary heart disease 913 861 Telangiectasis ileum 0 4 fetal buttock-thigh fibroblast #2, serum starved 1000 Brain skeletal muscle sprague1 whole tissue, individual animal, 10 weeks old, male Sprague Dawley skeletal muscle file:R3JW02103003 Source GEO sample is GSM15203 Last updated (according to GEO): May 28 2005 103 86 of neonatal brains Epithelium 861 of mouse brain 9 23 901 Cardiomyopathy, Dilated serotonin receptor 861 861 Brain Primary typical carcinoid 791 Source GEO sample is GSM17316 Last updated (according to GEO): May 28 2005 Normal human fetal cartilage from 18-22 weeks. Source GEO sample is GSM149643 Last updated (according to GEO): Jul 06 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with NGF (Nerve Growth Factor) for 60min Source GEO sample is GSM5702 Last updated (according to GEO): May 27 2005 G3 Iris CNS-SCsev_InjB7d-1B-s2 no additional Source GEO sample is GSM199165 Last updated (according to GEO): Jun 08 2007 Liver 1000 in brain 244 252 861 Cancer of Neck Macrophage 14smi106 CLL-21 320 306 Keywords = HIV Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.94 Subject: 1905 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM38995 Last updated (according to GEO): May 27 2005 from mouse colon 21 36 Brain 1000 1000 frontal lobe 132 118 from infections Skeletal bone 861 304 280 alcoholic cardiomyopathy NoCAD_replicate8 M_U133Plus_94_DLPFC 861 Glioblastoma Plasma 861 testis 52 58 Sample details: Three pools of rostral (R1-3), three pools of middle (M1-3), and three pools of caudal (C1-3) E13.5 MF1 neocortex were collected from 4 embryos. All possible 18 comparisons were carried out. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. Source GEO sample is GSM62833 Last updated (according to GEO): Aug 26 2005 intestine_PPARa-knockout_control_rep1 PCA-403 on UMich-10k Muscularis propria 896 1000 Hippocampus Sham 17 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107506 Last updated (according to GEO): May 01 2006 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114185 Last updated (according to GEO): Jun 16 2006 Normal Source GEO sample is GSM176354 Last updated (according to GEO): Apr 09 2007 VDXRHU_1771 CNS-SpinalCmod-Adult-28d-5A-s2 1000 Brain Transplant Series 19 , Transplant # 1 C6SPGFPslow1 spinal cord 46 56 cDNAs were generated from 5ug of total RNA per sample by reverse transcription (RT) for two hours at 42oC using the 3DNA SubmicroTM Oligo Expression Array Detection Kit (Genisphere, Hatfield, PA) and Superscript II (Invitrogen, Carlsbad, CA). For each microarray chip two consecutive hybridizations were performed with cDNAs and the fluorescent probes following the manufacture?s specifications. Briefly, in the first hybridization reaction the solution containing the mixture of cDNAs obtained from control and treated cells was loaded onto the CAG Human 19K array and incubated overnight at 55oC in a hybridization chamber (Genemachines, San Carlos, CA). The human 19K array (www.cag.icph.org/microarray_facility.htm) contains 60-mer oligonucleotides (Compugen, San Jose, CA) representing 18,861 human genes spotted onto poly-l-lysine coated glass microscope slides. In the second hybridization reaction Cy3 (green) and Cy5 (red) fluorescent probes were used to label the cDNAs from control and PGJ2-treated cells, respectively. The second hybridization was carried out for 3 hours at 65oC in the hybridization chambers. The arrays were scanned using an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) with laser intensities adjusted to bring the brightest spot just below saturation and the data extracted with the Axon GenePix Pro software. Source GEO sample is GSM98760 Last updated (according to GEO): May 31 2006 10 Bone marrow 0 NCI60.19_LABEL23EXTRACT22SUB3 Source GEO sample is GSM134085 Last updated (according to GEO): Aug 06 2007 10 Bone marrow 0 1000 Left Congenital Abnormality 853 1000 Coronary Arteriosclerosis Mice were sacrificed at 13 weeks of age. They can be used as controls for the 4 week swim 1 week rest mice. Keywords = exercise induced hypertrophy Source GEO sample is GSM2367 Last updated (according to GEO): May 27 2005 PGA-Pi3k_ntg_3119v2 Skeletal bone 861 Liver; day 14 postnatal_liver Keywords = mouse gene expression database Source GEO sample is GSM29368 Last updated (according to GEO): May 27 2005 no additional Source GEO sample is GSM199038 Last updated (according to GEO): Jun 08 2007 from the femurs 95 109 1000 Leukemia, Myelocytic, Acute Neoplasm 861 Liver; RegenerationSham 6 hrs Keywords = mouse gene expression database Source GEO sample is GSM29375 Last updated (according to GEO): May 27 2005 1000 Left Fluid-percussion head injury 83 110 brain, amygdala: Control-Hippocampus_e1_le2 861 Cancer of Neck Hippocampus 1000 901 Breast Carcinoma Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer. 901 Coronary artery EAE, 1,25(OH)2D3-treated #8 0029_1475_H95A2_T95-40_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A H9LMS00111006 Femur 1000 M_U133A_112_DLPFC Brain 861 Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183408 Last updated (according to GEO): Apr 23 2007 GSE2982 hippocampus rattus_norvegicus_strain iNP animal_number 10 Jejunum [JunctionChip 1 of 5] 1000 Solid tumor Immature B cells 1b 145 135 of epilepsy 861 Cerebral cortex Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11484 Last updated (according to GEO): May 28 2005 6 month oculomotor nucleus rep 2 588 570 activated microglia Replicate3_Voxel E9 7 cerebral cortex 21 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14540.gif Source GEO sample is GSM91511 Last updated (according to GEO): Sep 22 2006 1037 of transitional epithelium 1012 0029_1224_HU95A_KF0150_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Stomach Fundus 2 Normal brain, contralateral Cortex: Trizol Extraction42_le1 072801 Mock 01.00 hr. T-Cell 861 Cerebellum 12 0 ovarian tumor 913 Coronary heart disease Gene expression data from postmorten brain regions Source GEO sample is GSM145495 Last updated (according to GEO): Nov 20 2006 Abdominal aortic aneurysm 0 24 brain, cortex: 14dexp4_e1_le1 861 Epithelial Cells 17 0 Trigeminal ganglia 923 Optic Disk 1037 of transitional epithelium 1012 from the femurs 95 109 191 181 of ischemia Amygdaloid structure 1000 brain 0 5 Cerebral cortex 861 aortic biopsy stiff Keywords = pulse wave velocity, arterial stiffness Source GEO sample is GSM6181 Last updated (according to GEO): May 27 2005 456 427 in the embryonic basal ganglia 1000 Corpus Callosum NCI-H226 hgu95c Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184708 Last updated (according to GEO): Apr 26 2007 858 Prostatic Neoplasms 67 40 with coronary artery disease HUVEC isolate Z low serum media PlGF 24hours cf. #25 Source GEO sample is GSM12926 Last updated (according to GEO): May 28 2005 of somatomotor cortex 21 41 Primary tumor 19 32 Lymphoblastoid Cell Line for Individual 8015.5 log phase none Source GEO sample is GSM149624 Last updated (according to GEO): Jan 03 2007 925 891 that differentiated prostate cancer Congenital heart disease in Csx/ Nkx2.5 mutant embryos Blood B cells;anti-IgM 6h trigeminal_ganglia_3 19 0 human frontal cortex 1000 Malaria Saccule structure 1000 861 Hodgkin Disease GBM Treatment, type=remove Source GEO sample is GSM99577 Last updated (according to GEO): Apr 21 2006 4R 1 (Experiment 4R18h: Run 19869) Treatment, type=timepoint, description=Primary cortical neurons were treated for 18h with a new non competitive antagonist for nicotinic receptors (4R 2uM), and then the cells were harvested, measurement=18.0 h Source GEO sample is GSM96730 Last updated (according to GEO): Feb 14 2006 Keywords = Infectious diseases 1069 1099 healthy subject Source GEO sample is GSM211105 Last updated (according to GEO): Sep 10 2007 Ganglia, Spinal 1000 Treatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cells. Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 8 hours after lights on. Original RNA code = LC6A. Source GEO sample is GSM227406 Last updated (according to GEO): Sep 10 2007 basal ganglia Source GEO sample is GSM38975 Last updated (according to GEO): May 27 2005 Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation. Source GEO sample is GSM228475 Last updated (according to GEO): Sep 10 2007 at the Human Brain 744 761 M_U133A_93_AnCg Vestibular Nuclei Superior 6 Normal E2A-PBX1-#7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from the neocortex of wild-type mouse Source GEO sample is GSM172931 Last updated (according to GEO): Mar 08 2007 TEL-AML1-C43 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Colon (descending) [JunctionChip 5 of 5] 47 30 in prostate cancer Normal Source GEO sample is GSM176017 Last updated (according to GEO): Apr 09 2007 Amygdaloid structure 1000 MCF7 treated with vehicule for 24h Source GEO sample is GSM213330 Last updated (according to GEO): Jul 26 2007 Lymphoblastoid Cell Line for Individual 8051.3 log phase Fibroblasts 38 48 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155036 Last updated (according to GEO): Jun 04 2007 occipital_lobe_2 Source GEO sample is GSM80773 Last updated (according to GEO): Mar 31 2006 Epithelium of bronchus 983 1000 Coronary Arteriosclerosis We used the default settings of GCOS software to scan the chips. Source GEO sample is GSM148490 Last updated (according to GEO): Apr 16 2007 intermediolateral column motoneurons (IML) 24 brain 0 5 Brain 861 M_U133Plus_115_AnCg Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17074.gif Source GEO sample is GSM91582 Last updated (according to GEO): Sep 22 2006 GSE2018 Adipose tissue 1000 Blood 861 R463P00344 1000 Adenocarcinoma of large intestine Replicate1_Voxel F5 Laser captured visceral sensory neurons. Source GEO sample is GSM63654 Last updated (according to GEO): Dec 21 2005 Brain 861 pfc_1066_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A n/a Source GEO sample is GSM178065 Last updated (according to GEO): Jun 11 2007 such as hormones 901 916 PGA_PA-S_314 Lv2: Hippocampus_21PT-Y_rep7 Gonadectomized Dahl-Iwai Female LowSalt Cortex rat1 gdahl_cortexr_k_GX_1c_051702 Donor 3 Time point 12 hours Autologous control (uninfected) Source GEO sample is GSM2619 Last updated (according to GEO): May 27 2005 Hippocampus 861 +_6451_batch1 on NHGRI-6.7k Nasal Epithelium 865 Congenital chromosomal disease 901 Gene expression data from older male during 1 week of inadequate protein intake Source GEO sample is GSM209814 Last updated (according to GEO): Jul 11 2007 Seminoma 1000 of the stria terminalis rep1 26 53 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211315 Last updated (according to GEO): Jul 18 2007 GSE8070 none Source GEO sample is GSM149516 Last updated (according to GEO): Jan 03 2007 liver, wild type mice, control conditions Source GEO sample is GSM205766 Last updated (according to GEO): Jul 24 2007 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153490 Last updated (according to GEO): Jan 11 2007 SCG explant cultured for 65 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246069 Last updated (according to GEO): Dec 03 2007 Brain 1000 nostrils 156 164 0 Lung tissue 10 T178 83 69 Normal Thalamus brain 0 5 Wild type 8 wk old male FVB/NJ mouse bed nucleus of the stria terminalis Source GEO sample is GSM74938 Last updated (according to GEO): Feb 27 2007 280 275 Spleen Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211250 Last updated (according to GEO): Jul 18 2007 32 hr Hela Double Thymidine, exp2 X chromosome 736 747 mouse hippocampus 0 17 237 200 with idiopathic dilated cardiomyopathy Epithelium 865 Squamous cell carcinoma 6 0 24 Rat SCN Sample 10 (Technical replicate - 6 hr) human caudate nucleus Source GEO sample is GSM86887 Last updated (according to GEO): Feb 08 2006 Cerebral cortex 861 to the nose 599 609 Pool of 7 (1 utricle and 3 ampullae) at E14.5 Source GEO sample is GSM182606 Last updated (according to GEO): Aug 14 2007 Liver 1000 olfactory epithelium 194 213 PGA-lv_48h_519 total RNA derived from a leprosy lesion Source GEO sample is GSM6768 Last updated (according to GEO): May 27 2005 25 0 Lymph Node [JunctionChip 3 Resting Source GEO sample is GSM176001 Last updated (according to GEO): Apr 09 2007 Nd4: Hippocampus_5T-AU_rep7 such as the cochlea 313 332 901 Nervous system structure 861 Neoplasm Blood 1000 PriG_5%O2_Expt3_Day7_rep1 5 0 brain Gene expression data from postmorten brain regions Source GEO sample is GSM144991 Last updated (according to GEO): Nov 20 2006 17 0 Trigeminal ganglia NH 65h Communicable Diseases 1000 GSE56 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 0.25 hours after lights on. Original RNA code = LC37A. Source GEO sample is GSM227359 Last updated (according to GEO): Sep 10 2007 Utricle structure 861 1682 1657 in the contralateral knee pituitary Source GEO sample is GSM18862 Last updated (according to GEO): Sep 25 2006 GSE3634 PGA-E18.5_1A golub-leukemia C6SPGFPfast1 Pool Ts1Cje_P30_hyb2 Brain 861 from subcutaneous adipose tissue 25 56 Parkinson Disease 861 Utricle structure 1000 Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles. PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity. Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence. To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips. Source GEO sample is GSM136513 Last updated (according to GEO): Jun 05 2007 L_D2_Control_ZT 6_1 Parkinson Disease 1000 Arteries 861 DNA-EP-3W 43h-DMSO replication 1 Parkinson's model voxel D4 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with 2-Methyl-thio-ATP labeled with Cy5- time course with repeats. Date GSE370 Last Updated: May 29 2005 Contributers: Zhen Yan Robert Hsueh Angela Alexander Rebecca Hart Joella Grossoehme Sun Young Lee Sangdun Choi Yun Anna Cao Mi Sook Chang Jong-Woo Kim Includes GDS291. Update date: Nov 18 2003. Dataset description GDS291: Temporal analysis of effects induced by 100 uM 2-methyl-thio-ATP in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. Coronary heart disease 913 1000 Spleen with myocardial infarction 313 339 skin disorder 913 wt mouse number 3 Source GEO sample is GSM186711 Last updated (according to GEO): Jun 11 2007 of Parkinson's disease 450 471 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 7515 left_liver_lobe This is the mutant littermate at postnatal day 5 pooled 4 animals Lot batch = Source GEO sample is GSM4081 Last updated (according to GEO): May 28 2005 D_U133Plus_36_Amy Prostate carcinoma 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with 2-Methyl-thio-ATP for 120min Source GEO sample is GSM5427 Last updated (according to GEO): May 27 2005 ND015 1000 Cerebral cortex Starvation 916 1100 1087 heart failure Lymphoblastoid Cell Line for Individual 8083.3 log phase 1000 Prostate Pancreas at e13.5, Chip B, rep 2 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47539 Last updated (according to GEO): May 29 2005 GSE280 embryo_at_day1.5_rep1 DIF 3, chip MOE430A 913 Coronary heart disease brain, hippocampus: LH7_e1_le1 from liver 21 30 septum no access to cocaine replicate 2 Gene expression data from postmorten brain regions Source GEO sample is GSM145427 Last updated (according to GEO): Nov 20 2006 0 cortex 5 1000 Lung 667 643 on primary breast tumours total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Anti-IgM for 120min Source GEO sample is GSM5447 Last updated (according to GEO): May 27 2005 Ovarian_Tumor_Serous_KU-OS-022 stria terminalis 1000 901 Bone Marrow Skeletal bone 861 Renal Cell Carcinoma - Papillary types 1, and 2b, Normal Kidney Tissue 1000 Coronary Arteriosclerosis 1000 Cerebellum LDMTX_MP-DX-10 another 26 year old male thymus sprague2 861 HIV Infections brain, Superior Frontal Gyrus: Sample61_e1_le1 in the mammalian nervous system 110 141 R424P00100 1000 Brain 861 Pituitary Gland Medulla Oblongata 861 Timepoint6r 901 Bone Marrow 901 Nervous system structure frontal lobe 1000 Tumor__Leukemia_ALL-T_ALL_(22474)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene Signature for Aggression of Melanoma Metastases - Melanoma Metastasis (LeiFidler) Female 67.3 yr before antibody enrichment scan 1 (U133B) Retina 861 gene expression of 1 day LIF differentiated ESCs Source GEO sample is GSM181943 Last updated (according to GEO): Apr 12 2007 1000 Spinal Cord 923 Extracellular Matrix of mouse brain 9 23 Neurites 861 This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques P. Tremblay (jacques-p.tremblay@crchul.ulaval.ca; 2705 boulevard Laurier) for analysis. Stembase Experiment ID: E205 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205 SCGP Sample ID: S270 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=205#SAMPLE_247 Short description: Cells from sphere were incubated in a differentiation medium. They differentiated into neurons after 7 days in culture. Analysis requested: mouse genechips RNA concentration: 0.689 ug/uL Sample volume: 15 uL total Source GEO sample is GSM93614 Last updated (according to GEO): Jan 23 2006 C3H/HeJ bed nucleus of the stria terminalis rep1 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132526 Last updated (according to GEO): Feb 26 2007 Spleen vs CGS Treated B cell 60min (set1) 25 0 frontal cortex wistar 3662 Keywords = Infectious diseases 1133 1163 Alternative pre-mRNA splicing increases proteomic diversity and provides a potential mechanism underlying both phenotypic diversity and susceptibility to genetic disorders in human populations. To investigate the variation in splicing among humans on a genome-wide scale, we use a comprehensive exon-targeted microarray to examine alternative splicing in lymphoblastoid cell lines (LCLs) derived from the CEPH HapMap population. We show the identification of transcripts containing sequence verified exon skipping, intron retention, and cryptic splice site usage that are specific between individuals. A number of novel alternative splicing events with no previous annotations in either the RefSeq and EST databases were identified, indicating that we are able to discover de novo splicing events. Using family-based linkage analysis, we demonstrate Mendelian inheritance and segregation of specific splice isoforms with regulatory haplotypes for three genes: OAS1, CAST, and CRTAP. Allelic association was further used to identify individual SNPs or regulatory haplotype blocks linked to the alternative splicing event, taking advantage of the high-resolution genotype information from the CEPH HapMap population. In one candidate, we identified a regulatory polymorphism that disrupts a 5' splice site of an exon in the CAST gene, resulting in its exclusion in the mutant allele. This report illustrates that our approach can detect both annotated and novel alternatively spliced variants, and that such variation among individuals is heritable and genetically controlled. The nose 94 101 f2#172 versus pool Mouse Brain tissue 376 368 of brains Cerebellar Vermis AB Normal 27 0 Substantia nigra normal rep7 A HID U D089 39 21 from mammary glands Gene expression data from postmorten brain regions Source GEO sample is GSM145998 Last updated (according to GEO): Nov 20 2006 89 68 with tricuspid valves 121 102 in neurite outgrowth na Source GEO sample is GSM181303 Last updated (according to GEO): Apr 10 2007 1BJZ02022219_leukemiapromyelocytic(hl60) plasma cells 332 344 none Source GEO sample is GSM239883 Last updated (according to GEO): Dec 07 2007 Amyotrophic Lateral Sclerosis 1000 43 29 from the kidney 9 0 Blood Test A detailed description of this cell lines and the infection with prions, can be found in Schätzl et al., 1997. By single cell cloning consecutive subclones of ScGT1 cells were prepared. RNA was isolated from control and infected cell lines by the Trizol method. 20µg total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 30µl hybridisation buffer (6x SSC, 0,5% SDS 5 fold Denhardt's solution and 50% formamide) and mixed with 30µl of reference cDNA solution labelled with the second dye. This hybridisation mixture was placed on a pre hybriddised microarray, covered with cover slip, placed into a hybridisation chamber (Genomatix) and immersed in a thermostatic bath at 42°C for at least 16 hours. Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Maen intensities with substracted background were normalised so that the median of their rations has became 1 Keywords = prion Keywords = hypothalamus Keywords = GT1 Source GEO sample is GSM31112 Last updated (according to GEO): Oct 28 2005 Simple annotation: Reference verification, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10000.gif Source GEO sample is GSM78470 Last updated (according to GEO): Sep 22 2006 in blood 16 23 Exp A_4, 50mg/kg CPF Gene expression data of substantia nigra from postmortem brain of normal controls Source GEO sample is GSM184357 Last updated (according to GEO): May 29 2007 408 401 of axons Cell surface 861 Brain 1000 7 0 prostate 1000 Neck Utricle structure 1000 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 19 day time point Source GEO sample is GSM159800 Last updated (according to GEO): Apr 23 2007 PGA-MCR-CR-4h-1bAv2-s1 901 Malignant neoplasm of breast Basal Ganglia 1000 100339 195 180 atherosclerosis 861 Pancreas of primary fibroblasts 106 127 1255 1233 from other chromosomes 15 7 hindbrain Cerebral cortex 861 f2#36 versus pool Mouse Brain tissue Parkinson Disease 1000 umbilical cord_bpd: 9C 1094 1083 hair shafts Abdominal Aortic Aneurysm Female Pool CNS-SC_InjA24h-3B-s2 MP-6 HapMap CHB Female Source GEO sample is GSM159596 Last updated (according to GEO): Feb 01 2007 KT86_AR1 476_4d 1000 Spleen 1000 Heart failure no doxycycline, mutant Source GEO sample is GSM213387 Last updated (according to GEO): Jul 26 2007 10 7 Left spinalcord Source GEO sample is GSM18785 Last updated (according to GEO): Sep 25 2006 GM19201 Sprague-Dawley Male LowSalt Cortex rat709 sd_cortexr_k_709c_020802 Heart 1000 tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44879 Last updated (according to GEO): May 27 2005 in endothelial cells 1479 1498 Male Sprague-Dawley rats (400Ã?±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 8h after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44532 Last updated (according to GEO): Oct 28 2005 Hereditary Nonpolyposis Colorectal Neoplasms 947 Rats 240h after injection with dose kainate. Treatment, type=time_course, description=KA animals are treated with kainate., measurement=240.0 h Source GEO sample is GSM32095 Last updated (according to GEO): May 27 2005 hg_NY29 M_U133A_2_CB The epithelial cells 962 981 Nasal Epithelium Inhalation Formaldehyde 0ppm 24h ID57 40 21 from skeletal muscle Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16025.gif Source GEO sample is GSM91612 Last updated (according to GEO): Sep 22 2006 250 238 in the brains Primary tumor 19 32 n/a Source GEO sample is GSM177910 Last updated (according to GEO): Jun 11 2007 Congenital Abnormality 853 Female 66.6 yr after antibody enrichment scan 2 (U133B) Pancreas at e16.5, Chip C, rep 1 1000 Parietal Lobe Interatrial septum 865 1BJZ02022112_fetalbrain /2J pituitary gland rep2 3 26 connective tissue 1340 1357 Lda4 Ovarian_Tumor_Serous_CHTN-OS-072 Subject code A12 Arteries 861 DLCL-0020 brain, unknown: 00FA_e1_le1 Macrophage 14smi090 Normal Source GEO sample is GSM176125 Last updated (according to GEO): Apr 09 2007 experiment II LXSN replicate 2 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs//7254.gif Source GEO sample is GSM79922 Last updated (according to GEO): Sep 22 2006 spinal cord, ventral spinal cord: D60SODSP3_e1_le1 Neurodegenerative Disorders 901 Voxel E3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1418 Last updated (according to GEO): Nov 21 2005 MDA Mb231 1h 2 Control Gene expression data from postmorten brain regions Source GEO sample is GSM145150 Last updated (according to GEO): Nov 20 2006 PGA-swim_4w1w_s1124 Epithelium 861 4 0 Liver Control gray matter 2 Nrl ko samples were compared to wt at 2 months. Source GEO sample is GSM227467 Last updated (according to GEO): Sep 07 2007 none Source GEO sample is GSM246004 Last updated (according to GEO): Dec 03 2007 of the entorhinal cortex 1473 1496 Epithelium 861 560 528 epithelial ovarian adenocarcinoma Alzheimer's Disease 1000 694 679 then cerebellum Myocardium 861 1000 Cerebellum Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68274 Last updated (according to GEO): Jul 07 2006 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201261 Last updated (according to GEO): Jun 14 2007 7 cerebral cortex 21 CC237 Muscle 861 Frontal Cortex Source GEO sample is GSM107940 Last updated (according to GEO): Jun 06 2006 whole brain from wild-type littermate of nicotinic acetylcholine receptor subunit mutant mice Source GEO sample is GSM120576 Last updated (according to GEO): Sep 22 2006 Brain 861 Secondary malignant neoplasm of lung 901 Brain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145968 Last updated (according to GEO): Nov 20 2006 CNS-SpinalC-28dAdult-3A-s2 5 0 brain 1000 Brain 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113904 Last updated (according to GEO): Jun 16 2006 Ta gr2 tumour Source GEO sample is GSM2498 Last updated (according to GEO): May 27 2005 8 uterine horns 335 349 from colonic normal mucosa 21 47 prostate Source GEO sample is GSM203351 Last updated (according to GEO): Jun 21 2007 Normal Source GEO sample is GSM176276 Last updated (according to GEO): Apr 09 2007 Heart failure_LVAD_5 Myocardium 861 Utricle structure 1000 GSE755 R744P00748 from adult brain 686 701 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b101 Source GEO sample is GSM1988 Last updated (according to GEO): Nov 21 2005 Wild type inbred mice Source GEO sample is GSM82920 Last updated (according to GEO): Nov 10 2005 1000 Coronary Arteriosclerosis Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68267 Last updated (according to GEO): Jul 07 2006 GSE9391 Brain 861 ovarian tumor: endometrioid Source GEO sample is GSM139400 Last updated (according to GEO): Apr 09 2007 1000 Descending colon Posterior root of spinal nerve 861 861 Cerebral cortex This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis. Stembase Experiment ID: E189 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189 SCGP Sample ID: S231 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_189 Short description: RNA isolated from first passage retinal sphere cells. Estimated purity: > 90% RNA concentration: > 30.0 ng Num cells for RNA prep: ~160,000 Sample volume: 5.0 ul Source GEO sample is GSM87192 Last updated (according to GEO): Jan 19 2006 5 0 brain Brain 861 Arsenic-induced changes in gene expression in the neural tube of Folr2-/- KO mouse embryos 73 54 of hyperinsulinaemic tonsil_5 Source GEO sample is GSM80901 Last updated (according to GEO): Mar 31 2006 1000 Spleen KO-Nrf2-Male-2 wild-type mouse 2 Autistic Disorder 877 7 cerebral cortex 21 Stromal sarcoma 901 CD8+ T Lymphocytes_Healthy donor 3 HLA-matched Time 35_replicate 2 from liver 21 30 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113975 Last updated (according to GEO): Jun 16 2006 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228662 Last updated (according to GEO): Sep 11 2007 of infected skin 33 48 Dorsal Raphe Source GEO sample is GSM107967 Last updated (according to GEO): Jun 06 2006 NA19000 Gene expression data from postmorten brain regions Source GEO sample is GSM145696 Last updated (according to GEO): Nov 20 2006 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15714 Last updated (according to GEO): May 28 2005 Muscle 861 Leukemia, Lymphocytic, Chronic 884 Rat frontal cortex RNA - VH TTX Experiment Source GEO sample is GSM92301 Last updated (according to GEO): Jan 13 2006 I_U133A_33_CB 1000 Lung Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:285, Count:32 Corner- Avg:38232, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:14.069105,SFGene:All Background:Avg:538.48,Stdev:11.89,Max:554.2,Min:504.1 Noise:Avg:8.86,Stdev:0.20,Max:9.3,Min:8.2 RawQ:14.62 Keywords = ALL Source GEO sample is GSM3423 Last updated (according to GEO): May 27 2005 00291005H95A2-T01047v2p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A "Sample 61, <5 yr survival(32 months) age 38 erp yes" on vantveer-oligo 14 0 pineal sprague2 nostrils 156 164 gene expression data from ODC mouse skin samples Source GEO sample is GSM216659 Last updated (according to GEO): Aug 09 2007 To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132984 Last updated (according to GEO): Sep 12 2006 660 mesenchymal stem cell 639 1000 Trauma Prosencephalon 861 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225701 Last updated (according to GEO): Nov 05 2007 1000 Kidney Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 10 hours after lights on. Original RNA code = LC25A. Source GEO sample is GSM227360 Last updated (according to GEO): Sep 10 2007 146 133 from the liver 1000 Brain 1000 Liver 715 705 from livers 861 Cerebral cortex Coronary heart disease 913 brain 0 5 gene expression of 5 day LIF differentiated ESCs Source GEO sample is GSM181958 Last updated (according to GEO): Apr 12 2007 1000 Impaired cognition The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159961 Last updated (according to GEO): Feb 01 2007 High Fat Mouse 3 19 0 Head and neck cancer NA12004 Homozygous O377 mutant mouse line versus wildtype mice Source GEO sample is GSM86290 Last updated (according to GEO): Dec 08 2005 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15468.gif Source GEO sample is GSM84175 Last updated (according to GEO): Sep 22 2006 Brain 861 853 Blood Cells 861 Cerebral cortex Abdominal aortic aneurysm obtained from surgery to correct. Source GEO sample is GSM170554 Last updated (according to GEO): Jul 26 2007 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188756 Last updated (according to GEO): Jun 06 2007 Expression profiling of spinal cord section (T9) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31255 Last updated (according to GEO): May 27 2005 Gene expression data from colorectal adenoma. Source GEO sample is GSM215087 Last updated (according to GEO): Aug 02 2007 861 Blood Expression profiling of spinal cord section (T9) extracted from rats 14d following severe injury Source GEO sample is GSM31613 Last updated (according to GEO): May 27 2005 410_1 (cortex 19 25 Carcinoma, Large Cell 1000 CNS-RM_Mod24h-4A-s2 Spinal cord injury 9 26 0029_1426_H95A2_T96-167_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A DBA:2-1-2 perirhinal cortex 861 HIV Infections "Sample 35,>5 yr survival(125 months) age 54 erp yes" on vantveer-oligo H113 FC BA4 B Wild type 8 wk old male 129S6/SvEvTac mouse periaqueductal gray Source GEO sample is GSM74986 Last updated (according to GEO): Feb 27 2007 Exp B_4, 0.5mg/kg CPF of the normal mucosa 7 26 Coronary Arteriosclerosis 1000 SWR/J CHR, Rep2 Hereditary Nonpolyposis Colorectal Neoplasms 947 Neoplasm 861 3619 3606 in hippocampus Replicate 2 of 3 (same genotype, same age). All replicates were individual animals. Source GEO sample is GSM138272 Last updated (according to GEO): Sep 29 2006 913 Blood Cells Chromosomes 861 of foreskin fibroblasts 95 117 861 Colon Epithelium 865 Heart 1000 A/OVX/P4/1h/UTX 129/SvImJ WT Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203970 Last updated (according to GEO): Aug 02 2007 Blood 1000 127 114 from asthmatic ADR-RES_CL5002_UNKNOWN bronchial epithelia 224 243 Muscular Dystrophy, Duchenne 913 cardiac 746 752 Intermediolateral column, medial, and lateral motoneurons serotonin 1334 1343 f2#148 versus pool Mouse Brain tissue JMR-Sham21d-2aA-s2 n/a Source GEO sample is GSM177985 Last updated (according to GEO): Jun 11 2007 B10.PL mice with experimental autoimmune encephalomyelitis (MS model) were treated with either placebo or 200 ng 1,25(OH)2D3. Six hours later, the spinal cords were harvested and mRNA extracted for analysis. Naive mice served as controls. Keywords = Experimental autoimmune encephalomyelitis Keywords = multiple sclerosis Keywords = 1 Keywords = 25(OH)2D3 Source GEO sample is GSM13049 Last updated (according to GEO): May 28 2005 Female 71.4 yr after antibody enrichment scan 2 (U133B) GM19202 861 Hormones Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.94 Subject: 1905 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM38999 Last updated (according to GEO): May 27 2005 prostate Source GEO sample is GSM203331 Last updated (according to GEO): Jun 21 2007 PMN_LB_180min_Patient6 Gene expression data from postmorten brain regions Source GEO sample is GSM145351 Last updated (according to GEO): Nov 20 2006 84 74 in melanoma Neurosphere cultures were established from individually isolated E 14.5 forebrains of mouse embryos that carry a bcl2 transgene. Single-cell suspensions were prepared, seeded at 1x105 cells/ml and treated for two days with 150 nM Trichostatin A (TSA), 500 nM 5-Aza-2?-deoxycytidine (AzaC) or both compounds, or left untreated. Two independent experiments were performed. Source GEO sample is GSM8897 Last updated (according to GEO): Oct 28 2005 plasma cells 50 61 865 Disorder of artery Expression profiling of spinal cord section (T9) extracted from rats 72h following moderate injury Source GEO sample is GSM31583 Last updated (according to GEO): May 27 2005 Dioxin treated MCF7 breast cancer cells [HG-U133B] Exp 3 Normal epithelial cells were removed by dissection and digestion from bronchi of donor long tissue from normal subject. Source GEO sample is GSM3915 Last updated (according to GEO): May 27 2005 2500mg/kg APAP 6Hr rat 3595 blood vs. PC 6Hr rat 3586 blood Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD1 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD1 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36708 Last updated (according to GEO): May 27 2005 Primary Neoplasm 1000 onto a collagen 72 86 1000 Infection Skeletal bone 861 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184718 Last updated (according to GEO): Apr 26 2007 15 0 human cerebellum Gene expression data from rat lungs exposed to FiO2 of ~9.5%, SU5416, and Sorafenib (hypoxia-SU5416-Sorafenib). Source GEO sample is GSM201493 Last updated (according to GEO): Jun 14 2007 metanephric mesenchyme, LIF, 7 days, biological rep2 Heart Ventricle 1000 cerebral cortex 7 21 Low Freezing Source GEO sample is GSM92413 Last updated (according to GEO): Jan 13 2006 Occipital lobe 861 Blood 1000 brain, cochlea: [14] Sample #14_le1 6624_Lung did not develop PGD mouse brain contralateral LPS.RU486 Source GEO sample is GSM149762 Last updated (according to GEO): Mar 15 2007 15 7 brainstem of the stria terminalis rep2 21 48 Brain 1000 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181126 Last updated (according to GEO): Jul 12 2007 58 50 Eye C57BL 660 mesenchymal stem cell 639 861 Chromosomes Expression profiling of spinal cord section (T8) extracted from rats 14d following severe injury Source GEO sample is GSM31460 Last updated (according to GEO): May 27 2005 rad001 48h, biological rep1 861 Heart 861 Blood Prosencephalon 1000 1000 Leprosy none Source GEO sample is GSM246018 Last updated (according to GEO): Dec 03 2007 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15733 Last updated (according to GEO): May 28 2005 1000 Infection 861 Muscle Neoplasm Metastasis 947 PGA-HBE-Ctr-1aA-S2 from the right forebrain 21 44 Normal Source GEO sample is GSM175840 Last updated (according to GEO): Apr 09 2007 Heart 861 Heart 1000 7 0 Pancreas brain, cerebral cortex: NMDA10 5/7_le1 Wild type inbred mice Source GEO sample is GSM82913 Last updated (according to GEO): Nov 10 2005 165 155 of retinal none Source GEO sample is GSM210338 Last updated (according to GEO): Jul 16 2007 Wild type P104 mouse visual cortex ipsilateral to monocular enucleation Source GEO sample is GSM97223 Last updated (according to GEO): Feb 17 2006 491 477 to these tumors brain, unknown: 04JZ_e1_le1 of the olfactory bulbs 139 161 cerebral cortex 7 21 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201239 Last updated (according to GEO): Jun 14 2007 GBM Treatment, type=remove Source GEO sample is GSM99481 Last updated (according to GEO): Apr 21 2006 entorhinal cortex layer II stellate island cells Source GEO sample is GSM107534 Last updated (according to GEO): May 01 2006 Expression profiling of spinal cord section (T9) extracted from rats 28d following mild injury Source GEO sample is GSM31226 Last updated (according to GEO): May 27 2005 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114415 Last updated (according to GEO): Jun 16 2006 1000 Gelsolin /3T3 fibroblasts 478 493 129 109 of neurotransmitters Colon 1000 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155043 Last updated (according to GEO): Jun 04 2007 Intestines, Small 1000 Neostriatum 1000 CNS-RM_Ctr14d-2B-s2 hrs nasal epithelium 1126 1146 from liver 24 33 Aspartic Acid Conjugated Surface 32 hours Kidney 1000 5 0 brain Gene expression data from postmorten brain regions Source GEO sample is GSM145007 Last updated (according to GEO): Nov 20 2006 fetal lung fibroblast #3, asynchronous Lymphoblastoid Cell Line for Individual 8151.3 log phase 861 Blood Congenital Abnormality 1000 Cerebral cortex 861 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide Source GEO sample is GSM225349 Last updated (according to GEO): Aug 31 2007 Lymphoblastoid Cell Line for Individual 8055.4 log phase outer medulla 31 43 1000 Communicable Diseases from liver 21 30 861 Cancer of Neck 1000 Coronary Arteriosclerosis 1000 Brain 901 Mammary gland Epithelial Cells 901 M_U133A_26_AnCg 875 Cerebellar Diseases Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200625 Last updated (according to GEO): Jun 12 2007 Type 1 Diabetes patient and the timepoint 4 months after diagnosis. Source GEO sample is GSM228644 Last updated (according to GEO): Sep 11 2007 1000 Impaired cognition Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18934.gif Source GEO sample is GSM84137 Last updated (according to GEO): Sep 22 2006 of the stria terminalis 50 72 861 Asphyxia Liver Test (Blinded) Sample Source GEO sample is GSM130109 Last updated (according to GEO): Sep 18 2007 Nasal Epithelium Inhalation Formaldehyde 07ppm 24h ID133 Spinal Cord 1000 I_U133A_114_AnCg Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.86 Subject: 2822 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39019 Last updated (according to GEO): May 27 2005 DBA/2J Chronic morphine treated, striatum, biological replicate 2 Source GEO sample is GSM187990 Last updated (according to GEO): Jun 14 2007 mouse cerebral cortex, cox-2 WT, rep1 1000 Muscle Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11323 Last updated (according to GEO): May 28 2005 Female 65.9 yr after antibody enrichment scan 2 (U133B) Muscle Source GEO sample is GSM4295 Last updated (according to GEO): May 27 2005 Malignant Neoplasms 861 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181049 Last updated (according to GEO): Jul 12 2007 861 Cerebral cortex Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198624 Last updated (according to GEO): Jun 06 2007 with neoplastic disease 87 110 Gene expression data from rat metanephric mesenchymes cultured for 1 day in the absence of inducers Source GEO sample is GSM126190 Last updated (according to GEO): Dec 08 2006 105 80 of the ventral hippocampus Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2815 Source GEO sample is GSM2126 Last updated (according to GEO): Nov 21 2005 1000 Liver umbilical cord_bpd: 3E Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13422.gif Source GEO sample is GSM79659 Last updated (according to GEO): Sep 22 2006 main olfactory epithelium Source GEO sample is GSM18648 Last updated (according to GEO): May 27 2005 GSE952 1BRS02080874b_globus_pallidus G30 neurons from somatosensory cortex Source GEO sample is GSM63029 Last updated (according to GEO): Dec 01 2005 cerebellum sprague 3898 PGA-Pi3k_ca_2817v2 91 from the bone marrow 72 913 Myeloid Leukemia H9LMS00111505 with some respiratory epithelium. 1039 1072 1000 Globus Pallidus 0 Human Cortex 11 1000 Diabetes Mellitus MSE_D_678 Muscle 861 CNS-SC_CtrB30m-2bA-s2 OVAR_SKOV3 on Affymetrix GeneChip Human Full Length Array HuGeneFL NL-1698-A410-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11742.gif Source GEO sample is GSM76422 Last updated (according to GEO): Sep 22 2006 I_U133A_22_AnCg 861 Trachea 861 Ganglia, Sensory Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9863.gif Source GEO sample is GSM79915 Last updated (according to GEO): Sep 22 2006 Small cell carcinoma of lung 867 1000 Amygdaloid structure 201 174 at the longitudinal fissure R567P00147 at the Human Brain 746 763 I_95Av2_2822_Cg_1_GS 5 0 Muscle 1000 frontal lobe 1000 Communicable Diseases A HID U D018 1000 frontal lobe human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195340 Last updated (according to GEO): Jun 04 2007 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13147.gif Source GEO sample is GSM79688 Last updated (according to GEO): Sep 22 2006 brain 0 5 Muscular Dystrophy, Duchenne 1000 D_U133Plus_125_DLPFC Small cell carcinoma of lung 901 human frontal cortex Source GEO sample is GSM87042 Last updated (according to GEO): Feb 08 2006 67 40 with coronary artery disease 7 cerebral cortex 21 Standard affymetrix protocol Source GEO sample is GSM119725 Last updated (according to GEO): Jul 31 2007 brain, hippocampus: PR-CA1-9_e1_le1 1000 Cardiomyopathy, Alcoholic NA12751 growth 1, replicate 1 Normal Source GEO sample is GSM176135 Last updated (according to GEO): Apr 09 2007 Fluid-percussion head injury 83 110 13 7 cochlea Infection 861 Skeletal bone 861 Breast 1000 5 0 brain Hyperdip>50-C6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from hippocampus of one old SAMP8/Ta mouse Source GEO sample is GSM143752 Last updated (according to GEO): Jan 24 2007 Nose 1000 BL-C-TEST-18 on NHGRI-6.5k_b Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35372 Last updated (according to GEO): May 27 2005 344 328 Neurite outgrowth 861 Neoplasm Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162173 Last updated (according to GEO): Jun 12 2007 GSE4036 87 66 of the human skeleton 901 Muscular Dystrophies 69-96_Adeno PrefrontalCortex Source GEO sample is GSM18770 Last updated (according to GEO): Sep 25 2006 Mice sacrificed after swimming twice a day for 2 weeks. Keywords = exercise induced hypertrophy Source GEO sample is GSM2354 Last updated (according to GEO): May 27 2005 Category: Cell-line Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc69 Source GEO sample is GSM1875 Last updated (according to GEO): Nov 21 2005 5 0 Kidney Disorder of artery 865 15 0 human cerebellum GSE492 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188751 Last updated (according to GEO): Jun 06 2007 4535 4527 hepatoma Posterior root of spinal nerve 861 Bipolar Disorder 1000 30 0 ventral tegmental area sprague1 861 Brain Mouse old heart w/ a- & g-tocopherol agT-Ht-1 Epithelium 861 Nasal Epithelium Inhalation Formaldehyde 2ppm 6h ID206 D1_TP-12_I 861 Muscle 7 0 prostate 1100 1077 of Medulloblastoma - 8 - from SVG-A glial cells 21 43 Bone Marrow 1000 Voxel I3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1449 Last updated (according to GEO): Nov 21 2005 Mid secretory endometrium from normal patient Source GEO sample is GSM150223 Last updated (according to GEO): Dec 14 2006 into the damaged brain 2027 2049 amygdala_10 Source GEO sample is GSM80593 Last updated (according to GEO): Mar 31 2006 no additional Source GEO sample is GSM199125 Last updated (according to GEO): Jun 08 2007 Starvation 916 Mouse Kidney Female 3 (technical replicate) 901 Colon Richard Almon-25-1133800609542 25 7 Right Temporal Lobe Saline ip LPAM ILI 4hrs post ILI Cochlear structure 1000 Brain 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11275 Last updated (according to GEO): May 28 2005 A2780_cis_IC50_16h_2 from ventral prostate 21 41 heart 119 124 Gene expression data from postmorten brain regions Source GEO sample is GSM145039 Last updated (according to GEO): Nov 20 2006 Breast Carcinoma 983 1000 Impaired cognition Normal Source GEO sample is GSM176094 Last updated (according to GEO): Apr 09 2007 ovary_10 144 114 from a single adult spinal cord Nervous system structure 901 861 Heart 5 0 brain Hippocampus Source GEO sample is GSM53373 Last updated (according to GEO): Jul 06 2005 in each brain region. 1952 1973 Nose 1000 starved 27 33 brain, cerebral cortex: Rat_03-47_NroLep_Lipska_e1_le1 435 419 of the infection TUMOR 31 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A on muscle fibres 1413 1428 B2-16 on NCI-7.6k UET-13TR-EWS/FLI1 72hr tet+ Cortex_Control_rep6 (05SE1760) Gene expression of modiolus of newborn rats_cultivation_normoxia_repeat 1 inner ear kidney 37 43 Spleen 0 5 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114180 Last updated (according to GEO): Jun 16 2006 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114175 Last updated (according to GEO): Jun 16 2006 skeletal_muscle_4 Source GEO sample is GSM80792 Last updated (according to GEO): Mar 31 2006 collagen 301 309 MDA Mb231 6h 6 Control Fetal brains were obtained from 3 pregnant rats at pregnant day 17. Primary cortical neurons were isolated and pooled separately from each mother and plated onto 100mm ´ dishes, for a total of 4 plates from each pregnant rat. At Day in Vitro (DIV) 16, 3 of the 4 platesfrom the same mother, were exposed to either 1 or 3 MAC halothane (about 1% or 3%) or 3 MAC isoflurane (about 4%) in a gas tight chamber inside the culture incubator for 6 hr. The 4th plate from each mother treated with air were used (inside the same incubator, but outside the chamber) as controls. Isoflurane at 1 MAC was not conducted because of the complete lack of transcriptional response in the animals exposed to 1 MAC of isoflurane. The cells were recovered for an additional 6 hr, harvested, frozen by liquid nitrogen, and stored at ?80oC. Source GEO sample is GSM61779 Last updated (according to GEO): Oct 28 2005 Blood 1000 341 319 of primary glioblastoma 0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point, biological rep 4 Anxiety Disorders 901 Liver 1000 Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589?595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164?169.) Source GEO sample is GSM159482 Last updated (according to GEO): Jun 21 2007 Utricle and 3 ampullae at E14.5, replicate1 Skeletal bone 861 254 238 of neural retinas 5 0 brain brain, Left Parietal Lobe: Extract40_le1 861 Cancer of Neck Transplant Series 25 Right, Transplant # 5 216 Ganglia 210 Autistic Disorder 1000 335 325 The jejunum 1000 Modiolus anguli oris Standard Affymetrix Protocol Keywords = microarray Keywords = muscle Source GEO sample is GSM15939 Last updated (according to GEO): May 28 2005 1000 Structure of postcentral gyrus Parkinson's model voxel F1 E10.5 craniofacial tissue, first branchial arch: WT_MNA-3_e1_le1 T2+ gr ? tumour Source GEO sample is GSM2505 Last updated (according to GEO): May 27 2005 brain, cerebral cortex: Rat_03-25_NroLep_Lipska_e1_le1 1000 Spinal Cord 861 Nerve 861 Colon GC (HKG95N) rat cortex Treatment, type=time_course, measurement=7.0 d Source GEO sample is GSM53213 Last updated (according to GEO): Jul 06 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68247 Last updated (according to GEO): Jul 07 2006 Skeletal bone 861 Spleen vs CD27 Treated B cell 120min (set3) Replicate1_Voxel E11 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16211.gif Source GEO sample is GSM84134 Last updated (according to GEO): Sep 22 2006 Communicable Diseases 1000 Communicable Diseases 1000 GM18517 Infection 1000 1000 Encephalitis Tumor__Uterus_Adeno_2552 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene expression data from postmorten brain regions Source GEO sample is GSM145071 Last updated (according to GEO): Nov 20 2006 91 from the bone marrow 72 67 40 with coronary artery disease prostate Source GEO sample is GSM203378 Last updated (according to GEO): Jun 21 2007 NG007_b 320 291 of human oral epithelial cells 861 Malignant neoplasm of prostate Nose 1000 1000 Brain 15 0 human cerebellum dnEgr (dominant negative Egr)/EGFP infected SH-SY5Y/TrkA cells: infection (at t=-18 hours), NGF treatment (at t=0 hours), harvest for total RNA extraction (at t=3 hours). Replicate 3 Treatment, type=add Source GEO sample is GSM53383 Last updated (according to GEO): Jul 06 2005 long access to cocaine ,medial prefrontal cortex, 6 hrs/day access to cocaine Source GEO sample is GSM93874 Last updated (according to GEO): Jan 26 2006 Whole Brain 62 72 I_U133A_77_CB 5 0 brain Testis 861 KT78b_DT 1000 Brain 32h-AC replication 2 HMVEC-L stimulated with LPS for 24 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114561 Last updated (according to GEO): Sep 20 2006 Primary tumor 19 32 Brain 1000 Laser captured visceral sensory neurons. Source GEO sample is GSM63653 Last updated (according to GEO): Dec 21 2005 913 Coronary heart disease Coronary Arteriosclerosis 1000 human frontal cortex Source GEO sample is GSM87003 Last updated (according to GEO): Feb 08 2006 Male Sprague-Dawley rats (400Ã?±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 30min after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44473 Last updated (according to GEO): Oct 28 2005 1000 Rectum Epithelium of bronchus 983 216 200 of neural retinas 5 0 Spleen Ta gr2 tumour Source GEO sample is GSM2503 Last updated (according to GEO): May 27 2005 1502 1495 " tumors Molecular markers of early Parkinson's disease based on gene expression in blood. 901 frontal lobe Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141289 Last updated (according to GEO): Oct 26 2006 Brain 861 861 Cerebral cortex 1000 Hippocampus 70 40 without coronary artery disease Saccule structure 861 7 0 prostate 901 Bone Marrow short access to cocaine, amygdala, 1 hr/day access to cocaine Source GEO sample is GSM93829 Last updated (according to GEO): Jan 26 2006 from the right forebrain 21 44 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201274 Last updated (according to GEO): Jun 14 2007 Plasma 861 Arteries 861 KPeterson-Met-5box2-1G110-s2 5 0 brain 861 Cerebellum 901 frontal lobe 5 0 Spleen Primary Carcinoma 875 Gene expression data from whole brain infected mouse, day 3 Source GEO sample is GSM189644 Last updated (according to GEO): May 16 2007 5 0 Spleen leukemia 861 lg_NY11 Control total RNA was pooled from the kidney of five normal BALB/c mice. Total RNA was extracted from the kidney of BALB/c mice injected with anti-GBM antibody for 11 day. Source GEO sample is GSM15091 Last updated (according to GEO): May 28 2005 hippocampus: Sample #1_e1_le1 901 Coronary artery M_U133Plus_123_AnCg Kidney; Fetal Day 18.5 Keywords = mouse gene expression database Source GEO sample is GSM29363 Last updated (according to GEO): May 27 2005 Prosencephalon 861 of renin-angiotensin system 189 215 1000 Brain SN:Human Glioblastoma Biopsy 07082 262 diabetes 254 861 Nerve B220+CD25+sIg- Small Pre BII cells sorted out of mouse bone marrow, sort no. 8 Source GEO sample is GSM635 Last updated (according to GEO): Mar 17 2006 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5460.gif Source GEO sample is GSM93120 Last updated (according to GEO): Sep 22 2006 164 136 of the middle cerebral artery Blood Test (Blinded) Sample Source GEO sample is GSM129974 Last updated (according to GEO): Sep 18 2007 frontal cortex wistar 3658 whole tissue, individual animal, 10 weeks old, male Wistar frontal cortex file:p3658w Source GEO sample is GSM15117 Last updated (according to GEO): Oct 28 2005 Keywords = Heart 505 521 DR14d(3) 7 cerebral cortex 21 how tumor growth 1384 1399 255 234 with HIV encephalitis Nervous system structure 901 5 0 brain with Parkinson's disease 27 50 1000 Muscle 913 Coronary heart disease cortex Source GEO sample is GSM38978 Last updated (according to GEO): May 27 2005 19 0 human frontal cortex 901 lymph nodes 24 0 human prostate PC3 tumors DR48h(1) Obesity 0 6 Spinal Cord 1000 7 on NHGRI-13.8k 861 Lateral Sclerosis MCF7_CHX_E2_24h_rep3 NL-4083-A333-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1200 during bone remodeling 1178 Brain 861 C57BL/6J Basal Ganglia C 15 0 human cerebellum Carcinoma 861 Serum 16 3 hr Hela Double Thymidine, exp2 GM19100 1000 Seizures Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Source GEO sample is GSM15944 Last updated (according to GEO): May 28 2005 CNS-RM_CtrT0-2B-s2 861 Cerebral cortex Determination of gene expression changes in hindlimb muscle (gastrocnemius/soleus) of mdx (dystrophin-deficient) mice at postnatal ages 7, 14, 23, 28, 56, and 112.. Date GSE1025 Last Updated: May 29 2005 Contributers: JOhn D Porter Includes GDS639. Update date: Oct 05 2004. Dataset description GDS639: Temporal analysis of hindlimb gastrocnemius/soleus muscle from dystrophin-deficient mdx mice, a Duchenne muscular dystrophy (DMD) model. Postnatal ages 7 to 112 days examined. Results provide insight into mechanisms of muscular dystrophy pathogenesis.. Sample represents the supraoptic nucleus from 5 dehydrated animals (3 Days) Source GEO sample is GSM69459 Last updated (according to GEO): Dec 15 2005 Basal-like breast tumor cell line ME16C2 Keywords = Agilent microarray, Expression analysis, EGFR, Breast cancer growth Source GEO sample is GSM29516 Last updated (according to GEO): Dec 13 2006 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134639 Last updated (according to GEO): Jul 09 2007 Whole blood 0 10 S6_Muscle_Baseline_0min heart failure 583 595 Localized Malignant Neoplasm 853 31 21 spinal cord Hippocampus 1000 Primary tumor 19 32 1000 Brain Olfactory Epithelium 1000 607 597 the rectum 901 Bone Marrow brain, hindbrain and spinal cord: R0 aRNA Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198621 Last updated (according to GEO): Jun 06 2007 13 7 cochlea 144 114 from a single adult spinal cord human caudate nucleus Source GEO sample is GSM86905 Last updated (according to GEO): Feb 08 2006 Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging and comparing calorie restricted-fed 30-month-old to control-fed 30-month-old to investigate effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7458 Last updated (according to GEO): May 27 2005 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM79060 Last updated (according to GEO): Oct 24 2005 brain, cerebellum: Tg+/+_Crb3_e1_le1 Mouse Hypothalamus Male 1 Melanoma xenograft, MEA3_Lung_C (LeiFidler) ventral_tegmental_area_10 Control rats 240h after injection with PBS Treatment, type=time_course, description=Control animals are treated with PBS, measurement=240.0 h Source GEO sample is GSM32091 Last updated (according to GEO): May 27 2005 knockin mouse forebrain Treatment, type=time_course, measurement=4.0 weeks Source GEO sample is GSM53347 Last updated (according to GEO): Jul 06 2005 LCM oocytes_3wk ovary_FVB 1000 Parkinson Disease hPr1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Cortex_reserpine_treated_rep3 Nervous System; Fetal day 18.5 brain Keywords = mouse gene expression database Source GEO sample is GSM29417 Last updated (according to GEO): May 27 2005 11954 on TGRI-6.5k Heart 861 1000 Skeletal muscle structure 861 Blood CNS-SC_CtrAT0-2B-s2 Medulla 861 Nose 1000 39 21 of substantia nigra 20 0 human caudate nucleus Blood 861 5 0 Spleen heart failure 583 595 Myotubes 149 156 Amygdala Source GEO sample is GSM107913 Last updated (according to GEO): Jun 06 2006 858 Prostatic Neoplasms 114 101 brains quickly Medulla 861 Lymphoblastoid Cell Line for Individual 8190.5 log phase 320 306 Keywords = HIV proteoglycans 548 561 CNS-SpinalCmod-Adult-24h-4B-s2 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188691 Last updated (according to GEO): Jun 06 2007 1BJZ02061909_pituitary 5 0 brain Gene expression data from postmorten brain regions Source GEO sample is GSM145876 Last updated (according to GEO): Nov 20 2006 Ganglia, Spinal 923 19 0 The left hippocampus Heart 861 861 Oocytes Blood 1000 3rd 6hr C-DG 913 Acute leukemia liver_wildtype_WY14643_5d_rep3 Heart Ventricle 1000 983 Structure of horn of uterus 861 Colon with myocardial infarction 313 339 19 0 Head and neck cancer Heart failure 1000 Infection 861 JMR-MurSham24h-1dAv2-s2 Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. LDMTX_MP-DX-9 WGACON-148 A39 NES 142Q TG5 F1/2 A39 NES Htt exon 1 142Q Mouse 10.5 months Cerebellum Male Source GEO sample is GSM73187 Last updated (according to GEO): Sep 06 2005 1000 Hippocampus 861 Brain Cerebral cortex 861 1000 Prostate 861 Fibroid Tumor Brain 861 Expression profiling of human adult postmortem brain tissue from Down syndrome and healthy control subjects 293 270 in the spinal cord often 2334 2305 from wild type cerebral cortex Mouse Liver AIN Diet 8hr 1mg/kg Dex Injection, biological replicate D 20 0 human caudate nucleus 12 7 Cancer Animals were sacrificed and organs were rapidly frozen in liquid nitrogen, and subsequently stored at <ETH>80oC. Tissues were mechanically homogenized with a polytron and total cellular RNA was extracted using a commercially available reagent (TMTRIzol; Invitrogen). The poly-(A)+ fraction of the RNA was isolated by chromatography with oligo d(T) cellulose beads. For cDNA labeling, either 25 mg of total RNA or 2.5 mg of poly-(A) RNA was converted into cDNA using reverse transcriptase (RT; Super Script II, Invitrogen) and alternatively Cy5 or Cy3-labeled dCTP (1mM, Perkin Elmer-Cetus/NEN, Boston) in a reaction mixture containing 1.5 mL oligo (dT) (100pmol/ mL), 3 mL dNTP-dCTP (6.67mM each), 1 mL dCTP (2mM), 4 mL DTT (100mM), 8 mL 5 X RT Buffer (Invitrogen, California). The reactions were carried out at 42¼C for 3 hrs, after which the RNA was degraded by the addition of 0.5 mL RNase A (1 mg/mL) and 1.5 mL RNaseH 5 units/mL). Labeled cDNA was separated from unincorporated nucleotides (Qiagen column) and further concentrated by evaporation under vacuum. The arrays were pre-hybridized for 1-2hrs with DIGEasy hybridization buffer (Roche) containing 10ug/ml denatured salmon sperm DNA, and 10ug/ml yeast tRNA. The Cy5 and Cy3 labelled cDNAs were combined and hybridized in the same medium and incubated with the arrays for 16-18hrs at 37Co. Finally, the arrays were washed 3 x 10 mins in 0.1 x SSC (20 X SSC is 3M sodium chloride, 0.3 M sodium citrate, pH 7.0), 0.1%SDS at 50Co, and 4 x 3min in 0.1 x SSC at room temperature, and dried by centrifugation. Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray fluorescent scanner and image intensity data were extracted and analyzed with QuantArray 3.0 analysis software. Quantification data was imported in GeneSpring (Silicon Genetics). The import format was modified to maintain information relevant to user-contributed flagging as well as QC parameter furnished by the array manufacturer. Dye swap and Intensity-based normalization (Lowess) were performed using the default settings. Keywords = spleen Keywords = malaria Source GEO sample is GSM10997 Last updated (according to GEO): Oct 28 2005 75 65 Normal Skin 15564 on TGRI-6.5k CAD_replicate104 Blood Test (Blinded) Sample Source GEO sample is GSM130013 Last updated (according to GEO): Sep 18 2007 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153494 Last updated (according to GEO): Jan 11 2007 with experimental autoimmune encephalomyelitis 12 57 The nose 94 101 AML 51 on Affymetrix GeneChip Human Full Length Array HuGeneFL 3 CN B miRNAs and codon usage regulate striatal gene and protein expression in two mouse models of Parkinson?s disease Mammary Gland @ Preg1, biological rep1 Cerebellum Alzheimer's disease 3 SN:1010484 Source GEO sample is GSM115400 Last updated (according to GEO): Jun 20 2006 with autism spectrum disorder 37 65 n/a Source GEO sample is GSM177972 Last updated (according to GEO): Jun 11 2007 Gene expression profiles of kidney tissue from control-fed 5-month-old, control-fed 30-month-old and calorie restricted 30 month-old C57BL/6 mice. Last Updated (by provider): May 29 2005 Contributers: T Kayo Y Higami T A Prolla R Weindruch Includes GDS356. Update date: Jun 23 2003. Dataset description GDS356: Investigation of the effect of calorie restriction on the aging process. Gene expression profiles generated for control-fed 5 month, control-fed 30 month and calorie restricted 30 month C57BL/6 mice. Kidney tissue analyzed.. Includes GDS355. Update date: Jun 23 2003. Dataset description GDS355: Investigation of the effect of calorie restriction on the aging process. Gene expression profiles generated for control-fed 5 month, control-fed 30 month and calorie restricted 30 month C57BL/6 mice. Kidney tissue analyzed.. Occipital lobe 861 197 these ganglia 185 none Source GEO sample is GSM190782 Last updated (according to GEO): Jun 25 2007 Expression profiling of double negative thymocytes 766 750 in ischemic brain 1000 Mental Retardation CNS-SC_InjB4h-1C-s2 1000 Hippocampus dhanasekaran-prstate Bladder [JunctionChip 4 of 5] AD control Treatment, type=dissect Source GEO sample is GSM119646 Last updated (according to GEO): Jul 10 2006 91 from the bone marrow 72 Wild type voxel C1 40 21 from skeletal muscle Expression profiling of spinal cord section (T10) extracted from rats 4h following severe injury Source GEO sample is GSM31382 Last updated (according to GEO): May 27 2005 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211342 Last updated (according to GEO): Jul 18 2007 Nose 1000 156 141 in these cancers Normal__Uterus_UT_1 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Spleen 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145148 Last updated (according to GEO): Nov 20 2006 1000 Descending colon Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.98 Subject: 2672 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39006 Last updated (according to GEO): May 27 2005 Brain 861 Coronary heart disease 913 pull-downC_3, ZT6 27 0 cerebral cortex sprague 3915 17 7 hippocampus Expression profiling of spinal cord section (T8) extracted from rats 24h following laminectomy (sham) Lot batch = Source GEO sample is GSM4426 Last updated (according to GEO): May 28 2005 NHF3-hTERT_G1_C5_26553 1000 Brain Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15388.gif Source GEO sample is GSM84160 Last updated (according to GEO): Sep 22 2006 Halothane 5 exposures-1 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68314 Last updated (according to GEO): Jul 07 2006 MK C: MK control. Young male C57BL/6J mice received an injection of MK-801 (300 micro-g per g body weight). No other treatment administered. RNA from control mice were extracted 2 hours after experimental mice received their last shock treatment. Source GEO sample is GSM4566 Last updated (according to GEO): May 27 2005 1000 Brain after infection 147 161 1000 Brain Nasal Epithelium Inhalation Formaldehyde 6ppm 6h ID283 Skin 3 Disease 33 17 tibialis anterior Mature B cells 8b GSE4494 100 95 hearts Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 8846 blood Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum M7TW00122039 Mouse Liver Female 3 (technical replicate) Bone structure of tibia 1000 (GISTs 32 37 no additional Source GEO sample is GSM199235 Last updated (according to GEO): Jun 08 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM146031 Last updated (according to GEO): Nov 20 2006 1000 ovarian neoplasm Epithelial Cells 901 olfactory epithelium 194 213 P7_cy3_4 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184683 Last updated (according to GEO): Apr 26 2007 Myocardium 861 Cochlea at E11.5, replicate1 none Source GEO sample is GSM246007 Last updated (according to GEO): Dec 03 2007 1000 Brain Parkinson Disease 1000 Renal 177 181 SMCL-SMCL8t1-A356-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A D_U133A_96_HC the blood 393 402 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12352 Last updated (according to GEO): May 28 2005 T29__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225374 Last updated (according to GEO): Aug 31 2007 1000 Brain cerebral Source GEO sample is GSM67205 Last updated (according to GEO): Jan 19 2006 Mouse old heart C30-Ht-4 Subcutaneous Fat 1000 901 Heart Diseases WHOLEBLOOD(JJV) Source GEO sample is GSM18708 Last updated (according to GEO): Sep 25 2006 983 Structure of horn of uterus Ovary Source GEO sample is GSM18838 Last updated (according to GEO): Sep 25 2006 Mesenchymal Stem Cells 1000 I_U133A_19_DLPFC hippocampus 103 114 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16372.gif Source GEO sample is GSM91547 Last updated (according to GEO): Sep 22 2006 1000 Encephalitis V5-P392 RENAL 16 20 1000 ovarian neoplasm 2737 tumor cells 2747 CNS-SpinalCmod-Adult-24h-3B-s2 cerebral cortex 7 21 Liver (HBV+, HK1) 1000 Hippocampus Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152008 Last updated (according to GEO): Feb 06 2007 Cerebral cortex 861 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114404 Last updated (according to GEO): Jun 16 2006 PriG_5%O2_Expt1_Day3_rep1 Locus Coeruleus Source GEO sample is GSM107972 Last updated (according to GEO): Jun 06 2006 Sample 2 at Time 2 Source GEO sample is GSM113089 Last updated (according to GEO): Jun 06 2006 861 Malignant Neoplasms 220 184 in the developing trigeminal ganglion 901 Myeloid Leukemia brain 0 5 1000 medulloblastoma PGA-Csx_null_6b-m4 858 Prostatic Neoplasms Substantia nigra PD rep11 1000 ovarian neoplasm GBM Treatment, type=remove Source GEO sample is GSM99489 Last updated (according to GEO): Apr 21 2006 Cerebral cortex 861 Cortex Treatment, type=pharmacogenomic_treatment, description=Chronic Immobilization Stress Source GEO sample is GSM53311 Last updated (according to GEO): Jul 06 2005 Exp C_1, 5mg/kg CPF 1166 1151 of their tumours n/a Source GEO sample is GSM178054 Last updated (according to GEO): Jun 11 2007 M7TW00121818 Intestines, Small 1000 PCA22_localized prostate cancer 0 30 PBMCs-Type 1 Diabetes-IDDM54_T1D_4MO Neoplasm 1000 Spleen 0 5 861 Neoplasm 485 474 in the skin SN:Human Glioblastoma Biopsy 10392 n/a Source GEO sample is GSM178004 Last updated (according to GEO): Jun 11 2007 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13121.gif Source GEO sample is GSM79634 Last updated (according to GEO): Sep 22 2006 Sample 10 Treatment, type=pharmacogenomic_treatment, description=Neuronal cultures from cultures of rat cerebellar granule neurons will be treated with the chemical compound GW5074. Source GEO sample is GSM53251 Last updated (according to GEO): Jul 06 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145070 Last updated (according to GEO): Nov 20 2006 Whole blood 0 10 4525 4520 liver Heart Ventricle 1000 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160213 Last updated (according to GEO): Feb 08 2007 none Source GEO sample is GSM239849 Last updated (according to GEO): Dec 07 2007 HPB-ALL DMSO control 24h rep1 AKR/J Amygdala F normal testis 54 66 5_cerebral_cortex_time_0_#52 Prosencephalon 1000 861 Cerebellum 51 37 without malaria Carcinoma, Large Cell 888 Category: Tissue Rejection Subcategory: Kidney SCAR subcapsular Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=730560 LaserPower=2.081.3 Lot batch = LC17N031 Source GEO sample is GSM4783 Last updated (according to GEO): Nov 21 2005 Neoplasm 861 89 68 with tricuspid valves Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13416.gif Source GEO sample is GSM79645 Last updated (according to GEO): Sep 22 2006 Olfactory Epithelium 1000 Parkinson Disease 1000 RMS-T8 on NHGRI-6.5k_b Gene expression data from postmorten brain regions Source GEO sample is GSM145218 Last updated (according to GEO): Nov 20 2006 Heart 1000 adipose_tissue_4 Source GEO sample is GSM80583 Last updated (according to GEO): Mar 31 2006 21 adrenal medulla 7 1000 Infection 861 Cochlear structure Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11217 Last updated (according to GEO): May 28 2005 M_U133A_6_nAcc GM19172 90 year old female 0 Human Cortex 11 Hippocampus 0 10 R587P01067 Richard Almon-3-1133800608792 of coronary artery disease 317 342 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202689 Last updated (according to GEO): Jun 20 2007 Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers. SAMR1 Hippocampus Old Sample 2 Plasma 861 1BMH02022103_LymphomaRaji Donor 1 time point 0 autologous control (uninfected) Source GEO sample is GSM2591 Last updated (according to GEO): May 27 2005 Colonic mucous membrane 913 Experimental Autoimmune Encephalomyelitis 901 high gestational age Source GEO sample is GSM213081 Last updated (according to GEO): Jul 25 2007 1000 Brain metanephric mesenchyme, LIF, 1 day, biological rep1 21h-Control replication 1 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113968 Last updated (according to GEO): Jun 16 2006 metanephric mesenchyme, NGAL, 4 days, biological rep2 Mental Retardation 1000 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:248, Count:32 Corner- Avg:43803, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:17.496950,SFGene:All Background:Avg:346.00,Stdev:4.31,Max:359.2,Min:337.0 Noise:Avg:9.84,Stdev:0.35,Max:10.9,Min:8.9 RawQ:14.73 Keywords = ALL Source GEO sample is GSM3506 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145348 Last updated (according to GEO): Nov 20 2006 in the brain 150 162 MLL__3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Spinal Cord GM06994 M_U133Plus_124_nAcc 861 Cerebral cortex 5 0 brain cerebellum 7 16 Calcium-induced transcript variation in neuronal cells analyzed with exon microarrays. nerve, HumanSuralNerve: Human Schwann cell RNA extracts 329 Passage 3_le1 0 Human Cortex 11 Expression profiling of spinal cord section (T9) extracted from rats 30m following mild injury Lot batch = Source GEO sample is GSM4418 Last updated (according to GEO): May 28 2005 Putamen 4 Normal 202 175 at the longitudinal fissure Neoplasm 861 Gene expression profile of the cell line UB/OC-1 grown for 14 days under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1528 Last updated (according to GEO): May 27 2005 1000 Kidney AD-AD1T1-A383-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Brain (postcentral gyrus) [JunctionChip 4 of 5] Z4 juvenile biol repl 2 D_95Av2_3108_CB_0_GS 15 0 human cerebellum 1000 Brain Osteoblasts 1000 Posterior root of spinal nerve 861 01_0024_SepticShock_Day1_118 Cultured in DMEM with 10% FBS and penicillin (100U/ml)/streptomycin (100ug/ml). Media changed every other day. 37ºC, 5% CO2. Source GEO sample is GSM15789 Last updated (according to GEO): Oct 28 2005 Lymphoblastoid Cell Line for Individual 8053.3 log phase Appendix Source GEO sample is GSM19000 Last updated (according to GEO): Sep 25 2006 hrs nasal epithelium 1127 1147 none Source GEO sample is GSM244595 Last updated (according to GEO): Nov 23 2007 DR24h(1) of the atrial 647 659 1000 Brain 24 0 Substantia nigra PD rep10 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141278 Last updated (according to GEO): Oct 26 2006 Hypothalamic structure 861 thalamus_3 Source GEO sample is GSM80840 Last updated (according to GEO): Mar 31 2006 1000 frontal lobe 3792 0b 1BJZ02060515_IsletCell VDXIGRU_171260 865 Disorder of artery A/J Frontal Cortex D 861 Cerebral cortex CNS-SC_CtrB4h-2A-s2 5_cerebral_cortex_6hrs_sleep_deprivation_#70 Brain 1000 Osteoblasts 1000 Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68034.gif Source GEO sample is GSM137406 Last updated (according to GEO): Sep 26 2006 Mesenchymal Stem Cells 1000 Cerebral cortex 861 plasma cells 332 344 Ovary 1000 Bipolar Disorder 1000 88 68 with bicuspid valves iA50clone9+ M_U133A_96_HC Epithelium of bronchus 983 cardiac 763 769 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188786 Last updated (according to GEO): Jun 06 2007 cerebellum 7 16 Prosencephalon 1000 Saccule at E13.5, replicate1 human caudate nucleus Source GEO sample is GSM86903 Last updated (according to GEO): Feb 08 2006 SCG_control_24h_rep1 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11518 Last updated (according to GEO): May 28 2005 Brain 861 Lung 1000 MO_CTa_SON_NCBI Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD14 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD14 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36714 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145417 Last updated (according to GEO): Nov 20 2006 Ovarian_Tumor_Endometrioid_CHTN-OE-033 861 Blood 1000 Eye Haloperidol treated 12weeks AffyGC RMA rep7 40 21 from the hippocampus NHF1-hTERT_1.5Gy_2h_C3_20128 of the colon 28 39 1000 Temporal Lobe NasalRespMuc_0222ACJ3_31.txt cerebral cortex 7 21 1000 Brain of brains 87 95 858 Mesodermal cell 861 Nerve Liver 1000 213 of Turner's syndrome 232 Tract 861 Spleen 1000 1000 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145926 Last updated (according to GEO): Nov 20 2006 Macrophage 14smi061 with some respiratory epithelium. 1039 1072 Gene expression data from postmorten brain regions Source GEO sample is GSM145483 Last updated (according to GEO): Nov 20 2006 1000 Coronary Arteriosclerosis Salivary Glands 1000 Disease Source GEO sample is GSM175809 Last updated (according to GEO): Apr 09 2007 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13110.gif Source GEO sample is GSM79968 Last updated (according to GEO): Sep 22 2006 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188847 Last updated (according to GEO): Jun 06 2007 Muscle 861 plasma cells 332 344 24 0 human prostate PC3 tumors MGJZ030212014Ahippocampus Gene expression data from the neocortex of wild-type mouse Source GEO sample is GSM172935 Last updated (according to GEO): Mar 08 2007 HDMTX_MP-DX-5 of the most anterior dorsal root ganglia 23 62 9 0 Blood Test Liver 0 4 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11441 Last updated (according to GEO): May 28 2005 HapMap JPT Male Source GEO sample is GSM159622 Last updated (according to GEO): Feb 01 2007 277_1 breast 6 11 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3493.gif Source GEO sample is GSM93144 Last updated (according to GEO): Sep 22 2006 Macrophage smi45 Halothane/Isoflurane single and repetitive exposures Nose 1000 1000 Coronary Arteriosclerosis liver, PPARa-null mice, control conditions Source GEO sample is GSM205775 Last updated (according to GEO): Jul 24 2007 1000 Brain Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11671.gif Source GEO sample is GSM76424 Last updated (according to GEO): Sep 22 2006 Blood 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145978 Last updated (according to GEO): Nov 20 2006 Bone Marrow 1000 Brain [JunctionChip 1 of 5] Tumor__Leukemia_AML_AML_(14,PK)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Spinocerebellar ataxia type1 130 157 Spleen vs Insulin-like growth factor 1 gamma Treated B cell Parkinson Disease 861 ER negative human primary breast tumor EA02014_41301_H133A_JA-2038 spinal cord 399 410 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the lv samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12324 Last updated (according to GEO): May 28 2005 Lymphoblastoid Cell Line for Individual 8191.3 log phase from the cerebellum 20 38 healthy subject Source GEO sample is GSM211025 Last updated (according to GEO): Sep 10 2007 M7TW01010686 Early secretory endometrium from normal patient Source GEO sample is GSM150208 Last updated (according to GEO): Dec 14 2006 1000 Encephalitis 861 Blood 901 Mammary gland M_U133A_66_DLPFC Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203962 Last updated (according to GEO): Aug 02 2007 AR-Veh-1 Gene expression data from postmorten brain regions Source GEO sample is GSM144927 Last updated (according to GEO): Nov 20 2006 1000 Malaria 13 salivary gland 0 Brain 861 brain, cerebellum: RNA#7S_le1 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68263 Last updated (according to GEO): Jul 07 2006 0029_1355_H95A2_KF-182_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 283 280 (AML Vestibular organ at E10.5, replicate2 no additional Source GEO sample is GSM199415 Last updated (according to GEO): Jun 08 2007 trigeminal sensory ganglia 105 131 Brain 1000 Sum149_2 Colon Cancer 5 16 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159976 Last updated (according to GEO): Feb 01 2007 of the normal mucosa 7 26 Splenic Dendritic Cell Subsets peripheral blood-CD14Monocytes Source GEO sample is GSM18713 Last updated (according to GEO): Sep 25 2006 Post Natally excised Control 5 brainstem 7 15 858 Mesodermal cell Blood 861 Epithelium 861 by the liver 210 221 Ts1Cje-1-MGU74A GSE6509 in blood 16 23 Liver Test (Blinded) Sample Source GEO sample is GSM130091 Last updated (according to GEO): Sep 18 2007 913 Coronary heart disease P21 cochlear nuclei 0 18 277 271 Retinas 861 Cardiomyopathies brain, cerebral cortex: Nic1_le1 Ovary 1000 Communicable Diseases 1000 +_6470_batch1 on NHGRI-6.7k 1217 1206 in cartilage 861 Cerebral cortex Brain 1000 070302_HF_289MB Cerebral cortex 861 in extraocular muscle 41 61 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23743.gif Source GEO sample is GSM66583 Last updated (according to GEO): Sep 22 2006 Macrophages treated with LPS, 30 min, Replicate 1 Source GEO sample is GSM241140 Last updated (according to GEO): Nov 02 2007 Neoplasm Metastasis 1000 Primary tumor 19 32 36 0 Inflammatory myopathy specimen GEIM27 Cerebral cortex 861 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 14 hours after lights on. Original sample code = CM12A Source GEO sample is GSM227292 Last updated (according to GEO): Sep 10 2007 Expression profiling of spinal cord section (T8) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31396 Last updated (according to GEO): May 27 2005 59 35 out of mouse bone marrow PGC-1a null (PGC-1a-/- ) and wild-type (PGC-1a+/+) mice were obtained by breeding heterozygous (PGC-1a+/-) founder mice as described (Leone et al., 2005). Source GEO sample is GSM135226 Last updated (according to GEO): Oct 05 2006 Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1-Englow 3 Primary small cell lung carcinoma 3170 0 37 5 0 brain 50 41 mouse lung Starvation 916 Control_short-term Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.12 Subject: 3108 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39073 Last updated (according to GEO): May 27 2005 in bronchial epithelia 311 332 brain, cerebral cortex: 14998_e2_le1 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11469 Last updated (according to GEO): May 28 2005 b14 PGA-MCR-ctr-2h-1aAv2-s1 The most common congenital cardiac abnormalities 50 97 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198664 Last updated (according to GEO): Jun 06 2007 Prostate 2 Disease 0 17 Hubs in biological interaction networks exhibit low changes in expression in experimental asthma. 1000 Fibroblasts Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection). One of two samples from the same patient, different visits Source GEO sample is GSM36425 Last updated (according to GEO): May 27 2005 Richard Almon-2-1138200269414 77 year old male BTBR T+ tf/tf Cingulate Cortex C 861 Cerebral cortex 10 0 hippocampus Normal Source GEO sample is GSM175882 Last updated (according to GEO): Apr 09 2007 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201232 Last updated (according to GEO): Jun 14 2007 SN:Human Glioblastoma Biopsy 07088 5 0 brain Animals were sacrificed and organs were rapidly frozen in liquid nitrogen, and subsequently stored at <ETH>80oC. Tissues were mechanically homogenized with a polytron and total cellular RNA was extracted using a commercially available reagent (TMTRIzol; Invitrogen). The poly-(A)+ fraction of the RNA was isolated by chromatography with oligo d(T) cellulose beads. For cDNA labeling, either 25 mg of total RNA or 2.5 mg of poly-(A) RNA was converted into cDNA using reverse transcriptase (RT; Super Script II, Invitrogen) and alternatively Cy5 or Cy3-labeled dCTP (1mM, Perkin Elmer-Cetus/NEN, Boston) in a reaction mixture containing 1.5 mL oligo (dT) (100pmol/ mL), 3 mL dNTP-dCTP (6.67mM each), 1 mL dCTP (2mM), 4 mL DTT (100mM), 8 mL 5 X RT Buffer (Invitrogen, California). The reactions were carried out at 42¼C for 3 hrs, after which the RNA was degraded by the addition of 0.5 mL RNase A (1 mg/mL) and 1.5 mL RNaseH 5 units/mL). Labeled cDNA was separated from unincorporated nucleotides (Qiagen column) and further concentrated by evaporation under vacuum. The arrays were pre-hybridized for 1-2hrs with DIGEasy hybridization buffer (Roche) containing 10ug/ml denatured salmon sperm DNA, and 10ug/ml yeast tRNA. The Cy5 and Cy3 labelled cDNAs were combined and hybridized in the same medium and incubated with the arrays for 16-18hrs at 37Co. Finally, the arrays were washed 3 x 10 mins in 0.1 x SSC (20 X SSC is 3M sodium chloride, 0.3 M sodium citrate, pH 7.0), 0.1%SDS at 50Co, and 4 x 3min in 0.1 x SSC at room temperature, and dried by centrifugation. Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray fluorescent scanner and image intensity data were extracted and analyzed with QuantArray 3.0 analysis software. Quantification data was imported in GeneSpring (Silicon Genetics). The import format was modified to maintain information relevant to user-contributed flagging as well as QC parameter furnished by the array manufacturer. Dye swap and Intensity-based normalization (Lowess) were performed using the default settings. Keywords = spleen Keywords = malaria Source GEO sample is GSM11005 Last updated (according to GEO): Oct 28 2005 very early HCC Source GEO sample is GSM155987 Last updated (according to GEO): Jun 21 2007 D_95Av2_3023_DLPFC_0_GS 861 Cardiomyopathies Gene expression data Source GEO sample is GSM183184 Last updated (according to GEO): Jul 30 2007 Hypothalamus Source GEO sample is GSM107909 Last updated (according to GEO): Jun 06 2006 of Parkinson's disease 450 471 Wild type hippocampus CA1 region Source GEO sample is GSM88942 Last updated (according to GEO): Jan 04 2006 Brain 1000 Liver 1000 14 6 (thalamus 1301 CP48_11 Mouse Liver Male 3 Normal Source GEO sample is GSM176426 Last updated (according to GEO): Apr 09 2007 against malaria 446 460 Neoplasm 861 Mesenchymal Stem Cells 1000 Diet Induced Obese rat C3 Spleen vs Untreated B cell Time 0 (set15) 861 Bladder Neoplasm PGA-RnSalt_e_3w_1-m5 Buccal mucosa 1000 78 66 Control blood Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211318 Last updated (according to GEO): Jul 18 2007 Gene expression data from dorsal pancreas at e16.5, MG-U74A version2 Source GEO sample is GSM199452 Last updated (according to GEO): Jun 08 2007 S1P3-KO-hippocampus, biological rep1 (male) normal liver tissue Source GEO sample is GSM155989 Last updated (according to GEO): Jun 21 2007 brain, unknown: Sample58_e1_le1 3AJZ02022645_adrenal gland Endometrium 1000 Postnatal day 3 callosal projection neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription. Source GEO sample is GSM37085 Last updated (according to GEO): May 27 2005 Testis 1000 f2#152 versus pool Mouse Brain tissue Expression profiling of spinal cord section (T8) extracted from rats 4h following severe injury Source GEO sample is GSM31503 Last updated (according to GEO): May 27 2005 SK-MEL-28 hgu95d Fibroblasts 861 1000 Coronary Arteriosclerosis Cerebral cortex 1000 Duchenne muscular dystrophy 0 26 from a primary branch 21 41 5 0 Spleen obsessive-compulsive disorder 127 156 The effects of ionizing radiation (IR) on the temporal transcriptional response of lymphoblastoid cells were investigated in this study. We used oligonucleotide microarrays to assess mRNA levels of genes in lymphoblastoid cells at various time points within 24 h following gamma-irradiation. We identified 319 and 816 IR-responsive genes following 3 Gy and 10 Gy of IR exposure, respectively, with 126 genes in common between the two doses. A high percentage of IR-responsive genes are involved in the control of cell cycle, cell death, DNA repair, DNA metabolism, and RNA processing. We determined the temporal expression profiles of the IR-responsive genes and assessed effects of IR dose on this temporal pattern of expression. By combining dose-response data with temporal profiles of expression, we have identified sets of coordinately responding genes. Through a genomic approach, we characterized a set of genes that are implicated in cellular adaptation to IR stress. These findings will allow a better understanding of complex processes such as radiation-induced carcinogenesis and the development of biomarkers for radiation exposure. mouse brains 187 198 Muscular Dystrophies 901 P24 deprived visual cortex replicate 4 umbilical cord_nobpd: 6D Spleen 1000 HapMap YRI_parent Female Source GEO sample is GSM159676 Last updated (according to GEO): Feb 01 2007 Heart 1000 MDA Mb231 1h + 10 nM Cxcl12 1 Treated Lung tissue from C57BL/6 mice calorie restricted by 2/3 and sacrificed 24 hrs after the onset of calorie restriction. Lot batch = Source GEO sample is GSM4023 Last updated (according to GEO): May 28 2005 Nasal Epithelium 865 Standard Affymetrix Protocal Keywords = microarray Keywords = muscle Source GEO sample is GSM15777 Last updated (according to GEO): May 28 2005 BC214B-BE 861 Blood 1000 Cerebral cortex 4 0 Liver Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD11 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD11 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36677 Last updated (according to GEO): May 27 2005 988 980 cerebella cerebral cortex sprague 3916 all cortical minus the frontal cortex, individual animal, 10 weeks old, male Sprague Dawley cerebral cortex file:p3916w Source GEO sample is GSM15153 Last updated (according to GEO): Oct 28 2005 brain 0 5 1000 Brain 861 Pancreas Tumors 91 96 Blood Test (Blinded) Sample Source GEO sample is GSM129914 Last updated (according to GEO): Sep 18 2007 CNS-SMTC_Mod7d-2B-s2 24hr post 10Gy IR Cerebral cortex 1000 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211251 Last updated (according to GEO): Jul 18 2007 882-1 ovarian tumor: serous Source GEO sample is GSM139440 Last updated (according to GEO): Apr 09 2007 2034 2024 for livers Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68235 Last updated (according to GEO): Jul 07 2006 MGJZ030228017Alargeintestine 861 Pituitary Gland Epithelial Cells 1000 intestine_wildtype_treated_rep3 BALB/cByJ Basal Ganglia A General Paralysis 885 1000 adenoma 861 Blood 1794 1773 in experimental stroke spinal cord lower; lower half Source GEO sample is GSM18588 Last updated (according to GEO): May 27 2005 Ptdsr-/- fibroblast_rep14 861 Brain Lymphoblastoid Cell Line for Individual 8078.3 log phase 901 Caudate nucleus structure 52 35 bone marrow cell 1 WT 2 mon replicate 3 Retroviral vectors for the four factors were transfected into Fbx15 bgeo-KI MEF. Cells were cultured with ES cell condition and selected with G418 for 16 days. Source GEO sample is GSM119322 Last updated (according to GEO): May 18 2007 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160215 Last updated (according to GEO): Feb 08 2007 MammInvol_022QACHW_054.txt LungP5_022QAF70_077b.txt Pool of 11 saccules at E15 Source GEO sample is GSM182620 Last updated (according to GEO): Aug 14 2007 in plasma 666 675 To identify genes associated with lung cancer progression, we examined gene expression profiles of tumor cells from 20 patients with primary, untreated non-small cell lung cancer (10 adenocarcinomas (AC) and 10 squamous cell carcinomas (SCC)) in comparison to lung tissue of 23 patients with stage IIIB or stage IV non-small cell lung cancer (15 AC and 8 SCC). Bronchoscopical biopsies from patient with recurrent lung tumor were taken after initial treatment. Cancer cells were isolated using laser capture microdissection in order to obtain pure samples of tumor cells. For expression analysis, microarrays covering 8793 defined genes (Human HG Focus Array, Affymetrix) were used. Array data were normalized and analysed for significant differences using variance stabilizing transformation (VSN) and significance analysis of microarrays (SAM), respectively. Genes were considered to be up- or down-regulated when the ratio between primary and recurrent tumor samples were at least 1.5-fold differentially expressed with an estimated false discovery rate: < 5%. Based on differentially expressed genes, primary cancer samples could be separated from recurrent tumor samples. We identified 115 and 124 significantly regulates genes in AC and SCC, respectively. For example, in recurrent AC we found increased expression of genes related to the wingless (FZD6, RYK, MYC) and calcium (CALM1, ATB2B1, S100A2) signalling pathways which might play a role in metastasis of tumor cells. Other differentially expressed genes were related to cell cycle (CCND1, CDK2), transcription factors (TTF1, TAF2, YY1), nuclear mRNA splicing and mRNA processing (SFRS1, HNRPL), protein-nucleus import (NUTF2, KPNB1, NUP50) and chromatin modification (HIST1H4C, SMARCC1). In SCC, we found an increased expression of CTNNB1, an important mediator in wingless signalling pathway. Among the down-regulated genes in SCC, the utmost fraction belonged to genes coding for ubiquitin mediated proteolysis (UCHL1, PSMA3, COPS6) and ribosomal proteins (RPS26, RPL7A, RPS15). Other down regulated genes were related to transcription factors (TCEA2, TAF10), nuclear mRNA splicing and mRNA processing (SNRPD2, HNRPM). In conclusion, a distinct pattern of gene expression is found during the progression from primary carcinoma to recurrent NSCLC. Our microarray-based expression profiling revealed interesting novel candidate genes and pathways that may contribute to lung cancer progression. Last Updated (by provider): May 25 2007 Contributers: Judith Neukirchen Ulrich-Peter Rohr Helene Geddert Michael Rosskopf Ralf Kronenwett Astrid Rohrbeck Rainer Haas Guillermo Garcia-Pardillos human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195354 Last updated (according to GEO): Jun 04 2007 ES cell line was grown on irradiated MEF feeders using standard culture conditions. Feeders were then depleted and ES cells plated on gelatin for ~2 days. RNA was isolated using Trizol/RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol. Data were normalized by AffyMetrix MAS5.0 using defaults. Keywords = embryonic stem cholesterol transport Source GEO sample is GSM9272 Last updated (according to GEO): May 27 2005 17 7 hippocampus BC112A-AF tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44883 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T10) extracted from rats 24h following severe injury Source GEO sample is GSM31361 Last updated (according to GEO): May 27 2005 of the postmortem brains 674 698 Epithelial Cells 1000 Brain 861 normal 1112 Spleen 1000 5 0 brain 1000 Epithelial Cells 861 Colon Gene expression data from postmorten brain regions Source GEO sample is GSM145507 Last updated (according to GEO): Nov 20 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Dimaprit for 120min Source GEO sample is GSM5540 Last updated (according to GEO): May 27 2005 Obesity 1000 614 606 of tumors post HCMV infection 18 36 Gene expression data from rat metanephric mesenchymes cultured for 4 days in the presence of LIF Source GEO sample is GSM126200 Last updated (according to GEO): Dec 08 2006 1000 Hippocampus 1000 Uterine Fibroids 14 0 Small Intestine Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132558 Last updated (according to GEO): Feb 26 2007 mouse brains 187 198 23 11 of the kidney C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P32 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25129 Last updated (according to GEO): May 27 2005 cerebellum wistar 3885 whole tissue, individual animal, 10 weeks old, male Wistar cerebellum file:p3885w Source GEO sample is GSM15128 Last updated (according to GEO): Oct 28 2005 untransduced mammary epithelial cells passage 13 Source GEO sample is GSM5158 Last updated (according to GEO): May 27 2005 P104 non-deprived visual cortex replicate 2 Brain 861 Parkinson Disease 1000 104 frontal cortex 118 Leukemic fractions of ID49 AML patient have been hybridized. Source GEO sample is GSM103109 Last updated (according to GEO): Feb 26 2007 Basal- 0 5 1000 Liver the heart 987 996 Day 2_M_+RA_Achip 1000 Heart Alk shRNA, biological rep3 cortex 1942 1948 965 948 in the hippocampus Measles 861 Psychotic Disorders 1000 Kidney 861 M_U133Plus_93_HC Skeletal muscle structure 1000 Brain 861 PGA_PA-S_267 861 Colon Spinal Cord 861 Oat cell carcinoma 867 ovary 45 50 LPS plus IL-10, 30 min, Rep_1 of secondary brain damage 183 208 Parkinson Disease 861 1000 Brain brain, Left frontal Lobe: Extract22_le2 1000 Brain 1000 Liver /2J Amygdala A 3 16 Large-scale analysis of the human transcriptome. Fetal brain Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 138.01 Stdv: 3.97 Min: 130.94 Max: 146.00 Source GEO sample is GSM2883 Last updated (according to GEO): May 27 2005 Brain Stem 1000 Hormones 861 Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 72h. Lot batch = Source GEO sample is GSM1254 Last updated (according to GEO): May 28 2005 1000 Lung CurrentSmoker 1 Monocular deprivation left cortex, biological rep2 CHC MD-6 GM18852 Cockayne syndrome B wt-rescued cell Source GEO sample is GSM226620 Last updated (according to GEO): Sep 04 2007 Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589?595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164?169.) Source GEO sample is GSM159488 Last updated (according to GEO): Jun 21 2007 660 mesenchymal stem cell 639 1000 Retina RNA extracted from mouse brain Source GEO sample is GSM103419 Last updated (according to GEO): Sep 21 2006 Gene expression data from rat metanephric mesenchymes cultured for 2 days in the presence of the ANX fraction Source GEO sample is GSM126220 Last updated (according to GEO): Dec 08 2006 861 Blood 70 Embryonic Stem Cell 52 Large-scale analysis of the mouse transcriptome. dorsal root ganglion C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 383.45 Stdv: 15.22 Min: 361.32 Max: 408.85 Source GEO sample is GSM2992 Last updated (according to GEO): Mar 20 2006 mouse brain ipsilateral saline.RU486, biological rep4 M_U133Plus_125_CB 865 Disorder of artery 1000 Communicable Diseases 861 Asthma Male7, Olfactory RNA_Nasal olfactory epithelium_Tissue was preserved in RNA Later and collected from nose Saline ip saline ILI 24hrs post ILI sample A Cerebral cortex 1000 Lymphoblastoid Cell Line for Individual 8054.3 log phase R702P01103 901 Caudate nucleus structure D_U133A_63_Amy 789 768 primordial germ cells bronchial epithelia 224 243 NCI60.32_LABEL36EXTRACT35SUB3 Source GEO sample is GSM134150 Last updated (according to GEO): Aug 06 2007 GBM: 62A34 #7 67 40 with coronary artery disease cortex rattus_norvegicus_strain iNP animal_number 10 NL-1675-A409-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 225 203 from the mouse cochlea na Source GEO sample is GSM181291 Last updated (according to GEO): Apr 10 2007 Alzheimer's Disease 1000 RST-PVH3_2 16 0 Medulla_Oblongata pfc_1004_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Liver 0 4 FVB/NJ Amygdala D Spinal Cord 901 1000 Nervous system structure Gene expression data from postmorten brain regions Source GEO sample is GSM145451 Last updated (according to GEO): Nov 20 2006 Arteries 861 1000 Cerebral cortex by Rett syndrome 97 112 Epithelium 865 Anterior nares 1000 326 such as learning disorders 351 Expression profiling of spinal cord section (T10) extracted from rats 24h following severe injury Source GEO sample is GSM31354 Last updated (according to GEO): May 27 2005 861 Cerebral cortex Colon 1000 119 96 in embryonic stem cells 861 Nerve Menstrual phase - Follicular Source GEO sample is GSM175776 Last updated (according to GEO): Apr 09 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM144944 Last updated (according to GEO): Nov 20 2006 5 0 brain SCG_sema3A_12h_rep1 Primary Neoplasm 1000 24 skeletal muscle 10 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114265 Last updated (according to GEO): Jun 16 2006 1000 Carcinoma of lung 12 0 Uterus_Corpus 111 FC BA9 A MuscleRegen-ctx8.5d-1RLAv2-s2 Ventral Tegmental Area 1000 1000 Brain Sample45, Post Injury 24 hours Treatment, type=wait Source GEO sample is GSM53295 Last updated (according to GEO): Jul 06 2005 Whole neuroblastoma tumor_2182 Lymphoblastoid Cell Line for Individual 8080.4 log phase NCI60.55_LABEL59EXTRACT58SUB3 Source GEO sample is GSM134272 Last updated (according to GEO): Aug 06 2007 /HeJ mouse pituitary gland 27 52 Leg 56 Day mdx rep 3 Primary Neoplasm 1000 Colon 1000 Expression profiling of laminectomized raphe at 14d in rats Source GEO sample is GSM41517 Last updated (according to GEO): May 27 2005 Testis 1000 9 0 rat kidney Cerebellum Alzheimer's disease 6 MCF7 treated with E2 for 24h Source GEO sample is GSM213328 Last updated (according to GEO): Jul 26 2007 GBM Treatment, type=remove Source GEO sample is GSM99542 Last updated (according to GEO): Apr 21 2006 8814_Mock_1 Fibroblasts 1000 with some respiratory epithelium. 1039 1072 Expression profiling of spinal cord section (T8) extracted from rats 30m following mild injury Source GEO sample is GSM31440 Last updated (according to GEO): May 27 2005 Neoplasm 1000 Large-scale analysis of the human transcriptome. Lung Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 127.25 Stdv: 5.50 Min: 113.26 Max: 137.25 Source GEO sample is GSM2832 Last updated (according to GEO): Mar 20 2006 mouse brain contralateral LPS.RU486, biological rep2 Brain 1000 110 94 of heart failure lung Source GEO sample is GSM18949 Last updated (according to GEO): Sep 25 2006 f2#127 versus pool Mouse Brain tissue Communicable Diseases 861 Nervous system structure 901 Expression data from murine ventral prostate treated with placebo or RAD001 for 12h, 48h, 6d,9d, and 15d Intestinal Diseases 1000 Kidney [JunctionChip 3 of 5] 901 theca cell Integumentary system 1000 5.0 mg/kg MeHg forebrain at 3.0h Gene expression profile of the cell line UB/OC-1 grown for 7 days under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1540 Last updated (according to GEO): May 27 2005 zero_2 breast tumors 601 613 X-ray irradiation (2 Gy). Source GEO sample is GSM203982 Last updated (according to GEO): Jun 25 2007 1000 Carcinoma Chromosomes 861 CH2116 sensorimotor cortex 200 218 Skeletal bone 861 none Source GEO sample is GSM123195 Last updated (according to GEO): Jul 26 2006 861 Cerebral cortex Lymphoblastoid Cell Line for Individual 8065.3 log phase 966 Organ Human Sural Nerve Schwann Cell Donor 317 Passage 1 Treatment, type=add, description=growth factors heregulin and forskolin added Source GEO sample is GSM92231 Last updated (according to GEO): Jan 13 2006 Sample9, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53260 Last updated (according to GEO): Jul 06 2005 39 21 from mammary glands Gastrin infused gastrin Knockout replicate 2 786-0 hgu95a 1000 Cerebral cortex 861 Neoplasm Blood Test (Blinded) Sample Source GEO sample is GSM130011 Last updated (according to GEO): Sep 18 2007 CNS-SMTC_Ctr28d-1Bs2 1000 Spleen 861 Muscle Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202684 Last updated (according to GEO): Jun 20 2007 7 0 prostate Expression profiling of moderately injured raphe at 4h in rats Source GEO sample is GSM41613 Last updated (according to GEO): May 27 2005 with bipolar disorder 77 97 We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7. Source GEO sample is GSM200612 Last updated (according to GEO): Jul 12 2007 brain, hippocampus: Aldh5a1-/- #3403 Cort_e1_le1 PHG-CtrCM-1bAv2-s2 SWR/J ACU, Rep1 861 Breast 5 0 brain 91 from the bone marrow 72 Macrophages treated with LPS, 10 min, Replicate 1 Source GEO sample is GSM241128 Last updated (according to GEO): Nov 02 2007 468 459 the rectum MLL-C5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A temporal_lobe_8 brain, Posterior Singulate: Sample49_e1_le1 861 Brain Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226052 Last updated (according to GEO): Nov 02 2007 Testes_0225ACIN_113.txt Bone Marrow 1000 Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203965 Last updated (according to GEO): Aug 02 2007 PGA_PA-N_294 Huntington Disease 1000 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162185 Last updated (according to GEO): Jun 12 2007 1000 Hippocampus M_U133A_8_DLPFC GC (HKG41T) Expression profiling of spinal cord section (T10) extracted from rats 7d following laminectomy (sham) Lot batch = Source GEO sample is GSM6634 Last updated (according to GEO): May 28 2005 (cortex 19 25 Androgen Receptor (AR) is essential for the growth and progression of prostate cancer in both hormone-sensitive and hormone-refractory disease. We have designed a sequence-specific DNA binding polyamide (1) that targets the consensus androgen response element (ARE). This polyamide binds the PSA promoter ARE, inhibits androgen-induced expression of PSA and several other AR-regulated genes in cultured prostate cancer cells, and reduces AR occupancy at the PSA promoter and enhancer. Down-regulation of PSA by this polyamide was comparable to that produced by the synthetic anti-androgen bicalutamide (Casodex) at the same concentration. Genome-wide expression analysis reveals that a similar number of transcripts are affected by treatment with the polyamide and with bicalutamide. Direct inhibition of AR-DNA binding by sequence-specific DNA binding small molecules could offer an alternative approach to antagonizing AR activity. A polyamide (2) that targets a different DNA sequence is included as a control. Last Updated (by provider): May 04 2007 Contributers: Peter B Dervan Nicholas G Nickols Squamous cell carcinoma 884 Alzheimer's Disease 861 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:270, Count:32 Corner- Avg:37352, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:3.941622,SFGene:All Background:Avg:657.26,Stdev:6.43,Max:677.7,Min:641.9 Noise:Avg:12.21,Stdev:0.52,Max:14.7,Min:10.9 RawQ:16.85 Keywords = ALL Source GEO sample is GSM3395 Last updated (according to GEO): May 28 2005 660 mesenchymal stem cell 639 Gene expression data from a neocortex of saline-injected mouse Source GEO sample is GSM147396 Last updated (according to GEO): Jan 03 2007 Nasal Epithelium Inhalation Formaldehyde 07ppm 24h ID134 Brain 861 10 7 left nodose_nucleus_9 Source GEO sample is GSM80765 Last updated (according to GEO): Mar 31 2006 plasma cells 332 344 Retina 1000 901 Mammary gland Epithelial Cells 1000 M_U133Plus_121_HC Skin 1000 ventral spinal cord 13 31 Requirement for ERK MAP kinase in mouse preimplantation development Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68155 Last updated (according to GEO): Jul 07 2006 Cerebral cortex 1000 Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Globin reduction was performed according to the Affymetrix technical note. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183397 Last updated (according to GEO): Apr 23 2007 43h-CHX replication 2 Bone Marrow 1000 I_U133A_55_AnCg 663 mesenchymal stem cell 642 brain 0 5 Brain 1000 660 mesenchymal stem cell 639 Autistic Disorder 877 BL6:3-1 + 3-2 hypothalamus 276 271 Spleen 9 0 Blood Test 1000 Hippocampus Starvation 916 of oculomotor nuclei 240 259 144 114 from a single adult spinal cord 1037 of transitional epithelium 1012 Replicate1_Voxel B10 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68139 Last updated (according to GEO): Jul 07 2006 Whole Brain 73 83 1000 Cardiomyopathy, Alcoholic of the atrial 647 659 1000 Solid tumor 1000 Endometrium skeletal muscle, tibialis anterior: Innverated MCK::cre 1_e1_le1 peripheral blood-CD19BCells Source GEO sample is GSM18882 Last updated (according to GEO): Sep 25 2006 5 0 brain Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15019.gif Source GEO sample is GSM79811 Last updated (according to GEO): Sep 22 2006 chlorpromazine-treated mouse brain Peripheral Nerves 851 of coronary artery disease 258 284 861 Muscle HapMap YRI_parent Male Source GEO sample is GSM159683 Last updated (according to GEO): Feb 01 2007 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=0 (Non-acute rejection). Source GEO sample is GSM36427 Last updated (according to GEO): May 27 2005 1000 Uterus brain, Left frontal Lobe: Extract6_le2 Subject code A20EB Gene expression data from human colon tumor tissue Source GEO sample is GSM173355 Last updated (according to GEO): Apr 20 2007 21 0 acute myeloid leukemia I_U133Plus_110_Amy The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76954 Last updated (according to GEO): Oct 11 2005 325 319 cardiac 1000 Skeletal muscle structure the blood 393 402 Heart Atrium 1000 Osteoblasts 1000 seminoma specimen, pT1, patient age: 40y; W00 047 Head and neck cancer Source GEO sample is GSM155688 Last updated (according to GEO): Apr 24 2007 36 21 from whole brain Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151995 Last updated (according to GEO): Feb 06 2007 1000 Cerebral cortex neurological disease control sample x203 Oat cell carcinoma 888 17 7 hippocampus from liver 21 30 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188697 Last updated (according to GEO): Jun 06 2007 R541P00728 Gene expression data from human colon tumor tissue Source GEO sample is GSM173327 Last updated (according to GEO): Apr 20 2007 AD-167t1 (d dup)-A210-8 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156717 Last updated (according to GEO): Jan 22 2007 1424 1403 of the prostate gland umbilical cord_nobpd: 3A brain, left frontal temporal lobe: Extract42_le2 AD-366t1-A109-3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Neuroblastoma 861 SP-KO-Nrf2-Female-2 olfactory epithelium 194 213 Heart failure 871 Fetal brains were obtained from 3 pregnant rats at pregnant day 17. Primary cortical neurons were isolated and pooled separately from each mother and plated onto 100mm ´ dishes, for a total of 4 plates from each pregnant rat. At Day in Vitro (DIV) 16, 3 of the 4 platesfrom the same mother, were exposed to either 1 or 3 MAC halothane (about 1% or 3%) or 3 MAC isoflurane (about 4%) in a gas tight chamber inside the culture incubator for 6 hr. The 4th plate from each mother treated with air were used (inside the same incubator, but outside the chamber) as controls. Isoflurane at 1 MAC was not conducted because of the complete lack of transcriptional response in the animals exposed to 1 MAC of isoflurane. The cells were recovered for an additional 6 hr, harvested, frozen by liquid nitrogen, and stored at ?80oC. Source GEO sample is GSM61799 Last updated (according to GEO): Oct 28 2005 Pancreas at e15.5, Chip A, rep 2 966 Organ 1000 Amygdaloid structure 861 Substantia nigra structure GBM Treatment, type=remove Source GEO sample is GSM99461 Last updated (according to GEO): Apr 21 2006 Cells were either prestimulated (1_X) or not (0_X) for 18h with 100 ng/ml LPS. Media was exchanged and after 2h rest, cells either restimulated (X_1) or not (X_0) with again 100 ng/ml LPS. This resulted in 4 experimental conditions: 0_0, 0_1, 1_0 and 1_1. There were 3 biological replicates done, resulting in 12 arrays altogether. Source GEO sample is GSM213698 Last updated (according to GEO): Aug 01 2007 Basal 1000 ER-/LN+/Nevins7 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Bipolar Disorder Brain 861 /3T3 fibroblasts 295 310 The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale. Toward this end, we have designed custom arrays that interrogate the expression of the vast majority of protein-encoding human and mouse genes and have used them to profile a panel of 79 human and 61 mouse tissues. The resulting data set provides the expression patterns for thousands of predicted genes, as well as known and poorly characterized genes, from mice and humans. We have explored this data set for global trends in gene expression, evaluated commonly used lines of evidence in gene prediction methodologies, and investigated patterns indicative of chromosomal organization of transcription. We describe hundreds of regions of correlated transcription and show that some are subject to both tissue and parental allele-specific expression, suggesting a link between spatial expression and imprinting.. Date GSE1133.1 Last Updated: Contributers: John B Hogenesch John R Walker Gabriel Kreiman Tim Wiltshire David Block Mimi Hayakawa Hilmar Lapp Richard Soden Michael P Cooke Serge Batalov Keith A Ching Andrew I Su Jie Zhang Includes GDS596. Update date: May 14 2004. Dataset description GDS596: Gene atlas of human protein-encoding transcriptome. Examined gene expression profiles from 79 physiologically normal tissues obtained from various sources.. Includes GDS594. Update date: May 13 2004. Dataset description GDS594: Gene atlas of human protein-encoding transcriptome. Examined gene expression profiles from 79 physiologically normal tissues obtained from various sources.. lateral hypothalamus long access to cocaine replicate 1 heart_atrium_2 Anterior nares 1000 Nose 1000 1498 1476 in the small intestine DNA-48HRS 315-99_node none Source GEO sample is GSM239841 Last updated (according to GEO): Dec 07 2007 901 Myeloid Leukemia brain 0 5 1000 Substantia nigra structure Large-scale analysis of the human transcriptome. Ovary pool Source: CHTN, see PMID 11158614 Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 121.54 Stdv: 5.29 Min: 111.41 Max: 130.65 Source GEO sample is GSM2867 Last updated (according to GEO): Mar 20 2006 Neuroglia 901 brain, cortex: 28dsham3_e1_le1 hindbrain 1000 Wild type 8 wk old male C3H/HeJ mouse periaqueductal gray Source GEO sample is GSM107036 Last updated (according to GEO): Mar 05 2007 mouse hippocampus 0 16 901 Pituitary Gland 861 Adrenal Cortex 15 0 human cerebellum Gene expression profile of the cell line UB/OC-1 grown for 6 days under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1523 Last updated (according to GEO): May 27 2005 1000 Thymus Gland Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Dye-swap. Source GEO sample is GSM15952 Last updated (according to GEO): May 28 2005 The effects of chimeric EWS/ETS protein in human mesenchymal progenitor cells (MPCs). Breast 861 BTBR T+ tf/J_female_hypothalamus RNA isolated from fetal heart (predominantly valve and canal regions) Keywords = trisomy Keywords = heart Keywords = Down syndrome Source GEO sample is GSM22610 Last updated (according to GEO): May 27 2005 Richard Almon-42-1133800610073 78 73 rectum of mouse brain 9 23 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Insulin-like growth factor 1 for 120min Source GEO sample is GSM5622 Last updated (according to GEO): May 27 2005 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184779 Last updated (according to GEO): Apr 26 2007 1000 Spinal Cord 1000 Rectum Wild type inbred mice Source GEO sample is GSM82895 Last updated (according to GEO): Nov 10 2005 Spleen vs Untreated B cell Time 0 (set19) HapMap CHB Female Source GEO sample is GSM159597 Last updated (according to GEO): Feb 01 2007 67 40 with coronary artery disease in seminoma 357 368 Adenocarcinoma 861 7 frontal cortex 20 MuscleRegen-ctx20d-1RLAv2-s2 Melanoma xenograft, MEC2_Sub_C (LeiFidler) 1000 Glioblastoma 913 Coronary heart disease 861 Ganglia Hippocampus 861 of regenerating Dorsal Root Ganglia 21 55 Brain 861 20 0 human caudate nucleus Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16022.gif Source GEO sample is GSM91606 Last updated (according to GEO): Sep 22 2006 Gene expression data from human colon tumor tissue Source GEO sample is GSM173320 Last updated (according to GEO): Apr 20 2007 Serum cyc 0.5 C57 whole brain 3 mouse brain 478 489 GSE6937 4525 4520 liver 861 HIV Infections 2500mg/kg APAP 24Hr rat 3631 blood vs. 3616 PC 24Hr (pool) 61 50 Uterus C57BL HCC (HBV+, SF1, 1) In our original grant we proposed to use the NR3B-null mouse model to study the role of NR3B subunit in motor neuron function. We have now successfully generated NR3B null mice. Interestingly, NR3B-null mice invariably die at age P4-P8. Our preliminary examination indicates that the motor strength of these mice is severely impaired prior to death. As we continue to explore the cause of death in NR3B null mice, we propose to conduct gene profiling experiments to search for transcription changes in the brain related to ablation of the NR3B gene. We would like to use the facility provided by the NINDS/NIMH Microarray Consortium to identify true outlier genes that show abnormal expression patterns in these mice. Analysis of these outlier genes will help to identify changes in networks and pathways that may cause the death of NR3B-null mice. These studies will further help to elucidate the functional role of NR3B in motor neurons. We will compare samples from the hindbrain and spinal cord of wild type and NR3B null mice to identify true outlier genes that show abnormal expression patterns, which may be implicated in the death of NR3B-null mice We hypothesize that genes with their transcription level changing significantly by ablation of NR3B will be associated with the molecular mechanism underlying the death of motor neurons in NR3B null mice. As NR3B is expressed primarily in the hindbrain and spinal cord, we will first collect and analyze the hindbrain and spinal cord samples from NR3B null mice and wild-type controls in triplicate at two time points (P0 and P5). Total RNA from total 12 samples will be purified. Extracted RNAs will be treated for with DNase I to remove contaminating genomic DNA. The purified RNA will be sent to the NINDS/NIMH Microarray Consortium to generate biotin-labeled probe according to the Affymetrix protocol. These probes will be used to hybridize the GeneChip Mouse Genome 430 2.0 Array. The hybridization, scanning, and initial data analysis of these GeneChips will be conducted by the Consortium staff. We will analyze the collected data further after data collection. We will use computer software, GeneSpring (Silicon Genetics, Redwood City, CA), to analyze data from microarray experiments. We will first identify genes that show significant changes between wild-type and NR3B null mice by applying ANOVA analysis to sample groups of different ages. The genes identified in this manner will then be subjected to hierarchical (Gene tree) and nonhierarchical (K-means) cluster analysis, in order to group them according to similar expression patterns. Another clustering method, the self-organizing map, will be used to determine whether one gene cluster is a variant of another. Finally, the Principal Components Analysis (PCA) will be employed to analyze large sample groups, which may include experimental variability with respect to age, anatomical location and genotype. We will determine from these analysis whether further experiments are needed using different array platforms, such as Agillent Oligo Array. Last Updated (by provider): Jun 09 2006 Contributers: Dongxian Zhang 861 Blood 4525 4520 liver The epithelial cells 962 981 Exp 1 (+TNFa) Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp1214 Source GEO sample is GSM2171 Last updated (according to GEO): Nov 21 2005 Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1). NA12751 growth 1, replicate 2 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13423.gif Source GEO sample is GSM79661 Last updated (according to GEO): Sep 22 2006 1000 Retina no additional Source GEO sample is GSM199142 Last updated (according to GEO): Jun 08 2007 226 206 the cartilage anlagen HCC (HBV+, HK16) Substantia Nigra MME Sample3 RMA, MAS 5, dChip Brain 1000 1000 Spleen of caudal 93 101 102 67 in Emery-Dreifuss muscular dystrophy Lymphoblastoid Cell Line for Individual 8092.3 log phase I_95Av2_3023_Cg_0_GS 901 Bone Marrow 90 81 in stroke Coronary Arteriosclerosis 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145831 Last updated (according to GEO): Nov 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145992 Last updated (according to GEO): Nov 20 2006 Kidney Neoplasms 901 1000 Heart failure 84 69 by heart failure plasma cells 332 344 amygdala_4 Source GEO sample is GSM80568 Last updated (according to GEO): Mar 31 2006 Study the transcriptomic effects of the shear stress on cultured osteoblast-like MC3T3 cells Source GEO sample is GSM201209 Last updated (according to GEO): Jun 19 2007 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:275, Count:32 Corner- Avg:41417, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:5.686159,SFGene:All Background:Avg:328.66,Stdev:5.68,Max:345.4,Min:318.5 Noise:Avg:7.07,Stdev:0.19,Max:7.7,Min:6.6 RawQ:10.88 Keywords = ALL Source GEO sample is GSM3445 Last updated (according to GEO): May 27 2005 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184760 Last updated (according to GEO): Apr 26 2007 861 Colon 1000 Rett Syndrome 901 Malignant neoplasm of prostate tg-2 Expression profiling of spinal cord section (T9) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM4471 Last updated (according to GEO): May 28 2005 Disease Source GEO sample is GSM175808 Last updated (according to GEO): Apr 09 2007 Expression profiling of spinal cord section (T9) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM1326 Last updated (according to GEO): May 28 2005 1000 Left 106 of skeletal muscle 88 Tumor__Renal_Carcinoma_6727 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Exp C, Animal #1, 30mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 30mg/kg of CPF for 96 hours Source GEO sample is GSM246172 Last updated (according to GEO): Dec 03 2007 Gut 861 Nasal Epithelium Inhalation Formaldehyde 07ppm 5d ID138 160 119 by sporadic amyotrophic lateral sclerosis 5 0 brain 861 Infertility Voxel G4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1435 Last updated (according to GEO): Nov 21 2005 42 30 Control blood Myocardial Infarction 1000 brain, brainstem: cRNA-SOD-1 of peripheral blood 487 505 Prostate 861 Temporal Cortex Control (AD) 2 Saccule at E14.5, replicate1 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11460 Last updated (according to GEO): May 28 2005 861 Cerebral cortex brain 0 5 Cochlear nuclei 0 14 D_U133A_88_DLPFC We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201788 Last updated (according to GEO): Jun 20 2007 HapMap CEU_parent Male Source GEO sample is GSM159548 Last updated (according to GEO): Feb 01 2007 Normal Source GEO sample is GSM176408 Last updated (according to GEO): Apr 09 2007 To investigate the gene program activated by serotonergic hallucinogens in mouse somatosensory cortex, the effects of the 5-HT2A agonist (±)2,5-dimethoxy 4-iodoamphetamine (DOI) on gene expression was studied. The 5-HT2A serotonin receptor is a member of the 5-HT2 receptor subfamily of G protein?coupled receptors. The 5-HT2A receptor is thought to modulate processes related to cognition, appetite, mood, anxiety, sleep, and sexual behavior. Abnormal function of this receptor has been implicated in neuropsychiatric disorders such as major depression and schizophrenia. In particular, the 5-HT2A receptor has been implicated in the modulation of the mechanisms related to psychosis. We compared gene response patterns in the somatosensory cortical brain area, which has a high density of 5-HT2A receptors and has been implicated in the action of hallucinogenic drugs. Mice (strain 129Sv) were injected with DOI (2 mg/kg or 10 mg/kg) or vehicle, animals were sacrificed after 1 h, and somatosensory cortex samples dissected on ice for RNA extraction. Seven independent microarray hybridizations from seven different DOI- or vehicle-treated mouse pairs were performed. In this particular hybridization, 15 µg of RNA was used. Keywords = somatosensory cortex 5-HT2A receptor DOI Source GEO sample is GSM3383 Last updated (according to GEO): Oct 28 2005 1000 Hippocampus Acetaminophen 24hr Rat 3565 blood vs. Acetaminophen 24hr Rat Pooled Control blood Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242046 Last updated (according to GEO): Dec 04 2007 bronchial epithelia 224 243 skeletal muscle, tibialis anterior: Denervated 3-day MCK::cre 2_e1_le1 901 Somatic cell the blood 393 402 "Sample 19,>5 yr survival(69 months) age 48 erp yes" on vantveer-oligo Gene expression data from human colon tumor tissue Source GEO sample is GSM173361 Last updated (according to GEO): Apr 20 2007 29 0 cerebral cortex wistar ky 3910 Cerebral cortex 861 Brain 861 913 Coronary heart disease Large-scale analysis of the human transcriptome. Pancreas Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 193.42 Stdv: 7.54 Min: 178.05 Max: 208.95 Source GEO sample is GSM2872 Last updated (according to GEO): Mar 20 2006 Nucleus accumbens, male 10.5 week old c57bl/6J mouse, UNSUSCEPTIBLE group Source GEO sample is GSM224751 Last updated (according to GEO): Aug 31 2007 Epithelium 861 brain, amygdala: Stress-Hippocampus_e1_le2 bladder_control_pool-2 of mouse brain 9 23 Brain 1000 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162191 Last updated (according to GEO): Jun 12 2007 Thymosin 861 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25504.gif Source GEO sample is GSM81556 Last updated (according to GEO): Sep 22 2006 Nervous system structure 901 14 0 kidney sprague2 whole blood_100309 901 Impaired cognition prostate Source GEO sample is GSM203297 Last updated (according to GEO): Jun 21 2007 316 304 of the retina park_1154_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Parkinson 0 8 78 73 rectum brain, Medial Temporal Gyrus: Sample32_e1_le1 Autistic Disorder 877 CNS-SCsev_InjB4h-2C-s2 (No additional Information) Source GEO sample is GSM114400 Last updated (according to GEO): Jun 19 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145052 Last updated (according to GEO): Nov 20 2006 Brain 861 C57BL/6 benchmark dataset: Embryonic day 14.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25168 Last updated (according to GEO): May 27 2005 NG108 rat neuronal cell culture exposed to 0.25% DMSO (control) for two hours. 10 µg total RNA hybridized per chip. RNA STAT 60 used to extract RNA. Standard Affymetrix chip scaling factors used. No other data transformation. Source GEO sample is GSM1654 Last updated (according to GEO): Oct 28 2005 PrefrontalCortex Source GEO sample is GSM18930 Last updated (according to GEO): Sep 25 2006 861 Huntington Disease Nerve growth factor (NGF) is a neurotrophin that plays an important role in regulating the survival, growth, and differentiation of sympathetic neurons. Many in vitro studies indicate that Egr transcription factors are coupled to NGF signaling and are essential signaling mediators of NGF-dependent differentiation of sympathetic neurons, such as neuroblastoma cells and pheochromocytoma cells. Mice that are deficient for both Egr1 and Egr3 have profound sympathetic nerve system defects, including abnormal neuron degeneration and impaired differentiation (unpublished observations). To further understand the role of Egr genes in sympathetic neuron development, it is necessary to examine the signal transduction pathways involved in NGF-mediated Egr-dependent gene regulation. The results will be helpful in understanding the pathobiology of those diseases related to aberrant sympathetic neuron differentiation, such as neuroblastoma and dysautonomias, and may provide new insights into therapies for these refractory diseases. To identify NGF-mediated Egr-dependent target genes in human SH-SY5Y/TrkA neuroblastoma cells: Many potential Egr target genes have been described over the years. However, very few have been characterized to be involved in NGF-mediated sympathetic neuron differentiation. In order to further understand the role of Egr genes in sympathetic neuron development, it is necessary to examine the signal transduction pathways involved in NGF-mediated Egr-dependent gene regulation. Egr1 and Egr3 are rapidly induced after NGF treatment and Egr1 is involved in activation of the differentiation marker gene NPY in SH-SY5Y/TrkA cells. Therefore, SH-SY5Y/TtrkA cells appear to be an excellent model system to study the role of Egr transcription factors in sympathetic neuron differentiation in vitro. A dominant negative Egr molecule that specifically blocks transcriptional activity mediated by Egr transcription factors will be used in this study to identify Egr-dependent target genes. Egr1 and Egr3 are rapidly induced after NGF treatment in human SH-SY5Y/TrkA neuroblastoma cells, which in turn differentiate into sympathetic-like neurons. We hypothesize that Egr transcription factors are involved in activating downstream signaling pathways during NGF mediated differentiation of SH-SY5Y/TrkA cells. Moreover, we hypothesize that by using a dominant negative Egr (dnEgr) molecule that blocks all Egr mediated gene transcription and Affymetrix microarray analysis, it will be possible to identify NGF-mediated Egr transcription dependent gene regulatory networks that may be involved in growth and differentiation of neuroblastoma. An unbiased approach to understanding these gene regulatory networks may lead to new insights relating to NGF signaling involved in neuronal growth and differentiation. Human neuroblastoma SH-SY5Y/TrkA cells will be infected with either dnEgr-expressing adenovirus (SH-SY5Y/TrkA-dnEgr) or with EGFP-expressing control adenovirus (SH-SY5Y/TrkA-EGFP). Equivalent infection efficiency and lack of viral toxicity will be verified by EGFP fluorescence microscopy 24 hours after infection and the cells will be treated with NGF (100 ng/ml). Total RNA will be extracted from SH-SY5Y/TrkA (uninfected), SH-SY5Y/TrkA-dnEgr, and SH-SY5Y/TrkA-EGFP cells treated with NGF for 0, 1 hour and 3 hours. Total RNA will be prepared from all of the samples and a portion subjected to real-time PCR analysis to ensure that NGF mediated Egr gene induction was not altered by the context of viral infection. Pilot experiments demonstrate that Egr genes are still induced in the context of viral infection greater than 100-fold. Egr1 mRNA peak expression is known to occur at 1 hour and decrease by 3 hours after NGF treatment in all of the samples. The peak expression of Egr target genes is expected to occur later than Egr1 peak expression since Egr1 proteins need to be expressed first to initiate the transcription of target promoters. Therefore, the RNA samples from SH-SY5Y/TrkA-dnEgr and SH-SY5Y/TrkA-EGFP treated with NGF for 3 hours will be used to probe Affymetrix high-density human genome U133 Plus 2.0 Arrays to identify differentially expressed genes. RNA amplification for probe synthesis should not be necessary since we will provide 10 ug of intact total RNA for each sample. We will provide three sets of samples to perform the comparative microarray analysis twice from different starting materials and a nine-way comparative analysis of the data will be performed. We expect that cells containing high levels of dnEgr will inhibit NGF mediated Egr-dependent target gene expression and that these gene networks should be identifiable when compared to EGFP infected cells that have normal Egr gene transcriptional activity. Last Updated (by provider): Jul 06 2005 Contributers: W G Tourtellotte 1000 Cardiomyopathy, Alcoholic 861 Cerebral cortex Keywords = kidney 149 166 Sample 3 Treatment, type=add, description=low potassium Source GEO sample is GSM53241 Last updated (according to GEO): Jul 06 2005 5 0 Spleen 0 Human Cortex 11 B_D2_Control_ZT 6_2 brain, hindbrain and spinal cord: P5WT3_e1_le1 Fetal frontal cortex cocaine2 Abdominal aorta structure 1000 Expression profiling of spinal cord section (T9) extracted from rats 28d following moderate injury Source GEO sample is GSM31539 Last updated (according to GEO): May 27 2005 VIIcDG_Signal on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B Brain 1000 Small Intestine Jejunum 10 Normal Lung; Day 24 postnatal Keywords = mouse gene expression database Source GEO sample is GSM29382 Last updated (according to GEO): May 27 2005 334 320 Keywords = HIV Plasma 861 spinal cord 37 47 testis 52 58 Parkinson Disease 861 Cerebral cortex 861 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68197 Last updated (according to GEO): Jul 07 2006 CNS-SpinalCmod-Adult-4h-3B-s2 4 0 Brain 266 257 infection Brain 861 brain, unknown: Sample46_e1_le1 1000 Brain Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12513.gif Source GEO sample is GSM79924 Last updated (according to GEO): Sep 22 2006 Insulin Resistance 1000 Paravertebral Muscle 1 Disease 9 0 Blood Test 861 Blood the ventricular 1095 1109 Gene expression data from postmorten brain regions Source GEO sample is GSM145822 Last updated (according to GEO): Nov 20 2006 25 0 Superior_Cervical_Ganglion Heart failure 1000 Placenta BD Normal CNS-SMTC_Mod7d-4A-s2 Brain 861 C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 6hr after experimental mice received their last shock treatment. Source GEO sample is GSM4509 Last updated (according to GEO): May 27 2005 osteoblast 630 640 868 850 of medulloblastoma PriG_Expt3_Day0_rep1 Con (32 h) B on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A 5 0 Spleen no additional Source GEO sample is GSM199345 Last updated (according to GEO): Jun 08 2007 Stem cells 901 Mouse neuroblastoma (N2a) cells are available from the American Tissue Culture Collection (ATCC, number CCL-131). To generate cells expressing 3F4-tagged PrP, cells were stably transfected with Mo3F4 PrP in a pcDNA3.1/Zeo vector (Invitrogen, Leek, The Netherlands) and stable transfectants selected using Zeozine 300 ug/ml medium (Gilch et al, 2001, EMBO 20: 3957-3966). RNA was isolated from control and infected cell lines by the Trizol method. 20µg total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 30µl hybridisation buffer (6x SSC, 0,5% SDS 5 fold Denhardt's solution and 50% formamide) and mixed with 30µl of reference cDNA solution labelled with the second dye. This hybridisation mixture was placed on a pre hybriddised microarray, covered with cover slip, placed into a hybridisation chamber (Genomatix) and immersed in a thermostatic bath at 42°C for at least 16 hours. Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Maen intensities with substracted background were normalised so that the median of their rations has became 1 Keywords = prion Keywords = neuroblastoma Keywords = N2a Source GEO sample is GSM31108 Last updated (according to GEO): Oct 28 2005 Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 7 Male2, Olfactory RNA_Nasal olfactory epithleium_Tissue was preserved in RNA later and collected from nose NoCAD_replicate23 Nrl ko samples were compared to wt at 2 months. Source GEO sample is GSM227470 Last updated (according to GEO): Sep 07 2007 Epithelium 861 861 Medulla 36 from the facial nucleus 14 DNA-EP-4HRS_2 28 7 Superior Frontal Gyrus Nasal Epithelium 865 NA11831 none Source GEO sample is GSM149630 Last updated (according to GEO): Jan 03 2007 BUB/BnJ_female_hypothalamus The epithelial cells 962 981 861 Cerebral cortex 23 0 Substantia nigra PD rep2 1000 Brain 12 on NHGRI-13.8k 5_cerebral_cortex_12hrs_sleep_#35 Gene expression data from postmorten brain regions Source GEO sample is GSM145313 Last updated (according to GEO): Nov 20 2006 Serum cyc 2 hours 861 Aorta AML63 on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151977 Last updated (according to GEO): Feb 06 2007 ventral_tegmental_area_10 Source GEO sample is GSM80908 Last updated (according to GEO): Mar 31 2006 888 Large-Cell Lymphomas 30 19 (Extra Renal skin 80 83 C57BL/6 benchmark dataset: Embryonic day 14.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25170 Last updated (according to GEO): May 27 2005 901 Caudate nucleus structure Olfactory Epithelium 1000 CD3 + CD28 beads + FK506 06.00 hr. T-cell Paravertebral Muscle 6 Disease 0 29 CerebellumPeduncles Source GEO sample is GSM18916 Last updated (according to GEO): Sep 25 2006 rat cortex Treatment, type=time_course, measurement=0.1 d Source GEO sample is GSM53196 Last updated (according to GEO): Jul 06 2005 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15719 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145542 Last updated (according to GEO): Nov 20 2006 brain, contralateral Cortex: Trizol Extraction48_le1 Brain 861 Lymphoblastoid Cell Line for Individual 8049.3 log phase I_U133A_91_Amy D2_TP-48_C Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13112.gif Source GEO sample is GSM79972 Last updated (according to GEO): Sep 22 2006 Lung 861 Nicotinic Receptors 1000 Nasal Epithelium 865 Prosencephalon 861 WT biol repl3 Infection 1178 1187 from rat lungs 21 34 CNS-SpinalCmod-Adult-7d-3C-s2 seminoma specimen, pT1, pN1, patient age: 42y; W95 194 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188765 Last updated (according to GEO): Jun 06 2007 1000 Brain Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132547 Last updated (according to GEO): Feb 26 2007 Cerebral cortex 861 Blood Test (Blinded) Sample Source GEO sample is GSM129956 Last updated (according to GEO): Sep 18 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CGS for 30min Source GEO sample is GSM5511 Last updated (according to GEO): May 27 2005 Immune_CD4+_column purified_T-cells_antiCD3, antiCD28-activated Keywords = mouse gene expression database Source GEO sample is GSM29447 Last updated (according to GEO): May 27 2005 brain, hindbrain and spinal cord: P5WT2_e1_le1 Expression profiling of spinal cord section (T8) extracted from rats 4h following moderate injury Source GEO sample is GSM31464 Last updated (according to GEO): May 27 2005 Amplified RNA from lungs of ovalbumen sensitized and challenged C3H 1 mouse vs. pool of amplified RNA from lungs of control C3H mice. Source GEO sample is GSM6738 Last updated (according to GEO): Nov 21 2005 4 0 Colon 492 475 in the PCOS oocyte Spinal Cord 901 nasal epithelial cells 28 49 gene expression data from ODC mouse skin samples Source GEO sample is GSM216674 Last updated (according to GEO): Aug 09 2007 861 Extrinsic UB/OC-1 differentiation 19 0 human frontal cortex 1000 Brain 338 333 brain Gene expression data from postmorten brain regions Source GEO sample is GSM145011 Last updated (according to GEO): Nov 20 2006 Brain 861 221 212 hemorrhage Parkinson Disease 1000 Oj16: Hippocampus_5T-AI_rep8 4089 4084 liver Gene expression data from skeletal muscle following 30 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230430 Last updated (according to GEO): Sep 19 2007 1000 Heart failure Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141292 Last updated (according to GEO): Oct 26 2006 Head and neck cancer Source GEO sample is GSM155699 Last updated (according to GEO): Apr 24 2007 865 Disorder of artery 1000 Cerebellum 5 0 brain Liver 1000 mouse brains 187 198 none Source GEO sample is GSM241957 Last updated (according to GEO): Nov 29 2007 AcB55 #12246570 1000 Substantia nigra structure of parieto-occipital cortex 223 250 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92359 Last updated (according to GEO): Jan 13 2006 Postnatal day 3 corticospinal motor neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription. Source GEO sample is GSM37093 Last updated (according to GEO): May 27 2005 Vena Cava AB Normal UET-13 15 7 hindbrain 901 Connective Tissue 1000 Spleen Whole blood from a healthy control Source GEO sample is GSM153488 Last updated (according to GEO): Jan 11 2007 Normal Source GEO sample is GSM176350 Last updated (according to GEO): Apr 09 2007 43 0 Chorionic mesoderm-derived mesenchymal cells nasal epithelial cells 28 49 none Source GEO sample is GSM123197 Last updated (according to GEO): Jul 26 2006 1000 frontal lobe Mesenchymal Stem Cells 1000 Expression profiling of spinal cord section (T10) extracted from rats 24h following laminectomy (sham) Source GEO sample is GSM31274 Last updated (according to GEO): May 27 2005 660 mesenchymal stem cell 639 Stomach Cardiac 4 Normal Hippocampus VC mice off/on Dox (Reversal for 2 weeks) Acetaminophen 3hr Rat 2105 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool with mental retardation 241 263 Brain 1000 2nd 2hr C+S-DG normal 1502 in cellular blood 328 344 Whole Brain 62 72 Transcription profiling involves H3 methyltransferase G9a-deleted MEFs reconstituted with empty vector (delta), wild type FLAG-G9a (WT), FLAG-G9a K165A (K165A) or FLAG-G9a H1093K catalytic mutant (H1093K). Source GEO sample is GSM197741 Last updated (according to GEO): Jul 16 2007 Simple annotation: RNA coimmunoprecipitation, development Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8817.gif Source GEO sample is GSM78461 Last updated (according to GEO): Sep 22 2006 Epithelium of bronchus 983 129P3/J CHR, Rep2 Nose 1000 Prostate 16 Disease Parietal Lobe 9 Normal 1000 Bone Marrow 1000 Colon 861 Cerebral cortex Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Englow 1 Prostate 6 Disease collagen 302 310 1000 Histones none Source GEO sample is GSM149604 Last updated (according to GEO): Jan 03 2007 LPS tolerance in macrophages social phobia 190 203 brain, hippocampus: KA240-II_e1_le1 of somatomotor cortex 21 41 GC (HKG47T) Leukemia, Lymphocytic, Chronic 1000 Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22560 Last updated (according to GEO): May 27 2005 Parkinson's model voxel I3 no additional Source GEO sample is GSM199184 Last updated (according to GEO): Jun 08 2007 861 leukemia Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92371 Last updated (according to GEO): Jan 13 2006 Gene expression data from human colon tumor tissue Source GEO sample is GSM173350 Last updated (according to GEO): Apr 20 2007 30 15 bone marrow cell GM19240 cerebral cortex wistar ky 3911 all cortical minus the frontal cortex, individual animal, 10 weeks old, male Wistar Kyoto cerebral cortex file:p3911w Source GEO sample is GSM15148 Last updated (according to GEO): Oct 28 2005 Epithelium of bronchus 983 NCI60.52_LABEL56EXTRACT55SUB3 Source GEO sample is GSM134257 Last updated (according to GEO): Aug 06 2007 Thymus [JunctionChip 1 of 5] Fluid-percussion head injury 83 110 liver_PPARa-knockout_control_5d_rep3 DRG037_a Burkitt Lymphoma 1000 Infection 1000 Neoplasm 861 D2_TP-0_C PGA_IGF1R_1400 941 936 tumors plasma cells 50 61 5 0 brain outer medulla 31 43 Spleen vs BLC Treated B cell 120min (set2) Plasma 861 AD-AD16T2-A391-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Amygdaloid structure 1000 Down Syndrome 1000 Myocardium 861 901 Heart Diseases 129S6/SvEvTac hypothalamus rep2 (430 2.0 Array) 50 Cortex C57BL 61 Rat frontal cortex RNA - VH TTX Experiment Source GEO sample is GSM92311 Last updated (according to GEO): Jan 13 2006 Primary adenocarcinoma Source GEO sample is GSM16557 Last updated (according to GEO): May 28 2005 Medulla Oblongata 861 28 8 large B-cell lymphoma 11 0 Hypothalamus Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228607 Last updated (according to GEO): Sep 11 2007 of a colorectal adenoma 7 29 Pooled soleus RNA samples from five 8 wk old male C57BL10 mice Source GEO sample is GSM13736 Last updated (according to GEO): May 28 2005 901 Bone Marrow M_U133A_19_AnCg of cancer 222 230 Vestibular organ at E10.5, replicate1 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28462 Last updated (according to GEO): May 27 2005 12 0 ovarian tumor 5_cerebral_cortex_9hrs_sleep_deprivation_#22 90 81 in stroke Keywords = kidney 113 130 CurrentSmoker 82 5 0 brain 91 from the bone marrow 72 Mice on a mixed 129/SvJ and C57BL6/J background were sacrificed and livers frozen. RNA was isolated using RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol. Data were normalized by AffyMetrix MAS5.0 using defaults. Keywords = liver cholesterol abc Source GEO sample is GSM9281 Last updated (according to GEO): May 27 2005 CAD_replicate93 1000 ovarian neoplasm ESE_D_489 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156703 Last updated (according to GEO): Jan 22 2007 placebo 15d, biological rep6 861 Skeleton Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160728 Last updated (according to GEO): Sep 24 2007 f2#289 versus pool Mouse Brain tissue Duchenne muscular dystrophy 0 26 brain, amygdala: Stress-Hippocampus_e1_le3 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7602.gif Source GEO sample is GSM79898 Last updated (according to GEO): Sep 22 2006 18 0 Trisomy 21 sample 2 /HeJ periaqueductal gray rep2 3 31 HDMTX_MP-7 O377 homozygotes brains_0 1000 Brain 901 frontal lobe 1000 Endometriosis, site unspecified Sample 107 on vantveer-oligo D_U133Plus_106_nAcc 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart Keywords = Cardiac Keywords = Assist Device Keywords = LVAD Keywords = GATA-4 Keywords = Sprouty1 Keywords = microarray Keywords = heart failure Source GEO sample is GSM14844 Last updated (according to GEO): Oct 28 2005 D05 0h Media NA18633 1000 Brain 1000 Coronary Arteriosclerosis Liver Test (Blinded) Sample Source GEO sample is GSM130110 Last updated (according to GEO): Sep 18 2007 Spleen 0 5 Nervous system structure 901 7 cerebral cortex 21 406 395 whose hearts 1000 Structure of superior frontal gyrus 1037 of transitional epithelium 1012 255 234 with HIV encephalitis HCC-2998 hgu95c n/a Source GEO sample is GSM178042 Last updated (according to GEO): Jun 11 2007 Stem cells 901 0029_1436_H95A2_T97-0080_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A of mouse brain 9 23 KO_NP_mid_3 brain, hippocampus: CH5_e1_le1 361 335 hypertrophic cardiomyopathy 3AMH02082105_BM_CD33Myeloid A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke. White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by treatment (IV) with the catalytic antioxidant AEOL 10150 and then 6 hours of reperfusion; mRNA from a single brain #12. Source GEO sample is GSM2217 Last updated (according to GEO): May 27 2005 human frontal cortex Source GEO sample is GSM86996 Last updated (according to GEO): Feb 08 2006 HNC009 1000 Bone Marrow Cerebral cortex 861 9 0 Blood Test Spleen vs ELC Treated B cell 120min (set2) CNS-SC_CtrBT0-2B-s2 brain, Left frontal Lobe: Extract14_le1 To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at ?80C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at ?80°C before routine processing for GeneChip analysis. Source GEO sample is GSM28661 Last updated (according to GEO): Oct 28 2005 GM19101 20 0 human caudate nucleus Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:387, Count:32 Corner- Avg:36935, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:4.951684,SFGene:All Background:Avg:493.24,Stdev:7.44,Max:514.6,Min:480.1 Noise:Avg:11.19,Stdev:0.52,Max:12.8,Min:9.4 RawQ:14.58 Keywords = ALL Source GEO sample is GSM3435 Last updated (according to GEO): May 27 2005 Gene expression data from whole brain of uninfected mouse Source GEO sample is GSM189603 Last updated (according to GEO): May 16 2007 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 1 hours after lights on. Original RNA code = LC38A. Source GEO sample is GSM227404 Last updated (according to GEO): Sep 10 2007 1BJZ02081480a_Pons Plasma 861 Lymphoblastoid Cell Line for Individual 8201.6 log phase of a colorectal adenoma 7 29 1000 jejunum T23__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A MGMH030212053Bhypothalamus 1000 Skeletal muscle structure Thalamus Subthalamic Nucleus 2 Disease Normal Source GEO sample is GSM175902 Last updated (according to GEO): Apr 09 2007 Human Cell Line, adrenal medulla: RNA612_le1 "Brain, Cerebellum" brain, hippocampus: Aldh5a1-/- #3363 Cort_e1_le1 G9a-K165A Nose 861 3497 3480 by decapitation 2h Parkinson Disease 861 Skeletal muscle biopsy was obtained before a two-hours of hyperinsulinaemic (40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172129 Last updated (according to GEO): Feb 28 2007 Brain (thalamus) [JunctionChip 3 of 5] Brain 861 861 Brain 36 21 from hippocampus Nerve 1000 Muscular Atrophy 877 Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002. Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily. Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France). Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h. After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hippocampal gene expression analysis. From these same 5 mice, the hippocampus was dissected from the mice according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancourt, France), rinsed as described for livers, cut into 17-50 mg subsections, and frozen as described for livers. Hippocampal lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5). Hippocampal tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hippocampal RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips. Source GEO sample is GSM2559 Last updated (according to GEO): Oct 28 2005 Endothelial Cells 1000 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P7, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3225 Last updated (according to GEO): May 28 2005 brain, Left frontal Lobe: Extract27_le2 Osteoblasts 1000 Bone Marrow 1000 outer medulla 31 43 1000 Blood 13 0 G8 optic nerve Hereditary Diseases 913 Wild type voxel E3 PC 12Hr rat 4126 blood vs. 1500mg/kg APAP 12Hr rat 4133 blood 1187 1178 of cancers 7 cerebral cortex 21 67 52 descending colon 2hr post 10Gy IR cerebellum.3 Gene expression data from brain of adult rats Source GEO sample is GSM101039 Last updated (according to GEO): Feb 20 2007 24 skeletal muscle 10 Blood 1000 7 cerebral cortex 21 AMM_0_0_Female8_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111839 Last updated (according to GEO): Nov 21 2006 (cortex 19 25 280 263 the growth plates B74 on NCI-7.6k Communicable Diseases 1000 Epithelium of bronchus 983 T33__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A human cerebellum Source GEO sample is GSM87160 Last updated (according to GEO): Feb 08 2006 DLCL-0026 || lc4b066 NCI60.7_LABEL10EXTRACT9SUB3 Source GEO sample is GSM134027 Last updated (according to GEO): Aug 06 2007 530 519 in the brain in the heart 937 949 Gene expression data from B6xBALB F2 mouse lung Source GEO sample is GSM133470 Last updated (according to GEO): Apr 05 2007 with myocardial infarction 313 339 ovary 45 50 an induced moderate spinal cord injury 836 873 Brain Stem 1000 Study of in vitro granulocyte differentiation Source GEO sample is GSM137435 Last updated (according to GEO): Jun 06 2007 492 475 in the PCOS oocyte Brain 861 Brain 1000 Primary Neoplasm 1000 861 Myositis Lymphoblastoid Cell Line for Individual 8206.4 log phase 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113969 Last updated (according to GEO): Jun 16 2006 966 Hippocampus Zeitgeber Time Treatment, type=time_course, measurement=6.0 h Source GEO sample is GSM53327 Last updated (according to GEO): Jul 06 2005 858 Prostatic Neoplasms M_U133A_102_nAcc Gene expression data from postmorten brain regions Source GEO sample is GSM145610 Last updated (according to GEO): Nov 20 2006 pfc_1011_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A olfactory epithelium SR-A mutant, mouse 48 hpO Source GEO sample is GSM80212 Last updated (according to GEO): Oct 26 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lysophosphatidic Acid for 120min Source GEO sample is GSM5656 Last updated (according to GEO): May 27 2005 of the stria terminalis 51 73 of Parkinson's disease 450 471 osteoblast 627 637 M_U133A_91_AnCg none Source GEO sample is GSM244575 Last updated (according to GEO): Nov 23 2007 Voxel G4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1436 Last updated (according to GEO): Nov 21 2005 70 cortex 76 D_U133A_14_nAcc osteoblast 627 637 CNS-RM_Mod14d-4A-s2 acute myeloid leukemia Source GEO sample is GSM227442 Last updated (according to GEO): Sep 12 2007 brain 0 5 337 323 with adiposity Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28735 Last updated (according to GEO): May 27 2005 Brain 861 907 890 in the hippocampus heart failure 583 595 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211419 Last updated (according to GEO): Jul 18 2007 nasal epithelial cells 28 49 SN:Human Glioblastoma Biopsy 10397 Tacrine 2.7mg/kg/day from 5 weeks, from 5 weeks. Moclobemide 10mg/kg/day Creatine 1%w/v added to wet mash Lot batch = 5241 Source GEO sample is GSM13300 Last updated (according to GEO): May 28 2005 1000 Heart failure gfp pos. sorted cells from 3 disected e14.5 ganglionic eminences Treatment, type=wait Source GEO sample is GSM135772 Last updated (according to GEO): Sep 12 2006 RMS-T3 on NHGRI-6.5k_b Spleen 0 5 SmIntP1_0226AF6R_172.txt To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18423 Last updated (according to GEO): May 27 2005 1000 Cerebral cortex Operator Name: Sample Type: Sample Description: Comments: Reagents: Reagent Lot: Algorithm: Statistical Corner+ Avg:404, Count:32 Corner- Avg:39671, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:4.818338,SFGene:All Background:Avg:542.73,Stdev:10.40,Max:572.5,Min:520.5 Noise:Avg:14.47,Stdev:1.34,Max:19.9,Min:12.3 RawQ:15.60 Keywords = ALL Source GEO sample is GSM3466 Last updated (according to GEO): May 28 2005 mouse hippocampus, cox-1 knockout, rep3 Gene expression data from postmorten brain regions Source GEO sample is GSM145779 Last updated (according to GEO): Nov 20 2006 861 Oocytes Expression profiling of moderately injured raphe at 4h in rats Source GEO sample is GSM41621 Last updated (according to GEO): May 27 2005 Wild type 8 wk old male A/J mouse periaqueductal gray Source GEO sample is GSM74988 Last updated (according to GEO): Feb 27 2007 RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above Source GEO sample is GSM160005 Last updated (according to GEO): Feb 05 2007 23 6 (postcentral gyrus Spleen vs Untreated B cell Time 0 (set8) 861 Cerebral cortex GBM Treatment, type=remove Source GEO sample is GSM99572 Last updated (according to GEO): Apr 21 2006 HC103 CB A Heart 1000 GC (HKG24L) of Parkinson's disease 450 471 4525 4520 liver B6_Control_ZT 0_3 GSE9570 LDMTX_MP-6 Mid secretory endometrium from normal patient Source GEO sample is GSM150224 Last updated (according to GEO): Dec 14 2006 Normal__Ovary_OV_2 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Endometrium I_U133A_29_CB Plasma 861 Dahl-Iwai Male LowSalt OuterMedulla rat110 dahl_medullar_110_1_OM_053001 The genomic consequences of bursts of action potential firing induced (2 h pulse) by the treatment of cultured cortical neurons (9-11 DIV) with the GABAA receptor antagonist bicuculline (Bic, 50 ?M) and the potassium channel blocker 4-aminopyridine (4AP, 5 ?M). Source GEO sample is GSM144063 Last updated (according to GEO): Nov 24 2006 bladder_TaGL_pool-2 865 Disorder of artery 861 Breast tibiae 115 120 umbilical cord_nobpd: 2C We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7. Source GEO sample is GSM200740 Last updated (according to GEO): Jul 12 2007 19 0 human frontal cortex Cerebral cortex 861 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 5 day time point Source GEO sample is GSM159793 Last updated (according to GEO): Apr 23 2007 901 Coronary artery outer medulla 31 43 Plasma 861 no additional Source GEO sample is GSM199229 Last updated (according to GEO): Jun 08 2007 I_U133A_15_CB 861 Cerebellum Hippocampus Source GEO sample is GSM107921 Last updated (according to GEO): Jun 06 2006 41 29 Control blood 320 306 Keywords = HIV CSCC1 sample 1 CNS-RM_Ctr28d-2C-s2 Day 1 Mouse #13 - 3rd replicate Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 13 hours after lights on. Original RNA code = LC47A. Source GEO sample is GSM227357 Last updated (according to GEO): Sep 10 2007 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47530 Last updated (according to GEO): May 29 2005 Urethra 4 Normal no additional Source GEO sample is GSM199349 Last updated (according to GEO): Jun 08 2007 5 0 brain 254 238 of neural retinas 5 0 Spleen Pancreas 1000 1000 Muscle Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228655 Last updated (according to GEO): Sep 11 2007 1000 Brain brain, Entorhinal Cortex: 01-22 normal_e1_le1 brain_OFC_control C_mr202 of coronary artery disease 317 342 MuscleRegen-ctx10d-10LLA-s2 S11_Muscle_Baseline_0min 24 0 Proliferative endometrium Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit. Source GEO sample is GSM200589 Last updated (according to GEO): Jul 09 2007 1000 Brain NA19209 1000 Liver of somatomotor cortex 21 41 Pooled total RNA from (3) P27 L3-L5 Egr3-deficient spinal cords Treatment, type=acclimatization Source GEO sample is GSM32061 Last updated (according to GEO): May 27 2005 I_U133A_3_CB H Fast Rep 3 GM11839 861 Cerebral cortex 19 0 human frontal cortex none Source GEO sample is GSM239868 Last updated (according to GEO): Dec 07 2007 Corpus Callosum 4 Normal HapMap CEU_parent Male Source GEO sample is GSM159547 Last updated (according to GEO): Feb 01 2007 Blood 1000 A549/ATCC hgu95c Type 2 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228669 Last updated (according to GEO): Sep 11 2007 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b033 Source GEO sample is GSM1982 Last updated (according to GEO): Nov 21 2005 with mental retardation 241 263 VDXIGRU_254031 with Parkinson's disease 27 50 Transplant Series 36 , Transplant # 5 /3T3 fibroblasts 743 759 with autism spectrum disorder 37 65 PMN_control_0min_Patient14 Pool of 15 otic vesicles at E10 Source GEO sample is GSM182568 Last updated (according to GEO): Aug 14 2007 S1P3-KO-hippocampus, biological rep4 (female) 1000 Amygdaloid structure 1000 Cerebellum NCI60.56_LABEL60EXTRACT59SUB3 Source GEO sample is GSM134276 Last updated (according to GEO): Aug 06 2007 Acetaminophen 24hr Rat 7198 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool in bipolar disorder 1645 1663 1000 Brain brain, hippocampus: KA-6h-P15-III_e1_le1 Occipital lobe 861 Spleen vs Prostaglandin E2 Treated B cell 30min (set2) Pituitary Source GEO sample is GSM19021 Last updated (according to GEO): Sep 25 2006 brain, brainstem: PB4_e1_le1 hippocampus 7 17 Brain 1000 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15077.gif Source GEO sample is GSM91578 Last updated (according to GEO): Sep 22 2006 CCRF-CEM_I_CL7003_Leukemia on Affymetrix GeneChip Human Full Length Array HuGeneFL 732 719 in the jejunum A/OVX/no inj/0h/UTX 129/SvImJ WT Osteoblasts 1000 no additional Source GEO sample is GSM199197 Last updated (according to GEO): Jun 08 2007 GSE1606 20 9 Brain trauma 14 days age control RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis. Source GEO sample is GSM10046 Last updated (according to GEO): May 28 2005 in fibroblasts 1222 1236 Putamen 2 Normal Transitional epithelium 1000 NCI-H23 hgu95d 861 Ribosomal RNA CNS-SC_InjB7d-1B-s2 Whole blood 0 10 Transitional epithelium 1000 091211 OVR8 on Affymetrix GeneChip Human Full Length Array HuGeneFL ataxia 92 98 brain 0 5 The olfactory epithelium 0 23 JejuPrxTumor1022CAFBX_jtc.txt Lymphoblastoid Cell Line for Individual 8006.3 log phase Hoxb1 mutant E10.5, rep 1 (M5) Cortex_Control_rep4 (05SE734) AML_11 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A spinal cord 0 11 of prostate cancer 747 764 wildtype neonatal mouse brain3 (W-3) Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11499 Last updated (according to GEO): May 28 2005 Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep5 Structure of trigeminal ganglion 1000 LungE135_022KACGW_076.txt Large cell carcinoma of lung 937 901 Stem cells Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68298 Last updated (according to GEO): Jul 07 2006 such as drug addiction 83 104 nostrils 156 164 1037 of transitional epithelium 1012 prostate Source GEO sample is GSM203292 Last updated (according to GEO): Jun 21 2007 861 Brain 10 Bone marrow 0 no additional Source GEO sample is GSM199339 Last updated (according to GEO): Jun 08 2007 5 0 brain Date : 5/29/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 3 hrs post-injection Intervention : none Risk: estimated 20% increased risk for encephalopathy Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AO017 Source GEO sample is GSM12240 Last updated (according to GEO): May 28 2005 Liver [JunctionChip 4 of 5] in bronchial epithelia 121 144 tibiae 115 120 Mouse Liver AIN Diet 5wk Control, biological replicate B Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5459.gif Source GEO sample is GSM93151 Last updated (according to GEO): Sep 22 2006 265 in epithelial cells 283 Transplant Series 25 Right, Transplant # 1 starved 29 35 LCM 20 biological rep4 Oat cell carcinoma 867 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211292 Last updated (according to GEO): Jul 18 2007 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 5557 left_liver_lobe Primary tumor 19 32 67 52 descending colon This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM190915 Last updated (according to GEO): Sep 13 2007 329 306 valvular cardiomyopathy human caudate nucleus Source GEO sample is GSM86847 Last updated (according to GEO): Feb 08 2006 Fallopian Tube AB2 Normal mouse brains 187 198 Cerebral cortex 1000 1000 Brain Expression profiling of laminectomized raphe at 24h in rats Source GEO sample is GSM41523 Last updated (according to GEO): May 27 2005 337 323 with adiposity liver 184 189 Coronary heart disease 913 Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM107997 Last updated (according to GEO): Jun 06 2006 Frontal Lobe 3 Normal olfactory epithelium 194 213 70 40 without coronary artery disease prostate Source GEO sample is GSM203318 Last updated (according to GEO): Jun 21 2007 Osteoblasts 1000 "22 hr Hela Double Thymidine, exp3" Wild type 8 wk old male 129S6/SvEvTac mouse hypothalamus Source GEO sample is GSM74970 Last updated (according to GEO): Feb 27 2007 1000 Cardiomyopathy, Alcoholic mouse brain 478 489 SN:1006488 Source GEO sample is GSM115346 Last updated (according to GEO): Jun 20 2006 Liver 1000 Nervous system structure 901 A HID B D017 Lung 1000 heart 1169 1173 for osteoclasts 1125 1140 Spleen vs Prostaglandin E2 Treated B cell 60min (set3) Spleen vs Dimaprit Treated B cell 120min (set2) 1000 ovarian neoplasm The nose 94 101 861 Epithelial Cells 5 0 Spleen 7 Entorhinal Cortex 23 Spleen 1000 Bipolar Disorder DLBC57 on Affymetrix GeneChip Human Full Length Array HuGeneFL Expression profiling of spinal cord section (T10) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31667 Last updated (according to GEO): May 27 2005 Heart 861 256 235 dilated heart failure Wild type voxel A2 Rat vestibular ganglia_calretinin_negative_rep2 Expression profiling of naive raphe (T0) in rats Source GEO sample is GSM41554 Last updated (according to GEO): May 27 2005 116 in skeletal muscle 99 kidney 37 43 VP16-CREB hippocampus region Source GEO sample is GSM88939 Last updated (according to GEO): Jan 04 2006 Ventral Tegmental Area 884 1000 Rod Photoreceptors 13 0 jazaeri-breast 1000 Microphthalmos Infection 1000 Hoxb1 wt E10.5, rep 3 (W8) 715 702 After the eyes gene expression from allergen stimulated mouse lung Source GEO sample is GSM158136 Last updated (according to GEO): Jan 25 2007 frontal cortex 145 159 Blood Test (Blinded) Sample Source GEO sample is GSM129931 Last updated (according to GEO): Sep 18 2007 HapMap JPT Male Source GEO sample is GSM159628 Last updated (according to GEO): Feb 01 2007 36 21 from hippocampus total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD27 for 240min Source GEO sample is GSM5501 Last updated (according to GEO): May 27 2005 861 Brain advanced HCC Source GEO sample is GSM155963 Last updated (according to GEO): Jun 21 2007 RNA isolated from fetal cerebellum Keywords = trisomy Keywords = brain Keywords = Down syndrome Source GEO sample is GSM22585 Last updated (according to GEO): May 27 2005 1000 Secondary Glioblastoma PGA-HBE-CtrAir0h-1aA-S2 Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200636 Last updated (according to GEO): Jun 12 2007 901 Myeloid Leukemia Skeletal bone 861 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 1 - Pair 3 - MMN Source GEO sample is GSM49883 Last updated (according to GEO): Dec 20 2005 brain, Medial Temporal Gyrus: Sample27_e1_le1 983 pM category Brain 861 966 Hippocampus The nose 94 101 tongue_superior_part_w/_papillae_2 DBA-2J_male_hypothalamus Bmi-1 dependence distinguishes neural stem cell self-renewal from progenitor proliferation. Osteoblasts 1000 Transplant Series 36 , Transplant # 2 Brain_Rhab_10_AT/RT (Brain) on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Heart failure cortex 7 12 osteoblast 627 637 Lung 1000 43h-AM replication 2 Keywords = preimplantation Keywords = development Source GEO sample is GSM14711 Last updated (according to GEO): May 28 2005 Day 11 Mouse #73 - 3rd replicate Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7476 Last updated (according to GEO): May 27 2005 Skeletal bone 861 1000 Spinal Cord The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27030 Last updated (according to GEO): May 27 2005 Aortic Aneurysm 901 None Source GEO sample is GSM196061 Last updated (according to GEO): Jul 16 2007 DIF 3, chip MOE430B of Parkinson's disease 450 471 5 0 brain Ovary 1000 12 0 Blood B cells 0 Human Cortex 11 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28773 Last updated (according to GEO): May 27 2005 Donor E, after G-CSF Source GEO sample is GSM178558 Last updated (according to GEO): Aug 09 2007 Normal Source GEO sample is GSM176144 Last updated (according to GEO): Apr 09 2007 brain, cerebral cortex: 15000_e2_le1 16 0 Folate deficiency Heart Atrium 1000 of the atrial 647 659 normal human skeletal muscle sample 1 of the heart 842 854 human caudate nucleus Source GEO sample is GSM86908 Last updated (according to GEO): Feb 08 2006 Brain 861 1000 Large Intestine Pituitary Gland 2 Normal Wild-type-neocortex, biological rep7 (female) HapMap CEU_parent Female Source GEO sample is GSM159559 Last updated (according to GEO): Feb 01 2007 Cerebral cortex 1000 Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17266.gif Source GEO sample is GSM91499 Last updated (according to GEO): Sep 22 2006 CNS-SC_InjA7d-4C-s2 Brain 1000 Blood 1000 none Source GEO sample is GSM239927 Last updated (according to GEO): Dec 07 2007 to psychosis 673 685 brain, cerebral cortex: Nico 8/23_le1 1000 Lipids brain 0 5 715 702 After the eyes for defining the cancer ? 1163 1187 DCIS57 on harvard-12k 861 Blood Brain 861 ovary 45 50 Prostatic Diseases 913 17 7 hippocampus 861 HIV Infections Cerebellum_naive_ILS48_B 861 Acquired Immunodeficiency Syndrome nostrils 156 164 Primary Neoplasm 1000 14 7 amygdala 41 29 Control blood Dahl Salt Sensitive Rat Lung- Control 2 Muscle Source GEO sample is GSM4267 Last updated (according to GEO): May 27 2005 Blood Test (Blinded) Sample Source GEO sample is GSM130037 Last updated (according to GEO): Sep 18 2007 outer medulla 31 43 Muscle 861 MLL-#3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Medulla 861 123 86 of multipotent neural progenitor cells Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92382 Last updated (according to GEO): Jan 13 2006 1000 Amyotrophic Lateral Sclerosis 861 Thymus Gland Dendritic Cells, Exposed to Brugia malayi (5) - Repeat #1 mouse left hemi-diaphragm Source GEO sample is GSM53236 Last updated (according to GEO): Jul 06 2005 GSE422 Gene expression data from postmorten brain regions Source GEO sample is GSM145941 Last updated (according to GEO): Nov 20 2006 77 66 Normal Brain Frontal cortex 254 267 Wnt (0 h) B on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A 12 0 ovarian tumor 861 Brain of the colon 28 39 861 Cerebral cortex 1000 Globus Pallidus HC76 CN B Blood 861 1000 Leukemia, Myelocytic, Acute Gene expression data from rat lungs exposed to Normoxia (room air). Source GEO sample is GSM184873 Last updated (according to GEO): Jun 14 2007 5 0 Muscle Malignant neoplasm of urinary bladder 1000 Control hippocampus 2 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53448 Last updated (according to GEO): Jul 06 2005 Heart 861 Colon Cancer 5 16 AM Treatment, type=remove Source GEO sample is GSM99498 Last updated (according to GEO): Apr 21 2006 9 0 Blood Test Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 5480 blood Skeletal bone 861 Parkinson Disease 861 1000 Structure of middle cerebral artery RNA from three stroke patients was pooled. Source GEO sample is GSM239108 Last updated (according to GEO): Oct 29 2007 Skeletal muscle structure 901 whole blood_100190 /3T3 fibroblasts 478 493 brain, cerebral cortex: Rat_03-35_NroLep_Lipska_e1_le1 Brain 861 861 HIV Infections 6420_Lung did not develop PGD the heart 987 996 1000 Tongue 1000 Spleen Monocular deprivation left cortex, biological rep2 CHC MD-5 19 0 3AJZ02021913_ UTERUS left 35 38 233 215 cafe-au-lait spots 1000 Hippocampus 1100 1087 heart failure NCI60.42_LABEL46EXTRACT45SUB3 Source GEO sample is GSM134200 Last updated (according to GEO): Aug 06 2007 Wild-type striatal cells treated with 3NP Source GEO sample is GSM82442 Last updated (according to GEO): Jun 26 2007 neurological disease control sample x197 42 minus the frontal cortex 66 RENAL_7860 on Affymetrix GeneChip Human Full Length Array HuGeneFL CNS-SC_InjA4h-2A-s2 Hyperdip>50-C12 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 3AJZ02022103_leukemia, promyelocytic-HL-60 Abdominal aorta structure 865 mouse cerebral cortex from COX-2 heterozygous Source GEO sample is GSM121435 Last updated (according to GEO): Jan 31 2007 Recurrent Adenocarcinoma 3 1000 Mammary gland 1124 1117 histone- Osteoblasts 1000 LPS plus IL-10, 30 min, Rep_2 Normal Source GEO sample is GSM175829 Last updated (according to GEO): Apr 09 2007 ERalpha-CITED1 co-regulated genes expressed during pubertal mammary gland development: implications for breast cancer prognosis. 861 Brain Despite over 3,000 articles published on dystrophin in the last 15 years, the reasons underlying the progression of the human disease, differential muscle involvement, and disparate phenotypes in different species are not understood. The present experiment employed a screen of 12,488 mRNAs in 16-wk-old mouse mdx muscle at a time when the skeletal muscle is avoiding severe dystrophic pathophysiology, despite the absence of a functional dystrophin protein. A number of transcripts whose levels differed between the mdx and human Duchenne muscular dystrophy were noted. A fourfold decrease in myostatin mRNA in the mdx muscle was noted. Differential upregulation of actin-related protein 2/3 (subunit 4), beta-thymosin, calponin, mast cell chymase, and guanidinoacetate methyltransferase mRNA in the more benign mdx was also observed. Transcripts for oxidative and glycolytic enzymes in mdx muscle were not downregulated. These discrepancies could provide candidates for salvage pathways that maintain skeletal muscle integrity in the absence of a functional dystrophin protein in mdx skeletal muscle. of somatomotor cortex 21 41 1BJZ02022757_thymus 5 0 brain NA19172 Brain 861 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 2652 left_liver_lobe Gene expression data from postmorten brain regions Source GEO sample is GSM145270 Last updated (according to GEO): Nov 20 2006 Transplant Series 13 , PrimaryTumor 1000 Liver 38 CB B Huntington's disease (HD) is an inherited neurodegenerative disease caused by a glutamine repeat expansion in huntingtin protein. Transcriptional deregulation and altered energy metabolism have been implicated in HD pathogenesis. We report here that mutant huntingtin causes disruption of mitochondrial function by inhibiting expression of PGC-1alpha, a transcriptional coactivator that regulates several metabolic processes, including mitochondrial biogenesis and respiration. Mutant huntingtin represses PGC-1alpha gene transcription by associating with the promoter and interfering with the CREB/TAF4-dependent transcriptional pathway critical for the regulation of PGC-1alpha gene expression. Crossbreeding of PGC-1alpha knockout (KO) mice with HD knockin (KI) mice leads to increased neurodegeneration of striatal neurons and motor abnormalities in the HD mice. Importantly, expression of PGC-1alpha partially reverses the toxic effects of mutant huntingtin in cultured striatal neurons. Moreover, lentiviral-mediated delivery of PGC-1alpha in the striatum provides neuroprotection in the transgenic HD mice. These studies suggest a key role for PGC-1alpha in the control of energy metabolism in the early stages of HD pathogenesis. CNS-SpinalC-conAdult-24h-3A-s2 Untreated versus treated (bortezomib) breast cancer cells. Source GEO sample is GSM120354 Last updated (according to GEO): Jul 20 2006 NA Source GEO sample is GSM198901 Last updated (according to GEO): Jun 07 2007 43 0 Chorionic mesoderm-derived mesenchymal cells 1000 Brain 861 frontal lobe Transcriptional changes during neuronal death and replacement in the olfactory epithelium. mouse cerebral cortex from COX-1 WT Source GEO sample is GSM121421 Last updated (according to GEO): Jan 31 2007 Left hemidiaphragm 923 healthy subject Source GEO sample is GSM211028 Last updated (according to GEO): Sep 10 2007 skeletal muscle, tibialis anterior: Innvervated Control 2_e1_le1 brain 0 5 CNS-SMTC_Mod14d-4B-s2 345 319 the articular chondrocytes Wild type inbred mice Source GEO sample is GSM82896 Last updated (according to GEO): Nov 10 2005 B77 on NCI-7.6k 1000 Hereditary Diseases primary hepatocytes, mouse, treatment with WY14643 for 24h Source GEO sample is GSM205897 Last updated (according to GEO): Jul 24 2007 Prostate 1000 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM119702 Last updated (according to GEO): Jul 11 2006 1000 Brain Macrophage 14smi054 Structure of entorhinal cortex 1000 7 Entorhinal Cortex 23 5 0 brain Pituitary Gland, Posterior 1000 Gene expression data from human colon tumor tissue Source GEO sample is GSM173359 Last updated (according to GEO): Apr 20 2007 Normal Source GEO sample is GSM175883 Last updated (according to GEO): Apr 09 2007 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210419 Last updated (according to GEO): Jul 16 2007 hippocampal glutamatergic CA1 pyramidal neurons Source GEO sample is GSM35821 Last updated (according to GEO): May 27 2005 "Sample 34,>5 yr survival(123 months) age 54 erp yes" on vantveer-oligo 17 7 hippocampus 1000 Heart failure 17 7 hippocampus frontal lobe 1000 Cardiac 523 530 from colorectal adenoma 21 44 D_U133A_13_Amy M_U133A_52_DLPFC PC3 Treatment, type=incubate, description=Hypoxic preconditioning Source GEO sample is GSM107472 Last updated (according to GEO): May 01 2006 Muscle; Skeletal Keywords = mouse gene expression database Source GEO sample is GSM29403 Last updated (according to GEO): May 27 2005 BC2 Lymph Node X NCI reference brain, left frontal temporal lobe: Extract38_le1 1983 1969 adhering blood M_U133A_98_nAcc Colonic mucous membrane 913 Cerebral cortex 1000 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162174 Last updated (according to GEO): Jun 12 2007 861 Dislocations 858 Prostatic Neoplasms Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11227.gif Source GEO sample is GSM76464 Last updated (according to GEO): Sep 22 2006 Parkinson Disease 1000 embryo day 8.5 Source GEO sample is GSM18635 Last updated (according to GEO): May 27 2005 V5-P221 to the nose 599 609 cardiac 746 752 Spleen 1000 NA06994 861 Neoplasm 361 335 hypertrophic cardiomyopathy 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114479 Last updated (according to GEO): Jun 16 2006 HC80 CB B This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195237 Last updated (according to GEO): Sep 13 2007 stria terminalis 1000 HapMap YRI_parent Female Source GEO sample is GSM159697 Last updated (according to GEO): Feb 01 2007 no additional Source GEO sample is GSM199269 Last updated (according to GEO): Jun 08 2007 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:366, Count:32 Corner- Avg:40460, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:3.576670,SFGene:All Background:Avg:393.51,Stdev:6.89,Max:411.1,Min:376.0 Noise:Avg:8.31,Stdev:0.25,Max:9.0,Min:7.7 RawQ:12.20 Keywords = ALL Source GEO sample is GSM3412 Last updated (according to GEO): May 27 2005 M_U133A_10_CB 18 13 Cancer CNS-SMTC_Mod3mo-4A-s2 A/J bed nucleus of the stria terminalis rep1 Mouse old brain C30-Br-3 DLBC14 on Affymetrix GeneChip Human Full Length Array HuGeneFL RNA characterization of tissue from the injury site, 35 days post-injury. From the Christopher Reeve Paralysis Foundation Research Consortium microarray study (www.crpf.org/microarray) Source GEO sample is GSM49934 Last updated (according to GEO): May 27 2005 CCAT DTS Rep A3 myocardial infarction 383 403 Dahl-Iwai Male HighSalt OuterMedulla rat114 dahl_medullar_114_1_OM_053001 Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174518 Last updated (according to GEO): Mar 14 2007 Cochlear nucleus structure 901 Obesity 861 DLCL-0011 Autistic Disorder 877 Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 6622 blood Gene expression data from postmorten brain regions Source GEO sample is GSM144867 Last updated (according to GEO): Nov 20 2006 NCI60.11_LABEL14EXTRACT13SUB3 Source GEO sample is GSM134047 Last updated (according to GEO): Aug 06 2007 865 853 in M+ tumors 861 Brain thymus sprague1 whole tissue, individual animal, 10 weeks old, male Sprague Dawley thymus file:R3JW02103017 Source GEO sample is GSM15215 Last updated (according to GEO): May 28 2005 1000 Bronchi Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225938 Last updated (according to GEO): Nov 02 2007 Standard affymetrix protocol Source GEO sample is GSM119491 Last updated (according to GEO): Jul 31 2007 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy Keywords = pathological hypertrophy Keywords = rat Keywords = heart failure Keywords = cardiomyopathy Source GEO sample is GSM11896 Last updated (according to GEO): May 28 2005 171 158 of metastasis Secondary malignant neoplasm of lymph node 1000 Performed by UCI Microarray Facility. Source GEO sample is GSM203513 Last updated (according to GEO): Jun 22 2007 C57BL10 soleus sample 2 Proliferative endometrium from patient with endometriosis Source GEO sample is GSM150195 Last updated (according to GEO): Dec 14 2006 150mg/kg APAP 12Hr rat 4130 blood vs. PC 12Hr rat 4126 blood Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153476 Last updated (according to GEO): Jan 11 2007 660 mesenchymal stem cell 639 GSE1037 0029_1243_H95A2_KF0154_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A BALB/cJ strain, brain hemisphere, biological rep3 1000 Liver spleen.2 Epithelial Cells 901 5 0 brain Muscle 1000 the ventricular 1095 1109 Cerebellum Control (AD) 8 901 Cervical sympathetic ganglion 861 Cerebral cortex Normal Source GEO sample is GSM176075 Last updated (according to GEO): Apr 09 2007 1529 to the peritoneal cavity 1505 874 847 with a lymph node metastasis brain, cerebral cortex: NMDA30 5/7_le1 Pool of total RNA from 3 euploid cerebella at P15 postnatal stage Keywords = Down syndrome Keywords = Chromosme 21 Keywords = Transcriptome Keywords = Microarray Keywords = Brain Keywords = Cerebellum Keywords = Development Source GEO sample is GSM27475 Last updated (according to GEO): May 27 2005 861 Neoplasm 1000 Prostate Cerebral cortex 861 Heart 861 atrial septal defects 198 218 Gene expression data from postmorten brain regions Source GEO sample is GSM145833 Last updated (according to GEO): Nov 20 2006 861 Cochlear structure Skeletal bone 861 ER negative human primary breast tumor EA02014_41297_H133A_JA-2001 Ventral tegmental area 0 22 Intestines, Small 901 1000 Uterus Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11225 Last updated (according to GEO): May 28 2005 MCF10A_Treated_#4 hippocampal glutamatergic CA1 pyramidal neurons Treatment, type=behavioral_stimulus, description=These are control animals. Source GEO sample is GSM35843 Last updated (according to GEO): May 27 2005 Gene expression data from skeletal muscle following 30 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230433 Last updated (according to GEO): Sep 19 2007 Recurrent Adenocarcinoma 2 861 Prosencephalon HapMap CHB Female Source GEO sample is GSM159579 Last updated (according to GEO): Feb 01 2007 in the striatum 234 248 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/5100.gif Source GEO sample is GSM93130 Last updated (according to GEO): Sep 22 2006 of motor axon terminals. 333 357 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11503 Last updated (according to GEO): May 28 2005 Heart 861 Macrophages, Exposed to Leishmania major - Repeat #2 Skeletal muscle structure 1000 901 Nervous system structure Nose 1000 Organ 861 CCAT Full Length Rep A3 1000 Breast Carcinoma Chronic Lymphocytic Leukemia 19 47 861 Thymus Gland Lateral Sclerosis 901 861 Cardiomyopathies Menstrual phase - Follicular Source GEO sample is GSM175781 Last updated (according to GEO): Apr 09 2007 Dahl Salt Sensitive Rat Lung- Hypoxia with SU-5416 rep2b Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181048 Last updated (according to GEO): Jul 12 2007 1000 Heart failure Gene expression data from postmorten brain regions Source GEO sample is GSM145938 Last updated (according to GEO): Nov 20 2006 gene expression data from ODC mouse skin samples Source GEO sample is GSM216675 Last updated (according to GEO): Aug 09 2007 861 Cerebral cortex Liver Test (Blinded) Sample Source GEO sample is GSM130200 Last updated (according to GEO): Sep 18 2007 Neoplasm 861 865 Disorder of artery SNB-19 hgu95d f2#250 versus pool Mouse Brain tissue Heart Septal Defects, Atrial 1000 Small cell carcinoma of lung 1000 Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19205 Last updated (according to GEO): May 27 2005 Primary tumor 19 32 none Source GEO sample is GSM239854 Last updated (according to GEO): Dec 07 2007 starved 35 41 standard Affymetrix protocol, MAS 5.0 Source GEO sample is GSM9141 Last updated (according to GEO): May 28 2005 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 16 hours after lights on. Original sample code = CM49A Source GEO sample is GSM227350 Last updated (according to GEO): Sep 10 2007 2270 into the developing cortex 2296 Gloubus Pallidum Internal 7 Normal on the ventricles 598 614 1000 Down Syndrome ALL_6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A normal testis 54 66 Expression profiling of spinal cord section (T9) extracted from rats 24h following moderate injury Source GEO sample is GSM31533 Last updated (according to GEO): May 27 2005 Dahl Salt Sensitive Rat Lung- Hypoxia with SU-5416 rep2 Neostriatum 1000 cerebellum 7 16 Malignant Neoplasms 861 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Prostaglandin E2 for 240min Source GEO sample is GSM5740 Last updated (according to GEO): May 27 2005 ADH-1 ip saline ILI 48hrs post ILI hippocampus_4 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD27 for 120min Source GEO sample is GSM5497 Last updated (according to GEO): May 27 2005 NHF1-hTERT_G2_C5_16167 -_6537_batch1 on NHGRI-6.7k 901 frontal lobe Gene expression data from postmorten brain regions Source GEO sample is GSM145653 Last updated (according to GEO): Nov 20 2006 high gestational age Source GEO sample is GSM213090 Last updated (according to GEO): Jul 25 2007 Brain 861 5 0 Kidney Nothing in line. Source GEO sample is GSM154235 Last updated (according to GEO): Jul 05 2007 Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35387 Last updated (according to GEO): May 27 2005 Hippocampus 1000 1000 Brain Mouse ileum 0 10 Skeletal bone 861 PGA-swim_3w_s1097 5 0 Muscle HUVEC isolate 8 rich media control for #22 Source GEO sample is GSM12914 Last updated (according to GEO): May 28 2005 Olfactory Epithelium 1000 NoCAD_replicate12 Gene expression data from postmorten brain regions Source GEO sample is GSM144911 Last updated (according to GEO): Nov 20 2006 Subject code A50 1000 Prostate Molecular portraits of human breast tumours. HeLa CD4+ cells were transfected with an epitope-tagged eTat plasmid and selected with hygromycin. Cells were treated with hydroxyurea and collected @3 hours. Source GEO sample is GSM8697 Last updated (according to GEO): May 27 2005 Mouse ileum with B.thetaiotaomicron_A_5559 5 0 brain Cerebral cortex 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145235 Last updated (according to GEO): Nov 20 2006 2529 CP24_31 Predicting the clinical status of human breast cancer by using gene expression profiles. This is 8-week-old mouse untreated gastrocnemius muscle Source GEO sample is GSM4248 Last updated (according to GEO): May 27 2005 Coronary artery 901 mouse brains 187 198 A HID I D056 Whole Brain 62 72 1000 Brain 1000 Impaired cognition ovary 45 50 560 552 in brains Small cell carcinoma of lung 901 PMN_control_360min_Patient12 5 0 brain 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114267 Last updated (according to GEO): Jun 16 2006 1 of 3 replicates in treatment group Source GEO sample is GSM206022 Last updated (according to GEO): Jun 29 2007 healthy subject Source GEO sample is GSM211042 Last updated (according to GEO): Sep 10 2007 861 Spinal Cord Anterior nares 1000 Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell 240min (set3) NA Source GEO sample is GSM198910 Last updated (according to GEO): Jun 07 2007 T-ALL-C16 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Nasal Epithelium 901 Epithelial Cells 901 MuscleRegen-ctx6d-1RLAv2-s2 Standard Affymetrix Protocol Source GEO sample is GSM16505 Last updated (according to GEO): May 28 2005 Male 74.5 yr before antibody enrichment scan 1 (U133B) on the ventricles 598 614 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114464 Last updated (according to GEO): Jun 16 2006 Cerebral cortex 1000 Cerebral cortex 1000 GBM Treatment, type=remove Source GEO sample is GSM99447 Last updated (according to GEO): Apr 21 2006 Hypertensive disease 861 from colorectal adenoma 21 44 Squamous epithelial cell 861 "Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling." brain 0 5 from ventral prostate 21 41 Temporal Cortex Control (mTLE) 1 20 0 human caudate nucleus Brain 861 Virus Diseases 1000 no additional Source GEO sample is GSM199174 Last updated (according to GEO): Jun 08 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11519 Last updated (according to GEO): May 28 2005 Cerebral cortex 901 Abdomen 861 CS 21523A Information about the genes that are preferentially expressed during the course of Alzheimer?s disease (AD) could improve our understanding of the molecular mechanisms involved in the pathogenesis of this common cause of cognitive impairment in older persons, provide new opportunities in the diagnosis, early detection, and tracking of this disorder, and provide novel targets for the discovery of interventions to treat and prevent this disorder. Information about the genes that are preferentially expressed in relationship to normal neurological aging could provide new information about the molecular mechanisms that are involved in normal age-related cognitive decline and a host of age-related neurological disorders, and they could provide novel targets for the discovery of interventions to mitigate some of these deleterious effects. Aim 1. Collect brain samples from three Alzheimer?s Disease Centers (ADCs) for subsequent gene expression profiling. Individuals will be stratified with respect to diagnostic groups (using both clinical and neuropathological criteria), age groups, and APOE genotype. 150 individual brains will be sampled from the Arizona ADC, the Duke University ADC, and the Washington University ADC. Miniscule sample sizes (200 um of sectioned tissue) from six brain regions that are histopathologically or metabolically relevant to AD and aging will be collected, ensuring that this proposal does not deplete the national resource. Frozen and fixed samples will be sent to Phoenix, sectioned in a standardized fashion, and then returned. Aim 2. Tissue heterogeneity will be eliminated prior to expression profiling by performing laser capture microscopy on all brain regions. Aim 3. Expression profile LCM-captured cells on the Affymetrix U133 Plus 2.0 array (~55,000 transcripts), and quickly provide these data to the community at large. Aim 4. Identify pathogenic cascades related to each of the clinico-pathologic correlates using unsupervised and supervised analyses coupled with a hypothesis-driven approach. Aim 5. Validation of the expression correlates at the protein and functional levels. Scientific progress in the last few years has improved our understanding of AD and raised the hope of identifying treatments to halt the progression and prevent the onset of this disorder. For instance, researchers have begun to characterize the cascade of molecular events which lead to the major histopathological features of the disorder: neuritic plaques, which contain extra-cellular deposits of amyloid beta-peptides (Abeta); neurofibrillary tangles, which contain the hyperphosphorylated form of the intracellular, microtubule-associated protein, tau; and a loss of neurons and synapses. These molecular events provide targets for the development of promising new treatments. For example, A-beta has been postulated to trigger a cascade of events that are involved in the pathogenesis of AD. This proposal hopes to provide new information about the genes that are preferentially expressed in the development of AD histopathology, including the over-expression of APP, amyloid-induced neurotoxicity, and hyperphosphorylation of tau, as well as bring clarity to the metabolic abnormalities that seem to play a role in dementia and AD development and pathology. We will perform LCM on 6 brain regions with about 14 biological replicates per brain region. The brain regions are as follows: 1) entorhinal cortex 2) hippocampus 3) medial temporal gyrus 4) posterior cingulate 5) superior frontal gyrus and 6) primary visual cortex. We will collect layer III pyramidal cells from the white matter in each region, isolate total RNA from LCMed cell lysates, and perform double round amplification of each sample for array analysis. Last Updated (by provider): Jul 10 2006 Contributers: Dietrich A Stephan nerve, HumanSuralNerve: Human Schwann cell RNA extracts 351 Passage 1_le1 liver 0 5 1810 1796 the hippocampus in seminoma 28 38 Endometrium 21 Normal NA12750 growth 3 of Parkinson's disease 450 471 with myocardial infarction 313 339 d12 whole blood_102321 Spinal Cord 1000 WGACON-9 Epithelium of bronchus 983 Identification of Genetic Variants Contributing to Cisplatin-Induced Cytotoxicity using a Genome-wide Approach 861 Breast Average value of duplicate experiments of gut neurospheres (neurospheres of peripheral nervous system) of BMI-1 Knockout mice (postnatal day 0). The cRNAs were generated by two round amplifications. Source GEO sample is GSM9240 Last updated (according to GEO): May 27 2005 320-00_Adeno_p Systematic discovery and classification of ovarian fertility factors. Parkinson Disease 1000 Tumor__CNS_Glioblastoma_GlioB_5 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A The epithelial cells 962 981 Liver Test (Blinded) Sample Source GEO sample is GSM130065 Last updated (according to GEO): Sep 18 2007 12 frontal Lobe 23 mouse brain 478 489 Large-scale analysis of the human transcriptome. Kidney Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 173.70 Stdv: 9.65 Min: 148.80 Max: 185.59 Source GEO sample is GSM2830 Last updated (according to GEO): Mar 20 2006 1000 Amygdaloid structure blood, Blood: 6000_0100_le1 1000 Spleen Control total RNA was pooled from the kidney of five normal BALB/c mice. Total RNA was extracted from the kidney of BALB/c mice injected with anti-GBM antibody for 3 day. Source GEO sample is GSM15084 Last updated (according to GEO): May 28 2005 3-day-denervated tibialis anterior muscles from runx1f/- control mice Treatment, type=add, description=runx1f/- Source GEO sample is GSM99422 Last updated (according to GEO): Mar 08 2006 149 114 Keywords = Congestive heart failure 24 7 Right Frontal Lobe Total RNA extracted from the forebrain of a Tg+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144390 Last updated (according to GEO): Nov 14 2006 in the mammalian nervous system 110 141 Gene expression data from postmorten brain regions Source GEO sample is GSM145967 Last updated (according to GEO): Nov 20 2006 861 HIV Infections 335 325 The jejunum R621P01206 1000 Left dorsal root ganglion fisher1 Skeletal bone 861 cortex 27 33 1000 Muscular Atrophy AD-114T1-A9-1 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from postmorten brain regions Source GEO sample is GSM145160 Last updated (according to GEO): Nov 20 2006 K-562 hgu95d D_U133Plus_104_CB Normal Source GEO sample is GSM176179 Last updated (according to GEO): Apr 09 2007 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225659 Last updated (according to GEO): Aug 31 2007 861 Skeletal bone in neurodegenerative disorders 344 374 Gene expression data from dorsal pancreas at e15.5, MG-U74B version2 Source GEO sample is GSM199459 Last updated (according to GEO): Jun 08 2007 Retina 1000 human caudate nucleus Source GEO sample is GSM86836 Last updated (according to GEO): Feb 08 2006 M4 biol repl 2 17 7 hippocampus 1000 Structure of trigeminal ganglion Head and neck cancer Source GEO sample is GSM155700 Last updated (according to GEO): Apr 24 2007 Epithelial Cells 1000 primary cortical neurons sprague1 GBM: 99A6 Tissue Source GEO sample is GSM67230 Last updated (according to GEO): Jan 19 2006 HUVEC isolate 9 low serum media control for #8 Source GEO sample is GSM12900 Last updated (according to GEO): May 28 2005 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114443 Last updated (according to GEO): Jun 16 2006 osteoblast 630 640 ovary 45 50 outer medulla 31 43 Expression profiling of spinal cord section (T9) extracted from rats 24h following severe injury Lot batch = Source GEO sample is GSM7571 Last updated (according to GEO): May 28 2005 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153487 Last updated (according to GEO): Jan 11 2007 NA Source GEO sample is GSM84310 Last updated (according to GEO): Nov 21 2005 1000 Rectum Plasma 861 Fibroblasts 861 none Source GEO sample is GSM149550 Last updated (according to GEO): Jan 03 2007 Cerebellum_transgenic nuclear localization signal Htt exon1 18Q x50_16 months_replicate 1 brain, frontal cortex: ADX AM FC b_e1_le1 Obesity and fatty acid oxidation knockin mouse cerebellum Treatment, type=time_course, measurement=4.0 weeks Source GEO sample is GSM53343 Last updated (according to GEO): Jul 06 2005 HepG2 0h 3 Control D_U133Plus_92_HC Macrophages, Exposed to Brugia malayi (50) - Repeat #1 111 FC BA9 B Brain_MD_5_Medulloblastoma_Classic_D on Affymetrix GeneChip Human Full Length Array HuGeneFL brain, left frontal temporal lobe: Extract38_le2 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM79044 Last updated (according to GEO): Oct 24 2005 Expression profiling of spinal cord section (T9) extracted from rats 7d following severe injury Lot batch = Source GEO sample is GSM7593 Last updated (according to GEO): May 28 2005 liver_PPARa-knockout_WY14643_5d_rep2 Lymphoblastoid Cell Line for Individual 8185.4 log phase of somatomotor cortex 21 41 of Parkinson's disease 450 471 Richard Almon-9-1133800608979 86 70 Fetal liver cells Expression profile of genes in mouse brain Source GEO sample is GSM21051 Last updated (according to GEO): May 27 2005 Ganglia, Spinal 923 mammarygland.1 metanephric mesenchyme, LIF, 2 days, biological rep2 84 69 by heart failure 861 Muscle 861 Blood M_U133Plus_125_HC Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15385.gif Source GEO sample is GSM84154 Last updated (according to GEO): Sep 22 2006 M_U133A_101_AnCg SN:1011109;Fetal Cartilage, U133A validation Epithelium 861 cerebellum 7 16 high gestational age Source GEO sample is GSM213073 Last updated (according to GEO): Jul 25 2007 Expression profiling of spinal cord section (T10) extracted from rats 4h following mild injury Source GEO sample is GSM31337 Last updated (according to GEO): May 27 2005 benign prostate hyperplasia 37 63 Comprehensive description of the transcriptome of hypothalamo-neurohypophyseal system in euhydrated and dehydrated rat 1000 Brain 5 0 brain 64 47 that whole ovaries Anterior interpositus nucleus-centered deep cerebellar nuclei were sampled using syringe needles Source GEO sample is GSM84979 Last updated (according to GEO): Mar 29 2006 Sensitized on days 0 and 3 with ragweed pollen protein and alum, challenged intratrecheally on days 10 and 17 with ragweed pollen protein and sacrificed after 72h. Lot batch = Source GEO sample is GSM1278 Last updated (according to GEO): May 28 2005 brain, cerebral cortex: Total RNA extraction_le1 261167 11 0 Normal Brain Sample34, Post Injury 24 hours Treatment, type=wait Source GEO sample is GSM53285 Last updated (according to GEO): Jul 06 2005 of the stria terminalis rep1 20 47 Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 24h. Lot batch = Source GEO sample is GSM1233 Last updated (according to GEO): May 28 2005 osteoblast 627 637 of the kidney 568 581 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12673.gif Source GEO sample is GSM79959 Last updated (according to GEO): Sep 22 2006 1000 Spleen Primary tumor 19 32 BladdAd_022EAC39_087.txt heart 1169 1173 1000 Brain mouse hippocampus 0 17 in mouse hearts 40 54 MO_control_0min_Patient5 Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183407 Last updated (according to GEO): Apr 23 2007 cocaine naive, ventral tegmental area, 0 hrs/day access to cocaine Source GEO sample is GSM93859 Last updated (according to GEO): Jan 26 2006 1000 Spinal Cord MSS-Ctr9moM-1aAv2-s2 10 7 Left Liver 1000 A/J pituitary gland rep2 (430 2.0 Array) Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=810650 LaserPower=2.281.29 Lot batch = LC17N049 Source GEO sample is GSM4788 Last updated (according to GEO): Nov 21 2005 861 Huntington Disease comparison of olfactory-bulbectomized and sham-operated rats with depressive-like behaviour Source GEO sample is GSM247202 Last updated (according to GEO): Dec 11 2007 mouse brain contralateral control Source GEO sample is GSM149748 Last updated (according to GEO): Mar 15 2007 861 Aorta Juvenile astrocytoma 861 Myocardium 861 Stria 861 Aldosterone-producing adenoma (APA7) Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47524 Last updated (according to GEO): May 29 2005 607 597 the rectum Medulla Oblongata 861 1000 Retina P21 cochlear nuclei pooled from 5 pups for one replicate hybridization out of 3 replicates. Source GEO sample is GSM44857 Last updated (according to GEO): Jun 08 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with TGF-beta (transforming growth factor-beta) for 240min Source GEO sample is GSM5799 Last updated (according to GEO): May 27 2005 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181234 Last updated (according to GEO): Jul 12 2007 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc105 Source GEO sample is GSM1891 Last updated (according to GEO): Nov 21 2005 AcB61 #12243360 Hypertension, Pulmonary 1000 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184806 Last updated (according to GEO): Apr 26 2007 GRB14, GPD1, and GDF8 as potential network collaborators in weight loss-induced improvements in insulin action in human skeletal muscle. 1000 Neurodegenerative Disorders Brain 861 1000 Cerebral cortex Lymph node metastasis 19 40 CS-B cell UVC-irradiated (2hour) replicate 3 U133A Keywords = Heart 505 521 /6J Frontal Cortex C2 5 25 Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 72h. Lot batch = Source GEO sample is GSM1247 Last updated (according to GEO): May 28 2005 colon_cecum_1 Source GEO sample is GSM80624 Last updated (according to GEO): Mar 31 2006 Osteoblasts 1000 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225941 Last updated (according to GEO): Nov 02 2007 brain, Primary Visual Cortex: Sample66_e1_le1 Bone Marrow 1000 Brain 861 896 Myomatous neoplasm total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-beta (IFN beta) for 240min Source GEO sample is GSM5600 Last updated (according to GEO): May 27 2005 of the atrial 647 659 1000 Lung VDXIGRU_217320 D_U133A_53_DLPFC Brain 1000 CD rep 2 861 Neoplasm O377 homozygotes brains 10 232-97_node brain, cerebral cortex: Rat_02-43_VHL_Lipska_e1_le1 Anterior nares 1000 137T low-grade dysplastic liver tissue Source GEO sample is GSM155976 Last updated (according to GEO): Jun 21 2007 PHG-PCM-1bAv2-s2 Adenocarcinoma 861 M_U133A_33_DLPFC Osteoblasts 1000 Head and neck cancer Source GEO sample is GSM155718 Last updated (according to GEO): Apr 24 2007 144 114 from a single adult spinal cord Standard affymetrix protocol Source GEO sample is GSM119492 Last updated (according to GEO): Jul 31 2007 in adenocarcinoma 29 45 17 CN A 24 hr vehicle repl 1 N7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 0 Human Cortex 11 Parkinson Disease 1000 Sun179_BAV13 group ER negative human primary breast tumor EA02014_41290_H133A_JA-1938 Brain 861 "34 hr Hela Double Thymidine, exp3" Polyamide2_2 We will separately dissect the maxillary and mandibular branches of the E10.5 first branchial arch from wild type, dlx2, dlx1/2 and Dlx5/6 mutants. The tissues wil be flash frozen within 1 min of removal.We have not performed the dissections yet so we dont know how much RNA will be get from each sample, but previous experience suggests that we will need ~10 branchial arches/experiment. Treatment, type=nucleic_acid_extraction, description=We anticipate using this method as it was recommended by TGEN for small amounts of tissue. Source GEO sample is GSM107889 Last updated (according to GEO): Jun 06 2006 Carcinoma, Large Cell 867 868 850 of medulloblastoma Liver 1000 861 Heart Neoplasm 1000 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188735 Last updated (according to GEO): Jun 06 2007 autism 70 75 Category: Cell-line Subcategory: HMEC Scanning Software: unknown Software version: unknown Lot batch = 0096-5k Source GEO sample is GSM1941 Last updated (according to GEO): Nov 21 2005 4 0 Brain 9 0 Blood Test low-density lipoprotein receptor 467 499 Cerebral cortical contusion in rat 4 dpi, #2 bc-ZT15-3 Testis 1000 Chronic leukemia NOS 913 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour.This animal was sacrificed at 8 hours after lights on.Original sample code = CM24A Source GEO sample is GSM227342 Last updated (according to GEO): Sep 10 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11495 Last updated (according to GEO): May 28 2005 1000 Coronary Arteriosclerosis 36 0 Inflammatory myopathy specimen GEIM21 Brain 861 GSE7400 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188728 Last updated (according to GEO): Jun 06 2007 Gene expression data from dorsal pancreas at e14.5, MG-U74A version2 Source GEO sample is GSM199447 Last updated (according to GEO): Jun 08 2007 T03__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Caudate P4 Normal 901 Spinal Cord Whole Brain 62 72 10 7 Left na Source GEO sample is GSM181254 Last updated (according to GEO): Apr 10 2007 UT rep 3 CNS-SCsev_InjB4h-1B-s2 Hippocampus 861 91 from the bone marrow 72 Adrenal cortex [JunctionChip 2 of 5] standard Affymetrix protocol, MAS 5.0 Source GEO sample is GSM9140 Last updated (according to GEO): May 28 2005 Septum Source GEO sample is GSM107946 Last updated (according to GEO): Jun 06 2006 913 Localized Malignant Neoplasm 00291188H95A2-T00-0070v2p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Whole Brain Source GEO sample is GSM18763 Last updated (according to GEO): Sep 25 2006 Endometrium 1000 861 Blood oocyte 0 5 1000 Brain 36 21 from whole brain 117 cortex 123 in human brain 150 163 Gene expression data from human colon tumor tissue Source GEO sample is GSM173349 Last updated (according to GEO): Apr 20 2007 Tumor__Mesothelioma_235_T6 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A cell adhesion molecules 1397 1420 Wild type inbred mice Source GEO sample is GSM82901 Last updated (according to GEO): Nov 10 2005 (cortex 19 25 VDXOXFU_547 Colon 1000 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228613 Last updated (according to GEO): Sep 11 2007 26-3 spinal cord 4 19 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19222 Last updated (according to GEO): May 27 2005 CurrentSmoker 83 861 Brain 66 42 out of mouse bone marrow Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211287 Last updated (according to GEO): Jul 18 2007 T34__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Bone Marrow 1000 Olfactory Epithelium 1000 DLCL-0048 272 251 of the median eminence Epithelium 861 84 69 by heart failure zhang-affy-arabi-50806 S46 NLS 142Q TG3 F5/10 S46 NLS Htt exon 1 142Q Mouse 3.5 months Cerebellum Female Source GEO sample is GSM73211 Last updated (according to GEO): Sep 06 2005 Expression data with no treatment Source GEO sample is GSM230901 Last updated (according to GEO): Sep 20 2007 Brain_MD_37_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Prostate 861 Cerebral cortex 861 Occipital lobe 177 158 into chondrocytes to f2#9 versus pool Mouse Brain tissue Ovarian_Tumor_Mucinous_UM-OM-03 RENAL_CAKI1 on Affymetrix GeneChip Human Full Length Array HuGeneFL Parkinson Disease 861 in the left hemi-diaphragm 1289 1315 nostrils 156 164 Substantia Nigra 1 Normal Muscle; Skeletal Keywords = mouse gene expression database Source GEO sample is GSM29402 Last updated (according to GEO): May 27 2005 Expression data of substantia nigra from postmortem human brain of Parkinson's disease patients (PD) PGA-MFD-CtrPD5-2aCv2-s2 1000 Brain 861 Cancer of Neck GSE6976 3 min exposure to halothane, immediate perfusion with ice cold saline Keywords = Eckenhoff. anesthetics Source GEO sample is GSM5105 Last updated (according to GEO): Mar 17 2006 Brain 1000 1000 Brain Cockayne syndrome B cell Source GEO sample is GSM225385 Last updated (according to GEO): Sep 11 2007 osteoblast 627 637 From naive male C57BL/6 mice (20-25 g), a 4 mm diameter disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44476 Last updated (according to GEO): May 27 2005 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11340 Last updated (according to GEO): May 28 2005 of the atrial 647 659 1000 frontal lobe Lymphoblastoid Cell Line for Individual 8108.4 log phase 156 145 Their livers 861 Fissure 20 11 cord blood 861 Dislocations 52 CN A Spleen vs CpG-oligodeoxynucleotide Treated B cell 240min (set2) 8 0 G6 cornea Lung; Day 5 postnatal Keywords = mouse gene expression database Source GEO sample is GSM29384 Last updated (according to GEO): May 27 2005 Plasma 861 (cortex 19 25 NCI60.43_LABEL47EXTRACT46SUB3 Source GEO sample is GSM134209 Last updated (according to GEO): Aug 06 2007 after infection 158 172 Malignant Neoplasms 1000 brain, unknown: Sample51_e1_le1 AK_Control_ZT 0_1 1000 Uterus CC11+ sample 1 GSE402 23 0 locus coeruleus sprague1 Acetaminophen 3hr Rat 0186 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool Cerebral cortex 861 AD control Treatment, type=dissect Source GEO sample is GSM119653 Last updated (according to GEO): Jul 10 2006 Parkinson Disease 1000 90 81 in stroke MSS-Spa-M6moF-1bAv2-s2 A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism Source GEO sample is GSM5989 Last updated (according to GEO): Nov 21 2005 no additional Source GEO sample is GSM199295 Last updated (according to GEO): Jun 08 2007 Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153776 Last updated (according to GEO): Jan 19 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145261 Last updated (according to GEO): Nov 20 2006 This dataset contains the gene expression profile of a CD11c high, CD4 positive splenic dendritic cell population. The cells were processed following 2 hour incubation in tissue culture medium at 37 C. Global scaling was applied to Avg Difference intensity values. Keywords = mouse, dendritic cells, spleen Source GEO sample is GSM4757 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 The sample is a part of a series describing gene expression changes during postnatal development of the small intestine Source GEO sample is GSM198884 Last updated (according to GEO): Jun 11 2007 NA07056 1243 HP6_11 1000 Structure of parenchyma of lung Myocardium 861 Dystrophin 1000 8h mitotic selection testis 52 58 non-branched in vitro-formed UBs and MM, rep1 1000 Solid tumor 7 0 prostate Septum Source GEO sample is GSM107903 Last updated (according to GEO): Jun 06 2006 19 0 human frontal cortex Tumor__Bladder_TCC_B_0003 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Normal Source GEO sample is GSM176332 Last updated (according to GEO): Apr 09 2007 Epithelial Cells 901 Cardiac 523 530 Luminal breast tumor cell line BT474 Keywords = Agilent microarray, Expression analysis, EGFR, Breast cancer growth Source GEO sample is GSM29524 Last updated (according to GEO): Dec 13 2006 Expression data from mouse bone marrow macrophages from a strain intercross Brain 861 Muscle 1000 Lymphoblastoid Cell Line for Individual 8069.4 log phase 884 Organ of Corti 861 Cerebral cortex Nj14: Hippocampus_21PT-AU_rep8 Cerebral cortex 861 1000 medulloblastoma Experimental Autoimmune Encephalomyelitis 901 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184770 Last updated (according to GEO): Apr 26 2007 Spleen 1000 Prefrontal Cortex Source GEO sample is GSM105462 Last updated (according to GEO): Apr 17 2006 Adult occipital cortex cocaine4 1000 Muscle of orbit 1000 Amygdaloid structure Cerebral cortex 861 Brain 861 861 Cerebral cortex Bladder C100 on NCI-7.6k Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11333 Last updated (according to GEO): May 28 2005 Thyroid; Thyroid Keywords = mouse gene expression database Source GEO sample is GSM29443 Last updated (according to GEO): May 27 2005 69 CB B Nasal Epithelium Inhalation Formaldehyde 2ppm 8d ID223 Parkinson Disease 1000 966 Hippocampus Fertilized egg replication 1 0 27 32 12 frontal temporal lobe 1115 1102 cardiomyopathy 1000 jejunum placebo 6d, biological rep1 brain 0 5 Spleen vs Neuropeptide Y Treated B cell 30min (set2) GSE2502 Mouse Hypothalamus Male 2 (technical replicate) 091223 OVR18 on Affymetrix GeneChip Human Full Length Array HuGeneFL Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15769.gif Source GEO sample is GSM91610 Last updated (according to GEO): Sep 22 2006 /SvEvTac mouse periaqueductal gray 29 62 muscularis externa layers 785 809 brain 0 5 Gene expression data from purified granule neuron precursors. Source GEO sample is GSM148580 Last updated (according to GEO): Mar 14 2007 NCI/ADR-RES hgu95e Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181096 Last updated (according to GEO): Jul 12 2007 Normal human tissue:Normal Colon Keywords = Human, Normal Tissue, Normal Colon Source GEO sample is GSM44680 Last updated (according to GEO): May 27 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68137 Last updated (according to GEO): Jul 07 2006 AD control Treatment, type=dissect Source GEO sample is GSM119658 Last updated (according to GEO): Jul 10 2006 861 Neoplasm 156 145 Their livers 861 Cerebellum olfactory epithelium tissue 85 111 no additional Source GEO sample is GSM199418 Last updated (according to GEO): Jun 08 2007 184-96_node PBMCs-Type 1 Diabetes-IDDM47_T1D_4MO Bone Marrow 1000 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n095 Source GEO sample is GSM2077 Last updated (according to GEO): Nov 21 2005 Gene expression data from skeletal muscle following 30 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230454 Last updated (according to GEO): Sep 19 2007 1000 Lung 1000 Diabetes Mellitus, Non-Insulin-Dependent with some respiratory epithelium. 1039 1072 brain, cerebral cortex: 4R-4(2/5)_le1 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28799 Last updated (according to GEO): May 27 2005 Cultured_cortical_astrocyte_Cx43_null_rep1 nostrils 156 164 1000 Spleen 1000 Prostate Neurosphere cultures were established from individually isolated E 14.5 forebrains of mouse embryos that carry a bcl2 transgene. Single-cell suspensions were prepared, seeded at 1x105 cells/ml and treated for two days with 150 nM Trichostatin A (TSA), 500 nM 5-Aza-2?-deoxycytidine (AzaC) or both compounds, or left untreated. Two independent experiments were performed. Source GEO sample is GSM8901 Last updated (according to GEO): Oct 28 2005 Expression profiling of fast glial cells of obesity 321 331 Nose 1000 4535 4527 hepatoma embryonic hearts 1064 1079 plasma cells 50 61 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28472 Last updated (according to GEO): May 27 2005 huang-breast 0 11 Normal Source GEO sample is GSM176113 Last updated (according to GEO): Apr 09 2007 67 40 with coronary artery disease S3_IL6_1 Fibroblasts 861 Brain 861 eye, retina: 1 Retina at CT 12_e1_le1 861 Cerebral cortex on proliferating peripheral blood mononuclear cells 123 173 Epithelium 861 processed in batch 1 Source GEO sample is GSM90447 Last updated (according to GEO): Mar 20 2006 M_U133Plus_123_DLPFC I_U133Plus_108_AnCg 1000 Endometriosis, site unspecified hippocampus 7 17 1000 Brain Coronary Arteriosclerosis 1000 1000 Hippocampus 1000 Coronary Arteriosclerosis mouse brains 187 198 Bladder sample 1068-1 Cortex 0 5 Nervous system structure 901 901 Caudate nucleus structure 2061 2044 of the hippocampus 117 99 of the hypothalamus placebo 12h, biological rep1 heart failure 583 595 post-ES_EpiSC-7_P25 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188757 Last updated (according to GEO): Jun 06 2007 Occipital lobe 861 CNS-SC_Inj7d-2B-s2 BALB/cByJ Olfactory Bulb C P18 non-deprived visual cortex replicate 1 Skeletal muscle biopsy was obtained after a two-hours of hyperinsulinaemic (40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172138 Last updated (according to GEO): Feb 28 2007 FVB/NJ Hippocampus B Ganglia, Spinal 884 OltactoryEpithelium_mutant_biolrepli3 1000 Kidney emphysema. 257 267 Lymphoblastoid Cell Line for Individual 8164.4 log phase 69 50 Salivary gland C57BL plasma cells 50 61 A4 urethra_1 1000 Carcinoma brain, cerebral cortex: Co4 (2/5)_le1 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226165 Last updated (according to GEO): Nov 02 2007 1000 Malignant neoplasm of urinary bladder brain 0 5 cy3:SHR treated w/ nifedipine and then washed out, biological rep 4g; cy5:pool of 6 WKY control rats Epithelium 861 1000 Left Parkinson Disease 1000 1000 Cerebral cortex Skin 861 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162180 Last updated (according to GEO): Jun 12 2007 861 Neoplasm the blood 393 402 Standard Affymetrix Protocol Source GEO sample is GSM16500 Last updated (according to GEO): May 28 2005 1000 Encephalitis Job's patient Source GEO sample is GSM211089 Last updated (according to GEO): Sep 10 2007 Leg 112 Day control rep 2 A/J Hippocampus E total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Interferon-gamma (IFN gamma) labeled with Cy5- time course with repeats. Date GSE384 Last Updated: May 29 2005 Contributers: Joella Grossoehme Sun Young Lee Mi Sook Chang Robert Hsueh Zhen Yan Rebecca Hart Angela Alexander Sangdun Choi Yun Anna Cao Jong-Woo Kim Includes GDS305. Update date: Nov 18 2003. Dataset description GDS305: Temporal analysis of effects induced by 0.25 nM interferon gamma in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. 184B5 tibiae 115 120 Prediction of response and survival following chemotherapy in patients with advanced bladder cancer B6_Control_ZT 18_2 SN48h(3) 15 0 human cerebellum 861 Pancreas healthy subject Source GEO sample is GSM211128 Last updated (according to GEO): Sep 10 2007 no additional Source GEO sample is GSM199099 Last updated (according to GEO): Jun 08 2007 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 16 hours after lights on. Original sample code = CM13A Source GEO sample is GSM227308 Last updated (according to GEO): Sep 10 2007 Ovarian_Tumor_Endometrioid_CHTN-OE-047 80 68 Control blood 51 47 Lungs DLBC47 on Affymetrix GeneChip Human Full Length Array HuGeneFL EOM 28 Day mdx rep 3 Bone Marrow 1000 Cancers; Prox.Jejunum tumor Keywords = mouse gene expression database Source GEO sample is GSM29278 Last updated (according to GEO): May 27 2005 CNS WT 861 Lung 17 7 hippocampus NA18632 PHG-CtrCM-1aAv2-s2 PGA-E16.5_1 CNS-SpinalC-conAdult-48h-2A-s2 7 0 Pancreas osteoblast 627 637 861 Muscle Small Intestine Duodenum SG Normal Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:387, Count:32 Corner- Avg:36935, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:4.951684,SFGene:All Background:Avg:493.24,Stdev:7.44,Max:514.6,Min:480.1 Noise:Avg:11.19,Stdev:0.52,Max:12.8,Min:9.4 RawQ:14.58 Keywords = ALL Source GEO sample is GSM3437 Last updated (according to GEO): May 28 2005 of the normal mucosa 7 26 Ptdsr-/- fibroblast_rep4 Heart 861 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n091 Source GEO sample is GSM2035 Last updated (according to GEO): Nov 21 2005 of coronary artery disease 258 284 5 0 brain Mouse_E13.5_Front_Middle_Back_10 Date : 6/12/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 2.5 mg/kg Time : 3 hrs post-injection Intervention : none Risk: NOAEL (no increased risk for malformations) Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AO044 Source GEO sample is GSM12238 Last updated (according to GEO): May 28 2005 Expression profiling of spinal cord section (T9) extracted from rats 4h following moderate injury Source GEO sample is GSM31195 Last updated (according to GEO): May 27 2005 cerebellum sprague 3899 Gene expression data from brain of adult rats Source GEO sample is GSM101042 Last updated (according to GEO): Feb 20 2007 no additional Source GEO sample is GSM199313 Last updated (according to GEO): Jun 08 2007 CNS-SMTC_CtrT0-1B-s2 +_test-8_batch5 on NHGRI-6.7k bone; femur Source GEO sample is GSM18665 Last updated (according to GEO): May 27 2005 Infected with B. melitensis 16M and euthanized 3 days post-infection Source GEO sample is GSM155256 Last updated (according to GEO): Aug 08 2007 Normal Source GEO sample is GSM176411 Last updated (according to GEO): Apr 09 2007 861 Salivary Glands Neoplasm Metastasis 1000 outer medulla 31 43 901 frontal lobe T142 1000 Spleen 3AJZ02022756_trachea 5 0 Muscle Normal human tissue:Normal Corpus Keywords = Human, Normal Tissue, Normal Corpus Source GEO sample is GSM44696 Last updated (according to GEO): May 27 2005 Skeletal bone 861 10 Bone marrow 0 human cerebellum Source GEO sample is GSM87090 Last updated (according to GEO): Feb 08 2006 Brain 1000 HeLa cells were serum starved and either preincubated with DMSO (vehicle), preincubated with U0126 (10µM in DMSO) and infected with CVB3 (MOI 10), or preincubated with DMSO (vehicle) and infected with CVB3. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 0, 30 minutes, 3 and 9 hours following CVB3 infection (N=3 plates per time point), RNA was isolated, processed and hybridized to GeneChip®s (N=3 per sample). Date GSE697 Last Updated: Oct 28 2005 Contributers: Bobby Yanagawa Honglin Luo Timothy J Triche Raymond T Ng Ji Yuan Nana Rezai Jingchun Zhang Bruce M McManus Decheng Yang Zsuzsanna Hollander Includes GDS478. Update date: Nov 28 2003. Dataset description GDS478: Temporal analysis of in vitro model of coxsackievirus B3 (CVB3) infection. HeLa cells infected with either CVB3, CVB3 and U0126 (blocks cytokines and metalloproteinases) or control PBS, and samples examined at 0, 0.5, 3 and 9 hours after treatment.. 30 19 Solid tumor Gene expression of stria vascularis of newborn rats_cultivation_normoxia_repeat 2 inner ear 901 Malignant neoplasm of prostate KO_NP_mid_4 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 3426 left_liver_lobe D08 12h TLR2/1L park_1022_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A none Source GEO sample is GSM123182 Last updated (according to GEO): Jul 26 2006 C2C12_0.5_hr Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132499 Last updated (according to GEO): Feb 26 2007 Macrophage 14smi045 1000 hindbrain 1000 Kidney PGA-swim_2w_s1059 861 Cerebral cortex Medulla Oblongata 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145816 Last updated (according to GEO): Nov 20 2006 1000 Brain Pool of total RNA from 3 Ts1Cje cerebella (segmental trisomy of chromosome 16) at P15 postnatal stage Keywords = Down syndrome Keywords = Chromosome 21 Keywords = Transcriptome Keywords = Microarray Keywords = Brain Keywords = Cerebellum Keywords = Development Source GEO sample is GSM27481 Last updated (according to GEO): May 27 2005 5 0 brain Cerebellum 0 9 1000 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM144977 Last updated (according to GEO): Nov 20 2006 Expression profiling of spinal cord section (T9) extracted from rats 72h following moderate injury Source GEO sample is GSM31575 Last updated (according to GEO): May 27 2005 SCLC cell line Lu-134a M7TW00122062 After 2 week acclimation to 12 hr/12 hr light/dark regimen, c57/Bl6 mice were subjected to a 36 hour period of constant darkness. Aortae were subsequently harvested at 4 hour intervals to 48 hours. Duplicate microarrays were hybridized with biotin-labeled probes derived from aorta tissue (6 pooled aortae/timepoint). Keywords = aorta, murine, circadian Source GEO sample is GSM6090 Last updated (according to GEO): May 27 2005 tibiae 115 120 brain, Right Frontal Lobe: Extract54_le1 Expression profiling of spinal cord section (T9) extracted from rats 14d following mild injury Source GEO sample is GSM31299 Last updated (according to GEO): May 27 2005 plasma cells 332 344 15 0 human cerebellum Primary large cell neuroendocrine carcinoma 6042 0 47 Gene expression data from older female during 1 week of inadequate protein intake Source GEO sample is GSM209826 Last updated (according to GEO): Jul 11 2007 Spleen 0 5 Adrenal Medulla 1000 subthalamic_nucleus_4 Source GEO sample is GSM80829 Last updated (according to GEO): Mar 31 2006 Untreated Control 12weeks AffyGC RMA rep9 B_N1 on Affymetrix GeneChip Human Full Length Array HuGeneFL 2 month!Sample_source_name_ch1 = Post Natally excised Human lung tissue Source GEO sample is GSM107832 Last updated (according to GEO): May 04 2006 ISR16 Immature B cells 9 post-ES_EpiSC-7_P20 mouse cerebral cortex, cox-1 WT, rep3 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153458 Last updated (according to GEO): Jan 11 2007 Brain 861 PGA-MPF-BALB-saline-72h-1bAv2-s2 1000 Brain NCI60.34_LABEL38EXTRACT37SUB3 Source GEO sample is GSM134160 Last updated (according to GEO): Aug 06 2007 D_U133A_61_DLPFC 70 40 without coronary artery disease none Source GEO sample is GSM244620 Last updated (according to GEO): Nov 23 2007 041101_HF_330VC Replicate2_Voxel F3 Gene expression data from aldosterone-producing adenoma Source GEO sample is GSM211454 Last updated (according to GEO): Jul 18 2007 Large Pre-BII cells 10 Prosencephalon 1000 of the forebrain 2217 2232 Acetaminophen 24hr Rat 2507 blood vs. Acetaminophen 24hr Rat Pooled Control blood I_U133A_6_AnCg Simple annotation: Lymph node metastasis, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3959.gif Source GEO sample is GSM76455 Last updated (according to GEO): Sep 22 2006 Spinal Cord 1000 5 0 brain gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134645 Last updated (according to GEO): Jul 09 2007 Breast Carcinoma 861 Skeletal bone 861 M_95A_2822_Cg_1_GS cerebral cortex 7 21 Ptdsr-/- fibroblast_rep6 8077_Lung did not develop PGD Skeletal muscle structure 901 G1 Retina in brain damage 234 249 Diet induced changes in mouse liver mRNA profiles. One of 3 replicates of C57BL/6 mice maintained for 12 weeks on a high fat Western style diet. Keywords = LDL receptor deficiency, high fat diet, atherosclerosis, liver Source GEO sample is GSM5403 Last updated (according to GEO): May 27 2005 901 Caudate nucleus structure no doxycycline, mutant Source GEO sample is GSM213367 Last updated (according to GEO): Jul 26 2007 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228609 Last updated (according to GEO): Sep 11 2007 Gene expression data Source GEO sample is GSM230355 Last updated (according to GEO): Sep 19 2007 C57BL/6 benchmark dataset: Embryonic day 12.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25160 Last updated (according to GEO): May 27 2005 C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P10 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25144 Last updated (according to GEO): May 27 2005 Sph 1, chip MOE430B bone marrow-CD71EarlyErythroid Source GEO sample is GSM18748 Last updated (according to GEO): Sep 25 2006 PROSTATE_PC3 on Affymetrix GeneChip Human Full Length Array HuGeneFL hippocampus rattus_norvegicus_strain iP animal_number 1 278_1 Bipolar Disorder 1000 Measles 861 DBA/2J amygdala rep1 of parieto-occipital cortex 118 144 PC 12Hr rat 4126 blood vs. 2500mg/kg APAP 12Hr rat 4138 blood 114 101 brains quickly Disorder of artery 865 Gene expression data from colorectal adenoma. Source GEO sample is GSM215091 Last updated (according to GEO): Aug 02 2007 AD-323t1-A273-10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 0 Human Cortex 11 Spleen vs Untreated B cell 30min (set1) brain, cerebral cortex: NMDA30 6/24_le1 SN:1011113;Fetal Cartilage, U133A validation Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181122 Last updated (according to GEO): Jul 12 2007 0 Epithelial cells 15 Nose 1000 mefloquine-treated NG108 neuronal cells 2 Standard Affymetrix Protocol Source GEO sample is GSM16456 Last updated (according to GEO): May 28 2005 1000 Malignant Neoplasms in seminoma 28 38 Normal Source GEO sample is GSM176331 Last updated (according to GEO): Apr 09 2007 36 21 from hippocampus 7 cerebral cortex 21 91 from the bone marrow 72 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19260 Last updated (according to GEO): May 27 2005 nerve 0 5 9 0 Blood Test Down Syndrome 1000 Starvation 916 304 295 infection ventral striatum wistar ky 3959 freehand block dissections, removed only cortex, individual animal, 10 weeks old, male Wistar Kyoto ventral striatum file:p3959w Source GEO sample is GSM15181 Last updated (according to GEO): Oct 28 2005 0029_1208_H95A2_KF0076_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 258 245 from 6 brains brain, Entorhinal Cortex: Sample6_e1_le1 Structure of olfactory bulb 901 1571 1539 that cerebral cortical dysplasias C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P32 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25147 Last updated (according to GEO): May 27 2005 1784 HP24_21 Expression profiling of spinal cord section (T8) extracted from rats 24h following severe injury Source GEO sample is GSM31472 Last updated (according to GEO): May 27 2005 Endometrium 16 Normal 256 235 with HIV encephalitis V5-P222 Medulla Oblongata 861 LEUKEMIA 15 22 1000 Liver 1000 Liver cingulate cortex 861 861 Brain in cigulate cortex 26 44 RNA characterization of tissue from the injury site, 35 days post-injury. From the Christopher Reeve Paralysis Foundation Research Consortium microarray study (www.crpf.org/microarray) Source GEO sample is GSM49935 Last updated (according to GEO): May 27 2005 Cerebellum 1000 B195 DCs treated with isotype control antibody for 24 hrs in bronchial epithelia 311 332 Sample41, Post Injury 24 hours Treatment, type=wait Source GEO sample is GSM53252 Last updated (according to GEO): Jul 06 2005 901 Stem cells testis 52 58 1000 Brain Stem medial prefrontal cortex cocaine naive replicate 1 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27024 Last updated (according to GEO): May 27 2005 Pre-BI cells 3 Cerebral cortex 1000 901 Bone Marrow with mental retardation 241 263 5 0 brain Skeletal bone 861 male mhm chip 1 1000 Hippocampus Ischemia-reperfusion with AEOL 10150 #4 861 Spinal Cord 1000 Carcinoma 901 Mammary gland Nasal Epithelium 865 Y HID D039 no additional Source GEO sample is GSM199108 Last updated (according to GEO): Jun 08 2007 7 frontal cortex 20 brain, hippocampus: PR-CA1-1_e1_le1 tibiae 115 120 I_U133A_2_DLPFC D_U133A_51_CB H120 CN A Liver 1000 whole brains from nicotinic acetylcholine receptor subunit mutant mice and littermate controls spinal cord 0 11 AD-162t2-A230-8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 201 in the frontal cortex 221 24 0 human prostate PC3 tumors Blood; Fetal Day 14 Liver Hematopoietic Keywords = mouse gene expression database Source GEO sample is GSM29326 Last updated (according to GEO): May 27 2005 861 Cerebral cortex between the LAD artery 266 287 Naive, EAE placebo-treated and EAE 1,25(OH)2D3-treated groups very early HCC Source GEO sample is GSM155935 Last updated (according to GEO): Jun 21 2007 Tumor__Leukemia_ALL-B_ALL_(9335)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1.25 mg/kg 2CdA embryo at 3.0h Gene expression data from postmorten brain regions Source GEO sample is GSM144870 Last updated (according to GEO): Nov 20 2006 Saccule 0 6 607 597 the rectum Epithelial Cells 901 Cerebral cortex 1000 50 29 of human breast tumors Skin 861 680 654 with mesenchymal stem cells Mental Retardation 1000 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells cultured for 60min Source GEO sample is GSM5843 Last updated (according to GEO): May 27 2005 Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 2 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b103 Source GEO sample is GSM2014 Last updated (according to GEO): Nov 21 2005 TNFTG-3w-m-1 /6J cingulate cortex rep1 5 29 1000 Brain 1000 Axon Brain 1000 cy5:WKY control, biological rep 2r; cy3:pool of 6 WKY control rats 1000 Solid tumor sAPPalpha #2 1767 1754 Muscle atrophy 966 Hippocampus GSE6858 Met. Granulosa Cell Tumor (SF39, T2) PCA-405 on UMich-10k 861 Salivary Glands brain 0 5 Testis 861 Primary tumor 19 32 Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200643 Last updated (according to GEO): Jun 12 2007 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.12 Subject: 3108 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39069 Last updated (according to GEO): May 27 2005 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181216 Last updated (according to GEO): Jul 12 2007 PBMCs-Type 1 Diabetes-IDDM32_T1D_4MO KO-Nrf2-Female-2 861 Cerebellum A2780_cis_IC90_16h_5 GSE3131 of the saphenous artery 43 65 human caudate nucleus Source GEO sample is GSM86825 Last updated (according to GEO): Feb 08 2006 CNS-SMTC_Ctr4h-1B-s2 Pool of 12 cochlear tissues at E12.5 Source GEO sample is GSM182578 Last updated (according to GEO): Aug 14 2007 Tissue Source GEO sample is GSM67209 Last updated (according to GEO): Jan 19 2006 Heart Septal Defects, Atrial 1000 6421_Lung developed PGD 2N-1-MGU74B Wild type inbred mice Source GEO sample is GSM82976 Last updated (according to GEO): Nov 10 2005 from lateral geniculate nucleus 12 42 861 Medulla CT18-1 Tissue fiber 861 78 66 Control blood brain, Primary Visual Cortex: Sample69_e1_le1 NA12750 growth 1, replicate 5 Replicate3_Voxel B5 HCC (HBV+, HK64, T7) 854 843 These hearts Large-scale analysis of the mouse transcriptome. Thymus C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 255.22 Stdv: 13.71 Min: 226.28 Max: 275.98 Source GEO sample is GSM2987 Last updated (according to GEO): Mar 20 2006 medulla_7 CNS-SCsev_InjB14d-3B-s2 CLL-61 cerebellum 7 16 Hippocampus 1978 15 month Old MF-36 103 99 lens Epithelial Cells 1000 normal 1090 21 0 acute myeloid leukemia Blood 861 HOXB4 const_w/o TMX, 1hour, biological rep1 osteoblast 627 637 SN:1006731 Source GEO sample is GSM115356 Last updated (according to GEO): Jun 20 2006 861 Cerebral cortex r8 Gene expression data from whole brain infected mouse, day 6 Source GEO sample is GSM189622 Last updated (according to GEO): May 16 2007 the ventricular 1095 1109 Nanog-iPS MEF 20D18 B220+CD25+sIg- Large Pre BII cells sorted out of mouse bone marrow, sort no. 1 Source GEO sample is GSM616 Last updated (according to GEO): May 27 2005 from rat lungs 21 34 SON - 3d Dehydrated Source GEO sample is GSM69845 Last updated (according to GEO): Aug 15 2005 D_U133Plus_26_DLPFC_R Nose 1000 1000 Rectum of the stria terminalis 56 78 Primary tumor 19 32 Integumentary system 1000 15_0003_Control_Day1_19 861 Organ from the femurs 95 109 Endometrium 0 10 HME-CC Whole blood 0 10 Normal Source GEO sample is GSM176174 Last updated (according to GEO): Apr 09 2007 ovary 45 50 39 21 of substantia nigra of G protein? 285 297 I_U133A_21_DLPFC 5 0 brain 19 0 Head and neck cancer The epithelial cells 962 981 Myocardium 861 Brain of P10 wildtype C57Bl/6j mouse, replica W1 The use of genomic technology for assessing health risks associated with chemical exposure has significant potential, but its direct application has proven to be challenging for the toxicology and risk assessment communities. In this study, a method was established for analyzing dose-response microarray data using benchmark dose (BMD) calculations and gene ontology (GO) classification. Gene expression changes in the rat nasal epithelium following acute formaldehyde exposure were used as a case study. The gene expression data were first analyzed using a one-way analysis of variance to identify genes that showed significant dose-response behavior. These genes were then fit to a series of four statistical models (linear, 2 degrees polynomial, 3 degrees polynomial, and power model) and the least complex model that best described the data was selected. The genes were matched to their associated GO categories and the average BMD and benchmark dose lower confidence limit (BMDL) were calculated for each GO category. The results were used to identify doses at which individual cellular processes were altered. For the formaldehyde exposures, the BMD estimates for the GO categories related to cell proliferation and DNA damage were similar to those measured in previous studies using cell labelling indices and DNA-protein cross-links and consistent with the BMD estimated for rat nasal tumors. The method represents a significant advance in applying genomic information to risk assessment by allowing a comprehensive survey of molecular changes associated with chemical exposure and providing the capability to identify reference doses at which particular cellular processes are altered. from the femurs 95 109 GSE78 Nose 1000 Adenocarcinoma 861 861 Brain 913 Coronary heart disease between the LAD artery 266 287 G30-Amygdala-replicate1 5 0 Muscle 861 Cerebellum 17 7 hippocampus Identifying distinct classes of bladder carcinoma using microarrays. GBM Treatment, type=remove Source GEO sample is GSM99573 Last updated (according to GEO): Apr 21 2006 663 mesenchymal stem cell 642 Tumor__Prostate_Adeno_P_0025 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A GM18516 Expression profiling of spinal cord section (T9) extracted from rats 14d following mild injury Source GEO sample is GSM31201 Last updated (according to GEO): May 27 2005 rad001 12h, biological rep1 Aorta 3 Normal brain, Posterior Singulate: Sample45_e1_le1 1000 DNA, Mitochondrial 180 166 in the stomach nostrils 156 164 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=750710 LaserPower=2.231.29 Lot batch = LC17N045 Source GEO sample is GSM4794 Last updated (according to GEO): Nov 21 2005 G7 macula Nose 1000 1000 Brain stria terminalis 901 GSE4041 1000 Kidney G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Source GEO sample is GSM9643 Last updated (according to GEO): May 28 2005 861 Kidney brain, hippocampus: CON-CA1-22_e1_le1 Hippocampus 1000 3AJZ02081480a_Pons GC (HKG89T_1) Gene expression data from postmorten brain regions Source GEO sample is GSM144948 Last updated (according to GEO): Nov 20 2006 brain, cochlea: [9] Sample #9_le1 PGA_PA-N_322 mouse brains 187 198 861 Neoplasm GM10856_technical_rep_1 testis 52 58 144 114 from a single adult spinal cord B269 on Affymetrix GeneChip Human Full Length Array HuGeneFL B CELLS C on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A no additional Source GEO sample is GSM199048 Last updated (according to GEO): Jun 08 2007 GSE929 Gene expression data from a placenta with chronic malaria Source GEO sample is GSM183616 Last updated (according to GEO): Apr 23 2007 406 395 whose hearts Substantia Nigra Control Sample1 RMA, MAS 5, dChip Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132515 Last updated (according to GEO): Feb 26 2007 Co 1 (Experiment Nic 15 - Run 23145) Treatment, type=timepoint, measurement=0.0 m Source GEO sample is GSM96703 Last updated (according to GEO): Feb 14 2006 hippocampus 7 17 This SuperSeries is composed of the following subset Series: GSE8290: Comprehensive analysis of PPAR?-dependent regulation of hepatic lipid metabolism by expression profiling - 1 GSE8291: Comprehensive analysis of PPAR?-dependent regulation of hepatic lipid metabolism by expression profiling - 2 GSE8292: Comprehensive analysis of PPAR?-dependent regulation of hepatic lipid metabolism by expression profiling - 3 GSE8295: Comprehensive analysis of PPAR?-dependent regulation of hepatic lipid metabolism by expression profiling - 4 GSE8302: Comprehensive analysis of PPAR?-dependent regulation of hepatic lipid metabolism by expression profiling - 5 Last Updated (by provider): Contributers: Rinke Stienstra Merja Matilainen Michael Muller Philip J de Groot Maryam Rakhshandehroo Sander Kersten Linda M Sanderson Carsten Carlberg Pituitary Gland 1000 24 0 human prostate PC3 tumors 9 0 cerebellum dentate granule cells Source GEO sample is GSM35811 Last updated (according to GEO): May 27 2005 Lymphoblastoid Cell Line for Individual 8075.3 log phase Rogers-3U24NS043571-01S1 19 0 Head and neck cancer Dorsal #1 prostate Source GEO sample is GSM203288 Last updated (according to GEO): Jun 21 2007 septum long access to cocaine replicate 1 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the lv samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12330 Last updated (according to GEO): May 28 2005 Transitional epithelium 1000 tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44862 Last updated (according to GEO): Nov 21 2005 CNS-SCsev_InjA7d-1C-s2 9 0 BREAST_MDN Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3308 Last updated (according to GEO): Mar 21 2006 17 7 hippocampus 78 66 Control blood 497 487 metastasis amygdala short access to cocaine replicate 3 CHIPEXP_NAME: 230_2_050531tpj_60h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Isoproterenol TREAT_TOX_MECHANISM1: Heart_Cardiotoxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0.5 SAMPLING_TIME: 72 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197631 Last updated (according to GEO): Jun 01 2007 AKR/J Cingulate Cortex E Whole blood 0 10 Cerebral cortex 861 Parkinson's model voxel J3 15 0 human cerebellum 913 Coronary heart disease Medulla 861 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114477 Last updated (according to GEO): Jun 16 2006 organs 28 33 80 68 Control blood of the postmortem brains 665 689 WGACON-51 Control Source GEO sample is GSM176476 Last updated (according to GEO): Apr 09 2007 5 0 brain Intestines 861 Donor D, pre G-CSF Small cell carcinoma of lung 867 861 Spleen f2#58 versus pool Mouse Brain tissue of coronary artery disease 258 284 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68198 Last updated (according to GEO): Jul 07 2006 1000 Decapitation CNS-RM_Ctr4h-1A-s2 Whole blood 0 10 Organ 861 PGA-E13.5_3A 5 0 Spleen 1000 Liver 26 0 frontal cortex sprague 3937 no additional Source GEO sample is GSM199395 Last updated (according to GEO): Jun 08 2007 5 0 brain gene expression data from ODC mouse skin samples Source GEO sample is GSM216661 Last updated (according to GEO): Aug 09 2007 1000 Spleen Primary tumor 19 32 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118539 Last updated (according to GEO): Jul 11 2006 Spinal Cord 1000 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM112936 Last updated (according to GEO): Jun 16 2006 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211265 Last updated (according to GEO): Jul 18 2007 25 0 Lymph Node [JunctionChip 5 bronchus_3 none Source GEO sample is GSM239836 Last updated (according to GEO): Dec 07 2007 brain, unknown: Sample52_e1_le1 HDMTX-17 334 321 of endometrium Macrophage smi84 Epithelium of bronchus 983 Bone Marrow 1000 307_2 Gene expression data from postmorten brain regions Source GEO sample is GSM145242 Last updated (according to GEO): Nov 20 2006 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 4 hour after the last shock treatment. Source GEO sample is GSM4537 Last updated (according to GEO): May 27 2005 901 Myeloid Leukemia Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.71 Subject: 3023 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39053 Last updated (according to GEO): May 27 2005 on muscle fibres 285 301 Site: University of California, Davis Cohort: Male/Female Control Set Diagnosis: Control pH: 6.12 Subject: 3108 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39067 Last updated (according to GEO): May 27 2005 7 0 prostate Normal Source GEO sample is GSM176435 Last updated (according to GEO): Apr 09 2007 861 Colon Whole blood 0 10 Normal human tissue:Normal Placenta Keywords = Human, Normal Tissue, Normal Placenta Source GEO sample is GSM44681 Last updated (according to GEO): May 27 2005 Colonic mucous membrane 913 100 87 of hippocampus Normal Testis spinal cord Source GEO sample is GSM18944 Last updated (according to GEO): Sep 25 2006 Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.4 Subject: 2978 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39044 Last updated (according to GEO): May 27 2005 Lymphoblastoid Cell Line for Individual 8070.4 log phase Male 26.2 yr after antibody enrichment scan 2 (U133A) Lymphoblastoid Cell Line for Individual 8178.4 log phase I_U133Plus_38_Amy 12 0 ovarian tumor Gene expression data from brain hemispheres of experimentally naive male mice Source GEO sample is GSM172395 Last updated (according to GEO): Jun 27 2007 Gene expression data from a placenta with acute malaria Source GEO sample is GSM183618 Last updated (according to GEO): Apr 23 2007 HapMap CEU_parent Female Source GEO sample is GSM159573 Last updated (according to GEO): Feb 01 2007 none Source GEO sample is GSM239877 Last updated (according to GEO): Dec 07 2007 901 Autoimmune Diseases Gene expression of organ of Corti of newborn rats_cultivation_hypoxia_repeat 1 inner ear Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=710650 LaserPower=2.161.3 Lot batch = LC17N037 Source GEO sample is GSM4790 Last updated (according to GEO): Nov 21 2005 861 Glioma 1BMH02022808_Heart SCG explant cultured for 5 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246065 Last updated (according to GEO): Dec 03 2007 Tumor__Leukemia_ALL-T_ALL_(87_52)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A M_U133A_1_nAcc hippocampus 0 10 78 73 rectum 861 Hypersensitivity BAL_29_A1B0 Transplant Series 17 , Transplant # 4 5 0 brain 966 Hippocampus Heart failure 1000 from liver 21 30 b2 1000 Left adenocarcinoma 3479 0 18 NCI60.60_LABEL122EXTRACT62SUB3 Source GEO sample is GSM134294 Last updated (according to GEO): Aug 06 2007 Nasal Epithelium Inhalation Formaldehyde 07ppm 5d ID140 1000 Brain 15 0 human cerebellum 5 0 brain 861 Muscle PGA-RnSalt_c_15w_2-m5 cerebellum_3 Sample represents the Paraventricular nucleus from 5 dehydrated animals (3 Days) Source GEO sample is GSM69471 Last updated (according to GEO): Dec 16 2005 1000 Leukemia, Myelocytic, Acute Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92364 Last updated (according to GEO): Jan 13 2006 Four weeks expression data of the antipsychotics Clozapine and Haloperidol in the mouse brain (Affymetrix, GCRMA). 1000 Blood Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210373 Last updated (according to GEO): Jul 16 2007 119 96 in embryonic stem cells Squamous epithelial cell 861 36 0 Inflammatory myopathy specimen GEIM12 B2-22 on NCI-7.6k 1000 Median eminence of hypothalamus Large-scale analysis of the mouse transcriptome. Spleen C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 234.60 Stdv: 11.02 Min: 217.07 Max: 253.84 Source GEO sample is GSM2957 Last updated (according to GEO): Mar 20 2006 861 Spinal Cord Probeset expression data from NA12750 growth 3, replicate 5 Source GEO sample is GSM195202 Last updated (according to GEO): Aug 08 2007 861 Asphyxia 41 36 spleen Ovary 861 in childhood astrocytomas 64 88 human caudate nucleus Source GEO sample is GSM86867 Last updated (according to GEO): Feb 08 2006 Subject code A32 861 Brain CNS-RM_Ctr24h-2A-s2 Colon 861 (cortex 19 25 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202671 Last updated (according to GEO): Jun 20 2007 plasma cells 332 344 Accumbens P2 Disease Communicable Diseases 861 Brain 861 V5-P291 1000 Spleen rad001 9d, biological rep3 Investigation into murine dermal burn wound. Mouse thermal injury induced, and skin excised at different times post-injury. Source GEO sample is GSM7479 Last updated (according to GEO): May 27 2005 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184811 Last updated (according to GEO): Apr 26 2007 in high-grade papillary renal cell carcinoma 124 168 7 0 prostate BACKGROUND: Differences in ethanol metabolizing enzymes expressed in brain have been suggested to contribute to the significant differences in ethanol (alcohol) preference between inbred C57BL/6 and DBA/2 mouse strains. METHODS: We have utilized 2 different platforms of oligonucleotide microarray technology (CodeLink UniSet I BioArray from G.E. Healthcare and MG U74A v2.0 from Affymetrix) to simultaneously assess expression of alcohol and acetaldehyde metabolizing enzymes in the whole brain of naïve (no exposure to alcohol) C57BL/6 and DBA/2 mice. RESULTS: There were no significant differences between the 2 strains of mice in gene expression intensity for alcohol dehydrogenases (ADH), catalase, and a number of the cytochrome P450 family of genes, which can be involved in ethanol catabolism. However, significantly higher expression of mRNA for aldehyde dehydrogenase 2 (ALDH2), an isoform mainly responsible for the catabolism of acetaldehyde, was observed in whole brains of DBA/2 mice with both platforms. Aldehyde dehydrogenase 2 protein was also higher in DBA/2 brain. Expression of aldehyde dehydrogenase 1A1 (ALDH1A1) mRNA was found to be higher in brains of DBA/2 mice, when measured with the CodeLink platform, but not when measured with Affymetrix arrays or quantitative reverse transcriptase-real-time polymerase chain reaction (qRT-PCR). The ALDH1A1 protein, however, reflected the results obtained with the CodeLink arrays and was higher in DBA/2 brain, compared with brains of C57BL/6 mice. In contrast, the expression intensity for the aldehyde dehydrogenase 7A1 (ALDH7A1) mRNA and protein was significantly higher in C57BL/6 mice than DBA/2 mice. These expression differences are consistent with more rapid metabolism of acetaldehyde in brains of DBA/2 mice. CONCLUSIONS: The use of 2 different microarray platforms provides important cross-validation of many results, and some discrepancies can be resolved with qRT-PCR and immunoblotting. The expression differences that were validated may affect alcohol/aldehyde metabolism in brain and/or alcohol preference in the 2 strains of mice. 76 44 with nearly all cervical cancers 112 77 Keywords = congenital heart disease Brain 861 medial prefrontal cortex long access to cocaine replicate 1 Epithelium 861 5 0 brain Structure of olfactory bulb 901 /HeJ mouse pituitary gland 27 52 Fallopian Tube AB1 Normal due to prostate carcinoma 59 84 VDXOXFU_513 Transitional epithelium 1000 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy Keywords = pathological hypertrophy Keywords = rat Keywords = heart failure Keywords = cardiomyopathy Source GEO sample is GSM11885 Last updated (according to GEO): May 28 2005 Disorder of artery 865 1000 Cerebral cortex 66 CB A spinal cord 0 11 HC72 CN B Pyramidal neurons in hippocampus. Source GEO sample is GSM63043 Last updated (according to GEO): Dec 01 2005 Motor neurons obtained from a wild type mouse by laser capture microdissection. Source GEO sample is GSM113717 Last updated (according to GEO): Jun 09 2006 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19248 Last updated (according to GEO): May 27 2005 Disorder of artery 865 Neoplasm 861 vehicle treatment, 3 hour time point, biological replicate 3 Samples were immediately snap-frozen in liquid nitrogen and then stored in a -70° Celsius freezer until used for analysis. An area of lung tissue approximately 1 x 1 cm was isolated and excised using 2 staple lines from a 30 mm EndoGIA stapler (US Surgical, Norwalk, CT). Source GEO sample is GSM198661 Last updated (according to GEO): Jun 06 2007 1000 Brain Nrl ko samples were compared to wt at postnatal 2. Source GEO sample is GSM227451 Last updated (according to GEO): Sep 07 2007 5 0 Spleen BALB-c mice were given intratracheal saline. Lungs were harvested and frozen at 14d. Lot batch = Source GEO sample is GSM4154 Last updated (according to GEO): May 28 2005 1000 Substantia nigra structure CA96-116A 17 0 Normal Spinal Cord plasma cells 50 61 CAD_replicate20 192 184 20 tumors H126 CB B 10 0 fetal liver Rat vestibular ganglia stained with calretinin. Tissue is LCM captured, calretinin positive cells Source GEO sample is GSM100183 Last updated (according to GEO): Mar 13 2006 A HID B D092 Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2646.gif Source GEO sample is GSM72187 Last updated (according to GEO): Sep 22 2006 Nervous System; Olfactory Cortex Keywords = mouse gene expression database Source GEO sample is GSM29424 Last updated (according to GEO): May 27 2005 GSE701 ILS/ISS_cerebellum_naive_470 1000 Primary carcinoma of the liver cells 1000 Amygdaloid structure PGA-MCR-CR-12h-1aAv2-s1 Unfertilized egg replication 1 Keywords = preimplantation Keywords = development Source GEO sample is GSM14658 Last updated (according to GEO): May 28 2005 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc86 Source GEO sample is GSM1917 Last updated (according to GEO): Nov 21 2005 B6:2-7 cerebellum 12 Parietal Lobe 24 Coronary Artery 1 Normal mouse brain contralateral LPS.Dmso, biological rep2 large adenomas 673 687 Acetaminophen 6hr Rat 1376 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool 1115 1102 cardiomyopathy Gene expression data from UET-13TR-EWS/ERG cells incubated in the absence of tetracycline for 48 hours Source GEO sample is GSM214926 Last updated (according to GEO): Aug 02 2007 Normal Brain 20 0 human caudate nucleus 1000 Cerebral cortex CNS-RM_Mod14d-4B-s2 Tumor__Mesothelioma_165_T5 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A PBMCs-Type 1 Diabetes-IDDM57_T1D_4MO Brain_Aged_Salineip_4hr_mouse1 (OP1_#61) female MhmBN chip 46 BT-549 hgu95b Expression profiling of spinal cord section (T10) extracted from rats 0h following laminectomy (naïve) Source GEO sample is GSM31304 Last updated (according to GEO): Oct 28 2005 861 Immune system CNS-SMTC_Mod7d-1B-s2 BC206A-BE A/J cingulate cortex rep3 Fibroblasts 1000 R7N 10 HMVEC-L stimulated without LPS for 8 hours c08R4 Transplant Series 42 , Transplant # 4 Acetaminophen 6hr Rat 3942 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool 2551 2541 decapitated Cerebral cortex 1000 of human gastric cancer 614 637 brain, amygdala: Amygdala 8_le1 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11585 Last updated (according to GEO): May 28 2005 UET-13TR-EWS/ERG 48hr the blood 393 402 1000 Hypothalamic structure lateral hypothalamus 24 44 875 Subcutaneous Tissue Cerebellum 1000 Sample Type: cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 15 ppm, 6 h time point Source GEO sample is GSM159771 Last updated (according to GEO): Apr 23 2007 IM-5_PRE Transitional epithelium 1000 Ovary 1000 brain_OFC_bipolar B_mr91 Normal Source GEO sample is GSM175841 Last updated (according to GEO): Apr 09 2007 B6:16-2 olfactory bulbs KPeterson-Met-2box1G110-s2 mouse brain 478 489 cerebellum_2 Migration Source GEO sample is GSM19103 Last updated (according to GEO): May 27 2005 5 0 Spleen Spleen vs BLC Treated B cell 60min (set1) brain, cerebral cortex: Egr1/Egr3 double knockout 3_e1_le1 261247 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11456 Last updated (according to GEO): May 28 2005 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162183 Last updated (according to GEO): Jun 12 2007 2_cerebral_cortex_9hrs_sleep_deprivation_#3 Prostate carcinoma 861 Brain 861 Low-density CCg progenitors treated with FBS to derive Astrocytes Source GEO sample is GSM47555 Last updated (according to GEO): Jun 10 2005 mouse cerebral cortex 0 20 Spleen vs MIP3-alpha Treated B cell 240min (set1) Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211302 Last updated (according to GEO): Jul 18 2007 Recurrent tumor grade 3 164 187 901 Stem cells U251_CL12009_CNS of the postmortem brains 674 698 spinal cord 13 23 SCG_control_24h_rep2 brain, cerebral cortex: Rat_02-40_VHL_Lipska_e1_le1 Gene expression data from epididymal fat tissues. Source GEO sample is GSM215574 Last updated (according to GEO): Aug 07 2007 649 634 cervical cancers Liver 1000 CNS-SpinalCsev-Adult-28d-4A-s2 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16472.gif Source GEO sample is GSM84158 Last updated (according to GEO): Sep 22 2006 5 0 brain nasal epithelial cells 28 49 Gene expression data from brain hemispheres of experimentally naive male mice Source GEO sample is GSM172403 Last updated (according to GEO): Jun 27 2007 Expression profiling of medulloblastoma 110 94 of heart failure Gene expression data from a EFT cell line expressing EWS/ERG Source GEO sample is GSM213312 Last updated (according to GEO): Jul 26 2007 CNS-SpinalCmod-Adult-24h-1C-s2 from whole tumor 21 36 The epithelial cells 962 981 Normal Source GEO sample is GSM176277 Last updated (according to GEO): Apr 09 2007 SCG explant cultured for 5 hours in vitro Source GEO sample is GSM246021 Last updated (according to GEO): Dec 03 2007 Skin 861 913 frontal lobe Nucleus Accumbends, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231033 Last updated (according to GEO): Sep 26 2007 7 cerebral cortex 21 673 659 by decapitation Clone 8.1 chip 3 no PDGF Prostate 861 Multiple Myeloma 1000 /SvEvTac cingulate cortex rep1 5 34 901 Myeloid Leukemia spinal cord 0 11 Primary tumor 19 32 Heart 1000 5 0 brain Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n100 Source GEO sample is GSM2056 Last updated (according to GEO): Nov 21 2005 NA11839 278 255 ischemic cardiomyopathy Total RNA extracted from the cerebellum of a Lh+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144418 Last updated (according to GEO): Nov 14 2006 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5833 Last updated (according to GEO): May 27 2005 HD4b Neoplasm 861 Myocardium 861 8814_Infect_1 30 0 Fetal occipital cortex cocaine3 861 Nicotinic Receptors 7 frontal cortex 20 rat cortex Treatment, type=time_course, measurement=3.0 d Source GEO sample is GSM53204 Last updated (according to GEO): Jul 06 2005 Plasma 861 NCI60.52_LABEL56EXTRACT55SUB3 Source GEO sample is GSM134258 Last updated (according to GEO): Aug 06 2007 Y HID D038 acute myocardial infarction 251 277 plasma cells 50 61 Cerebellum 1000 913 Coronary heart disease "40 hr Hela Double Thymidine, exp3" TUMOR 4 0 6 GSE3778 RNA from muscle biopsy specimen Source GEO sample is GSM3710 Last updated (according to GEO): May 27 2005 osteoblast 630 640 HapMap CEU_parent Female Source GEO sample is GSM159525 Last updated (according to GEO): Feb 01 2007 mid back fibroblast (1.3F), serum starved mammary epithelial cells Source GEO sample is GSM5164 Last updated (according to GEO): May 27 2005 Hippocampus 1000 Bone Marrow 1000 11_0013_Control_Day1_47 Infection 861 901 Heart failure tumors 454 459 db/db 8wk 3 861 Immune system Gene expression data from postmorten brain regions Source GEO sample is GSM145120 Last updated (according to GEO): Nov 20 2006 406 395 whose hearts 34 27 in lungs RNA from Lymphoblastoid Cell Line from this individual Source GEO sample is GSM213295 Last updated (according to GEO): Jul 26 2007 PriG_5%O2_Expt2_Day11_rep2 Left 1000 861 Brain RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above Source GEO sample is GSM160009 Last updated (according to GEO): Feb 05 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11579 Last updated (according to GEO): May 28 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68133 Last updated (according to GEO): Jul 07 2006 Ataxia 1000 Arteries 861 Richard Almon-21-1138200270102 nic 1 (Experiment Neuroprotection4- Run 21823) Treatment, type=timepoint, description=Same sample used for Experiment Neuroprotection4-Run 14985, samples were rerun due to oven failure, measurement=0.0 h Source GEO sample is GSM96688 Last updated (according to GEO): Feb 14 2006 5 0 brain 7 cerebral cortex 21 1000 Rectum from the right forebrain 21 44 Heart 1000 5 0 Spleen CAD_replicate33 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.12 Subject: 3108 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39075 Last updated (according to GEO): May 27 2005 Adenocarcinoma of lung 1000 23 0 large intestine sprague1 PP243_infected_Skin biopsy 1000 Endometrium 4_cerebral_cortex_12hrs_sleep_deprivation_#26 brain, amygdala: pADX AM A_e1_le1 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195266 Last updated (according to GEO): Sep 13 2007 225 203 from the mouse cochlea Pool of 16 vestibular tissues at E11 Source GEO sample is GSM182592 Last updated (according to GEO): Aug 14 2007 Prosencephalon 861 no additional Source GEO sample is GSM199390 Last updated (according to GEO): Jun 08 2007 D_95Av2_3108_DLPFC_0_GS GBM: 69A29 from the right forebrain 21 44 46 8 in docetaxel-refractory prostate cancer 861 Breast 901 Myeloid Leukemia Neural tube, control, GD9:12, C214260 1000 Brain Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc78 Source GEO sample is GSM1897 Last updated (according to GEO): Nov 21 2005 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9925.gif Source GEO sample is GSM79889 Last updated (according to GEO): Sep 22 2006 Heart 1000 AcB61 #12243339 861 Cardiomyopathies Disease Source GEO sample is GSM176399 Last updated (according to GEO): Apr 09 2007 no doxycycline, wt Source GEO sample is GSM213388 Last updated (according to GEO): Jul 26 2007 22 19 left GSE7814 Menstruation blood, HRF treatment, primary E5HRF 19 0 Head and neck cancer brain_DLPFC_bipolar B_mr946 Simple annotation: Metastatic tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13111.gif Source GEO sample is GSM79969 Last updated (according to GEO): Sep 22 2006 Chromosomes 861 Gene expression data from the right forebrain of C57BL mouse received Haloperidol oral treatment for twelve weeks. Source GEO sample is GSM148670 Last updated (according to GEO): Dec 12 2006 Expression profiling of somatomotor cortex extracted from rats at 7d following sham surgery Source GEO sample is GSM41668 Last updated (according to GEO): May 27 2005 TAp63 alpha 24h without induction s1 LEUK_HL60 on Affymetrix GeneChip Human Full Length Array HuGeneFL 13 0 Nervous System 19 0 human frontal cortex 7 frontal cortex 20 thymus Source GEO sample is GSM18668 Last updated (according to GEO): May 27 2005 Voxel H2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1439 Last updated (according to GEO): Nov 21 2005 1000 Spleen Disease Source GEO sample is GSM176086 Last updated (according to GEO): Apr 09 2007 PC 6Hr rat 3586 blood vs. 2500mg/kg APAP 6Hr rat 3598 blood 1000 Milk Normal__Colon_CR_9 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A plus_720_1 24 0 human prostate PC3 tumors tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44887 Last updated (according to GEO): May 27 2005 ovarian tumor: mucinous Source GEO sample is GSM139428 Last updated (according to GEO): Apr 09 2007 human cerebellum Source GEO sample is GSM87140 Last updated (according to GEO): Feb 08 2006 67 50 Gall bladder C57BL Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132511 Last updated (according to GEO): Feb 26 2007 1000 Prostate Liver 1000 cerebral_cortex_4 3616 PC 24Hr (pool) vs.1500mg/kg APAP 24Hr rat 3625 blood 901 Myeloid Leukemia 7 0 prostate Gene expression data from postmorten brain regions Source GEO sample is GSM144937 Last updated (according to GEO): Nov 20 2006 cerebral cortex 7 21 Leg 28 Day mdx rep 2 Untreated versus treated (bortezomib) breast cancer cells. Source GEO sample is GSM120345 Last updated (according to GEO): Jul 20 2006 Category: Cell-line Subcategory: Breast HMEC-C isolate from clonetics, used by chuck perou for PNAS 1999 paper Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc94 Source GEO sample is GSM1863 Last updated (according to GEO): Nov 21 2005 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD21 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD21 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36695 Last updated (according to GEO): May 27 2005 1445 1430 in aged cochlea I_U133A_34_AnCg GSE6355 861 Cerebellum NA18558 Acetaminophen 24hr Rat 9999 blood vs. Acetaminophen 24hr Rat Pooled Control blood Lymphoblastoid Cell Line for Individual 8128.3 log phase 91 from the bone marrow 72 Gene expressions affected by TNF alpha Source GEO sample is GSM189807 Last updated (according to GEO): May 21 2007 NA19119 nostrils 156 164 CH1810 SCG explant cultured for 24 hours in vitro Source GEO sample is GSM246035 Last updated (according to GEO): Dec 03 2007 Brain 1000 gum fibroblast, serum starved CNS-SMTC_Mod24h-4C-s2 rat cortex Treatment, type=time_course, measurement=3.0 d Source GEO sample is GSM53208 Last updated (according to GEO): Jul 06 2005 Expression profiling of spinal cord section (T8) extracted from rats 30m following mild injury Source GEO sample is GSM31436 Last updated (according to GEO): May 27 2005 Mesenchymal Stem Cells 1000 144 114 from a single adult spinal cord C16 on NCI-7.6k GSE3571 361 343 of mouse Chromosome of somatomotor cortex 21 41 Heart 861 Multiclass cancer diagnosis using tumor gene expression signatures. PCA121_Iocally advanced hormone sensitive PCA lateral motoneurons (LMN) 26 VDXOXFU_194 Spleen vs Lipopolysaccharide (LPS) Treated B cell 120min (set1) Effects of SOCS3 on transcriptional response of macrophages to IL-6. Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Replicate 2 after stimulation for 100 minutes with 10 ng/ml IL-6. Source GEO sample is GSM6082 Last updated (according to GEO): Mar 17 2006 of prefrontal cortex 86 105 1000 Spleen Occipital region 983 18 0 Trisomy 21 sample 4 nasal epithelial cells 28 49 Epithelium 861 Heart failure 1000 1000 Hereditary Diseases To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18435 Last updated (according to GEO): May 27 2005 901 Caudate nucleus structure 1000 Mitral Valve 1000 Coronary Arteriosclerosis Nasal Epithelium 901 861 Nerve Brain 1000 Control brainstem 5 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53444 Last updated (according to GEO): Jul 06 2005 78 73 rectum Myocardium sample was obtained from a 42 years old female congestive heart failure subject. High quality sample. Keywords = Congestive heart failure, eNOS, gene, dimethylarginine dimethylaminohydrolase Source GEO sample is GSM6540 Last updated (according to GEO): May 28 2005 hippocampal glutamatergic CA1 pyramidal neurons Source GEO sample is GSM35799 Last updated (according to GEO): May 27 2005 10 7 Left frontal cortex Source GEO sample is GSM18595 Last updated (according to GEO): May 27 2005 Malignant neoplasm of prostate 1000 Craniocerebral Trauma 861 Primary tumor 19 32 Ileum [JunctionChip 4 of 5] 5 0 brain 861 Coxsackievirus Infections cerebral_cortex_5 healthy control sample x050 I_U133A_1_AnCg 1000 Parietal Lobe Dioxin treated MCF7 breast cancer cells [HG-U133B] Exp 2 861 Substantia nigra structure from ventral prostate 21 41 861 Brain total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-gamma (IFN gamma) for 120min Source GEO sample is GSM5609 Last updated (according to GEO): May 27 2005 1000 Hippocampus 5 0 brain 56 32 out of mouse bone marrow Mesenchymal Stem Cells 1000 5 hr Hela Double Thymidine, exp2 Normal__Cerebellum_Brain_Ncer_S-125 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A DLCL-0034 || lc8n109 plasma cells 50 61 mouse brains 187 198 in visual cortex 87 103 Temporal Lobe 4 Normal 19 0 Head and neck cancer BC208A-BE 9 0 Blood Test Blood Test (Blinded) Sample Source GEO sample is GSM130049 Last updated (according to GEO): Sep 18 2007 small intestine PPARalpha knockout mice, treated with WY14,643 for 5 days. The WY14.643 was present in the diet at 0.1% w/w. Source GEO sample is GSM124318 Last updated (according to GEO): Jun 28 2007 The Hay Wells syndrome-derived TAp63alphaQ540L mutant has impaired transcriptional and cell growth regulatory activity. Macrophage smi69 MGJZ030211071Bdorsalstriatum Whole blood 0 10 861 Epithelial Cells Skeletal bone 861 865 Disorder of artery brain, Primary Visual Cortex: Sample64_e1_le1 1000 Aorta Squamous cell carcinoma 875 WGACON-38 Nasal Epithelium 901 brain, hippocampus: Aldh5a1-/- #3363 Cereb_e1_le1 cells stimulated with lipoprotein prep 2, biological rep2 0 Human Cortex 11 1000 Brain BL6:3-1 hippocampus 245 218 of parieto-occipital cortex metastasis 603 612 Coronary heart disease 913 of Parkinson's disease 450 471 Esophagus 3 Normal Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for twelve weeks.. Source GEO sample is GSM148657 Last updated (according to GEO): Dec 12 2006 brain, Medial Temporal Gyrus: Sample30_e1_le1 NCI60.9_LABEL12EXTRACT11SUB3 Source GEO sample is GSM134035 Last updated (according to GEO): Aug 06 2007 of the actin cytoskeleton 841 865 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118559 Last updated (according to GEO): Jul 11 2006 GBM: 32A6 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211257 Last updated (according to GEO): Jul 18 2007 Normal Breast-Norway1 with autism spectrum disorder 37 65 of the mammalian nervous system 46 76 901 Coronary artery amygdala_3 S5_Muscle_Baseline_0min Knockout saline, biological replicate 5 0029_1291_H95A2_KF-097_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174503 Last updated (according to GEO): Mar 14 2007 1000 Hypothalamic structure PBMCs-Type 1 Diabetes-IDDM39_T1D_1MO Mouse Liver AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate C B6 2000-2 Heart Expression profiling of spinal cord section (T9) extracted from rats 4h following laminectomy (sham) Lot batch = Source GEO sample is GSM4482 Last updated (according to GEO): May 28 2005 Thyroid carcinoma 901 CNS-SpinalCmod-Adult-4h-4C-s2 Epithelium of bronchus 983 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188834 Last updated (according to GEO): Jun 06 2007 ISR22-Fv2E-PERK AP20187 8hr2 RNA from an 2nm AP20187 treated (8hr) Fv2E expressing fibroblast cell line in an eIF2 alpha AA (mutant) background. AP20187 activates the kinase activity of the Fv2E-PERK chimera. The eIF2 alpha AA background was used in order to determine whether genes activated through Fv2E-PERK required eIF2alpha phosphorylation. The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules. Source GEO sample is GSM10910 Last updated (according to GEO): May 28 2005 19 0 Head and neck cancer cerebellum wistar ky 3890 whole tissue, individual animal, 10 weeks old, male Wistar Kyoto cerebellum file:p3890w Source GEO sample is GSM15133 Last updated (according to GEO): Oct 28 2005 CNS-SCsev_InjA14d-2B-s2 AML_9 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A cerebellum wistar 3886 Liver Test (Blinded) Sample Source GEO sample is GSM130085 Last updated (according to GEO): Sep 18 2007 5 0 brain Vestibular organ 0 15 Hereditary Malignant Neoplasm 876 Gene expression data from brain of adult rats Source GEO sample is GSM101047 Last updated (according to GEO): Feb 20 2007 Job's patient Source GEO sample is GSM211012 Last updated (according to GEO): Sep 10 2007 Epithelium 861 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9927.gif Source GEO sample is GSM79892 Last updated (according to GEO): Sep 22 2006 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153344 Last updated (according to GEO): Dec 27 2006 H9RGV00110702 Gene expression data Source GEO sample is GSM183169 Last updated (according to GEO): Jul 30 2007 VDXRHU_5232 10 7 Left 22 0 Mammary Gland @ Invo2 Gene expression data from postmorten brain regions Source GEO sample is GSM145706 Last updated (according to GEO): Nov 20 2006 Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174527 Last updated (according to GEO): Mar 14 2007 Sham infected HIGK cells, biological rep3 1000 jejunum "Sample 97, BRCA1 mutation(101 months) age 41 erp no" on vantveer-oligo 2CdA: PK11195 intervention at 3.0h Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225754 Last updated (according to GEO): Nov 02 2007 Healthy donor SN31_vs_Pool D_U133A_44_DLPFC Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589?595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164?169.) Source GEO sample is GSM159480 Last updated (according to GEO): Jun 21 2007 Neoplasm 861 Expression profiling of somatomotor cortex extracted from rats at 4h following moderate injury Source GEO sample is GSM44453 Last updated (according to GEO): May 27 2005 Mesenchymal Stem Cells 1000 10 7 Left 0 Human Cortex 11 Cerebral cortical contusion in rat, 4 dpi #1 NG108 rat neuronal cell culture exposed to 4400 ng/ml mefloquine (treated) for two hours. 10 µg total RNA hybridized per chip. RNA STAT 60 used to extract RNA. Standard Affymetrix chip scaling factors used. No other data transformation. Source GEO sample is GSM1669 Last updated (according to GEO): Oct 28 2005 1000 Left S1P2-KO-hippocampus, biological rep4 (male) Tumor__Melanoma_94_I_191 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 861 Neoplasm 11 CN B Coronary Arteriosclerosis 1000 923 Ganglia, Spinal at the Human Brain 743 760 from rat lungs 21 34 Neoplasm 861 Transitional epithelium 1000 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11480 Last updated (according to GEO): May 28 2005 PBMCs-Type 1 Diabetes-IDDM43_T1D_New Neoplasm 861 brain, Left Temporal Lobe: Extract45_le2 30 19 Solid tumor 861 Astrocytoma 12 hr Hela Double Thymidine, exp2 CAD_replicate47 304 280 alcoholic cardiomyopathy 091201 OVR1 on Affymetrix GeneChip Human Full Length Array HuGeneFL 875 Neoplasms, Embryonal Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225720 Last updated (according to GEO): Nov 02 2007 Sample details: Three pools of rostral (R1-3), three pools of middle (M1-3), and three pools of caudal (C1-3) E13.5 MF1 neocortex were collected from 4 embryos. All possible 18 comparisons were carried out. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. Source GEO sample is GSM62821 Last updated (according to GEO): Aug 26 2005 Mesenchymal Stem Cells 1000 Prostate carcinoma 1000 A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism Source GEO sample is GSM5975 Last updated (according to GEO): Nov 21 2005 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27039 Last updated (according to GEO): May 27 2005 Bronchopulmonary Dysplasia 901 40 29 from kidneys Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28731 Last updated (according to GEO): May 27 2005 5 0 brain 1000 Cardiomyopathy, Alcoholic Predicting the clinical status of human breast cancer by using gene expression profiles. Primary Neoplasm 1000 whole blood_101644 336 320 Keywords = aorta BACKGROUND: Immune complexes may cause an irreversible onset of chronic renal disease. Most patients with chronic renal disease undergo a final common pathway, marked by glomerulosclerosis and interstitial fibrosis. We attempted to draw a molecular map of anti-glomerular basement membrane (GBM) glomerulonephritis in mice using oligonucleotide microarray technology. METHODS: Kidneys were harvested at days 1, 3, 7, 11, and 16 after inducing glomerulonephritis by using anti-GBM antibody. In parallel with examining the biochemical and histologic changes, gene expression profiles were acquired against five pooled control kidneys. Gene expression levels were cross-validated by either reverse transcription-polymerase chain reaction (RT-PCR), real-time PCR, or immunohistochemistry. RESULTS: Pathologic changes in anti-GBM glomerulonephritis were confirmed in both BALB/c and C57BL/6 strains. Among the 13,680 spotted 65mer oligonucleotides, 1112 genes showing significant temporal patterns by permutation analysis of variance (ANOVA) with multiple testing correction [false discovery ratio (FDR) < 0.05] were chosen for cluster analysis. From the expression profile, acute inflammatory reactions characterized by the elevation of various cytokines, including interleukin (IL)-1 and IL-6, were identified within 3 days of disease onset. After 7 days, tissue remodeling response was prominent with highly induced extracellular-matrix (ECM) genes. Although cytokines related to lymphocyte activation were not detected, monocyte or mesangial cell proliferation-related genes were increased. Tumor necrosis factor-alpha (TNF-alpha) and nuclear factor-kappaB (NF-kappaB) pathway were consistently activated along the entire disease progression, inducing various target genes like complement 3, IL-1b, IL-6, Traf1, and Saa1. CONCLUSION: We made a large-scale gene expression time table for mouse anti-GBM glomerulonephritis model, providing a comprehensive overview on the mechanism governing the initiation and the progression of inflammatory renal disease. 861 Brain 20 0 amygdala sprague 3950 from the femurs 95 109 Spleen 0 5 1000 Kidney olfactory epithelium 194 213 H9RGV00102612 Lymphoblastoid Cell Line for Individual 8127.4 log phase bonemarrow Source GEO sample is GSM18751 Last updated (according to GEO): Sep 25 2006 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153327 Last updated (according to GEO): Dec 27 2006 5 0 brain SNU423 cells Chronic leukemia NOS 913 PriG_5%O2_Expt2_Day11_rep1 To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at ?80C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at ?80°C before routine processing for GeneChip analysis. Source GEO sample is GSM28667 Last updated (according to GEO): Oct 28 2005 Cerebral cortex 861 Brain 861 Prostatitis on UMich-10k labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156160 Last updated (according to GEO): Jan 22 2007 Brain 861 Carcinoma, Large Cell 884 58 41 with endometriosis of the nasal epithelial cells? 1237 1266 Mesenchymal Stem Cells 1000 Expression profiling of spinal cord section (T8) extracted from rats 14d following severe injury Source GEO sample is GSM31470 Last updated (according to GEO): May 27 2005 10 7 Left Gene expression data from postmorten brain regions Source GEO sample is GSM145087 Last updated (according to GEO): Nov 20 2006 1000 Brain Control rats 6h after injection with PBS Treatment, type=time_course, description=Control animals are treated with PBS, measurement=6.0 h Source GEO sample is GSM32076 Last updated (according to GEO): May 27 2005 Bladder sample 810-1 Hypothalamus RYGB-Success Repl1 875 Muscle Plasma 861 human caudate nucleus Source GEO sample is GSM86893 Last updated (according to GEO): Feb 08 2006 1000 Mammary gland DLCL-0005 || lc4b064 1000 Structure of trigeminal ganglion Low-Density Lipoproteins 923 ileum (pool of 4 animals)_72h monoassociation with L.innocua_A_5547 Source GEO sample is GSM161568 Last updated (according to GEO): Feb 14 2007 B305 immature DCs without IFN alpha treatment total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lipopolysaccharide (LPS) for 60min Source GEO sample is GSM5665 Last updated (according to GEO): May 27 2005 NHE1 null mutation hippocampus-1 Primary Neoplasm 1000 Whole Brain 62 72 PGA-HMO-NonObese-3aUA-s2 Female 21.5 yr after antibody enrichment scan 2 (U133B) Infection 861 fetal_lung 0 9 1BJZ02022866_bonemarrow 12 0 ovarian tumor Gene expression data from postmorten brain regions Source GEO sample is GSM145013 Last updated (according to GEO): Nov 20 2006 rat hippocampus Treatment, type=time_course, measurement=1.0 h Source GEO sample is GSM32128 Last updated (according to GEO): May 27 2005 Colon 1000 Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID321 Liver 1000 5 0 brain 861 Colon /testicles 202 212 11 0 Fetal brains Y SIT D074 19 0 human frontal cortex 36 21 from whole brain Muscle; Smooth - Bladder- day 1 postnatal male Keywords = mouse gene expression database Source GEO sample is GSM29405 Last updated (according to GEO): May 27 2005 cerebellum 7 16 CCC103B GRP sample 4 Nasal Epithelium Inhalation Formaldehyde 2ppm 19d ID234 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120674 Last updated (according to GEO): May 14 2007 5 0 Spleen plasma cells 50 61 /3T3 fibroblasts 478 493 10 7 left Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy, pathological hypertrophy, rat, heart failure, cardiomyopathy Source GEO sample is GSM12321 Last updated (according to GEO): May 28 2005 Expression profiling of spinal cord section (T10) extracted from rats 4h following moderate injury Source GEO sample is GSM31342 Last updated (according to GEO): May 27 2005 the heart 986 995 901 theca cell The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160198 Last updated (according to GEO): Feb 08 2007 Nasal Epithelium Inhalation Formaldehyde 0ppm 19d ID76 861 Cerebellum brain, forebrain: Sample7_e1_le1 CCAT Full Length Rep B2 144 114 from a single adult spinal cord A/J amygdala rep1 After 2 week acclimation to 12 hr/12 hr light/dark regimen, c57/Bl6 mice were subjected to a 36 hour period of constant darkness. Aortae were subsequently harvested at 4 hour intervals to 48 hours. Duplicate microarrays were hybridized with biotin-labeled probes derived from aorta tissue (6 pooled aortae/timepoint). Source GEO sample is GSM6096 Last updated (according to GEO): May 27 2005 Testi_GermCell Source GEO sample is GSM18985 Last updated (according to GEO): Sep 25 2006 Ts1Cje-5-MGU74B 7 0 prostate R7N 6 WGACON-265 TUMOR 12 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Brain NORMAL 8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Replicate1_Voxel E6 861 Colon The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160219 Last updated (according to GEO): Feb 08 2007 Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174515 Last updated (according to GEO): Mar 14 2007 Skeletal bone 1000 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195265 Last updated (according to GEO): Sep 13 2007 Myocardium 861 Substantia Nigra MME Sample1 RMA, MAS 5, dChip HC69 CB A rat cortex Treatment, type=time_course, measurement=14.0 d Source GEO sample is GSM53221 Last updated (according to GEO): Jul 06 2005 Study of in vitro granulocyte differentiation Source GEO sample is GSM137475 Last updated (according to GEO): Jun 06 2007 normal lung 992 1002 brain_DLPFC_bipolar C_mr545 Parkinson Disease 861 94 68 dorsal tongue surface C57BL 901 Spinal Cord PGA-Band_4h_10-m5 Vestibular organ 0 15 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188745 Last updated (according to GEO): Jun 06 2007 Hippocampus_WildType_rep2 78 73 rectum ventral tegmental area sprague1 HapMap YRI_parent Male Source GEO sample is GSM159714 Last updated (according to GEO): Feb 01 2007 Mammary Neoplasms 884 Craniocerebral Trauma 861 GBM Treatment, type=remove Source GEO sample is GSM99601 Last updated (according to GEO): Apr 21 2006 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3504.gif Source GEO sample is GSM76428 Last updated (according to GEO): Sep 22 2006 BC112B-BE Brain 861 #18 (isolate 36 low serum media VEGF-A 42hours) Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM Source GEO sample is GSM207687 Last updated (according to GEO): Jul 09 2007 15 0 human cerebellum total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Insulin-like growth factor 1 for 60min Source GEO sample is GSM5618 Last updated (according to GEO): May 27 2005 12 frontal Lobe 23 Female 26.5 yr before antibody enrichment scan 1 (U133B) 40 21 from dorsal pancreas 19 0 human frontal cortex hippocampus rattus_norvegicus_strain iNP animal_number 12 Whole blood 0 10 Richard Almon-44-1138200270774 Heart 861 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156596 Last updated (according to GEO): Jan 22 2007 Mouse model of congenital heart disease. Wild-type embyronic day 9.5 mouse. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2282 Last updated (according to GEO): May 27 2005 brain, Entorhinal Cortex: 95-08 normal_e1_le1 Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92290 Last updated (according to GEO): Jan 13 2006 Male; Testes Keywords = mouse gene expression database Source GEO sample is GSM29397 Last updated (according to GEO): May 27 2005 Squamous cell carcinoma 5 0 24 Large cell carcinoma of lung 901 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228586 Last updated (according to GEO): Sep 11 2007 osteoblast 630 640 861 Retina PBMCs-Type 1 Diabetes-IDDM50_T1D_1MO Macrophage smi118 VDXGUYU_4061 of hypertension 44 58 Epithelial Cells 901 cortex 7 12 7 cerebral cortex 21 human caudate nucleus Source GEO sample is GSM86915 Last updated (according to GEO): Feb 08 2006 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28452 Last updated (according to GEO): May 27 2005 (1 utricle 11 20 in brain 295 303 dopamine receptors 1349 1366 Heart 861 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with ELC for 30min Source GEO sample is GSM5546 Last updated (according to GEO): May 27 2005 CCRF-CEM DMSO control 24h rep1 901 Coronary artery GBM Treatment, type=remove Source GEO sample is GSM99544 Last updated (according to GEO): Apr 21 2006 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15467.gif Source GEO sample is GSM84173 Last updated (according to GEO): Sep 22 2006 1000 Encephalitis Lymphoblastoid Cell Line for Individual 8167.4 log phase 5 0 brain in human gastric cancers 37 60 901 Brain Neoplasms Lymphoblastic Leukemia 901 by the liver 210 221 Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P14, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day. Source GEO sample is GSM3217 Last updated (according to GEO): May 28 2005 PGA-MPF-BALB-saline-14d-1aAv2-s2 Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213475 Last updated (according to GEO): Jul 31 2007 GBM Treatment, type=remove Source GEO sample is GSM99472 Last updated (according to GEO): Apr 21 2006 osteoblast 630 640 901 Mammary gland M_U133A_31_nAcc 21-3 spinal cord 3 18 1000 Encephalitis liver 0 5 C57BL/6J periaqueductal gray rep2 (430 2.0 Array) Cancers; Colon Tumor Keywords = mouse gene expression database Source GEO sample is GSM29262 Last updated (according to GEO): May 27 2005 T57__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 27 0 dorsal root ganglion fisher1 Mesenchymal Stem Cells 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM144949 Last updated (according to GEO): Nov 20 2006 59 50 Epidermis Morula replication 4 Keywords = preimplantation Keywords = development Source GEO sample is GSM14690 Last updated (according to GEO): May 28 2005 mouse cerebral cortex 0 21 78 66 Control blood Haloperidol treated 12weeks AffyGC RMA rep10 1000 Hippocampus Coronary heart disease 913 Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231053 Last updated (according to GEO): Sep 26 2007 kidney 176 182 gene expression of 2 day RA differentiated ESCs Source GEO sample is GSM181969 Last updated (according to GEO): Apr 12 2007 Whole Brain 62 72 858 Prostatic Neoplasms 7 0 prostate Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:179, Count:32 Corner- Avg:32377, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:10.951877,SFGene:All Background:Avg:533.85,Stdev:14.67,Max:561.2,Min:501.0 Noise:Avg:9.33,Stdev:0.31,Max:10.1,Min:8.3 RawQ:14.88 Keywords = ALL Source GEO sample is GSM3426 Last updated (according to GEO): May 28 2005 breast basal- 491 503 Blood 1000 35 0 Inflammatory myopathy specimen GEIM7 HA96-37A Spleen vs MIP3-alpha Treated B cell 240min (set3) 5 0 brain 5 0 brain 861 Blood Adult murine BM, Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1+Englow 4 Cerebral cortex 861 1000 Amygdaloid structure Tumor__CNS_Medulloblastoma_M33 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Corticospinal Motor Neurons P6 1 858 Mesodermal cell Gene expression data from human prostate tissue with 90 percent tumor content Source GEO sample is GSM119314 Last updated (according to GEO): Feb 23 2007 Cerebral cortex 861 1000 Communicable Diseases Bone Marrow 1000 Neoplasm 861 I_U133A_13_CB 129/SvImJ Cerebellum B Wild type 8 wk old male FVB/NJ mouse periaqueductal gray Source GEO sample is GSM74996 Last updated (according to GEO): Feb 27 2007 BPH-39 on UMich-10k Brain 1000 7 0 prostate Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM80011 Last updated (according to GEO): Oct 26 2005 PGA_MI_nilv_24h_362 no additional Source GEO sample is GSM199084 Last updated (according to GEO): Jun 08 2007 Integumentary system 1000 Human muscle cultures were prepared from progenitor satellite cells isolated from a muscle biopsy of a 16-donor subject through an explant-reexplant technique (5). Biopsies were obtained with informed consent and approval of the Human Use Committee of the Hospital Vall d?Hebrón, Barcelona. A batch of cells isolated after 1 explant and 4 consecutive subcultures at dilution (1:3) were induced to differentiate for 15 days and then weekly monitored for the stated parameters. Growth medium was DMEM:MEM-199 3:1, supplemented with 10 % fetal bovine serum (FBS), 10 µg/ml insulin, 2 mM glutamine, 25 ng/ml fibroblast growth factor (FGF) and 10 ng/ml epidermal growth factor (EGF). Differentiating medium had the same composition except FGF and EGF. Cultures were kept at 37ºC in a humidified 5% CO2 atmosphere. Source GEO sample is GSM19155 Last updated (according to GEO): Oct 28 2005 861 Cerebral cortex Utricle structure 1000 of somatomotor cortex 21 41 Malignant Neoplasms 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145232 Last updated (according to GEO): Nov 20 2006 82 53 with congestive heart failure N5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A umbilical cord_nobpd: 6A of human cytomegalovirus infection 11 44 V5-P266 60 23 a prevalent neurodegenerative disorder ISR5 D_U133A_18_HC Impact of viral infection on the gene expression profiles of proliferating normal human peripheral blood mononuclear cells infected with HIV type 1 RF. 861 Kidney 1037 of transitional epithelium 1012 ileum 1000 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211277 Last updated (according to GEO): Jul 18 2007 Pancreas at e15.5, Chip B, rep 2 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27028 Last updated (according to GEO): May 27 2005 (cortex 19 25 The nose 94 101 Parkinson Disease 861 Si9_3, mouse, SW, infected, 9 days post infection_rep 3 Skeletal bone 861 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195353 Last updated (according to GEO): Jun 04 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145187 Last updated (according to GEO): Nov 20 2006 Intraabdominal stromo vascular fraction, rep3 MDA Mb231 1h 3 Control Arteries 861 1000 Liver 1000 Liver adenoma 861 CNS-SpinalCmod-Adult-28d-3A-s2 1000 medulloblastoma Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5457.gif Source GEO sample is GSM93150 Last updated (according to GEO): Sep 22 2006 Examining the effects of tTA expression in mouse hearts Source GEO sample is GSM15070 Last updated (according to GEO): May 28 2005 Blood Test (Blinded) Sample Source GEO sample is GSM129933 Last updated (according to GEO): Sep 18 2007 ALL B-cell39 on Affymetrix GeneChip Human Full Length Array HuGeneFL 26 0 frontal cortex sprague 3936 of the central nervous system 61 89 Normal__Breast_BR_3 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Adenovirus 133 142 CH1814 acute myeloid leukemia Source GEO sample is GSM227414 Last updated (according to GEO): Sep 12 2007 Skeletal bone 861 NoCAD_replicate40 1000 Lymphoma Cerebellum 5 Normal no additional Source GEO sample is GSM199351 Last updated (according to GEO): Jun 08 2007 Pancreas at e12.5, Chip C, rep 1 Interatrial septum 865 Cerebral cortex 901 NMDA 10 (5/7) (Experiment NMDA1-Run 9136) Treatment, type=time_course, description=samples are treated for 10, 30 or 60 min with NMDA 1mM, the agonist is then washed out and the cells are harvested 24h later, measurement=10.0 m Source GEO sample is GSM96710 Last updated (according to GEO): Feb 14 2006 1000 Lung Transplant Series 34 , PrimaryTumor D_U133A_95_CB 1000 Communicable Diseases Brain 1000 Tumor__Bladder_TCC_9858 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Parkinson Disease 1000 24 0 Proliferative endometrium Epithelium 861 901 Coronary artery ANIMALS Patched heterozygous mice (Goodrich et al., 1997) were obtained from Matthew Scott?s lab at Stanford, and maintained by breeding with 129X1/SvJ mice from Jackson Laboratories. Math1-GFP transgenic mice (Lumpkin et al., 2003) were provided by Jane Johnson at UT Southwestern Medical Center. Math1-GFP/patched+/- mice were generated by crossing patched heterozygotes with Math1-GFP mice, and then backcrossing to Math1-GFP mice three times before further analysis. All mice were maintained in the Cancer Center Isolation Facility at Duke University Medical Center. ISOLATION OF CELLS Granule cell precursors (GCPs) were isolated from 7-day-old (P7) patched+/- mice; preneoplastic cells were obtained from 6 week-old patched mutants; and tumor cells were obtained from 10-25-week old patched mutants displaying physical and behavioral signs of medulloblastoma. Cells were isolated from each source using a protocol described in (Wechsler- Reya and Scott, 1999). Briefly, cerebella were digested in solution containing 10 U/ml papain Oliver et al. Pre-Neoplastic Stage of Medulloblastoma - 8 - (Worthington, Lakewood, NJ) and 250 U/ml DNase (Sigma) and triturated to obtain a cell suspension. This suspension was centrifuged through a step gradient of 35% and 65% Percoll (Amersham Biosciences, Piscataway, NJ), and cells were harvested from the 35%-65% interface. Cells were resuspended in serum-free culture medium consisting of Neurobasal containing B27 supplement, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen, Carlsbad, California) and counted on a hemacytometer. Cells used for RNA isolation were centrifuged and flash frozen in liquid nitrogen. For proliferation assays or immunostaining, cells were plated on poly-D-lysine (PDL)-coated tissue culture vessels and incubated in serum-free culture medium. MICROARRAY HYBRIDIZATION AND ANALYSIS RNA from GCPs, pre-neoplastic cells and tumor cells (isolated as described above, but not FACS-sorted) and from normal adult cerebellum (not dissociated) was converted to cDNA using the Superscript Choice cDNA kit (Invitrogen) and a T7-dT(24) primer (Genset/Proligo, Boulder, CO). cRNA was generated using a T7-transcription/labeling kit from Enzo Life Sciences and hybridized to Affymetrix U74Av2 chips (Affymetrix, Santa Clara, CA). Chips were scanned, and hybridization data were acquired using Affymetrix Suite 5.0 software. Affymetrix CEL files were normalized and quantified using Bioconductor software with the gcRMA model to quantify gene expression levels (Gentleman and Carey, 2002). Unsupervised principal components analysis (PCA) was used to identify the relationships among normal adult cerebellum, GCPs, pre-neoplastic cells and tumor cells based on expression profiles. To identify genes that were differentially expressed among GCPs, pre-neoplastic cells and tumor cells, supervised analysis was carried out. A gene-by-gene ANOVA model with three groups (GCP, pre-neoplastic, tumor) was used to fit the log2-transformed intensities. To correct for multiple comparisons, the nominal p-value was adjusted using the false discovery rate (Benjamini and Hochberg, 1995). Genes were considered to be differentially expressed if they satisfied all of the following criteria: a difference in expression greater than 1.9-fold between any two groups, a maximum absolute intensity difference larger than 32 units, and an adjusted pvalue < 0.01. There were 118 genes that met these criteria. The identities of differentially expressed genes were verified by integrating data from the Affymetrix and Unigene databases. Gene functions were determined using information from Gene Ontology, Unigene, LocusLink and PubMed databases. Clustering was performed with Cluster and Treeview (Eisen et al., 1998). All statistical analysis was performed using R-1.7 software (Dalgaard, 2002). Results were visualized with Spotfire 6.0 (Somerville, MA). CORRESPONDING AUTHOR Robert J. Wechsler-Reya* Dept. of Pharmacology & Cancer Biology, Duke University Medical Center Box 3813, Durham, NC 27710 Phone: 919-613-8754. Fax: 919-668-3556. Email: rw.reya@duke.edu Keywords = medulloblastoma Keywords = brain tumor Source GEO sample is GSM45625 Last updated (according to GEO): Oct 28 2005 BCR-ABL-#6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A IDC41 on harvard-12k 17 7 hippocampi Neoplasm 861 GM10835 Structure of olfactory bulb 1000 16 7 cerebellum A_1 15 7 brainstem Hypothalamic structure 861 Saphenous Vein 2 Normal Expression of VP16-CREB, a constitutively active form of CREB, in hippocampal neurons of the CA1 region lowers the threshold for eliciting the late, persistent phase of long-term potentiation (L-LTP) in the Schaffer collateral pathway. This VP16-CREB-mediated L-LTP differs from the conventional late phase of LTP in not being dependent on new transcription. This finding suggests that in the transgenic mice the mRNA transcript(s) encoding the protein(s) necessary for this form of L-LTP might already be present in CA1 neurons in the basal condition. We used high-density oligonucleotide arrays to identify the mRNAs differentially expressed in the hippocampus of transgenic and wild-type mice. We then explored the contribution of the most prominent candidate genes revealed by our screening, namely prodynorphin, BDNF, and MHC class I molecules, to the facilitated LTP of VP16-CREB mice. We found that the overexpression of brain-derived neurotrophic factor accounts for an important component of this phenotype. HMVEC-L stimulated with LPS for 4 hours L04R1 690 685 Tumors Cerebral cortex 861 PC 6Hr rat 3586 blood vs. 150mg/kg APAP 6Hr rat 3588 blood 1000 Cardiomyopathies Mouse neuroblastoma (N2a) cells are available from the American Tissue Culture Collection (ATCC, number CCL-131). To generate cells expressing 3F4-tagged PrP, cells were stably transfected with Mo3F4 PrP in a pcDNA3.1/Zeo vector (Invitrogen, Leek, The Netherlands) and stable transfectants selected using Zeozine 300 ug/ml medium (Gilch et al, 2001, EMBO 20: 3957-3966). RNA was isolated from control and infected cell lines by the Trizol method. 20µg total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 30µl hybridisation buffer (6x SSC, 0,5% SDS 5 fold Denhardt's solution and 50% formamide) and mixed with 30µl of reference cDNA solution labelled with the second dye. This hybridisation mixture was placed on a pre hybriddised microarray, covered with cover slip, placed into a hybridisation chamber (Genomatix) and immersed in a thermostatic bath at 42°C for at least 16 hours. Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Maen intensities with substracted background were normalised so that the median of their rations has became 1 Keywords = prion Keywords = neuroblastoma Keywords = N2a Source GEO sample is GSM31103 Last updated (according to GEO): Oct 28 2005 1 Retina 13 20 with some respiratory epithelium. 1039 1072 -_6936_batch1 on NHGRI-6.7k 1000 Carcinoma Neurosphere cultures were established from individually isolated E 14.5 forebrains of mouse embryos that carry a bcl2 transgene. Single-cell suspensions were prepared, seeded at 1x105 cells/ml and treated for two days with 150 nM Trichostatin A (TSA), 500 nM 5-Aza-2?-deoxycytidine (AzaC) or both compounds, or left untreated. Two independent experiments were performed. Source GEO sample is GSM8900 Last updated (according to GEO): Oct 28 2005 DCN_SHAM_A brain, Right Temporal Parietal: Extract85_le2 I_U133A_3_AnCg VDXIGRU_256209 G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage. Source GEO sample is GSM9641 Last updated (according to GEO): May 28 2005 f2#191 versus pool Mouse Brain tissue Parkinson Disease 1000 861 Brain MuscleRegen-ctx5.5d-2LLAv2-s2 in bronchial epithelia 311 332 Expression profiling of spinal cord section (T10) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM4465 Last updated (according to GEO): May 28 2005 sAPPalpha #3 Large-scale analysis of the mouse transcriptome. Dorsal root ganglion C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 356.69 Stdv: 12.12 Min: 341.69 Max: 379.74 Source GEO sample is GSM2993 Last updated (according to GEO): May 27 2005 Gene expression data from whole tumor Source GEO sample is GSM182289 Last updated (according to GEO): Apr 16 2007 ovary 45 50 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14939 Last updated (according to GEO): Oct 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145640 Last updated (according to GEO): Nov 20 2006 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184768 Last updated (according to GEO): Apr 26 2007 between the LAD artery 266 287 1000 Hippocampus 1000 Prostate carcinoma brain, Left frontal Lobe: Extract14_le2 ProstateCancer-12 on NHGRI-6.5k_c 861 Cardiomyopathies Nose 1000 A2780_oxa_IC90_24h Exp A_3, 10mg/kg CPF 117 112 Lipids PGA-MFD-CtrPD1-2aAv2-s2b labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156562 Last updated (according to GEO): Jan 22 2007 861 Cerebral cortex 3_hypothalamus_12hrs_sleep_deprivation_#104 umbilical cord_bpd: 8I Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell 30min (set1) Organ 966 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114266 Last updated (according to GEO): Jun 16 2006 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225700 Last updated (according to GEO): Nov 05 2007 1000 Structure of superior frontal gyrus Cerebral cortex 861 MELANOMA 18 25 NZW/LacJ_female_hypothalamus Source GEO sample is GSM138571 Last updated (according to GEO): Apr 18 2007 40 21 from skeletal muscle Macrophage smi66 5 0 brain The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159954 Last updated (according to GEO): Feb 01 2007 12 The inner ear 0 whole blood_100981 E2A-PBX1-#3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Skeletal bone 1000 Kidney 23 13 spinal cord human cerebellum Source GEO sample is GSM87082 Last updated (according to GEO): Feb 08 2006 861 Retina f2#303 versus pool Mouse Brain tissue spinal cord 13 23 HL-60(TB) hgu95a 261 234 of activating immunoglobulin 23 16 in brain +_6302_batch4 on NHGRI-6.7k 861 Neoplasm Mesenchymal Stem Cells 1000 TUMOR 7 0 6 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195349 Last updated (according to GEO): Jun 04 2007 Autistic Disorder 877 Brain 861 7 cerebral cortex 21 Spleen vs TGF-beta Treated B cell 240min (set2) cocaine naive,medial prefrontal cortex, 0 hrs/day access to cocaine Source GEO sample is GSM93867 Last updated (according to GEO): Jan 26 2006 CNS-SC_InjA4h-3B-s2 after infection. 236 252 Total RNA was extracted from umbilical subcutaneous adipose tissue from an individual affected with FCHL and exhibiting the USF1 susceptibility haplotype Source GEO sample is GSM9043 Last updated (according to GEO): May 28 2005 of neurite outgrowth 597 616 1000 Rectum Brain 1000 Multiple Sclerosis 1000 of mouse brain 9 23 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211262 Last updated (according to GEO): Jul 18 2007 1000 Leukemia, Myelocytic, Acute 89 70 isolated theca cells 861 Blood Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211293 Last updated (according to GEO): Jul 18 2007 25 7 Right Temporal Lobe infection 278 287 Spinal Cord 10 Normal stria terminalis 1000 OlfactoryBulb Source GEO sample is GSM19020 Last updated (according to GEO): Sep 25 2006 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19220 Last updated (according to GEO): May 27 2005 Parkinson's disease sample x184 0 30 infection 255 264 320 306 Keywords = HIV 5 0 brain 5 0 Spleen 329 306 valvular cardiomyopathy Heart 1000 Prostate 861 ALS gray matter 4 Sporadic 858 Mesodermal cell ANIMALS Patched heterozygous mice (Goodrich et al., 1997) were obtained from Matthew Scott?s lab at Stanford, and maintained by breeding with 129X1/SvJ mice from Jackson Laboratories. Math1-GFP transgenic mice (Lumpkin et al., 2003) were provided by Jane Johnson at UT Southwestern Medical Center. Math1-GFP/patched+/- mice were generated by crossing patched heterozygotes with Math1-GFP mice, and then backcrossing to Math1-GFP mice three times before further analysis. All mice were maintained in the Cancer Center Isolation Facility at Duke University Medical Center. ISOLATION OF CELLS Granule cell precursors (GCPs) were isolated from 7-day-old (P7) patched+/- mice; preneoplastic cells were obtained from 6 week-old patched mutants; and tumor cells were obtained from 10-25-week old patched mutants displaying physical and behavioral signs of medulloblastoma. Cells were isolated from each source using a protocol described in (Wechsler- Reya and Scott, 1999). Briefly, cerebella were digested in solution containing 10 U/ml papain Oliver et al. Pre-Neoplastic Stage of Medulloblastoma - 8 - (Worthington, Lakewood, NJ) and 250 U/ml DNase (Sigma) and triturated to obtain a cell suspension. This suspension was centrifuged through a step gradient of 35% and 65% Percoll (Amersham Biosciences, Piscataway, NJ), and cells were harvested from the 35%-65% interface. Cells were resuspended in serum-free culture medium consisting of Neurobasal containing B27 supplement, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen, Carlsbad, California) and counted on a hemacytometer. Cells used for RNA isolation were centrifuged and flash frozen in liquid nitrogen. For proliferation assays or immunostaining, cells were plated on poly-D-lysine (PDL)-coated tissue culture vessels and incubated in serum-free culture medium. MICROARRAY HYBRIDIZATION AND ANALYSIS RNA from GCPs, pre-neoplastic cells and tumor cells (isolated as described above, but not FACS-sorted) and from normal adult cerebellum (not dissociated) was converted to cDNA using the Superscript Choice cDNA kit (Invitrogen) and a T7-dT(24) primer (Genset/Proligo, Boulder, CO). cRNA was generated using a T7-transcription/labeling kit from Enzo Life Sciences and hybridized to Affymetrix U74Av2 chips (Affymetrix, Santa Clara, CA). Chips were scanned, and hybridization data were acquired using Affymetrix Suite 5.0 software. Affymetrix CEL files were normalized and quantified using Bioconductor software with the gcRMA model to quantify gene expression levels (Gentleman and Carey, 2002). Unsupervised principal components analysis (PCA) was used to identify the relationships among normal adult cerebellum, GCPs, pre-neoplastic cells and tumor cells based on expression profiles. To identify genes that were differentially expressed among GCPs, pre-neoplastic cells and tumor cells, supervised analysis was carried out. A gene-by-gene ANOVA model with three groups (GCP, pre-neoplastic, tumor) was used to fit the log2-transformed intensities. To correct for multiple comparisons, the nominal p-value was adjusted using the false discovery rate (Benjamini and Hochberg, 1995). Genes were considered to be differentially expressed if they satisfied all of the following criteria: a difference in expression greater than 1.9-fold between any two groups, a maximum absolute intensity difference larger than 32 units, and an adjusted pvalue < 0.01. There were 118 genes that met these criteria. The identities of differentially expressed genes were verified by integrating data from the Affymetrix and Unigene databases. Gene functions were determined using information from Gene Ontology, Unigene, LocusLink and PubMed databases. Clustering was performed with Cluster and Treeview (Eisen et al., 1998). All statistical analysis was performed using R-1.7 software (Dalgaard, 2002). Results were visualized with Spotfire 6.0 (Somerville, MA). Keywords = cerebellar granule cell precursors (GCPs) Source GEO sample is GSM45616 Last updated (according to GEO): Oct 28 2005 Mouse Kidney Male 1 (technical replicate) with Parkinson's disease 27 50 olfactory epithelium 194 213 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68129 Last updated (according to GEO): Jul 07 2006 Parkinson's model voxel E2 SCG_sema3A_40h_rep1 D_U133Plus_73_DLPFC 1000 Cardiomyopathy, Alcoholic 294 267 benign prostatic hyperplasia I_U133Plus_125_Amy PCA-50 on UMich-10k spleen 264 269 Day 1 Mouse #11 - 1st replicate 861 Brain Brain 861 2_hypothalamus_time_0_#118 Wild type 8 wk old male C57BL/6J mouse hypothalamus Source GEO sample is GSM74975 Last updated (according to GEO): Feb 27 2007 AD control Treatment, type=dissect Source GEO sample is GSM119686 Last updated (according to GEO): Jul 10 2006 Liver 1000 Communicable Diseases 1000 Neural tube, treated, GD9:12, T215587 Cultured_cortical_astrocyte_Cx43_null_rep3 861 Brain nostrils 156 164 kidney_medulla_4 Source GEO sample is GSM80734 Last updated (according to GEO): Mar 31 2006 Muscle 861 2782 2774 28S rRNA Postnatal day 14 corticospinal motor neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription. Source GEO sample is GSM37098 Last updated (according to GEO): May 27 2005 Heart 1000 5 0 brain KT36_N Sun185_BAV13 group human cerebellum Source GEO sample is GSM87108 Last updated (according to GEO): Feb 08 2006 trauma 277 283 I_U133A_5_CB 861 Carcinoma adenoma 861 Gene expression data from B6xBALB F2 mouse lung Source GEO sample is GSM133479 Last updated (according to GEO): Apr 05 2007 T39__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 281_1 none Source GEO sample is GSM239855 Last updated (according to GEO): Dec 07 2007 in the cerebellum 29 45 341 332 the tumors Brain 861 Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep7 Brain 861 none Source GEO sample is GSM244644 Last updated (according to GEO): Nov 23 2007 Balb/c day 3, biological rep 4, tech rep 1 human cerebellum Source GEO sample is GSM87091 Last updated (according to GEO): Feb 08 2006 atrial septal defects 198 218 Neoplasm 861 Endometrium 0 10 plasma cells 332 344 Supranuclear Palsy, Progressive 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Tumor necrosis factor-alpha for 30min Source GEO sample is GSM5800 Last updated (according to GEO): May 27 2005 Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200624 Last updated (according to GEO): Jun 12 2007 Laser Capture Microdissection (LCM) to isolate tissue sections of the hippocampus area of wild type mice brains Source GEO sample is GSM208599 Last updated (according to GEO): Jul 12 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM146045 Last updated (according to GEO): Nov 20 2006 1000 Neoplasm 80 neurological diseases 101 of the postmortem brains 664 688 Plasma 861 from olfactory epithelium tissue 24 55 Bone marrow, Mesenchymal stem cells: T3-101103_e1_le1 7 0 Synovium RNA isolated from fetal cerebrum Keywords = trisomy 13 Keywords = brain Keywords = Patau syndrome Source GEO sample is GSM22615 Last updated (according to GEO): May 27 2005 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19066.gif Source GEO sample is GSM91551 Last updated (according to GEO): Sep 22 2006 Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 9676 blood days nasal epithelium 1126 1147 Gene expression data from postmorten brain regions Source GEO sample is GSM146007 Last updated (according to GEO): Nov 20 2006 Liver (HBV+, HK10) of brain cerebella 96 113 brain, hippocampus: Hippocampus 4_le1 Male 26.2 yr before antibody enrichment scan 1 (U133A) lymphnode 0 8 NA Source GEO sample is GSM198933 Last updated (according to GEO): Jun 07 2007 1000 Carcinoma, Embryonal in Mouse Brain 40 53 Low-density CCg progenitors treated with FBS to derive Astrocytes Source GEO sample is GSM47551 Last updated (according to GEO): Jun 10 2005 861 Kidney nasal epithelial cells 28 49 0 Human Cortex 11 1000 Carcinoma T16__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A frontal cortex wistar 3922 whole tissue, individual animal, 10 weeks old, male Wistar frontal cortex file:p3922w Source GEO sample is GSM15159 Last updated (according to GEO): Oct 28 2005 "36 hr Hela Double Thymidine, exp3" VDXKIU_15E7 Mesenchymal Stem Cells 1000 Macrophage smi94 901 frontal lobe Liver 1000 950 Blood Cells Effects of SOCS3 on the transcriptional response of bone marrow-derived macrophages to IL-6. Fetal liver cells from SOCS3+/+ or SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Macrophages were either unstimulated, or stimulated for 100 or 400 minutes with 10 ng/ml IL-6. Last Updated (by provider): Jun 15 2005 Contributers: E Parganas P Murray Y Takahashi R Rutschman J Mages A Pauleau J Ihle R Lang Includes GDS325. Update date: Apr 17 2003. Dataset description GDS325: Bone marrow-derived macrophages from mice that had received fetal liver cells from SOCS3+/+ or SOCS3-/- embryos analyzed. Macrophages either unstimulated, or stimulated for 100 or 400 minutes with 10 ng/ml IL-6.. blood 0 5 pM category 1000 1345 1323 by cervical dislocation bc-ZT15-1 1000 Cerebral cortex Lymphoblastoid Cell Line for Individual 8157.5 log phase 1000 Bronchi 5 0 Muscle Epithelium of bronchus 983 NCI60.44_LABEL48EXTRACT47SUB3 Source GEO sample is GSM134216 Last updated (according to GEO): Aug 06 2007 861 Hippocampus Spleen [JunctionChip 5 of 5] 1000 Brain Brain 861 861 Blood Cochlear nucleus structure 901 days nasal epithelium 1126 1147 Epithelium 865 GM12005 Individual array of a bladder cancer expression experiment. Source GEO sample is GSM180995 Last updated (according to GEO): Apr 12 2007 Primary large cell carcinoma 3259 1000 Muscle 12 0 ovarian tumor Lymphoblastoid Cell Line for Individual 8061.3 log phase in fibroblasts 1222 1236 from ventral prostate 21 41 gene expression data from ODC mouse skin samples Source GEO sample is GSM216653 Last updated (according to GEO): Aug 09 2007 164 136 of the middle cerebral artery Blood 1000 neural progenitor cells 403 426 The epithelial cells 962 981 plasma cells 332 344 Primary Neoplasm 1000 17 7 hippocampus Germ free Corpus 1 Subject code A26 Parkinson's model voxel H1 GSE1556 Ovarian_Tumor_Endometrioid_CHTN-OE-038 Spleen 1000 brain, Left frontal Lobe: Extract26_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM145215 Last updated (according to GEO): Nov 20 2006 Abdominal aortic aneurysm obtained from surgery to correct. Source GEO sample is GSM170568 Last updated (according to GEO): Jul 26 2007 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201753 Last updated (according to GEO): Jun 20 2007 P14 cochlear nuclei pooled from 5 pups for one replicate hybridization out of 2 replicates. Source GEO sample is GSM44854 Last updated (according to GEO): Jun 08 2005 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11346 Last updated (according to GEO): May 28 2005 1000 Coronary Arteriosclerosis Mental Retardation 1000 Voxel J1 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1453 Last updated (according to GEO): Nov 21 2005 1792 1787 livers bronchial epithelia 224 243 AT2-hTERT_1.5Gy_6h_C3_26770 D_U133Plus_114_HC 2500 mg/kg X 12 hr Source GEO sample is GSM129875 Last updated (according to GEO): Sep 18 2007 MucOlfEpith_022SACIG_030.txt CONTROL_1 Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19194 Last updated (according to GEO): May 27 2005 None Source GEO sample is GSM214245 Last updated (according to GEO): Aug 01 2007 Muscle 861 I_U133Plus_126_AnCg Kidney 1000 Brain 861 51 CN A Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184709 Last updated (according to GEO): Apr 26 2007 67 40 with coronary artery disease M-16-2-LI on UMich-10k D2_SleepDep_ZT 6_3 865 Disorder of artery 40 16 in human optic nerve head 1836 1821 locus coeruleus from brain 21 30 861 Adipose tissue Spleen vs CGS Treated B cell 30min (set2) D_U133A_19_nAcc in the hippocampus 115 132 Normal Source GEO sample is GSM176265 Last updated (according to GEO): Apr 09 2007 PGA-RnSalt_h_15w_3-m5 Parkinson Disease 861 Liver 0 4 Substantia nigra PD rep10 Pituitary Gland 861 CNS-SC_CtrB14d-1A-s2 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15952.gif Source GEO sample is GSM84131 Last updated (according to GEO): Sep 22 2006 Saline control-neocortex, biological rep4 Blood 1000 of lung cancer 35 49 SN:1029731;Fetal Cartilage, biological rep2 validation Congenital Abnormality 853 Nose 1000 Mental Retardation 1000 TEL-AML1-R3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Low Freezing Source GEO sample is GSM92414 Last updated (according to GEO): Jan 13 2006 Primary typical carcinoid 4423 Source GEO sample is GSM17321 Last updated (according to GEO): May 28 2005 GSE5281 19 0 Embryonal carcinoma Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35377 Last updated (according to GEO): May 27 2005 C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 4hr after experimental mice received their last shock treatment. Source GEO sample is GSM4495 Last updated (according to GEO): May 27 2005 substantia_nigra_1 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188758 Last updated (according to GEO): Jun 06 2007 Neoplasm 861 1000 Lipids Mouse old brain C30-Br-5 5 0 brain 1000 Heart failure Brain Amygdala Source GEO sample is GSM18927 Last updated (according to GEO): Sep 25 2006 Brain 861 96 84 of diaphragm SN:1007093 Source GEO sample is GSM115370 Last updated (according to GEO): Jun 20 2006 GC (HKG18T) Substantia nigra PD rep5 32h-AM replication 1 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225753 Last updated (according to GEO): Nov 02 2007 TEL-AML1-#2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Cerebellum 0 9 PGA-lv_8w_340 the heart 987 996 KO_NP_med_3 nostrils 156 164 ABSTRACT: BACKGROUND: Hypertension is a complex disease with many contributory genetic and environmental factors. We aimed to identify common targets for therapy by gene expression profiling of a resistance artery taken from animals representing two different models of hypertension. We studied gene expression and morphology of a saphenous artery branch in normotensive WKY rats, spontaneously hypertensive rats (SHR) and adrenocorticotropic hormone (ACTH)-induced hypertensive rats. RESULTS: Differential remodeling of arteries occurred in SHR and ACTH-treated rats, involving changes in both smooth muscle and endothelium. Increased expression of smooth muscle cell growth promoters and decreased expression of growth suppressors confirmed smooth muscle cell proliferation in SHR but not in ACTH. Differential gene expression between arteries from the two hypertensive models extended to the renin-angiotensin system, MAP kinase pathways, mitochondrial activity, lipid metabolism, extracellular matrix and calcium handling. In contrast, arteries from both hypertensive models exhibited significant increases in caveolin-1 expression and decreases in the regulators of G-protein signalling, Rgs2 and Rgs5. Increased protein expression of caveolin-1 and increased incidence of caveolae was found in both smooth muscle and endothelial cells of arteries from both hypertensive models. CONCLUSIONS: We conclude that the majority of differences in gene expression found in the saphenous artery taken from rats with two different forms of hypertension reflect distinctive morphological and physiological alterations. However, changes in common to caveolin-1 expression and G protein signalling, through attenuation of Rgs2 and Rgs5, may contribute to hypertension through augmentation of vasoconstrictor pathways and provide potential targets for common drug development. DBA/2J Amygdala B 884 Structure of horn of uterus Brain 1000 1000 Solid tumor Transcription profiling time series of finite life span and immortal non-malignant human mammary epithelial cell lines 427 407 Keywords = Alzheimer? plasma cells 332 344 Gene expression data from postmorten brain regions Source GEO sample is GSM146009 Last updated (according to GEO): Nov 20 2006 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113960 Last updated (according to GEO): Jun 16 2006 1433 1414 extracellular-matrix Gene expression data from postmorten brain regions Source GEO sample is GSM145661 Last updated (according to GEO): Nov 20 2006 mouse brain 478 489 Ovarian Diseases 877 nostrils 156 164 6,18,30 month oculomotor nucleus and spinal cord Source GEO sample is GSM74339 Last updated (according to GEO): Sep 16 2005 861 Brain 1000 Brain Injuries primary breast tumors 154 175 1000 frontal lobe Heart 861 at the Human Brain 745 762 CNS-SC_CtrBT0-2A-s2 Communicable Diseases 861 81 CB B Parkinson Disease 861 /J mouse pituitary gland 25 48 Control 5 (Experiment Neuroprotection4- Run 21823) Treatment, type=timepoint, description=Same sample used for Experiment Neuroprotection4-Run 14985, samples were rerun due to oven failure, measurement=0.0 h Source GEO sample is GSM96687 Last updated (according to GEO): Feb 14 2006 D_U133Plus_118_nAcc Gene expression data from human colon tumor tissue Source GEO sample is GSM173353 Last updated (according to GEO): Apr 20 2007 WGACON-26 AD-250t1-A166-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A atrial septal defects 198 218 in mdx muscle 886 898 OVCAR-5 hgu95a Spleen vs BAFF Treated B cell 30min (set3) 861 Neoplasm 1BMH02020805_LymphomaRaji Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68358 Last updated (according to GEO): Jul 07 2006 5 0 brain 913 Blood Cells Ovarian Diseases 877 1000 Retina Parkinson Disease 861 1000 Brain brain 0 5 Anterior nares 1000 423 386 with idiopathic dilated cardiomyopathy 091225 OVR21 on Affymetrix GeneChip Human Full Length Array HuGeneFL human frontal cortex Source GEO sample is GSM86961 Last updated (according to GEO): Feb 08 2006 57 39 with endometriosis SN:1006725 Source GEO sample is GSM115351 Last updated (according to GEO): Jun 20 2006 brain, hippocampus: KA240-I_e1_le1 1000 Brain Ovary 1000 of regenerating Dorsal Root Ganglia 21 55 337 323 with adiposity 215 199 of neural retinas 14 7 amygdala 158 133 with ataxia telangiectasia Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11603 Last updated (according to GEO): May 28 2005 processed in batch 1 Source GEO sample is GSM90449 Last updated (according to GEO): Mar 20 2006 BC38 CAD_replicate91 19 0 human frontal cortex Liver 0 4 983 Cervix carcinoma gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134617 Last updated (according to GEO): Jul 09 2007 WGACON-73 5 0 brain CNS-SpinalCmod-Adult-48h-1C-s2 Expression profile of genes in mouse brain Source GEO sample is GSM21056 Last updated (according to GEO): May 27 2005 62 CN B 19 0 Embryonal carcinoma 61 41 from postmortem brain 928 Synapses 2531 CP24_33 Epithelial Cells 1000 Kidney 861 mouse hippocampus from COX-1 WT Source GEO sample is GSM121437 Last updated (according to GEO): Jan 31 2007 Malignant neoplasm of prostate 1000 total RNA derived from a leprosy lesion Source GEO sample is GSM6771 Last updated (according to GEO): May 27 2005 Abnormal development of the prefrontal cortex (PFC) is associated with a number of neuropsychiatric disorders that have an onset in childhood or adolescence. Although the basic laminar structure of the PFC is established in utero, extensive remodeling continues into adolescence. To map the overall pattern of changes in cortical gene transcripts during post-natal development, we made serial measurements of mRNA levels in mouse PFC using oligonucleotide microarrays. We observed changes in mRNA transcripts consistent with known post-natal morphological and biochemical events. Overall, most transcripts that changed significantly showed a progressive decrease in abundance after birth, with the majority of change between post-natal weeks 2 and 4. Genes with cell proliferative, cytoskeletal, extracellular matrix, plasma membrane lipid / transport, protein folding, and regulatory functions had decreases in mRNA levels. Quantitative PCR verified the microarray results for six selected genes: DNA methyltransferase 3A (Dnmt3a), procollagen, type III, alpha 1 (Col3a1), solute carrier family 16 (monocarboxylic acid transporters), member 1 (Slc16a1), MARCKS-like 1 (Marcksl1), nidogen 1 (Nid1) and 3-hydroxybutyrate dehydrogenase (heart, mitochondrial) (Bdh). Last Updated (by provider): Oct 04 2006 Contributers: Allan B Okey Paul C Boutros Hubert H Van Tol Olga Likhodi Mawahib O Semeralul Albert H Wong Includes GDS2135. Update date: Mar 13 2007. Dataset description GDS2135: Analysis of prefrontal cortex (PFC) of animals at 2 to 10 weeks of age. Although the basic laminar structure of the PFC is established in utero, extensive remodeling continues into adolescence. Results map the overall pattern of changes in cortical gene transcripts during postnatal development.. na Source GEO sample is GSM181274 Last updated (according to GEO): Apr 10 2007 5 0 brain ND010 human frontal cortex Source GEO sample is GSM87046 Last updated (according to GEO): Feb 08 2006 1000 Structure of corneal epithelium Mice sacrificed after swimming twice a day for 2 weeks. Keywords = exercise induced hypertrophy Source GEO sample is GSM2352 Last updated (according to GEO): May 27 2005 Primary tumor 19 32 16 7 cerebellum 7 0 prostate Measles 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145773 Last updated (according to GEO): Nov 20 2006 DR72h(2) 1000 Prostate Pooled EDL RNA samples from five 8 wk old male C57BL10 mice Source GEO sample is GSM13673 Last updated (according to GEO): May 28 2005 Performed by UCI Microarray Facility. Source GEO sample is GSM203588 Last updated (according to GEO): Jun 22 2007 Brain 861 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169501 Last updated (according to GEO): Feb 21 2007 Nose 1000 brain 0 5 Normal Source GEO sample is GSM176140 Last updated (according to GEO): Apr 09 2007 Intestines 861 Donor 3 Time point 72 hours Autologous control (uninfected) Source GEO sample is GSM2625 Last updated (according to GEO): May 27 2005 Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=0 (Non-acute rejection). Source GEO sample is GSM36430 Last updated (according to GEO): May 27 2005 n/a Source GEO sample is GSM177971 Last updated (according to GEO): Jun 11 2007 GSE138 Malignant neoplasm of ovary 901 ISR20-Fv2E-PERK UT2 RNA from an untreated Fv2E-PERK expressing fibroblast cell line in an eIF2 alpha AA (mutant) background. The eIF2 alpha AA background was used in order to determine whether genes activated through Fv2E-PERK required eIF2alpha phosphorylation. The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules. Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10903 Last updated (according to GEO): May 28 2005 Muscle Fibers 861 861 Cerebellum Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211364 Last updated (according to GEO): Jul 18 2007 normal testis 54 66 myometrium_3 To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18447 Last updated (according to GEO): May 27 2005 Cardiovascular system 861 cy3:SHR treated w/ nifedipine, biological rep 3g; cy5:pool of 6 WKY control rats brain, cerebral cortex: Control 1_le1 Head and neck cancer Source GEO sample is GSM155648 Last updated (according to GEO): Apr 24 2007 Fibroblasts 861 Malignant Neoplasms 861 Abdominal aortic aneurysm 0 24 of regenerating Dorsal Root Ganglia 21 55 brain, cortex: Sample19_e1_le1 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:364, Count:32 Corner- Avg:36544, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:15.267480,SFGene:All Background:Avg:408.40,Stdev:5.81,Max:426.0,Min:399.9 Noise:Avg:9.27,Stdev:0.43,Max:10.8,Min:8.4 RawQ:13.27 Keywords = ALL Source GEO sample is GSM3509 Last updated (according to GEO): May 28 2005 ovarian tumor: endometrioid Source GEO sample is GSM139387 Last updated (according to GEO): Apr 09 2007 Liver Test (Blinded) Sample Source GEO sample is GSM130073 Last updated (according to GEO): Sep 18 2007 D_U133A_54_nAcc Muscle_adequate protein_male_rep3 of regenerating Dorsal Root Ganglia 21 55 20 0 atrioventricular_node LCM 20 biological rep2 DLCL-0023 || lc8n098 Bmi1 Mel18 shRNA, biological rep3 5 0 brain 1000 Carcinoma of bladder Wild type olfactory epithlium 0 h replicate1 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27744.gif Source GEO sample is GSM66594 Last updated (according to GEO): Sep 22 2006 Expression profiling of spinal cord section (T9) extracted from rats 72h following moderate injury Source GEO sample is GSM31580 Last updated (according to GEO): May 27 2005 1050 1032 mature hippocampus Stem cells 901 Mental disorders 884 days nasal epithelium 1127 1148 Bone Marrow 1000 standard Affymetrix protocol, MAS 5.0 Source GEO sample is GSM9136 Last updated (according to GEO): May 28 2005 The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76953 Last updated (according to GEO): Oct 11 2005 5 0 Spleen Lymphoblastoid Cell Line for Individual 8206.3 log phase Muscle 861 Aortic Aneurysm, Abdominal 1000 Gene expression data from a primary branch of the saphenous artery of 16 week old ACTH-treated male Wistar-Kyoto rats Source GEO sample is GSM198860 Last updated (according to GEO): Nov 28 2007 Fibroblasts 1000 H131 CN B RNA isolated from fetal cerebrum Keywords = trisomy 13 Keywords = brain Keywords = Patau syndrome Source GEO sample is GSM22705 Last updated (according to GEO): May 27 2005 none Source GEO sample is GSM123269 Last updated (according to GEO): Jul 27 2006 Normal Source GEO sample is GSM175928 Last updated (according to GEO): Apr 09 2007 P18 non-deprived visual cortex replicate 2 Neoplasm 861 N2_d3 #1(16012165010069) 861 Ribosomal RNA Control, 48.00 hr. T-Cell 5 0 brain normal testis 54 66 Ovary 1000 umbilical cord_nobpd: 5F 0029_1225_H95A2_KF0157_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A DBA 2:1-2 CA3 Blood 861 adenocarcinoma 3088 0 18 Universal Mouse Reference RNA Source GEO sample is GSM93427 Last updated (according to GEO): Jan 23 2006 253 246 ischemia brain 0 5 7 0 Lymphoma with those of normal mucosa 476 502 Cortex 0 5 SF-539 hgu95a Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2668.gif Source GEO sample is GSM72140 Last updated (according to GEO): Sep 22 2006 olfactory bulb 192 206 cerebral cortex 7 21 5 0 brain 913 Acute leukemia 1000 Brown Fat Gene expression data from mouse colon Source GEO sample is GSM198111 Last updated (according to GEO): Aug 22 2007 861 Nervous system structure Heterozygote TG e13.5 U74Bv21 AD-241t1x-A160-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 21 0 Normal Skeletal Muscle Muscle Fibers 1000 91 from the bone marrow 72 1000 Lung AML cDNA hybridization-ID43-L Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM80013 Last updated (according to GEO): Oct 26 2005 3160 3147 of spinal cord Wild type inbred mice Source GEO sample is GSM83001 Last updated (according to GEO): Nov 10 2005 Cerebral cortex 861 Cochlea 0 6 Epithelium 861 865 Disorder of artery 861 Malignant neoplasm of prostate JMR-MurSham8h-1bAv2-s2 Gene expression data from epididymal fat tissues. Source GEO sample is GSM215581 Last updated (according to GEO): Aug 07 2007 Colonic mucous membrane 913 480_4d from the femurs 95 109 CH2112 stria terminalis 901 103 85 of a past infection Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184676 Last updated (according to GEO): Apr 26 2007 brain, hippocampus: KA-24h-P15-I_e1_le1 1000 Brain Wild type inbred mice Source GEO sample is GSM82908 Last updated (according to GEO): Nov 10 2005 Medulla Oblongata 861 T265_Infect_1 1000 Communicable Diseases 1811 1797 the hippocampus 129S6/SvEvTac pituitary gland rep2 (430 2.0 Array) 279 266 from 6 brains 453 434 The descending colon myocardial infarction 383 403 Replicate2_Voxel A5 schizophrenia 559 572 Ataxia 1000 7 cerebral cortex 21 BALB/c_OVA Replicate 4 Cerebellum 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Insulin-like growth factor 1 for 60min Source GEO sample is GSM5617 Last updated (according to GEO): May 27 2005 1000 Cerebellum Epithelium 861 MCF7 human breast cancer cells treated with DMSO and used as a control in a 2 platform, three replicate experiment Source GEO sample is GSM188021 Last updated (according to GEO): May 11 2007 ISR14 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169491 Last updated (according to GEO): Feb 21 2007 GBM Treatment, type=remove Source GEO sample is GSM99557 Last updated (according to GEO): Apr 21 2006 NCI60.60_LABEL122EXTRACT62SUB3 Source GEO sample is GSM134298 Last updated (according to GEO): Aug 06 2007 Control brainstem 4 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53443 Last updated (according to GEO): Jul 06 2005 CC11- sample 1 Motor neurons obtained from a SOD1 mutant mouse by laser capture microdissection. Source GEO sample is GSM113722 Last updated (according to GEO): Jun 09 2006 691 686 hearts 865 Disorder of artery Spleen vs CpG-oligodeoxynucleotide Treated B cell 240min (set1) B Cells AntiCD40+Il4 30H 1 Activated Gene expression data from na?ve DIV 14 cortical neuron i.e. non activated state Source GEO sample is GSM100448 Last updated (according to GEO): Mar 15 2006 Adenocarcinoma 861 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13424.gif Source GEO sample is GSM79662 Last updated (according to GEO): Sep 22 2006 Pituitary Gland 861 660 mesenchymal stem cell 639 MSS-Spa3+moM-1aAv2-s2 Tumor__Leukemia_ALL-T_ALL(14402)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Brain 1000 Gene expression data from mouse primary visual cortex Source GEO sample is GSM101724 Last updated (according to GEO): Jun 15 2006 out of tibias 2763 2775 1224 1210 on chromosome 9 Expression profiling of somatomotor cortex extracted from rats at 28d following moderate injury Source GEO sample is GSM41721 Last updated (according to GEO): May 27 2005 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153358 Last updated (according to GEO): Dec 27 2006 1000 Cerebrovascular accident 16h2 901 frontal lobe of mouse brain 9 23 660 mesenchymal stem cell 639 human cerebellum Source GEO sample is GSM87178 Last updated (according to GEO): Feb 08 2006 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225684 Last updated (according to GEO): Nov 05 2007 Entorhinal Cortex 7 23 1000 Descending colon HOXB4ERT_+10nM TMX, 1hour, biological rep1 Type 1 Diabetes patient and the timepoint 1 month after diagnosis. Source GEO sample is GSM228647 Last updated (according to GEO): Sep 11 2007 striatum_wildtype_6S brain, Superior Frontal Gyrus: Sample59_e1_le1 bc-ZT9-1 Brain 861 Saccule structure 861 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 2 - Pair 4 - MMN Source GEO sample is GSM49890 Last updated (according to GEO): Dec 20 2005 Neoplasm 861 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184769 Last updated (according to GEO): Apr 26 2007 901 Myeloid Leukemia Expression profiling of spinal cord section (T9) extracted from rats 28d following severe injury Source GEO sample is GSM31609 Last updated (according to GEO): May 27 2005 Wild type inbred mice Source GEO sample is GSM83033 Last updated (according to GEO): Nov 10 2005 Epithelium of bronchus 983 1000 ovarian neoplasm Brain 1000 Normal Source GEO sample is GSM176228 Last updated (according to GEO): Apr 09 2007 Large cell neuroendocrine carcinoma 901 1000 Muscle V5-P085 Expression profiling of spinal cord section (T9) extracted from rats 24h following moderate injury Source GEO sample is GSM31193 Last updated (according to GEO): May 27 2005 Lymphoblastoid Cell Line for Individual 8046.4 log phase CNS-RM_Mod7d-2A-s2 VDXOXFU_220 B6EntorhinalCortex(1a)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B V5-P165 Cerebral cortex 861 923 Carcinoma in Situ 901 frontal lobe Synapses 928 cerebral cortex 7 21 Blood 1000 in blood 16 23 Cerebellum 861 Blood 1000 none Source GEO sample is GSM149648 Last updated (according to GEO): Jan 03 2007 R7E 9 861 Blood Pooled total RNA from (3) P27 L3-L5 Egr3-deficient spinal cords Source GEO sample is GSM32063 Last updated (according to GEO): May 27 2005 861 HIV Infections Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b021 Source GEO sample is GSM1987 Last updated (according to GEO): Nov 21 2005 5 0 Spleen neurological disease control sample x156 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13132.gif Source GEO sample is GSM79652 Last updated (according to GEO): Sep 22 2006 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2775 Source GEO sample is GSM2094 Last updated (according to GEO): Nov 21 2005 Gene expression data from PD1 Foxo3 wild-type ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203840 Last updated (according to GEO): Aug 02 2007 1000 Brain 1000 Endometrium Transitional epithelium 1000 Brain 1000 Coronary artery 901 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113966 Last updated (according to GEO): Jun 16 2006 Blood 1000 prostate Source GEO sample is GSM203275 Last updated (according to GEO): Jun 21 2007 no additional Source GEO sample is GSM199126 Last updated (according to GEO): Jun 08 2007 /tf Basal Ganglia A 10 28 normal human skeletal muscles 55 83 HapMap CEU_parent Female Source GEO sample is GSM159549 Last updated (according to GEO): Feb 01 2007 C3H 2-1-2 Testes Skeletal muscle biopsy was obtained before a two-hours of hyperinsulinaemic (40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172140 Last updated (according to GEO): Feb 28 2007 861 frontal lobe MSM/Ms_male_hypothalamus E6, E7, hTERT, endometrial cell 3AMH02030705_Lung Macrophages treated with LPS plus IL-10, 10 min, Replicate 3 Source GEO sample is GSM241133 Last updated (according to GEO): Nov 02 2007 1068 on whole ganglia 1052 No IR control 1000 Hypertrophic Cardiomyopathy Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174512 Last updated (according to GEO): Mar 14 2007 The pigmented portion of ciliary epithelium in the adult mammalian eye harbors mitotically quiescent retinal sphere cells, which are capable of self-renewal and differentiating into retinal neurons when assayed in vitro; however, very little is known about the molecular mechanism controlling the proliferation and differentiation of these adult retinal stem cells or their molecular resemblance to mutipotent stem/progenitor cells during early eye development. This experiment studies the gene expression of first passage and primary human and mouse retinal sphere cells. Last Updated (by provider): Nasal Epithelium 901 Brain 1000 MGJZ030211002Badrenalgland pooled RNA of the kidney of 36 day old rats Source GEO sample is GSM86650 Last updated (according to GEO): Jun 12 2006 EWS-C10 on NHGRI-6.5k_b Brain 1000 "16h Thy-Noc, Exp4" Testis 861 861 Skeletal bone 8 hr vehicle repl 2 901 Autoimmune Diseases 1000 frontal lobe 10 Bone marrow 0 Hyperdip>50-C2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2650.gif Source GEO sample is GSM72202 Last updated (according to GEO): Sep 22 2006 G42 neurons from cingulate cortex Source GEO sample is GSM63021 Last updated (according to GEO): Dec 01 2005 67 40 with coronary artery disease Gene expression data from postmorten brain regions Source GEO sample is GSM146003 Last updated (according to GEO): Nov 20 2006 Tonsil GC B Lung 861 PGA-MurLungRag-rwp-72h-1bAv2-s2 olfactory epithelium tissue 85 111 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11326 Last updated (according to GEO): May 28 2005 176 132 to those with a normal tricuspid aortic valve NB-T-TEST-14 on NHGRI-6.5k_b brain, brainstem: PB5_e1_le1 Brain 1000 Spleen 0 5 901 Somatic cell striatum 32 40 88 68 with bicuspid valves Ovarian Diseases 877 Leg 14 Day Control rep 3 nerve 0 5 Parkinson's model voxel C4 of atrophied skeletal muscle 166 193 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47531 Last updated (according to GEO): May 29 2005 N/A Source GEO sample is GSM4319 Last updated (according to GEO): May 28 2005 Cerebral cortex 1000 Liver 1000 Biopsy of the normal mucosa of the colon from patient #3 Nrl ko 2 mon replicate 3 the ventricular 1095 1109 861 Hippocampus 11_0011_Control_Day1_49 JMR-MurSham72h-1cAv2-s2 SN:1010455 Source GEO sample is GSM115396 Last updated (according to GEO): Jun 20 2006 Sample 1 at Time 1 Source GEO sample is GSM113085 Last updated (according to GEO): Jun 06 2006 Type 1 Diabetes patient and the timepoint 1 month after diagnosis. Source GEO sample is GSM228605 Last updated (according to GEO): Sep 11 2007 Healthy donor SN_19_vs_Pool Testis 861 R437P00057 Investigation into murine dermal burn wound. Mouse thermal injury induced, and skin excised at different times post-injury. Source GEO sample is GSM7485 Last updated (according to GEO): May 27 2005 Cochlear structure 1000 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5822 Last updated (according to GEO): May 27 2005 brain, hippocampus: Sham PM Hip_e1_le1 The epithelial cells 962 981 MP-DX-9 Mesenchymal Stem Cells 1000 no additional Source GEO sample is GSM199241 Last updated (according to GEO): Jun 08 2007 Brain 861 901 Heart failure Gene expression data from rat metanephric mesenchymes cultured for 5 days in the presence of LIF Source GEO sample is GSM126202 Last updated (according to GEO): Dec 08 2006 of the tumors 271 283 1000 frontal lobe Wild type inbred mice Source GEO sample is GSM82941 Last updated (according to GEO): Nov 10 2005 673 659 by decapitation kidney 37 43 of somatomotor cortex 21 41 Ovarian_Tumor_Endometrioid_CHTN-OE-087 Myocardium 861 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151972 Last updated (according to GEO): Feb 06 2007 Studies using mice with beta4 nicotinic acetylcholine receptor (nAChR) subunit deficiency (beta4-/- mice) helped reveal the roles of this subunit in bradycardiac response to vagal stimulation, nicotine-induced seizure activity and anxiety. In order to identify genes that might be related to beta4-containing nAChRs activity, we compared the mRNA expression profiles of brains from beta4-/- and wild-type mice using Affymetrix U74Avr2 microarray. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Sep 22 2006 Contributers: Merav Kedmi Avi Orr-Urtreger 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14944 Last updated (according to GEO): Oct 28 2005 of the stria terminalis rep2 16 43 HNC2855 1000 Eye NA07345 853 Refractory Carcinoma Endometrium 18 Normal 1000 Mammary gland ABSTRACT: BACKGROUND: The ability of a neuron to regenerate functional connections after injury is influenced by both its intrinsic state and also by extrinsic cues in its surroundings. Investigations of the transcriptional changes undergone by neurons during in vivo models of injury and regeneration have revealed many transcripts associated with these processes. Because of the complex milieu of interactions in vivo, these results include not only expression changes directly related to regenerative outgrowth and but also unrelated responses to surrounding cells and signals. In vitro models of neurite outgrowth provide a means to study the intrinsic transcriptional patterns of neurite outgrowth in the absence of extensive extrinsic cues from nearby cells and tissues. RESULTS: We have undertaken a genome-wide study of transcriptional activity in embryonic superior cervical ganglia (SCG) and dorsal root ganglia (DRG) during a time course of neurite outgrowth in vitro. Gene expression observed in these models likely includes both developmental gene expression patterns and regenerative responses to axotomy, which occurs as the result of tissue dissection. Comparison across both models revealed many genes with similar gene expression patterns during neurite outgrowth. These patterns were minimally affected by exposure to the potent inhibitory cue Semaphorin3A, indicating that this extrinsic cue does not exert major effects at the level of nuclear transcription. We also compared our data to several published studies of DRG and SCG gene expression in animal models of regeneration, and found the expression of a large number of genes in common between neurite outgrowth in vitro and regeneration in vivo. CONCLUSIONS: Many gene expression changes undergone by SCG and DRG during in vitro outgrowth are shared between these two tissue types and in common with in vivo regeneration models. This suggests that the genes identified in this in vitro study may represent new candidates worthy of further study for potential roles in the therapeutic regrowth of neuronal connections. 901 Coronary artery brain, cochlea: [10] Sample #10_le1 1000 Communicable Diseases 861 Cerebral cortex Exp A, Animal #1, 1mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours Source GEO sample is GSM246132 Last updated (according to GEO): Dec 03 2007 Macrophage smi106_2 Coronary heart disease 913 861 Blood Muscle 861 3792 12a of mouse brain 9 23 51 48 (ALS 5 0 Spleen Gene expression data from experimental treatment D-UT = 48h after PMA induced differentiated SH-SY5Y cells. Source GEO sample is GSM102875 Last updated (according to GEO): May 11 2006 Gastrin infused gastrin Knockout replicate 1 Brain of P10 Gja9 (+/-) C57Bl/6j mouse, replica H1 Disease Source GEO sample is GSM176440 Last updated (according to GEO): Apr 09 2007 Frontal_Cerebrocortex_Vehicle_6hr_rep2 CNS-SC_CtrBT0-1B-s2 to the nose 599 609 901 Coronary artery Baseline comparison of global gene expression in ILS and ISS cerebellum to find differences in the naive state. Source GEO sample is GSM69659 Last updated (according to GEO): Oct 28 2005 Mutations in dystrophin are the proximate cause of Duchenne muscular dystrophy (DMD), but pathogenic mechanisms linking the absence of dystrophin from the sarcolemma to myofiber necrosis are not fully known. The muscular dystrophies also have properties not accounted for by current disease models, including the temporal delay to disease onset, broad species differences in severity, and diversity of skeletal muscle responses. To address the mechanisms underlying the differential targeting of muscular dystrophy, we characterized temporal expression profiles of the diaphragm in dystrophin-deficient (mdx) mice between postnatal days 7 and 112 using oligonucleotide microarrays and contrasted these data with published hindlimb muscle data. Although the diaphragm and hindlimb muscle groups differ in severity of response to dystrophin deficiency, and exhibited substantial divergence in some transcript categories including inflammation and muscle-specific genes, our data show that the general mechanisms operative in muscular dystrophy are highly conserved. The two muscle groups principally differed in expression levels of differentially regulated genes, as opposed to the non-conserved induced/repressed transcripts defining fundamentally distinct mechanisms. We also identified a postnatal divergence of the two wild-type muscle group expression profiles that temporally correlated with the onset and progression of the dystrophic process. These findings support the hypothesis that conserved disease mechanisms interacting with baseline differences in muscle group-specific transcriptomes underlie their differential responses to DMD. We further suggest that muscle group-specific transcriptional profiles contribute toward the muscle targeting and sparing patterns observed for a variety of metabolic and neuromuscular diseases. Nervous system structure 901 Sample26, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53277 Last updated (according to GEO): Jul 06 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145197 Last updated (according to GEO): Nov 20 2006 brain 0 5 1000 Structure of parenchyma of lung Utricle and 3 ampullae at E12.5, replicate2 Gloubus Pallidum Internal 6 Normal HCC-2998 hgu95a 5 0 brain Intestines 861 brain, unknown: C4A_e1_le1 901 Cerebral cortex Gene expression data from older male during 1 week of adequate protein intake Source GEO sample is GSM209819 Last updated (according to GEO): Jul 11 2007 Trachea 2 Normal Transitional epithelium 1000 CNS-SC_InjA7d-3B-s2 Gene expression data from whole tumor Source GEO sample is GSM182286 Last updated (according to GEO): Apr 16 2007 861 Cardiomyopathies Gene expression data of substantia nigra from postmortem brain of normal controls Source GEO sample is GSM184354 Last updated (according to GEO): May 29 2007 cerebellum 7 16 AKR-J_male_hypothalamus Gene expression data from postmorten brain regions Source GEO sample is GSM145910 Last updated (according to GEO): Nov 20 2006 brain 0 5 Gastrin-CCK double Knockout fundic RNA Source GEO sample is GSM108494 Last updated (according to GEO): May 03 2007 Expression profiling of somatomotor cortex extracted from rats at 24h following sham surgery Source GEO sample is GSM41644 Last updated (according to GEO): May 27 2005 Control Abdominal Aorta 4-M Spleen 0 5 Liver 0 4 brain, amygdala: Sham PM A b_e1_le1 90 81 in stroke tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44872 Last updated (according to GEO): May 27 2005 Job's patient Source GEO sample is GSM211095 Last updated (according to GEO): Sep 10 2007 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201258 Last updated (according to GEO): Jun 14 2007 865 Disorder of artery 1000 Neoplasm Spleen vs Insulin-like growth factor 1 Treated B cell 120min (set1) C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P10 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25132 Last updated (according to GEO): May 27 2005 Sample represents the Neurointermediate lobe of the Pituitary from 5 dehydrated animals (3 Days) Source GEO sample is GSM69784 Last updated (according to GEO): Dec 15 2005 CNS-SMTC_Mod3mo-3A-s2 Skeletal bone 861 861 Cerebral cortex Cerebral cortex 861 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3317 Last updated (according to GEO): Mar 21 2006 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM79043 Last updated (according to GEO): Oct 24 2005 Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM107995 Last updated (according to GEO): Jun 06 2006 with Parkinson's disease 27 50 GSE6778 embryonic hearts 1064 1079 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153463 Last updated (according to GEO): Jan 11 2007 plasma cells 332 344 plasma cells 50 61 Gene expression data from human colon tumor tissue Source GEO sample is GSM173362 Last updated (according to GEO): Apr 20 2007 7 frontal cortex 20 Spleen vs 2-Methyl-thio-ATP Treated B cell 120min (set2) Normal Source GEO sample is GSM176374 Last updated (according to GEO): Apr 09 2007 1000 Pancreas 913 Coronary heart disease 1000 Skeletal muscle structure Comparison of genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules.. Date GSE700 Last Updated: May 29 2005 Contributers: P D Lu D Scheuner S J Marciniak H P Harding Y Zhang D Ron I Novoa R J Kaufman C Jousse Includes GDS405. Update date: Nov 06 2003. Dataset description GDS405: Examination of genes induced during the integrated stress response (ISR). ISR induced by tunicamycin or AP20187 in fibroblasts carrying mutations in ATF4 and PERK (ISR signaling molecules), and in eIF2alpha mutant or wildtype PERK-expressing fibroblasts.. Neoplasm 1000 Pooled soleus RNA samples from five 8 wk old male mdx mice Source GEO sample is GSM13738 Last updated (according to GEO): May 28 2005 stria terminalis 901 Expression profiling of spinal cord section (T9) extracted from rats 24h following moderate injury Source GEO sample is GSM31531 Last updated (according to GEO): May 27 2005 NHF3-hTERT_1.5Gy_6h_C3_21250 26 15 endometrioid 329 306 valvular cardiomyopathy B220+c-kit+ Pre BI cells sorted out of mouse bone marrow, sort no. 2 Source GEO sample is GSM655 Last updated (according to GEO): May 27 2005 1000 Cerebellum brain, unknown: 03BV_e1_le1 HBEC Source GEO sample is GSM18973 Last updated (according to GEO): Sep 25 2006 female mhm chip 3 Dahl-Iwai Male LowSalt Cortex rat111 dahl_cortexr_k_111c_072001 Heart 861 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153501 Last updated (according to GEO): Jan 11 2007 GC (HKG52T) 901 Demyelinating Diseases Knockout 5 months old, male Source GEO sample is GSM154340 Last updated (according to GEO): Jan 09 2007 278 255 ischemic cardiomyopathy pfc_1057_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Gene expression data from postmorten brain regions Source GEO sample is GSM145224 Last updated (according to GEO): Nov 20 2006 M_U133A_55_AnCg Blood 1000 of the postmortem brains 656 680 PGA-E18.5_2 prostate Source GEO sample is GSM203346 Last updated (according to GEO): Jun 21 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11254 Last updated (according to GEO): May 28 2005 1000 Aorta 277 271 Retinas tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44865 Last updated (according to GEO): May 27 2005 This sample has two chips, therefore the values represent the average of the features from both chips. Source GEO sample is GSM227420 Last updated (according to GEO): Sep 12 2007 1000 Brain The epithelial cells 962 981 A HID U D020 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108609 Last updated (according to GEO): Aug 22 2006 1000 Heart Nasal Epithelium 901 Primary adenocarcinoma Source GEO sample is GSM16558 Last updated (according to GEO): May 28 2005 plasma cells 50 61 Prosencephalon 861 R460P00321 (utricle 265 273 1000 Retina HUVEC isolate 36 low serum media control for #18 Source GEO sample is GSM12910 Last updated (according to GEO): May 28 2005 861 Mammary gland none Source GEO sample is GSM244572 Last updated (according to GEO): Nov 23 2007 Parkinson Disease 861 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113917 Last updated (according to GEO): Jun 16 2006 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184692 Last updated (according to GEO): Apr 26 2007 Basal Ganglia 901 1000 Bronchi This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195242 Last updated (according to GEO): Sep 13 2007 The virB operon, encoding a Type IV secretion system (T4SS), is essential for intracellular survival and persistent infection by Brucella spp. To better understand the role of the T4SS in evading host defence mechanisms and establishing chronic infection, we compared transcriptional profiles of the host response to infection with wild-type and virB mutant Brucella strains. Analysis of gene expression profiles in murine splenocytes 3 days after inoculation with wild-type Brucella strains revealed an inflammatory response, with a prominent upregulation of genes induced by both type I and type II interferons. Real-time RT-PCR showed that a group of genes from these pathways were induced by day 3 post infection and declined to baseline levels by day 7. In contrast, neither of the two virB mutant strains elicited a proinflammatory gene expression profile, demonstrating that the T4SS was required to trigger this response. Infection studies using type I interferon receptor knockout mice showed that a lack of type I interferon signalling did not affect Brucella replication during the first 4 weeks of infection. Thus, induction of type I interferons does not appear to be an essential mechanism by which the T4SS promotes persistent infection by Brucella. the blood 393 402 Nose 1000 Mesenchymal Stem Cells 1000 Fibroblasts 1000 17 7 hippocampus GBM Treatment, type=remove Source GEO sample is GSM99438 Last updated (according to GEO): Apr 21 2006 Compare the brain transcriptomes of Gja9 (-/-) and Gja9 (+/-) mice with that of wildtype mice to detect transcriptomic alterationss induced by total or partial ablation of Gja9 Source GEO sample is GSM146899 Last updated (according to GEO): Nov 29 2006 of the postmortem brains 656 680 Heart Septal Defects, Atrial 1000 DBA/2J_female_hypothalamus Source GEO sample is GSM138569 Last updated (according to GEO): Apr 18 2007 #27 (isolate V low serum media control) Heart 861 peripheral blood-CD19BCells Source GEO sample is GSM18723 Last updated (according to GEO): Sep 25 2006 processed in batch 2 Source GEO sample is GSM90452 Last updated (according to GEO): Mar 20 2006 H118 CB B /3T3 fibroblasts 743 759 9 0 Blood Test Gene expression data from aneurismal tissues obtained from patients with tricuspid valves. Source GEO sample is GSM116797 Last updated (according to GEO): Jun 28 2006 CNS-SMTC_Mod28d-3A-s2 COID-3580-A302-5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Autistic Disorder 877 Extracellular Matrix 911 nostrils 156 164 Whole Brain 62 72 10 0 Endometrium Brain 1000 Cortex from rats with cerebral cortical contusion 1 day post injury, injured cortex (ipsilateral side) -uninjured cortex (contralateral side) were hybridised onto a 6240 cDNA probe microarray. Expression ratios were calculated using injured/ un-injured cortex Source GEO sample is GSM76158 Last updated (according to GEO): Sep 29 2005 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228660 Last updated (according to GEO): Sep 11 2007 smooth muscle 1305 1317 mouse brain 478 489 Large-Cell Lymphomas 888 the blood 393 402 17 7 hippocampus 7 0 prostate 180 169 like asthma in the mouse brain 75 92 HapMap YRI_parent Female Source GEO sample is GSM159691 Last updated (according to GEO): Feb 01 2007 Brain (hippocampus) [JunctionChip 2 of 5] Gene expression data from postmorten brain regions Source GEO sample is GSM146023 Last updated (according to GEO): Nov 20 2006 Large cell neuroendocrine carcinoma 901 NCI60.15_LABEL19EXTRACT18SUB3 Source GEO sample is GSM134068 Last updated (according to GEO): Aug 06 2007 Plasma 861 no additional Source GEO sample is GSM199036 Last updated (according to GEO): Jun 08 2007 Normal Source GEO sample is GSM175948 Last updated (according to GEO): Apr 09 2007 14 hr Hela Double Thymidine, exp2 Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD34 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD34 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36710 Last updated (according to GEO): May 27 2005 GBM Treatment, type=remove Source GEO sample is GSM99440 Last updated (according to GEO): Apr 21 2006 1000 Malignant tumor of colon Expression profile of genes in mouse brain Source GEO sample is GSM21041 Last updated (according to GEO): May 27 2005 901 Caudate nucleus structure 1000 Lung NCI60.41_LABEL45EXTRACT44SUB3 Source GEO sample is GSM134195 Last updated (according to GEO): Aug 06 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM146035 Last updated (according to GEO): Nov 20 2006 865 Disorder of artery Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 23 hours after lights on. Original RNA code = LC53A. Source GEO sample is GSM227358 Last updated (according to GEO): Sep 10 2007 A HID B D090 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108589 Last updated (according to GEO): Aug 22 2006 healthy control sample x044a Whole Brain 62 72 Lmna H222P homozygous male 6 91 from the bone marrow 72 Spleen vs Interferon-gamma (IFN gamma) Treated B cell 120min (set1) Gene expression data from brain of adult rats Source GEO sample is GSM101031 Last updated (according to GEO): Feb 20 2007 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151986 Last updated (according to GEO): Feb 06 2007 Sample is skeletal muscle from nonobese patient undergoing elective abdominal surgery Source GEO sample is GSM3991 Last updated (according to GEO): May 28 2005 12mo Control #2 Spleen 1000 Whole blood 0 10 CNS-SC_CtrB7d-1A-s2 CNS-SpinalCsev-Adult-4h-3C-s2 Mesenchymal Stem Cells 1000 Muscular Dystrophies 861 901 Intestines, Small C3H/HeJ Basal Ganglia C 1000 Hypertrophic Cardiomyopathy 901 Stem cells 26 15 endometrioid 1000 medulloblastoma Category: Tissue Rejection Subcategory: Kidney Diabetes reccurence in biopsy also Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=710640 LaserPower=1.951.34 Lot batch = LC17N102 Source GEO sample is GSM4823 Last updated (according to GEO): Nov 21 2005 Large cell neuroendocrine carcinoma 901 1000 Brain 67 52 descending colon Primary large cell carcinoma 2985 0 32 brain, cerebellum: Stg+/+_Crb3_e1_le1 5 0 brain Gene expression data from postmorten brain regions Source GEO sample is GSM145526 Last updated (according to GEO): Nov 20 2006 adenocarcinoma 3336 0 18 361 335 hypertrophic cardiomyopathy WGACON-257 shipp-dlbcl Occipital lobe 861 Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68035.gif Source GEO sample is GSM137408 Last updated (according to GEO): Sep 26 2006 861 Colon Blood Test (Blinded) Sample Source GEO sample is GSM129967 Last updated (according to GEO): Sep 18 2007 Collagen 1000 CAD_replicate22 Brain 1000 Posterior root of spinal nerve 861 Cerebellum 1000 none Source GEO sample is GSM149512 Last updated (according to GEO): Jan 03 2007 861 Neoplasm I + P T-Cell 12.00 hr. affy original enzo kit processing Source GEO sample is GSM120462 Last updated (according to GEO): Jul 17 2006 861 Intestines M_U133A_14_HC 1000 Bone Marrow 1000 Spleen Gene expression data from rat lungs exposed to FiO2 of ~9.5%, SU5416, and Sorafenib (hypoxia-SU5416-Sorafenib). Source GEO sample is GSM201491 Last updated (according to GEO): Jun 14 2007 Primary tumor 19 32 Organotypic hippocampal slice cultures of male, postnatal day 15 mice (C57B6/SJL) were maintained in culture for 15 days and treated with phosphate buffered saline (vehicle) for an additional 24 h. Cultures were maintained on filter inserts in Neurobasal media with B-27 supplement (Invitrogen) and 1mM glutamine. The sample consists of 12 slices from 4 mice. Data were analyzed with MAS 5.0 and scaled to 2500. Keywords = Alzheimer?s disease Keywords = neuroprotection Keywords = sAPPalpha Source GEO sample is GSM26700 Last updated (according to GEO): Oct 28 2005 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11309 Last updated (according to GEO): May 28 2005 57 39 with endometriosis BAL_31_A0B1 GC (HKG62T) Epithelial Cells 901 1000 Cerebrovascular accident T4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Adipose Tissue Subcutaneous 4 Normal Gene expression data from aneurismal tissues obtained from patients with tricuspid valves. Source GEO sample is GSM116802 Last updated (according to GEO): Jun 28 2006 Infection 1000 Superior Frontal Gyrus_2-4y_RTT Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=780580 LaserPower=4.323.78 Lot batch = LC17N006 Source GEO sample is GSM4811 Last updated (according to GEO): Nov 21 2005 A number of studies have shown that cigarette smoking produces a field defect, such that genetic mutations induced by smoking occur throughout the lung and its intra and extra-pulmonary airways. Based on this concept, we have begun this study, which has as its goal the definition of the normal airway transcriptome, an analysis of how that transcriptome is affected by cigarette smoke, and to explore the reversibility of altered gene expression when smoking has been discontinued. We have obtained brushings from intra-pulmonary airways (the right upper lobe carina) and scrapings from the buccal mucosa, from normal smoking and non-smoking volunteers (including 34 Current Smokers, 23 Never Smokers and 18 Former Smokers). RNA was isolated from these samples and gene expression profiles from intra-pulmonary airway epithelial cells were analyzed using Affymetrix U133A human gene expression arrays. All microarray data from the experiments described above have been stored, preprocessed and analyzed in a relational MySQL database that is accessible through our website at http://pulm.bumc.bu.edu/aged. Date GSE994 Last Updated: May 29 2005 Contributers: Jennifer Beane Frank Schembri John Palma Gang Liu Jerome Brody Avrum Spira Xuemei Yang Vishal Shah Includes GDS534. Update date: May 02 2004. Dataset description GDS534: Analysis of cigarette smoking-induced changes in bronchial epithelia, and reversibility of effects when smoking is discontinued. May provide insight to molecular events leading to chronic obstructive pulmonary disease (COPD) and lung cancer.. Mouse_E13.5_Front_Middle_Back_14 Olfactory Epithelium 1000 54 50 Bone abd skin fibroblast (1.4BF), serum starved Probeset expression data from NA12750 growth 3, replicate 4 Source GEO sample is GSM195201 Last updated (according to GEO): Aug 08 2007 KO-Nrf2-Female-1 1000 Infection 901 Caudate nucleus structure Oat cell carcinoma 867 MGJZ030228092Avomeralnasalorgan(VMO) cerebral cortex 7 21 Whole blood from a patient with progressive supranuclear palsy Source GEO sample is GSM153440 Last updated (according to GEO): Jan 11 2007 with epithelial ovarian cancer 523 553 Skeletal muscle structure 1000 Epithelial Cells 901 Transitional epithelium 1000 c7.2 1000 Eye B6:16-1 olfactory bulbs 2897 2889 28S rRNA Muscular Dystrophy, Duchenne 913 5 0 brain 1000 Retina D_U133A_39_DLPFC Kidney YC-3B 861 Cerebral cortex DR7d(1) C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 4 hour after the last shock treatment. Source GEO sample is GSM4532 Last updated (according to GEO): May 27 2005 "Sample 1,>5 yr survival(150 months) age 43 erp yes" on vantveer-oligo Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225940 Last updated (according to GEO): Nov 02 2007 HOP-62 hgu95a Spleen vs Untreated B cell 240min (set1) H85 CB B total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lysophosphatidic Acid for 240min Source GEO sample is GSM5660 Last updated (according to GEO): May 27 2005 913 Coronary heart disease aa_NY218 SF-295 hgu95d ER negative human primary breast tumor EA02014_41274_H133A_JA-1563 Fibroblasts 1000 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153339 Last updated (according to GEO): Dec 27 2006 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153495 Last updated (according to GEO): Jan 11 2007 Macrophage smi98 none Source GEO sample is GSM123239 Last updated (according to GEO): Jul 26 2006 Brain 861 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68196 Last updated (according to GEO): Jul 07 2006 1000 Coronary Arteriosclerosis MO_CTb_SON_NCBI Richard Almon-48-1133800610245 M_U133A_29_nAcc Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15731 Last updated (according to GEO): May 28 2005 NCI-H460 hgu95a 0 Lung tissue 10 DLCL-0027 || lc8n095 GC (HKG56T) OCI Ly13.2 DCN_U7_C 1000 Cerebral cortex Heart 1000 Wild type P46 mouse visual cortex contralateral to monocular enucleation Source GEO sample is GSM97216 Last updated (according to GEO): Feb 17 2006 5 0 Spleen of the heart 842 854 Prefrontal Cortex 0 16 Skeletal Muscle [JunctionChip 2 of 5] brain, cerebral cortex: NMDA 180 4_le1 41 21 in serum lipoproteins 3AJZ02022643_kidney Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11439 Last updated (according to GEO): May 28 2005 Large-scale analysis of the mouse transcriptome. Skeletal muscle C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 347.91 Stdv: 14.18 Min: 323.71 Max: 371.58 Source GEO sample is GSM2951 Last updated (according to GEO): Mar 20 2006 Mouse Testis 1 Brain_MD_13_Medulloblastoma_Classic_D on Affymetrix GeneChip Human Full Length Array HuGeneFL 29 DNA damage 20 4525 4520 liver no doxycycline, no AAT Source GEO sample is GSM213374 Last updated (according to GEO): Jul 26 2007 ALS gray matter 6 Sporadic Gene expression data from brain of adult rats Source GEO sample is GSM101055 Last updated (according to GEO): Feb 20 2007 Lung; Fetal Day 18.5 Keywords = mouse gene expression database Source GEO sample is GSM29390 Last updated (according to GEO): May 27 2005 Bone structure of tibia 1000 913 Coronary heart disease HL-60(TB) hgu95d human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195351 Last updated (according to GEO): Jun 04 2007 Obsessive-Compulsive Disorder 1000 Human Sural Nerve Schwann Cell Donor 317 Passage 1 Treatment, type=add, description=growth factors heregulin and forskolin added Source GEO sample is GSM92238 Last updated (according to GEO): Jan 13 2006 plasma cells 332 344 primary hepatocytes, human, treatment with WY14643 (12h) Source GEO sample is GSM205901 Last updated (according to GEO): Jul 24 2007 KT65_DT 3-day-denervated tibialis anterior muscles from runx1f/-; MCK::cre mice Treatment, type=remove, description=runx1f/-; MCK::cre Source GEO sample is GSM99427 Last updated (according to GEO): Mar 08 2006 1000 Brain 65 24 from umbilical subcutaneous adipose tissue Nasal Epithelium 901 43 0 Chorionic mesoderm-derived mesenchymal cells Osteoblasts 1000 of the small intestine 97 118 to the nose 599 609 Primary Carcinoma 876 1000 Pancreas Simple annotation: Lymph node metastasis, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11580.gif Source GEO sample is GSM76454 Last updated (according to GEO): Sep 22 2006 brain, cerebellum: 6 hrs B GW_e1_le1 48 33 for 72hrs- lungs the blood 393 402 no additional Source GEO sample is GSM199155 Last updated (according to GEO): Jun 08 2007 AD-346t1a-A124-3 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 9 0 Blood Test myocardial infarction 383 403 normal testis 54 66 Primary tumor 19 32 0 Human Cortex 11 none Source GEO sample is GSM239958 Last updated (according to GEO): Dec 07 2007 861 Cerebral cortex CNS-SpinalCsev-Adult-24h-3A-s2 cerebellum sprague 3900 whole tissue, individual animal, 10 weeks old, male Sprague Dawley cerebellum file:p3900w Source GEO sample is GSM15142 Last updated (according to GEO): Oct 28 2005 osteoblast 630 640 Expression profiling of laminectomized raphe at 14d in rats Source GEO sample is GSM41518 Last updated (according to GEO): May 27 2005 prostate Source GEO sample is GSM203302 Last updated (according to GEO): Jun 21 2007 Skeletal bone 861 Primary Neoplasm 1000 5 0 brain Cerebellum 1000 total RNA from biosource CC#42a Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92469 Last updated (according to GEO): Jan 13 2006 Hippocampus 861 Brain 861 M_U133A_2_nAcc GSE90 brain 0 5 NCI60.23_LABEL27EXTRACT26SUB3 Source GEO sample is GSM134107 Last updated (according to GEO): Aug 06 2007 HSC_12Months_p53_het_A GSE3111 Gene expression data from older female during 1 week of adequate protein intake Source GEO sample is GSM209827 Last updated (according to GEO): Jul 11 2007 with mental retardation 241 263 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225744 Last updated (according to GEO): Nov 02 2007 15 0 human cerebellum Central gray substance of midbrain 861 U87 parent chip 1 /HeJ mouse periaqueductal gray 27 56 Tumor__Lymphoma_Large_B-Cell_L_B_CELL_S98_12569_R on Affymetrix GeneChip Human 35K SubA Array Hu35k-A frontal lobe 1000 861 Blood Liver 861 GSE2164 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells cultured for 30min Source GEO sample is GSM5840 Last updated (according to GEO): May 27 2005 Synapses 928 Spleen 0 5 Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Meningioma Primary Grade 2. Source GEO sample is GSM108046 Last updated (according to GEO): Jun 06 2006 Cerebral cortex 1000 Glutamic Acid Conjugated Surface 32 hours Anteroventral Thalamic Nucleus 913 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lipopolysaccharide (LPS) for 120min Source GEO sample is GSM5667 Last updated (according to GEO): May 27 2005 1000 Brain 1000 Brain Smooth Muscle Tissue 1000 Nodose Ganglion 1000 HA01-149A Standard Affymetrix procedure Source GEO sample is GSM133014 Last updated (according to GEO): Aug 28 2007 16 on NHGRI-13.8k 10 weeks Source GEO sample is GSM147514 Last updated (according to GEO): Dec 01 2006 863 836 of severe autoimmune disease Carcinoma, Large Cell 884 HapMap CEU_parent Male Source GEO sample is GSM159524 Last updated (according to GEO): Feb 01 2007 Ventral Tegmental Area 1000 Neoplasm 861 in bronchial epithelia 311 332 24 0 human prostate PC3 tumors 246-97_SCC_c left 22 25 5 0 brain Nothing in line. Source GEO sample is GSM154215 Last updated (according to GEO): Jul 05 2007 M_U133Plus_77_nAcc 17 7 hippocampus GSE8733 brain, amygdala: Amygdala 10_le1 AML mRNA hybridization to HGU133 Plus 2.0 884 Joint contracture of unspecified site these tumors 337 348 1000 Prostate brain, hippocampus: Sham AM Hip b_e1_le1 5 0 Muscle Normal Source GEO sample is GSM176448 Last updated (according to GEO): Apr 09 2007 268 253 of brain tumors Bladder sample 1379-1 folatedeficientAs10ppm2 Standard Affymetrix procedure Source GEO sample is GSM133012 Last updated (according to GEO): Aug 28 2007 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153341 Last updated (according to GEO): Dec 27 2006 100 88 after stroke Lymphoblastoid Cell Line for Individual 8076.4 log phase 1000 Cerebral cortex brain, Right Frontal Lobe: Extract58_le1 Lymphoblastoid Cell Line for Individual 8120.4 log phase "Sample 39,>5 yr survival(132 months) age 46 erp yes" on vantveer-oligo Skeletal bone 861 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5819 Last updated (according to GEO): May 27 2005 pfc_1060_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 27 0 Substantia nigra normal rep6 Mesenchymal Stem Cells 1000 jazaeri-breast Bone Marrow 1000 Keywords = Heart 505 521 27 7 Medial Temporal Gyrus 1000 Immunoglobulins 17 7 hippocampus 1000 Spleen 1000 Cerebral cortex of Parkinson's disease 450 471 osteoblast 630 640 Communicable Diseases 1000 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9930.gif Source GEO sample is GSM79907 Last updated (according to GEO): Sep 22 2006 660 mesenchymal stem cell 639 Liver Test (Blinded) Sample Source GEO sample is GSM130154 Last updated (according to GEO): Sep 18 2007 CA95-198A folatesufficientAs0ppm3 brain, Left Parietal Lobe: Extract39_le2 M_U133A_11_DLPFC (No additional Information) Source GEO sample is GSM114436 Last updated (according to GEO): Jun 19 2006 204 178 below thoracic vertebrae T9 GC (HKG65T) of the normal mucosa 7 26 1000 Communicable Diseases 38 21 from a hippocampus Normal Source GEO sample is GSM176029 Last updated (according to GEO): Apr 09 2007 129P3/J SAL, Rep2 1035 1009 of peripheral blood B cells 861 Brain three semi-circular canals 288 313 Category: Lymphoma Classification Subcategory: Follicular Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b097 Source GEO sample is GSM1992 Last updated (according to GEO): Nov 21 2005 plasma cells 50 61 Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep8 CNS-SC_InjA7d-2C-s2 testis 52 58 1000 ovarian neoplasm Blood Test (Blinded) Sample Source GEO sample is GSM129979 Last updated (according to GEO): Sep 18 2007 olfactory epithelium 194 213 olfactory epithelium 194 213 1000 Prostate total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD27 for 30min Source GEO sample is GSM5485 Last updated (according to GEO): May 27 2005 35 0 Inflammatory myopathy specimen GEIM3 67 40 with coronary artery disease 861 Cancer of Neck Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68184 Last updated (according to GEO): Jul 07 2006 861 Basal ANIMALS Patched heterozygous mice (Goodrich et al., 1997) were obtained from Matthew Scott?s lab at Stanford, and maintained by breeding with 129X1/SvJ mice from Jackson Laboratories. Math1-GFP transgenic mice (Lumpkin et al., 2003) were provided by Jane Johnson at UT Southwestern Medical Center. Math1-GFP/patched+/- mice were generated by crossing patched heterozygotes with Math1-GFP mice, and then backcrossing to Math1-GFP mice three times before further analysis. All mice were maintained in the Cancer Center Isolation Facility at Duke University Medical Center. ISOLATION OF CELLS Granule cell precursors (GCPs) were isolated from 7-day-old (P7) patched+/- mice; preneoplastic cells were obtained from 6 week-old patched mutants; and tumor cells were obtained from 10-25-week old patched mutants displaying physical and behavioral signs of medulloblastoma. Cells were isolated from each source using a protocol described in (Wechsler- Reya and Scott, 1999). Briefly, cerebella were digested in solution containing 10 U/ml papain Oliver et al. Pre-Neoplastic Stage of Medulloblastoma - 8 - (Worthington, Lakewood, NJ) and 250 U/ml DNase (Sigma) and triturated to obtain a cell suspension. This suspension was centrifuged through a step gradient of 35% and 65% Percoll (Amersham Biosciences, Piscataway, NJ), and cells were harvested from the 35%-65% interface. Cells were resuspended in serum-free culture medium consisting of Neurobasal containing B27 supplement, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen, Carlsbad, California) and counted on a hemacytometer. Cells used for RNA isolation were centrifuged and flash frozen in liquid nitrogen. For proliferation assays or immunostaining, cells were plated on poly-D-lysine (PDL)-coated tissue culture vessels and incubated in serum-free culture medium. MICROARRAY HYBRIDIZATION AND ANALYSIS RNA from GCPs, pre-neoplastic cells and tumor cells (isolated as described above, but not FACS-sorted) and from normal adult cerebellum (not dissociated) was converted to cDNA using the Superscript Choice cDNA kit (Invitrogen) and a T7-dT(24) primer (Genset/Proligo, Boulder, CO). cRNA was generated using a T7-transcription/labeling kit from Enzo Life Sciences and hybridized to Affymetrix U74Av2 chips (Affymetrix, Santa Clara, CA). Chips were scanned, and hybridization data were acquired using Affymetrix Suite 5.0 software. Affymetrix CEL files were normalized and quantified using Bioconductor software with the gcRMA model to quantify gene expression levels (Gentleman and Carey, 2002). Unsupervised principal components analysis (PCA) was used to identify the relationships among normal adult cerebellum, GCPs, pre-neoplastic cells and tumor cells based on expression profiles. To identify genes that were differentially expressed among GCPs, pre-neoplastic cells and tumor cells, supervised analysis was carried out. A gene-by-gene ANOVA model with three groups (GCP, pre-neoplastic, tumor) was used to fit the log2-transformed intensities. To correct for multiple comparisons, the nominal p-value was adjusted using the false discovery rate (Benjamini and Hochberg, 1995). Genes were considered to be differentially expressed if they satisfied all of the following criteria: a difference in expression greater than 1.9-fold between any two groups, a maximum absolute intensity difference larger than 32 units, and an adjusted pvalue < 0.01. There were 118 genes that met these criteria. The identities of differentially expressed genes were verified by integrating data from the Affymetrix and Unigene databases. Gene functions were determined using information from Gene Ontology, Unigene, LocusLink and PubMed databases. Clustering was performed with Cluster and Treeview (Eisen et al., 1998). All statistical analysis was performed using R-1.7 software (Dalgaard, 2002). Results were visualized with Spotfire 6.0 (Somerville, MA). Source GEO sample is GSM45621 Last updated (according to GEO): Oct 28 2005 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc81 Source GEO sample is GSM1868 Last updated (according to GEO): Nov 21 2005 Pancreas at e13.5, Chip B, rep 1 spinal cord lower; lower half Source GEO sample is GSM18589 Last updated (according to GEO): May 27 2005 36 21 from whole brain 861 Ovary We analyzed gene expression patterns in human gastric cancers by using cDNA microarrays representing approximately 30,300 genes. Expression of PLA2G2A, a gene previously implicated as a modifier of the Apc(Min/+) (multiple intestinal neoplasia 1) mutant phenotype in the mouse, was significantly correlated with patient survival. We confirmed this observation in an independent set of patient samples by using quantitative RT-PCR. Beyond its potential diagnostic and prognostic significance, this result suggests the intriguing possibility that the activity of PLA2G2A may suppress progression or metastasis of human gastric cancer. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Last Updated (by provider): Jan 10 2006 Contributers: Xin Chen [Switched to use HGCtry2 by Gemma] Primary large cell lung carcinoma 1870 Source GEO sample is GSM18311 Last updated (according to GEO): May 27 2005 19 0 The left hippocampus ADH-1 ip LPAM ILI 24hrs post ILI sample B Brain 1000 901 frontal lobe Prostate 22 Normal D_U133A_66_HC 861 Retinal macula Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141272 Last updated (according to GEO): Oct 26 2006 1000 Cerebral cortex 1000 Kidney Oculomotor nucleus 1000 gene expression data from melanoma xenografts following ILI with saline Source GEO sample is GSM213630 Last updated (according to GEO): Jul 27 2007 05_0007_SepticShock_Day1_3 Gene expression data from PD7 Foxo3 wild-type ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203827 Last updated (according to GEO): Aug 02 2007 89 70 isolated theca cells 1000 Skin Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolism. 145 134 liver damage 861 Anterior 9 0 Blood Test Starvation 916 901 Coronary artery Macrophages, Exposed to Toxoplasma gondii - Repeat #1 between the LAD artery 266 287 Standard Affymetrix Protocal Keywords = microarray Keywords = muscle Source GEO sample is GSM15771 Last updated (according to GEO): May 28 2005 5 0 brain Gene expression data from postmorten brain regions Source GEO sample is GSM144953 Last updated (according to GEO): Nov 20 2006 na Source GEO sample is GSM180464 Last updated (according to GEO): Apr 05 2007 gene expression of 2 day RA differentiated ESCs Source GEO sample is GSM181967 Last updated (according to GEO): Apr 12 2007 17 7 hippocampus Liver 1000 1000 Heart failure Testi_Intersitial Source GEO sample is GSM18987 Last updated (according to GEO): Sep 25 2006 Con (48 h) B on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A Prostate carcinoma 901 bone marrow-CD71EarlyErythroid Source GEO sample is GSM18907 Last updated (according to GEO): Sep 25 2006 913 Coronary heart disease frontal lobe 901 Infection 861 Mouse model of congenital heart disease in Csx/Nkx2.5 mutant embryos. Homozygous mutant mouse at embyronic day 9.5. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2274 Last updated (according to GEO): May 27 2005 plasma cells 50 61 Amygdala Treatment, type=pharmacogenomic_treatment, description=Chronic Immobilization Stress Source GEO sample is GSM53299 Last updated (according to GEO): Jul 06 2005 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11337 Last updated (according to GEO): May 28 2005 M_U133Plus_124_AnCg 0 Lung tissue 10 1000 Breast Carcinoma Prosencephalon 1000 DLCL-0004 21 0 cerebellum wistar 3884 861 Occipital lobe CCRF-CEM_II_CL7003_Leukemia on Affymetrix GeneChip Human Full Length Array HuGeneFL To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28465 Last updated (according to GEO): May 27 2005 91 from the bone marrow 72 Gene expression data from postmorten brain regions Source GEO sample is GSM145023 Last updated (according to GEO): Nov 20 2006 nasal epithelial cells 28 49 C20 on NCI-7.6k Expression profiling of spinal cord section (T9) extracted from rats 0 following laminectomy (naïve) Lot batch = Source GEO sample is GSM1337 Last updated (according to GEO): Oct 28 2005 26 15 endometrioid NCI60.46_LABEL50EXTRACT49SUB3 Source GEO sample is GSM134225 Last updated (according to GEO): Aug 06 2007 Gene expression data from brain of adult rats Source GEO sample is GSM101025 Last updated (according to GEO): Feb 20 2007 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28453 Last updated (according to GEO): May 27 2005 1000 Brain plasma cells 332 344 MGJZ030228033Bspleen Parietal Lobe 7 Normal 3 0 Lung FSCC17 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1266 1249 in the cerebellum Medulla 861 Corner+ Avg:444, Count:32 Corner- Avg:45544, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:2.378481,SFGene:All Background:Avg:481.97,Stdev:8.21,Max:502.2,Min:450.2 Noise:Avg:17.00,Stdev:0.54,Max:18.7,Min:15.1 RawQ:19.54 Source GEO sample is GSM3482 Last updated (according to GEO): May 27 2005 Brain 861 1000 Hippocampus 861 Cerebellum PP243_infected_DC Diaphragm 7 Day control rep 2 NCI60.29_LABEL33EXTRACT32SUB3 Source GEO sample is GSM134139 Last updated (according to GEO): Aug 06 2007 Brain 1000 Spleen vs Untreated B cell Time 0 (set3) 861 Brain 660 mesenchymal stem cell 639 1812 of lytic bone 1800 G1E_7_A Spleen vs fMLP Treated B cell 5 0 brain of coronary artery disease 258 284 Sample is skeletal muscle from a morbidly obese patient undergoing elective abdominal surgery Source GEO sample is GSM3985 Last updated (according to GEO): May 28 2005 Lmna H222P heterozygous male 3 brain, Right Frontal Lobe: Extract60_le2 Hippocampus 1000 861 Heart failure osteoblast 627 637 124 105 persistent infection cingulate cortex 861 UO-31 hgu95d PMN_LB_360min_Patient11 We used manual macrodissection or laser capture microdissection (LCM) to isolate tissue sections of the hippocampus area of Ras-GRF1 wild type and knockout mice brains, and analyzed their transcriptional patterns using commercial oligonucleotide microarrays. Comparison between the transcriptomes of macrodissected and microdissected samples showed that the LCM samples allowed detection of significantly higher numbers of differentially expressed genes, with higher statistical rates of significance. These results validate LCM as a reliable technique for in vivo genomic studies in the brain hippocampus, where contamination by surrounding areas (not expressing Ras-GRF1) increases background noise and impairs identification of differentially expressed genes. Comparison between wild type and knockout LCM hippocampus samples revealed that Ras-GRF1 elimination caused significant gene expression changes, mostly affecting signal transduction and related neural processes. The list of 36 most differentially expressed genes included loci concerned mainly with Ras/G protein signaling and cytoskeletal organization (i.e. 14-3-3gamma/zeta, Kcnj6, Clasp2) or related, cross-talking pathways (i.e. jag2, decorin, strap). Consistent with the phenotypes shown by Ras-GRF1 knockout mice, many of these differentially expressed genes play functional roles in processes such as sensory development and function (i.e. Sptlc1, antiquitin, jag2) and/or neurological development/neurodegeneration processes affecting memory and learning. Indeed, potential links to neurodegenerative diseases such as Alzheimer disease (AD) or Creutzfeldt-Jacobs disease (CJD), have been reported for a number of differentially expressed genes identified in this study (Ptma, Aebp2, Clasp2, Hebp1, 14-3-3gamma/zeta, Csnk1delta, etc.). These data, together with the previously described role of IRS and insulin (known Ras-GRF1 activators) in AD, warrant further investigation of a potential functional link of Ras-GRF1 to neurodegenerative processes. Heart Ventricle 1000 hrs nasal epithelium 1126 1146 between the LAD artery 266 287 Femur 1000 5 0 Spleen Ventral tegmental area, male 10.5 week old c57bl/6J mouse, UNSUSCEPTIBLE group Source GEO sample is GSM224742 Last updated (according to GEO): Aug 31 2007 occipital_lobe_10 1000 Ischemia Normal Source GEO sample is GSM175938 Last updated (according to GEO): Apr 09 2007 Expression Studies of Melanotransferrin in Mouse Brain 5 0 brain NCI60.42_LABEL46EXTRACT45SUB3 Source GEO sample is GSM134203 Last updated (according to GEO): Aug 06 2007 Gene expression profile of the cell line UB/OC-1 grown for 4 days under differentiating conditions (39C). This data set is a replica experiment of sample GSM1521. Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1531 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28779 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM144895 Last updated (according to GEO): Nov 20 2006 66 42 out of mouse bone marrow with recurrent lung tumor 400 424 1000 Brain R536P00445 PGA-Band_1h_16-m5 EWS-C6 on NHGRI-6.5k_b Pool of 3 non-inner ear tissue samples at E9.5; 14 at E10; 4 at E10.5 Source GEO sample is GSM182624 Last updated (according to GEO): Aug 14 2007 I_95Av2_3076_CB_1_GS cerebellum 7 16 Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242086 Last updated (according to GEO): Dec 04 2007 334 320 Keywords = HIV 257 242 of uterine horns PGA_PA-D_82 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68291 Last updated (according to GEO): Jul 07 2006 plasma cells 332 344 Liver 1000 Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002. Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Part of the medium chain triacylglycerol oil in control diet was replaced with: 1.1% fungal oil and 1.9% fish oil. Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily. Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France). Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h. After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hippocampal gene expression analysis. From these same 5 mice, the hippocampus was dissected from the mice according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancourt, France), rinsed as described for livers, cut into 17-50 mg subsections, and frozen as described for livers. Hippocampal lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5). Hippocampal tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hippocampal RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips. Source GEO sample is GSM2564 Last updated (according to GEO): Mar 17 2006 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114452 Last updated (according to GEO): Jun 16 2006 Lung; Fetal Day 16.5 Keywords = mouse gene expression database Source GEO sample is GSM29389 Last updated (according to GEO): May 27 2005 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15756 Last updated (according to GEO): May 28 2005 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 23.75 hours after lights on. Original RNA code = LC36A. Source GEO sample is GSM227389 Last updated (according to GEO): Sep 10 2007 5 0 Spleen Structure of superior frontal gyrus 1000 Dahl-Iwai Male HighSalt Cortex rat112 dahl_cortexr_k_112c_072001 PGA-MFD-CtrPD1-1aCv2-s2 brain, frontal cortex: pADX PM DR_e1_le1 10 Bone marrow 0 Liver 1000 none Source GEO sample is GSM239959 Last updated (according to GEO): Dec 07 2007 B39 on NCI-7.6k ciliary_ganglion Source GEO sample is GSM18845 Last updated (according to GEO): Sep 25 2006 901 Caudate nucleus structure Alzheimer's Disease 1000 3AJZ02052309_Islet SCG explant cultured for 12 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246066 Last updated (according to GEO): Dec 03 2007 1000 Caudate nucleus structure Dendritic Cells, CD8+ subset - Expt #2 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188781 Last updated (according to GEO): Jun 06 2007 HapMap CEU_parent Male Source GEO sample is GSM159558 Last updated (according to GEO): Feb 01 2007 innervated tibialis anterior muscles from runx1f/- control mice Treatment, type=add, description=runx1f/- Source GEO sample is GSM99430 Last updated (according to GEO): Mar 08 2006 Brain 861 control 4 weeks Treatment, type=time_course, measurement=4.0 weeks Source GEO sample is GSM107862 Last updated (according to GEO): Jun 06 2006 none Source GEO sample is GSM239943 Last updated (according to GEO): Dec 07 2007 Hyperdip>50-R4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Neuraxis Affymetrix RGU34A 0H A Lymphoblastoid Cell Line for Individual 8135.4 log phase Skeletal bone 861 1000 Asthma 1000 frontal lobe Parkinson Disease 1000 spinal cord 37 47 RXF 393 hgu95a 2526 in the trigeminal ganglion 2500 1000 Brain to the renin-angiotensin system 888 919 V5-P090 Prosencephalon 861 A HID B D091 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108590 Last updated (according to GEO): Aug 22 2006 in brain 758 765 D_U133A_32_Amy Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15523.gif Source GEO sample is GSM84142 Last updated (according to GEO): Sep 22 2006 Measles 861 Spleen vs Platelet activating factor Treated B cell 30min (set2) HOP-92 hgu95e extracellular matrix 984 1003 906 Microtubule-Associated Proteins 1000 Hippocampus 1000 Seizures 11 0 Hypothalamus NCI-H522 hgu95a f2#279 versus pool Mouse Brain tissue Brain area 8/9_8yp_RTT B6:25-16-30 choroid plexus starved 41 47 7 0 prostate Bone Marrow 1000 201 in the frontal cortex 221 M_U133A_27_CB Hoxb1 mutant E10.5, rep 2 (M6) 6,18,30 month oculomotor nucleus and spinal cord Source GEO sample is GSM74341 Last updated (according to GEO): Sep 16 2005 brain, Right Cerebellum: Extract53_le1 24 CB B 7 cerebral cortex 21 mouse hippocampus, cox-2 heterozygous, rep1 Creatine-treated, biological rep5 Spleen vs ELC Treated B cell 30min (set3) of the hippocampus 528 545 1000 Brain Cerebral cortex 861 hindbrain 1000 Standard Affymetrix Protocol on total RNA extracted from brain tissue Source GEO sample is GSM101415 Last updated (according to GEO): Mar 28 2006 mouse brains 187 198 We will separately dissect the maxillary and mandibular branches of the E10.5 first branchial arch from wild type, dlx2, dlx1/2 and Dlx5/6 mutants. The tissues wil be flash frozen within 1 min of removal.We have not performed the dissections yet so we dont know how much RNA will be get from each sample, but previous experience suggests that we will need ~10 branchial arches/experiment. Treatment, type=nucleic_acid_extraction, description=We anticipate using this method as it was recommended by TGEN for small amounts of tissue. Source GEO sample is GSM107890 Last updated (according to GEO): Jun 06 2006 861 Encephalitis I_U133A_48_CB Neoplasm 861 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. 4h after sham surgery, a 7 mm disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44486 Last updated (according to GEO): May 27 2005 EAE, placebo-treated #10 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184752 Last updated (according to GEO): Apr 26 2007 40 21 from dorsal pancreas 5 0 brain CAD_replicate107 1000 Cerebral cortex Neoplasm 861 913 Coronary heart disease 12 frontal Lobe 23 10 7 Left Gene expression data from postmorten brain regions Source GEO sample is GSM145389 Last updated (according to GEO): Nov 20 2006 201 197 liver 62 38 out of mouse bone marrow Gene expression data from postmorten brain regions Source GEO sample is GSM145047 Last updated (according to GEO): Nov 20 2006 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68181 Last updated (according to GEO): Jul 07 2006 Fibroblasts 861 15 0 human cerebellum effect of +/- mutations in ES cells. Date GSE614 Last Updated: Jul 27 2006 Contributers: Derek J Symula Includes GDS434. Update date: Nov 14 2003. Dataset description GDS434: Transcriptional profiling of embryonic stem (ES) cell lines with mutations affecting cholesterol transport and metabolism. Abca1 +/- and Cdk4 +/- ES lines compared with controls.. Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep7 Tumor__Bladder_TCC_94_I_229 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 10 7 Left na Source GEO sample is GSM181307 Last updated (according to GEO): Apr 10 2007 Vastus lateralis muscle biopsy from healthy 25 year old male volunteer. Analysis done with Affymetrix Microarray Suite 5.0 software Source GEO sample is GSM2391 Last updated (according to GEO): May 27 2005 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 21d after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44481 Last updated (according to GEO): May 27 2005 NZB/BINJ_male_hypothalamus Source GEO sample is GSM184211 Last updated (according to GEO): Apr 26 2007 Greater sac of peritoneum 1000 in bronchial epithelia 311 332 MO_control_0min_Patient4 GSE867 Treated Source GEO sample is GSM175972 Last updated (according to GEO): Apr 09 2007 G42-LGN replicate1 901 Coronary artery 861 Infertility GSE8314 Adipose tissue 901 gene expression data from ODC mouse skin samples Source GEO sample is GSM216676 Last updated (according to GEO): Aug 09 2007 5 0 Muscle 1000 medulloblastoma Epithelial Cells 1000 #20 (isolate V rich media PlGF 24hours) 15 0 human cerebellum Normal human tissue:Normal Pancreas Keywords = Human, Normal Tissue, Normal Pancreas Source GEO sample is GSM44677 Last updated (according to GEO): May 27 2005 Heart [JunctionChip 5 of 5] Spleen 1000 C3H-HeOuJ mice exposed to filterd air for 72hrs- lungs were removed-frozen in liquid nitrogen-RNA extraction. Lot batch = Source GEO sample is GSM4017 Last updated (according to GEO): May 28 2005 861 Neoplasm 166 156 of retinal TUMOR 21 0 7 adenoma 861 861 Heart Keywords = kidney 236 253 Endometrium/Ovary-Disease 4 NCI-H522 hgu95c CNS-SpinalC-conAdult-24h-2B-s2 3wkC 1000 Cerebral cortex 861 Brain Spleen vs NGF (Nerve Growth Factor)Treated B cell 60min (set1) Blood samples from apparently healthy blood donors were collected in PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Gene expression profiles were assessed using HG-U133A arrays. Source GEO sample is GSM183416 Last updated (according to GEO): Apr 23 2007 SN:Human Glioblastoma Biopsy 10412 Normal Source GEO sample is GSM175864 Last updated (according to GEO): Apr 09 2007 M7TW00122035 Normal__Peripheral_Blood_Poly_POLY2 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene expression data from liver Source GEO sample is GSM243354 Last updated (according to GEO): Nov 16 2007 Sun176_BAV13 group DBA whole brain 2B 861 Neoplasm 901 Caudate nucleus structure 1000 hindbrain D_U133A_1_DLPFC adipose_tissue_3 Source GEO sample is GSM80580 Last updated (according to GEO): Mar 31 2006 +_6582_batch1 on NHGRI-6.7k Expression data after reversal of DNA methylation Source GEO sample is GSM230912 Last updated (according to GEO): Sep 20 2007 861 Brain processed in batch 6 Source GEO sample is GSM90431 Last updated (according to GEO): Mar 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145856 Last updated (according to GEO): Nov 20 2006 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201252 Last updated (according to GEO): Jun 14 2007 WGACON-179 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:523, Count:32 Corner- Avg:38268, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:10.581564,SFGene:All Background:Avg:529.04,Stdev:29.11,Max:602.6,Min:483.5 Noise:Avg:16.79,Stdev:1.70,Max:23.5,Min:13.4 RawQ:16.87 Keywords = ALL Source GEO sample is GSM3459 Last updated (according to GEO): May 28 2005 human peripheral blood derived monocytes, 8 hour LPS stimulation, biological rep1 Source GEO sample is GSM126998 Last updated (according to GEO): Aug 15 2006 from colonic normal mucosa 21 47 1000 Brain 983 Occipital lobe Gene expression data from colonic normal mucosa. Source GEO sample is GSM215071 Last updated (according to GEO): Aug 02 2007 861 Neoplasm 1000 Communicable Diseases M_U133A_23_AnCg 1059 1043 in breast tumors 1000 Pituitary Gland This is the fifth replicate for the SNc neurons which were captured using LCM. Source GEO sample is GSM19321 Last updated (according to GEO): May 27 2005 adenoma 861 861 Pituitary Gland brain 0 5 1BJZ02022640_trachea 1575 such as Alzheimer disease 1599 Brain 1000 brain, unknown: 03BI_e1_le1 497_11d Type 1 Diabetes patient and the timepoint 1 month after diagnosis. Source GEO sample is GSM228657 Last updated (according to GEO): Sep 11 2007 1000 Brain thymus sprague2 whole tissue, individual animal, 10 weeks old, male Sprague Dawley thymus file:R3JW02103018 Source GEO sample is GSM15216 Last updated (according to GEO): May 28 2005 CAD_replicate70 Cancers; Colon Tumor Keywords = mouse gene expression database Source GEO sample is GSM29263 Last updated (according to GEO): May 27 2005 Renal Cell Carcinoma 913 Uterus Source GEO sample is GSM18960 Last updated (according to GEO): Sep 25 2006 Liver 1000 855 846 ER- tumors Ovarian_Tumor_Serous_KU-OS-015 Colon Cecum 10 Normal FVB/NJ Frontal Cortex C s8 24 0 human prostate PC3 tumors Kidney YC-1A 40 21 from dorsal pancreas 91 from the bone marrow 72 1000 Bone Marrow 5 0 Spleen Category: Cell-line Subcategory: Breast isolate obtained from ATCC Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc15 Source GEO sample is GSM1864 Last updated (according to GEO): Nov 21 2005 in the mammalian nervous system 110 141 L_B6_Control_ZT 6_3 861 Cerebral cortex GBM: 90A20 Gene expression data from postmorten brain regions Source GEO sample is GSM145336 Last updated (according to GEO): Nov 20 2006 brain 0 5 brain, hippocampus: Ctr-6h-P15-III_e1_le1 Pancreas Source GEO sample is GSM18818 Last updated (according to GEO): Sep 25 2006 Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108048 Last updated (according to GEO): Jun 06 2006 Neoplasm 861 Epithelium 861 Bipolar Disorder 861 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228597 Last updated (according to GEO): Sep 11 2007 Coronary heart disease 913 Expression profiling of spinal cord section (T8) extracted from rats 7d following severe injury Source GEO sample is GSM31499 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM176039 Last updated (according to GEO): Apr 09 2007 15 0 human cerebellum The sample is a part of a series describing gene expression changes during postnatal development of the small intestine Source GEO sample is GSM198941 Last updated (according to GEO): Jun 11 2007 lymphomaburkittsDaudi Source GEO sample is GSM18895 Last updated (according to GEO): Sep 25 2006 none Source GEO sample is GSM244561 Last updated (according to GEO): Nov 23 2007 HDMTX_MP-DX-10 421 412 infection Gene expression data from postmorten brain regions Source GEO sample is GSM146077 Last updated (according to GEO): Nov 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145435 Last updated (according to GEO): Nov 20 2006 304 280 alcoholic cardiomyopathy AD-375t1-A115-3 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 14 7 amygdala Muscle 861 I_U133Plus_123_AnCg Macrophages treated with LPS plus IL-10, 30 min, Replicate 2 Source GEO sample is GSM241144 Last updated (according to GEO): Nov 02 2007 26 0 cerebral cortex wistar 3904 umbilical cord_bpd: 2B Disorder of artery 865 with myocardial infarction 313 339 861 Oocytes 32 F arm fibroblast LS10, serum starved Leukemia, Lymphocytic, Chronic 1000 1000 Cochlear structure Leukemic fractions of ID09 AML patient have been hybridized. Source GEO sample is GSM103098 Last updated (according to GEO): Feb 26 2007 Simple annotation: Normal tissue, Eye Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18601.gif Source GEO sample is GSM66569 Last updated (according to GEO): Sep 22 2006 Substantia nigra PD rep3 Communicable Diseases 1000 Sample48, Post Injury 24 hours Treatment, type=wait Source GEO sample is GSM53298 Last updated (according to GEO): Jul 06 2005 PCA11_localized prostate cancer Liver 1000 14 0 spleen sprague1 216 200 of neural retinas Leukemia, Myelocytic, Acute 1000 H121 CN A DRG_sema3A_40h_rep1 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211326 Last updated (according to GEO): Jul 18 2007 861 Cerebral cortex BALB/cByJ Amygdala A Sample4, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53255 Last updated (according to GEO): Jul 06 2005 brain_DLPFC_bipolar C_mr418 853 Spinal Injuries 861 Hereditary Diseases KT126_AR1 Ventral tegmental area 0 22 Primary Neoplasm 1000 Localized Carcinoma 853 Brain (cerebellum) [JunctionChip 2 of 5] Category: Cell-line Subcategory: Reproducibility Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp3318 Source GEO sample is GSM2134 Last updated (according to GEO): Nov 21 2005 Expression profiling of spinal cord section (T9) extracted from rats 4h following severe injury Lot batch = Source GEO sample is GSM7583 Last updated (according to GEO): May 28 2005 gene expression from allergen stimulated mouse lung Source GEO sample is GSM158141 Last updated (according to GEO): Jan 25 2007 Brain 1000 Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181998 Last updated (according to GEO): Apr 13 2007 1000 Medulla Oblongata HCC (HBV+, SF32) Gene expression data from 9A1 BMEL cells cultured under basal conditions. Source GEO sample is GSM160071 Last updated (according to GEO): Jul 11 2007 1000 Malaria brain, Left frontal Lobe: Extract24_le2 Microdissected area # 2 of 2182 tumor Mammary Gland @ Lac2, biological rep4 Gene expression data from postmorten brain regions Source GEO sample is GSM145796 Last updated (according to GEO): Nov 20 2006 Disease Source GEO sample is GSM176250 Last updated (according to GEO): Apr 09 2007 RNA from three stroke patients was pooled. Source GEO sample is GSM239107 Last updated (according to GEO): Oct 29 2007 park_1157_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Heart Septal Defects 884 A HID B D012 Axon 861 7 0 Pancreas Affymetrix protocol Source GEO sample is GSM213815 Last updated (according to GEO): Aug 02 2007 Human fibroblast-derived, pluripotent cell lines are described that have normal karyotypes, express high levels of telomerase activity, and express both cell surface markers and genes that characterize human embryonic stem (ES) cells. Last Updated (by provider): Nov 22 2007 Contributers: Kim Smuga-Otto Ron Stewart Junying Yu James A Thomson Karen J Heidarsdottir PGA-Pi3k_dn_1451v2 cy5:WKY treated w/ angtiotensin, biological rep 5r; cy3:pool of 6 WKY control rats plasma cells 332 344 Melanoma xenograft, MED1_Lung_B (LeiFidler) Female8, Respiratory RNA_Nasal respiratory epithelium_Tissue was preserved in RNA later and collected from nose The epithelial cells 962 981 for liver 26 35 M_U133A_31_DLPFC Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211229 Last updated (according to GEO): Jul 18 2007 901 Myeloid Leukemia Gene-expression profiles in hereditary breast cancer. with mental retardation 241 263 RPMI-8226 hgu95b human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195338 Last updated (according to GEO): Jun 04 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM144946 Last updated (according to GEO): Nov 20 2006 in brain 294 302 processed in batch 4 Source GEO sample is GSM90414 Last updated (according to GEO): Mar 20 2006 Nose 1000 5 0 brain Gene expression data from rat lungs exposed to FiO2 of ~9.5% (hypoxia). Source GEO sample is GSM184877 Last updated (according to GEO): Jun 14 2007 In innate immune responses, activation of Toll-like receptors (TLRs) triggers direct antimicrobial activity against intracellular bacteria, which in murine, but not human, monocytes and macrophages is mediated principally by nitric oxide. We report here that TLR activation of human macrophages up-regulated expression of the vitamin D receptor and the vitamin D-1-hydroxylase genes, leading to induction of the antimicrobial peptide cathelicidin and killing of intracellular Mycobacterium tuberculosis. We also observed that sera from African-American individuals, known to have increased susceptibility to tuberculosis, had low 25-hydroxyvitamin D and were inefficient in supporting cathelicidin messenger RNA induction. These data support a link between TLRs and vitamin D-mediated innate immunity and suggest that differences in ability of human populations to produce vitamin D may contribute to susceptibility to microbial infection. BTBR T+ tf/tf Frontal Cortex B olfactory epithelium 194 213 Medulla 861 High Freezing Source GEO sample is GSM92418 Last updated (according to GEO): Jan 13 2006 861 Chondrocytes CNS-SCsev_InjA4h-2B-s2 Normal Spinal Cord PGA_PA-D_132 A2780_oxa_IC50_16h_1 3AJZ02051604_CerebellumPeduncles 1BMH02082909_PB_CD56NKCells fetalbrain Source GEO sample is GSM18786 Last updated (according to GEO): Sep 25 2006 In this time course pregnant CD-1 (outbred) dams were exposed to the 2-chloro analogue of 2'-deoxyadenosine (a metabolic toxin) on 8 d.p.c. The test dose of 2.5 mg/kg 2CdA was modeled for a 5% increased risk of microphthalmia in term fetuses. Exposed embryos were co-treated with PK11195, a nontoxic ligand of the mitochondrial peripheral-type benzodiazepine receptor (Bzrp) that effectively blocks p53 protein induction and developmental toxicity induced with 2CdA. Sampling intervals were anchored to the conditional biomarker (p53 protein induction) expressed in 2CdA-treated embryos between 3.0- and 4.5h post-exposure. Since p53 protein induction has been defined as a critical event in 2CdA-induced microphthalmia, these sampling intervals represent times before (3.0h), during (4.5h), and after (6.0h) this critical event. No p53 induction is observed in embryos co-treated with 2CdA and PK11195. All measurements were on RNA from the embryonic headfold.. Date GSE1070 Last Updated: May 29 2005 Contributers: Jeffrey H Charlap Thomas B Knudsen Amar V Singh Kimberly R Nemeth Includes GDS632. Update date: Jul 14 2004. Dataset description GDS632: Temporal analysis of ocular teratogen 2-chloro-2'deoxyadenosine (2CdA) exposure in developing embryos, intervention with PK11195, and induction of microphthalmia (small eye syndrome). Embryonic headfold examined at 3, 4.5, and 6 hours.. Wild type 8 wk old male FVB/NJ mouse pituitary gland Source GEO sample is GSM75007 Last updated (according to GEO): Feb 27 2007 Cerebral cortex 861 1000 Brain Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19219 Last updated (according to GEO): May 27 2005 GSE7694 Conventional Corpus 2 6 (cerebral cortex 21 Y VIS D065 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108649 Last updated (according to GEO): Aug 22 2006 Neoplasm 861 Lymphoblastoid Cell Line for Individual 8178.3 log phase Mesenchymal Stem Cells 1000 901 Coronary artery of brain cortex 25 39 Mesenchymal Stem Cells 1000 Normal Source GEO sample is GSM176175 Last updated (according to GEO): Apr 09 2007 10 7 Left Cochlea 0 6 Expression profiling of spinal cord section (T10) extracted from rats 28d following severe injury Source GEO sample is GSM31364 Last updated (according to GEO): May 27 2005 of somatomotor cortex 21 41 4535 4527 hepatoma Midbrain 4 Normal Wild-type-hippocampus, biological rep9 (female) Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2724 Source GEO sample is GSM2109 Last updated (according to GEO): Nov 21 2005 861 Cerebral cortex Normal human tissue:Normal Prostate Keywords = Human, Normal Tissue, Normal Prostate Source GEO sample is GSM44678 Last updated (according to GEO): May 27 2005 41 30 PCOS oocytes 1000 Endometriosis, site unspecified /HeJ Cerebellum A 3 19 Heart Septal Defects, Atrial 1000 from colonic normal mucosa 21 47 Lymphoblastoid Cell Line for Individual 8129.3 log phase Lung 1283 1286 in the brain 150 162 superficial 946 956 Tumor__Breast_Adeno_mBRT1_(8697) on Affymetrix GeneChip Human 35K SubA Array Hu35k-A TestiSeminiferousTubule Source GEO sample is GSM18990 Last updated (according to GEO): Sep 25 2006 testis 52 58 129:3-1-2 perirhinal cortex 266 257 infection occipital_lobe_9 Levitiracetam brainstem 1 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53426 Last updated (according to GEO): Jul 06 2005 cingulate cortex 861 Liver; RegenerationSham 6 hrs Keywords = mouse gene expression database Source GEO sample is GSM29374 Last updated (according to GEO): May 27 2005 atrial septal defects 198 218 861 Ventral Tegmental Area 1000 Descending colon 4 0 Liver Cardiac 523 530 865 Disorder of artery Macrophage 14smi048 Blood Test (Blinded) Sample Source GEO sample is GSM129962 Last updated (according to GEO): Sep 18 2007 NAP-104 on UMich-10k Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92355 Last updated (according to GEO): Jan 13 2006 CNS-RM_Ctr7d-2A-s2 201 in the frontal cortex 221 CNS-SC_InjB14d-2B-s2 GBM Treatment, type=remove Source GEO sample is GSM99561 Last updated (according to GEO): Apr 21 2006 brainstem 7 15 Gene expression data from postmorten brain regions Source GEO sample is GSM145088 Last updated (according to GEO): Nov 20 2006 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153486 Last updated (according to GEO): Jan 11 2007 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=800650 LaserPower=2.121.28 Lot batch = LC17N057 Source GEO sample is GSM4799 Last updated (according to GEO): Nov 21 2005 Cochlear nucleus structure 1000 1000 Diabetes Mellitus Spleen 1000 861 Mammary gland Leukemic fractions of ID05 AML patient have been hybridized. Source GEO sample is GSM102918 Last updated (according to GEO): Feb 26 2007 Hyperdip>50-C33 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 5 0 brain 861 Dislocations 901 Heart Diseases bronchial epithelia 224 243 Expression profile of genes in mouse brain Source GEO sample is GSM21046 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM176336 Last updated (according to GEO): Apr 09 2007 of mouse brain 9 23 861 Brain Healthy patient. Source GEO sample is GSM228665 Last updated (according to GEO): Sep 11 2007 2362 2347 of schizophrenia osteoblast 627 637 of the postmortem brains 674 698 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM79048 Last updated (according to GEO): Oct 24 2005 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11581.gif Source GEO sample is GSM76457 Last updated (according to GEO): Sep 22 2006 CS-B wt-rescued cell UVC-irradiated (12hour) replicate 2 U133B 1000 Hippocampus Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.71 Subject: 3023 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39054 Last updated (according to GEO): May 27 2005 660 mesenchymal stem cell 639 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68188 Last updated (according to GEO): Jul 07 2006 of hormone resistant prostate cancer 26 61 of parieto-occipital cortex 223 250 T6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Brain 1000 Callosal Neurons E18 2 38 21 from a hippocampus Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16259.gif Source GEO sample is GSM91530 Last updated (according to GEO): Sep 22 2006 Epithelial Cells 901 Bone marrow [JunctionChip 1 of 5] Nose 1000 Brain 1000 no additional Source GEO sample is GSM199098 Last updated (according to GEO): Jun 08 2007 after trauma 697 709 861 Cerebral cortex human caudate nucleus Source GEO sample is GSM86857 Last updated (according to GEO): Feb 08 2006 RNA from muscle biopsy specimen Source GEO sample is GSM3716 Last updated (according to GEO): May 27 2005 brain 0 5 Spinal Cord 901 The epithelial cells 962 981 T Cells Resting 30h 1 Resting A2780_cis_IC90_0h_2 Central gray substance of midbrain 861 1000 Hippocampus Transcription profiling involves H3 methyltransferase G9a-deleted MEFs reconstituted with empty vector (delta), wild type FLAG-G9a (WT), FLAG-G9a K165A (K165A) or FLAG-G9a H1093K catalytic mutant (H1093K). Source GEO sample is GSM197740 Last updated (according to GEO): Jul 16 2007 adLacZ8 1000 Mammary gland 858 Mesodermal cell L_AK_SleepDep_ZT 6_1 M_U133A_46_DLPFC PGA-MCR-CR-24h-1bAv2-s1 Lymphoblastoid Cell Line for Individual 8169.3 log phase Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153357 Last updated (according to GEO): Dec 27 2006 1000 Down Syndrome ABSTRACT: BACKGROUND: General somatic sensation is conveyed to the central nervous system at cranial levels by the trigeminal ganglion (TG), and at spinal levels by the dorsal root ganglia (DRG). Although these ganglia have similar functions, they have distinct embryological origins, in that both contain neurons originating from the neural crest, while only the TG includes cells derived from the placodal ectoderm. RESULTS: Here we use microarray analysis of E13.5 embryos to demonstrate that the developing DRG and TG have very similar overall patterns of gene expression. In mice lacking the POU-domain transcription factor Brn3a, the DRG and TG exhibit many common changes in gene expression, but a subset of Brn3a target genes show increased expression only in the TG. In the wild-type TG these Brn3a-repressed genes are silent, yet their promoter regions exhibit histone H3-acetylation levels similar to constitutively transcribed gene loci. This increased H3-acetylation is not observed in the DRG, suggesting that chromatin modifications play a role in cell-specific target gene regulation by Brn3a. CONCLUSION: These results demonstrate that one developmental role of Brn3a is to repress potential differences in gene expression between sensory neurons generated at different axial levels, and to regulate a convergent program of developmental gene expression, in which functionally similar populations of neurons are generated from different embryological substrates. in bronchial epithelia 311 332 CNS-SpinalC-conAdult-4h-1B-s2 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11592 Last updated (according to GEO): May 28 2005 Hypertensive disease 861 861 Retina Testis 1000 Expression data from pre natal and post natal CCAM samples and relative controls 31 21 spinal cord Heart 1000 Liver 0 4 1000 Liver due to severe encephalopathy 437 465 PHA, 06.00 hr. T-Cell, Repeat. Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12668.gif Source GEO sample is GSM79930 Last updated (according to GEO): Sep 22 2006 Colonic mucous membrane 913 pinealgland.3 Blood 861 NCI60.48_LABEL52EXTRACT51SUB3 Source GEO sample is GSM134238 Last updated (according to GEO): Aug 06 2007 TEL-AML1-C28 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Parkinson Disease 1000 embryonic hearts 1064 1079 1000 Mental Retardation 43 0 Chorionic mesoderm-derived mesenchymal cells 1000 Amygdaloid structure Human Hypothalamus Female 3 Gene expression data from human colon tumor tissue Source GEO sample is GSM173342 Last updated (according to GEO): Apr 20 2007 5 0 brain 1000 Left WGACON-147 861 Blood MGMH030212037Bthyroid of psychiatric disorder 1814 1837 Normal Source GEO sample is GSM176098 Last updated (according to GEO): Apr 09 2007 "16 hr Hela Double Thymidine, exp3" 1000 Uterus ER negative human primary breast tumor EA02014_41261_H133A_JA-1060 hippocampus sprague 3957 whole tissue, individual animal, 10 weeks old, male Sprague Dawley hippocampus file:p3957w Source GEO sample is GSM15179 Last updated (according to GEO): Oct 28 2005 B325 on Affymetrix GeneChip Human Full Length Array HuGeneFL Normal Source GEO sample is GSM176324 Last updated (according to GEO): Apr 09 2007 on the X chromosome 869 888 Replicate 1 of 3 (same genotype, same age). All replicates were individual animals. Source GEO sample is GSM138277 Last updated (according to GEO): Sep 29 2006 Spleen vs MIP3-alpha Treated B cell 30min (set2) Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 h time point Source GEO sample is GSM159757 Last updated (according to GEO): Apr 23 2007 Spinal Cord 3 Normal Structure of trigeminal ganglion 1000 Expression profiling of somatomotor cortex extracted from rats at 28d following moderate injury Source GEO sample is GSM41718 Last updated (according to GEO): May 27 2005 Bic/4AP(3) of somatomotor cortex 21 41 901 Caudate nucleus structure mouse brain ipsilateral LPS.RU486, biological rep5 "36h Thy-Noc, Exp4" mild cognitive impairment - primary visual cortex 4 Expression profiling of spinal cord section (T9) extracted from rats 48h following moderate injury Source GEO sample is GSM31550 Last updated (according to GEO): May 27 2005 436 of stem cells 424 134 116 with Endometriosis FVB-3wk-m-3 Adenocarcinoma 861 Brain 861 GSE1008 1000 Prostate Normal__Lung_LU_2 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Migration Source GEO sample is GSM19104 Last updated (according to GEO): May 27 2005 wt mouse number 2 Source GEO sample is GSM186667 Last updated (according to GEO): Jun 11 2007 Heart 1000 24 0 Proliferative endometrium cingulate cortex 861 Subject code A11EB 36 0 Inflammatory myopathy specimen GEIM17 Duchenne muscular dystrophy 0 26 Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 10 brain, Medial Temporal Gyrus: Sample37_e1_le1 brain, Left frontal Lobe: Extract24_le1 for liver 26 35 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5837 Last updated (according to GEO): May 27 2005 This is replicate 1 of the naive samples from passive avoidance trained rats. Source GEO sample is GSM17395 Last updated (according to GEO): Aug 22 2007 858 Mesodermal cell of somatomotor cortex 21 41 Myocardium 861 Muscle 861 Adipose tissue 884 SNU398 cells 330 324 uterus Stria 861 NA Source GEO sample is GSM198899 Last updated (according to GEO): Jun 07 2007 Gene expression data from liver Source GEO sample is GSM243382 Last updated (according to GEO): Nov 16 2007 Gene expression data from whole tumor Source GEO sample is GSM182308 Last updated (according to GEO): Apr 16 2007 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188803 Last updated (according to GEO): Jun 06 2007 ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes(delta-inlAB)_A_5551 Source GEO sample is GSM161577 Last updated (according to GEO): Apr 23 2007 Whole Brain 62 72 Gene expression regulated by DACH1-9 861 Hippocampus Muscle 861 brain, SNc and VTA: SNc2_e1_le1 VDXKIU_15E6 Lymphoblastoid Cell Line for Individual 8120.3 log phase 26 11 /Ovary-Disease 8 in synaptic 2348 2358 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3474.gif Source GEO sample is GSM93142 Last updated (according to GEO): Sep 22 2006 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:595, Count:32 Corner- Avg:33202, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:5.146851,SFGene:All Background:Avg:632.03,Stdev:10.66,Max:661.0,Min:610.6 Noise:Avg:13.36,Stdev:0.48,Max:14.8,Min:11.9 RawQ:16.73 Keywords = ALL Source GEO sample is GSM3427 Last updated (according to GEO): May 27 2005 A498 hgu95d Cerebellum 1000 skeletal.muscle.2 Expression profiling of somatomotor cortex extracted from rats at 7d following sham surgery Source GEO sample is GSM41669 Last updated (according to GEO): May 27 2005 861 Longitudinal X50 NLS 18Q TG2 F2/35 X50 NLS Htt exon 1 18Q Mouse 16 months Cerebellum Male Source GEO sample is GSM73194 Last updated (according to GEO): Sep 06 2005 GSE1068 660 mesenchymal stem cell 639 I_U133A_91_CB 30 0 Fetal occipital cortex cocaine1 861 Down Syndrome brain, cerebral cortex: Rat_03-04_NroLep_Lipska_e1_le1 Diet induced changes in mouse liver mRNA profiles. One of 3 replicates of C57BL/6 mice maintained for 12 weeks on a high fat Western style diet. Keywords = LDL receptor deficiency, high fat diet, atherosclerosis, liver Source GEO sample is GSM5404 Last updated (according to GEO): May 27 2005 H117 CN A GBM Treatment, type=remove Source GEO sample is GSM99448 Last updated (according to GEO): Apr 21 2006 ER negative human primary breast tumor EA02014_41280_H133A_JA-1661 in the brain 104 115 prostate Source GEO sample is GSM203308 Last updated (according to GEO): Jun 21 2007 861 Cerebellum 1000 Spleen Brain 861 MDA Mb231 6h 4 Control Liver (HBV+, HK38) Bmi-1 and Mel-18 are close structural homologues that belong to the polycomb group (PcG) of transcriptional regulators of homeotic gene expression in development. They are believed to stably maintain repression of gene expression by altering the state of chromatin at specific promoters. A number of clinical and experimental observations have also implicated Bmi-1 in tumorigenesis and stem cell maintenance. Bmi-1 overexpression or amplification has been observed in a number of human malignancies, particularly in B-cell lymphomas, medulloblastomas and breast cancer. We report here that shRNA-mediated knock-down of either Bmi-1 or Mel-18 in human medulloblastoma DAOY cells results in the inhibition of proliferation, loss of clonogenic survival and anchorage-independent growth, and suppression of xenograft tumor formation in nude mice. Furthermore, overexpression of both Bmi-1 and Mel-18 significantly increased clonogenic survival of Rat1 fibroblasts. In contrast, stable downregulation of Bmi-1 or Mel-18 alone did not affect the growth of SK-OV-3 or U2OS cancer cell lines or normal human WI38 fibroblasts. Gene expression analysis of shRNA-expressing DAOY cells has demonstrated a significant overlap in the Bmi-1- and Mel-18-regulated genes and revealed novel gene targets under their control. Taken together, these results suggest that Bmi-1 and Mel-18 might have overlapping functions in human tumorigenesis. Last Updated (by provider): May 22 2007 Contributers: Michael D Jones Dmitri Wiederschain Paul Fordjour Michael P Morrissey John D Benson TEL-AML1-C38 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Liver (HBV+, HK46) Muscular Dystrophies 901 5 0 brain D01 24h Media A HID I D083 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108601 Last updated (according to GEO): Aug 22 2006 UBOC1 Exp A Day 8 (a) MGMH030228087Bembryoday9.5 Primary Neoplasm 1000 861 Brain Spinal Cord 901 Whole blood 0 10 D_U133Plus_122_HC CNS-SpinalCmod-Adult-72h-3C-s2 4 0 Brain Roux-en-Y gastric bypass (RYGB) is the most effective therapy for morbid obesity, but it has a ~20% failure rate. We used our established RYGB model in diet-induced obese (DIO) Sprague-Dawley rats, which reproduces human bi-phasic body weight (BW) loss pattern, to determine mechanisms contributing to success (RGYB-S) or failed (RYGB-F) RYGB. DIO rats were randomized to RYGB, sham operated Obese, and sham operated obese pair fed-linked to RYGB (PF) groups. BW, caloric intake (CI) and fecal output (FO) were recorded daily for 90 days, food efficiency (FE) was calculated, and morphologic changes were determined. Gut, adipose and thyroid hormones were measured in plasma. Mitochondrial respiratory complexes in skeletal muscle, expression of energy-related hypothalamic and fat peptides, receptors and enzymes were quantified. A 25% failure rate occurred. RYGB-S, RYGB-F and PF rats vs. Obese showed rapid BW decrease, followed by sustained BW loss in RYGB-S. RYGB-F and PF gradually increased BW. Expression profiling of both CNS (hypothalamus) and peripheral tissues (subcutaneous abdominal fat) strongly supported the involvement of a number of metabolic and feeding-related genes in the differential outcomes. Last Updated (by provider): Jun 29 2007 Contributers: Chung Chen Ana Guijarro Akio Inui Susumu Suzuki Michael M Meguid Paul S Brookes Akira Niijima Henriette Kirchner Sergiy Nadtochiy Frank A Middleton Primary Carcinoma 876 1000 Cochlear structure RNA isolated from post-mortem tissues Source GEO sample is GSM6836 Last updated (according to GEO): May 28 2005 mild cognitive impairment - hippocampus 4 Spleen 0 5 Y VIS D030 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108647 Last updated (according to GEO): Aug 22 2006 H120 CN B Male 74.5 yr after antibody enrichment scan 2 (U133A) 861 Gland structure 861 Brain Wild type P24 mouse visual cortex contralateral to monocular enucleation Source GEO sample is GSM97210 Last updated (according to GEO): Feb 17 2006 Heart 1000 274 in Parkinson's disease 295 Levitiracetam hippocampus 3 Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53435 Last updated (according to GEO): Jul 06 2005 UET-13TR-EWS/FLI1 48hr tet+ Melanoma metastatic cell line A375, biological rep10 (LeiFidler) D_U133A_28_HC brain, frontal cortex: pADX AM LC b_e1_le1 20 0 human caudate nucleus AML 66 0 5 This is a wildtype littermate at postnatal day 1 pool of 5 animals Lot batch = Source GEO sample is GSM4053 Last updated (according to GEO): May 28 2005 Adult murine BM, Lin-Sca1-Kit+Itga2b+Slamf1+ 2 Primary tumor 19 32 Anterior nares 1000 brain 0 5 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3313 Last updated (according to GEO): Mar 21 2006 testis 52 58 Cerebral cortex 861 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225674 Last updated (according to GEO): Nov 02 2007 Transitional epithelium 1000 organs 28 33 17 7 hippocampus Whole brain 0 10 1319 1312 seizure Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response Gene expression data from mammary glands of involuting mice Source GEO sample is GSM202702 Last updated (according to GEO): Jun 20 2007 None Source GEO sample is GSM214202 Last updated (according to GEO): Aug 01 2007 Brain 861 447 425 to human schizophrenia 861 Pineal gland Nasal Epithelium 901 GSE3652 Brain 1000 20 0 human caudate nucleus Parkinson's disease sample x032 0 30 Samp10 Hippocampus Old Sample 1 OVCAR-3_CL6001_Ovarian on Affymetrix GeneChip Human Full Length Array HuGeneFL ChWK3 861 Gland structure 1000 Encephalitis HCC (HBV+, SF15) nucleus accumbens, whole wistar1 NA Source GEO sample is GSM198928 Last updated (according to GEO): Jun 07 2007 occipital regions 163 179 embryo_at_day2.5_rep1 0 Human Cortex 11 Gloubus Pallidum Internal 2 Disease Fat Pair-Fed Repl3 with acute measles 20 37 ISR23 24 skeletal muscle 10 861 Cerebellum Alzheimer's Disease 1000 Skeletal bone 861 Muscular Dystrophies 1000 Lymphoblastoid Cell Line for Individual 8108.5 log phase Tumor__Lung_Adeno_H_20154 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Myocardium 861 from the femurs 95 109 865 Disorder of artery Expression profiling of spinal cord section (T9) extracted from rats 28d following severe injury Source GEO sample is GSM31610 Last updated (according to GEO): May 27 2005 CNS_SNB75 on Affymetrix GeneChip Human Full Length Array HuGeneFL Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28757 Last updated (according to GEO): May 27 2005 1000 frontal lobe stomach Source GEO sample is GSM18658 Last updated (according to GEO): May 27 2005 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:204, Count:32 Corner- Avg:38726, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:6.096644,SFGene:All Background:Avg:515.16,Stdev:16.02,Max:542.9,Min:478.8 Noise:Avg:10.41,Stdev:0.39,Max:11.8,Min:9.5 RawQ:14.37 Keywords = ALL Source GEO sample is GSM3447 Last updated (according to GEO): May 27 2005 5 0 brain olfactory epithelium 194 213 Cerebellum_naive_ILS51_B GSE3551 f2#39 versus pool Mouse Brain tissue Plasma 861 30 19 Solid tumor 963 948 between adenomas 1000 Hyperthyroidism Spleen vs Prostaglandin E2 Treated B cell 240min (set3) brain, adrenal medulla: 7C_e1_le1 KPeterson-NonMet-4box2-1G110-s2 1000 Primary carcinoma of the liver cells brain, Entorhinal Cortex: Sample13_e1_le1 Exp 2 (-TNFa) 1000 Cerebellum /3T3 fibroblasts 295 310 1000 Tibialis anterior muscle structure Small Intestine; d14 small intestine Keywords = mouse gene expression database Source GEO sample is GSM29296 Last updated (according to GEO): May 27 2005 Epithelium of bronchus 983 1000 Left 67 52 descending colon 913 Coronary heart disease human cerebellum Source GEO sample is GSM87070 Last updated (according to GEO): Feb 08 2006 Lymphoma (Burkitts Daudi) [JunctionChip 5 of 5] Liver (HBV+, HK14) V5-P426 NHF10-hTERT_G0_C5_26580 10 weeks Source GEO sample is GSM147459 Last updated (according to GEO): Dec 01 2006 human cerebellum Source GEO sample is GSM87112 Last updated (according to GEO): Feb 08 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145950 Last updated (according to GEO): Nov 20 2006 none Source GEO sample is GSM210300 Last updated (according to GEO): Jul 16 2007 folatesufficientAs0ppm1 Parkinson Disease 861 Skeletal muscle structure 901 Lymphoblastic Leukemia 901 SK-OV-3 hgu95a Testis 1000 Macrophage smi43 of the stria terminalis rep1 19 46 Heart 1000 91 from the bone marrow 72 brain, amygdala: Amygdala 7_le1 NA12749 growth 1 Menstrual phase - Follicular Source GEO sample is GSM175767 Last updated (according to GEO): Apr 09 2007 Healthy patient. Source GEO sample is GSM228562 Last updated (according to GEO): Sep 11 2007 1000 Caudate nucleus structure Spleen 1000 Brain 861 Mammary Gland @ Lac2, biological rep3 organs 28 33 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withTerbutaline for 240min Source GEO sample is GSM5788 Last updated (according to GEO): May 27 2005 brain, cerebral cortex: Rat_03-63_NroLep_Lipska_e1_le1 Ovarian_Tumor_Serous_UM-OS-11 Large-scale analysis of the human transcriptome. CD34+Thy+ hematopoetic stem cells, GCSF-treated patients Source: Internal GNF, mail mcooke@gnf.org Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 94.48 Stdv: 3.30 Min: 88.09 Max: 100.63 Source GEO sample is GSM2857 Last updated (according to GEO): Mar 20 2006 NHE1 null mutation brain stem-diencephalon-2 in abdominal aortic aneurysms 219 247 osteoblast 627 637 861 Lipoproteins Cy3-labeled cDNA from brains of neonatal Cx43 null C57BL mice was compared to Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice. Keywords = Cx43 null neonatal mouse brain Source GEO sample is GSM34870 Last updated (according to GEO): Jun 19 2007 Normal__Whole_Brain_BRAIN_5 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Gene expression data from postmorten brain regions Source GEO sample is GSM145608 Last updated (according to GEO): Nov 20 2006 972 Structure of middle temporal gyrus plasma cells 332 344 Brain_Aged_LPSip_4hr_mouse1 (OL1_#67) SCG_sema3A_12h_rep2 Cerebral cortex 1000 Distinctive molecular profiles of high-grade and low-grade gliomas based on oligonucleotide microarray analysis. cortex rattus_norvegicus_strain iP animal_number 2 913 Coronary heart disease 217 192 of doublings somatic cells 1000 Infection 1000 Uterine Fibroids 25 7 Right Parietal Lobe Epithelium 861 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225696 Last updated (according to GEO): Nov 05 2007 Spleen vs CD40 Treated B cell 120min (set1) 861 Brain Gene expression in brain Homer1a-expressing cells after sleep deprivation 411_2 the blood 393 402 Communicable Diseases 861 Lung tissue from C57BL/6 mice that were always fed by 2/3 and sacrificed 4hrs after the onset of calorie-restriction in calorie-restricted mice. Lot batch = Source GEO sample is GSM4043 Last updated (according to GEO): May 28 2005 Mice sacrificed after swimming twice a day for 4 weeks. Keywords = exercise induced hypertrophy Source GEO sample is GSM2358 Last updated (according to GEO): May 27 2005 Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2674.gif Source GEO sample is GSM72171 Last updated (according to GEO): Sep 22 2006 brain 0 5 Olfactory Epithelium 1000 Keywords = kidney 113 130 Caudal 1000 neurological disease control sample x151 18 0 Extraocular muscle 1000 Cardiomyopathy, Alcoholic PMN_LB_360min_Patient15 "Sample 3,>5 yr survival(128 months) age 41 erp no" on vantveer-oligo human cerebellum Source GEO sample is GSM87081 Last updated (according to GEO): Feb 08 2006 of the atrial 647 659 Fibroblasts 861 NCI60.26_LABEL30EXTRACT29SUB3 Source GEO sample is GSM134123 Last updated (according to GEO): Aug 06 2007 137-96_Adeno Heart 1000 ovarian tumor: serous Source GEO sample is GSM139439 Last updated (according to GEO): Apr 09 2007 1000 Heart Head and neck cancer Source GEO sample is GSM155673 Last updated (according to GEO): Apr 24 2007 1000 Spinal Cord brain, hippocampus: P5 Isocaloric diet_e1_le1 Colorectal cancer patient SC11_vs_Pool Uterus Source GEO sample is GSM18800 Last updated (according to GEO): Sep 25 2006 amygdala rattus_norvegicus_strain iP animal_number 1 brain, amygdala: Amygdala 1_le1 plasma cells 332 344 2_cerebral_cortex_6hrs_sleep_deprivation_#47 umbilical cord_bpd: 3B eye 0 3 Transcriptional changes during neuronal death and replacement in the adult olfactory epithelium 361 335 hypertrophic cardiomyopathy 861 Thymus Gland 861 Cardiomyopathies NCI60.47_LABEL51EXTRACT50SUB3 Source GEO sample is GSM134232 Last updated (according to GEO): Aug 06 2007 901 Bone Marrow 129Midbrain(2)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B Malignant neoplasm of breast 1000 Pancreas at e14.5, Chip B, rep 1 Neuroglia 901 P7 cochlear nuclei pooled from 5 pups for one replicate hybridization. Source GEO sample is GSM44850 Last updated (according to GEO): Jun 08 2005 5 0 brain +_7164_batch2 on NHGRI-6.7k Osteoblasts 1000 1115 1102 cardiomyopathy Prosencephalon 861 medial motoneurons (MMN) 22 bone_marrow_1 Source GEO sample is GSM80576 Last updated (according to GEO): Mar 31 2006 Primary Neoplasm 1000 of muscular dystrophy pathogenesis. 270 305 Trauma 1000 3 0 Lung 861 Brain CNS-SpinalCmod-Adult-12h-1C-s2 C57BL/6J Amygdala E Muscle 1000 brain, Right Frontal Lobe: Extract57_le2 Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP). Source GEO sample is GSM160719 Last updated (according to GEO): Sep 24 2007 Acetaminophen 3hr Rat 2360 blood vs. Acetaminophen 3hr Rat Pooled Control blood spinal cord 13 23 67 40 with coronary artery disease PP149_unifected_Skin biopsy Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68121 Last updated (according to GEO): Jul 07 2006 T55__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A WM1205, no treatment 212 197 atherosclerosis Tolerizing allografts 7 days No.3 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with MIP3-alpha (Macrophage inflammatory protein-3) for 30min Source GEO sample is GSM5688 Last updated (according to GEO): May 27 2005 Head and neck cancer Source GEO sample is GSM155724 Last updated (according to GEO): Apr 24 2007 S5_Muscle_Insulin_30min 6 0 Cancers 861 Hippocampus PGA-Band_Sham_48h_16-m5 NOS exp1 control Ischemia-reperfusion with AEOL 10150 #12 Aortic aneurysm without mention of rupture NOS 901 PBMCs-Type 1 Diabetes-IDDM39_T1D_4MO 861 Brain Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68315 Last updated (according to GEO): Jul 07 2006 Brain 861 organs 497 503 Brain 861 total RNA from biosource CC#4S Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92483 Last updated (according to GEO): Jan 13 2006 CD34-positive fractions were used for mRNA preparation, which was hybridized to HGU 133 Plus 2.0 arrays. Last Updated (by provider): May 31 2007 Disorder of artery 865 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23729.gif Source GEO sample is GSM81560 Last updated (according to GEO): Sep 22 2006 Normal Source GEO sample is GSM175927 Last updated (according to GEO): Apr 09 2007 Cerebellum 1000 m1-carcinoma2 Diaphragm 14 day mdx rep 3 Cerebellum Source GEO sample is GSM53374 Last updated (according to GEO): Jul 06 2005 1000 Endometriosis, site unspecified Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68158 Last updated (according to GEO): Jul 07 2006 1000 Atherosclerosis UBOC1 Exp A Day 1 (b) NCI60.22_LABEL26EXTRACT25SUB3 Source GEO sample is GSM134100 Last updated (according to GEO): Aug 06 2007 1000 Left Clone 3.1 chip 3 Cerebellum_nontransgenic control S25_3 months_replicate 1 Nervous system structure 901 15 0 human cerebellum Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression.<BR> <LI><u>Brain:</u></LI><BR> GSM2558: Control<bR> GSM2559: Control <bR> GSM2560: Fungal oil (AA)<bR> GSM2561: Fungal oil (AA)<bR> GSM2562: Fish oil (DHA)<bR> GSM2563: Fish oil (DHA)<bR> GSM2564: Fish and Fungal oil (DHA + AA)<bR> <LI><u>Liver:</u></LI><bR> GSM2565: Control <bR> GSM2566: Control<bR> GSM2567: Control<bR> GSM2568: Control<bR> GSM2569: Fungal oil (AA)<bR> GSM2570: Fungal oil (AA)<bR> GSM2571: Fish oil (DHA)<bR> GSM2572: Fish oil (DHA)<bR> GSM2573: Fish + Fungal oil (DHA +AA)<bR> GSM2574: Fish + Fungal oil (DHA +AA)<bR> . Date GSE91 Last Updated: Jul 21 2005 Contributers: A Berger B German Matthew-Alan Roberts D Vilanova D M Mutch Includes GDS168. Update date: Apr 22 2003. Dataset description GDS168: Dietary effects of long chain polyunsaturated fatty acids from arachidonate-rich fungal oil and fish oil on hepatic and hippocampal gene expression. Identified broad-spectrum effects on major lipid metabolism transcription factors.. Includes GDS169. Update date: Jul 23 2003. Dataset description GDS169: Dietary effects of long chain polyunsaturated fatty acids from arachidonate-rich fungal oil and fish oil on hepatic and hippocampal gene expression. Identified broad-spectrum effects on major lipid metabolism transcription factors.. Spinal Cord 901 Wild type inbred mice Source GEO sample is GSM83007 Last updated (according to GEO): Nov 10 2005 CNS-SMTC_Mod7d-4C-s2 1000 ovarian neoplasm Epithelium 966 Postnatal day 14 callosal projection neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription. Source GEO sample is GSM37088 Last updated (according to GEO): May 27 2005 Plasma 861 Ovarian Follicle 1000 of the postmortem brains 674 698 Two 90 minute exposures (3 hr recovery in between) to 0.8% halothane every day for 5 days, for a total of 10 exposures Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5108 Last updated (according to GEO): Mar 17 2006 To investigate the gene program activated by serotonergic hallucinogens in mouse somatosensory cortex, the effects of the 5-HT2A agonist (±)2,5-dimethoxy 4-iodoamphetamine (DOI) on gene expression was studied. The 5-HT2A serotonin receptor is a member of the 5-HT2 receptor subfamily of G protein?coupled receptors. The 5-HT2A receptor is thought to modulate processes related to cognition, appetite, mood, anxiety, sleep, and sexual behavior. Abnormal function of this receptor has been implicated in neuropsychiatric disorders such as major depression and schizophrenia. In particular, the 5-HT2A receptor has been implicated in the modulation of the mechanisms related to psychosis. We compared gene response patterns in the somatosensory cortical brain area, which has a high density of 5-HT2A receptors and has been implicated in the action of hallucinogenic drugs. Mice (strain 129Sv) were injected with DOI (2 mg/kg or 10 mg/kg) or vehicle, animals were sacrificed after 1 h, and somatosensory cortex samples dissected on ice for RNA extraction. Seven independent microarray hybridizations from seven different DOI- or vehicle-treated mouse pairs were performed. In this particular hybridization, 15 µg of RNA was used. Keywords = somatosensory cortex 5-HT2A receptor DOI Source GEO sample is GSM3382 Last updated (according to GEO): Oct 28 2005 Heart 861 65 50 Small intestine Spleen vs Untreated B cell Time 0 (set7) 6,18,30 month oculomotor nucleus and spinal cord Source GEO sample is GSM74343 Last updated (according to GEO): Sep 16 2005 1BMH02022704_Thyroid skeletal Source GEO sample is GSM67247 Last updated (according to GEO): Jan 19 2006 with myocardial infarction 313 339 1000 Neuroglia Skin 1000 GSE1077 Abdominal aorta structure 1000 Anterior nares 1000 nasal epithelial cells 28 49 1000 Brain BCR-ABL-R2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A SN:1006735 Source GEO sample is GSM115359 Last updated (according to GEO): Jun 20 2006 cingulate cortex 901 healthy control sample x177 Plasma 861 Summary: We build a model for the molecular and cellular events underlying phenotypic discordance in glycine receptor defects (beta subunit). Some mice progress and die, while their littermates recover and get better, despite the same mutation on an inbred genetic background. We find evidence for glycine neurotransmitter toxicity and loss of glycinergic interneurons early in the disease, but some mice are able to keep things going until they can over-express homomeric alpha1 channels, whereupon they recover. In the mice progressing towards lethality, neurotransmitter toxicity too quickly extends to GABAergic interneurons and motorneurons, and they lose their window of time to upregulate the alpha1 glycine receptor, and they crash and burn. Importantly, human patients with glycine receptor defects typically show a resolution of their phenotype with age, and we propose that the same remodeling events are occuring in human patients. Hypothesis: Our data suggests that functional recovery of GlyRb mutant mice is likely due to expression of homomeric glycine receptors, rescue from excitotoxicity, and subsequent neuronal remodeling. We propose that human patients with hyperekplexia (mutations of glycine receptors) show remodeling similar to that of the recovering spastic mice, as human patients also show a lessening of symptoms as a function of age. Specific Aim: Murine models for human Startle Disease show clinical variability between littermates. Here, we determined the molecular remodeling of spastic GlyRb mutant spinal cord through the course of the disease, and develop a model for clinical disparity between littermates. At young ages, all animals were spastic, showed loss of glycine receptors, increased expression of vesicular glycine/GABA transporter and NMDA receptors, induction of activated caspase3, and preferential loss of glycinergic interneurons consistent with neurotransmitter toxicity model. Those littermates that recovered from symptoms showed strong over-expression of the GlyRa1 subunit, and increased myelination and synaptic plasticity. Littermates that showed a deteriorating clinical course failed to over-express GlyRa1, and also showed relative loss of gephyrin. These molecular changes were associated with preferential loss of GABAergic interneurons, and extensive motorneuron loss. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): May 29 2005 Contributers: Eric Hoffman Includes GDS967. Update date: Jan 03 2005. Dataset description GDS967: Analysis of spinal cords from glycine receptor beta subunit mutants with alleviating or severe spastic symptoms. Mutants at various ages up to 6 months examined. Results provide insight into the basis for tendency of hyperekplexia (startle disease) symptoms to alleviate with age.. total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Sphingosine-1-phosphate for 240min Source GEO sample is GSM5753 Last updated (according to GEO): May 27 2005 Metastatic tumor 19 35 in the mammalian nervous system 110 141 brain, frontal cortex: Sham PM LC b_e1_le1 the blood 393 402 Bipolar Disorder 913 in the cerebellum 1485 1501 Cerebral cortex 861 pfc_1065_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 611 593 from the six brains Gene expression data on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203960 Last updated (according to GEO): Aug 02 2007 11 4 branched PGA-HBE-NormOz0h-1aA-S2 brain 0 5 rat lungs 1876 1884 Callosal Neurons P6 2 TEL-AML1-C16 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A The nose 94 101 67 52 descending colon WGACON-72 Stem cells 901 SN:Human Glioblastoma Biopsy 06732 Amino terminated Surface 6 hours Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188783 Last updated (according to GEO): Jun 06 2007 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188859 Last updated (according to GEO): Jun 06 2007 1000 Prostate 5 0 Spleen 913 Blood Cells rat model organism with depression left untreated or treated with reserpine Source GEO sample is GSM247179 Last updated (according to GEO): Dec 11 2007 accumbens_3 Primary tumor 19 32 rat cortex Treatment, type=time_course, measurement=3.0 d Source GEO sample is GSM53210 Last updated (according to GEO): Jul 06 2005 1BJZ02053102_HBEC Expression profiling of spinal cord section (T9) extracted from rats 28d following moderate injury Source GEO sample is GSM31554 Last updated (according to GEO): May 27 2005 C57BL/6J amygdala rep1 Disease Source GEO sample is GSM176439 Last updated (according to GEO): Apr 09 2007 Low Freezing Source GEO sample is GSM92422 Last updated (according to GEO): Jan 13 2006 TUMOR 22 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A brain 0 5 Liver 0 4 Ganglia, Spinal 923 Normal__Lung_HCTN_LUN2_(18763_A2A) on Affymetrix GeneChip Human 35K SubA Array Hu35k-A human cerebellum Source GEO sample is GSM87097 Last updated (according to GEO): Feb 08 2006 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47522 Last updated (according to GEO): May 29 2005 against breast cancer 172 193 brain, unknown: 00ME_e1_le1 total RNA from biosource CC#12S Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92487 Last updated (according to GEO): Jan 13 2006 406 395 whose hearts of fibroblasts 107 120 5 0 brain B6_Control_ZT 6_2 lymph nodes 944 Morula replication 1 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68361 Last updated (according to GEO): Jul 07 2006 We build a model for the molecular and cellular events underlying phenotypic discordance in glycine receptor defects (beta subunit). Some mice progress and die, while their littermates recover and get better, despite the same mutation on an inbred genetic background. We find evidence for glycine neurotransmitter toxicity and loss of glycinergic interneurons early in the disease, but some mice are able to keep things going until they can over-express homomeric alpha1 channels, whereupon they recover. In the mice progressing towards lethality, neurotransmitter toxicity too quickly extends to GABAergic interneurons and motorneurons, and they lose their window of time to upregulate the alpha1 glycine receptor, and they crash and burn. Importantly, human patients with glycine receptor defects typically show a resolution of their phenotype with age, and we propose that the same remodeling events are occuring in human patients. Source GEO sample is GSM31007 Last updated (according to GEO): May 27 2005 19 0 Head and neck cancer Using microarray-based profiling of isogenic prostate cancer xenograft models, we found that a modest increase in androgen receptor mRNA was the only change consistently associated with the development of resistance to antiandrogen therapy. This increase in androgen receptor mRNA and protein was both necessary and sufficient to convert prostate cancer growth from a hormone-sensitive to a hormone-refractory stage, and was dependent on a functional ligand-binding domain. Androgen receptor antagonists showed agonistic activity in cells with increased androgen receptor levels; this antagonist-agonist conversion was associated with alterations in the recruitment of coactivators and corepressors to the promoters of androgen receptor target genes. Increased levels of androgen receptor confer resistance to antiandrogens by amplifying signal output from low levels of residual ligand, and by altering the normal response to antagonists. These findings provide insight toward the design of new antiandrogens. HCC (HBV+, HK11) 30 0 ventral tegmental area sprague2 GM19161 occipital regions 125 141 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD40 for 30min Source GEO sample is GSM5493 Last updated (according to GEO): May 27 2005 Macrophage smi119_2 Communicable Diseases 1000 901 Coronary artery Infection 861 IDC65 on harvard-12k In our original grant we proposed to use the NR3B-null mouse model to study the role of NR3B subunit in motor neuron function. We have now successfully generated NR3B null mice. Interestingly, NR3B-null mice invariably die at age P4-P8. Our preliminary examination indicates that the motor strength of these mice is severely impaired prior to death. As we continue to explore the cause of death in NR3B null mice, we propose to conduct gene profiling experiments to search for transcription changes in the brain related to ablation of the NR3B gene. We have previously used the UCLA array facility provided by the NINDS/NIMH Microarray Consortium to identify genes that show abnormal expression patterns in these mice using whole brain samples. Now, we would like to use the same approach to analyze pure motor neuron samples obtained by Laser Capture Microdisection (LCM). As these samples are of small size we need to use RNA amplification method. We would like to compare probes from two amplification methods to see which one gives the best result. We will collect the cDNA probe obtained by RNA-based single primer isothermal amplification developed by Nugen, Inc. and the aRNA probe obtained from T7-based RNA amplification. Both the hybridization intensity and the percentage of the present call of these two types of probe will be analyzed. The cDNA probe obtained by RNA-based single primer isothermal amplification developed by Nugen, Inc. may have some advantage over the aRNA probe obtained from T7-based RNA amplification. Two samples will be processed by either RNA-based single primer isothermal amplification developed by Nugen or T7-based RNA amplification to obtain cDNA or aRNA probes, respectively. For each sample we will use 600 motor neurons obtained by LCM. Both types of probe will be labeled by biotin and hybridize to Affymetrix GeneChip Mouse Genome 430 2.0 Array. Data analysis will be performed by array facility. Last Updated (by provider): Jun 09 2006 Contributers: Dongxian Zhang ATCC number CRL-1502 Source GEO sample is GSM6815 Last updated (according to GEO): May 27 2005 SON - 3d Dehydrated Source GEO sample is GSM69844 Last updated (according to GEO): Aug 15 2005 Macrophage smi57 3 bone 0 /3T3 fibroblasts 478 493 We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7. Source GEO sample is GSM200743 Last updated (according to GEO): Jul 12 2007 Spleen vs IL4 Treated B cell 240min (set3) 5 0 Spleen 1000 Bregma Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11542 Last updated (according to GEO): May 28 2005 brain, ipsi HC: Trizol Extraction18_le1 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16868.gif Source GEO sample is GSM91509 Last updated (according to GEO): Sep 22 2006 Wild type inbred mice Source GEO sample is GSM82946 Last updated (according to GEO): Nov 10 2005 865 Disorder of artery HMVEC-L stimulated with LPS for 24 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114563 Last updated (according to GEO): Sep 20 2006 prostate Source GEO sample is GSM203304 Last updated (according to GEO): Jun 21 2007 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215063 Last updated (according to GEO): Aug 02 2007 /J periaqueductal gray rep2 1 27 "tauopathies." 859 872 Myocardium 861 36 21 from hippocampus Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11577 Last updated (according to GEO): May 28 2005 Nasal Epithelium 901 Trigeminal ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until enough tissue was harvested to be pooled by genotype. Approximately 10-12 ganglia were pooled for a single analysis, which was extracted using the RNeasy system (Qiagen). Source GEO sample is GSM89137 Last updated (according to GEO): Dec 23 2005 Cerebral cortex 861 Spleen vs Anti-IgM Treated B cell 346 314 in the posterior pituitary gland Lymphoblastoid Cell Line for Individual 8199.5 log phase Localized Malignant Neoplasm 875 KPeterson-NonMet-4+box2-1G110-s2 f2#212 versus pool Mouse Brain tissue 5 0 brain 876 869 amygdala Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep2 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11226 Last updated (according to GEO): May 28 2005 966 Branch Whole Brain 62 72 -_6716_batch3 on NHGRI-6.7k AML61 on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211276 Last updated (according to GEO): Jul 18 2007 none Source GEO sample is GSM149553 Last updated (according to GEO): Jan 03 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145873 Last updated (according to GEO): Nov 20 2006 Trasnsformed Lymphocytes Bipolar Disorder 0 40 from progenitor satellite cells 36 66 human cerebellum Source GEO sample is GSM87151 Last updated (according to GEO): Feb 08 2006 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9963.gif Source GEO sample is GSM79803 Last updated (according to GEO): Sep 22 2006 OccipitalLobe Source GEO sample is GSM18772 Last updated (according to GEO): Sep 25 2006 NCI60.23_LABEL27EXTRACT26SUB3 Source GEO sample is GSM134106 Last updated (according to GEO): Aug 06 2007 5 0 Muscle FBooth-CON-3Av2-s2 1000 Carcinoma of bladder 861 Cerebral cortex 20 0 Mammary Gland @ Lac1 4 0 Brain human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195323 Last updated (according to GEO): Jun 04 2007 cy3:WKY control, biological rep 4g; cy5:pool of 6 WKY control rats Cerebral cortex 861 1000 Prostate 901 Epithelial Cells GSE380 5 0 Spleen 861 Ventral Tegmental Area Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 9 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10705 Last updated (according to GEO): May 28 2005 1BJZ02060505_CingulateCortex 7 0 Pancreas Coronary heart disease 913 256 235 with HIV encephalitis 861 Cardiomyopathies 901 Hepatocyte lateral motoneurons (LMN) 19 Neoplasm 861 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19244 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM175860 Last updated (according to GEO): Apr 09 2007 ileum 0 4 Prostate Source GEO sample is GSM18958 Last updated (according to GEO): Sep 25 2006 1000 Hippocampus 5 0 Spleen Muscle 1000 Neoplasm 861 IM-6_PRE Cerebral cortex 861 0 Human Cortex 11 5 0 brain Brain 861 lymphomaburkittsDaudi Source GEO sample is GSM18737 Last updated (according to GEO): Sep 25 2006 in hepatocellular carcinoma 355 382 861 medulloblastoma CS-B cell UVC-irradiated (12hour) replicate 1 U133B Femur 1000 from hippocampus 57 72 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162171 Last updated (according to GEO): Jun 12 2007 D_U133A_89_DLPFC T-ALL-C15 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Skin 152 155 prostate Source GEO sample is GSM203342 Last updated (according to GEO): Jun 21 2007 Brain 861 human cerebellum Source GEO sample is GSM87130 Last updated (according to GEO): Feb 08 2006 Brain 861 C3H/HeJ pituitary gland rep1 (430 2.0 Array) Laser Capture Microdissection (LCM) to isolate tissue sections of the hippocampus area of wild type mice brains Source GEO sample is GSM209491 Last updated (according to GEO): Jul 12 2007 gene expression data from ODC mouse skin samples Source GEO sample is GSM216672 Last updated (according to GEO): Aug 09 2007 40 21 from the hippocampus Spleen vs CD40 Treated B cell 120min (set3) 335 325 The jejunum 65 50 Snout epidermis 861 Cerebellum Trigeminal Ganglion Source GEO sample is GSM53320 Last updated (according to GEO): Jul 06 2005 Disease Source GEO sample is GSM176377 Last updated (according to GEO): Apr 09 2007 brain 0 5 DLBC53 on Affymetrix GeneChip Human Full Length Array HuGeneFL 901 Autoimmune Diseases Squamous cell carcinoma 4 0 24 GM12812 CNS-SMTC_Ctr28d-2C-s2 Liver 1000 HDMTX-22 MAS 5.0, scaled to 500; Affymetrix data Mining Tool 3.0; dChip was used to determine differentially expressed genes (MBEI); Statistical Analysis of Microarrays(SAM), as described in Miller et al. 2004. Source GEO sample is GSM108085 Last updated (according to GEO): Sep 12 2006 no additional Source GEO sample is GSM199193 Last updated (according to GEO): Jun 08 2007 CSCC1 sample 2 AD-118t1-A13-1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A placenta; females with E18 embryos Source GEO sample is GSM18683 Last updated (according to GEO): May 27 2005 of the stria terminalis rep2 16 43 1000 Brain Injuries C57BL/6J Hippocampus C A HID B D014 Cockayne syndrome B wt-rescued cell Source GEO sample is GSM226630 Last updated (according to GEO): Sep 04 2007 Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 5402 blood Cx43 KO cortical astrocytes 1 1000 Spleen 901 theca cell Female; Uterus-virgin estrus Keywords = mouse gene expression database Source GEO sample is GSM29334 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T9) extracted from rats 28d following moderate injury Source GEO sample is GSM31549 Last updated (according to GEO): May 27 2005 AD-247t1-A164-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A m1-WT5 Normal Source GEO sample is GSM176383 Last updated (according to GEO): Apr 09 2007 TK-10_CL9024_RENAL R524P00603 in the mammalian nervous system 110 141 9 0 Blood Test Five different human MPNST cell lines, mock treated or infected with G207. Source GEO sample is GSM215821 Last updated (according to GEO): Aug 07 2007 Liver 0 4 40 21 from the hippocampus AD-262t1a-A259-10 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A salivary.gland.3 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153480 Last updated (according to GEO): Jan 11 2007 129EntorhinalCortex(1a)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B Gene expression data from prostate cancer samples Parkinson's disease sample x153 0 30 GSE4097 Replicate3_Voxel A9 278 255 ischemic cardiomyopathy cortex 1017 1022 VDXKIU_15H3 processed in batch 7 Source GEO sample is GSM90429 Last updated (according to GEO): Mar 20 2006 AD-315t1-A270-10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A brain 0 5 Epithelium of bronchus 983 Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14356.gif Source GEO sample is GSM79625 Last updated (according to GEO): Sep 22 2006 human caudate nucleus Source GEO sample is GSM86837 Last updated (according to GEO): Feb 08 2006 24 0 Colorectal Adenocarcinoma C3H-HeOuJ mice exposed to ozone for 72hrs- lungs were removed-frozen in liquid nitrogen-RNA extraction. Lot batch = Source GEO sample is GSM4018 Last updated (according to GEO): May 28 2005 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. 4h after sham surgery, a 7 mm disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44528 Last updated (according to GEO): May 27 2005 Renin-Angiotensin System 923 13 0 heart sprague1 Primary tumor 19 32 HA00-13B 0 Human Cortex 11 during neurite outgrowth 28 51 353 of the pituitary gland 331 MDA Mb231 Treated 2 Treated 861 Nerve Bone Marrow 1000 Disorder of artery 865 Epithelial Cells 901 1000 Chromosomes cerebellum wistar 3889 Epithelial Cells 861 Brain 1000 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2789 Source GEO sample is GSM2105 Last updated (according to GEO): Nov 21 2005 65 61 Lungs 964 Body of uterus hypothalamus hypohydration Normal Source GEO sample is GSM176069 Last updated (according to GEO): Apr 09 2007 GSE7761 Myocardial Infarction 1000 858 Prostatic Neoplasms 129/SvImJ Amygdala A outer medulla 31 43 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM79050 Last updated (according to GEO): Oct 24 2005 861 Basal 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114398 Last updated (according to GEO): Jun 16 2006 gruvberger-estrogen 1000 frontal lobe 861 Acquired Immunodeficiency Syndrome 129S1/SvImJ_male_hypothalamus control (unstimulated) cells, biological rep2 PGA-HMO-Obese-7aUA-s2 91 from the bone marrow 72 Cerebral cortex 1000 1000 Hypothalamic structure Muscle 861 Testis 1000 Pool Ts1Cje_P0_hyb2 1000 Chronic Obstructive Airway Disease brain, cortex: norm3_e1_le1 Coronary Arteriosclerosis 1000 DLCL-0035 1000 Atherosclerosis 1000 Liver 1000 Hippocampus 990 from cancer cells 1006 HNC3003 Stem cells 901 Liver 1000 no additional Source GEO sample is GSM199312 Last updated (according to GEO): Jun 08 2007 NH 82h Zeitgeber Time Treatment, type=time_course, measurement=6.0 h Source GEO sample is GSM53326 Last updated (according to GEO): Jul 06 2005 1000 Hippocampus Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25639.gif Source GEO sample is GSM81567 Last updated (according to GEO): Sep 22 2006 1000 Endometriosis, site unspecified Wild type 8 wk old male C3H/HeJ mouse bed nucleus of the stria terminalis Source GEO sample is GSM106999 Last updated (according to GEO): Mar 05 2007 AK_SleepDep_ZT 12_2 166 156 of retinal 861 Cerebral cortex Brain_Wild-type_MiceNoB4394 861 Kidney Cerebral cortex 1000 861 Encephalitis Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225660 Last updated (according to GEO): Aug 31 2007 with myocardial infarction 313 339 brain, brainstem: CB6_e1_le1 Skeletal bone 861 Large-scale analysis of the mouse transcriptome. Spinal cord, upper half C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 237.26 Stdv: 6.00 Min: 227.49 Max: 250.70 Source GEO sample is GSM2920 Last updated (according to GEO): Mar 20 2006 M_U133A_86_DLPFC Prostate 861 in the brain 150 162 in brain 66 73 mouse hippocampus 0 16 0 Human Cortex 11 Human Cell Line, adrenal medulla: RNA616_le1 from mouse colon 21 36 14 0 G1 Ciliary body Plasma 861 large cell lung carcinoma 2985 Source GEO sample is GSM17352 Last updated (according to GEO): May 28 2005 Infected 6 weeks prior with Htt-N171-19Q-expressing recombinant lentivirus Source GEO sample is GSM34376 Last updated (according to GEO): Oct 16 2006 Expression profiling of spinal cord section (T9) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM6661 Last updated (according to GEO): May 28 2005 NA19003 Adenoma 0 6 Female mice used were SvJ/129, 10-16 weeks of age, with both copies of the Hoxa-10 gene (GenBank # NM_008263) present (wildtype). These mice were littermates of Hoxa-10-/- mice used in parallel experiments. 14 days after ovariectomy, mice were injected subcutaneously with progesterone dissolved in sesame oil (Sigma; 0.2mg/0.1mL/mouse), followed by sacrifice and removal of uterine horns at 6 hours after injection. 8 uterine horns from 4 mice were pooled to form one sample. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix. Source GEO sample is GSM3041 Last updated (according to GEO): May 27 2005 Parkinson Disease 1000 17 6 (hippocampus Expression profiling of spinal cord section (T9) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM6663 Last updated (according to GEO): May 28 2005 Leukemia, Lymphocytic, Chronic 1000 AD-374t1-A114-3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A heart 1169 1173 none Source GEO sample is GSM244571 Last updated (according to GEO): Nov 23 2007 pituitary_gland_4 Source GEO sample is GSM80819 Last updated (according to GEO): Mar 31 2006 5 0 Muscle total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Leukotriene B4 (LTB4) for 120min Source GEO sample is GSM5679 Last updated (according to GEO): May 27 2005 Dahl Salt Sensitive Rat Lung- Hypoxia alone rep4 Wild type voxel H4 with Alzheimer's disease 27 50 /cByJ Cerebellum A 4 21 Large-scale analysis of the mouse transcriptome. Hypothalamus C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 329.47 Stdv: 7.51 Min: 319.02 Max: 343.31 Source GEO sample is GSM2915 Last updated (according to GEO): Mar 17 2006 Pool of 9 saccules at E13.5 Source GEO sample is GSM182614 Last updated (according to GEO): Aug 14 2007 Olfactory Epithelium 1000 Nose 1000 in the mammalian nervous system 110 141 1000 Cerebral cortex 861 Blood H9LMS00111502 Lung 861 Pool of 11 cochlear tissues at E12 Source GEO sample is GSM182576 Last updated (according to GEO): Aug 14 2007 Cockayne syndrome B wt-rescued cell Source GEO sample is GSM226619 Last updated (according to GEO): Sep 04 2007 /3T3 fibroblasts 478 493 861 Epidermis nostrils 156 164 processed in batch 3 Source GEO sample is GSM90444 Last updated (according to GEO): Mar 20 2006 Abdominal aorta structure 865 Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep1 Anterior 861 Bipolar Disorder 913 GBM Treatment, type=remove Source GEO sample is GSM99585 Last updated (according to GEO): Apr 21 2006 Heart 1000 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16190.gif Source GEO sample is GSM84165 Last updated (according to GEO): Sep 22 2006 Liver 1000 Liver 861 1000 Hippocampus Male 68.4 yr before antibody enrichment scan 1 (U133B) 38 year old female Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28706 Last updated (according to GEO): May 27 2005 NA18621 Malignant Glioma 1000 861 Cerebellum mouse cerebral cortex 0 20 brain_DLPFC_bipolar B_mr520 Spleen vs BLC Treated B cell 30min (set3) Ta gr2 tumour Source GEO sample is GSM2492 Last updated (according to GEO): May 27 2005 Spinal Cord 901 Primary tumor 19 32 219 197 in the small intestine Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188788 Last updated (according to GEO): Jun 06 2007 brain 0 5 left hemi-diaphragm 27 45 22-oct-2002-liverD-Mu11KsubBsc 7 cortex 12 Diversity of gene expression in adenocarcinoma of the lung. 858 Prostatic Neoplasms of AML 926 931 Hippocampus 861 861 Cerebral cortex This is the sixth replicate for the VTA neurons which were captured using LCM. Source GEO sample is GSM19339 Last updated (according to GEO): May 27 2005 of epithelial ovarian cancer 124 152 human cerebellum Source GEO sample is GSM87141 Last updated (according to GEO): Feb 08 2006 M_U133A_29_AnCg 1201 of epithelial cells 1219 Brain 861 Spleen vs Interferon-gamma (IFN gamma) Treated B cell 60min (set2) human melanoma metastatic cell line A375 Source GEO sample is GSM155035 Last updated (according to GEO): Jun 04 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145678 Last updated (according to GEO): Nov 20 2006 1000 Atherosclerosis Hippocampus 1000 432_1 HC73 FC BA4 A This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12346 Last updated (according to GEO): May 28 2005 prostate Source GEO sample is GSM203376 Last updated (according to GEO): Jun 21 2007 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114254 Last updated (according to GEO): Jun 16 2006 Brain 1000 R496P00521 during neurite outgrowth 98 121 Normal Source GEO sample is GSM175814 Last updated (according to GEO): Apr 09 2007 17 7 hippocampus no additional Source GEO sample is GSM199325 Last updated (according to GEO): Jun 08 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145524 Last updated (according to GEO): Nov 20 2006 5 0 brain skeletal Source GEO sample is GSM67250 Last updated (according to GEO): Jan 19 2006 in the trisomic cerebellum 1096 1122 Heart 861 861 Hippocampus Fibroblasts 861 7 frontal cortex 20 8 uterine horns 411 425 1000 Left 14 0 Locus Coeruleus NA18572 Kidney 1000 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155049 Last updated (according to GEO): Jun 04 2007 Acetaminophen 6hr Rat 4550 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool 1000 Substantia nigra structure The nose 94 101 V5-P154 Spleen vs BLC Treated B cell 60min (set2) mouse brain contralateral RU486 Source GEO sample is GSM149760 Last updated (according to GEO): Mar 15 2007 Treated Source GEO sample is GSM176469 Last updated (according to GEO): Apr 09 2007 Brain 1000 hippocampal glutamatergic CA3 pyramidal neurons Source GEO sample is GSM35804 Last updated (according to GEO): May 27 2005 MAS 5.0, scaled to 500; Affymetrix data Mining Tool 3.0; dChip was used to determine differentially expressed genes (MBEI); Statistical Analysis of Microarrays(SAM), as described in Miller et al. 2004. Source GEO sample is GSM108091 Last updated (according to GEO): Sep 12 2006 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28702 Last updated (according to GEO): May 27 2005 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47533 Last updated (according to GEO): May 29 2005 human caudate nucleus Source GEO sample is GSM86884 Last updated (according to GEO): Feb 08 2006 GBM Treatment, type=remove Source GEO sample is GSM99598 Last updated (according to GEO): Apr 21 2006 5 0 Spleen brain, cerebellum: Stg+/+_Crb2_e1_le1 Normal Source GEO sample is GSM176041 Last updated (according to GEO): Apr 09 2007 brain, Left frontal Lobe: Extract34_le1 G30-CingulateCortex replicate1 139-96_LCLC Cerebellum Alzheimer's disease 10 osteoblast 627 637 7 cerebral cortex 21 P7 cochlear nuclei pooled from 5 pups for one replicate hybridization. Source GEO sample is GSM44851 Last updated (according to GEO): Jun 08 2005 NA18622 pfc_1055_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 1000 Cerebral cortex AT2-hTERT_1.5Gy_6h_C5_26746 The prefrontal cortex was dissected from each individual C57Bl/6J mouse. Targets from three biological replicates at each of ZT 3, 9, 15, and 21 were generated and the expression profiles were determined using Affymetrix MOE430_v2 arrays. Comparisons among the sample groups allow the identification of genes under the control of circadian system, homeostatic sleep mechanism, or genes induced or suppressed by environmental responses. We identified 3,944 transcripts corresponding to 2,966 genes, with oscillating expression levels. Genes with cycling expression during the day:night cycle include several known core clock genes. We also show that 14% of genes identified in our study were previously identified as clock controlled or sleep/wakefulness induced genes in the mouse liver and SCN, rat cortex and cerebellum, or Drosophila head. Cycling genes in the mouse prefrontal cortex fall into eight temporal categories with distinct functional attributes, as assessed by the Gene Ontology classification and by the analysis of enriched transcription factor binding sites. Our analysis demonstrates that about 10% of transcripts have oscillating expression patterns in the mouse prefrontal cortex. Functional annotation of these genes with respect to oscillatory expression will be important for the selection of candidate genes for behavioral mutants in the mouse and for genetic studies of disorders associated with anomalies in the sleep:wake cycle. Last Updated (by provider): Feb 05 2007 Contributers: Maja Bucan Sridhar Hannenhalli Shuzhang Yang Otto Valladares Kai Wang 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114456 Last updated (according to GEO): Jun 16 2006 966 Hippocampus Expression profiling of spinal cord section (T10) extracted from rats 7d following mild injury Source GEO sample is GSM31340 Last updated (according to GEO): May 27 2005 Exp C_2, control (0mg/kg) CPF human cerebellum Source GEO sample is GSM87074 Last updated (according to GEO): Feb 08 2006 861 Occipital lobe mouse brain contralateral LPS.RU486 Source GEO sample is GSM149763 Last updated (according to GEO): Mar 15 2007 Gene expression data from the hippocampus of wild-type mouse Source GEO sample is GSM172952 Last updated (according to GEO): Mar 08 2007 Gene expression data from a placenta with chronic malaria Source GEO sample is GSM183619 Last updated (according to GEO): Apr 23 2007 50 43 jejunum Whole Brain 73 83 plasma cells 332 344 Laser capture lung cancer cells Source GEO sample is GSM191059 Last updated (according to GEO): May 25 2007 12 frontal Lobe 23 putamen_3 Source GEO sample is GSM80581 Last updated (according to GEO): Mar 31 2006 Ta gr2 tumour Source GEO sample is GSM2494 Last updated (according to GEO): Mar 21 2006 M_U133A_68_HC We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201792 Last updated (according to GEO): Jun 20 2007 15 0 human cerebellum Nervous system structure 901 HapMap CEU_parent Female Source GEO sample is GSM159514 Last updated (according to GEO): Feb 01 2007 GSE1830 Melanoma metastatic cell line A375, biological rep10 (LeiATCC) of the prefrontal cortex 21 44 Mature B cells 3b brain, cerebellum: RNA#2_le1 1786 HP24_23 Muscle Source GEO sample is GSM4265 Last updated (according to GEO): May 27 2005 prostate Source GEO sample is GSM203344 Last updated (according to GEO): Jun 21 2007 Dark rearing, biological rep3 CNS-SC_InjA4h-2C-s2 Gene expression data from brain of adult rats Source GEO sample is GSM101015 Last updated (according to GEO): Feb 20 2007 Expression profiling of spinal cord section (T10) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM4454 Last updated (according to GEO): May 28 2005 Prosencephalon 861 Hippocamus and amygdala expression was examined in naïve, conditioned stimulus exposed, and fear conditioned mice 30 minutes after behavioral manipulation Last Updated (by provider): Mar 24 2006 Contributers: Ted Abel Includes GDS1903. Update date: Jun 09 2006. Dataset description GDS1903: Comparison of amygdalae and hippocampi of animals subjected to classical fear conditioning (CFC), which consists of a 3-minute exposure to the conditioning chamber, a 30-second exposure to tone, and a 2-second, 1.5-mA footshock. CFC induced greater gene expression changes in the amygdala.. 4 0 Blood HapMap JPT Female Source GEO sample is GSM159648 Last updated (according to GEO): Feb 01 2007 Schizophrenia 1000 Lymphoblastoid Cell Line for Individual 8203.4 log phase Job's patient Source GEO sample is GSM211081 Last updated (according to GEO): Sep 10 2007 Normal Source GEO sample is GSM176415 Last updated (according to GEO): Apr 09 2007 15 0 skeletal muscle We performed the GeneChip analysis to identify multiple extracellular determinants such as cytokines, cell membrane-bound molecules, and matrix responsible for cardiomyogenic differentiation, and evaluated the statistical significance of differential gene expression by the NIA array analysis (http://lgsun.grc.nia.nih.gov/ANOVA/) (Bioinformatics 21: 2548), a web-based tool for microarrays data analysis. Last Updated (by provider): Jul 24 2007 Contributers: A Umezawa Y Takahashi H Makino K Matsumoto I Komuro R Ishii D Kami H Saito I Shiojima M Watanabe Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132524 Last updated (according to GEO): Feb 26 2007 Entorhinal Cortex 7 23 1000 Diabetes Mellitus WGACON-35 1634 1609 Creutzfeldt-Jacobs disease 861 Blood Baseline comparison of global gene expression in ILS and ISS cerebellum to find differences in the naive state. Source GEO sample is GSM69657 Last updated (according to GEO): Oct 28 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68251 Last updated (according to GEO): Jul 07 2006 accumbens_5 PGA_IGF1R_1055 1000 Coronary Arteriosclerosis Ovary 1000 901 frontal lobe Skeletal bone 861 AA Treatment, type=remove Source GEO sample is GSM99504 Last updated (according to GEO): Apr 21 2006 PAX sample 6 5 0 brain cerebral_cortex_8 Source GEO sample is GSM80641 Last updated (according to GEO): Mar 31 2006 EKVX__CL1008_NSCLC We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201809 Last updated (according to GEO): Jun 20 2007 1000 frontal lobe Parkinson Disease 861 human frontal cortex Source GEO sample is GSM86956 Last updated (according to GEO): Feb 08 2006 brain damage 306 317 HMEC 184 day 5 sample 1 1000 Hippocampus 1000 Brain Rat SCN Sample 14 (Technical replicate - 30 hr) 858 Mesodermal cell 913 Coronary heart disease Acetaminophen 6hr Rat 9754 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool Gene expression data from postmorten brain regions Source GEO sample is GSM145306 Last updated (according to GEO): Nov 20 2006 FVB/NJ hypothalamus rep1 (430 2.0 Array) brain, cerebral cortex: 14990_e2_le1 Central gray substance of midbrain 861 861 Cancer of Neck hippocampus rattus_norvegicus_strain iNP animal_number 9 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15400.gif Source GEO sample is GSM84188 Last updated (according to GEO): Sep 22 2006 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210396 Last updated (according to GEO): Jul 16 2007 DLCL-0005 52 37 without malaria R6/1 wildtype, brain hemisphere Source GEO sample is GSM83866 Last updated (according to GEO): Apr 20 2007 2_hypothalamus_9hrs_sleep_#92 how obesity 275 285 901 Nervous system structure Infertility 861 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11558 Last updated (according to GEO): May 28 2005 Trauma 1000 861 Liver S10_Muscle_Baseline_0min Lung (fetal) [JunctionChip 1 of 5] 151 110 of non-insulin-dependent diabetes mellitus 1BJZ02051614_ParietalLobe Heart Septal Defects 884 /SvEvTac mouse cingulate cortex 29 59 Normal Source GEO sample is GSM176418 Last updated (according to GEO): Apr 09 2007 213 205 of cancer 1000 Cerebrum Wild type 8 wk old male C3H/HeJ mouse cingulate cortex Source GEO sample is GSM74949 Last updated (according to GEO): Feb 27 2007 H9RGV00110703 The transmission of information about the photic environment to the circadian clock involves a complex array of neurotransmitters, receptors, and second messenger systems. Using laser capture microscopy and microarray analysis, a population of genes rapidly induced by light in the suprachiasmatic nucleus is identified. Last Updated (by provider): Oct 31 2007 Contributers: Veronica M Porterfield Eric M Mintz Amygdala Source GEO sample is GSM107958 Last updated (according to GEO): Jun 06 2006 in the hearts 120 132 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11532 Last updated (according to GEO): May 28 2005 Laser capture lung cancer cells Source GEO sample is GSM191010 Last updated (according to GEO): May 25 2007 Disease Source GEO sample is GSM175995 Last updated (according to GEO): Apr 09 2007 14 NT C4 Treatment, type=add, description=10ng/mL Ciliary neurotrophiic factor, 4d Source GEO sample is GSM92496 Last updated (according to GEO): Jan 13 2006 1000 Prostate mouse brain 478 489 Lymphoblastoid Cell Line for Individual 8207.3 log phase Mesenchymal Stem Cells 1000 Primary tumor 19 32 1000 Synovial Membrane amygdala 25 33 CT50-1 1018 1005 into the brain brain, cerebral cortex: NMDA1H 6/24_le1 1000 Brain ERMS-T-TEST-10 on NHGRI-6.5k_b Plasma 861 SiHa sample 2 Lymphoma (Burkitts Raji) [JunctionChip 1 of 5] 352 347 brain total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5821 Last updated (according to GEO): May 27 2005 comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247396 Last updated (according to GEO): Dec 11 2007 Chronic Lymphocytic Leukemia 19 47 AT3-hTERT_1.5Gy_2h_C3_27044 The nose 94 101 1000 Cerebral cortex 1000 jejunum 1000 Prostate in multiple myeloma 87 106 662 by motor cortex 677 Posterior root of spinal nerve 861 1000 Structure of parenchyma of lung 0 Human Cortex 11 Neoplasm 861 Balb/c day 1, biological rep 3, tech rep 2 861 Blood on dendrites 282 293 Spleen 1000 Wild type 8 wk old male C3H/HeJ mouse cingulate cortex Source GEO sample is GSM74948 Last updated (according to GEO): Feb 27 2007 CNS-SpinalC-conAdult-28d-2A-s2 129Cortex(2)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B 5 0 brain leukemia 1000 normal 1473 Balb/c day 1, biological rep 4, tech rep 2 2nd 6hr C+S-CA1 human frontal cortex Source GEO sample is GSM86952 Last updated (according to GEO): Feb 08 2006 Secondary malignant neoplasm of lymph node 1000 1000 Rectum 1000 Brain Lung 1000 43h-CHX replication 3 Keywords = preimplantation Keywords = development Source GEO sample is GSM14729 Last updated (according to GEO): May 28 2005 BACKGROUND: The causes and clinical course of acute rejection vary, and it is not possible to predict graft outcome reliably on the basis of available clinical, pathological, and genetic markers. We hypothesized that previously unrecognized molecular heterogeneity might underlie some of the variability in the clinical course of acute renal allograft rejection and in its response to treatment. METHODS: We used DNA microarrays in a systematic study of gene-expression patterns in biopsy samples from normal and dysfunctional renal allografts. A combination of exploratory and supervised bioinformatic methods was used to analyze these profiles. RESULTS: We found consistent differences among the gene-expression patterns associated with acute rejection, nephrotoxic effects of drugs, chronic allograft nephropathy, and normal kidneys. The gene-expression patterns associated with acute rejection suggested at least three possible distinct subtypes of acute rejection that, although indistinguishable by light microscopy, were marked by differences in immune activation and cellular proliferation. Since the gene-expression patterns pointed to substantial variation in the composition of immune infiltrates, we used immunohistochemical staining to define these subtypes further. This analysis revealed a striking association between dense CD20+ B-cell infiltrates and both clinical glucocorticoid resistance (P=0.01) and graft loss (P<0.001). CONCLUSIONS: Systematic analysis of gene-expression patterns provides a window on the biology and pathogenesis of renal allograft rejection. Biopsy samples from patients with acute rejection that are indistinguishable on conventional histologic analysis reveal extensive differences in gene expression, which are associated with differences in immunologic and cellular features and clinical course. The presence of dense clusters of B cells in a biopsy sample was strongly associated with severe graft rejection, suggesting a pivotal role of infiltrating B cells in acute rejection. NINDS Rat Neuron Parkinsons 15 0 human cerebellum 861 Heart failure Epithelium 861 Kidney (fetal) [JunctionChip 5 of 5] Gene expression data Source GEO sample is GSM230358 Last updated (according to GEO): Sep 19 2007 Normal Source GEO sample is GSM176363 Last updated (according to GEO): Apr 09 2007 to the nose 599 609 E-Cadherin 1000 no additional Source GEO sample is GSM199254 Last updated (according to GEO): Jun 08 2007 ER-/LN-/Marks220 on Affymetrix GeneChip Human Full Length Array HuGeneFL 277 271 Retinas 901 Bone Marrow 15 0 human cerebellum 3AJZ02081480b_Pons none Source GEO sample is GSM123228 Last updated (according to GEO): Jul 26 2006 testis Source GEO sample is GSM18705 Last updated (according to GEO): May 27 2005 days nasal epithelium 1126 1147 1000 Communicable Diseases Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181175 Last updated (according to GEO): Jul 12 2007 92 38 of nicotinic acetylcholine receptor subunit mutant mice Epithelium 861 brain, unknown: R1C_e1_le1 Spleen 0 5 n/a Source GEO sample is GSM178082 Last updated (according to GEO): Jun 11 2007 1606 1588 in small intestine 9 0 Blood Test H9LMS99081103 ovarian tumor: endometrioid Source GEO sample is GSM139399 Last updated (according to GEO): Apr 09 2007 YFPH-Amygdala-replicate3 861 Cardiomyopathies Supranuclear Palsy, Progressive 1000 Normal human tissue:Normal Brain Keywords = Human, Normal Tissue, Normal Brain Source GEO sample is GSM44690 Last updated (according to GEO): May 27 2005 Normal Source GEO sample is GSM175872 Last updated (according to GEO): Apr 09 2007 osteoblast 627 637 Brain 861 Olfactory Epithelium 1000 0029_1244_H95A2_KF0153_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A PGA-HMO-Obese-6aUA-s2 Gene expression data from postmorten brain regions Source GEO sample is GSM145368 Last updated (according to GEO): Nov 20 2006 1000 Descending colon Gene expression data from B6xBALB F2 mouse lung Source GEO sample is GSM133478 Last updated (according to GEO): Apr 05 2007 61 41 from postmortem brain Compare the transcriptomes of Cx43 null and Cx43 siRNA treated cortical astrocytes with the transcriptome of the wildtype cortical astrocytes Source GEO sample is GSM200839 Last updated (according to GEO): Jun 19 2007 PGA_MI_ilv_24h_361 Lung tissue from C57BL/6 mice that were always fed by 2/3 and sacrificed 2hrs after the onset of calorie-restriction in calorie-restricted mice. Lot batch = Source GEO sample is GSM4041 Last updated (according to GEO): May 28 2005 PMN_control_360min_Patient14 861 Colon Tumor__Colorectal_Adeno_0001c040_CC on Affymetrix GeneChip Human 35K SubA Array Hu35k-A human cerebellum Source GEO sample is GSM87180 Last updated (according to GEO): Feb 08 2006 Leukemia, Lymphocytic, Chronic 1000 HDMTX-DX-20 865 Disorder of artery Gene expression data from postmorten brain regions Source GEO sample is GSM145222 Last updated (according to GEO): Nov 20 2006 SCN2.2 Sample 4 (Exp#1-12 hr a) 191 181 of ischemia Expression profiling of spinal cord section (T9) extracted from rats 48h following moderate injury Source GEO sample is GSM31561 Last updated (according to GEO): May 27 2005 RMS-T2 on NHGRI-6.5k_b 1000 Brain 80 year old male Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD2 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD2 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36703 Last updated (according to GEO): May 27 2005 OCI Ly1 BALB-RAG_PBS Replicate 4 767 751 in ischemic brain 1000 frontal lobe Neoplasm 861 Substantia nigra structure 1000 from colonic normal mucosa 21 47 MGMH030311036Athymus Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181235 Last updated (according to GEO): Jul 12 2007 988 980 cerebella Gene expression data from retinas of two young SAMR1TA mice Source GEO sample is GSM143745 Last updated (according to GEO): Jan 24 2007 966 Hippocampus plasma cells 332 344 H131 FC BA4 B 601 593 in muscle 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114269 Last updated (according to GEO): Jun 16 2006 gene expression data from ODC mouse skin samples Source GEO sample is GSM216669 Last updated (according to GEO): Aug 09 2007 hippocampal glutamatergic CA1 pyramidal neurons Source GEO sample is GSM35815 Last updated (according to GEO): May 27 2005 brain 0 5 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28455 Last updated (according to GEO): May 27 2005 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19226 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM146043 Last updated (according to GEO): Nov 20 2006 with myocardial infarction 313 339 861 Neoplasm 94 61 after human immunodeficiency virus Heart Septal Defects, Atrial 1000 Normal Adrenal Gland (AN11) Structure of parenchyma of lung 901 8 0 G7 cornea 17 7 hippocampus 278 255 ischemic cardiomyopathy Breast Diseases 913 Y HID D002 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108630 Last updated (according to GEO): Aug 22 2006 CLL-70;Lymph node B_AK_SleepDep_ZT 6_1 1000 Cerebral cortex no additional Source GEO sample is GSM199089 Last updated (according to GEO): Jun 08 2007 861 Neoplasm 5 0 brain Heart 1000 Nasal Epithelium 865 1000 frontal lobe cerebellum 7 16 pituitary Source GEO sample is GSM18613 Last updated (according to GEO): May 27 2005 WT-Nrf2-Male-2 of parieto-occipital cortex 118 144 Disease Source GEO sample is GSM176316 Last updated (according to GEO): Apr 09 2007 Richard Almon-35-1138200270524 Neostriatum 1000 atrioventricular_node Source GEO sample is GSM19008 Last updated (according to GEO): Sep 25 2006 Effects of SOCS3 on transcriptional response of macrophages to IL-6. Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Replicate 1 after stimulation for 100 minutes with 10 ng/ml IL-6. Source GEO sample is GSM6076 Last updated (according to GEO): May 27 2005 Fibroblasts 861 Structure of vastus lateralis muscle 1000 Blood 861 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211403 Last updated (according to GEO): Jul 18 2007 folatedeficientAs10ppm1 Treated Source GEO sample is GSM175963 Last updated (according to GEO): Apr 09 2007 Primary large cell carcinoma 745 0 31 1000 Hypothalamic structure Balb/c day 3, biological rep 2, tech rep 1 203 193 of retinal A3 from brain 21 30 Ganglia 861 24 7 Right Frontal Lobe 861 Cardiomyopathies 10 7 Left Spleen vs Interferon-beta (IFN beta) Treated B cell 120min (set3) f2#13 versus pool Mouse Brain tissue 1000 medulloblastoma metanephric mesenchyme, ANX, 4 days, biological rep1 913 Coronary heart disease Primary carcinoma of the liver cells 1000 Prosencephalon 1000 Spleen vs Untreated B cell Time 0 (set26) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. brain, cerebral cortex: PC20_e1_le1 861 Cardiomyopathies rat_hepatocytes_control_pooled 1000 Myosin ATPase 17 0 Malignant melanoma bronchial epithelia 224 243 B2-1 on NCI-7.6k 14 7 amygdala Brain 861 1000 Brain Animals were sacrificed and organs were rapidly frozen in liquid nitrogen, and subsequently stored at <ETH>80oC. Tissues were mechanically homogenized with a polytron and total cellular RNA was extracted using a commercially available reagent (TMTRIzol; Invitrogen). The poly-(A)+ fraction of the RNA was isolated by chromatography with oligo d(T) cellulose beads. For cDNA labeling, either 25 mg of total RNA or 2.5 mg of poly-(A) RNA was converted into cDNA using reverse transcriptase (RT; Super Script II, Invitrogen) and alternatively Cy5 or Cy3-labeled dCTP (1mM, Perkin Elmer-Cetus/NEN, Boston) in a reaction mixture containing 1.5 mL oligo (dT) (100pmol/ mL), 3 mL dNTP-dCTP (6.67mM each), 1 mL dCTP (2mM), 4 mL DTT (100mM), 8 mL 5 X RT Buffer (Invitrogen, California). The reactions were carried out at 42¼C for 3 hrs, after which the RNA was degraded by the addition of 0.5 mL RNase A (1 mg/mL) and 1.5 mL RNaseH 5 units/mL). Labeled cDNA was separated from unincorporated nucleotides (Qiagen column) and further concentrated by evaporation under vacuum. The arrays were pre-hybridized for 1-2hrs with DIGEasy hybridization buffer (Roche) containing 10ug/ml denatured salmon sperm DNA, and 10ug/ml yeast tRNA. The Cy5 and Cy3 labelled cDNAs were combined and hybridized in the same medium and incubated with the arrays for 16-18hrs at 37Co. Finally, the arrays were washed 3 x 10 mins in 0.1 x SSC (20 X SSC is 3M sodium chloride, 0.3 M sodium citrate, pH 7.0), 0.1%SDS at 50Co, and 4 x 3min in 0.1 x SSC at room temperature, and dried by centrifugation. Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray fluorescent scanner and image intensity data were extracted and analyzed with QuantArray 3.0 analysis software. Quantification data was imported in GeneSpring (Silicon Genetics). The import format was modified to maintain information relevant to user-contributed flagging as well as QC parameter furnished by the array manufacturer. Dye swap and Intensity-based normalization (Lowess) were performed using the default settings. Keywords = spleen Keywords = malaria Source GEO sample is GSM11001 Last updated (according to GEO): Oct 28 2005 VDXRHU_1472 1000 Encephalitis Prediction and Testing of Novel Networks Regulating Embryonic Stem Cell Self-Renewal and Commitment 57 39 with endometriosis 4535 4527 hepatoma A39 NES 142Q TG6 F1/4 A39 NES Htt exon 1 142Q Mouse 10.5 months Cerebellum Female Source GEO sample is GSM73188 Last updated (according to GEO): Sep 06 2005 amygdala 24 32 Normal Source GEO sample is GSM176162 Last updated (according to GEO): Apr 09 2007 Gene expression data from dorsal pancreas at e12.5, MG-U74B version2 Source GEO sample is GSM199454 Last updated (according to GEO): Jun 08 2007 of the small intestine 97 118 1000 Spleen Acetaminophen 6hr Rat 9934 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28760 Last updated (according to GEO): May 27 2005 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210392 Last updated (according to GEO): Jul 16 2007 Cerebral cortex 1000 Communicable Diseases 861 Mouse ileum with L.monocytogenes(delta-inlA)_B_5546 7 frontal cortex 20 olfactory epithelium 194 213 HC80 CB A Cerebellum 1000 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169485 Last updated (according to GEO): Feb 21 2007 Endometrium 1000 brain 0 5 GSE5808 NCI-H322 hgu95a 5 0 brain 15 7 hindbrain R484P00306 Voxel I2 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1448 Last updated (according to GEO): Nov 21 2005 Y SIT D070 1000 Spinal Cord Liver Test (Blinded) Sample Source GEO sample is GSM130177 Last updated (according to GEO): Sep 18 2007 ER+/LN+/Nevins6 on Affymetrix GeneChip Human Full Length Array HuGeneFL 865 Ovarian Diseases 861 Cerebral cortex 12 frontal Lobe 23 7 0 prostate 865 Disorder of artery CNS-SC_CtrB7d-2C-s2 901 Coronary artery for liver 26 35 Laser Capture Microdissection (LCM) to isolate tissue sections of the hippocampus area of Rasgrf1 knockout mice brains Source GEO sample is GSM209507 Last updated (according to GEO): Jul 12 2007 Immunoglobulins 861 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:265, Count:32 Corner- Avg:37187, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:7.325640,SFGene:All Background:Avg:391.32,Stdev:10.27,Max:422.7,Min:375.6 Noise:Avg:8.95,Stdev:0.47,Max:10.4,Min:7.8 RawQ:12.57 Keywords = ALL Source GEO sample is GSM3417 Last updated (according to GEO): May 27 2005 1000 Descending colon NH 67h GSE6536 Whole Brain 73 83 Ptdsr-/- fibroblast_rep2 T2+ gr3 tumour Source GEO sample is GSM2509 Last updated (according to GEO): Mar 21 2006 05_0007_SepticShock_Day3_2 neurological disease control sample x087 Normal Source GEO sample is GSM175907 Last updated (according to GEO): Apr 09 2007 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with BLC labeled with Cy5- time course with repeats. Date GSE373 Last Updated: May 29 2005 Contributers: Sangdun Choi Mi Sook Chang Jong-Woo Kim Yun Anna Cao Zhen Yan Sun Young Lee Robert Hsueh Joella Grossoehme Angela Alexander Rebecca Hart Includes GDS294. Update date: Nov 18 2003. Dataset description GDS294: Temporal analysis of effects induced by 0.2 uM B-lymphocyte chemoattractant in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. Brain 861 B240 monocytes treated with isotype control antibody for 24 hrs GSE7586 34 16 of stria vascularis hypothalamus_2 Embryo_E11.5_Foxo3 Wt_Female parietal_lobe_4 Source GEO sample is GSM80747 Last updated (according to GEO): Mar 31 2006 no additional Source GEO sample is GSM199277 Last updated (according to GEO): Jun 08 2007 GC (HKG66T) Communicable Diseases 1000 brain 0 5 91 from the bone marrow 72 129:24-3 cerebellum 2093 2071 in the embryonic brain Gene expression data from postmorten brain regions Source GEO sample is GSM145702 Last updated (according to GEO): Nov 20 2006 GBM: 5A4 Spleen vs Untreated B cell Time 0 (set10) WGACON-109 NA Source GEO sample is GSM198938 Last updated (according to GEO): Jun 07 2007 human caudate nucleus Source GEO sample is GSM86869 Last updated (according to GEO): Feb 08 2006 1000 Benign prostatic hypertrophy Healthy patient. Source GEO sample is GSM228663 Last updated (according to GEO): Sep 11 2007 of somatomotor cortex 21 41 H111 CB B 1000 Spleen RST-PVH_1 Epithelium 861 Heart 861 1000 Colon Disorder of artery 865 1000 Myositis none Source GEO sample is GSM210341 Last updated (according to GEO): Jul 16 2007 11 Bone marrow 0 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225714 Last updated (according to GEO): Nov 05 2007 of their peripheral neurite 383 410 colon_cecum_3 Source GEO sample is GSM80625 Last updated (according to GEO): Mar 31 2006 of Parkinson's disease 450 471 Diaphragm 14 Day control rep 3 Temporal neocortex mTLE 9 M_U133Plus_115_DLPFC 19 0 Head and neck cancer 861 Heart 861 Coxsackievirus Infections 141 of cardiopulmonary diseases 167 C57L/J_male_hypothalamus Disorder of artery 865 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184776 Last updated (according to GEO): Apr 26 2007 /3T3 fibroblasts 743 759 Lymphoblastic Leukemia 901 4535 4527 hepatoma Head and neck cancer Source GEO sample is GSM155677 Last updated (according to GEO): Apr 24 2007 in oculomotor nuclei 995 1014 Congenital Abnormality 853 olfactory Source GEO sample is GSM67236 Last updated (according to GEO): Jan 19 2006 f2#309 versus pool Mouse Brain tissue WT_IL-6_0_rep2 GM18871_technical_rep_1 Investigation into murine dermal burn wound. Mouse thermal injury induced, and skin excised at different times post-injury. Source GEO sample is GSM7484 Last updated (according to GEO): May 27 2005 861 Carcinoma 1000 Brain 23 0 mammary epithelial cells 1000 Cerebral cortex 5 0 brain CNS-SC_InjB30m-4B-s2 H9LMS00111007 Gene expression data from postmorten brain regions Source GEO sample is GSM145275 Last updated (according to GEO): Nov 20 2006 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2851 Source GEO sample is GSM2093 Last updated (according to GEO): Nov 21 2005 Brain 1000 861 Pain 0 Human Cortex 11 5 0 brain 28 0 frontal cortex wistar ky 3930 brain, cerebral cortex: Sham13_e1_le1 Expression profiling of spinal cord section (T8) extracted from rats 14d following mild injury Source GEO sample is GSM31426 Last updated (according to GEO): May 27 2005 Testis 861 V5-P170 heart_atrium_1 Gene expression data of substantia nigra from postmortem brain of PD patients Source GEO sample is GSM184371 Last updated (according to GEO): May 29 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11292 Last updated (according to GEO): May 28 2005 Kidney 861 D_U133Plus_78_CB Chronic leukemia NOS 913 361 335 hypertrophic cardiomyopathy Wild type inbred mice Source GEO sample is GSM82995 Last updated (according to GEO): Nov 10 2005 by the liver 210 221 Balb/c to C57/BL6 with anti CD80/86 mAb Source GEO sample is GSM8937 Last updated (according to GEO): May 28 2005 CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of DC, recombinant human (rh) IL-4 and rhGMCSF were added to the culture at 50 ng/ml on days 1, 3, and 5 of culture. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5125 Last updated (according to GEO): Oct 28 2005 V5-P565 R592P01081 Neoplasm 861 12 0 ovarian tumor from whole tumor 21 36 1907 1879 of adhering connective tissue Gene expression data from postmorten brain regions Source GEO sample is GSM145137 Last updated (according to GEO): Nov 20 2006 Trigeminal Ganglia 5 Normal 27 0 cerebral cortex sprague 3919 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211383 Last updated (according to GEO): Jul 18 2007 Squamous cell carcinoma 4 CNS-RM_Ctr24h-1A-s2 R430P00182 Parkinson's model voxel A1 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28471 Last updated (according to GEO): May 27 2005 M_U133A_54_nAcc 861 HIV Infections NG001_c Standard Affymetrix Protocal Keywords = microarray Keywords = muscle Source GEO sample is GSM15767 Last updated (according to GEO): May 28 2005 spinal_cord_5 Source GEO sample is GSM80794 Last updated (according to GEO): Mar 31 2006 Brain 1000 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181164 Last updated (according to GEO): Jul 12 2007 Oculomotor nucleus 1000 GSE2872 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169482 Last updated (according to GEO): Feb 21 2007 1000 HIV Infections PGA-Csx_null_2b-m4 Colon (transverse) [JunctionChip 1 of 5] 660 mesenchymal stem cell 639 the spinal cords 144 159 B220hi sIgM+ Mature B cells sorted out of mouse bone marrow, sort no. 1 Source GEO sample is GSM647 Last updated (according to GEO): Mar 20 2006 0 Human Cortex 11 To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18442 Last updated (according to GEO): May 27 2005 Spleen 1000 acute myeloid leukemia Source GEO sample is GSM227437 Last updated (according to GEO): Sep 12 2007 Spleen vs MIP3-alpha Treated B cell 120min (set2) 24 0 human prostate PC3 tumors striatum 30 38 Fibroblasts 1000 NHF10-hTERT_M_C5_U26594 bronchial epithelia 224 243 9 0 lymph node gene expression data from ODC mouse skin samples Source GEO sample is GSM216666 Last updated (according to GEO): Aug 09 2007 Kidney YC-2A The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169484 Last updated (according to GEO): Feb 21 2007 none Source GEO sample is GSM239856 Last updated (according to GEO): Dec 07 2007 Ganglia, Spinal 923 human cerebellum Source GEO sample is GSM87152 Last updated (according to GEO): Feb 08 2006 The epithelial cells 962 981 Hoxb1 wt E10.5, rep 2 (W6) 865 Disorder of artery rat hippocampus Treatment, type=time_course, measurement=240.0 h Source GEO sample is GSM32148 Last updated (according to GEO): May 27 2005 Amygdaloid structure 1000 "Sample 29,>5 yr survival(137 months) age 52 erp yes" on vantveer-oligo in traumatic brain injury 992 1017 "24h Thy-Noc, Exp4" 8 uterine horns 411 425 IMR90 from the ES(IMR90)-3 sample Expression profiling of somatomotor cortex extracted from rats at 14d following moderate injury Source GEO sample is GSM41694 Last updated (according to GEO): May 27 2005 Vagina 9 Normal Gene Expression Profile of NHE1 Null Mutation in mouse hearts 40 54 M_U133A_56_AnCg Alzheimer's Disease 1000 Central gray substance of midbrain 861 12 frontal Lobe 23 10 7 Left Expression profiling of somatomotor cortex extracted from rats at 4h following moderate injury Lot batch = Source GEO sample is GSM41998 Last updated (according to GEO): May 27 2005 861 Substantia nigra structure 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114438 Last updated (according to GEO): Jun 16 2006 Brain 861 Anterior nares 1000 none Source GEO sample is GSM244606 Last updated (according to GEO): Nov 23 2007 Sample 12 Treatment, type=pharmacogenomic_treatment, description=Neuronal cultures from cultures of rat cerebellar granule neurons will be treated with the chemical compound GW5074. Source GEO sample is GSM53242 Last updated (according to GEO): Jul 06 2005 158 of embryonic stem cells 136 "Sample 52, <5 yr survival(19 months) age 45 erp yes" on vantveer-oligo Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15686 Last updated (according to GEO): May 28 2005 861 Malignant neoplasm of prostate Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 9709 blood 129/SvImJ Olfactory Bulb B Human Hypothalamus Male 2 (technical replicate) We build a model for the molecular and cellular events underlying phenotypic discordance in glycine receptor defects (beta subunit). Some mice progress and die, while their littermates recover and get better, despite the same mutation on an inbred genetic background. We find evidence for glycine neurotransmitter toxicity and loss of glycinergic interneurons early in the disease, but some mice are able to keep things going until they can over-express homomeric alpha1 channels, whereupon they recover. In the mice progressing towards lethality, neurotransmitter toxicity too quickly extends to GABAergic interneurons and motorneurons, and they lose their window of time to upregulate the alpha1 glycine receptor, and they crash and burn. Importantly, human patients with glycine receptor defects typically show a resolution of their phenotype with age, and we propose that the same remodeling events are occuring in human patients. Source GEO sample is GSM30989 Last updated (according to GEO): May 27 2005 thymocytes_DN2_2 H9LMS99090508 AD-AD3T1-A385-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A with some respiratory epithelium. 1039 1072 861 Cerebral cortex Nrl ko samples were compared to wt at postnatal 2. Source GEO sample is GSM227450 Last updated (according to GEO): Sep 07 2007 0029_1265_H95A2_KF151_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Disease Source GEO sample is GSM176083 Last updated (according to GEO): Apr 09 2007 Expression profiling of somatomotor cortex extracted from rats at 14d following sham surgery Source GEO sample is GSM41636 Last updated (according to GEO): May 27 2005 Primary large cell neuroendocrine carcinoma 5883 0 47 We have generated a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, we analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct subclasses of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients. 5 0 brain 19 0 Head and neck cancer Temporal Cortex Alzheimer's disease 1 Skeletal bone 861 19 0 human frontal cortex 17 7 hippocampus Morphine effects on striatal transcriptome in four inbred mouse strains brain 0 5 901 Myeloid Leukemia Jejunum 2 [JunctionChip 3 of 5] Liver Test (Blinded) Sample Source GEO sample is GSM130162 Last updated (according to GEO): Sep 18 2007 1000 Hippocampus Normal Source GEO sample is GSM176264 Last updated (according to GEO): Apr 09 2007 PGA_MI_ilv_1h_395 none Source GEO sample is GSM239906 Last updated (according to GEO): Dec 07 2007 HCC (HBV+, HK47) Spleen vs Untreated B cell Time 0 (set4) Malignant Neoplasms 861 Spleen vs Interferon-beta (IFN beta) Treated B cell 120min (set2) Mouse Liver AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate B healthy control sample x171 Brain 1000 a debilitating autoimmune disease 27 59 Spleen 0 5 no additional Source GEO sample is GSM199234 Last updated (according to GEO): Jun 08 2007 165-96_Adeno Femur 1000 Serum 02 Cerebral cortex 861 Brain 861 36 21 from whole brain C57BL10 quadriceps sample 1 1000 Heart failure 1000 Structure of parenchyma of lung ProstateCancer-13 on NHGRI-6.5k_c 861 Ribosomal RNA Substantia nigra PD rep1 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11459 Last updated (according to GEO): May 28 2005 366 354 encephalitis 2nd 4hr C-DG Oat cell carcinoma 867 Spleen 1000 68 54 /- mouse retina mouse cerebral cortex, cox-1 WT, rep1 metastatic transitional cell carcinoma 108 145 32 21 from retinas na Source GEO sample is GSM181273 Last updated (according to GEO): Apr 10 2007 from colonic normal mucosa 21 47 adrenalgland Source GEO sample is GSM18789 Last updated (according to GEO): Sep 25 2006 NA18960 Acetaminophen 3hr Rat 7365 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool 5 0 brain 133 94 in ovarian endometrioid adenocarcinomas Microarray analysis of postictal transcriptional regulation of neuropeptides. 23 0 mammary epithelial cells 983 Structure of horn of uterus Brain_MD_57_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 ovarian neoplasm Chronic Lymphocytic Leukemia 19 47 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225682 Last updated (according to GEO): Nov 05 2007 Substantia Nigra Reticulata 3 Disease Lymphoblastic Leukemia 901 1000 Structure of atrioventricular node Abdominal aorta collected during autopsy within 24 hours post mortem Source GEO sample is GSM170562 Last updated (according to GEO): Jul 26 2007 7 0 prostate 7676 on TGRI-6.5k the blood 393 402 Gene expression data from postmorten brain regions Source GEO sample is GSM145714 Last updated (according to GEO): Nov 20 2006 Heart 1000 60 50 Lymph node Liver 1000 Gene expression data from brain of adult rats Source GEO sample is GSM101043 Last updated (according to GEO): Feb 20 2007 Primary Neoplasm 1000 with myocardial infarction 313 339 short access to cocaine, ventral tegmental area, 1 hr/day access to cocaine Source GEO sample is GSM93861 Last updated (according to GEO): Jan 26 2006 T-ALL-C26 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Dahl Salt Sensitive Rat Lung- Hypoxia, SU-5416, and Sorafenib rep4 901 Neurodegenerative Disorders Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16527.gif Source GEO sample is GSM91591 Last updated (according to GEO): Sep 22 2006 91 from the bone marrow 72 88 68 with bicuspid valves Large Pre-BII cells 8b Bone marrow [JunctionChip 4 of 5] 1000 Substantia nigra structure striatum rattus_norvegicus_strain iNP animal_number 8 Adult Mouse Brain Gene Expression accumbens rattus_norvegicus_strain iP animal_number 5 Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles. PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity. Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence. To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips. Source GEO sample is GSM136527 Last updated (according to GEO): Jun 05 2007 cocaine naive, ventral tegmental area 0 37 acute myeloid leukemia Source GEO sample is GSM227444 Last updated (according to GEO): Sep 12 2007 AD control Treatment, type=dissect Source GEO sample is GSM119645 Last updated (according to GEO): Jul 10 2006 Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174508 Last updated (according to GEO): Mar 14 2007 Myocardial Infarction 1000 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225358 Last updated (according to GEO): Aug 31 2007 1000 Primary carcinoma of the liver cells PGA_MI_nilv_48h_351 66 42 out of mouse bone marrow Treated Source GEO sample is GSM176475 Last updated (according to GEO): Apr 09 2007 OA 1 Primary Neoplasm 1000 PGA-MLS-RA-1aAv2-s1 Hippocampus 1000 BAL_4_A0B0 brain 0 5 Colon 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Dimaprit for 240min Source GEO sample is GSM5543 Last updated (according to GEO): May 27 2005 brain, unknown: 03CA_e1_le1 MLL__1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gloubus Pallidum External 4 Disease BREAST_MCF7ADRr on Affymetrix GeneChip Human Full Length Array HuGeneFL Pressure-overload induced hypertrophy model. Mouse was sacrificed 8 weeks after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2263 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145498 Last updated (according to GEO): Nov 20 2006 SN:1022965;Fetal Cartilage, biological rep2 validation 1000 Brain Nose 1000 mild cognitive impairment - middle temporal gyrus 5 Temporal Cortex Control (AD) 5 Malignant neoplasm of prostate 1000 ovarian tumor: endometrioid Source GEO sample is GSM139386 Last updated (according to GEO): Apr 09 2007 Epithelium 861 GSE2866 861 Neoplasm Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211301 Last updated (according to GEO): Jul 18 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL4 for 60min Source GEO sample is GSM5629 Last updated (according to GEO): May 27 2005 5 0 brain Total RNA extracted from the cerebellum of a Tg-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144395 Last updated (according to GEO): Nov 14 2006 Parkinson's disease sample x092 0 30 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withTerbutaline for 120min Source GEO sample is GSM5786 Last updated (according to GEO): May 27 2005 DLCL-0031 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23626.gif Source GEO sample is GSM81544 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145392 Last updated (according to GEO): Nov 20 2006 1403 1381 in primary human tumors brain, hippocampus: PR-CA3-A3_e1_le1 1000 Urine amygdala, central nucleus sprague2 whole tissue, pool of 5 animals, 20 weeks old, male Sprague Dawley amygdala, central nucleus file:p3942w Source GEO sample is GSM15175 Last updated (according to GEO): May 28 2005 Gene expression from Dendritic cells from human subject with pustule former phenotype infected with H. ducreyi. Source GEO sample is GSM128976 Last updated (according to GEO): Sep 13 2007 olfactory epithelium 194 213 prostate Source GEO sample is GSM203293 Last updated (according to GEO): Jun 21 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11219 Last updated (according to GEO): May 28 2005 Nervous system structure 901 861 Cardiomyopathies 913 Coronary heart disease Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19239 Last updated (according to GEO): May 27 2005 Expression profiling of somatomotor cortex extracted from rats at 28d following moderate injury Source GEO sample is GSM41714 Last updated (according to GEO): May 27 2005 Trachea [JunctionChip 2 of 5] 901 Neuroglia Adrenal cortex [JunctionChip 1 of 5] BALB/cByJ_female_hypothalamus Mature B cells 11b 660 mesenchymal stem cell 639 Chronic leukemia NOS 853 OBX Day 1,# 2 HapMap CEU_parent Female Source GEO sample is GSM159543 Last updated (according to GEO): Feb 01 2007 Keywords = Infectious diseases 1133 1163 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160201 Last updated (according to GEO): Feb 08 2007 Muscle 861 NCI60.35_LABEL39EXTRACT38SUB3 Source GEO sample is GSM134165 Last updated (according to GEO): Aug 06 2007 Gene expression data from a hippocampus of saline-injected mouse Source GEO sample is GSM147418 Last updated (according to GEO): Jan 03 2007 human cerebellum Source GEO sample is GSM87084 Last updated (according to GEO): Feb 08 2006 Normal Source GEO sample is GSM176051 Last updated (according to GEO): Apr 09 2007 1000 frontal lobe BCR-ABL-#7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 15 0 human cerebellum total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Insulin-like growth factor 1 for 120min Source GEO sample is GSM5620 Last updated (according to GEO): May 27 2005 Stomach 1000 Parkinson's disease sample x106 0 30 cardiac 746 752 tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44899 Last updated (according to GEO): May 27 2005 n/a Source GEO sample is GSM177946 Last updated (according to GEO): Jun 11 2007 Spleen 1000 Transitional epithelium 1000 Brain 861 Pancreas at e16.5, Chip A, rep 2 1000 Brain 1000 Kidney SP-KO-Nrf2-Female-1 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Prostaglandin E2 for 120min Source GEO sample is GSM5739 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM146069 Last updated (according to GEO): Nov 20 2006 329 306 valvular cardiomyopathy 901 Aortic valve structure 1000 Hippocampus brain, cerebral cortex: Rat_02-131_TTX_Lipska_e1_le1 17 7 hippocampus Nose 1000 Epithelium 861 HapMap CHB Female Source GEO sample is GSM159580 Last updated (according to GEO): Feb 01 2007 1000 Down Syndrome Replicate 2 of 3 (same genotype, same age). All replicates were individual animals. Source GEO sample is GSM138275 Last updated (according to GEO): Sep 29 2006 (1 utricle 10 19 M_U133A_11_nAcc 663 mesenchymal stem cell 642 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2726 Source GEO sample is GSM2110 Last updated (according to GEO): Nov 21 2005 Locus Coeruleus Source GEO sample is GSM107931 Last updated (according to GEO): Jun 06 2006 9 0 Blood Test Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162194 Last updated (according to GEO): Jun 12 2007 Changes in mouse liver mRNA profiles following intraperitoneal cytokine injection. One of 2 replicates of albumin-cre(+) Socs3(-/fl) mice, injected with phosphate-buffered saline, and killed after 4h. Source GEO sample is GSM5957 Last updated (according to GEO): May 27 2005 Tumor__Ovary_Adeno_H_6206 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A outer medulla 31 43 Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 5 of Parkinson's disease 450 471 wild type placebo 15d, biological rep3 175 157 in the hypothalamus MLL_14 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A The most common congenital cardiac abnormalities 50 97 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9962.gif Source GEO sample is GSM79802 Last updated (according to GEO): Sep 22 2006 CNS-SpinalCsev-Adult-28d-3C-s2 Blood B cells || lc8n076 Cerebellum 1000 Simple annotation: Normal tissue, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27746.gif Source GEO sample is GSM66559 Last updated (according to GEO): Sep 22 2006 Normal Small Intestine CNS-RM_Mod28d-2B-s2 Met. Ovarian Granulosa Cell Tumor (SF39, T1) Kainate-neocortex, biological rep5 Lymphoblastoid Cell Line for Individual 8087.3 log phase DLBC25 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Coronary Arteriosclerosis Plasma 861 256 235 dilated heart failure Malignant Neoplasms 861 30 19 Solid tumor 1000 Brain Substantia nigra PD rep13 hedenfalk-familial Probeset expression data from NA12751 growth 2, replicate 2 Source GEO sample is GSM195209 Last updated (according to GEO): Aug 08 2007 pinealgland.1 Spleen vs Untreated B cell 240min (set4) thioridazine-treated mouse brain Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 7743 left_liver_lobe 861 Brain 913 Coronary heart disease mouse brain ipsilateral LPS Source GEO sample is GSM149773 Last updated (according to GEO): Mar 15 2007 Spleen 1000 1000 Spleen 40 21 from dorsal pancreas cingulate cortex 1000 AD control Treatment, type=dissect Source GEO sample is GSM119629 Last updated (according to GEO): Jul 10 2006 Gene expression data from human colon tumor tissue Source GEO sample is GSM173368 Last updated (according to GEO): Apr 20 2007 plasma cells 50 61 cingulate cortex 1000 Probeset expression data from NA12749 growth 1 Source GEO sample is GSM201534 Last updated (according to GEO): Aug 08 2007 GSE4595 Liver 1000 ct-1 Brain 861 Brain 861 wild type placebo 12h, biological rep1 none Source GEO sample is GSM210325 Last updated (according to GEO): Jul 16 2007 PMN_control_360min_Patient1 1000 adenoma 923 Aortic Aneurysm, Thoracic from brain 21 30 EOM 14 Day mdx rep 3 of coronary artery disease 317 342 brain 0 5 Primary Neoplasm 1000 Papillary renal cell carcinoma (RCC) represents 10% to 15% of adult renal neoplasms; however, the molecular genetic events that are associated with the development and progression of sporadic papillary RCC remain largely unclear. Papillary RCCs can be divided into two subtypes based on histologic, cytogenetic, and gene expression differences. Type 1 tumors ( approximately 60-70%) are generally low grade with favorable outcome, whereas type 2 tumors ( approximately 30-40%) are associated with increased cytogenetic complexity, high tumor grade, and poor prognosis. In this study, computational analysis of gene expression data derived from papillary RCC revealed that a transcriptional signature indicative of MYC pathway activation is present in high-grade type 2 papillary RCC. The MYC signature is associated with amplification of chromosome 8q and overexpression of MYC that maps to chromosome 8q24. The importance of MYC activation was confirmed by both pharmacologic and short interfering RNA-mediated inhibition of active Myc signaling in a cell line model of type 2 papillary RCC. These results provide both computational and genetic evidence that activation of Myc is associated with the aggressiveness of papillary type 2 RCC. Therefore, it will be useful to consider inhibition of components of the MYC signaling pathway as avenues for therapeutic intervention in high-grade papillary RCC. 861 Hypothalamic structure Liver 1000 Bone Marrow 1000 9 0 Blood Test Gene expression data from a primary branch of the saphenous artery of 16 week old ACTH-treated male Wistar-Kyoto rats Source GEO sample is GSM198861 Last updated (according to GEO): Nov 28 2007 1000 Heart This dataset contains the gene expression profile of a CD11c high, CD4 negative, CD8 negative ("Double negative") splenic dendritic cell population. The cells were processed directly after isolation. Global scaling was applied to Avg Difference intensity values. Keywords = mouse, dendritic cells, spleen Source GEO sample is GSM4710 Last updated (according to GEO): May 27 2005 from the olfactory epithelium tissue 172 208 Prefrontal Cortex Source GEO sample is GSM105466 Last updated (according to GEO): Apr 17 2006 Male 68.4 yr after antibody enrichment scan 2 (U133A) brain, cerebral cortex: NIC + NMDA 5_le1 amygdala wistar 3720 BT-474/ATCC Laser capture lung cancer cells Source GEO sample is GSM191028 Last updated (according to GEO): May 25 2007 Heart 1000 RNAtotSD_20, ZT6 ovarian tumor: serous Source GEO sample is GSM139455 Last updated (according to GEO): Apr 09 2007 B220+c-kit+ Pre BI cells sorted out of mouse bone marrow, sort no. 3 Source GEO sample is GSM656 Last updated (according to GEO): Mar 17 2006 Melanoma xenograft, SM_Lung_A (LeiFidler) gene expression of 1 day RA differentiated ESCs Source GEO sample is GSM181962 Last updated (according to GEO): Apr 12 2007 Adrenal medulla [JunctionChip 2 of 5] 861 Neoplasm Expression profiling of spinal cord section (T9) extracted from rats 30m following mild injury Source GEO sample is GSM1323 Last updated (according to GEO): Jun 06 2005 Brain 861 of the postmortem brains 673 697 97 84 in the cornea 91 from the bone marrow 72 Primary Neoplasm 1000 GSE9788 CC304 Ta gr3 tumour Source GEO sample is GSM2507 Last updated (according to GEO): Mar 21 2006 567 548 the descending colon Gene expression data from postmorten brain regions Source GEO sample is GSM144968 Last updated (according to GEO): Nov 20 2006 to the nose 599 609 Mesenchymal Stem Cells 1000 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181129 Last updated (according to GEO): Jul 12 2007 Normal human fetal cartilage from 18-22 weeks. Source GEO sample is GSM149642 Last updated (according to GEO): Jul 06 2007 I_U133A_52_AnCg C3H-HeJ mice were exposed to filtered air. Lungs were removed-frozen in liquid nitrogen-RNA extraction. Lot batch = Source GEO sample is GSM4012 Last updated (according to GEO): May 28 2005 Cerebellum 1000 Melanoma metastatic cell line A375, biological rep6 (LeiATCC) Epithelial Cells 1000 13 6 Awn Hair Whole blood 0 10 38 21 from a hippocampus GSE713 26 0 frontal cortex sprague 3933 Melanoma xenograft, MEC2_Sub_B (LeiFidler) 1000 Cerebellum 43 0 Chorionic mesoderm-derived mesenchymal cells Epithelium 861 D_U133A_7_DLPFC Nodose Ganglion 1000 Clone 8.1 plus PDGF chip 2 olfactory epithelium SR-A mutant, mouse 48 hpO Source GEO sample is GSM80210 Last updated (according to GEO): Oct 26 2005 7 0 prostate TUMOR 21 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 54 32 in the developing brain D07 12h TLR2/1L in human skeletal muscle 35 59 Gene expression data from PD3 Foxo3 wild-type ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203846 Last updated (according to GEO): Aug 02 2007 Cerebral cortex 861 Hep3B cells in the brain 150 162 861 Testis Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 20 hours after lights on. Original RNA code = LC51A. Source GEO sample is GSM227376 Last updated (according to GEO): Sep 10 2007 onto a collagen 71 85 1000 Liver Cerebellum 1000 Cerebral Cortex 10 Normal Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132492 Last updated (according to GEO): Feb 26 2007 brain, cerebral cortex: Rat_02-56_VHL_Lipska_e1_le1 AML cDNA hybridization-ID60-L GSE6764 Laser captured visceral sensory neurons. Source GEO sample is GSM63670 Last updated (according to GEO): Dec 21 2005 5 0 Spleen 9 0 lymph node mod097_10nM-3 Brain 861 Mesenchymal stem cells 4029 4050 Approximately 10 pairs of the most anterior dorsal root ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until sufficient tissue was harvested to be pooled by genotype. Ganglia from 5 embryos were pooled for a single analysis and RNA extracted using the RNeasy system (Qiagen). Source GEO sample is GSM132426 Last updated (according to GEO): Aug 30 2006 Epithelium 861 Cerebral cortex 1000 5 0 Spleen Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19211 Last updated (according to GEO): May 27 2005 rat cortex Treatment, type=time_course, measurement=3.0 d Source GEO sample is GSM53205 Last updated (according to GEO): Jul 06 2005 Ventral Tegmental Area 8 Normal plasma cells 50 61 D_U133Plus_113_Amy 1000 Myosin Heavy Chains Ta gr3 tumour Source GEO sample is GSM2516 Last updated (according to GEO): Mar 21 2006 SHR rep2 Two groups of 3 days old mice were treated with oil or retinoic acid. At day 4 one half of each group was treated with saline solution or dexametasone. Lungs were removed snap frozed for RNA extraction Source GEO sample is GSM4143 Last updated (according to GEO): May 27 2005 966 Hippocampus CNS-SCsev_InjA28d-3A-s2 Euploid sample 1 (Astrocyte) 861 Encephalitis 3AJZ02022220_leukemia, promyelocytic-HL-60 Skeletal bone 1000 861 Asthma 1000 Skeletal muscle structure Coronary heart disease 913 NA Source GEO sample is GSM198905 Last updated (according to GEO): Jun 07 2007 901 Parietal Lobe MGJZ030207020Alymphnode 660 mesenchymal stem cell 639 5 0 brain Cerebral cortex 1000 PGA-RnSalt_e_6w_3-m5 GSE8407 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211269 Last updated (according to GEO): Jul 18 2007 Spinal Cord 1000 DLCL-0035 || lc4b035 Brain 1000 infection 255 264 Spleen vs 2-Methyl-thio-ATP Treated B cell Date 3/16/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : headfold Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 2.5 mg/kg Time : 3.0 hrs post-injection Intervention : 4.0 mg/kg PK11195 co-administered Risk: remediated Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 16-20 headfolds pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = PK11195 Keywords = embryo Keywords = microphthalmia Lot batch = AM080 Source GEO sample is GSM12202 Last updated (according to GEO): May 28 2005 Nrf2 Knockout vs. Wildtype mice Muscular Dystrophies 901 901 Tenascin SVG-A subclone 3-D6 GeneChip U133B Tissue homogenate from cingulate cortex from GIN mouse (Gad1 inhibitory ref. (pubmed id:10777798) ). Source GEO sample is GSM64188 Last updated (according to GEO): Dec 01 2005 SCG_control_65h_rep2 Gene expression data from postmorten brain regions Source GEO sample is GSM145504 Last updated (according to GEO): Nov 20 2006 1000 Prostate Transplant Series 25 Left, Transplant # 2 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162165 Last updated (according to GEO): Jun 12 2007 5 0 brain Cochlear structure 1000 CD28 beads 24.00 hr. T-Cell mdx5cv diaphragm sample 1 Exp 4 (-TNFa) Brain 1000 Neoplasm 861 144 109 Keywords = congenital heart disease 861 Acquired Immunodeficiency Syndrome Gene expression data from postmorten brain regions Source GEO sample is GSM145834 Last updated (according to GEO): Nov 20 2006 C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 4hr after experimental mice received their last shock treatment. Source GEO sample is GSM4517 Last updated (according to GEO): May 27 2005 26 15 endometrioid MuscleRegen-ctx3d-1RLAv2-s2 1000 Myositis 4 0 Lungs with some respiratory epithelium. 1039 1072 Sprague-Dawley Male LowSalt OuterMedulla rat708 sd_medullar_k_708r_om_070302 from whole tumor 21 36 f2#38 versus pool Mouse Brain tissue dorsal root ganglion 0 19 Voxel B3 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1395 Last updated (according to GEO): Nov 21 2005 prostate Source GEO sample is GSM203283 Last updated (according to GEO): Jun 21 2007 heart 1169 1173 Nervous system structure 901 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Insulin-like growth factor 1 for 30min Source GEO sample is GSM5616 Last updated (according to GEO): May 27 2005 Neoplasm 861 brain 0 5 861 Cerebellum Control 3 (Experiment Neuroprotection4- Run 14985) Treatment, type=timepoint, measurement=0.0 h Source GEO sample is GSM96671 Last updated (according to GEO): Feb 14 2006 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11451 Last updated (according to GEO): May 28 2005 Endometrium-Normal 5 266 257 infection CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of DC, recombinant human (rh) IL-4 and rhGMCSF were added to the culture at 50 ng/ml on days 1, 3, and 5 of culture. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5142 Last updated (according to GEO): Oct 28 2005 Entorhinal Cortex 7 23 Plasma 861 AD-226t2-A151-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Lung (fetal) [JunctionChip 4 of 5] Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47516 Last updated (according to GEO): May 29 2005 with autism spectrum disorder 37 65 Expression profiling of somatomotor cortex extracted from rats at 14d following sham surgery Source GEO sample is GSM41637 Last updated (according to GEO): May 27 2005 CNS-SC_InjB7d-3C-s2 T_active_022WAFCZ_093.txt A/J pituitary gland rep1 (430 2.0 Array) 32 21 from retinas PGA-E16.5_3A Normal Source GEO sample is GSM175988 Last updated (according to GEO): Apr 09 2007 Expression profiling of spinal cord section (T8) extracted from rats 7d following severe injury Source GEO sample is GSM31502 Last updated (according to GEO): May 27 2005 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2826 Source GEO sample is GSM2131 Last updated (according to GEO): Nov 21 2005 Leukemia, Myelocytic, Acute 1000 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27044 Last updated (according to GEO): May 27 2005 WGACON-6 Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles. PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity. Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence. To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips. Source GEO sample is GSM136526 Last updated (according to GEO): Jun 05 2007 Tumor__Breast_Adeno_mBRT2_(9078) on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Adenocarcinoma 861 Liver gene transcription during energy balance perturbations in C57/BL/J6 mice. Heart Septal Defects, Atrial 1000 N19__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211393 Last updated (according to GEO): Jul 18 2007 C3H 2-1 Heart AD-299t1-A235-8 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Liver 1000 hypothalamus_10 Source GEO sample is GSM80684 Last updated (according to GEO): Mar 31 2006 Medulla 861 Spleen vs MIP3-alpha Treated B cell 60min (set3) 1500mg/kg APAP 6Hr rat 3593 blood vs. PC 6Hr rat 3586 blood 101095 Gene expression of transplanted hearts Nasal Epithelium 901 1000 Descending colon 861 Cerebral cortex spinal_cord_2 Source GEO sample is GSM80785 Last updated (according to GEO): Mar 31 2006 1000 Spleen 1000 Hippocampus Stria 861 3 hrs Pre-clamp sample 4 cerebral_cortex_5 Source GEO sample is GSM80627 Last updated (according to GEO): Mar 31 2006 861 Colon 913 Coronary heart disease Mental Retardation 1000 Replicate 3 of 3 (same genotype, same age). All replicates were individual animals. Source GEO sample is GSM138276 Last updated (according to GEO): Sep 29 2006 91 80 from bronchi COLON_KM12 on Affymetrix GeneChip Human Full Length Array HuGeneFL cerebral cortex 7 21 Cystic fibrosis transmembrane conductance regulator (Cftr) knockout mice present the clinical features of low body weight and intestinal disease permitting an assessment of the interrelatedness of these phenotypes in a controlled environment. To identify intestinal alterations which affect body weight in CF mice the histological phenotypes of crypt-villus axis height, goblet cell hyperplasia, and mast cell infiltrate were measured, cardiac blood samples assessed, and gene expression profiling of the ileum was completed for 12 week old (C57BL/6xBALB) F2 Cftrtm1UNC and non-CF mice presenting a range of body weight. Crypt-villus axis height decreased with increasing weight in CF, but not control, mice. Goblet cell hyperplasia and mast cell infiltration in the submucosa and muscularis externa layers of the CF intestine, were identified to be independent of bodyweight. Blood triglyceride levels were found to be significantly lower in CF mice than control mice (p = 3.02 x 10-5) but were not dependent on CF mouse body weight. By expression profiling, genes of DNA replication and lipid metabolism were among those altered in CF mice relative to non-CF controls; and no differences in gene expression were measured between samples from CF mice in the 25th and 75th percentile for weight. This study indicates that the absence of Cftr leads to altered morphology in the CF intestine the extent of which is correlated with body weight in CF mice while CF related changes in blood triglyceride levels and in the intestinal gene expression profile were not dependent on body weight in this model. Last Updated (by provider): Apr 05 2007 Contributers: Daryl H Humes Juan C Carnale-Zambrano Christina H Haston Maya C Poffenberger Sean M Cory mammary_gland_10 Source GEO sample is GSM80716 Last updated (according to GEO): Mar 31 2006 human cerebellum Source GEO sample is GSM87103 Last updated (according to GEO): Feb 08 2006 Epithelium 861 Epididymis [JunctionChip 3 of 5] Gene expression data from postmorten brain regions Source GEO sample is GSM146015 Last updated (according to GEO): Nov 20 2006 Cerebral cortex 861 no additional Source GEO sample is GSM199251 Last updated (according to GEO): Jun 08 2007 40 hr Hela Double Thymidine, exp2 midbrain_2 Source GEO sample is GSM80700 Last updated (according to GEO): Mar 31 2006 1000 Axon 861 Heart failure 1000 Antibodies UET-13TR-EWS/ERG 24hr tet+ 901 Temporal Lobe Plasma 861 861 Cerebellum plasma cells 50 61 Wild type inbred mice Source GEO sample is GSM82928 Last updated (according to GEO): Nov 10 2005 saphenous_vein_2 Corpus Callosum 2 Normal Heart Atrium 1000 Normal Source GEO sample is GSM176387 Last updated (according to GEO): Apr 09 2007 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5812 Last updated (according to GEO): May 27 2005 Endometrium 1000 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68120 Last updated (according to GEO): Jul 07 2006 861 Blood 1000 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM144972 Last updated (according to GEO): Nov 20 2006 HapMap YRI_parent Male Source GEO sample is GSM159686 Last updated (according to GEO): Feb 01 2007 "Sample 72, <5 yr survival(36 months) age 39 erp yes" on vantveer-oligo Brain 1000 Muscular Dystrophies 901 6, 18, 30 month F344BN oculomotor nucleus and spinal cord Source GEO sample is GSM74334 Last updated (according to GEO): Sep 16 2005 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11262 Last updated (according to GEO): May 28 2005 1000 Malaria, Cerebral C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 4hr after experimental mice received their last shock treatment. Source GEO sample is GSM4512 Last updated (according to GEO): May 27 2005 eTat - Noco6hr - 1 Occipital lobe 983 ileum 861 256 235 dilated heart failure lethal status epilepticus 229 253 Muscular Dystrophy, Duchenne 913 861 Gland structure 861 Cardiomyopathies 28 0 Adult frontal cortex cocaine2 Affymetrix GeneChip® Mouse Genome 430 2.0 Array Source GEO sample is GSM197114 Last updated (according to GEO): May 31 2007 Liver 0 4 5 0 brain Brain 1000 Midbrain 3 Normal labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156710 Last updated (according to GEO): Jan 22 2007 A/J Frontal Cortex F 134 115 by CO2 asphyxiation 132 from mouse cortex 149 1000 Maxilla Cerebral cortex 861 C57BL/10Jmale_hypothalamus Large-scale analysis of the human transcriptome. Kidney Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 148.60 Stdv: 7.22 Min: 138.96 Max: 166.76 Source GEO sample is GSM2843 Last updated (according to GEO): Mar 20 2006 43 0 Chorionic mesoderm-derived mesenchymal cells gene expression from allergen stimulated mouse lung Source GEO sample is GSM158145 Last updated (according to GEO): Jan 25 2007 Experimental Autoimmune Encephalomyelitis 1000 00291191H95A2-KF67v2p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Normal Source GEO sample is GSM176428 Last updated (according to GEO): Apr 09 2007 Prosencephalon 861 Isograft 70 days No.1 Coxsackievirus Infections 861 660 mesenchymal stem cell 639 brain, frontal cortex: ADX PM LC_e1_le1 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188815 Last updated (according to GEO): Jun 06 2007 Brain 861 Classification of antipsychotic drugs by gene expression in the frontal cortex of mice. 65 50 Large intestine Epithelial Cells 1000 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188769 Last updated (according to GEO): Jun 06 2007 20 0 human caudate nucleus Brain 861 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210403 Last updated (according to GEO): Jul 16 2007 Cerebral cortex 861 15 0 human cerebellum Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22568 Last updated (according to GEO): May 27 2005 Acetaminophen 6hr Rat 7334 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool Wild type inbred mice Source GEO sample is GSM82957 Last updated (according to GEO): Nov 10 2005 Affymetrix RGU34A Naive C 861 Carcinoma of coronary artery disease 258 284 Adrenal Gland Cortex 3 Normal PrimaryConj1 B220Low sIgM+ immature B cells sorted out of mouse bone marrow, sort no. 11 Source GEO sample is GSM612 Last updated (according to GEO): Mar 17 2006 post HCMV infection 18 36 Cardiac 523 530 1357 1347 in adenomas Epithelium 861 Mesenchymal Stem Cells 1000 whole blood_101794 ATCC number CRL-1502 Source GEO sample is GSM6810 Last updated (according to GEO): May 27 2005 Macrophages treated with LPS plus IL-10, 20 min, Replicate 3 Source GEO sample is GSM241139 Last updated (according to GEO): Nov 02 2007 5 0 Spleen GSE3963 118 101 anterior commisure Plasma 861 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211288 Last updated (according to GEO): Jul 18 2007 1000 Encephalitis CNS-SC_CtrA30m-2C-s2 861 Stem cells CD28 beads 02.00 hr. T-Cell Tumor__Lymphoma_Follicular_FSCC_S93_11021 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A NA18969 1000 Heart fetal buttock-thigh fibroblast #1, serum starved whole brain from wild-type littermate of nicotinic acetylcholine receptor subunit mutant mice Source GEO sample is GSM120574 Last updated (according to GEO): Sep 22 2006 1000 Decapitation 1000 Organ of Corti brain, Left frontal Lobe: Extract17_le1 N-2_PRE PGA-swim_4w1w_s1128 Brain 1000 Normal Source GEO sample is GSM175826 Last updated (according to GEO): Apr 09 2007 NA Source GEO sample is GSM198937 Last updated (according to GEO): Jun 07 2007 SN:1007082 Source GEO sample is GSM115363 Last updated (according to GEO): Jun 20 2006 Expression profiling of spinal cord section (T9) extracted from rats 28d following moderate injury Source GEO sample is GSM31541 Last updated (according to GEO): May 27 2005 NA12751 growth 1, replicate 5 NORMAL 1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Interatrial septum 865 of cancer 2098 2106 of somatomotor cortex 21 41 ALS model Source GEO sample is GSM75484 Last updated (according to GEO): Mar 06 2006 mouse hippocampus 0 17 Plasma 861 61 50 Spinal cord Voxel A4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1387 Last updated (according to GEO): Nov 21 2005 Liver pars nervosa of hypophysis 1000 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13099.gif Source GEO sample is GSM79906 Last updated (according to GEO): Sep 22 2006 for liver 26 35 Diabetes Mellitus 1000 1000 Coronary Arteriosclerosis Lung 861 Fibroblasts 861 Normal Source GEO sample is GSM175987 Last updated (according to GEO): Apr 09 2007 hippocampus Source GEO sample is GSM36005 Last updated (according to GEO): May 27 2005 H123 CB A Transitional epithelium 1000 Cerebellum 861 61 45 from 12 cochleas C57BL/6 benchmark dataset: Embryonic day 12.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25156 Last updated (according to GEO): May 27 2005 brain, cerebellum: RNA#21*_le1 0 Lung tissue 10 1000 Oocytes Brain 861 f2#177 versus pool Mouse Brain tissue Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:299, Count:32 Corner- Avg:40383, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:4.527624,SFGene:All Background:Avg:496.28,Stdev:77.48,Max:682.9,Min:347.6 Noise:Avg:11.61,Stdev:1.35,Max:14.8,Min:7.9 RawQ:13.98 Keywords = ALL Source GEO sample is GSM3409 Last updated (according to GEO): May 27 2005 861 Brain Plasma 861 Neoplasm 861 6 month spinal cord rep 1 of hippocampi 86 98 1238 1229 brain stem The nose 94 101 5 0 brain Pool of total RNA from 3 Ts1Cje cerebella (segmental trisomy of chromosome 16) at P0 postnatal stage Keywords = Down syndrome Keywords = Chromosome 21 Keywords = Transcriptome Keywords = Microarray Keywords = Brain Keywords = Cerebellum Keywords = Development Source GEO sample is GSM27479 Last updated (according to GEO): May 27 2005 myocardial infarction 383 403 Myocardium 861 Study of in vitro granulocyte differentiation Source GEO sample is GSM137452 Last updated (according to GEO): Jun 06 2007 AML-35 on Affymetrix GeneChip Human Full Length Array HuGeneFL total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withSLC (Secondary lymphoid-organ chemokine) for 30min Source GEO sample is GSM5769 Last updated (according to GEO): May 27 2005 Examining the effects of tTA expression in mouse hearts Source GEO sample is GSM15061 Last updated (according to GEO): May 28 2005 Cardiac 523 530 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28758 Last updated (according to GEO): May 27 2005 Infection 861 CNS-SpinalC-4hAdult-1A-s2 0029_1479_H95A2_T95-162_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 5 0 brain Brain 861 10 0 Huntington? Brain 1000 N/A Source GEO sample is GSM96292 Last updated (according to GEO): Feb 13 2006 861 Chromosomes T Cells Resting 30h 2 Resting in somatosensory cortex 26 49 E6.5_rep1 f2#271 versus pool Mouse Brain tissue 1000 Pituitary Gland Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 1391 blood Intestine_6wk_FVB_Female RD-ES Macrophage smi60 FVB/NJ Olfactory Bulb A Gene expression data from postmorten brain regions Source GEO sample is GSM146059 Last updated (according to GEO): Nov 20 2006 Liver 1000 Gene expression data from mouse primary visual cortex Source GEO sample is GSM101711 Last updated (according to GEO): Mar 27 2006 A HID U D042 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108610 Last updated (according to GEO): Aug 22 2006 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 72h after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44520 Last updated (according to GEO): May 27 2005 C57BL/6J Acute morphine treated, striatum, biological replicate 2 Source GEO sample is GSM187978 Last updated (according to GEO): Jun 14 2007 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195239 Last updated (according to GEO): Sep 13 2007 Cerebral cortex 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145028 Last updated (according to GEO): Nov 20 2006 Normal Source GEO sample is GSM176035 Last updated (according to GEO): Apr 09 2007 SCLC cell line DMS79 EWS-T12 on NHGRI-6.5k_b Date 1/19/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : headfold Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 2.5 mg/kg Time : 3.0 hrs post-injection Intervention : none Risk: benchmark dose modeled for 5% increased risk of microphthalmia Conditional biomarker: post-injection interval prior to p53 protein induction Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 16-20 headfolds pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = embryo Keywords = threshold Lot batch = AH606 Source GEO sample is GSM12066 Last updated (according to GEO): May 28 2005 Phenytoin hippocampus 4 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53422 Last updated (according to GEO): Aug 05 2005 Simple annotation: FNH, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10015.gif Source GEO sample is GSM79842 Last updated (according to GEO): Sep 22 2006 Parkinson Disease 861 Brain (amygdala) [JunctionChip 4 of 5] D01 12h Media 1000 Leukemia, Myelocytic, Acute Ta gr2 tumour Source GEO sample is GSM2531 Last updated (according to GEO): Mar 21 2006 Heart 1000 Liver Test (Blinded) Sample Source GEO sample is GSM130122 Last updated (according to GEO): Sep 18 2007 Temporal neocortex mTLE 8 Laser capture lung cancer cells Source GEO sample is GSM191056 Last updated (according to GEO): May 25 2007 901 Coronary artery 861 Malignant Neoplasms Ganglia 861 Spleen vs Terbutaline Treated B cell 30min (set3) Bone Marrow 1000 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156588 Last updated (according to GEO): Jan 22 2007 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181152 Last updated (according to GEO): Jul 12 2007 1000 ovarian neoplasm Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210384 Last updated (according to GEO): Jul 16 2007 1000 Brain 188 169 of hyperinsulinaemic Lung 861 CNS-RM_Mod4h-3B-s2 MALME-3M hgu95d 861 Mammary gland MGJZ030312083Ab220+bcell no additional Source GEO sample is GSM199350 Last updated (according to GEO): Jun 08 2007 Pool of 6 saccules at E14.5 Source GEO sample is GSM182618 Last updated (according to GEO): Aug 14 2007 spinal cord 0 11 Gene expression profile of presenilin conditional double knockout cerebral cortex, comparing to control. Age of mice: 6 months Source GEO sample is GSM22351 Last updated (according to GEO): May 27 2005 HapMap JPT Male Source GEO sample is GSM159641 Last updated (according to GEO): Feb 01 2007 Total RNA extracted from the cerebellum of a Lh-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144414 Last updated (according to GEO): Nov 14 2006 3AMH02030703_Uterus Simple annotation: Cell-cycle, Mitotic selection Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16425.gif Source GEO sample is GSM79628 Last updated (according to GEO): Sep 22 2006 B6_Control_ZT 12_1 Arteries 861 185 169 of microphthalmia Whole blood 0 10 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18914.gif Source GEO sample is GSM84182 Last updated (according to GEO): Sep 22 2006 2_cerebral_cortex_time_0_#39 Neoplasm 861 Coronary heart disease 913 Collagen 1000 Whole blood 0 10 Medulla Oblongata 861 small intestine PPARa knockout mice, fasted for 24 hours Source GEO sample is GSM154796 Last updated (according to GEO): Jul 04 2007 150 mg/kg X 24 hr Source GEO sample is GSM129830 Last updated (according to GEO): Sep 18 2007 with autism spectrum disorder 37 65 928 Hyperinsulinism Corl51 SCLC cell line 366 354 encephalitis Mouse retinal sphere RNA-3, chip MOE430B 2500 mg/kg X 12 hr Source GEO sample is GSM129876 Last updated (according to GEO): Sep 18 2007 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:364, Count:32 Corner- Avg:36544, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:15.267480,SFGene:All Background:Avg:408.40,Stdev:5.81,Max:426.0,Min:399.9 Noise:Avg:9.27,Stdev:0.43,Max:10.8,Min:8.4 RawQ:13.27 Keywords = ALL Source GEO sample is GSM3475 Last updated (according to GEO): May 28 2005 1000 medulloblastoma brain, brainstem: D60SODFNMN1_e1_le1 Spleen 1000 861 Colon 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201240 Last updated (according to GEO): Jun 14 2007 Adipose Tissue 5 Normal Corpus Callosum 10 Normal 861 Blood 861 Amyotrophic Lateral Sclerosis Skeletal bone 861 966 Hippocampus BXD 5_M7SS02080620 875 Acute leukemia cerebellum 7 16 228 219 Hippocampi oral_mucosa_3 Source GEO sample is GSM80778 Last updated (according to GEO): Mar 31 2006 156 145 Their livers c_NY101 865 Disorder of artery breast cancers 75 89 ScGT1_1 5 0 brain SN:1010429 Source GEO sample is GSM115393 Last updated (according to GEO): Jun 20 2006 HCC-2998 hgu95e Parkinson's disease sample x110 gene expression data from the Superior Frontal Gyrus of 2y-old normal girl, RNA labeled and hybridized Dec. 2001 Source GEO sample is GSM160306 Last updated (according to GEO): Feb 05 2007 Normal Source GEO sample is GSM175958 Last updated (according to GEO): Apr 09 2007 fetal buttock-thigh fibroblast #3, asynchronous 23 0 mammary epithelial cells 1000 Brain 913 Coronary heart disease Bone Marrow 1000 C57BL/6 benchmark dataset: Embryonic day 18.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25181 Last updated (according to GEO): May 27 2005 no additional Source GEO sample is GSM199070 Last updated (according to GEO): Jun 08 2007 healthy subject Source GEO sample is GSM211125 Last updated (according to GEO): Sep 10 2007 Parkinson Disease 1000 Epithelial cells from Astmatic subject were removed by dissection and digestion from bronchi of donor long tissue from normal subject. Source GEO sample is GSM3913 Last updated (according to GEO): May 27 2005 GCP.4 P2A_KIDNEY_3 TEL-AML1-#10 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Head and neck cancer Source GEO sample is GSM155722 Last updated (according to GEO): Apr 24 2007 Gene expression profile of the cell line UB/OC-1 grown at 33C (undifferentiated, day 0). This data set is a replica experiment of sample GSM1517. Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1529 Last updated (according to GEO): May 27 2005 CHIPEXP_NAME: 230_2_050531tpj_36h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Isoproterenol TREAT_TOX_MECHANISM1: Heart_Cardiotoxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0.5 SAMPLING_TIME: 1 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197610 Last updated (according to GEO): Jun 01 2007 These data were used as preliminary results for paper: Maternal Cocaine Administration Alters DNA Methylation in Hippocampal Neurons of Neonatal and Prepubertal Mice Svetlana I. Novikova, Fang He, Jie Bai, Nicholas J. Curtufello, Ashiwel S. Undie and Michael S. Lidow Source GEO sample is GSM154049 Last updated (according to GEO): Jan 19 2007 GBM Treatment, type=remove Source GEO sample is GSM99474 Last updated (according to GEO): Apr 21 2006 Zeitgeber Time Treatment, type=time_course, measurement=12.0 h Source GEO sample is GSM53335 Last updated (according to GEO): Jul 06 2005 39 21 from mammary glands Spleen 1000 VDXIGRU_211980 B_N2 on Affymetrix GeneChip Human Full Length Array HuGeneFL 7 cerebral cortex 21 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211360 Last updated (according to GEO): Jul 18 2007 GSE5388 111 90 of mental retardation Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 23.75 hours after lights on. Original sample code = CM18A Source GEO sample is GSM227352 Last updated (according to GEO): Sep 10 2007 occipital regions 163 179 901 Caudate nucleus structure 861 Myopathy adult fibroblasts 1412 1428 Nj15: Hippocampus_21PT-AI_rep6 1000 Spleen cerebellum 7 16 5 0 Tonsil 361 335 hypertrophic cardiomyopathy 32h-AC replication 2 Keywords = preimplantation Keywords = development Source GEO sample is GSM14717 Last updated (according to GEO): May 28 2005 Whole Brain 73 83 SCG_sema3A_12h_rep1 blood, Blood: 2391_0102_le1 I_U133A_81_AnCg 861 Gland structure 0 Human Cortex 11 Gene expression data from a neocortex from mouse injected 10 mg/kg nicotine Source GEO sample is GSM147411 Last updated (according to GEO): Jan 03 2007 90 81 in stroke 861 Brain Colon 1000 to the nose 599 609 no additional Source GEO sample is GSM199078 Last updated (according to GEO): Jun 08 2007 The aged mouse was injected intraperitoneal (ip) with saline (~100ul/mouse) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use. Source GEO sample is GSM73016 Last updated (according to GEO): Sep 07 2005 Adenocarcinoma 861 with myocardial infarction 313 339 Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 14 hours after lights on. Original sample code = CM48A Source GEO sample is GSM227311 Last updated (according to GEO): Sep 10 2007 Coronary Arteriosclerosis 1000 liver_PPARa-knockout_WY14643_6h_rep3 Primary tumor 19 32 861 Neoplasm Ovary_PD7_Foxo3 Wt_Replica 3 NZB-BlNJ_male_hypothalamus Source GEO sample is GSM138582 Last updated (according to GEO): Apr 18 2007 Saline ip saline ILI 4hrs post ILI sample A 1000 Lung spinal cord, ventral spinal cord: D28WTSP1 e1 le1 Wild type 8 wk old male FVB/NJ mouse pituitary gland Source GEO sample is GSM75008 Last updated (according to GEO): Feb 27 2007 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225957 Last updated (according to GEO): Nov 02 2007 from the right forebrain 21 44 Myocardium 861 I_95Av2_2978_AnCg_0_GS 861 Immediate hypersensitivity no doxycycline, wt Source GEO sample is GSM213371 Last updated (according to GEO): Jul 26 2007 Skin 1000 Pituitary Gland 861 A/J periaqueductal gray rep2 (430 2.0 Array) Gene expression data from postmorten brain regions Source GEO sample is GSM145951 Last updated (according to GEO): Nov 20 2006 GM19143 UterPreg45_022CACHU_111.txt 26 16 of modiolus Balb/c day 6, biological rep 3, tech rep 2 ProstateCancer-14 on NHGRI-6.5k_c Category: Lymphoma Classification Subcategory: Chronic Lymphocytic Leukemia Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n118 Source GEO sample is GSM2082 Last updated (according to GEO): Nov 21 2005 Normal Source GEO sample is GSM176070 Last updated (according to GEO): Apr 09 2007 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12540.gif Source GEO sample is GSM79809 Last updated (according to GEO): Sep 22 2006 Ovary Source GEO sample is GSM18998 Last updated (according to GEO): Sep 25 2006 1000 Structure of corneal epithelium 2nd 1hr C-CA1 plasma cells 50 61 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195231 Last updated (according to GEO): Sep 13 2007 178 157 from normal myometrium Whole blood 0 10 704 693 /db kidneys HCC (HBV+, SF18) Mesenchymal Stem Cells 1000 n/a Source GEO sample is GSM177934 Last updated (according to GEO): Jun 11 2007 Affymetrix RGU34A 24HA Microarray analysis of the developing cortex. human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155059 Last updated (according to GEO): Jun 04 2007 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92329 Last updated (according to GEO): Jan 13 2006 brain, unknown: R1B_e1_le1 Heart 1000 brain, Right Frontal Lobe: Extract58_le2 M_U133Plus_114_nAcc Normal__Breast_BR_1 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A VDXOXFU_245 Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.4 Subject: 2978 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39047 Last updated (according to GEO): May 27 2005 HeartVentr22TAFIE_081.txt 1000 Mammary gland 10 0 spinal cord prostate Source GEO sample is GSM203265 Last updated (according to GEO): Jun 21 2007 Communicable Diseases 1000 mouse hippocampus from COX-1 WT Source GEO sample is GSM121438 Last updated (according to GEO): Jan 31 2007 I_U133Plus_73_Amy Stomach Cardiac 1 Normal umbilical cord_nobpd: 3F Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16660.gif Source GEO sample is GSM81546 Last updated (according to GEO): Sep 22 2006 Large-scale analysis of the mouse transcriptome. Liver C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 233.37 Stdv: 7.07 Min: 222.16 Max: 244.82 Source GEO sample is GSM2934 Last updated (according to GEO): Mar 20 2006 Parkinson Disease 861 bc-ZT21-2 1000 Rectum hip_1016_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Brain 1000 olfactory epithelium 194 213 17 7 hippocampi nasal epithelial cells 28 49 Primary Carcinoma 875 21 6 (corpus callosum Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188707 Last updated (according to GEO): Jun 06 2007 nodose_nucleus_1 plasma cells 50 61 intermediolateral column motoneurons (IML) 12 861 Cardiomyopathies After 2 week acclimation to 12 hr/12 hr light/dark regimen, c57/Bl6 mice were subjected to a 36 hour period of constant darkness. Aortae were subsequently harvested at 4 hour intervals to 48 hours. Duplicate microarrays were hybridized with biotin-labeled probes derived from aorta tissue (6 pooled aortae/timepoint). Source GEO sample is GSM6097 Last updated (according to GEO): May 27 2005 1000 Spleen 4_cerebral_cortex_12hrs_sleep_#34 Diurnally regulated gene expression in the prefrontal cortex of C57Bl/6J mice at Zeitgeber Time (ZT) 3, 9, 15, and 21. 304 280 alcoholic cardiomyopathy 663 mesenchymal stem cell 642 Neocortical astrocyte 2 H132 CN A ALL B-cell46 on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132551 Last updated (according to GEO): Feb 26 2007 15 CN B In our original grant we proposed to use the NR3B-null mouse model to study the role of NR3B subunit in motor neuron function. We have now successfully generated NR3B null mice. Interestingly, NR3B-null mice invariably die at age P4-P8. Our preliminary examination indicates that the motor strength of these mice is severely impaired prior to death. As we continue to explore the cause of death in NR3B null mice, we propose to conduct gene profiling experiments to search for transcription changes in the brain related to ablation of the NR3B gene. We have used the facility provided by the NINDS/NIMH Microarray Consortium to identify genes that show abnormal expression patterns in these mice. We would like to compare these changes with that opccured in SOD1 mice, a mouse model of motor neuron diseases. Analysis of these genes will help to identify changes in networks and pathways that may cause the death of NR3B-null mice. These studies will further help to elucidate the functional role of NR3B in motor neurons. We will compare samples from motor neurons of wild type and SOD1 mice to identify genes that show abnormal expression patterns, which may be implicated in the death of SOD1 mice and shared with the same changes in NR3B-null mice. We hypothesize that genes with their transcription level changing significantly in SOD1 mutant mice will be associated with the molecular mechanism underlying the death of motor neurons. We like to compare motor neuron and spinal cord smaples from SOD1 mice at the age prior to the disease onset. Total RNA from total 9 samples will be purified, each from ~200 motor neurons obtained by Laser Capture Microdissection and the total spinal cord. Extracted RNAs will be subjected to one or two rounds of amplification and the obtained cRNA will be biotinylated. The purified cRNA will be sent to the NINDS/NIMH Microarray Consortium be used to hybridize the GeneChip Mouse Genome 430 2.0 Array. The hybridization, scanning, and initial data analysis of these GeneChips will be conducted by the Consortium staff. We will analyze the collected data further after data collection. We will first identify genes that show significant changes between wild-type and SOD1 mice and then compare that with the result from NR3B null mice. Last Updated (by provider): Jun 09 2006 Contributers: Dongxian Zhang from aorta 100 110 901 Spinal Cord 42-95_SCC bladder_T2-4_pool-2 cardiac 763 769 Gene expression data from controls Source GEO sample is GSM231003 Last updated (according to GEO): Sep 21 2007 10 7 Left CNS-SCsev_InjB14d-2C-s2 1000 Coronary Arteriosclerosis 3rd 2hr C-CA1 861 Cerebral cortex 1000 Brain 112 98 from the kidney Gene expression data from postmorten brain regions Source GEO sample is GSM145119 Last updated (according to GEO): Nov 20 2006 5 0 brain 1000 Left Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141293 Last updated (according to GEO): Oct 26 2006 A VIS D033 OCI Ly3 Expression profiling of spinal cord section (T10) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM4464 Last updated (according to GEO): May 28 2005 ramaswamy-cancer 0 15 Gene expression data from PD14 Foxo3 Null ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203838 Last updated (according to GEO): Aug 02 2007 Ovary 1000 within the brain 656 672 human frontal cortex Source GEO sample is GSM86976 Last updated (according to GEO): Feb 08 2006 in rat cerebral cortex 18 39 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16712.gif Source GEO sample is GSM91493 Last updated (according to GEO): Sep 22 2006 Nasal Epithelium 865 P24 deprived visual cortex replicate 1 1000 Brain ProstateCancer-1 on NHGRI-6.5k_c 1037 of transitional epithelium 1012 Neoplasm 861 Skeletal bone 861 Melanoma metastatic cell line A375, biological rep8 (LeiFidler) Anterior nares 1000 Alzheimer's Disease 1000 A/J Olfactory Bulb E KT1002b_N TS13 sample 1 (cerebrum) 861 Blood P1_KIDNEY_5 H9LMS00111003 5 0 brain Disease Source GEO sample is GSM175918 Last updated (according to GEO): Apr 09 2007 176 166 bone marrow in breast 1043 1052 Brain 861 338 333 brain JMR-RatInj72h-3aA-s2 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc61 Source GEO sample is GSM1852 Last updated (according to GEO): Nov 21 2005 NZB/BlNJ_female_hypothalamus A549_CL1004__NSCLC Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211268 Last updated (according to GEO): Jul 18 2007 The etiology of the central nervous system (CNS) alterations after human immunodeficiency virus (HIV) infection, such as dementia and encephalitis, remains unknown. We have used microarray analysis in a monkey model of neuroAIDS to identify 98 genes, many previously unrecognized in lentiviral CNS pathogenesis, whose expression is significantly up-regulated in the frontal lobe of simian immunodeficiency virus-infected brains. Further, through immunohistochemical illumination, distinct classes of genes were found whose protein products localized to infiltrating macrophages, endothelial cells and resident glia, such as CD163, Glut5, and ISG15. In addition we found proteins induced in cortical neurons (ie, cyclin D3, tissue transglutaminase, alpha1-antichymotrypsin, and STAT1), which have not previously been described as participating in simian immunodeficiency virus or HIV-related CNS pathology. This molecular phenotyping in the infected brains revealed pathways promoting entry of macrophages into the brain and their subsequent detrimental effects on neurons. These data support the hypothesis that in HIV-induced CNS disease products of activated macrophages and astrocytes lead to CNS dysfunction by directly damaging neurons, as well as by induction of altered gene and protein expression profiles in neurons themselves which are deleterious to their function. Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92282 Last updated (according to GEO): Jan 13 2006 Expression profiling of spinal cord section (T8) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM6645 Last updated (according to GEO): May 28 2005 858 Prostatic Neoplasms Expression profiling of spinal cord section (T9) extracted from rats 21d following moderate injury Source GEO sample is GSM31526 Last updated (according to GEO): May 27 2005 of prion disease 188 204 hypothalamus sprague1 whole tissue, pool of 5 animals, 16 weeks old, male Sprague Dawley hypothalamus file:R3MH02061102 Source GEO sample is GSM15233 Last updated (according to GEO): May 28 2005 Cord blood, primary UCB302-D7 HCT-116_CL4003_COLON osteoblast 630 640 SCG_control_65h_rep1 1000 Neurotransmitters Arteries 861 1000 Brain Neoplasm 861 adenoma 861 Blood 1000 Spinal Cord 1000 40 25 in breast cancer ER negative human primary breast tumor EA02014_41298_H133A_JA-2007 Amygdala 4 Normal 50 43 jejunum NCI60.15_LABEL19EXTRACT18SUB3 Source GEO sample is GSM134067 Last updated (according to GEO): Aug 06 2007 Plasma 861 I_U133Plus_120_CB of female Wistar soleus muscle 84 113 861 Neoplasm 1000 Lung Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188853 Last updated (according to GEO): Jun 06 2007 NCI60.49_LABEL53EXTRACT52SUB3 Source GEO sample is GSM134243 Last updated (according to GEO): Aug 06 2007 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 1 - Pair 2 - IML Source GEO sample is GSM49879 Last updated (according to GEO): Dec 20 2005 901 Bone Marrow 453 434 The descending colon Colon 1000 39 27 the maxillary Brain 1000 1000 medulloblastoma golub-leukemia 0 13 CS-B wt-rescued cell UVC-irradiated (12hour) replicate 1 U133A Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3882 Last updated (according to GEO): May 27 2005 NCI60.25_LABEL29EXTRACT28SUB3 Source GEO sample is GSM134118 Last updated (according to GEO): Aug 06 2007 P7_cy3_3 Expression profiling of spinal cord section (T10) extracted from rats 4h following laminectomy (sham) Lot batch = Source GEO sample is GSM6632 Last updated (according to GEO): May 28 2005 Week 1 Control Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211337 Last updated (according to GEO): Jul 18 2007 stria terminalis 1000 Probeset expression data from NA12751 growth 3, replicate 2 Source GEO sample is GSM195214 Last updated (according to GEO): Aug 08 2007 1000 ovarian neoplasm 963 944 of Rat1 fibroblasts no additional Source GEO sample is GSM199172 Last updated (according to GEO): Jun 08 2007 Cultured in DMEM with 10% FBS and penicillin (100U/ml)/streptomycin (100ug/ml). Media changed every other day. 37ºC, 5% CO2. Source GEO sample is GSM15787 Last updated (according to GEO): Oct 28 2005 Plasma 861 Stem cells 901 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188829 Last updated (according to GEO): Jun 06 2007 Colon 1000 PriG_5%O2_Expt1_Day5_rep1 We build a model for the molecular and cellular events underlying phenotypic discordance in glycine receptor defects (beta subunit). Some mice progress and die, while their littermates recover and get better, despite the same mutation on an inbred genetic background. We find evidence for glycine neurotransmitter toxicity and loss of glycinergic interneurons early in the disease, but some mice are able to keep things going until they can over-express homomeric alpha1 channels, whereupon they recover. In the mice progressing towards lethality, neurotransmitter toxicity too quickly extends to GABAergic interneurons and motorneurons, and they lose their window of time to upregulate the alpha1 glycine receptor, and they crash and burn. Importantly, human patients with glycine receptor defects typically show a resolution of their phenotype with age, and we propose that the same remodeling events are occuring in human patients. Source GEO sample is GSM30992 Last updated (according to GEO): May 27 2005 Serum 12 366 354 encephalitis 256 235 with HIV encephalitis Subject code A2 with some respiratory epithelium. 1039 1072 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 1 hour following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM11033 Last updated (according to GEO): May 28 2005 1000 Cerebellum TemporalLobe Source GEO sample is GSM18753 Last updated (according to GEO): Sep 25 2006 10 week mutant spinal cord rep 1 861 Blood Cerebral cortex 861 66 56 femur C57BL D_95Av2_3108_AnCg_0_GS Mental Retardation 1000 lateral hypothalamus 24 44 ileum (pool of 4 animals)_Germ-free_A_5553 Source GEO sample is GSM161581 Last updated (according to GEO): Apr 23 2007 Medulla 861 1000 Liver 669 stem cells 660 Spleen vs fMLP Treated B cell 60min (set2) MuscleRegen-ctx7d-1RLbAv2-s2 Brain 1000 Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231046 Last updated (according to GEO): Sep 26 2007 brain, cortex: 14dsham1_e1_le1 36 21 from whole brain Nrf2 +/+ mice (C57B6/SJL) were crossed with nrf2 -/- mice (C57B6/129SVJ) to generate mice heterozygous for nrf2. Interbreeding these heterozygotes generated the double-knockout mice (nrf2 -/-) as well as the corresponding littermate controls (nrf2 +/+). Mice were housed in plastic cages on a bedding of wood chips and maintained at ~22C, ~60% relative humidity, and a 12 hr light/dark cycle. The animals were fed with mouse diet 5015, which includes 30 IU/g of vitamin A and 35 IU/kg of vitamin E, (LabDiet, Richmond, IN) and drinking water ad libitum. All animal protocols were approved by the Institutional Animal Use and Care Committee at the University of Wisconsin-Madison. Total RNA was extracted from livers and spleens isolated from male and female nrf2 wildtype and knockout mice at 5 months of age (prior to the development of severe autoimmune disease). Keywords = Nrf2 Keywords = liver Source GEO sample is GSM13439 Last updated (according to GEO): May 28 2005 Parkinson 0 8 KT76_AR2/DT/IN spinal cord 1845 1855 1000 Lung NA Source GEO sample is GSM84315 Last updated (according to GEO): Dec 01 2005 Standard Affymetrix Protocol Keywords = microarray Keywords = muscle Source GEO sample is GSM15941 Last updated (according to GEO): May 28 2005 BALB/c_OVA Replicate 1 comparison of olfactory-bulbectomized and sham-operated rats with depressive-like behaviour Source GEO sample is GSM247200 Last updated (according to GEO): Dec 11 2007 spinal cord 13 23 Medulla 861 with myocardial infarction 313 339 Cerebellum 0 9 total RNA from biosource CC#12 Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92477 Last updated (according to GEO): Jan 13 2006 1000 Cerebral cortex Primary tumor 19 32 Ovary 1000 Wild type 8 wk old male DBA/2J mouse hypothalamus Source GEO sample is GSM74978 Last updated (according to GEO): Feb 27 2007 n/a Source GEO sample is GSM178051 Last updated (according to GEO): Jun 11 2007 1000 Cartilage 12 frontal Lobe 23 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28802 Last updated (according to GEO): May 27 2005 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151994 Last updated (according to GEO): Feb 06 2007 Olfactory Epithelium 1000 GRP sample 11 from the right forebrain 21 44 5 0 brain ventral tegmental area 24 46 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225679 Last updated (according to GEO): Nov 05 2007 26-2 spinal cord 4 19 Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Last Updated (by provider): Jun 12 2007 Contributers: Arneet L Saltzman Brendan J Frey Tomas Babak Wen Zhang Derek van der Kooy Timothy R Hughes Christine Misquitta Yoseph Barash Qun Pan Joanna Ip Sandrine Willaime-Morawek Matthew Fagnani Benjamin J Blencowe Aviad Rozenhek Naveed Mohammad Ofer Shai Leo Lee Female; Uterus - virgin-diestrus Keywords = mouse gene expression database Source GEO sample is GSM29332 Last updated (according to GEO): May 27 2005 Normal__Kidney_Norm_627 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Parkinson Disease 861 metanephric mesenchyme, LIF, 3 days, biological rep2 placenta-0735-uninflamed-uninfected-rep1 1000 Pituitary Gland 5 0 blood Whole Brain 73 83 HCC (HBV+, HK56) IleumSBR_22QAFB6_177.txt 913 Coronary heart disease CNS-RM_Ctr14d-1C-s2 from metastases 803 817 861 Mammary gland Total RNA was extracted from umbilical subcutaneous adipose tissue from an individual affected with FCHL and exhibiting the USF1 protective haplotype Source GEO sample is GSM9048 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145440 Last updated (according to GEO): Nov 20 2006 928 Endometrium 1933 tumor cells 1943 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159979 Last updated (according to GEO): Feb 01 2007 329 306 valvular cardiomyopathy f2#209 versus pool Mouse Brain tissue 2-cell embryo replication 2 Keywords = preimplantation Keywords = development Source GEO sample is GSM14668 Last updated (according to GEO): May 28 2005 17 7 hippocampus with acute measles 20 37 Parkinson's disease sample x109 0 30 928 Endometrium Spleen 0 5 484_7d HDMTX_MP-5 brain, cerebral cortex: Rat_03-12_NroLep_Lipska_e1_le1 male C57BL6, double amplification Source GEO sample is GSM5434 Last updated (according to GEO): May 27 2005 5 0 Kidney Adipose Tissue 3 Normal 89 70 isolated theca cells PGA-RnSalt_c_15w_1-m5 Abdomen 861 Sample 111 on vantveer-oligo Expression profiling of spinal cord section (T10) extracted from rats 30m following mild injury Source GEO sample is GSM31324 Last updated (according to GEO): May 27 2005 78 73 rectum Gene expression data from postmorten brain regions Source GEO sample is GSM145966 Last updated (according to GEO): Nov 20 2006 TEL-AML1-C52 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Infection Substantia nigra normal rep5 Epithelium 861 Leg 7 Day mdx rep 1 1000 Heart between the LAD artery 266 287 Array representing response of human foreskin fibroblasts at 12 h post infection with HCMV Source GEO sample is GSM10348 Last updated (according to GEO): May 27 2005 HC66 CB A 15 0 human cerebellum labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156604 Last updated (according to GEO): Jan 22 2007 Nrf2 +/+ mice (C57B6/SJL) were crossed with nrf2 -/- mice (C57B6/129SVJ) to generate mice heterozygous for nrf2. Interbreeding these heterozygotes generated the double-knockout mice (nrf2 -/-) as well as the corresponding littermate controls (nrf2 +/+). Mice were housed in plastic cages on a bedding of wood chips and maintained at ~22C, ~60% relative humidity, and a 12 hr light/dark cycle. The animals were fed with mouse diet 5015, which includes 30 IU/g of vitamin A and 35 IU/kg of vitamin E, (LabDiet, Richmond, IN) and drinking water ad libitum. All animal protocols were approved by the Institutional Animal Use and Care Committee at the University of Wisconsin-Madison. Total RNA was extracted from livers and spleens isolated from male and female nrf2 wildtype and knockout mice at 5 months of age (prior to the development of severe autoimmune disease). Keywords = Nrf2 Keywords = liver Source GEO sample is GSM13436 Last updated (according to GEO): May 28 2005 BAL_19_A0B0 114 101 brains quickly HMVEC-L stimulated with LPS for 4 hours L04R3 Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108003 Last updated (according to GEO): Jun 06 2006 Interatrial septum 865 CNS-SpinalCmod-Adult-72h-1A-s2 Total RNA from cultured modiolus, pool from 12 cochleas; used as control for hypoxia. Source GEO sample is GSM124571 Last updated (according to GEO): Aug 04 2006 Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153778 Last updated (according to GEO): Jan 19 2007 1000 Brain 3x3 Pooling Strategy. See Nadler et al., 2006 Source GEO sample is GSM114474 Last updated (according to GEO): Jun 16 2006 861 Malignant neoplasm of prostate GM12249 1000 Structure of middle temporal gyrus 90minplus.1 none Source GEO sample is GSM244548 Last updated (according to GEO): Nov 23 2007 V5-P069 I_U133A_60_Amy Expression profiling of spinal cord section (T10) extracted from rats 28d following severe injury Source GEO sample is GSM31372 Last updated (according to GEO): May 27 2005 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181093 Last updated (according to GEO): Jul 12 2007 63 50 Amygdala C57BL basal culture, 9A1, rep 2 0 Human Cortex 11 spleen 301 306 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM226151 Last updated (according to GEO): Nov 02 2007 24 0 human prostate PC3 tumors C57BL/6 benchmark dataset: Embryonic day 18.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25182 Last updated (according to GEO): May 27 2005 Retina 1000 Comprehensive analysis of PPARa-dependent regulation of hepatic lipid metabolism by expression profiling - Rattus norvegicus Liver 1000 ALS model Source GEO sample is GSM75487 Last updated (according to GEO): Mar 06 2006 vascular disease 142 157 Replicate2_Voxel A7 Laser captured visceral sensory neurons. Source GEO sample is GSM63676 Last updated (according to GEO): Dec 21 2005 98 86 of aged brain Gastrin Knockout fundus replicate 1 R7N 3 Gene expression data from postmorten brain regions Source GEO sample is GSM145304 Last updated (according to GEO): Nov 20 2006 Human retinal sphere RNA-2, chip HG-U133A #22 (isolate 8 rich media plGF 24hours) Prostate carcinoma 1000 861 Amygdaloid structure Laser capture lung cancer cells Source GEO sample is GSM191021 Last updated (according to GEO): May 25 2007 901 Stem cells Whole blood 0 10 SN:1006732 Source GEO sample is GSM115357 Last updated (according to GEO): Jun 20 2006 seminoma specimen, pT1, patient age: 51y; W02 116 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211431 Last updated (according to GEO): Jul 18 2007 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211231 Last updated (according to GEO): Jul 18 2007 of mouse brain 9 23 GSE4492 in the brain 150 162 366 354 encephalitis Liver Test (Blinded) Sample Source GEO sample is GSM130123 Last updated (according to GEO): Sep 18 2007 none Source GEO sample is GSM239921 Last updated (according to GEO): Dec 07 2007 861 Blood rat cortex Treatment, type=time_course, measurement=0.1 d Source GEO sample is GSM53203 Last updated (according to GEO): Jul 06 2005 Bladder sample 1164-1 Osteoblasts 1000 Parkinson? 0 9 Gene expression data from mouse colon Source GEO sample is GSM198116 Last updated (according to GEO): Aug 22 2007 Epithelial Cells 901 in cellular blood 327 343 Proteoglycan 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145906 Last updated (according to GEO): Nov 20 2006 I_U133A_71_DLPFC B6_SleepDep_ZT 12_2 for liver 26 35 Bone Marrow 1000 Heart 1000 Individual LCL vs Pooled control LCLs Source GEO sample is GSM3324 Last updated (according to GEO): Mar 21 2006 D_U133A_92_DLPFC Gene expression data from PD7 Foxo3 wild-type ovary sample on Affymetrix Mouse Genome 430 2.0 chip. Source GEO sample is GSM203826 Last updated (according to GEO): Aug 02 2007 5 0 brain infection 278 287 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11256 Last updated (according to GEO): May 28 2005 Experimental Autoimmune Encephalomyelitis 901 865 Ovarian Diseases brain, Right Frontal Temporal: Extract67_le1 1000 Liver none Source GEO sample is GSM123190 Last updated (according to GEO): Jul 26 2006 124T Tissue Source GEO sample is GSM67225 Last updated (according to GEO): Jan 19 2006 T-ALL-#2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A NCI60.9_LABEL12EXTRACT11SUB3 Source GEO sample is GSM134037 Last updated (according to GEO): Aug 06 2007 testis 52 58 Anterior nares 1000 RMS-C9 on NHGRI-6.5k_b Gene expression data from postmorten brain regions Source GEO sample is GSM144877 Last updated (according to GEO): Nov 20 2006 HeLa sample 2 Primary Neoplasm 1000 D_U133A_3_HC EOM 112 Day Control rep 2 M_U133A_41_AnCg nasal epithelial cells 28 49 retina 7 12 Autistic Disorder 877 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3306 Last updated (according to GEO): Mar 21 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145272 Last updated (according to GEO): Nov 20 2006 GSE96 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114176 Last updated (according to GEO): Jun 16 2006 865 Disorder of artery 225 210 atherosclerosis from the right forebrain 21 44 Biopsy of the normal mucosa of the colon from patient #18 adenocarcinoma 3479 Gene expression data from postmorten brain regions Source GEO sample is GSM145364 Last updated (according to GEO): Nov 20 2006 Parkinson Disease 1000 in blood 16 23 days nasal epithelium 1127 1148 43 20 of human breast tumours D_U133A_15_HC dorsal_root_ganglia_1 Source GEO sample is GSM80611 Last updated (according to GEO): Mar 31 2006 Cerebral cortex 1000 Colon 1000 BACKGROUND: Progressive neurological dysfunction is a key aspect of human aging. Because of underlying differences in the aging of mice and humans, useful mouse models have been difficult to obtain and study. We have used gene-expression analysis and polymorphism screening to study molecular senescence of the retina and hippocampus in two rare inbred mouse models of accelerated neurological senescence (SAMP8 and SAMP10) that closely mimic human neurological aging, and in a related normal strain (SAMR1) and an unrelated normal strain (C57BL/6J). RESULTS: The majority of age-related gene expression changes were strain-specific, with only a few common pathways found for normal and accelerated neurological aging. Polymorphism screening led to the identification of mutations that could have a direct impact on important disease processes, including a mutation in a fibroblast growth factor gene, Fgf1, and a mutation in and ectopic expression of the gene for the chemokine CCL19, which is involved in the inflammatory response. CONCLUSION: We show that combining the study of inbred mouse strains with interesting traits and gene-expression profiling can lead to the discovery of genes important for complex phenotypes. Furthermore, full-genome polymorphism detection, sequencing and gene-expression profiling of inbred mouse strains with interesting phenotypic differences may provide unique insights into the molecular genetics of late-manifesting complex diseases. 941 Recurrent tumor Wild type 8 wk old male 129S6/SvEvTac mouse pituitary gland Source GEO sample is GSM107041 Last updated (according to GEO): Mar 05 2007 Lymphoblastoid Cell Line for Individual 8182.3 log phase TNFTG-3w-m-3 1000 Myeloid Leukemia, Chronic liver 0 5 D_U133A_98_Amy Squamous cell carcinoma 3 Pool of 7 saccules at E12.5 Source GEO sample is GSM182611 Last updated (according to GEO): Aug 14 2007 Barcode: 251316210185 Source GEO sample is GSM159387 Last updated (according to GEO): Jul 17 2007 1000 Liver D_U133A_81_DLPFC cy5:SHR treated w/ nifedipine and then washed out, biological rep 4r; cy3:pool of 6 WKY control rats of coronary artery disease 317 342 Mammary Gland @ Lac1, biological rep3 Blood Test (Blinded) Sample Source GEO sample is GSM129966 Last updated (according to GEO): Sep 18 2007 testis 52 58 from ventral prostate 21 41 KHG-HG-4Av2-s2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Voxel D4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1411 Last updated (according to GEO): Nov 21 2005 12 0 ovarian tumor NG010_c Male Sprague-Dawley rats (400Ã?±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 72h after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44484 Last updated (according to GEO): Oct 28 2005 Small cell carcinoma of lung 901 SN7d(1) CLL-14 || lc8n118 0 Human Cortex 11 Liver Test (Blinded) Sample Source GEO sample is GSM130127 Last updated (according to GEO): Sep 18 2007 Gene expression data from mouse primary visual cortex Source GEO sample is GSM101698 Last updated (according to GEO): Mar 27 2006 1000 Organ of Corti Epithelium 861 medulla_1 PGA-MurLungRag-pbs-24h-1aCv2-s2 MCF7_CHX_E2_24h_rep1 Heart 1000 from mouse colon 21 36 Brain 861 NL-504-A407?-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A D_U133Plus_123_nAcc Exp B_2, 30mg/kg CPF Locus Coeruleus Source GEO sample is GSM107932 Last updated (according to GEO): Jun 06 2006 SCG explant cultured for 24 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246041 Last updated (according to GEO): Dec 03 2007 Double KO 1 Thymus, Whole thymus: Amplified mRNA_le1 of endothelial cells 629 648 human frontal cortex Source GEO sample is GSM86934 Last updated (according to GEO): Feb 08 2006 Medulla 861 901 Hepatocyte Affymetrix GeneChip® Mouse Genome 430 2.0 Array Source GEO sample is GSM197123 Last updated (according to GEO): May 31 2007 Whole Brain 62 72 RNA isolated from fetal cerebellum Keywords = trisomy Keywords = brain Keywords = Down syndrome Source GEO sample is GSM22587 Last updated (according to GEO): May 27 2005 seminoma specimen, pT2, patient age: 31y; W03 033 Testis 861 trigeminal_ganglia_2 Source GEO sample is GSM80876 Last updated (according to GEO): Mar 31 2006 1106 1090 that the cochleae -_6080_batch3 on NHGRI-6.7k Gene expression data from the hippocampus of S1P3-knockout mouse Source GEO sample is GSM172972 Last updated (according to GEO): Mar 08 2007 Replicate3_Voxel C3 of the postmortem brains 674 698 of the atrial 647 659 865 Disorder of artery 861 Carcinoma adACN3 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184778 Last updated (according to GEO): Apr 26 2007 26 hr Hela Double Thymidine, exp2 that fibroblasts 450 465 dorsal striatum 0 14 861 Encephalitis V5-P083 Wild type voxel G2 1000 Brain Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184812 Last updated (according to GEO): Apr 26 2007 Secondary malignant neoplasm of lymph node 1000 Coronary Arteriosclerosis 1000 Parkinson Disease 1000 Putamen 1 Normal prostate Source GEO sample is GSM203364 Last updated (according to GEO): Jun 21 2007 Date 3/9/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : headfold Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 2.5 mg/kg Time : 4.5 hrs post-injection Intervention : 4.0 mg/kg PK11195 co-administered Risk: remediated Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 16-20 headfolds pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = PK11195 Keywords = embryo Keywords = microphthalmia Lot batch = AM040 Source GEO sample is GSM12206 Last updated (according to GEO): May 28 2005 1221 1205 in breast tumours osteoblast 627 637 Parkinson Disease 1000 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225748 Last updated (according to GEO): Nov 02 2007 Plasma 861 Placenta [JunctionChip 2 of 5] Control 3 Primary large cell neuroendocrine carcinoma 1408 0 47 Female 26.5 yr before antibody enrichment scan 1 (U133A) osteoblast 627 637 Bone Marrow 1000 Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181047 Last updated (according to GEO): Jul 12 2007 Epithelial Cells 901 60 36 of newborn rats inner ear Transplant Series 10 , Transplant # 1 Normal human tissue:Normal Bone Marrow Keywords = Human, Normal Tissue, Normal Bone Marrow Source GEO sample is GSM44693 Last updated (according to GEO): May 27 2005 Heart 1000 Day 1_L_+RA_Achip BALB/cByJ Frontal Cortex A contralateral Cortex 7 27 none Source GEO sample is GSM210340 Last updated (according to GEO): Jul 16 2007 human caudate nucleus Source GEO sample is GSM86843 Last updated (according to GEO): Feb 08 2006 Brain 861 B6_Control_ZT 18_3 embryo_released_at_day3.5_rep2 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.13 Subject: 1871 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39046 Last updated (according to GEO): May 27 2005 22 0 Mammary Gland @ Preg12 159T mefloquine-treated NG108 neuronal cells 6 testis 52 58 Total RNA extracted from the cerebellum of a Tg+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144400 Last updated (according to GEO): Nov 14 2006 frontal cortex 0 13 913 Acute leukemia Epithelium of bronchus 983 GSE2595 osteoblast 627 637 BCR-ABL-R1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Skeletal muscle structure 901 starved 143 149 Cerebellum Control (AD) 6 Tumor__Leukemia_ALL-T_ALL_(17269)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 861 Blood 36 21 from whole brain Large-scale analysis of the mouse transcriptome. Olfactory bulb C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 463.21 Stdv: 16.59 Min: 433.07 Max: 491.87 Source GEO sample is GSM2926 Last updated (according to GEO): May 27 2005 ER-/LN+/Marks214 on Affymetrix GeneChip Human Full Length Array HuGeneFL Myocardial Infarction 1000 n/a Source GEO sample is GSM177954 Last updated (according to GEO): Jun 11 2007 748-1 861 Bone Marrow Spleen 1000 Parkinson Disease 1000 Muscle 861 The hypothalamo-neurohypophyseal system (HNS) is crucial for osmoregulation. The HNS consists of the magnocellular neurons (MCNs) of the hypothalamus that have their axons terminating in the posterior pituitary. The HNS exerts its role in water balance via the release of the anti-diuretic hormone vasopressin (VP). Following dehydration VP is released into the general circulation. By binding to V2-type receptors located in the kidney, VP decrease the amount of water lost in urine. An osmotic stimulus also elicits an increase in VP gene expression and a functional remodelling of the entire HNS. We want to understand this plasticity in terms of the co-ordinated reprogramming of gene expression. We thus used Affymetrix U34a rat GeneChips to examine the dynamics of gene expression plasticity over the duration of a dehydration stimulus. Arrays were probed in triplicate with targets derived from SON of control rats, and rats dehydrated for 1 and for 3 days. Transcripts were thus identified that respond early to dehydration (up- or down-regulated after only 1day of dehydration), or that respond late (up- or down-regulated at 3 days of dehydration).  Last Updated (by provider): Oct 28 2005 Contributers: Thomas Thykjaer Torben Orntoft Charles C Hindmarch Mohamed T Ghorbel D1_TP-48_C from colorectal adenoma 21 44 660 mesenchymal stem cell 639 Brain_MD_59_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression data from the neocortex of S1P2-knockout mouse Source GEO sample is GSM172941 Last updated (according to GEO): Mar 08 2007 HCC (HBV+, HK7) Brain 861 between the hepatic sinusoidal endothelium 1443 1484 GSE6008 WGACON-96 Early secretory endometrium from patient with endometriosis Source GEO sample is GSM150203 Last updated (according to GEO): Dec 14 2006 1000 frontal lobe Effects of SOCS3 on transcriptional response of macrophages to IL-6. Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Replicate 2 unstimulated. Source GEO sample is GSM6078 Last updated (according to GEO): Mar 10 2006 17 7 hippocampus 861 Blood HapMap CEU_parent Male Source GEO sample is GSM159519 Last updated (according to GEO): Feb 01 2007 plasma cells 332 344 Acetaminophen 24hr Rat 2486 blood vs. Acetaminophen 24hr Rat Pooled Control blood Brain 861 Normal__Germinal_Center_GC3 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 1000 Leukemia, Myelocytic, Acute NG108 rat neuronal cell culture exposed to 0.25% DMSO (control) for two hours. 10 µg total RNA hybridized per chip. RNA STAT 60 used to extract RNA. Standard Affymetrix chip scaling factors used. No other data transformation. Source GEO sample is GSM1658 Last updated (according to GEO): Oct 28 2005 1000 Spleen Blood 861 TUMOR 26 0 7 ovarian tumor: serous Source GEO sample is GSM139464 Last updated (according to GEO): Apr 09 2007 R724P00901 1000 jejunum 0029_1425_H95A2_T96-159_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A LCM 20 biological rep1 Analysis of target genes induced by the Amyloid Precursor Protein Intracellular Domain (AICD) Source GEO sample is GSM93710 Last updated (according to GEO): Jan 25 2006 D_U133A_5_nAcc 861 Cancer of Neck "6h Thy-Noc, Exp4" Gene expression data from liver Source GEO sample is GSM243353 Last updated (according to GEO): Nov 16 2007 901 Optic Nerve 901 Stem cells Normal human tissue samples from ten post-mortem donors were processed to generate total RNA, which was subsequently analyzed for gene expression using Affymetrix U133 plus 2.0 arrays. Donor information: Donor 1 - 25 year old male; donor 2 - 38 year old male; donor 3 - 39 year old female; donor 4 - 30 year old male; donor 5 - 35 year old male; donor 6 - 52 year old male; donor 7 - 50 year old female; donor 8 - 48 year old female; donor 9 - 53 year old female; donor 10 - 23 year old female Last Updated (by provider): Mar 30 2006 Contributers: Richard B Roth 1000 Liver Cirrhosis 13 0 Nervous System We build a model for the molecular and cellular events underlying phenotypic discordance in glycine receptor defects (beta subunit). Some mice progress and die, while their littermates recover and get better, despite the same mutation on an inbred genetic background. We find evidence for glycine neurotransmitter toxicity and loss of glycinergic interneurons early in the disease, but some mice are able to keep things going until they can over-express homomeric alpha1 channels, whereupon they recover. In the mice progressing towards lethality, neurotransmitter toxicity too quickly extends to GABAergic interneurons and motorneurons, and they lose their window of time to upregulate the alpha1 glycine receptor, and they crash and burn. Importantly, human patients with glycine receptor defects typically show a resolution of their phenotype with age, and we propose that the same remodeling events are occuring in human patients. Source GEO sample is GSM30991 Last updated (according to GEO): May 27 2005 19 0 human frontal cortex Gene expression data from brain of adult rats Source GEO sample is GSM101023 Last updated (according to GEO): Feb 20 2007 PGA-MPF-C57-saline-24h-2bAv2-s1 Kidney 861 1000 Cochlear structure AML cDNA hybridization-ID10-L 1000 Encephalitis total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lysophosphatidic Acid for 120min Source GEO sample is GSM5655 Last updated (according to GEO): May 27 2005 n/a Source GEO sample is GSM178043 Last updated (according to GEO): Jun 11 2007 Nasal Epithelium Inhalation Formaldehyde 07ppm 19d ID156 861 HIV Infections 131 125 retina hrs nasal epithelium 1127 1147 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211376 Last updated (according to GEO): Jul 18 2007 with Alzheimer's disease 27 50 sodium retention 959 974 507 499 of cornea Macrophage smi87 Spleen vs Untreated B cell 240min (set2) 77 from Down syndrome 60 rat cortex Treatment, type=time_course, measurement=14.0 d Source GEO sample is GSM53222 Last updated (according to GEO): Jul 06 2005 861 Anterior DBA/2J Olfactory Bulb B 0 Lung tissue 10 861 Brain in bronchial epithelia 311 332 KT1021b_CAN olfactory epithelium wild type mouse 8 hpO Source GEO sample is GSM80190 Last updated (according to GEO): Oct 26 2005 GSE2874 Normal Stomach Gene expression from Dendritic cells from human subject with pustule former phenotype uninfected. Source GEO sample is GSM128972 Last updated (according to GEO): Sep 13 2007 NA18987 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225706 Last updated (according to GEO): Nov 05 2007 hg_NY15 Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.12 Subject: 3108 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39074 Last updated (according to GEO): May 27 2005 1000 Rectum Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10035.gif Source GEO sample is GSM76409 Last updated (according to GEO): Sep 22 2006 the heart 987 996 861 Cerebral cortex total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lysophosphatidic Acid for 60min Source GEO sample is GSM5653 Last updated (according to GEO): May 27 2005 36 21 from whole brain Knockout cocaine, biological replicate 3 1443 1432 PCOS oocytes Nervous system structure 901 1000 Amyotrophic Lateral Sclerosis Brain 1000 Expression profiling of spinal cord section (T9) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM6667 Last updated (according to GEO): May 28 2005 HUVEC isolate 36 low serum media VEGF-A 42hours cf. #17 Source GEO sample is GSM12911 Last updated (according to GEO): May 28 2005 875 Blood Cells hippocampus Source GEO sample is GSM36010 Last updated (according to GEO): May 27 2005 867 Large-Cell Lymphomas Myopathy 875 Hippocampus 1988 15 month Old Tissue Source GEO sample is GSM67217 Last updated (according to GEO): Jan 19 2006 Brain 861 861 Rett Syndrome total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5813 Last updated (according to GEO): May 27 2005 SQ-SQ13t1-A364-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A D01 24h TLR2/1L Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181202 Last updated (according to GEO): Jul 12 2007 100T Compare the transcriptomes of Cx43 null and Cx43 siRNA treated cortical astrocytes with the transcriptome of the wildtype cortical astrocytes Source GEO sample is GSM200841 Last updated (according to GEO): Jun 19 2007 HOXB4 const_+10nM TMX, 1hour, biological rep2 Dorsal Root Ganglia 5 Normal Malignant tumor of colon 901 Squamous epithelial cell 913 mouse brain ipsilateral LPS Source GEO sample is GSM149774 Last updated (according to GEO): Mar 15 2007 875 Subcutaneous Tissue 52 37 without malaria 901 Caudate nucleus structure 6,18,30 month oculomotor nucleus and spinal cord Source GEO sample is GSM74344 Last updated (according to GEO): Sep 16 2005 from brain 21 30 SmIntP145_0223AF77_173.txt D_U133A_9_HC D_U133A_11_nAcc Macrophage 14smi041 Hyperdip>50-R3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A I_U133A_74_AnCg Liver Test (Blinded) Sample Source GEO sample is GSM130131 Last updated (according to GEO): Sep 18 2007 kidney Source GEO sample is GSM18955 Last updated (according to GEO): Sep 25 2006 gene expression data from melanoma xenografts following ILI with melphalan Source GEO sample is GSM213641 Last updated (according to GEO): Jul 27 2007 5 0 brain 91 from the bone marrow 72 1000 Cochlear structure Acetaminophen 6hr Rat 1871 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool putamen_9 Low-density CCg progenitors treated with RA/Fsk to derive Neurons Source GEO sample is GSM47560 Last updated (according to GEO): Jun 10 2005 858 Prostatic Neoplasms brain 0 5 Blood Test (Blinded) Sample Source GEO sample is GSM130045 Last updated (according to GEO): Sep 18 2007 Amyotrophic Lateral Sclerosis 1000 D_U133Plus_1_DLPFC plasma cells 50 61 substantia_nigra_3 Starvation 916 WGACON-255 hypothalamus_8 Source GEO sample is GSM80669 Last updated (according to GEO): Mar 31 2006 Human mammary epithelium and breast cancer 1000 Lung Lymphoblastoid Cell Line for Individual 8124.3 log phase CO_NP_med_2 Gene expression data from postmorten brain regions Source GEO sample is GSM145492 Last updated (according to GEO): Nov 20 2006 Animal models represent a very useful tool for the study of depressive-like behaviour and for the evaluation of the therapeutic efficacy of antidepressants. Nevertheless, gene expression patterns of these different animal models and whether genes classically associated to human major depression are present in these genetic profiles remain unknown. Gene expression was evaluated in an animal model of depression: corticosterone-treated rats. Gene expression analyses were carried out using the Affymetrix® GeneChip® technology. Last Updated (by provider): Dec 11 2007 Contributers: David Arteta Leyre Uriguen Javier Meana Rebeca Diez-Alarcia Alvaro Diaz Angel Pazos Marcel Ferrer-Alcon outer medulla 31 43 osteoblast 627 637 Brain 1000 Brain 1000 178 164 Atherosclerosis Septicemia 1000 HS 578T hgu95b Germ free Jejenum 1 Macrophage 14smi107 Lymphoblastoid Cell Line for Individual 8069.3 log phase Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184678 Last updated (according to GEO): Apr 26 2007 901 theca cell Cerebral cortex 1000 Spinal Cord 1000 Brain 1000 Cerebral cortex 1000 Gene expression data from experimental treatment D-CD = Differentiated and control decoy transfected cells. Source GEO sample is GSM102881 Last updated (according to GEO): May 11 2006 human caudate nucleus Source GEO sample is GSM86863 Last updated (according to GEO): Feb 08 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Anti-IgM for 30min Source GEO sample is GSM5441 Last updated (according to GEO): May 27 2005 Skeletal muscle structure 861 Gene expression data from postmorten brain regions Source GEO sample is GSM144931 Last updated (according to GEO): Nov 20 2006 with experimental autoimmune encephalomyelitis 12 57 SN:Human Glioblastoma Biopsy 10453 human cerebellum Source GEO sample is GSM87116 Last updated (according to GEO): Feb 08 2006 1000 Kidney Failure, Chronic Skeletal bone 861 861 Cerebellum Ovary 1 Normal liver, PPARa-null mice, control conditions Source GEO sample is GSM205820 Last updated (according to GEO): Jul 24 2007 BC710A-BE 129Amygdala(1b)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B 269801AC_4 150 mg/kg X 12 hr Source GEO sample is GSM129856 Last updated (according to GEO): Sep 18 2007 osteoblast 627 637 BREAST_MDN on Affymetrix GeneChip Human Full Length Array HuGeneFL Trigeminal ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until enough tissue was harvested to be pooled by genotype. Approximately 10-12 ganglia were pooled for a single analysis, which was extracted using the RNeasy system (Qiagen). Source GEO sample is GSM89140 Last updated (according to GEO): Dec 23 2005 brain, cerebral cortex: Rat_02-140_TTX_Lipska_e1_le1 human peripheral blood derived monocytes, no stimulation, biological rep1 Source GEO sample is GSM126988 Last updated (according to GEO): Aug 15 2006 Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit. Source GEO sample is GSM200592 Last updated (according to GEO): Jul 09 2007 861 frontal lobe n/a Source GEO sample is GSM177931 Last updated (according to GEO): Jun 11 2007 1037 of transitional epithelium 1012 1000 Ventricular septum M_U133A_75_AnCg PGA-MFD-MutantPD1-2aAv2-s2a Head and neck cancer Source GEO sample is GSM155697 Last updated (according to GEO): Apr 24 2007 Posterior root of spinal nerve 861 I_U133Plus_113_CB human cerebellum Source GEO sample is GSM87135 Last updated (according to GEO): Feb 08 2006 NCI60.41_LABEL45EXTRACT44SUB3 Source GEO sample is GSM134197 Last updated (according to GEO): Aug 06 2007 Brain (postcentral gyrus) [JunctionChip 1 of 5] 1000 Medulla Oblongata LDMTX_MP-DX-5 Nasal Epithelium 865 284 272 of the tumor Pancreas at e14.5, Chip C, rep 2 26 11 /Ovary-Disease 1 1000 Neuraxis IMR-90 cells: Collagen Mesh Time Course Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11570 Last updated (according to GEO): May 28 2005 with autism spectrum disorder 37 65 1000 Brain T265_Mock_1 T3 treatment for ind H Hypothalamus 4 Normal M_U133A_78_nAcc brain, contralateral Cortex: Trizol Extraction16_le1 27 7 Medial Temporal Gyrus O377 homozygotes brains 4 Primary large cell neuroendocrine carcinoma 6564 0 47 To investigate the phenotype associated with estrogen receptor alpha (ER) expression in breast carcinoma, gene expression profiles of 58 node-negative breast carcinomas discordant for ER status were determined using DNA microarray technology. Using artificial neural networks as well as standard hierarchical clustering techniques, the tumors could be classified according to ER status, and a list of genes which discriminate tumors according to ER status was generated. The artificial neural networks could accurately predict ER status even when excluding top discriminator genes, including ER itself. By reference to the serial analysis of gene expression database, we found that only a small proportion of the 100 most important ER discriminator genes were also regulated by estradiol in MCF-7 cells. The results provide evidence that ER+ and ER- tumors display remarkably different gene-expression phenotypes not solely explained by differences in estrogen responsiveness. 861 Colon accumbens rattus_norvegicus_strain iNP animal_number 9 Mc3: Hippocampus_5T-Y_rep4 brain, unknown: 03EH_e1_le1 Cardiac-specific TNF-alpha transgenic mouse is an excellent model to study the pathologenesis of heart failure. Affytrix U74V2A was used to analyzed the gene expression profile of mice at the time point of compensated hypertrophy and dilated heart failure Source GEO sample is GSM8983 Last updated (according to GEO): May 28 2005 s42 PGA-Band_48h_8-m5 midbrain_5 Nasal Epithelium Instilation Formaldehyde 400mM 6h ID374 Murine Neurofibromatosis nucleus accumbens ctrl replicate 2 129:4-4 striatum 1215 1204 /db kidneys 17 7 hippocampus Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3293 Last updated (according to GEO): Mar 21 2006 Brain 1000 81 CB A Hippocampus 1000 1000 Intestines, Small 1967 1957 by seizures 26 15 endometrioid Cerebral cortex 1000 Neurites 861 30 19 Solid tumor 861 Cerebral cortex Regulator of G signaling 16 is a marker for the distinct ER stress state associated with aggregated mutant alpha 1antitrypsin Z in the classical form of alpha 1antitrypsin deficiency. Cochlear structure 1000 Gene expression data from human prostate tissue with 90 percent tumor content Source GEO sample is GSM119315 Last updated (according to GEO): Feb 23 2007 1000 Cerebral cortex R527P00606 Osteoblasts 1000 KT1001a(2)_AR1 Peritneum 1 Normal 1BJZ02051610_OccipitalLobe WT P2 replicate 2 Prostate 861 Human aging is associated with skeletal muscle atrophy and functional impairment (sarcopenia). Multiple lines of evidence suggest that mitochondrial dysfunction is a major contributor to sarcopenia. We evaluated whether healthy aging was associated with a transcriptional profile reflecting mitochondrial impairment and whether resistance exercise could reverse this signature to that approximating a younger physiological age. Skeletal muscle biopsies from healthy older (N = 25) and younger (N = 26) adult men and women were compared using gene expression profiling, and a subset of these were related to measurements of muscle strength. 14 of the older adults had muscle samples taken before and after a six-month resistance exercise-training program. Before exercise training, older adults were 59% weaker than younger, but after six months of training in older adults, strength improved significantly (P<0.001) such that they were only 38% lower than young adults. As a consequence of age, we found 596 genes differentially expressed using a false discovery rate cut-off of 5%. Prior to the exercise training, the transcriptome profile showed a dramatic enrichment of genes associated with mitochondrial function with age. However, following exercise training the transcriptional signature of aging was markedly reversed back to that of younger levels for most genes that were affected by both age and exercise. We conclude that healthy older adults show evidence of mitochondrial impairment and muscle weakness, but that this can be partially reversed at the phenotypic level, and substantially reversed at the transcriptome level, following six months of resistance exercise training. Last Updated (by provider): Jul 16 2007 Contributers: Alan Hubbard Kenneth Beckman Simon Melov Mark A Tarnopolsky Krysta Felkey Primary tumor 19 32 D_U133Plus_73_HC Spleen vs Leukotriene B4 (LTB4)Treated B cell 120min (set3) Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 5 day time point Source GEO sample is GSM159734 Last updated (according to GEO): Apr 23 2007 CLL-62 Communicable Diseases 901 DNA damage caused by UV radiation initiates cellular recovery mechanisms, which involve activation of DNA damage response pathways, cell cycle arrest and apoptosis. To assess cellular transcriptional responses to UVC-induced DNA damage we compared time course responses of human skin fibroblasts to low and high doses of UVC radiation known to induce a transient cellular replicative arrest or apoptosis, respectively. UVC radiation elicited >3-fold changes in 460 out of 12,000 transcripts and 89% of these represented downregulated transcripts. Only 5% of the regulated genes were common to both low and high doses of radiation. Cells inflicted with a low dose of UVC exhibited transcription profiles demonstrating transient regulation followed by recovery, whereas the responses were persistent after the high dose. A detailed clustering analysis and functional classification of the targets implied regulation of biologically divergent responses and suggested involvement of transcriptional and translational machinery, inflammatory, anti-proliferative and anti-angiogenic responses. The data support the notion that UVC radiation induces prominent, dose-dependent downregulation of transcription. However, the data strongly suggest that transcriptional repression is also target gene selective. Furthermore, the results demonstrate that dose-dependent induction of cell cycle arrest and apoptosis by UVC radiation are transcriptionally highly distinct responses.. Date GSE713 Last Updated: Jun 15 2005 Contributers: Massimiliano Gentile Marikki Laiho Leena Latonen Includes GDS400. Update date: Oct 08 2003. Dataset description GDS400: Temporal analysis of differences in WS1 human skin fibroblast gene expression response to low (10 J/m2; induces transient cellular replicative arrest) or high (50 J/m2; induces apoptosis) doses of short wavelength UV radiation (UVC; 254 nm).. Blood 861 brain, hippocampus: KA-24h-P15-II_e1_le1 7 0 prostate Male 24.2 yr before antibody enrichment scan 1 (U133B) Cerebral cortex 1000 no additional Source GEO sample is GSM199137 Last updated (according to GEO): Jun 08 2007 liver, PPARa-null mice, control conditions Source GEO sample is GSM205819 Last updated (according to GEO): Jul 24 2007 normal testis 54 66 of the heart 842 854 myometrium_9 Source GEO sample is GSM80719 Last updated (according to GEO): Mar 31 2006 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28728 Last updated (according to GEO): May 27 2005 HapMap CHB Male Source GEO sample is GSM159586 Last updated (according to GEO): Feb 01 2007 78 66 Control blood 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114442 Last updated (according to GEO): Jun 16 2006 park_1149_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 73 cortex 79 Mouse neuroblastoma 0 18 Epithelial Cells 1000 22 17 (heart total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Lipopolysaccharide (LPS) labeled with Cy5- time course with repeats. Date GSE389 Last Updated: May 29 2005 Contributers: Rebecca Hart Joella Grossoehme Jong-Woo Kim Robert Hsueh Sangdun Choi Zhen Yan Mi Sook Chang Sun Young Lee Angela Alexander Yun Anna Cao Includes GDS310. Update date: Nov 18 2003. Dataset description GDS310: Temporal analysis of effects induced by 40 ug/ml lipopolysaccharide in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. CAD_replicate7 Prosencephalon 1000 JMR-MurInj72h-1cAv2-s2 MO_control_0min_Patient10 Wild type 8 wk old male A/J mouse hypothalamus Source GEO sample is GSM74973 Last updated (according to GEO): Feb 27 2007 NCI-H226 hgu95a HCC (HBV+, HK44) 1000 Bregma Gene expression data from postmorten brain regions Source GEO sample is GSM145687 Last updated (according to GEO): Nov 20 2006 Congenital Abnormality 853 Prostate 11 Disease 0 18 Gene expression data from postmorten brain regions Source GEO sample is GSM145184 Last updated (according to GEO): Nov 20 2006 (cortex 19 25 of mouse brain 9 23 HTI-286 in docetaxel-refractory prostate cancer (Dye flip2) Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_4 months_replicate 3 1000 Cerebral cortex Replicate2_Voxel F2 660 mesenchymal stem cell 639 CNS-SpinalCmod-Adult-48h-3C-s2 Epithelial Cells 1000 cortex 7 12 Chancroids 1000 1000 frontal lobe Brain_MD_27_Medulloblastoma_Classic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL SK-BR-3 861 Skeletal bone Zeitgeber Time Treatment, type=timepoint, description=Zeitgeber Time, measurement=6.0 h Source GEO sample is GSM53325 Last updated (according to GEO): Jul 06 2005 Parkinson Disease 861 901 Breast Carcinoma puroD replicate 1 12 frontal Lobe 23 406 395 whose hearts Acetaminophen 3hr Rat 7532 blood vs. Acetaminophen 3hr Rat Pooled Control blood Craniocerebral Trauma 861 GI_dev, small bowel fetal day 16.5 Keywords = mouse gene expression database Source GEO sample is GSM29291 Last updated (according to GEO): May 27 2005 13 0 Normal Trachea Laser capture lung cancer cells Source GEO sample is GSM191051 Last updated (according to GEO): May 25 2007 86 of epithelial cells 104 1000 Brain 80 67 duodenum C57BL Liver (HBV+, HK31) Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211298 Last updated (according to GEO): Jul 18 2007 31 adrenal medulla 17 Lda2a Total RNA extracted from the cerebellum of a stg-/- mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144394 Last updated (according to GEO): Nov 14 2006 of the heart 842 854 Epithelial Cells 901 45 33 in the kidney 1000 frontal lobe Whole Brain 62 72 1000 Lung Primary large cell neuroendocrine carcinoma 1408 Source GEO sample is GSM17332 Last updated (according to GEO): May 28 2005 332 327 liver none Source GEO sample is GSM246016 Last updated (according to GEO): Dec 03 2007 M7TW00121391 Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks The nose 94 101 /3T3 fibroblasts 295 310 Parkinson's disease sample x108 Mammary; Lactating Keywords = mouse gene expression database Source GEO sample is GSM29401 Last updated (according to GEO): May 27 2005 1000 Cartilage Normal Source GEO sample is GSM175871 Last updated (according to GEO): Apr 09 2007 352 347 brain Neuraxis 1000 NA18593 brain 0 5 metanephric mesenchyme, control, 1 day, biological rep1 861 Cerebral cortex NA18980 Muscle_adequate protein_male_rep4 9 0 Blood Test ramaswamy-cancer 1000 Brain Brain_Rhab_2_AT/RT (Renal) on Affymetrix GeneChip Human Full Length Array HuGeneFL heart.1 7 0 prostate CAD_replicate27 The epithelial cells 962 981 of the postmortem brains 656 680 Cerebral cortex 861 the infection 46 58 Spleen vs Insulin-like growth factor 1 Treated B cell 120min (set2) Balb/c day 1, biological rep 3, tech rep 1 Spleen vs 2-Methyl-thio-ATP Treated B cell 120min (set1) Rp1 knockout mice retinal development GSE3637 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225944 Last updated (according to GEO): Nov 02 2007 FSCC9 on Affymetrix GeneChip Human Full Length Array HuGeneFL Skeletal muscle structure 1000 Pooled soleus RNA samples from five 8 wk old male mdx mice Source GEO sample is GSM13740 Last updated (according to GEO): May 28 2005 AD-340t1a-A122-3 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Acute myocardial infarction 1000 brain, cerebral cortex: Rat_02-53_VHL_Lipska_e1_le1 Neoplasm 861 9 0 Blood Test plasma cells 50 61 Epithelium 861 knockin mouse cerebellum Treatment, type=time_course, measurement=4.0 weeks Source GEO sample is GSM53342 Last updated (according to GEO): Jul 06 2005 1000 Cerebral cortex Neoplasm 1000 Hypertensive Rat Kidney Study: Gender-Selective Responses to Salt in Dahl-Iwai & Sprague-Dawley Rats Tumor__Leukemia_ALL-B_ALL_(20414)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A in the adult heart 44 61 none Source GEO sample is GSM123210 Last updated (according to GEO): Jul 26 2006 Neoplasm 861 I_U133A_75_AnCg 1000 Liver human caudate nucleus Source GEO sample is GSM86820 Last updated (according to GEO): Feb 08 2006 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14958 Last updated (according to GEO): Oct 28 2005 Skeletal bone 861 865 Ovarian Diseases such as panic disorder 103 125 1000 Cerebral cortex Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153347 Last updated (according to GEO): Dec 27 2006 from ventral prostate 21 41 Fibroblasts 861 Entorhinal Cortex 7 23 Bone structure of tibia 1000 1000 Endometriosis, site unspecified 861 Neoplasm 1338 1316 of experimental asthma Control Source GEO sample is GSM176477 Last updated (according to GEO): Apr 09 2007 3 0 Lung of mouse brain 9 23 CNS-SMTC_Mod3mo-2A-s2 1000 hindbrain 1000 Nervous system structure BTBR T+ tf-tf_male_hypothalamus Source GEO sample is GSM138578 Last updated (according to GEO): Apr 18 2007 Expression profiling of somatomotor cortex extracted from rats at 3 months following sham surgery Source GEO sample is GSM41653 Last updated (according to GEO): May 27 2005 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184677 Last updated (according to GEO): Apr 26 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Bombesin for 30min Source GEO sample is GSM5476 Last updated (according to GEO): May 27 2005 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225942 Last updated (according to GEO): Nov 02 2007 Sun186_BAV13 group Laser microdissection and microarray analysis of the hippocampus of Rasgrf1 knockout mice 913 Coronary heart disease PGA_MI_ilv_4h_391 Blood 861 Lymphoblastoid Cell Line for Individual 8168.3 log phase 70 40 without coronary artery disease 861 Blood Heart 1000 923 Blood Cells NoCAD_replicate25 V5-P260 Cerebral cortex 861 1000 Heart 858 Mesodermal cell Large-scale analysis of the human transcriptome. Adrenal gland Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 171.56 Stdv: 6.73 Min: 156.65 Max: 180.66 Source GEO sample is GSM2827 Last updated (according to GEO): May 27 2005 from the femurs 95 109 861 Cerebral cortex 1000 Hippocampus Dahl-Iwai Female LowSalt Cortex rat105 dahl_cortexr_k_105c_072001 Pooled quad RNA samples from five 8 wk old male mdx5cv mice Source GEO sample is GSM13731 Last updated (according to GEO): May 28 2005 1000 Lung Wild type voxel I3 Transplant Series 13 , Transplant # 1 ovarian tumor: serous Source GEO sample is GSM139457 Last updated (according to GEO): Apr 09 2007 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134607 Last updated (according to GEO): Jul 09 2007 HMEC X Confluent HMEC Gene expression data from postmorten brain regions Source GEO sample is GSM145099 Last updated (according to GEO): Nov 20 2006 Probeset expression data from NA12751 growth 2 Source GEO sample is GSM201539 Last updated (according to GEO): Aug 08 2007 D2_TP-72_C C57L/J Cerebellum C 733 724 lipofuscin 567 548 the descending colon Male 25.2 yr after antibody enrichment scan 2 (U133A) The nose 94 101 64 47 that whole ovaries Cancers; Colon Tumor Keywords = mouse gene expression database Source GEO sample is GSM29264 Last updated (according to GEO): May 27 2005 AR-R-10pM human caudate nucleus Source GEO sample is GSM86875 Last updated (according to GEO): Feb 08 2006 1000 Kidney Failure, Chronic IDC102 on harvard-12k brain, cerebral cortex: Sham1_e1_le1 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211365 Last updated (according to GEO): Jul 18 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11289 Last updated (according to GEO): May 28 2005 Bone Marrow 1000 1000 Cerebral cortex D_U133A_17_HC TEL-AML1-C34 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Lung hippocampus_2 G2 Nasal Retina Ovarian_Tumor_Serous_CU-OS-05 861 Coxsackievirus Infections Mental disorders 901 Diaphragm 23 Day mdx rep 3 988 980 cerebella Macrophage smi91 24 a genetic disease 40 81 73 by trauma Anterior nares 1000 bone marrow-CD33myeloid Source GEO sample is GSM18710 Last updated (according to GEO): Sep 25 2006 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201241 Last updated (according to GEO): Jun 14 2007 861 Cerebral cortex Liver 1000 /SvEvTac periaqueductal gray rep2 5 37 43h-DMSO replication 3 Keywords = preimplantation Keywords = development Source GEO sample is GSM14727 Last updated (according to GEO): May 28 2005 132 121 like asthma The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27017 Last updated (according to GEO): May 27 2005 Medulla Oblongata 861 Brain 1000 none Source GEO sample is GSM149629 Last updated (according to GEO): Jan 03 2007 saphenous_vein_3 Synapses 928 43 0 Chorionic mesoderm-derived mesenchymal cells 102 86 of the brainstem AML_27 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Human Sural Nerve Schwann Cell Donor 317 Passage 1 Treatment, type=add, description=growth factors heregulin and forskolin added Source GEO sample is GSM92234 Last updated (according to GEO): Jan 13 2006 U87 glioblastoma cell, clone 3.1 (neo-resistant negative control) Keywords = bioinformatics Keywords = gene expression Keywords = cancer Keywords = platelet-derived growth factor Keywords = sterol regulatory element binding protein Keywords = glioblastoma multiformae Keywords = microarray Source GEO sample is GSM34580 Last updated (according to GEO): May 27 2005 Brain_Melanotransferrin Knockout_affs275-1096 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3325 Last updated (according to GEO): Mar 21 2006 1000 Hippocampus human frontal cortex Source GEO sample is GSM87027 Last updated (according to GEO): Feb 08 2006 901 Caudate nucleus structure HUMANCULTUREDADIPOCYTE Source GEO sample is GSM18816 Last updated (according to GEO): Sep 25 2006 CurrentSmoker 113 Bladder 1000 SN:1010515 Source GEO sample is GSM115403 Last updated (according to GEO): Jun 20 2006 Gene expression data from whole brain of uninfected mouse Source GEO sample is GSM189602 Last updated (according to GEO): May 16 2007 gene expression from allergen stimulated mouse lung Source GEO sample is GSM158143 Last updated (according to GEO): Jan 25 2007 Spleen 1000 Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 2789 blood cerebral cortex 7 21 f2#277 versus pool Mouse Brain tissue "2h Thy-Noc, Exp4" WGACON-250 pooled RNA of the kidney of 36 day old rats Source GEO sample is GSM86652 Last updated (according to GEO): Jun 12 2006 54h-AM replication 2 901 frontal lobe 983 Occipital lobe Standard Affymetrix Protocol Keywords = microarray Keywords = muscle Source GEO sample is GSM15937 Last updated (according to GEO): May 28 2005 from colorectal adenoma 21 44 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15954.gif Source GEO sample is GSM84133 Last updated (according to GEO): Sep 22 2006 Cardiac 523 530 hypothalamus_4 Source GEO sample is GSM80693 Last updated (according to GEO): Mar 31 2006 Epithelium of bronchus 983 861 Heart Diseases DBA whole brain 3A Brain 1000 660 mesenchymal stem cell 639 Total RNA from brain sample of NR3B knockout mice at P0. Treatment, type=purify, measurement=0.0 years Source GEO sample is GSM113683 Last updated (according to GEO): Jun 09 2006 Cerebellum Control (AD) 3 712 698 of each tumour Infected 6 weeks prior with Htt-N171-19Q-expressing recombinant lentivirus Source GEO sample is GSM33273 Last updated (according to GEO): Oct 16 2006 861 Cerebral cortex heart 1169 1173 CNS-SMTC_Mod24h-4A-s2 In human anxiety disorders 75 100 76 40 in human mesenchymal progenitor cells 1000 Retina Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=1 (Acute rejection). One of two samples from the same patient, different visits. Source GEO sample is GSM36432 Last updated (according to GEO): May 27 2005 brain 0 5 861 Mammary gland Brain 1000 5 0 Spleen Testis 861 Wild type voxel A4 1000 ovarian neoplasm Diet Induced Obese rat C7 112 98 from the kidney Parkinson's disease sample x109 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113898 Last updated (according to GEO): Jun 16 2006 WT cortical astrocytes 1 1037 of transitional epithelium 1012 Macrophages, Baseline - Repeat #2 Epithelium 861 brain, cerebral cortex: Sham12_e1_le1 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11604 Last updated (according to GEO): May 28 2005 Prostate 4 Disease 0 17 RPMI-8226_II_CL7010_Leukemia on Affymetrix GeneChip Human Full Length Array HuGeneFL skin 80 83 30 0 Adult occipital cortex cocaine1 This is a wildtype littermate at postnatal day 5 pool of 5 animals Lot batch = Source GEO sample is GSM4061 Last updated (according to GEO): May 28 2005 GSE5287 Brain 1000 Primary Neoplasm 1000 Coronary heart disease 913 HC62 CN B HCC (HBV+, HK84) of 2182 tumor 24 36 primary tumors selectively 1027 1052 141 137 Brain 1000 Liver Cell source of DN2_1, DN3_1, and DN4_1 are identical. Cell source of DN2_2, DN3_2, and DN4_2 are identical. Cell source of DN2_3, DN3_3, and DN4_3 are identical. Cell source of DN2_4, DN3_4, and DN4_4 are identical. Each cell sorce was derived from four mice. Source GEO sample is GSM188619 Last updated (according to GEO): May 16 2007 Parkinson Disease 861 CNS-SCsev_InjB7d-2C-s2 861 Amygdaloid structure G4 optic nerve HCC-2998 hgu95b Prosencephalon 1000 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12542.gif Source GEO sample is GSM79813 Last updated (according to GEO): Sep 22 2006 of mouse brain 9 23 Ganglia, Spinal 923 Expression profiling of spinal cord section (T8) extracted from rats 4h following mild injury Source GEO sample is GSM31450 Last updated (according to GEO): May 27 2005 441 423 in the hippocampus CNS-SpinalCsev-Adult-24h-4B-s2 Whole blood 0 10 Synovium; chronic arthritis Keywords = mouse gene expression database Source GEO sample is GSM29440 Last updated (according to GEO): May 27 2005 Voxel D4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1412 Last updated (according to GEO): Nov 21 2005 Myocardial Infarction 1000 1000 Bregma from colonic normal mucosa 21 47 CNS-SMTC_Mod4h-2C-s2 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120692 Last updated (according to GEO): May 14 2007 Brain Injuries 861 Neurodegenerative Disorders 901 nmd untreated 1 1BJZ02031098_lymphomaburkittsDaudi Myocardium 861 ovary Source GEO sample is GSM18623 Last updated (according to GEO): May 27 2005 Heart 861 from the right forebrain 21 44 Simple annotation: Lymph node metastasis, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3499.gif Source GEO sample is GSM76472 Last updated (according to GEO): Sep 22 2006 861 Hippocampus Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for twelve weeks.. Source GEO sample is GSM148665 Last updated (according to GEO): Dec 12 2006 Study of in vitro granulocyte differentiation Source GEO sample is GSM137456 Last updated (according to GEO): Jun 06 2007 HCC (HK41) Whole blood from a healthy control Source GEO sample is GSM153444 Last updated (according to GEO): Jan 11 2007 N/A Source GEO sample is GSM4321 Last updated (according to GEO): May 28 2005 no additional Source GEO sample is GSM199211 Last updated (according to GEO): Jun 08 2007 Liver 1000 258 245 of each tumor Heart failure 1000 861 Cerebral cortex 176 166 bone marrow of Alzheimer? 77 89 Infected 6 weeks prior with GFP-expressing recombinant lentivirus Source GEO sample is GSM34392 Last updated (according to GEO): Oct 16 2006 colon_cecum_10 CAD_replicate66 Lymphoblastoid Cell Line for Individual 8123.4 log phase 93 of cardiopulmonary diseases 119 Prosencephalon 1000 861 Cerebral cortex Spleen vs Untreated B cell Time 0 (set18) 861 Bladder 1000 Brain ileum 1000 CT22-1 Myocardial Infarction 1000 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17076.gif Source GEO sample is GSM91584 Last updated (according to GEO): Sep 22 2006 861 Cerebral cortex Osteoblasts 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145037 Last updated (according to GEO): Nov 20 2006 Hypothalamus RYGB- 0 17 861 Cancer of Neck mammarygland.2 a unique leukemia 81 98 ALL-T-cell-2 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Acquired Immunodeficiency Syndrome IGF1 and IGF1 receptors (IGF1R) are present in the adult heart and have been shown to be essential for myocardial performance. Insulin-like growth factor 1 (IGF1) is produced in numerous tissues particularly by the liver in response to growth hormone stimulation and is an important factor in the regulation of post-natal growth and development. We have generated and characterized transgenic mice over-expressing the IGF1R. We crossed IGF1R transgenic mice with dominant negative (dn)PI3K (p110) and with constitutively active (ca)PI3K(p110) transgenic mice. Expression profiling was performed on the ventricles of IGF1R, IGF1R-caPI3K, IGF1R-dnPI3K, caPI3K, dnPI3K transgenic female mice at 3 months of age. Non-transgenic littermates were used as controls. Keywords = insulin growth factor, IGF, cardiac, hypertrophy Source GEO sample is GSM18362 Last updated (according to GEO): May 27 2005 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3280 Last updated (according to GEO): Mar 21 2006 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156587 Last updated (according to GEO): Jan 22 2007 Mouse old brain w/ a- & g-tocopherol agT-Br-2 Pancreas Bone Marrow 1000 Expression profiling of spinal cord section (T8) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM4452 Last updated (according to GEO): May 28 2005 CS-B cell unirradiated replicate 2 U133B 1000 Prostate 26 15 endometrioid brain, cerebral cortex: PC6_e1_le1 mouse brain ipsilateral control Source GEO sample is GSM149768 Last updated (according to GEO): Mar 15 2007 3 hrs Post-clamp sample 5 dorsal_root_ganglia_5 Dissection of E16.5 cortex for RNA extraction. Cortex Hemispheres of E16.5 mice were divided into the medial (R1), dorsal (R2), ventral (R3), lateral (R4), and occipital regions (R5). Preparation of RNA and Synthesis of cDNA. Poly A+ RNA was obtained through twice column procedures with oligo dT cellulose column (New England Biolabs, Beverly, MA) and was used for synthesis of cDNA. 1ug of polyA+ RNA was converted into double-stranded cDNA by reverse transcription using ReverTra Ace (ToYoBo, Japan) with oligo dT(24) primers containing the T7 RNA polymerase promotor sequence (Amersham Pharmacia Biotech, Japan). The integrity of RNA was confirmed by agarose electrophoresis and RNA contents were analyzed by measuring the optical density at 260 nm. Target preparation and array processing. The following procedures including preparation of cRNA targets, hybridization, washing, staining, and scanning were performed as described in the Expression Analysis Technical Manual (Affymetrix, CA). Briefly, biotin-labeled antisense cRNA targets were synthesized in in vitro transcription reaction system (IVT) using cDNA as template (ENZO BioArrayTM HighYieldTM RNA Transcription Labeling kit with T7 RNA polymerase, Enzo, NY). The cRNA targets were size-fragmented to 35-200 bp in a buffer containing potassium and magnesium acetate at 94 °C for 35 minutes and were used for hybridization as cRNA targets. The hybridization cocktail [containing 10 ug of target cRNA, control oligo BS (Affymetrix), and Eukaryotic Hybridization controls (Affymetrix)] was hybridized with a mouse U74A array at 42 °C for 16 hours in GeneChip Hybridization Oven 640. Washing and staining were performed after hybridization under the fluidics station protocol, EuGE-WS2, on GeneChip Fluidics Station 400. Then, we scanned the array twice on HP GeneArrayTM scanner. Experiments were repeated twice with independent dissection. Data analysis. To quantify the expression level of a transcript, the average difference value (Adv) was calculated from the intensities against the probe cells using the global methods of normalization by Microarray Suite ver. 4.0 (Affymetrix). Keywords = mouse Keywords = cortex Keywords = development Keywords = regional Keywords = gene expression Keywords = medial Keywords = dorsal Keywords = lateral Keywords = rostral Keywords = occipital Source GEO sample is GSM14593 Last updated (according to GEO): Oct 28 2005 cortex rattus_norvegicus_strain iP animal_number 4 1000 Spleen Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:248, Count:32 Corner- Avg:43803, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:17.496950,SFGene:All Background:Avg:346.00,Stdev:4.31,Max:359.2,Min:337.0 Noise:Avg:9.84,Stdev:0.35,Max:10.9,Min:8.9 RawQ:14.73 Keywords = ALL Source GEO sample is GSM3507 Last updated (according to GEO): May 28 2005 TUMOR 27 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A HCC (HBV+, HK9) nipple_cross-section_2 Lymphoblastoid Cell Line for Individual 8089.3 log phase Epithelium 861 striatum 30 38 Cerebral cortex 861 M_U133Plus_121_DLPFC Mental Retardation 1000 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs//7346.gif Source GEO sample is GSM79987 Last updated (according to GEO): Sep 22 2006 1000 Primary carcinoma of the liver cells 1000 Brain LT-Hematopoietic stem cell isolated by flow cytometry Source GEO sample is GSM149526 Last updated (according to GEO): Apr 27 2007 Nose 1000 285_2 Cerebellum 1000 brain, hippocampus: Wt #3396 Cort_e1_le1 Structure of entorhinal cortex 1000 Wild type inbred mice Source GEO sample is GSM82984 Last updated (according to GEO): Nov 10 2005 861 Pancreas 216 195 dilated heart failure Breast Carcinoma 983 Bone Marrow 1000 10_0012_SepticShock_Day1_64 901 Contact hypersensitivity 1000 Cerebral cortex The AIN-centered DCN of delayed-type eyeblink conditioned mice: 3-d paired training and sham negative control groups JejunTumorNew_0221AFCA_jtc.txt 17 7 hippocampus Plasma 861 Endothelial Cells 1000 Brain 1000 in the heart 460 472 Olfactory Epithelium 1000 Osteoblasts 1000 861 Acquired Immunodeficiency Syndrome Aorta 1000 in bronchial epithelia 311 332 Salivary Gland [JunctionChip 5 of 5] Acetaminophen 24hr Rat 8089 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool brain 0 5 Fibroblasts 1000 Pooled total RNA from (3) P27 L3-L5 wild type spinal cords Treatment, type=acclimatization Source GEO sample is GSM32062 Last updated (according to GEO): May 27 2005 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3498.gif Source GEO sample is GSM76471 Last updated (according to GEO): Sep 22 2006 A2780_cis_IC50_16h_1 Pool of 9 non-inner ear tissue samples at E9 Source GEO sample is GSM182623 Last updated (according to GEO): Aug 14 2007 Spleen vs Insulin-like growth factor 1 Treated B cell 60min (set3) mouse brain contralateral LPS Source GEO sample is GSM149753 Last updated (according to GEO): Mar 15 2007 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19231 Last updated (according to GEO): May 27 2005 40 year old male 861 Cerebellum DLBC1 on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression data from postmorten brain regions Source GEO sample is GSM145245 Last updated (according to GEO): Nov 20 2006 Muscle 861 40 21 from the hippocampus Neoplasm 861 adenoma 861 Tumor__Pancreas_Adeno_Pan_3T on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Heart failure_LVAD_6 Mental disorders 901 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Anti-IgM for 60min Source GEO sample is GSM5445 Last updated (according to GEO): May 27 2005 Primary tumor 19 32 Richard Almon-27-1138200270289 335 325 The jejunum 372 355 in small intestine doxycycline, mutant Source GEO sample is GSM213383 Last updated (according to GEO): Jul 26 2007 brain, unknown: Sample59_e1_le1 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134606 Last updated (according to GEO): Jul 09 2007 Primary tumor 19 32 Osteoblasts 1000 stria terminalis 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145032 Last updated (according to GEO): Nov 20 2006 Expression profiling of spinal cord section (T8) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM6641 Last updated (according to GEO): May 28 2005 pM category 983 Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=740580 LaserPower=2.031.32 Lot batch = LC17N029 Source GEO sample is GSM4781 Last updated (according to GEO): Nov 21 2005 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b024 Source GEO sample is GSM2004 Last updated (according to GEO): Nov 21 2005 1000 Hippocampus 5 0 brain Spleen 1000 Neoplasm 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145531 Last updated (according to GEO): Nov 20 2006 176 166 bone marrow 861 Cancer of Neck 12 frontal Lobe 23 thymocytes_DN2_4 knock-in mouse cerebellum Treatment, type=time_course, measurement=11.0 weeks Source GEO sample is GSM53353 Last updated (according to GEO): Jul 06 2005 Heart failure sample 1 CurrentSmoker 116 Brain 861 Heart 861 Primary Neoplasm 1000 NA12750 growth 2, replicate 2 91 FC BA9 A HSC_12Months_p53_het_B Brain 1000 39 21 from mammary glands Gene expression data from postmorten brain regions Source GEO sample is GSM145890 Last updated (according to GEO): Nov 20 2006 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5456.gif Source GEO sample is GSM93149 Last updated (according to GEO): Sep 22 2006 Monocular deprivation right cortex, biological rep1 CHB MD-1 SN:1006573 Source GEO sample is GSM115348 Last updated (according to GEO): Jun 20 2006 1037 of transitional epithelium 1012 Congenital Abnormality 861 ADH180 on harvard-12k Hyperdip>50-C39 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD28 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD28 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36716 Last updated (according to GEO): May 27 2005 Untreated versus treated (bortezomib), untranformed MCF10A and Transformed (see Adler et al, Nature Gen. 2006) Source GEO sample is GSM120282 Last updated (according to GEO): Jul 20 2006 861 Malignant Neoplasms Bic/4AP/EGTA 861 Heart failure XX1_InX Parkinson 0 8 861 Muscle 61 41 from postmortem brain west-breast from nose 100 108 Thalamus 8 Normal AML cDNA hybridization-ID59-L Circadian Profiling of NIH3T3 Fibroblasts: Comparison with Rhythmic Gene Expression in SCN2.2 Cells and the Rat SCN mouse brains 187 198 1375 1357 of the cytoskeleton of the postmortem brains 666 690 nodose_nucleus_3 Source GEO sample is GSM80770 Last updated (according to GEO): Mar 31 2006 1000 Brain 1000 Breast Carcinoma Expression profiling of spinal cord section (T10) extracted from rats 14d following severe injury Source GEO sample is GSM31348 Last updated (according to GEO): May 27 2005 Ventral Tegmental Area 1000 basal culture, 9A1, rep 1 Olfactory Epithelium 1000 1000 Spleen Brain 861 Ganglia 861 Mental Retardation 1000 913 Bipolar Disorder mammary_gland_9 Source GEO sample is GSM80726 Last updated (according to GEO): Mar 31 2006 Primary Carcinoma 876 from ventral prostate 21 41 Neoplasm 861 HapMap YRI_parent Male Source GEO sample is GSM159701 Last updated (according to GEO): Feb 01 2007 101075 Lung tissue from C57BL/6 mice that were always fed by 2/3 and sacrificed. Lot batch = Source GEO sample is GSM4036 Last updated (according to GEO): May 28 2005 5wkB from the nasal septum 655 676 314-99_SCLC 24 skeletal muscle 10 Nrl ko samples were compared to wt at postnatal 10. Source GEO sample is GSM227460 Last updated (according to GEO): Sep 07 2007 CLL-66;SL106 865 Disorder of artery Parkinson Disease 1000 Gloubus Pallidum External 5 Normal Wild type voxel C3 DLCL-0008 Kidney 861 Bipolar Disorder 1000 Expression data with no treatment Source GEO sample is GSM230905 Last updated (according to GEO): Sep 20 2007 Muscle 861 Date : 3/29/2002 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 6.0 hrs post-injection Intervention : 4.0 mg/kg PK11195 co-administered Risk: anticipated remediation to <10% malformations Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots Keywords = methylmercury Keywords = PK11195 Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = SC851 Source GEO sample is GSM12265 Last updated (according to GEO): May 28 2005 CNS-SC_CtrB14h-1B-s2 DLBC15 on Affymetrix GeneChip Human Full Length Array HuGeneFL Replicate3_Voxel A3 R745P00782 /2J pituitary gland rep1 3 26 Brain 1000 75-95_combined Gene expression data from postmorten brain regions Source GEO sample is GSM145722 Last updated (according to GEO): Nov 20 2006 CNS-SCsev_InjA28d-2C-s2 861 Hypothalamic structure Autistic Disorder 1000 BarCode:251316210194 Source GEO sample is GSM159389 Last updated (according to GEO): Jul 17 2007 plasma cells 50 61 Tract 861 striatum rattus_norvegicus_strain iP animal_number 1 901 frontal lobe CNS-RM_Ctr28d-2B-s2 HC105 FC BA4 A Lymphoblastoid Cell Line for Individual 8213.4 log phase 1000 Brain Injuries Metastatic tumor 19 35 Neoplasm Metastasis 1000 SK-ES1 NHF1-hTERT_M_C3_16181 Lung [JunctionChip 5 of 5] 861 Cerebral cortex R564P00721 Gene expression data from postmorten brain regions Source GEO sample is GSM145713 Last updated (according to GEO): Nov 20 2006 1000 Malignant neoplasm of prostate Gene expression data from liver Source GEO sample is GSM243406 Last updated (according to GEO): Nov 16 2007 MSE_D_543 Brain 861 Sample35, Post Injury 24 hours Treatment, type=wait Source GEO sample is GSM53286 Last updated (according to GEO): Jul 06 2005 KO_sham_mid_1 Macrophages treated with LPS, 30 min, Replicate 3 Source GEO sample is GSM241142 Last updated (according to GEO): Nov 02 2007 MCF7 pre-treated for 1h with cycloheximide, treated with E2 for 24h Source GEO sample is GSM213318 Last updated (according to GEO): Jul 26 2007 Expression profiling of spinal cord section (T9) extracted from rats 4h following moderate injury Source GEO sample is GSM31568 Last updated (according to GEO): May 27 2005 1000 Encephalitis Gene expression data from mouse primary visual cortex Source GEO sample is GSM101728 Last updated (according to GEO): Jun 15 2006 Replicate1_Voxel F2 pfc_1043_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A 1727 1700 inflammatory bowel diseases 1000 Descending colon 5 0 brain Epithelium of bronchus 983 Gene expression data from mouse primary visual cortex Source GEO sample is GSM101712 Last updated (according to GEO): Mar 27 2006 Testis 861 1000 Cardiomyopathy, Alcoholic ross-adipogenesis Liver 1000 Pituitary Gland 861 1037 of transitional epithelium 1012 Brain 1000 stomach_pyloric_3 Source GEO sample is GSM80815 Last updated (according to GEO): Mar 31 2006 1000 Stomach Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=760550 LaserPower=2.041.3 Lot batch = LC17N034 Source GEO sample is GSM4785 Last updated (according to GEO): Nov 21 2005 861 medulloblastoma GC (HKG3N) 5 0 brain labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156698 Last updated (according to GEO): Jan 22 2007 7 cerebral cortex 21 Plasma 861 Huntington Disease 1000 Carcinoma, Large Cell 888 Medulla Oblongata 861 Keywords = kidney 149 166 an adenovirus 57 69 S46 WT7 F5/55 S46 wild type Mouse 10 months Cerebellum Female Source GEO sample is GSM73217 Last updated (according to GEO): Sep 06 2005 A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism Source GEO sample is GSM5990 Last updated (according to GEO): Nov 21 2005 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12355 Last updated (according to GEO): May 28 2005 X chromosome 737 748 Gene expression data from postmorten brain regions Source GEO sample is GSM145134 Last updated (according to GEO): Nov 20 2006 Nervous system structure 901 39 21 of substantia nigra Array analysis of gene expression in connexin-43 null astrocytes. Abdominal aortic aneurysm obtained from surgery to correct. Source GEO sample is GSM170553 Last updated (according to GEO): Jul 26 2007 Transitional epithelium 1000 of cancers 661 670 brain 0 5 Hypothalamic structure 1000 JMR-MurInj72h-2cAv2-s2 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211425 Last updated (according to GEO): Jul 18 2007 into squamous, large cell 271 296 ileum 1000 Malignant neoplasm of breast 1000 1212 1188 for the SALS spinal cord 456 441 sporadic tumors Gastrointestinal stromal tumors with KIT mutations exhibit a remarkably homogeneous gene expression profile. 1000 Heart Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225945 Last updated (according to GEO): Nov 02 2007 5 0 Spleen 1000 Left Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181071 Last updated (according to GEO): Jul 12 2007 CNS-SMTC_Mod14d-1B-s2 352 347 brain 5 0 Spleen HapMap CHB Male Source GEO sample is GSM159618 Last updated (according to GEO): Feb 01 2007 BL6:4-1 + 4-2 BNST K-562 (CL7005) LEUKEMIA Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68343 Last updated (according to GEO): Jul 07 2006 Skeletal muscle structure 901 1000 Transverse B458 on Affymetrix GeneChip Human Full Length Array HuGeneFL Spleen vs Bombesin Treated B cell Carcinoma, Large Cell 923 861 Cerebellum BXD11_M7SS02042206 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11252 Last updated (according to GEO): May 28 2005 skin 80 83 1000 Tongue Bladder sample 1145-1 to malaria 1158 1167 1000 Encephalitis Liver 0 4 1000 Brain Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3871 Last updated (according to GEO): May 27 2005 cardiac 763 769 from the right forebrain 21 44 CNS-SCsev_InjA24h-2B-s2 none Source GEO sample is GSM190787 Last updated (according to GEO): Jun 25 2007 tibiae 115 120 Phenytoin hippocampus 1 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53419 Last updated (according to GEO): Jul 06 2005 salivary_gland_3 Source GEO sample is GSM80822 Last updated (according to GEO): Mar 31 2006 Male Sprague-Dawley albino rats (Charles River) initially weighting approximately 200 grams were randomly assigned to one of the following: 1) olanzapine (2 mg/kg/day, I.P.) (N=20) or 2) Saline (N=20) and administered olanzapine or saline for 21 days. Frontal cortex (N=4/group) was dissected and homogenized for microarray, QPCR and western blotting following previous methods (Fatemi et al. 2003; Brooks et al. 2003). RNA isolation, cDNA preparation, microarray hybridization and QPCR followed previous methods (Brooks et al. 2003). Last Updated (by provider): Apr 10 2007 Contributers: Teri J Reutiman Peter Fried Andrew I Brooks David A Pearce Timothy D Folsom S H Fatemi Christopher Bell Lisa Nos Anne V Snow Acetaminophen 24hr Rat 9540 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool Gene expression data from postmorten brain regions Source GEO sample is GSM145497 Last updated (according to GEO): Nov 20 2006 12 Parietal Lobe 24 A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke. White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by treatment (IV) with the catalytic antioxidant AEOL 10150 and then 6 hours of reperfusion; third replicate; pooled mRNA from 6 brains. Source GEO sample is GSM2215 Last updated (according to GEO): May 27 2005 SN12h(2) A HID I D052 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225666 Last updated (according to GEO): Nov 02 2007 Donor 2 Time Point 48 hours Autologous control (uninfected) Source GEO sample is GSM2613 Last updated (according to GEO): May 27 2005 160 145 in the midbrain from cingulate cortex 376 396 Haloperidol treated 4weeks AffyGC RMA rep1 no additional Source GEO sample is GSM199385 Last updated (according to GEO): Jun 08 2007 between the LAD artery 266 287 corticosterone_treated_rep9 (06SE466) 1000 Neuraxis dentate granule cells Source GEO sample is GSM35840 Last updated (according to GEO): May 27 2005 Simple annotation: Development, development Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50642.gif Developmental Stage: E8.25 Source GEO sample is GSM229810 Last updated (according to GEO): Nov 06 2007 1000 Skin for liver 26 35 Epithelium 861 Coronary artery 901 Nose 1000 wild type placebo 12h, biological rep4 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181136 Last updated (according to GEO): Jul 12 2007 Leukemia, Myelocytic, Acute 861 276 270 Retinas of underlying brain 171 190 General somatic sensation is conveyed to the central nervous system at cranial levels by the trigeminal ganglion (TG), and at spinal levels by the dorsal root ganglia (DRG). Although these ganglia have similar functions, they have distinct embryological origins, in that both contain neurons originating from the neural crest, while only the TG includes cells derived from the placodal ectoderm. Here we use microarray analysis of E13.5 embryos to demonstrate that the developing DRG and TG have very similar overall patterns of gene expression. In mice lacking the POU-domain transcription factor Brn3a the DRG and TG exhibit many common changes in downstream gene expression, but a subset of genes show increased expression only at cranial levels. Although silent in wild-type ganglia, the promoter regions of genes which are activated in the absence of Brn3a also exhibit increased histone H3-acetylation at levels similar to constitutively transcribed gene loci, and this H3-acetylation is tissue-specific for genes which are increased only in the TG. These results demonstrate that one developmental role of Brn3a is to repress potential differences in gene expression between sensory neurons generated at different axial levels, and to regulate a convergent program of developmental gene expression, in which functionally similar populations of neurons are generated from different embryological substrates. Note: 11 samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: GSM89134, GSM89136, GSM89135, GSM89141, GSM89137, GSM89142, GSM89133, GSM89143, GSM89140, GSM89139, GSM89138, Last Updated (by provider): Apr 30 2007 Contributers: Eric E Turner Natalia Fedtsova Iain Dykes Lanier Jason Sani R Eng of caudal 93 101 Structure of blastomere 913 256 235 dilated heart failure ALL_23 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Pancreas 1000 Brain 1000 M_95Av2_3108_DLPFC_0_GS 861 Cerebellum Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181195 Last updated (according to GEO): Jul 12 2007 Gene expression data from SVG-A glial cells. Source GEO sample is GSM189708 Last updated (according to GEO): May 16 2007 NA18974 hrs nasal epithelium 1126 1146 1000 Coronary Arteriosclerosis 861 Neoplasm Meningioma Primary Grade 2 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM108004 Last updated (according to GEO): Jun 06 2006 B344 on Affymetrix GeneChip Human Full Length Array HuGeneFL Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour. This animal was sacrificed at 11 hours after lights on. Original sample code = CM44A Source GEO sample is GSM227296 Last updated (according to GEO): Sep 10 2007 813 with cell proliferative, cytoskeletal, extracellular matrix 754 1000 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145138 Last updated (according to GEO): Nov 20 2006 HC52 FC BA4 A 861 Myositis NA Source GEO sample is GSM84319 Last updated (according to GEO): Dec 01 2005 BL6:3-3 hippocampus 99 FC BA9 B Cerebral cortex 1000 adenoma 861 Comparison of gene expression profiles across the normal human body CNS-SpinalCmod-Adult-28d-2B-s2 cortex 7 12 2737 tumor cells 2747 1000 Prostate 858 Mesodermal cell (cortex 19 25 Blood 1000 bronchus_3 Source GEO sample is GSM80579 Last updated (according to GEO): Mar 31 2006 GM07019 brain, cerebral cortex: Rat_03-44_NroLep_Lipska_e1_le1 MCF7_EtOH_24h_rep1 861 Cerebral cortex GSE5666 Testis 1000 Wild type 8 wk old male A/J mouse cingulate cortex Source GEO sample is GSM74943 Last updated (according to GEO): Feb 27 2007 861 Prostate carcinoma 23 0 mammary epithelial cells 1000 frontal lobe Met. Colon Cancer (SF38) 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113965 Last updated (according to GEO): Jun 16 2006 5 0 brain Replicate1_Voxel E2 /J pituitary gland rep1 1 23 901 frontal lobe Gene expression data from rat metanephric mesenchymes cultured for 1 day in the absence of inducers Source GEO sample is GSM126189 Last updated (according to GEO): Dec 08 2006 The induction of specific tolerance would be the ultimate achievement in transplant immunology, but the precise mechanisms of immunologic tolerance remain largely unknown. Here, we investigated global gene expression analysis in tolerizing murine cardiac allografts by means of oligonucleotide microarrays. Tolerance induction was achieved in cardiac allografts from BALB/c to C57BL/6 mice by daily intraperitoneal injection of anti-CD80 and anti-CD86 monoclonal antibodies (mAbs). Comparative analysis revealed 64 genes to be induced more extensively in the tolerizing than in the syngeneic isografts, and 16 genes than in the rejecting allografts. Two genes were specifically upregulated in the tolerizing allografts. In the tolerizing allografts there were induced marked expressions of a number of genes for pro-inflammatory factors, including interferon-gamma-inducible cytokines and chemokines, as well as apoptosis-related genes, which were also upregulated in the rejecting allografts. Moreover, these gene expression patterns continued to be upregulated more than 70 days posttransplant. These results provide evidence that immunologic tolerance can be induced and maintained in the presence of prominent pro-inflammatory gene expression in vivo. Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11310 Last updated (according to GEO): May 28 2005 861 Integumentary system NORMAL 9 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1653 1648 livers Brain_MD_40_Medulloblastoma_Desmoplastic_A on Affymetrix GeneChip Human Full Length Array HuGeneFL 39 27 the maxillary 4089 4084 liver Paravertebral Muscle 9 Disease 0 29 19 0 Head and neck cancer 861 Spinal Cord 861 Cerebral cortex Sham Day 5,# 3 n/a Source GEO sample is GSM178071 Last updated (according to GEO): Jun 11 2007 DRG_control_24h_rep1 Prosencephalon 861 43h-AM replication 3 Job's patient Source GEO sample is GSM211082 Last updated (according to GEO): Sep 10 2007 0 Human Cortex 11 HapMap CHB Female Source GEO sample is GSM159590 Last updated (according to GEO): Feb 01 2007 19 0 Head and neck cancer Dioxin-induced gene expression changes in MCF-7 human breast cancer cells 19 0 human frontal cortex Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer. This sample is from recombinant inbred strain BXD16 ; a cross of C57BL/6 and DBA/2 mice Keywords = This sample is from recombinant inbred strain BXD16 Keywords = a cross of C57BL/6 and DBA/2 mice Source GEO sample is GSM36705 Last updated (according to GEO): May 27 2005 days nasal epithelium 1127 1148 PBMCs-Type 1 Diabetes-IDDM37_T1D_New Brain 861 861 Hypersensitivity D_U133A_7_Amy CON(DR)(1) Backskin_DN-CLIM_P23_rep3 A HID B D090 D_U133A_98_nAcc 40 21 from dorsal pancreas liver_wildtype_control_6h_rep1 n/a Source GEO sample is GSM177951 Last updated (according to GEO): Jun 11 2007 Nose 1000 Myocardium 861 Chronic Lymphocytic Leukemia 19 47 Abdomen 861 12 frontal Lobe 23 861 Colon HapMap YRI_parent Female Source GEO sample is GSM159720 Last updated (according to GEO): Feb 01 2007 of 10 saccules 5 18 12314 on TGRI-6.5k Cerebral cortex 861 1000 Spleen 102 62 in pediatric acute lymphoblastic leukemia The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169490 Last updated (according to GEO): Feb 21 2007 180-96_Adeno 1000 Coronary Arteriosclerosis none Source GEO sample is GSM149600 Last updated (according to GEO): Jan 03 2007 Cerebral cortex 861 861 Blood Complete or partial monosomy with respect to the X chromosome is the genetic basis of Turner syndrome in human females. Individuals with Turner syndrome have a spectrum of anatomical, physiological and behavioral phenotypes with expressivity dependent on the extent of monosomy and the parental origin of the single X. Parent-of-origin influences on social cognition in Turner syndrome might be due to the presence of imprinted genes on the X. Imprinting of X-linked genes has also been implicated in the male prevalence of autistic spectrum disorders, in male sexual orientation and in the developmental delay of XO mouse embryos. The only molecular evidence for X-chromosome imprinting, however, concerns X-chromosome inactivation in specific circumstances and does not account for these phenotypes. Using a mouse model for Turner syndrome, we searched for locus-specific imprinting of X-linked genes in developing brain. We identified a cluster of X-linked genes containing at least three genes that show transcriptional repression of paternal alleles. Imprinting of these three genes, Xlr3b, Xlr4b and Xlr4c, is independent of X-chromosome inactivation and has a dynamic and complex pattern of tissue and stage specificity. 901 Caudate nucleus structure cerebral cortex 7 21 TAp63 alpha Q540L 24h without induction s1 MSE_N_626 861 Cerebellum 901 Hepatocyte 923 Amyotrophic Lateral Sclerosis Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 2 - Pair 5 - IML Source GEO sample is GSM49898 Last updated (according to GEO): Dec 20 2005 M_95A_2822_CB_1_GS Expression data after reversal of DNA methylation Source GEO sample is GSM230900 Last updated (according to GEO): Sep 20 2007 Epithelium of bronchus 983 861 Fissure Spinal Injuries 913 Blood Test (Blinded) Sample Source GEO sample is GSM129920 Last updated (according to GEO): Sep 18 2007 The AIN-centered DCN of delayed-type eyeblink conditioned mice: 7-d paired and 7-d unpaired training groups 17 7 hippocampus Cerebral cortex 1000 Epithelium 861 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141310 Last updated (according to GEO): Oct 26 2006 Sample 3 at Time 3 Source GEO sample is GSM113092 Last updated (according to GEO): Jun 06 2006 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114388 Last updated (according to GEO): Jun 16 2006 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215054 Last updated (according to GEO): Aug 02 2007 Anterior nares 1000 1000 frontal lobe brain, cerebral cortex: Rat_03-41_NroLep_Lipska_e1_le1 1000 Retina autism 0 5 1000 Neuraxis 82 60 in retinitis pigmentosa 901 Nervous system structure GSE4031 CF knockout HMCF CHN310 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188768 Last updated (according to GEO): Jun 06 2007 Normal Source GEO sample is GSM175857 Last updated (according to GEO): Apr 09 2007 Hormones 1000 320 306 Keywords = HIV 753 748 brain Primary large cell carcinoma 1997 1000 Kidney NA Source GEO sample is GSM84311 Last updated (according to GEO): Nov 21 2005 none Source GEO sample is GSM244632 Last updated (according to GEO): Nov 23 2007 Blood 1000 Myocardium 861 901 Temporal Lobe 1000 Amygdaloid structure MLL__7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 4176 tumor cells 4187 JMR-RatInj72h-2aA-s2 on progenitor oval cells 1515 1538 /Ovary 14 Disease 11 27 Prosencephalon 861 5 0 Spleen GSE4810 Site: University of Michigan Cohort: Male/Female Control Set Diagnosis: Control pH: 6.84 Subject: 2835 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39029 Last updated (according to GEO): May 27 2005 Obese 892 896 Cerebral cortex 861 Epithelium 865 AML_6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Anterior nares 1000 861 Acquired Immunodeficiency Syndrome Bone Marrow 1000 Brain 861 We report a comprehensive analysis of gene expression differences between sexes in multiple somatic tissues of 334 mice derived from an intercross between inbred mouse strains C57BL/6J and C3H/HeJ. The analysis of a large number of individuals provided the power to detect relatively small differences in expression between sexes, and the use of an intercross allowed analysis of the genetic control of sexually dimorphic gene expression. Microarray analysis of 23,574 transcripts revealed that the extent of sexual dimorphism in gene expression was much greater than previously recognized. Thus, thousands of genes showed sexual dimorphism in liver, adipose, and muscle, and hundreds of genes were sexually dimorphic in brain. These genes exhibited highly tissue-specific patterns of expression and were enriched for distinct pathways represented in the Gene Ontology database. They also showed evidence of chromosomal enrichment, not only on the sex chromosomes, but also on several autosomes. Genetic analyses provided evidence of the global regulation of subsets of the sexually dimorphic genes, as the transcript levels of a large number of these genes were controlled by several expression quantitative trait loci (eQTL) hotspots that exhibited tissue-specific control. Moreover, many tissue-specific transcription factor binding sites were found to be enriched in the sexually dimorphic genes. no additional Source GEO sample is GSM199090 Last updated (according to GEO): Jun 08 2007 E2A-PBX1-#6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 3AJZ02081478b_Superior_Cervical_Ganglion in adipocytes 882 894 1000 Retina Brain 861 Brain (caudate nucleus) [JunctionChip 2 of 5] DCIS79 on harvard-12k Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n129 Source GEO sample is GSM2044 Last updated (according to GEO): Nov 21 2005 Muscle biopsies taken from vastus lateralis muscle of 15 men and 15 women after 3 days of standardized diet and activity to examine effects of sex and age Subjects were either young adults (7 men and 7 women, 20-29 yr old) or older (8 men and 8 women, 65-75 yr old) Affymetrix U133A and U133B arrays were scanned both before (S1) and after (S2) antibody enhancement. This file has U133A S1 data. Effects of age were computed for men and women separately with an alternative method previously and data submitted as GSE362 (men) and GSE674 (women). Last Updated (by provider): Nov 23 2007 Contributers: Stephen Welle CC010 Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174510 Last updated (according to GEO): Mar 14 2007 Spinal Cord 861 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68286 Last updated (according to GEO): Jul 07 2006 Brain 1000 ER+/LN-/Marks210 on Affymetrix GeneChip Human Full Length Array HuGeneFL Nasal Epithelium 865 Gene expression data from rat lungs exposed to FiO2 of ~9.5% and SU-5416 (hypoxia-SU-5416). Source GEO sample is GSM184881 Last updated (according to GEO): Jun 14 2007 1000 Uterus Organotypic hippocampal slice cultures of male, postnatal day 15 mice (C57B6/SJL) were maintained in culture for 11 days and treated with 1 nM sAPPalpha (sAPPalpha) for an additional 24 h. Cultures were maintained on filter inserts in Neurobasal media with B-27 supplement (Invitrogen) and 1 mM glutamine. The sample consists of 11 slices from 4 mice. Data were analyzed with MAS 5.0 and scaled to 2500. Keywords = Alzheimer?s disease Keywords = neuroprotection Keywords = sAPPalpha Source GEO sample is GSM26705 Last updated (according to GEO): Oct 28 2005 The nose 94 101 861 Asphyxia days nasal epithelium 1126 1147 DIV14 cortical neuron, KCl 2 5 0 brain 395 390 spleen PBMCs-Type 2 Diabetes-T2D_10_New 10 Bone marrow 0 nic + nmda2 (Experiment Neuroprotection4- Run 14985) Treatment, type=timepoint, description=primary cortical neurons were treated for 18 h with nicotine 10uM ,NMDA 1mM was added for 30 min, both agonists were then washed out and the cells were harvested 24h later, measurement=24.0 h Source GEO sample is GSM96737 Last updated (according to GEO): Feb 14 2006 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120675 Last updated (according to GEO): May 14 2007 Brain 861 f2#75 versus pool Mouse Brain tissue frontal cortex wistar ky 3929 whole tissue, individual animal, 10 weeks old, male Wistar Kyoto frontal cortex file:p3929w Source GEO sample is GSM15166 Last updated (according to GEO): Oct 28 2005 13 7 cochlea GSE386 cocaine naive, ventral tegmental area 0 37 861 Brain 1000 Descending colon 861 Cancer of Neck 266 257 infection Epithelial Cells 1000 of Parkinson's disease 450 471 901 theca cell C3H/HeJ Basal Ganglia F Gene expression data from colorectal adenoma. Source GEO sample is GSM215095 Last updated (according to GEO): Aug 02 2007 Expression profiling of somatomotor cortex extracted from rats at 4h following moderate injury Source GEO sample is GSM44455 Last updated (according to GEO): May 27 2005 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195355 Last updated (according to GEO): Jun 04 2007 at the Human Brain 746 763 Ovary 1000 human caudate nucleus Source GEO sample is GSM86904 Last updated (according to GEO): Feb 08 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-beta (IFN beta) for 30min Source GEO sample is GSM5592 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T9) extracted from rats 28d following severe injury Source GEO sample is GSM31604 Last updated (according to GEO): May 27 2005 861 Cerebral cortex Melanoma xenograft, MED1_Sub_A (LeiFidler) Parkinson Disease 861 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11554 Last updated (according to GEO): May 28 2005 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Leukotriene B4 (LTB4) for 240min Source GEO sample is GSM5683 Last updated (according to GEO): May 27 2005 Gene expression data from the neocortex of S1P3-knockout mouse Source GEO sample is GSM172947 Last updated (according to GEO): Mar 08 2007 1000 Infection Cerebral cortex 861 short access to cocaine ,medial prefrontal cortex, 1 hr/day access to cocaine Source GEO sample is GSM93870 Last updated (according to GEO): Jan 26 2006 Colonic mucous membrane 913 MuscleRegen-ctx3d-2RLAv2-s2 Wild type inbred mice Source GEO sample is GSM82925 Last updated (according to GEO): Nov 10 2005 B220+CD25+sIg- Large Pre BII cells sorted out of mouse bone marrow, sort no. 1_2 Source GEO sample is GSM618 Last updated (according to GEO): Mar 17 2006 NH 63h the blood 393 402 progenitor cells 545 561 861 HIV Infections CNS-SC_InjA14d-4C-s2 Female mice used were 129/SvImJ wildtype (Jackson Lab), 10-16 weeks of age. 14 days after ovariectomy, the mice were sacrifice and uterine horns were removed. 8 uterine horns from 4 mice were pooled to form one sample. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix. Source GEO sample is GSM3053 Last updated (according to GEO): May 27 2005 medial prefrontal cortex short access to cocaine replicate 3 1338 in the prefrontal cortex 1361 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 24 h time point Source GEO sample is GSM159820 Last updated (according to GEO): Apr 23 2007 225 209 of microphthalmia fibroblasts 606 617 A2780_cis_IC90_0h_1 22 17 (heart with mental retardation 241 263 320 291 of human oral epithelial cells 1000 Spleen 1000 Glioma digested Treatment, type=time_course, measurement=1.0 d Source GEO sample is GSM113321 Last updated (according to GEO): Jun 07 2006 Primary Neoplasm 1000 spleen 164 170 1000 Brain Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211331 Last updated (according to GEO): Jul 18 2007 Gene expression data of substantia nigra from postmortem brain of normal controls Source GEO sample is GSM184362 Last updated (according to GEO): May 29 2007 nic + nmda5 (Experiment Neuroprotection4- Run 21823) Treatment, type=timepoint, description=Same sample used for Experiment Neuroprotection4-Run 14985, samples were rerun due to oven failure, measurement=0.0 h Source GEO sample is GSM96702 Last updated (according to GEO): Feb 14 2006 PBMCs-Healthy-H122_Healthy 12 frontal Lobe 23 Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 7067 blood Squamous cell carcinoma 884 Granulocyte-colony stimulating factor (G-CSF) is used to boost granulocyte counts in immunocompromised patients, but its effects on the immune system may be counter productive. We tested the hypothesis that G-CSF mobilized peripheral blood stem cell (PBSC) products are immunologically down regulated based on gene microarray analysis. Ten peripheral blood samples from normal donors for allogeneic PBSC transplantation were obtained before and after administration of G-CSF and tested on Affymetrix Human U133 Plus 2.0 GeneChip® microarrays. Significant changes in gene expression after G-CSF mobilization were reported by controlling the false discovery rate at 5%. Immune-related genes (335) were isolated from the data set and categorized according to probe set annotations and a thorough, independent literature search. We found that G-CSF up-regulated inflammatory and neutrophil activation pathway gene expression; however, adaptive immune-related gene expression, such as antigen presentation, co-stimulation, T cell activation and cytolytic effector pathways, were generally down-regulated. Thus, despite significant increases in stem cells, lymphocytes and antigen presenting cells, G-CSF mobilized PBSC allografts exhibit a suppressive adaptive immune-related gene expression profile. Our data provides an explanation for the potentially immunosuppressive effects observed after G-CSF administration. Last Updated (by provider): Aug 09 2007 Contributers: Matthew Buzzeo Vijay Reddy ovarian tumor: serous Source GEO sample is GSM139448 Last updated (according to GEO): Apr 09 2007 To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at ?800C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at ?80°C before routine processing for GeneChip analysis. Source GEO sample is GSM28658 Last updated (according to GEO): Oct 28 2005 n/a Source GEO sample is GSM177901 Last updated (according to GEO): Jun 11 2007 Mice sacrificed after swimming twice a day for 4 weeks. Keywords = exercise induced hypertrophy Source GEO sample is GSM2360 Last updated (according to GEO): May 27 2005 Biopsy of the normal mucosa of the colon from patient #25 1007 995 to M0 tumors 4M_A31103 Cerebral cortex 1000 Rat SCN Sample 4 (Exp 1 - 18 hr) the ventricular 1095 1109 19 0 amygdala wistar 3720 43 0 Chorionic mesoderm-derived mesenchymal cells Immature Dcs treated with IFN alpha HOXB4ERT_w/o TMX, 4 hours, biological rep1 861 Pancreas Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211321 Last updated (according to GEO): Jul 18 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145325 Last updated (according to GEO): Nov 20 2006 FVB/NJ hypothalamus rep1 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10158.gif Source GEO sample is GSM79651 Last updated (according to GEO): Sep 22 2006 medulla_7 Source GEO sample is GSM80721 Last updated (according to GEO): Mar 31 2006 brain, hippocampus: KA72-III_e1_le1 Spleen 1000 Bone Marrow 1000 na Source GEO sample is GSM181296 Last updated (according to GEO): Apr 10 2007 NO_KIDNEY_9 38 25 normal ovaries 66 50 Tongue epidermis Disorder of artery 865 cy3:SHR treated w/ nifedipine, biological rep 4g; cy5:pool of 6 WKY control rats Phenytoin frontal cortex 4 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53464 Last updated (according to GEO): Jul 06 2005 testis 52 58 T-47D hgu95b Macrophage 14smi017 n/a Source GEO sample is GSM177980 Last updated (according to GEO): Jun 11 2007 HNN039 "14h Thy-Noc, Exp4" Epithelial Cells 901 1000 Coronary Arteriosclerosis TEL-AML1-C35 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Small Intestine; Duodenum Keywords = mouse gene expression database Source GEO sample is GSM29297 Last updated (according to GEO): May 27 2005 Acetaminophen 24hr Rat 0504 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool Gene expression data from postmorten brain regions Source GEO sample is GSM145527 Last updated (according to GEO): Nov 20 2006 861 Cerebellum Mesenchymal Stem Cells 1000 1 year!Sample_source_name_ch1 = Post Natally excised Human lung tissue Source GEO sample is GSM107829 Last updated (according to GEO): May 04 2006 Macrophages treated with LPS plus IL-10, 30 min, Replicate 1 Source GEO sample is GSM241143 Last updated (according to GEO): Nov 02 2007 GSE5504 Brain 861 from the forebrain 20 37 861 Colon myocardial infarction 383 403 65 61 Lungs B220+CD25+sIg- Small Pre BII cells sorted out of mouse bone marrow, sort no. 10 Source GEO sample is GSM633 Last updated (according to GEO): Mar 17 2006 5 0 brain infection 433 442 C57BL/6J cingulate cortex rep1 brain, cerebellum: RNA#11*_le1 74 66 seizures of somatomotor cortex 21 41 Prefrontal cortex of schizophrenic, bipolar, and control subjects. This is the "McLean 66" 861 Cancer of Neck Cortex 0 5 Entorhinal Cortex 7 23 1000 ovarian neoplasm 0 Human Cortex 11 Gene expression data from postmorten brain regions Source GEO sample is GSM145118 Last updated (according to GEO): Nov 20 2006 Neoplasm 861 Human Hypothalamus Female 4 (technical replicate) 19 0 Head and neck cancer Pineal gland 1000 Normal Source GEO sample is GSM175876 Last updated (according to GEO): Apr 09 2007 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153469 Last updated (according to GEO): Jan 11 2007 Cochlea_WT_9mo_1 58 39 from the spinal cord of somatomotor cortex 21 41 S3_Muscle_Insulin_30min 3 min exposure to halothane, immediate perfusion with ice cold saline Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5090 Last updated (according to GEO): May 27 2005 Ischemia-reperfusion #2 prostate Source GEO sample is GSM203348 Last updated (according to GEO): Jun 21 2007 with progressive supranuclear palsy 27 61 that adenovirus 207 221 20 0 human caudate nucleus seminoma specimen, pT1, patient age: 36y; W00 223 901 Intestines, Small Replicate3_Voxel C5 NeverSmoker 48 1000 Brain of regenerating Dorsal Root Ganglia 21 55 E7, hTERT, neural differentiation, bone marrow cell 5 CNS-SC_InjB7d-1A-s2 Liver 1000 Mesentery 1000 5 0 Spleen 67 40 with coronary artery disease AD 2hr C+S-CA1 5 0 brain heart failure 583 595 Microarray analysis of NL and PCOS oocytes (P5) 432 409 with those from adenomas of parieto-occipital cortex 122 148 ISR6 Nose 1000 leukemia lymphoblastic (MOLT-4) Source GEO sample is GSM18887 Last updated (according to GEO): Sep 25 2006 Pooled gastroc RNA samples from five 8 wk old male mdx mice Source GEO sample is GSM13679 Last updated (according to GEO): May 28 2005 1BJZ02053110_PrefrontalCortex 1000 Retina Gene expression data from postmorten brain regions Source GEO sample is GSM146017 Last updated (according to GEO): Nov 20 2006 HeartHDmekt_022GACJ5_123t.txt prostate Source GEO sample is GSM203358 Last updated (according to GEO): Jun 21 2007 5 0 brain Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153493 Last updated (according to GEO): Jan 11 2007 The aim was to carry out global analysis of gene expression changes occurring in the normal pubertal mouse mammary gland from the appearance to the regression of terminal end buds. Last Updated (by provider): May 09 2007 Contributers: Jean McBryan Finian Martin Cerebral cortex 861 1000 Brain C57BL/6J Hippocampus B nucleus accumbens_shell sprague2 Half-moon-shaped NAc shell samples were obtained with a 12 gauge punch of the remaining ventromedial shell tissue, pool of 5 animals, 20 weeks old, male Sprague Dawley nucleus accumbens shell file:R3MH01112101 Source GEO sample is GSM15226 Last updated (according to GEO): Oct 28 2005 in bronchial epithelia 311 332 To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132970 Last updated (according to GEO): Sep 12 2006 Laser captured visceral sensory neurons. Source GEO sample is GSM63685 Last updated (according to GEO): Dec 21 2005 Gene profiling in spinal cord injury shows role of cell cycle in neuronal death. Integumentary system 861 mouse hippocampus from COX-2 knockout Source GEO sample is GSM121445 Last updated (according to GEO): Jan 31 2007 MLL_11 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with ELC for 240min Source GEO sample is GSM5558 Last updated (according to GEO): May 27 2005 459 450 infection Neoplasm 861 Replicate1_Voxel A3 Spleen vs ELC Treated B cell 240min (set1) plasma cells 332 344 brain, amygdala: Amygdala 4_le1 Heart 861 1000 Brain Myocardium 861 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211373 Last updated (according to GEO): Jul 18 2007 bc-ZT15-2 Richard Almon-43-1138200270742 H111 CB A osteoblast 627 637 1143_24d CAD_replicate63 KO_IL-6_0_rep2 acute myeloid leukemia Source GEO sample is GSM227423 Last updated (according to GEO): Sep 12 2007 Cerebellum 1000 861 Heart 2754 2741 of spinal cord mouse brain ipsilateral LPS Source GEO sample is GSM149772 Last updated (according to GEO): Mar 15 2007 12 frontal Lobe 23 Brain 1000 861 Gland structure Brain [JunctionChip 5 of 5] Parkinson's disease sample x200 from the right forebrain 21 44 861 Blood Blood 861 /3T3 fibroblasts 478 493 861 Heart Diseases 1000 Carcinoma of bladder 165 155 of retinal 19 0 human frontal cortex 1000 Spleen Wild type 8 wk old male A/J mouse periaqueductal gray Source GEO sample is GSM107031 Last updated (according to GEO): Mar 05 2007 Lymphoblastoid Cell Line for Individual 8026.3 log phase WGACON-15 861 Cancer of Neck Richard Almon-16-1133800609214 0 Human Cortex 11 91 from the bone marrow 72 329 306 valvular cardiomyopathy MF-14 without visceral metastases 1151 1178 from nose 100 108 Hereditary Nonpolyposis Colorectal Neoplasms 947 Brain 861 23 0 mammary epithelial cells Acetaminophen 6hr Rat 7270 blood vs. Acetaminophen 6hr Rat Pooled Control blood Primary large cell neuroendocrine carcinoma 6042 1037 of transitional epithelium 1012 11_0017_SepticShock_Day1_41 NHF1-hTERT_S_C5_16137 B_N6 on Affymetrix GeneChip Human Full Length Array HuGeneFL 1000 Acquired Immunodeficiency Syndrome 5 0 Spleen Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159811 Last updated (according to GEO): Apr 23 2007 Primary tumor 19 32 Sample details: Three pools of rostral (R1-3), three pools of middle (M1-3), and three pools of caudal (C1-3) E13.5 MF1 neocortex were collected from 4 embryos. All possible 18 comparisons were carried out. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. Source GEO sample is GSM62831 Last updated (according to GEO): Aug 26 2005 colon.2 H9LMS00092710 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11539 Last updated (according to GEO): May 28 2005 37 18 of the failing heart CAD_replicate15 BPH-24 on NHGRI-6.5k_c Gene expression data from postmorten brain regions Source GEO sample is GSM145207 Last updated (according to GEO): Nov 20 2006 TEL-AML1-C17 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A GSE7469 TNFTG-3w-f-2 Rat frontal cortex RNA - VH TTX Experiment Source GEO sample is GSM92307 Last updated (according to GEO): Jan 13 2006 S12_Muscle_Insulin_240min "26h Thy-Noc, Exp4" 1607 1593 in the amygdala of the heart 842 854 Sample represents the Paraventricular nucleus from 5 dehydrated animals (3 Days) Source GEO sample is GSM69472 Last updated (according to GEO): Dec 16 2005 after stroke 238 250 901 frontal lobe 904 894 to seizures Ganglia 861 P104 deprived visual cortex replicate 1 5 0 brain mouse brain contralateral control, biological rep3 Ganglia, Spinal 923 Posterior root of spinal nerve 861 MALME-3M_CL10002_MELANOMA 15 0 human cerebellum G30-CingulateCortex replicate3 I_95Av2_2978_CB_0_GS E6.75_rep1 Bilateral olfactory bulbectomies were performed on male C57Bl/6 mice(6 week old) and olfactory epithelium tissue collected 7 days post-bulbectomy. Total RNA was extracted from the olfactory epithelium tissue. Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol. Keywords = olfaction Keywords = neurogenesis Keywords = apoptosis Keywords = gene silencing Keywords = microarray, transcription factor Source GEO sample is GSM45688 Last updated (according to GEO): Oct 28 2005 Parkinson 0 8 brain 0 5 901 Malignant neoplasm of breast Anterior nares 1000 This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195264 Last updated (according to GEO): Sep 13 2007 34 16 of stria vascularis SR-A mutant olfactory epithlium 2 hpO replicate2 Osteoblasts 1000 Macrophage 14smi057 brain, cerebral cortex: PC5_e1_le1 3_hypothalamus_9hrs_sleep_#107 861 Heart Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Source GEO sample is GSM15943 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145556 Last updated (according to GEO): Nov 20 2006 Primary Neoplasm 1000 Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 9203 left_liver_lobe Expression profiling of spinal cord section (T8) extracted from rats 4h following laminectomy (sham) Lot batch = Source GEO sample is GSM4428 Last updated (according to GEO): May 28 2005 Ovary_PD1_Foxo3 Null_Replica 3 RNA of Kidney was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 biological replicates were analyzed. Keywords = db/m mice Keywords = kidney Source GEO sample is GSM9928 Last updated (according to GEO): May 27 2005 Femur 1000 861 Nerve Primary Carcinoma 876 Primary large cell neuroendocrine carcinoma 5883 Source GEO sample is GSM17330 Last updated (according to GEO): May 28 2005 Blood 1000 Human lung tissue 28 44 1000 Descending colon brain 0 5 5 0 brain from colorectal adenoma 21 44 Squamous cell carcinoma 923 brain_DLPFC_bipolar C_mr951 1000 frontal lobe Inflammatory response to titanium dioxide particles exposure is enhanced during pregnancy brain 0 5 Gene expression data from aneurismal tissues obtained from patients with bicuspid valves. Source GEO sample is GSM116782 Last updated (according to GEO): Jun 28 2006 660 mesenchymal stem cell 639 of metastasis 1019 1031 FBooth-CON-1Av2-s2 Brain 861 858 Prostatic Neoplasms Skeletal muscle biopsy was obtained before a 3-hour hyperinsulinemic (infusion rate 40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172150 Last updated (according to GEO): Feb 28 2007 in seminoma 28 38 861 Infection Nerve 1000 UACC-257 hgu95e ve_2m57 14 7 amygdala 1000 ovarian neoplasm R7E 3 Spinal muscular atrophy with respiratory distress type 1 (SMARD1) is an infantile autosomal-recessive motor neuron disease caused by mutations in the immunoglobulin micro-binding protein 2. We investigated the potential of a spinal cord neural stem cell population isolated on the basis of aldehyde dehydrogenase (ALDH) activity to modify disease progression of nmd mice, an animal model of SMARD1. ALDH(hi)SSC(lo) stem cells are self-renewing and multipotent and when intrathecally transplanted in nmd mice generate motor neurons properly localized in the spinal cord ventral horns. Transplanted nmd animals presented delayed disease progression, sparing of motor neurons and ventral root axons and increased lifespan. To further investigate the molecular events responsible for these differences, microarray and real-time reverse transcription-polymerase chain reaction analyses of wild-type, mutated and transplanted nmd spinal cord were undertaken. We demonstrated a down-regulation of genes involved in excitatory amino acid toxicity and oxidative stress handling, as well as an up-regulation of genes related to the chromatin organization in nmd compared with wild-type mice, suggesting that they may play a role in SMARD1 pathogenesis. Spinal cord of nmd-transplanted mice expressed high transcript levels for genes related to neurogenesis such as doublecortin (DCX), LIS1 and drebrin. The presence of DCX-expressing cells in adult nmd spinal cord suggests that both exogenous and endogenous neurogeneses may contribute to the observed nmd phenotype amelioration. The muscular dystrophies also 208 236 1000 Descending colon Normal Source GEO sample is GSM176206 Last updated (according to GEO): Apr 09 2007 hippocampus 161 172 Testi-GermCell Source GEO sample is GSM18986 Last updated (according to GEO): Sep 25 2006 8076_Lung did not develop PGD Balb/c day 6, biological rep 1, tech rep 1 Liver Test (Blinded) Sample Source GEO sample is GSM130118 Last updated (according to GEO): Sep 18 2007 human caudate nucleus Source GEO sample is GSM86830 Last updated (according to GEO): Feb 08 2006 D_U133A_37_nAcc ALL B-cell47 on Affymetrix GeneChip Human Full Length Array HuGeneFL ovarian tumor: mucinous Source GEO sample is GSM139433 Last updated (according to GEO): Apr 09 2007 Hoxb1 mutant mRNA levels in rhombomere 4 at E10.5 Thyroid Source GEO sample is GSM18961 Last updated (according to GEO): Sep 25 2006 DBA whole brain 1 M_U133Plus_16_HC low gestational age Source GEO sample is GSM213102 Last updated (according to GEO): Jul 25 2007 Myocardial Infarction 1000 wild type placebo 15d, biological rep2 19 0 human frontal cortex 9 0 rat kidney M_U133Plus_119_HC NG020_a 861 hair Cerebral cortex 861 5 0 Spleen 27 0 Substantia nigra normal rep5 coronary_artery_4 Source GEO sample is GSM80610 Last updated (according to GEO): Mar 31 2006 Starvation 916 Nose 1000 Whole blood from a healthy control Source GEO sample is GSM153425 Last updated (according to GEO): Jan 11 2007 Keywords = kidney 149 166 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11247 Last updated (according to GEO): May 28 2005 embryonic hearts 1064 1079 63 50 Striatum C57BL Craniocerebral Trauma 861 861 Blood Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213470 Last updated (according to GEO): Jul 31 2007 human caudate nucleus Source GEO sample is GSM86821 Last updated (according to GEO): Feb 08 2006 1000 Lymphoma 1000 Brain AMM_0_0_Male10_Olfact_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111841 Last updated (according to GEO): Nov 21 2006 Macrophage smi71 1000 Brain Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211396 Last updated (according to GEO): Jul 18 2007 Ovary 1000 67 40 with coronary artery disease Whole blood 0 10 Myocardial Infarction 1000 Normal Source GEO sample is GSM176454 Last updated (according to GEO): Apr 09 2007 PGA_MI_ilv_8w_332 338 333 brain 1000 Large Intestine Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b053 Source GEO sample is GSM1978 Last updated (according to GEO): Nov 21 2005 in bronchial epithelia 311 332 Embryonal carcinoma, NCR-G4, adherent PC5 Treatment, type=incubate, description=Hypoxic preconditioning Source GEO sample is GSM107474 Last updated (according to GEO): May 01 2006 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202669 Last updated (according to GEO): Jun 20 2007 861 Brain cardiac 746 752 of central neurites 419 437 CNS-SpinalCmod-Adult-4h-2B-s2 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Platelet activating factor labeled with Cy5- time course with repeats. Date GSE394 Last Updated: May 29 2005 Contributers: Joella Grossoehme Rebecca Hart Robert Hsueh Sangdun Choi Zhen Yan Angela Alexander Jong-Woo Kim Sun Young Lee Yun Anna Cao Mi Sook Chang Includes GDS315. Update date: Nov 18 2003. Dataset description GDS315: Temporal analysis of effects induced by 100 nM platelet activating factor in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. 1365 1343 in immature hippocampus mouse brains 187 198 Thymosin 861 HapMap YRI_parent Female Source GEO sample is GSM159700 Last updated (according to GEO): Feb 01 2007 Leukemia Chronic Myelogenous (K562) [JunctionChip 3 of 5] jzo027-rp1-v5_u74av2-met 9275 on TGRI-6.5k of the mouse brain 224 241 1000 Brain The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160335 Last updated (according to GEO): Feb 08 2007 Subject code A47 processed in batch 2 Source GEO sample is GSM90440 Last updated (according to GEO): Mar 20 2006 no additional Source GEO sample is GSM199220 Last updated (according to GEO): Jun 08 2007 Bone Marrow 901 M7TW01013110 Nd8: Hippocampus_21PT-AU_rep7 of the heart 842 854 Spleen 0 5 861 Chromosomes Timecourse of TLR2/1 stimulated human dendritic cells with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225881 Last updated (according to GEO): Aug 31 2007 1000 Heart failure embryonic hearts 1064 1079 68 52 of breast cancer 1000 Endometriosis, site unspecified no additional Source GEO sample is GSM199300 Last updated (according to GEO): Jun 08 2007 Gene expression data from NICM NYHA III-IV CHF patients Source GEO sample is GSM231007 Last updated (according to GEO): Sep 21 2007 Female mice used were SvJ/129, 10-16 weeks of age; Hoxa-10+/+ and Hoxa-10-/- littermates were used in parallel experiments. 14 days after ovariectomy, mice were injected subcutaneously with progesterone dissolved in sesame oil (Sigma; 0.2mg/0.1mL/mouse), followed by sacrifice and removal of uterine horns at 6 hours after injection. 8 uterine horns from 4 mice were pooled to form one sample. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix. The 6 samples were obtained and processed in two batches: (1: GSM3047 and GSM3041), and (2: GSM3048, GSM3049, GSM3042, and GSM3043). Last Updated (by provider): May 29 2005 Contributers: Hyunjung Lim Mylene W Yao George M Church Daniel J Schust Richard L Maas Sung E Choe Sebastien Michaud Yueyun Ding Anna Farago Includes GDS187. Update date: May 03 2004. Dataset description GDS187: Hoxa-10 +/+ and Hoxa-10 -/- littermates injected 14 days after ovariectomy with either progesterone in sesame oil, or just sesame oil. Uterine horns removed for analysis 6 hours after injection.. cingulate cortex 901 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132538 Last updated (according to GEO): Feb 26 2007 861 Cerebellum Wild type 8 wk old male 129S6/SvEvTac mouse cingulate cortex Source GEO sample is GSM74941 Last updated (according to GEO): Feb 27 2007 mRNA was isolated after 4 hours of incubation from IMR-90 cells seeded onto a collagen/chondroitin sulfate tissue engineering scaffold mesh material. Cells were seeded at a density of 1 x 10^6 cells/ mesh, and this chip represents a pooling of cells from 4 meshes. Keywords = tissue engineering mesh, collagen, chondroitin sulfate, biomaterials design Source GEO sample is GSM6059 Last updated (according to GEO): May 27 2005 1000 Brain 691 652 from magnocellular neuron axon terminals none Source GEO sample is GSM246010 Last updated (according to GEO): Dec 03 2007 Expression profiling of somatomotor cortex extracted from rats at 3 months following moderate injury Source GEO sample is GSM41725 Last updated (according to GEO): May 27 2005 1000 Cerebral cortex Replicate2_Voxel F5 no additional Source GEO sample is GSM199094 Last updated (according to GEO): Jun 08 2007 1000 Cerebral cortex Haloperidol treated 4weeks AffyGC RMA rep3 Skeletal_Muscle_Psoas Source GEO sample is GSM18854 Last updated (according to GEO): Sep 25 2006 Kidney Cortex 3 Normal 1000 Brain mouse cerebral cortex 0 21 ovarian tumor: serous Source GEO sample is GSM139467 Last updated (according to GEO): Apr 09 2007 868 850 of medulloblastoma Fibroblasts 1000 1000 Bipolar Disorder ALS model Source GEO sample is GSM75507 Last updated (according to GEO): Mar 06 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145379 Last updated (according to GEO): Nov 20 2006 Total RNA extracted from the forebrain of a Stg+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144389 Last updated (according to GEO): Nov 14 2006 infection 453 461 Neoplasm Metastasis 861 WGACON-17 Acetaminophen 3hr Rat 8282 blood vs. Acetaminophen 3hr Rat Pooled Control blood 69 61 of tumors total spinal cord 0 16 ovary 180 185 GC (HKG34N) from brain 21 30 total RNA from biosource CC#18 Treatment, type=dissect, description=dissection from cerebellar tissue Source GEO sample is GSM92464 Last updated (according to GEO): Jan 13 2006 Wildtype cocaine, biological replicate 1 Spleen vs Leukotriene B4 (LTB4)Treated B cell 120min (set2) Fibroblasts 861 Identification of putative learning and memory genes in the dentate gyrus of aged rats following the Morris Water Maze HMVEC-L stimulated with LPS for 24 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114562 Last updated (according to GEO): Sep 20 2006 6 (cerebral cortex 21 913 Spinal Injuries of the normal mucosa 7 26 rodentium infection 784 803 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211367 Last updated (according to GEO): Jul 18 2007 1000 Brain Stem Cerebral cortex 861 Lymphoblastoid Cell Line for Individual 8094.4 log phase with progressive supranuclear palsy 27 61 Whole Brain 73 83 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM160202 Last updated (according to GEO): Feb 08 2007 CNS-SC_CtrA14d-2A-s2 Leukemia, Lymphocytic, Chronic 1000 67 40 with coronary artery disease R7E 5 in human liver cancers" 65 87 40 CB A Expression profiling of laminectomized raphe at 3mo in rats Source GEO sample is GSM41536 Last updated (according to GEO): May 27 2005 Gene expression data from the hippocampus of wild-type mouse Source GEO sample is GSM172957 Last updated (according to GEO): Mar 08 2007 1000 Primary carcinoma of the liver cells 21 0 acute myeloid leukemia 861 Blood The sample is a part of a series describing gene expression changes during postnatal development of the small intestine Source GEO sample is GSM198827 Last updated (according to GEO): Jun 11 2007 91 from the bone marrow 72 Knockout cocaine, biological replicate 1 axon pathfinding. 349 366 CAD_replicate110 To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour intervals cells from a single plate were harvested and pooled for total RNA extraction. Keywords = Suprachiasmatic Nucleus / Circadian Pacemaker / Clock / Oscillator / SCN2.2 /. Source GEO sample is GSM28459 Last updated (according to GEO): May 27 2005 901 Myeloid Leukemia Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153377 Last updated (according to GEO): Dec 27 2006 M7TW00122036 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11549 Last updated (according to GEO): May 28 2005 Cerebellum 1000 Spleen 1000 3 0 Lung mouse brain ipsilateral LPS.RU486, biological rep3 923 Subcutaneous Fat 04_0004_SepticShock_Day3_9 na Source GEO sample is GSM181265 Last updated (according to GEO): Apr 10 2007 Primary small cell lung carcinoma 544 Source GEO sample is GSM17335 Last updated (according to GEO): May 28 2005 trigeminal_ganglia_4 HDMTX_MP-DX-8 923 Ganglia, Spinal 861 Cerebral cortex Brain_MD_20_Medulloblastoma_Classic_D on Affymetrix GeneChip Human Full Length Array HuGeneFL Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225934 Last updated (according to GEO): Nov 02 2007 BCR-ABL-#4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 930 914 in the cerebellum Spleen vs Bombesin Treated B cell 30min (set2) Simple annotation: Reference verification, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9990.gif Source GEO sample is GSM78465 Last updated (according to GEO): Sep 22 2006 Multiple System Atrophy 1000 WGACON-212 Nasal Epithelium 901 Lymphoblastoid Cell Line for Individual 8020.4 log phase Donor A, pre G-CSF Normal Source GEO sample is GSM176386 Last updated (according to GEO): Apr 09 2007 H1 Human Embryonic Stem cell (H1LESC) M_U133A_48_DLPFC_R GSE582 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114239 Last updated (according to GEO): Jun 16 2006 Neoplasm 861 LDMTX_MP-7 Gene expression comparison of mouse ES cells and EpiSCs brain, cerebellum: RNA#10S_le1 post HCMV infection 68 86 hrs nasal epithelium 1127 1147 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188729 Last updated (according to GEO): Jun 06 2007 1000 Liver 1000 Structure of superior cervical ganglion Replicate3_Voxel D8 tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44864 Last updated (according to GEO): May 27 2005 ventral_tegmental_area_1 cy5:SHR treated w/ nifedipine and then washed out, biological rep 5r; cy3:pool of 6 WKY control rats 861 Ribosomal RNA 23 0 3AJZ02022222_ leukemia D_U133Plus_116_HC brain, cochlea: [15] Sample #15_le1 Type 1 Diabetes patient and the timepoint at diagnosis. Source GEO sample is GSM228592 Last updated (according to GEO): Sep 11 2007 Malignant Neoplasms 861 Plasma 861 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181207 Last updated (according to GEO): Jul 12 2007 Cerebral cortex 1000 in brains 65 73 858 Mesodermal cell folatesufficientAs1ppm2 nostrils 156 164 861 Glioblastoma brain, cerebral cortex: Rat_03-64_NroLep_Lipska_e1_le1 901 Coronary artery Abdominal aorta collected during autopsy within 24 hours post mortem Source GEO sample is GSM170557 Last updated (according to GEO): Jul 26 2007 Acetaminophen 6hr Rat 8897 left_liver_lobe vs. Control Acetaminophen 6hr Rat left_liver_lobe Pool Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11257 Last updated (according to GEO): May 28 2005 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11595 Last updated (according to GEO): May 28 2005 A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke. White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by treatment (IV) with the catalytic antioxidant AEOL 10150 and then 6 hours of reperfusion; mRNA from a single brain #16. Source GEO sample is GSM2220 Last updated (according to GEO): May 27 2005 Large Intestine; Proximal Colon Keywords = mouse gene expression database Source GEO sample is GSM29306 Last updated (according to GEO): May 27 2005 cerebral cortex 7 21 Brain 861 CF control DFW CHN312 Epithelium of bronchus 983 TEL-AML1-C9 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Lymphoblastoid Cell Line for Individual 8163.4 log phase Skeletal muscle biopsy was obtained before a 3-hour hyperinsulinemic (infusion rate 40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172166 Last updated (according to GEO): Feb 28 2007 of regenerating Dorsal Root Ganglia 21 55 4 0 Heart Spleen vs CD40 Treated B cell 30min (set3) 20 0 human caudate nucleus Type 1 Diabetes patient and the timepoint 4 months after diagnosis. Source GEO sample is GSM228627 Last updated (according to GEO): Sep 11 2007 LPS plus IL-10, 20 min, Rep_3 R428P00155 Autistic Disorder 877 Nervous System; Striatum Keywords = mouse gene expression database Source GEO sample is GSM29429 Last updated (according to GEO): May 27 2005 11 Bone marrow 0 left 22 25 Gene expression data from postmorten brain regions Source GEO sample is GSM145857 Last updated (according to GEO): Nov 20 2006 7 cerebral cortex 21 Plasma 861 5 0 brain 861 Blood Brain 861 1000 Brain 5 0 brain 861 Brain Bone Marrow 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM144997 Last updated (according to GEO): Nov 20 2006 1BJZ02030473_bonemarrow Brain 1000 1037 of transitional epithelium 1012 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141322 Last updated (according to GEO): Oct 26 2006 osteoblast 627 637 Examining the effects of tTA expression in mouse hearts Source GEO sample is GSM15066 Last updated (according to GEO): May 28 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68151 Last updated (according to GEO): Jul 07 2006 Mesenchymal Stem Cells 1000 913 frontal lobe 901 Heart failure Spleen 1000 human frontal cortex Source GEO sample is GSM86967 Last updated (according to GEO): Feb 08 2006 Cerebral cortex 1000 853 Refractory Carcinoma Control 4 (Experiment Neuroprotection4- Run 21823) Treatment, type=timepoint, description=Same sample used for Experiment Neuroprotection4-Run 14985, samples were rerun due to oven failure, measurement=0.0 h Source GEO sample is GSM96686 Last updated (according to GEO): Feb 14 2006 31 0 Cerebellum Alzheimer's disease 1 Lymphoblastoid Cell Line for Individual 8121.4 log phase Cerebral cortex 861 Twelve weeks expression data of the antipsychotics Clozapine and Haloperidol in the mouse brain (Affymetrix, GCRMA). 20 0 human caudate nucleus Normal Source GEO sample is GSM176072 Last updated (according to GEO): Apr 09 2007 with mental retardation 241 263 Oat cell carcinoma 867 2.5 mg/kg 2CdA exposure Transitional epithelium 1000 B220Low sIgM+ immature B cells sorted out of mouse bone marrow, sort no. 9 Source GEO sample is GSM641 Last updated (according to GEO): Mar 20 2006 Category: Cell-line Subcategory: HMEC Scanning Software: unknown Software version: unknown Lot batch = 0129-5k Source GEO sample is GSM1942 Last updated (according to GEO): Nov 21 2005 pfc_1037_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Epithelium 861 Muscular Atrophy 886 Lung 1000 9 0 Blood Test 901 Heart failure normal testis 54 66 19 0 Head and neck cancer whole blood_101832 CAF 1852 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A C57BL/6 benchmark dataset: Embryonic day 18.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25184 Last updated (according to GEO): May 27 2005 brain 0 5 20 0 human caudate nucleus Normal Source GEO sample is GSM175889 Last updated (according to GEO): Apr 09 2007 NA12814 5 0 brain Day 3_M_-LIF_Achip medial motoneurons (MMN) 15 Knockout 8 months old, male Source GEO sample is GSM154345 Last updated (according to GEO): Jan 09 2007 SCG explant cultured for 2 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246026 Last updated (according to GEO): Dec 03 2007 bc-ZT21-1 1000 frontal lobe Standard Affymetrix Protocol Source GEO sample is GSM16502 Last updated (according to GEO): May 28 2005 26 15 endometrioid 1000 Lung 17 7 hippocampus PGA-MurLungRag-rwp-72h-1bBv2-s2 heart_ventricle_1 Source GEO sample is GSM80657 Last updated (according to GEO): Mar 31 2006 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM80012 Last updated (according to GEO): Oct 26 2005 Heart Source GEO sample is GSM18952 Last updated (according to GEO): Sep 25 2006 midbrain_9 Source GEO sample is GSM80705 Last updated (according to GEO): Mar 31 2006 Wild type voxel D2 1000 Spleen Gene expression data from postmorten brain regions Source GEO sample is GSM145579 Last updated (according to GEO): Nov 20 2006 Brain 1000 Parkinson Disease 1000 CAKI-1_CL9015_Renal on Affymetrix GeneChip Human Full Length Array HuGeneFL Untreated LNCaP cells stimulated with DHT, biological replicate 2 Source GEO sample is GSM187372 Last updated (according to GEO): May 04 2007 B220+c-kit+ Pre BI cells sorted out of mouse bone marrow, sort no. 1 Source GEO sample is GSM653 Last updated (according to GEO): Mar 10 2006 plasma cells 332 344 1653 1648 livers 1100 1087 heart failure total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5836 Last updated (according to GEO): May 27 2005 Biopsy of the normal mucosa of the colon from patient #26 Gene expression data from postmorten brain regions Source GEO sample is GSM145098 Last updated (according to GEO): Nov 20 2006 Lymphoblastoid Cell Line for Individual 8003.4 log phase 52 8 in docetaxel-refractory prostate cancer_docet Olfactory Epithelium 1000 Gene expression data from human colon tumor tissue Source GEO sample is GSM173330 Last updated (according to GEO): Apr 20 2007 Diaphragm 7 day mdx rep 1 15 0 human cerebellum 452 433 The descending colon liver 0 5 Structure of horn of uterus 983 Myocardium 861 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM119706 Last updated (according to GEO): Jul 11 2006 of coronary artery disease 258 284 861 Cerebral cortex Skeletal bone 861 f2#357 versus pool Mouse Brain tissue SN:Human Glioblastoma Biopsy 07085 Pooled TA RNA samples from five 8 wk old male mdx5cv mice Source GEO sample is GSM13748 Last updated (according to GEO): May 28 2005 CNS-SCsev_InjA7d-2B-s2 DMN-NF1Hippo32d-1aAv2-s2 1000 Neoplasm Metastasis of the heart 278 290 861 Cerebral cortex Stem cells 1000 Occipital lobe 861 Transitional epithelium 1000 -_7636_batch1 on NHGRI-6.7k PHA, 48.00 hr. T-Cell, Repeat. Ovary 1000 The nose 94 101 none Source GEO sample is GSM239838 Last updated (according to GEO): Dec 07 2007 Triple selected polyA RNA for liver, kidney, ovary, testis, was obtained from Ambion (Austin, TX). Total RNA was obtained form Ambion for hypothalamus samples. All RNA samples had an agilent ratio greater than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of 10 different animals. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Mouse, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19235 Last updated (according to GEO): May 27 2005 7 cerebral cortex 21 Nasal Epithelium 865 GM18913 Skeletal bone 861 1000 Cerebral cortex GSE5944 1000 Skeletal muscle structure 287 260 at the longitudinal fissure 1000 Amyotrophic Lateral Sclerosis CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of M?, rhM?CSF was added at 1000 U/ml on the same days. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5144 Last updated (according to GEO): Sep 08 2006 I_U133A_102_Amy Postnatal day 6 corticospinal motor neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription. Source GEO sample is GSM37095 Last updated (according to GEO): May 27 2005 Whole blood from a healthy control Source GEO sample is GSM153428 Last updated (according to GEO): Jan 11 2007 D_U133A_109_DLPFC plasma cells 332 344 26 15 endometrioid B6_Control_ZT 12_3 Coronary artery 901 Sprague-Dawley Male HighSalt Cortex rat712 sd_cortexr_k_712c_020802 Nose 1000 cerebral cortex 7 21 Ovarian_Tumor_Endometrioid_CHTN-OE-039 Murine NK cells were compared at rest and following 24 hours of IL-15 stimulation for their mRNA expression profiles on the Affymetrix MOE430_2 microarray platform. Additional comparators included resting bulk splenocytes. Last Updated (by provider): May 09 2007 Contributers: Todd A Fehniger Timothy J Ley OccipitalLobe Source GEO sample is GSM18773 Last updated (according to GEO): Sep 25 2006 Neutralization of transthyretin reverses the neuroprotective effects of secreted amyloid precursor protein (APP) in APPSW mice resulting in tau phosphorylation and loss of hippocampal neurons: support for the amyloid hypothesis. V5-P254 osteoblast 627 637 Brain 1000 n/a Source GEO sample is GSM178073 Last updated (according to GEO): Jun 11 2007 70 40 without coronary artery disease Bone Marrow 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11324 Last updated (according to GEO): May 28 2005 processed in batch 7 Source GEO sample is GSM90430 Last updated (according to GEO): Mar 20 2006 5 0 Spleen Parkinson Disease 861 Subject code A9 Total RNA extracted from the forebrain of a Lh+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144391 Last updated (according to GEO): Nov 14 2006 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201271 Last updated (according to GEO): Jun 14 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145770 Last updated (according to GEO): Nov 20 2006 2500 mg/kg X 24 hr Source GEO sample is GSM129851 Last updated (according to GEO): Sep 18 2007 nucleus accumbens ctrl replicate 4 Macrophage smi102 Cerebellum 1000 Epithelium 861 Brain 1000 32 0 Cerebellum Alzheimer's disease 10 Disease Source GEO sample is GSM176252 Last updated (according to GEO): Apr 09 2007 thalamus_2 Source GEO sample is GSM80839 Last updated (according to GEO): Mar 31 2006 Control rat 3 ventral tegmental area Source GEO sample is GSM32162 Last updated (according to GEO): May 27 2005 Effect of Acute Physiologic Hyperinsulinemia on Gene Expression in Human Skeletal Muscle in vivo 1000 Brain Stem Neuroblastoma 1000 R441P00225 Primary tumor 19 32 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118356 Last updated (according to GEO): Jul 11 2006 861 Cerebral cortex of coronary artery disease 258 284 Ischemia-reperfusion with AEOL 10150 #16 GIN (Gad1 inhibitory ref. (pubmed id:10777798) ) neurons from cingulate cortex Source GEO sample is GSM63019 Last updated (according to GEO): Dec 01 2005 brain_OFC_control C_mr206 129S6/SvEvTac bed nucleus of the stria terminalis rep2 JMR-RatSham24hf-1aA-s2 1000 Obesity Brain 861 443_2 plasma cells 50 61 S10_Muscle_Insulin_240min Total RNA extracted from the cerebellum of a Tg+/+ mutant mouse Treatment, type=sacrifice Source GEO sample is GSM144417 Last updated (according to GEO): Nov 14 2006 mouse cerebral cortex 0 20 The epithelial cells 962 981 320 306 Keywords = HIV Fibroblast growth factor 9 has oncogenic activity and is a downstream target of Wnt signaling in ovarian endometrioid adenocarcinomas. aml8-aml8_924_ab_hu68_abms on Affymetrix GeneChip Human Full Length Array HuGeneFL Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11287 Last updated (according to GEO): May 28 2005 Parkinson Disease 1000 of left ventricular hypertrophy 83 113 M_95A_1871_DLPFC_0_GS brain, ipsi Cortex: Trizol Extraction35_le1 1000 frontal lobe 1000 Decapitation NA Source GEO sample is GSM198923 Last updated (according to GEO): Jun 07 2007 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n105 Source GEO sample is GSM2038 Last updated (according to GEO): Nov 21 2005 1000 Spleen R662P00808 9 of prefrontal cortex 28 Gene expression data from postmorten brain regions Source GEO sample is GSM145701 Last updated (according to GEO): Nov 20 2006 861 Bladder Substantia Nigra Pars Compacta 1 Disease Spinal Injuries 913 none Source GEO sample is GSM244534 Last updated (according to GEO): Nov 23 2007 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12506.gif Source GEO sample is GSM79902 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145725 Last updated (according to GEO): Nov 20 2006 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188789 Last updated (according to GEO): Jun 06 2007 Normal Source GEO sample is GSM176232 Last updated (according to GEO): Apr 09 2007 3 min exposure to halothane, immediate perfusion with ice cold saline Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5087 Last updated (according to GEO): Mar 17 2006 1000 Lung Cerebral cortex 1000 861 Neoplasm 913 Coronary heart disease Standard affymetrix protocol Source GEO sample is GSM119722 Last updated (according to GEO): Jul 31 2007 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15527.gif Source GEO sample is GSM84145 Last updated (according to GEO): Sep 22 2006 43 29 from the kidney I_U133A_6_DLPFC Brain 1000 f2#104 versus pool Mouse Brain tissue Muscular Dystrophies 901 453 434 The descending colon 4_cerebral_cortex_3hrs_sleep_deprivation_#66 "Sample 41,>5 yr survival(82 months) age 54 erp yes" on vantveer-oligo brain, cochlea: [18] Sample #18_le1 0 Human Cortex 11 hrs nasal epithelium 1126 1146 in neurite outgrowth 959 978 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 4 hour after the last shock treatment. Source GEO sample is GSM4527 Last updated (according to GEO): May 27 2005 Mesentery 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145237 Last updated (according to GEO): Nov 20 2006 GSE401 1000 Muscle Mouse ileum with L.monocytogenes_D_5550 Wild type hippocampus region Source GEO sample is GSM88936 Last updated (according to GEO): Jan 04 2006 Lungs 153 157 660 mesenchymal stem cell 639 1000 Spleen tTA +Doxy 7488 WGACON-140 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11582 Last updated (according to GEO): May 28 2005 25 0 endothelial cells sprague2 E7, hTERT, neural differentiation, bone marrow cell 1000 frontal lobe Fibroblasts 1000 of 11 saccules 5 18 216 200 of neural retinas KT34b_AR2 Sample Type: cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, air control, 6 h time point Source GEO sample is GSM159787 Last updated (according to GEO): Apr 23 2007 blood, adrenal medulla: BG +/- replicate 3_e1_le1 NA Source GEO sample is GSM84333 Last updated (according to GEO): Dec 01 2005 AD control Treatment, type=dissect Source GEO sample is GSM119664 Last updated (according to GEO): Jul 10 2006 34 brain cortex 45 1000 Brain Keywords = Heart 505 521 Lymphoblastoid Cell Line for Individual 8045.3 log phase Infected 6 weeks prior with Htt-N171-19Q-expressing recombinant lentivirus Source GEO sample is GSM34375 Last updated (according to GEO): Oct 16 2006 20 0 human caudate nucleus Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2670.gif Source GEO sample is GSM72166 Last updated (according to GEO): Sep 22 2006 Brain 861 Brain 861 NCI-H23 hgu95c no additional Source GEO sample is GSM199231 Last updated (according to GEO): Jun 08 2007 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19470.gif Source GEO sample is GSM91607 Last updated (according to GEO): Sep 22 2006 Tacrine 2.7mg/kg/day from 5 weeks Moclobemide 10mg/kg/day Creatine 1%w/v added to wet mash Lot batch = 5217 Source GEO sample is GSM13357 Last updated (according to GEO): May 28 2005 MuscleRegen-ctx1d-1RLAv2-s2 1000 Spinal Cord 12 0 ovarian tumor Cerebral cortex 861 9 0 Blood Test Replicate2_Voxel B2 Treated Source GEO sample is GSM175964 Last updated (according to GEO): Apr 09 2007 5 0 brain 1000 Spleen D_U133A_49_Amy Testis 861 M7TW00122047 861 Lymph Category: Tissue Rejection Subcategory: Kidney Experimenter: Minnie Sarwal Scanning Software: GenePix Software version: Pro Scanning parameters: PMTVolts=780650 LaserPower=2.271.27 Lot batch = LC17N048 Source GEO sample is GSM4787 Last updated (according to GEO): Nov 21 2005 Gene expression data from liver Source GEO sample is GSM243390 Last updated (according to GEO): Nov 16 2007 Tumor__Ovary_Adeno_mOVT2_(I)_(9334) on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Femur 1000 660 mesenchymal stem cell 639 861 Acquired Immunodeficiency Syndrome Nanog-iPS cells Source GEO sample is GSM190250 Last updated (according to GEO): May 18 2007 human cerebellum Source GEO sample is GSM87059 Last updated (according to GEO): Feb 08 2006 Tumor__Mesothelioma_74_T6 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 129S6/SvEvTac hippocampus rep1 PMN_LB_360min_Patient5 Communicable Diseases 901 3AMH02022605_Brain Amygdala AD-260t1a-A172-4 * on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Mouse neuroblastoma 0 18 Normal human fetal cartilage from 18-22 weeks. Source GEO sample is GSM149641 Last updated (according to GEO): Jul 06 2007 1BRS02080872b_atrioventricular_node Central gray substance of midbrain 861 861 Cerebral cortex 660 mesenchymal stem cell 639 Coronary heart disease 913 GSE8011 320 306 Keywords = HIV 1000 Infection in seminoma 28 38 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14937 Last updated (according to GEO): Oct 28 2005 brain, cerebral cortex: PC12_e1_le1 in the brain 150 162 Wild type inbred mice Source GEO sample is GSM82967 Last updated (according to GEO): Nov 10 2005 WT P2 replicate 1 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134638 Last updated (according to GEO): Jul 09 2007 vagina_8 Spinal Cord 1000 atrial septal defects 198 218 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114216 Last updated (according to GEO): Jun 16 2006 254 238 of neural retinas Fluid-percussion head injury 83 110 Primary Neoplasm 1000 Macrophage 14smi115 Brain 1000 Expression profiling of laminectomized raphe at 28d in rats Source GEO sample is GSM41531 Last updated (according to GEO): May 27 2005 db/m 8wk 1 WGACON-65 ES cell control, RNA 296 Plasma 861 Heart Ventricle 1000 Gene expression data from a primary branch of the saphenous artery of 16 week old spontaneously hypertensive (SHR) rats Source GEO sample is GSM198865 Last updated (according to GEO): Nov 28 2007 1000 Trachea n/a Source GEO sample is GSM177948 Last updated (according to GEO): Jun 11 2007 91 from the bone marrow 72 nico 18h + nmda 1h 9/06/02 (Experiment Neuroprotection3- Run 13276) Treatment, type=timepoint, description=primary cortical neurons were treated for 18 h with nicotine 10uM then NMDA 1 mM was added and the cells were harvested 1h later, measurement=19.0 h Source GEO sample is GSM96735 Last updated (according to GEO): Feb 14 2006 NL-2378-A412-7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Spleen 264 269 Normal Thymus GSE3071 1000 Descending colon The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169498 Last updated (according to GEO): Feb 21 2007 Olfactory Epithelium 1000 14 saline D_U133A_33_DLPFC Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159733 Last updated (according to GEO): Apr 23 2007 183 177 retinas WGACON-242 Gene expression data from hippocampus of one young SAMP10//Ta mouse Source GEO sample is GSM143750 Last updated (according to GEO): Jan 24 2007 Donor 1 Time point 48 hours post infection with HIV-1, RF Source GEO sample is GSM2604 Last updated (according to GEO): May 27 2005 Gene expression data from experimental treatment UD = Undifferentiated SH-SY5Y cells, i.e. before PMA induced differentiation (UD). Source GEO sample is GSM102825 Last updated (according to GEO): May 11 2006 Metabolic Diseases 1000 12 frontal Lobe 23 1000 Brain AML 51 0 5 brain 0 5 Exercised Induced Hypertrophy Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11272 Last updated (according to GEO): May 28 2005 Parkinson Disease 861 1000 frontal lobe Job's patient Source GEO sample is GSM211136 Last updated (according to GEO): Sep 10 2007 67 40 with coronary artery disease Structure of olfactory bulb 901 MGMH030211062Bamygdala Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc8n012 Source GEO sample is GSM2067 Last updated (according to GEO): Nov 21 2005 50 43 jejunum Gene expression profile of the cell line UB/OC-1 grown for 14 days under differentiating conditions (39C) Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1544 Last updated (according to GEO): May 27 2005 Cultured_cortical_astrocyte_Cx43_siRNA_rep4 from the entorhinal cortex 963 988 Leukemia, Lymphocytic, Acute 1000 PGA-MPF-C57-saline-72h-1bAv2-s2 3170 Pulmonary Hypertension 3149 SCG_control_12h_rep2 eicosanoid hormones 902 921 with autism spectrum disorder 37 65 9 0 Blood Test Timed pregnant C57Bl6 mice were exposed to ethanol during gestational day 15 to day 18 and ethanol exposed fetuses were delivered by cessarian section on gestational day 19. Alcohol exposed fetuses were compared to control timed preg Source GEO sample is GSM116864 Last updated (according to GEO): Jul 03 2006 453 434 The descending colon of somatomotor cortex 21 41 Neurites 861 1000 Cerebral cortex 1607 1590 with schizophrenia Mesenchymal Stem Cells 1000 928 Hyperinsulinism brain, hippocampus: Ctr-240h-P15-III_e1_le1 CH2110 Blood supply aspects 896 ND007 Primary adenocarcinoma 0 21 Kidney 1000 977 occipital regions 993 brain 0 5 861 Spinal Cord AML cDNA hybridization-ID29-L 114 101 brains quickly Normal Trachea 861 Colon Exp C_3, 10mg/kg CPF, 1st repeat Postnatal day 6 callosal projection neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription. Source GEO sample is GSM37086 Last updated (according to GEO): May 27 2005 1000 Descending colon Large cell carcinoma of lung 937 Gene expression data from brain of adult rats Source GEO sample is GSM101030 Last updated (according to GEO): Feb 20 2007 747 tumor cells 757 human cerebellum Source GEO sample is GSM87175 Last updated (according to GEO): Feb 08 2006 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28813 Last updated (according to GEO): May 27 2005 861 Cerebral cortex HCT-116 hgu95e Parkinson's disease sample x187 30 0 ventral tegmental area sprague1 Activated Source GEO sample is GSM176000 Last updated (according to GEO): Apr 09 2007 nic 1 (Experiment Neuroprotection4- Run 14985) Treatment, type=timepoint, description=primary cortical neurons were treated for 18 h with nicotine 10uM , agonist was then washed out and the cells were harvested 24h later, measurement=18.0 h Source GEO sample is GSM96725 Last updated (according to GEO): Feb 14 2006 278 255 ischemic cardiomyopathy 861 Cerebral cortex 551 521 of autistic spectrum disorders Neoplasm 1000 B029 on Affymetrix GeneChip Human Full Length Array HuGeneFL SCN2.2 Sample 21 (Exp#3-6 hr) Brain 1000 Heart Septal Defects 884 1000 Spleen Embryonic day 18.5 corticospinal motor neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription. Source GEO sample is GSM37091 Last updated (according to GEO): May 27 2005 Spleen vs Platelet activating factor Treated B cell 60min (set3) 1000 Lipids Whole brain 0 10 human peripheral blood derived monocytes, 8 hour LPS stimulation, biological rep2 Source GEO sample is GSM126999 Last updated (according to GEO): Aug 15 2006 Frontal cortex 254 267 41 29 Control blood mouse hippocampus 0 16 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47532 Last updated (according to GEO): May 29 2005 1000 Brain brain 0 5 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210390 Last updated (according to GEO): Jul 16 2007 Intestines 861 HapMap CHB Male Source GEO sample is GSM159607 Last updated (according to GEO): Feb 01 2007 1000 Descending colon Study the transcriptomic effects of the shear stress on cultured osteoblast-like MC3T3 cells Source GEO sample is GSM201214 Last updated (according to GEO): Jun 19 2007 Left 1000 from brain 21 30 Spleen 0 5 Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242066 Last updated (according to GEO): Dec 04 2007 brain, cerebral cortex: Co 7/8 RC_le1 Infection 1000 5 0 brain no additional Source GEO sample is GSM199223 Last updated (according to GEO): Jun 08 2007 CH1811 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 11.75 hours after lights on. Original RNA code = LC27A. Source GEO sample is GSM227400 Last updated (according to GEO): Sep 10 2007 38 21 of Medulloblastoma C79 on NCI-7.6k Control rats 24h after injection with PBS Treatment, type=time_course, description=Control animals are treated with PBS, measurement=24.0 h Source GEO sample is GSM32082 Last updated (according to GEO): May 27 2005 Expression data from transgenic mice (6 wk) inducibly expresssing human alpha1-antitrypsin in the liver Osteoblasts 1000 1000 Optic Nerve 1000 Brain Control, 02.00 hr. T-Cell Malignant Neoplasms 1000 A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke. White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by treatment (IV) with the catalytic antioxidant AEOL 10150 and then 6 hours of reperfusion; mRNA from a single brain #14. Source GEO sample is GSM2219 Last updated (according to GEO): May 27 2005 Sample Type: human total RNA Sample User: dpatel Experiment User: jmorris Algorithm: Statistical Corner+ Avg:265, Count:32 Corner- Avg:39620, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:6.320118,SFGene:All Background:Avg:279.64,Stdev:2.80,Max:289.3,Min:274.2 Noise:Avg:6.89,Stdev:0.23,Max:7.9,Min:6.4 RawQ:10.33 Keywords = ALL Source GEO sample is GSM3465 Last updated (according to GEO): May 27 2005 Substantia nigra PD rep15 Prostate 861 Rat frontal cortex RNA - VH Lesion Experiment Source GEO sample is GSM92289 Last updated (according to GEO): Jan 13 2006 brain, cerebral cortex: 15006_e2_le1 A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism Source GEO sample is GSM5978 Last updated (according to GEO): Nov 21 2005 Gene expression data from the neocortex of wild-type mouse Source GEO sample is GSM172928 Last updated (according to GEO): Mar 08 2007 Disorder of artery 865 cy5:WKY treated w/ angtiotensin, biological rep 4r; cy3:pool of 6 WKY control rats 1000 Cardiomyopathy, Alcoholic between the LAD artery 266 287 temporal_lobe_1 Brain 861 Normal Source GEO sample is GSM176389 Last updated (according to GEO): Apr 09 2007 Heart 861 901 Connective Tissue 861 Prostate carcinoma brain 0 5 Duodenum 1000 C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 1hr after experimental mice received their last shock treatment. Source GEO sample is GSM4505 Last updated (according to GEO): May 27 2005 D_U133Plus_16_HC Nervous Sysem; Peripheral, Sensory-dorsal root ganglion Keywords = mouse gene expression database Source GEO sample is GSM29432 Last updated (according to GEO): May 27 2005 1000 Left CS-B cell UVC-irradiated (12hour) replicate 3 U133B Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 0.25 hours after lights on. Original RNA code = LC1A. Source GEO sample is GSM227353 Last updated (according to GEO): Sep 10 2007 901 Heart failure none Source GEO sample is GSM244625 Last updated (according to GEO): Nov 23 2007 19 0 human frontal cortex PBMCs-Type 1 Diabetes-IDDM41_T1D_4MO Normal Fetal Lung Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188861 Last updated (according to GEO): Jun 06 2007 none Source GEO sample is GSM210329 Last updated (according to GEO): Jul 16 2007 Seminoma 1000 liver_PPARa-knockout_WY14643_5d_rep3 CH2115 Normal Source GEO sample is GSM176341 Last updated (according to GEO): Apr 09 2007 1000 frontal lobe Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92363 Last updated (according to GEO): Jan 13 2006 1000 Coronary Arteriosclerosis 1000 Hippocampus whole blood_100760 861 Longitudinal Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. Source GEO sample is GSM112316 Last updated (according to GEO): Jun 06 2006 1848 1840 The brain T256 HeLa CD4+ cells were transfected with an epitope-tagged eTat plasmid and selected with hygromycin. Cells were treated with nocodazole and collected @9 hours. Source GEO sample is GSM8709 Last updated (according to GEO): May 27 2005 42 30 Control blood CNS-SC_InjB14d-1A-s2 861 Cerebellum Brain 1000 1000 Infection 5 0 Spleen Human lung tissue 54 70 Brain 861 subthalamic_nucleus_8 Source GEO sample is GSM80856 Last updated (according to GEO): Mar 31 2006 CNS-SC_InjA4h-1A-s2 515 490 during malarial infection Wild type voxel F3 long access to cocaine ,medial prefrontal cortex, 6 hrs/day access to cocaine Source GEO sample is GSM93875 Last updated (according to GEO): Jan 26 2006 Cerebral cortex 861 The nose 94 101 in the olfactory epithelium 62 89 20 0 human caudate nucleus 1000 Spleen Ovarian_Tumor_Serous_CHTN-OS-046 2nd 2hr C-DG human frontal cortex Source GEO sample is GSM87009 Last updated (according to GEO): Feb 08 2006 861 Cerebral cortex 1000 Leukemia, Myelocytic, Acute substantia_nigra_2 Postnatal Development of Mouse Cochlear Nucleus SN:1010410 Source GEO sample is GSM115391 Last updated (according to GEO): Jun 20 2006 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141297 Last updated (according to GEO): Oct 26 2006 913 Coronary heart disease Liver (HBV+, HK89) Gene expression data from a EFT cell line expressing EWS/FLI1 typeI Source GEO sample is GSM213306 Last updated (according to GEO): Jul 26 2007 Lung 861 Brain 861 256 235 with HIV encephalitis cerebellum 0 9 41 29 Control blood Neoplasm 861 M_U133A_68_DLPFC ovary 45 50 865 Disorder of artery 1000 Left 901 Nervous system structure NA19141 901 Mammary gland 1000 Cerebellum for hereditary non-polyposis colon cancer 340 380 PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls. All samples were normalized with quantile normalization and summarized using RMA. Source GEO sample is GSM135576 Last updated (according to GEO): Dec 19 2006 Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242084 Last updated (according to GEO): Dec 04 2007 f2#44 versus pool Mouse Brain tissue Parkinson Disease 861 Corticospinal Motor Neurons P3 3 Brain 1000 gangliocytoma 1000 CNS-SpinalCsev-Adult-28d-3A-s2 HOXB4ERT-LSK+ cells_ 1 hour after TMX withdrawal Source GEO sample is GSM228749 Last updated (according to GEO): Sep 13 2007 5 0 brain Cardiovascular Diseases 1000 Blood 1000 861 Cardiomyopathies 042601_HF_357FL normal testis 54 66 Pool of 9 cochlear tissues at E13.5 Source GEO sample is GSM182582 Last updated (according to GEO): Aug 14 2007 brain, hippocampus: KA-1h-P15-III_e1_le1 RNA isolated from post-mortem tissues Source GEO sample is GSM6832 Last updated (according to GEO): May 28 2005 Malignant neoplasm of breast 983 Heart Ventricle 1000 none Source GEO sample is GSM244600 Last updated (according to GEO): Nov 23 2007 of somatomotor cortex 21 41 Epithelial Cells 1000 Voxel C4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1404 Last updated (according to GEO): Nov 21 2005 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188701 Last updated (according to GEO): Jun 06 2007 1000 Brain Collagen 1000 861 Brain 941 Heart failure striatum 33 41 PMN_control_0min_Patient13 Volunteer patients underwent bronchoscopy from which RNA was extracted using a commercial RNA extraction kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. Keywords = Homo Sapiens, bronchial epithelia, molecular screen for smoking related changes to transcript levels in bronchial epithelia Source GEO sample is GSM15684 Last updated (according to GEO): May 28 2005 24 0 human prostate PC3 tumors mild cognitive impairment - entorhinal cortex 1 large cell lung carcinoma 2081 0 29 The nose 94 101 Spleen 1000 Normal epithelial cells were removed by dissection and digestion from bronchi of donor long tissue from normal subject. Source GEO sample is GSM3918 Last updated (according to GEO): May 27 2005 short access to cocaine, amygdala, 1 hr/day access to cocaine Source GEO sample is GSM93830 Last updated (according to GEO): Jan 26 2006 brain 0 5 1000 Retina NHF3-hTERT_M_C5_26559 Plasma 861 of Parkinson's disease 450 471 BACKGROUND Cisplatin-containing chemotherapy is the standard of care for patients with locally advanced and metastatic transitional cell carcinoma of the urothelium. The response rate is around 50% and tumor derived molecular prognostic markers are needed for estimation of response and survival. METHODS Affymetrix GeneChip expression profiling was carried out using tumor material from 30 patients. A set of genes having an expression with high correlation to survival time after chemotherapy was identified. Two of these genes were selected for validation by immunohistochemistry (IHC) in tumor tissue from 149 cisplatin treated patients having complete follow-up data. RESULTS Fifty-five differentially expressed genes correlated significantly to survival time. Two of these (Emmprin and Survivin) were validated using IHC, and multivariate analysis (n=145) identified Emmprin expression (hazard ratio 2.38; p<0.0001) and Survivin expression (hazard ratio 2.34; p<0.0001) as independent prognostic markers for poor outcome, together with the presence of visceral metastases (hazard ratio 2.72; p<0.0001). In the good prognosis group of patients without visceral metastases, both markers showed significant discriminating power as supplemental risk factors (p<0.0001). Within this group of patients, the subgroups of patients with no positive, one positive or two positive IHC stainings (Emmprin and Survivin) had estimated 5-year survival rates (+- SE) of 35.6+-?%, 6.3+-?%, and 0+?%, respectively. Response to chemotherapy could also be predicted with an OddsRatio of 4.60 (2.13-9.93) and 2.59 (1.25-5.38) for Emmprin and Survivin respectively. CONCLUSION Emmprin and Survivin proteins were identified as strong independent prognostic predictors for response and survival after cisplatin-containing chemotherapy in patients with bladder cancer. Last Updated (by provider): Jul 31 2007 Adipocytes 1000 1000 Lymphoma Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM79056 Last updated (according to GEO): Oct 24 2005 BC123B-BE adrenal_gland_cortex_4 Exp A_1, 1mg/kg CPF 1000 Cerebral cortex Bone Marrow 1000 Brain 861 Collagen 861 of the normal mucosa 7 26 CAD_replicate10 NORMAL 4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A high gestational age Source GEO sample is GSM213089 Last updated (according to GEO): Jul 25 2007 HapMap JPT Female Source GEO sample is GSM159624 Last updated (according to GEO): Feb 01 2007 NCI-H226 hgu95d from liver 21 30 Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep2 Wild type 8 wk old male C57BL/6J mouse cingulate cortex Source GEO sample is GSM74947 Last updated (according to GEO): Feb 27 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11581 Last updated (according to GEO): May 28 2005 Cortex Treatment, type=pharmacogenomic_treatment, description=Handled (no stress) control Source GEO sample is GSM53314 Last updated (according to GEO): Jul 06 2005 none Source GEO sample is GSM123254 Last updated (according to GEO): Jul 26 2006 Anterior nares 1000 R704P01242 PGA-MPF-C57-saline-14d-1aAv2-s2 Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Source GEO sample is GSM200644 Last updated (according to GEO): Jun 12 2007 Infection 1000 I_U133A_75_CB 1000 Maxilla 59 50 Brown fat 1000 jejunum 913 Coronary heart disease 20 0 human caudate nucleus 0 Human Cortex 11 Branch 861 975 962 in trisomy 21 9 0 rat kidney Spinal Cord 1000 861 Stem cells PriG_5%O2_Expt1_Day14_rep1 B2-10 on NCI-7.6k 901 Caudate nucleus structure Collagen 1000 f2#27 versus pool Mouse Brain tissue 861 Kidney NCI60.56_LABEL60EXTRACT59SUB3 Source GEO sample is GSM134277 Last updated (according to GEO): Aug 06 2007 7 cerebral cortex 21 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120662 Last updated (according to GEO): May 14 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with IL4 for 120min Source GEO sample is GSM5637 Last updated (according to GEO): May 27 2005 CNS-SC_CtrA7d-2A-s2 18 0 Trigeminal_Ganglion Gene expression data from whole brain infected mouse, day 1 Source GEO sample is GSM189609 Last updated (according to GEO): May 16 2007 7 cortex 12 0029_1474_H95A2_T95-31_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Cerebellum 0 Human Cortex 11 Normal Source GEO sample is GSM176239 Last updated (according to GEO): Apr 09 2007 Parkinson Disease 1000 Occipital lobe 861 none Source GEO sample is GSM244568 Last updated (according to GEO): Nov 23 2007 Expression profiling of laminectomized raphe at 24h in rats Source GEO sample is GSM41527 Last updated (according to GEO): May 27 2005 Y SIT D034 brain 0 5 11 0 Fetal brains Hippocampus_Rasgrf1KO_rep1 1000 Parkinson Disease MOLT-4 hgu95c from colorectal adenoma 21 44 Brain 1000 endometrium_3 WGACON-102 GM19205 kidney 0 5 Analysis of gene expression during neurite outgrowth and regeneration. total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withTerbutaline for 30min Source GEO sample is GSM5780 Last updated (according to GEO): May 27 2005 1500mg/kg APAP 6Hr rat 3594 blood vs. PC 6Hr rat 3586 blood Gene expression data from postmorten brain regions Source GEO sample is GSM145009 Last updated (according to GEO): Nov 20 2006 Brain 861 Pressure-overload induced hypertrophy model. Mouse was sacrificed 24 hours after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2255 Last updated (according to GEO): May 27 2005 70 40 without coronary artery disease 1000 Cerebral cortex Wild type inbred mice Source GEO sample is GSM82894 Last updated (according to GEO): Nov 10 2005 Cell source of DN2_1, DN3_1, and DN4_1 are identical. Cell source of DN2_2, DN3_2, and DN4_2 are identical. Cell source of DN2_3, DN3_3, and DN4_3 are identical. Cell source of DN2_4, DN3_4, and DN4_4 are identical. Each cell sorce was derived from four mice. Source GEO sample is GSM188620 Last updated (according to GEO): May 16 2007 NA18577 Adenocarcinoma 861 for liver 26 35 Hippocampus 1995 15 month Old 1000 Carcinoma 1000 Communicable Diseases Epithelial Cells 901 Brain 861 Liver 0 4 Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242053 Last updated (according to GEO): Dec 04 2007 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc5b040 Source GEO sample is GSM1960 Last updated (according to GEO): Nov 21 2005 Ovary_PD3_Foxo3 Null_Replica 1 Liver 1000 861 Myositis PMN_control_0min_Patient7 Whole Brain 62 72 VDXKIU_15E8 1000 Hippocampus Patient4F N10__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Colon mdx gastroc sample 2 GM18500 adenocarcinoma 3336 Control Acetaminophen 24hr Rat left_liver_lobe Pool vs. Acetaminophen 24hr Rat 9537 left_liver_lobe total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-gamma (IFN gamma) for 60min Source GEO sample is GSM5606 Last updated (according to GEO): May 27 2005 Disorder of artery 865 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28701 Last updated (according to GEO): May 27 2005 of the postmortem brains 676 700 Hippocampus 1000 00291189H95A2-T00-0109v2p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A none Source GEO sample is GSM239900 Last updated (according to GEO): Dec 07 2007 Chromosomes 861 M_U133A_71_HC 923 Congestive heart failure Colonic mucous membrane 913 Muscle 861 Fluid-percussion head injury 86 113 NHF3-hTERT_G2_C3_26558 1000 Spinal Cord KidFA_022YAFIP_fa2.txt 268 263 Spleen plasma cells 50 61 plasma cells 50 61 1000 Brain Benign prostatic hypertrophy 884 Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Source GEO sample is GSM188833 Last updated (according to GEO): Jun 06 2007 Normal Source GEO sample is GSM175947 Last updated (according to GEO): Apr 09 2007 Adipose tissue 901 B6 2000-1 Muscle Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT) Source GEO sample is GSM213479 Last updated (according to GEO): Jul 31 2007 Left hemidiaphragm 923 thymocytes_DN3_2 1000 Spleen 315 271 of transient middle cerebral artery occlusion Expression profiling of moderately injured raphe at 28d in rats Source GEO sample is GSM41587 Last updated (according to GEO): May 27 2005 Skin 1000 16 6 (transverse 5 0 TONGUE Squamous epithelial cell 861 1000 Amyotrophic Lateral Sclerosis Colorectal cancer patient SC16_vs_Pool vestibular_nuclei_superior_3 Source GEO sample is GSM80880 Last updated (according to GEO): Mar 31 2006 Liver 1000 Large-scale analysis of the human transcriptome. Salivary gland Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 98.28 Stdv: 4.13 Min: 90.98 Max: 105.48 Source GEO sample is GSM2834 Last updated (according to GEO): Mar 20 2006 12 frontal Lobe 23 Gene expression data from 9A1 BMEL cells cultured under basal conditions. Source GEO sample is GSM160072 Last updated (according to GEO): Jul 11 2007 Brain 1000 Primary tumor 19 32 from mouse colon 21 36 7 frontal cortex 20 C57BL/10Jmale_hypothalamus Source GEO sample is GSM184196 Last updated (according to GEO): Apr 26 2007 Mouse strain = BALB/c Age: Adult (>30 postnatal) One adult animal (postnatal 30 day or beyond) was used for each replicate adult sample Total RNA was extracted using RNeasy Midi Kit, according to manufacturerÆs instructions (Qiagen). The quality of the samples was checked with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA). Standard Affymetrix Protocol was used for RNA sample labeling with ENZO BioArray HighYield RNA Transcript Labeling Kit Keywords = Cerebellum, microarray, development, glycoconjugates, glycosyltransferases, proteoglycans, gene expression Lot batch = Source GEO sample is GSM29632 Last updated (according to GEO): Oct 28 2005 13 6 Awn Hair MuscleRegen-ctx6.5d-2RLAv2-s2 1000 Congestive heart failure 43h-AC replication 2 D_U133A_91_Amy 913 Blood Cells Muscle Cells 913 861 Neoplasm Normal Source GEO sample is GSM176022 Last updated (according to GEO): Apr 09 2007 50 43 jejunum 17 7 hippocampus CA97-14B Timepoint4 Ovarian Follicle 1000 Nerve Sheath Tumors 861 from ventral prostate 21 41 General Paralysis 885 cingulate cortex 861 K562_II_CL7005_Leukemia on Affymetrix GeneChip Human Full Length Array HuGeneFL The epithelial cells 962 981 Control 5 (Experiment Neuroprotection4- Run 14985) Treatment, type=timepoint, measurement=0.0 h Source GEO sample is GSM96673 Last updated (according to GEO): Feb 14 2006 861 Brain 5 0 brain 901 frontal lobe Mesenchymal Stem Cells 1000 SmIntP1_022BAFB9_172.txt Brain (amygdala) [JunctionChip 5 of 5] Affymetrix protocol Source GEO sample is GSM213816 Last updated (according to GEO): Aug 02 2007 ovarian tumor: endometrioid Source GEO sample is GSM139385 Last updated (according to GEO): Apr 09 2007 GSE5587 Coronary artery 901 913 Muscular Dystrophy, Duchenne olfactory epithelium 194 213 861 Fissure Nervous system structure 901 24 7 Right Frontal Lobe 1000 Leukemia, Myelocytic, Acute cy3:SHR treated w/ nifedipine and then washed out, biological rep 1g; cy5:pool of 6 WKY control rats experiment I, passage 9, replicate 2 43 0 Chorionic mesoderm-derived mesenchymal cells Biological replicate 1 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181094 Last updated (according to GEO): Jul 12 2007 67 40 with coronary artery disease 1000 Spleen Parkinson's disease sample x187 0 30 Large-scale analysis of the human transcriptome. Brain, amygdala Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 395.90 Stdv: 15.76 Min: 369.58 Max: 425.26 Source GEO sample is GSM2884 Last updated (according to GEO): Mar 20 2006 skeletal_muscle_5 Source GEO sample is GSM80796 Last updated (according to GEO): Mar 31 2006 176 166 bone marrow Brain 861 1000 Liver oral_mucosa_1 Heart Ventricle 1000 TEL-AML1-C2 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from colonic normal mucosa. Source GEO sample is GSM215052 Last updated (according to GEO): Aug 02 2007 /HeJ periaqueductal gray rep2 3 31 Bone marrow, Mesenchymal stem cells: T5-181203_e1_le1 663 mesenchymal stem cell 642 Gene expression of organ of Corti of newborn rats_repeat 2 inner ear Expression data with no treatment Source GEO sample is GSM230899 Last updated (according to GEO): Sep 20 2007 875 Blood Cells Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID49 41/OVX/P4/6h/UTX 129 Hoxa-10+/+ The epithelial cells 962 981 Replicate3_Voxel E1 M-18-35-LI on UMich-10k 23 0 hippocampus sprague 3957 PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls. All samples were normalized with quantile normalization and summarized using RMA. Source GEO sample is GSM135280 Last updated (according to GEO): Dec 19 2006 861 Cancer of Neck 928 Endometrium Replicate2_Voxel C11 of mature hepatocytes 1144 1165 /2J pituitary gland rep2 3 26 PGA-RnSalt_h_3w_3-m5 Heart failure sample 7 Control 7 Gene expression data from postmorten brain regions Source GEO sample is GSM145021 Last updated (according to GEO): Nov 20 2006 H126 FC BA4 B 40 21 from dorsal pancreas Brain 861 5 0 Spleen Tumor__Lymphoma_Large_B-Cell_L_B_CELL_S94_17150_R on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Brain 1000 testis 52 58 Parkinson Disease 1000 pfc_1003_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 1 hours after lights on. Original RNA code = LC2A. Source GEO sample is GSM227366 Last updated (according to GEO): Sep 10 2007 H9RGV00102602 as the sole chromosomal abnormality 360 394 D_95Av2_2672_Cg_0_GS SN:1010514 Source GEO sample is GSM115402 Last updated (according to GEO): Jun 20 2006 Keywords = Infectious diseases 1133 1163 Spleen 1000 1000 Hippocampus Parkinson Disease 861 Nose 1000 Brain 861 SCN2.2 Sample 12 (Exp#2-0 hr) 861 Neoplasm Testis 861 10 weeks Source GEO sample is GSM147462 Last updated (according to GEO): Dec 01 2006 Biopsy of a colorectal adenoma from patient #20 RNAtotC_24, ZT6 osteoblast 630 640 Kidney [JunctionChip 5 of 5] Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132514 Last updated (according to GEO): Feb 26 2007 Male Sprague-Dawley albino rats (Charles River) initially weighting approximately 200 grams were randomly assigned to one of the following: 1) olanzapine (2 mg/kg/day, I.P.) (N=20) or 2) Saline (N=20) and administered olanzapine or saline for 21 days. Frontal cortex (N=4/group) was dissected and homogenized for microarray, QPCR and western blotting following previous methods (Fatemi et al. 2003; Brooks et al. 2003). RNA isolation, cDNA preparation, microarray hybridization and QPCR followed previous methods (Brooks et al. 2003). Keywords = olanzapine Keywords = frontal cortex Source GEO sample is GSM48559 Last updated (according to GEO): Apr 10 2006 Control male 2 BACKGROUND: Correlation of risk factors with genomic data promises to provide specific treatment for individual patients, and needs interpretation of complex, multivariate patterns in gene expression data, as well as assessment of their ability to improve clinical predictions. We aimed to predict nodal metastatic states and relapse for breast cancer patients. METHODS: We analysed DNA microarray data from samples of primary breast tumours, using non-linear statistical analyses to assess multiple patterns of interactions of groups of genes that have predictive value for the individual patient, with respect to lymph node metastasis and cancer recurrence. FINDINGS: We identified aggregate patterns of gene expression (metagenes) that associate with lymph node status and recurrence, and that are capable of predicting outcomes in individual patients with about 90% accuracy. The metagenes defined distinct groups of genes, suggesting different biological processes underlying these two characteristics of breast cancer. Initial external validation came from similarly accurate predictions of nodal status of a small sample in a distinct population. INTERPRETATION: Multiple aggregate measures of profiles of gene expression define valuable predictive associations with lymph node metastasis and disease recurrence for individual patients. Gene expression data have the potential to aid accurate, individualised, prognosis. Importantly, these data are assessed in terms of precise numerical predictions, with ranges of probabilities of outcome. Precise and statistically valid assessments of risks specific for patients, will ultimately be of most value to clinicians faced with treatment decisions. 10 7 left from ventral prostate 21 41 P2B_KIDNEY_7 IGF1 and IGF1 receptors (IGF1R) are present in the adult heart and have been shown to be essential for myocardial performance. Insulin-like growth factor 1 (IGF1) is produced in numerous tissues particularly by the liver in response to growth hormone stimulation and is an important factor in the regulation of post-natal growth and development. We have generated and characterized transgenic mice over-expressing the IGF1R. We crossed IGF1R transgenic mice with dominant negative (dn)PI3K (p110) and with constitutively active (ca)PI3K(p110) transgenic mice. Expression profiling was performed on the ventricles of IGF1R, IGF1R-caPI3K, IGF1R-dnPI3K, caPI3K, dnPI3K transgenic female mice at 3 months of age. Non-transgenic littermates were used as controls. Keywords = insulin growth factor, IGF, cardiac, hypertrophy Source GEO sample is GSM18366 Last updated (according to GEO): May 27 2005 Plasma 861 nipple_cross-section_4 FSCC1 on Affymetrix GeneChip Human Full Length Array HuGeneFL mRNA was isolated after 4 hours of incubation from IMR-90 cells seeded onto a collagen/chondroitin sulfate tissue engineering scaffold mesh material. Cells were seeded at a density of 1 x 10^6 cells/ mesh, and this chip represents a pooling of cells from 4 meshes. Keywords = tissue engineering mesh, collagen, chondroitin sulfate, biomaterials design Source GEO sample is GSM6058 Last updated (according to GEO): May 27 2005 Spinal Cord 1000 CNS-SMTC_Mod4h-3A-s2 T30__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Melanoma xenograft, MEA2_Lung_B (LeiFidler) Gonadectomized Dahl-Iwai Female LowSalt Cortex rat3 gdahl_cortexr_k_GX_3c_051702 SON - 1d Dehydrated Source GEO sample is GSM69841 Last updated (according to GEO): Aug 15 2005 Exp B, Animal #3, control (0mg/kg) CPF Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours Source GEO sample is GSM246147 Last updated (according to GEO): Dec 03 2007 861 Fibroid Tumor brain 0 5 Mucous Membrane 861 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17075.gif Source GEO sample is GSM91583 Last updated (according to GEO): Sep 22 2006 Normal bronchial epithelial cell, primary 1000 Retina healthy subject Source GEO sample is GSM211079 Last updated (according to GEO): Sep 10 2007 GPX-000048 mouse brain ipsilateral control, biological rep1 Parkinson Disease 861 GSE430 8-cell embryo replication 2 Keywords = preimplantation Keywords = development Source GEO sample is GSM14684 Last updated (according to GEO): May 28 2005 post infection 28 41 M_U133A_21_DLPFC 96 FC BA9 B D_U133A_23_nAcc Cerebral Cortex 7 Normal Conventional Corpus 3 Laser capture lung cancer cells Source GEO sample is GSM191027 Last updated (according to GEO): May 25 2007 1000 Rectum Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174511 Last updated (according to GEO): Mar 14 2007 Colon Carcinoma 1000 This is the sixth replicate for the SNc neurons which were captured using LCM. Source GEO sample is GSM19323 Last updated (according to GEO): May 27 2005 1000 Cerebral cortex 5 0 brain GSE388 Myocardium 861 Synovium; acute arthritis Keywords = mouse gene expression database Source GEO sample is GSM29437 Last updated (according to GEO): May 27 2005 22-oct-2002-liverF-Mu11KsubAsc D_U133A_6_DLPFC Lung cancer 1000 Spleen D01 6h TLR2/1L 5 0 Spleen Tumors 91 96 4 0 Liver Gene expression data from rat metanephric mesenchymes cultured for 7 days in the presence of the ANX fraction Source GEO sample is GSM126227 Last updated (according to GEO): Dec 08 2006 1000 Brain 1000 Brain CNS-SpinalCsev-Adult-24h-1B-s2 untreated B Treatment, type=time_course, measurement=1.0 weeks Source GEO sample is GSM107848 Last updated (according to GEO): Jun 06 2006 liver_PPARa-knockout_WY14643_6h_rep1 LDMTX_MP-11 Blood 1000 41 36 spleen Gastrointestinal Stromal Tumors 966 Myometrium 49 Disease 7 0 Melanoma 1000 Intestines, Small human frontal cortex Source GEO sample is GSM87037 Last updated (according to GEO): Feb 08 2006 injured cortex 69 82 1000 Stem cells MCF7 human breast cancer cells treated with DMSO and used as a control in a 2 platform, three replicate experiment Source GEO sample is GSM188017 Last updated (according to GEO): May 11 2007 27 7 Medial Temporal Gyrus Human Hypothalamus Male 5 Acetaminophen 3hr Rat 8846 blood vs. Acetaminophen 3hr Rat Pooled Control blood Gene expression data from colorectal adenoma. Source GEO sample is GSM215103 Last updated (according to GEO): Aug 02 2007 GC (HKG13T) Large-scale analysis of the human transcriptome. Fetal brain Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 130.69 Stdv: 5.98 Min: 119.54 Max: 139.58 Source GEO sample is GSM2895 Last updated (according to GEO): Mar 20 2006 6 0 G4 lens D_U133Plus_126_HC Disorder of artery 865 HDMTX-DX-2 Kidney 1000 1000 Brain 913 Acute leukemia 17 7 hippocampus mouse hippocampus, cox-2 heterozygous, rep2 total RNA from mouse (male c57BL/6) spleen total RNA from untreated mouse (male c57BL/6) B cells Source GEO sample is GSM5835 Last updated (according to GEO): May 27 2005 1960 1950 hippocampus Exp C, Animal #1, 5mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 5mg/kg of CPF for 96 hours Source GEO sample is GSM246164 Last updated (according to GEO): Dec 03 2007 Epithelial Cells 1000 Primary Neoplasm 1000 Pool of 9 cochlear tissues at E12 Source GEO sample is GSM182577 Last updated (according to GEO): Aug 14 2007 Experimental Autoimmune Encephalomyelitis 901 861 Blood Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68326 Last updated (according to GEO): Jul 07 2006 865 Disorder of artery CNS-RM_CtrT0-4A-s2 NCI60.44_LABEL48EXTRACT47SUB3 Source GEO sample is GSM134217 Last updated (according to GEO): Aug 06 2007 of regenerating Dorsal Root Ganglia 21 55 M7TW00121827 between the LAD artery 266 287 D2_TP-72_I 1000 Brain 19 0 Head and neck cancer Brain 861 CVB3_S-0.5h-3 0 Human Cortex 11 RXF-393_CL9016__RENAL of the colon 28 39 Gene expression correlates of clinical prostate cancer behavior. normal human skeletal muscle sample 10 5 0 brain human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM155044 Last updated (according to GEO): Jun 04 2007 1000 Spleen 1000 Left Breast 1000 Standard Affymetrix Protocol Source GEO sample is GSM16499 Last updated (according to GEO): May 28 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145008 Last updated (according to GEO): Nov 20 2006 1000 Brain No_DHT_control_1 of somatomotor cortex 21 41 129P3/J SAL, Rep3 Medulla Oblongata 861 CNS-SC_CtrA14d-1B-s2 LymphNodUn_022VAFD5_0951.txt Gene expression data from colonic normal mucosa. Source GEO sample is GSM215056 Last updated (according to GEO): Aug 02 2007 AD-268t1(dup b4)-A93-3 ** on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A (cortex 19 25 Primary adenocarcinoma 0 21 158 memory disorders 173 /SvEvTac pituitary gland rep1 5 33 5 0 Spleen 1000 Spleen Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3281 Last updated (according to GEO): Mar 21 2006 901 Coronary artery Expression profiling of spinal cord section (T8) extracted from rats 30m following laminectomy (sham) Source GEO sample is GSM31405 Last updated (according to GEO): May 27 2005 Nose 1000 of the small intestine 97 118 62 CN A e_B7 M_U133A_5_AnCg 11 0 Fetal brains Mesenchymal Stem Cells 1000 Blood 861 1119 1100 into the hippocampus Parkinson's model voxel G4 861 Neoplasm Large-scale analysis of the human transcriptome. Testis Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 215.15 Stdv: 8.48 Min: 197.86 Max: 228.62 Source GEO sample is GSM2823 Last updated (according to GEO): Mar 20 2006 C3H/HeJ hypothalamus rep2 (430 2.0 Array) Gene expression data from the right forebrain of C57BL mouse received no treatment for twelve weeks. Source GEO sample is GSM148686 Last updated (according to GEO): Dec 12 2006 Mouse model of congenital heart disease in Csx/Nkx2.5 mutant embryos. Homozygous mutant mouse at embyronic day 9.5. Keywords = congenital heart disease, Csx, Nkx2.5 Source GEO sample is GSM2276 Last updated (according to GEO): May 27 2005 Spleen 1000 brain, cortex: Sample14_e1_le1 of regenerating Dorsal Root Ganglia 21 55 Cerebral cortex 1000 0 Human Cortex 11 ileum 0 4 Gene expression data from whole brain infected mouse, day 1 Source GEO sample is GSM189611 Last updated (according to GEO): May 16 2007 human frontal cortex Source GEO sample is GSM86950 Last updated (according to GEO): Feb 08 2006 861 Cerebellum brain, hippocampus: KA-6h-P15-II_e1_le1 Heart 1000 1000 Maxilla AdrenalCortex Source GEO sample is GSM18996 Last updated (according to GEO): Sep 25 2006 Myocardial Infarction 1000 334 320 Keywords = HIV whole blood_100603 Macrophage 14smi063 Collagen 1000 Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2672.gif Source GEO sample is GSM72168 Last updated (according to GEO): Sep 22 2006 Muscle 861 43h-AC replication 1 Keywords = preimplantation Keywords = development Source GEO sample is GSM14719 Last updated (according to GEO): May 28 2005 Schwann cells, expanded in number by exposure to growth factors in vitro, could be useful in nervous system repair. Our previous results suggest that long term exposure to heregulin and forskolin changes the functional properties of the human Schwann cells, including the ability to myelinate axons after transplantation. Here, we propose to determine the molecular changes in the Schwann cells that occur as a result of extended growth with mitogenic factors. We believe that the information obtained in these studies will provide clues about mechanisms underlying the already observed changes in function. This information will aid in the prediction of the safety and efficacy of neural repair approaches that use cultured, expanded Schwann cells. Finally this data may provide clues into the mechanisms underlying normal human Schwann cell function. To use gene array analysis to compare gene expression profiles in early and late passage human Schwann cells exposed to the growth factors heregulin and forskolin. Observed changes in the function of human Schwann cells, including their capacity for growth and differentiation, after prolonged exposure to heregulin and forskolin, are caused by changes in the gene expression profiles in these cells. Nerves from four different donors were obtained within 12-15 h postmortem, with full consent for research from the families of the donors (faxed). IRB approval not required because subjects were officially dead at nerve harvest (IRB confirmation faxed). The nerve tissue obtained consisted of the lower 15 cm of nerve extending from mid calf to ankle. Endoneurial fascicles were dissected from short (1-2 cm) nerve fragments and cultured with heregulin and forskolin for 1 week. The nerve fascicles were then treated overnight with collagenase and dispase and dissociated by gentle trituration. Cells were plated at low density on laminin coated dishes and maintained in culture with mitogens for 3 passages. Schwann cell purities during this period were > 95%. RNA was extracted from the cells at passage 1 ( i.e. after 2 population doublings) and passage 3 (i.e. after 8 population doublings) from the following donors: SN HSC 330, age 51; SN HSC 317, age 29; SN HSC 329, age 20 and SN HSC 351, age 42. Thus eight samples (2 groups, 4 independent samples per group) are to be analyzed. Because both groups in this comparison have been exposed to mitogens, differences in gene expression profiles will be interpreted as indicative of changes caused by prolonged versus short term exposure to mitogens. More RNA was prepared from each group of cells than was needed for gene array analysis to allow confirmation of differentially-expressed gene transcripts by real-time RT-PCR. Since the main purpose of this project is to detect any major changes in the molecular properties of the Schwann cells, we propose that these samples be analyzed using Affymetrix U133 + 2 arrays containing the complete human genome and request Option 1: Start to Finish Profiling of all samples. We have contacted Dr Stanley Nelson at UCLA and discussed the project with him. We request that the samples be analyzed in the UCLA facility. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Jan 13 2006 Contributers: Mary B Bunge Includes GDS1869. Update date: Jun 14 2006. Dataset description GDS1869: Analysis of passage 1 and passage 3 Schwann cell cultures obtained from four donors and maintained in the presence of the heregulin and forskolin. Heregulin and forskolin synergistically drive Schwann cell proliferation in vitro.. 1000 Lipids stria terminalis 1000 Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B. Source GEO sample is GSM162187 Last updated (according to GEO): Jun 12 2007 Adenocarcinoma 4 Hypertension 22 33 861 Acquired Immunodeficiency Syndrome 1000 Hippocampus prefrontal cortex sprague2 331 307 in central nervous system Spleen vs BAFF Treated B cell 30min (set2) 1000 Solid tumor from brain 21 30 Gene expression data from UET-13TR-EWS/FLI1 cells incubated in the absence of tetracycline for 72 hours Source GEO sample is GSM214920 Last updated (according to GEO): Aug 02 2007 in blood 16 23 of epithelial ovarian cancer 124 152 Neoplasm 861 5 0 brain Macrophages treated with LPS, 10 min, Replicate 3 Source GEO sample is GSM241130 Last updated (according to GEO): Nov 02 2007 1000 Spleen PGA-E13.5_1A Wild type 8 wk old male FVB/NJ mouse pituitary gland Source GEO sample is GSM107051 Last updated (according to GEO): Mar 05 2007 I_U133A_31_Amy 15 7 hindbrain Liver 0 4 with acute measles 20 37 Neural system-enriched gene expression: relationship to biological pathways and neurological diseases. Liver 1000 7 cerebral cortex 21 Gene expression data from postmorten brain regions Source GEO sample is GSM144989 Last updated (according to GEO): Nov 20 2006 Mental disorders 1000 1000 Coronary Arteriosclerosis Blood Test (Blinded) Sample Source GEO sample is GSM129940 Last updated (according to GEO): Sep 18 2007 Abdominal aorta structure 1000 short access to cocaine, lateral hypothalamus, 1 hr/day access to cocaine Source GEO sample is GSM93841 Last updated (according to GEO): Jan 26 2006 902 Aortic Aneurysm, Thoracic GC (HKG56N) This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195241 Last updated (according to GEO): Sep 13 2007 GC (HKG34L) 861 Gland structure 486_9d Aorta 1000 to HCMV infection 33 49 to the nose 599 609 1000 Lung Cochlea 0 6 1500 mg/kg X 24 hr Source GEO sample is GSM129888 Last updated (according to GEO): Sep 18 2007 adenoma 861 36 21 from whole brain Congenital Abnormality 853 Nose 1000 Diaphragm 7 day control rep 3 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184749 Last updated (according to GEO): Apr 26 2007 Mature B cells 3-2b Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184759 Last updated (according to GEO): Apr 26 2007 1000 adenoma GSE8599 wild-type mouse forebrain Treatment, type=time_course, measurement=4.0 weeks Source GEO sample is GSM53350 Last updated (according to GEO): Jul 06 2005 Abdominal aorta structure 1000 16 0 Medulla_Oblongata 861 Brain Squamous cell carcinoma 884 gfp pos. sorted cells from 3 disected e14.5 ganglionic eminences Treatment, type=wait Source GEO sample is GSM135775 Last updated (according to GEO): Sep 12 2006 Prostate 861 1000 Liver pre-mesenchymal stem cells 3781 3806 861 Malignant Neoplasms Liver 0 4 Disorder of artery 865 none Source GEO sample is GSM244553 Last updated (according to GEO): Nov 23 2007 Gene expression data from the hippocampus of S1P3-knockout mouse Source GEO sample is GSM172976 Last updated (according to GEO): Mar 08 2007 901 Caudate nucleus structure Coronary artery 901 in peripheral blood 837 856 Probeset expression data from NA12750 growth 1, replicate 2 Source GEO sample is GSM195192 Last updated (according to GEO): Aug 08 2007 1000 Temporal Lobe 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14938 Last updated (according to GEO): Oct 28 2005 human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195335 Last updated (according to GEO): Jun 04 2007 Bone Marrow 1000 1000 Left Epithelial Cells 1000 1000 Uterus Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35383 Last updated (according to GEO): May 27 2005 Leukemia, Lymphocytic, Chronic 884 Average value of triplicate experiments of brain neurospheres of WT (wild type) mice (postnatal day 0). The cRNAs for hybridization were generated by one round RNA amplification. Source GEO sample is GSM9250 Last updated (according to GEO): May 27 2005 CNS-SMTC_Mod3mo-4C-s2 Cord blood, primary UCB302 f2#183 versus pool Mouse Brain tissue Gene expression data from UET-13TR-EWS/ERG cells incubated in the absence of tetracycline for 72 hours Source GEO sample is GSM214927 Last updated (according to GEO): Aug 02 2007 olfactory bulb 0 13 406 395 whose hearts 1000 Skeletal muscle structure of lower leg none Source GEO sample is GSM123208 Last updated (according to GEO): Jul 26 2006 B6_Control_ZT 18_1 861 Gland structure 29 0 H13B Human Embryonic Stem cell Neural induction of ES by N2B27 monolayer culture Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): Jan 23 2006 Contributers: Mark G Carter Alexei A Sharov Minoru S Ko Kazuhiro Aiba Chiara Foroni Angelo L Vescovi brain, cerebral cortex: Sham8_e1_le1 Liver 0 4 Gene expression data from the right forebrain of C57BL mouse received no treatment for twelve weeks. Source GEO sample is GSM148679 Last updated (according to GEO): Dec 12 2006 861 Skeletal bone 1000 Malignant Neoplasms Parkinson Disease 861 Brain 1000 cortex 7 12 1000 Cerebellum D_U133Plus_87_CB total spinal cord 0 16 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3339 Last updated (according to GEO): May 27 2005 M7TW00121357 1000 Spleen Sham 1 f2#238 versus pool Mouse Brain tissue GSE5883 Medulla Oblongata 861 861 Neoplasm Blood 861 cerebral cortex 7 21 for liver 26 35 1000 Cerebellum normal testis 54 66 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11479.gif Source GEO sample is GSM79868 Last updated (according to GEO): Sep 22 2006 SN:1010399 Source GEO sample is GSM115382 Last updated (according to GEO): Jun 20 2006 AD control Treatment, type=dissect Source GEO sample is GSM119620 Last updated (according to GEO): Jul 10 2006 Cerebral cortex 861 1000 Lung (cortex 19 25 Blood 861 1000 Brain Samp10 Hippocampus Young Sample 1 923 Immune Complex Diseases /J periaqueductal gray rep1 1 27 The association between large tumor size and metastatic risk in a majority of clinical cancers has led to questions as to whether these observations are causally related or whether one is simply a marker for the other. This is partly due to an uncertainty about how metastasis-promoting gene expression changes can arise in primary tumors. We investigated this question through the analysis of a previously defined "lung metastasis gene-expression signature" (LMS) that mediates experimental breast cancer metastasis selectively to the lung and is expressed by primary human breast cancer with a high risk for developing lung metastasis. Experimentally, we demonstrate that the LMS promotes primary tumor growth that enriches for LMS(+) cells, and it allows for intravasation after reaching a critical tumor size. Clinically, this corresponds to LMS(+) tumors being larger at diagnosis compared with LMS(-) tumors and to a marked rise in the incidence of metastasis after LMS(+) tumors reach 2 cm. Patients with LMS-expressing primary tumors selectively fail in the lung compared with the bone or other visceral sites and have a worse overall survival. The mechanistic linkage between metastasis gene expression, accelerated tumor growth, and likelihood of metastatic recurrence provided by the LMS may help to explain observations of prognostic gene signatures in primary cancer and how tumor growth can both lead to metastasis and be a marker for cells destined to metastasize. spleen_1 Source GEO sample is GSM80807 Last updated (according to GEO): Mar 31 2006 Brain 861 Normal Source GEO sample is GSM175908 Last updated (according to GEO): Apr 09 2007 PMN_control_0min_Patient12 peripheral blood-CD14Monocytes Source GEO sample is GSM18872 Last updated (according to GEO): Sep 25 2006 M_U133A_66_nAcc 1000 frontal lobe Gene expression data from liver Source GEO sample is GSM243395 Last updated (according to GEO): Nov 16 2007 Olfactory Epithelium 1000 D_U133A_96_nAcc Nasal Epithelium 901 Primary tumor 19 32 Laser capture lung cancer cells Source GEO sample is GSM190996 Last updated (according to GEO): May 25 2007 1000 Congestive heart failure 1000 Nose Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118544 Last updated (according to GEO): Jul 11 2006 861 Cerebral cortex Macrophage smi40 MPL13E_Treated Oj3: Hippocampus_5T-AI_rep9 brain, Right Frontal Lobe: Extract61_le2 Cockayne syndrome B wt-rescued cell Source GEO sample is GSM226621 Last updated (according to GEO): Sep 04 2007 1000 Infection Parkinson's disease sample x006 0 30 Pregnant Swiss Webster mice were used as a model because cocaine treatment in these animals has been shown to result in offspring with reduced cerebral cortical mass. Source GEO sample is GSM153767 Last updated (according to GEO): Jan 19 2007 /Ovary 18 Disease 11 27 313 290 with distensible aorta. C3H/HeJ periaqueductal gray rep1 (430 2.0 Array) Vastus lateralis muscle biopsy from 73 year old healthy male. Analysis done with Affymetrix Microarray Suite 5.0 software. Keywords = muscle, aging Source GEO sample is GSM2399 Last updated (according to GEO): May 27 2005 1000 Brain Expression profiling of spinal cord section (T8) extracted from rats 4h following mild injury Source GEO sample is GSM31449 Last updated (according to GEO): May 27 2005 Balb/c day 3, biological rep 4, tech rep 2 Infection 1176 1185 9 0 Blood Test Gene expression data from DAOY cells stably expressing Mel18 shRNA Source GEO sample is GSM182009 Last updated (according to GEO): Apr 23 2007 Bladder sample 1178-1 Muscle 861 pooled RNA of the kidney of 36 day old rats Source GEO sample is GSM86662 Last updated (according to GEO): Jun 12 2006 Sprague-Dawley Female HighSalt OuterMedulla rat706 sd_medullar_k_706r_om_070302 Brain - Right Motor Cortex Description Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP) and harvested at the beginning (0 h) of pressure experiment #3 (PE3). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11369 Last updated (according to GEO): Dec 15 2006 Nervous system structure 901 Liver 1000 Liver 1000 23 0 mammary epithelial cells human caudate nucleus Source GEO sample is GSM86855 Last updated (according to GEO): Feb 08 2006 +_test-9_batch5 on NHGRI-6.7k human caudate nucleus Source GEO sample is GSM86816 Last updated (according to GEO): Feb 08 2006 89 69 in Ewing family tumor SN:1022907;Fetal Cartilage, biological rep2 validation Structure of trigeminal ganglion 1000 Aldosterone-producing adenoma (APA13) Bone Marrow 1000 f2#178 versus pool Mouse Brain tissue PMN_control_180min_Patient2 91 from the bone marrow 72 Brain 861 adenocarcinoma 3193 166 135 of surrounding carcinoma in situ SCN2.2 Sample 18 (Exp#2-36 hr) Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211258 Last updated (according to GEO): Jul 18 2007 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Interferon-beta (IFN beta) for 60min Source GEO sample is GSM5595 Last updated (according to GEO): May 27 2005 CingulateCortex Source GEO sample is GSM18940 Last updated (according to GEO): Sep 25 2006 mdx soleus sample 2 Normal Breast1 Gene expression data from mammary glands of pregnant mice Source GEO sample is GSM202680 Last updated (according to GEO): Jun 20 2007 Neurites 861 Heart 1000 brain 0 5 Isolated adipocytes 0 18 onto a collagen 71 85 5 0 Spleen Pancreas [JunctionChip 3 of 5] GSE4623 901 Mammary gland 901 Autoimmune Diseases 25 0 Superior_Cervical_Ganglion Skin 1000 TUMOR 16 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Y SIT D073 The first letter of the title refers to the age of the animal: 3 months (Y) 24 months (A) The second word in the title refers to the treatment: hidden platform (HID) visible platform (VIS) yoke control, no platform (YOKE) cage control (SIT) The next letter, if present, corresponds to: learning unimpaired (U) learning impaired (I) learning intermediate (B) Source GEO sample is GSM108642 Last updated (according to GEO): Aug 22 2006 Liver 0 4 1100 1087 heart failure Diaphragm 23 Day mdx rep 2 Cerebral cortex 861 1000 Cardiomyopathy, Alcoholic none Source GEO sample is GSM239932 Last updated (according to GEO): Dec 07 2007 VDXGUYU_4060 mouse brains 187 198 of coronary artery disease 317 342 1000 Descending colon Primary tumor 19 32 NA19192 Colon 1000 /3T3 fibroblasts 743 759 Pool of 10 (1 utricle and 3 ampullae) at E13 Source GEO sample is GSM182600 Last updated (according to GEO): Aug 14 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145578 Last updated (according to GEO): Nov 20 2006 NFIA E18KO3 GC (HKG45T) Knockout 5 months old, female Source GEO sample is GSM154341 Last updated (according to GEO): Jan 09 2007 LungP24_022HAF79_077d.txt I_U133A_112_Amy folatesufficientAs1ppm4 Heart 861 at the Human Brain 744 761 1074 1056 of neuropathic pain prostate Source GEO sample is GSM203372 Last updated (according to GEO): Jun 21 2007 PMN_control_360min_Patient5 17 7 hippocampus Lymphoblastoid Cell Line for Individual 8109.3 log phase total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Dimaprit for 60min Source GEO sample is GSM5535 Last updated (according to GEO): May 27 2005 NA18968 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with SDF1 alpha (Stromal cell derived factor-1) for 30min Source GEO sample is GSM5755 Last updated (according to GEO): May 27 2005 Blood 1000 1037 of transitional epithelium 1012 Lung; Adult Keywords = mouse gene expression database Source GEO sample is GSM29376 Last updated (according to GEO): May 27 2005 Wild type inbred mice Source GEO sample is GSM83038 Last updated (according to GEO): Nov 10 2005 of the heart 842 854 KO_NP_med_1 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3305 Last updated (according to GEO): Mar 21 2006 Replicate3_Voxel D7 Cerebral cortex 861 V5-P381 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226163 Last updated (according to GEO): Nov 02 2007 GM12750 Expression profiling of spinal cord section (T8) extracted from rats 7d following laminectomy (sham) Source GEO sample is GSM31410 Last updated (according to GEO): May 27 2005 1000 Coronary Arteriosclerosis 861 Blood in fibroblasts 1323 1337 I_U133A_28_DLPFC spinal cord 0 11 Cardiomyopathies 1000 high gestational age Source GEO sample is GSM213123 Last updated (according to GEO): Jul 25 2007 Kidney 56 62 Lymphoblastoid Cell Line for Individual 8198.4 log phase 1000 Neurodegenerative Disorders nasal epithelial cells 28 49 Testis 861 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 3 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10959 Last updated (according to GEO): May 27 2005 15 0 human cerebellum 1000 Brain Injuries Control male 7 CH2122 Wild-type 3 months old, female Source GEO sample is GSM154348 Last updated (according to GEO): Jan 09 2007 RENAL_UO31 on Affymetrix GeneChip Human Full Length Array HuGeneFL Huntington's disease (HD) pathology is well understood at a histological level but a comprehensive molecular analysis of the effect of the disease in the human brain has not previously been available. To elucidate the molecular phenotype of HD on a genome-wide scale, we compared mRNA profiles from 44 human HD brains with those from 36 unaffected controls using microarray analysis. Four brain regions were analyzed: caudate nucleus, cerebellum, prefrontal association cortex [Brodmann's area 9 (BA9)] and motor cortex [Brodmann's area 4 (BA4)]. The greatest number and magnitude of differentially expressed mRNAs were detected in the caudate nucleus, followed by motor cortex, then cerebellum. Thus, the molecular phenotype of HD generally parallels established neuropathology. Surprisingly, no mRNA changes were detected in prefrontal association cortex, thereby revealing subtleties of pathology not previously disclosed by histological methods. To establish that the observed changes were not simply the result of cell loss, we examined mRNA levels in laser-capture microdissected neurons from Grade 1 HD caudate compared to control. These analyses confirmed changes in expression seen in tissue homogenates; we thus conclude that mRNA changes are not attributable to cell loss alone. These data from bona fide HD brains comprise an important reference for hypotheses related to HD and other neurodegenerative diseases. human cerebellum Source GEO sample is GSM87102 Last updated (according to GEO): Feb 08 2006 26 15 endometrioid olfactory epithelium 194 213 It is well known that many genes are expressed in the retina where they show a clear daily pattern of expression. Although several studies have investigated gene expression in the retina, no study ? so far - has investigated the daily and the circadian pattern of gene expression using microarray. In the present study we propose to investigate the daily and circadian pattern of expression in the retina. To determine gene expression in the retina in Light:Dark cycles and in constant condition (constant dim light) in the rat. We hypothesize that (a) different genes are expressed in different retinal layers and (b) the pattern of expression of the same genes can differ among the different layers. Wistar rats (3 for each time point) will be killed in the middle of the day (ZT6) and in the middle of the night (ZT18). Eyeballs will be collected and the retina will be removed and immediately frozen and then stored at -80 oC. The same experiment will be repeated on animals that have been maintained in constant dim light for 3. Retinas (3 for each time point) will be obtained from animal killed at CT6 (middle subjective day) and CT 18 (middle subjectice night) and stored at ? 80 oC. The samples will be then shipped to NINDS-NIMH array facility for analysis.. Date GSE2868 Last Updated: Oct 28 2005 Contributers: G Tosini Includes GDS1759. Update date: Jun 16 2006. Dataset description GDS1759: Analysis of retinas under a light-dark cycle at Zeitgeber times (ZT) 6 and 18 or in constant dim light at circadian times (CT) 6 and 18. Gene expression in retinas compared to that in pineal glands.. Expression profiles of different mouse tissue samples profiles.. Date GSE2178 Last Updated: May 29 2005 Contributers: Michael Mucenski Bruce J Aronow Belinda Peach Mitchell Cohen Amy Moseley Susan E Waltz John Maggio Sandra Degen Steve Potter Thomas Doetschman Chris Erwin Joanna A Groden James Lessard Linda Parysek R Hirsch MaryBeth Genter Jianhua Zhang Kathleen Anderson Jonathan D Katz John Dedman Michael Lehman Jorge A Bezerra Michael D Bates Ming Xu Dan Wiginton Jeff A Molkentin Includes GDS1322. Update date: Nov 09 2005. Dataset description GDS1322: Gene expression profiles across a wide variety of tissue samples. The tissues examined include nervous system, skeletal muscle, male and female reproductive organs, gastrointestinal tract, as well as organs in a developmental context including lung, liver, kidney, and heart.. bc-ZT3-3 158 153 (NIDDM no additional Source GEO sample is GSM199081 Last updated (according to GEO): Jun 08 2007 Diaphragm 28 Day control rep 3 3 0 Lung 1000 Kidney Epithelium 861 of the stria terminalis rep2 19 46 to the nose 599 609 Whole Brain 62 72 418 391 with a lymph node metastasis no additional Source GEO sample is GSM199187 Last updated (according to GEO): Jun 08 2007 Male Sprague-Dawley rats (400±25 g) were anesthetized with sodium pentobarbital. Fluid-percussion head injury with a brief 2.5 atm pressure pulse leading to deformation of underlying brain. 8h after surgery, a 7 mm disk of parieto-occipital cortex, centered on the point of impact of the injury and containing the contusion area, was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44531 Last updated (according to GEO): May 27 2005 901 Heart Diseases Control brainstem 2 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53441 Last updated (according to GEO): Jul 06 2005 861 Cerebral cortex Parkinson's disease sample x122 Mouse Kidney Male 2 (technical replicate) Gene expression data from postmorten brain regions Source GEO sample is GSM145480 Last updated (according to GEO): Nov 20 2006 Gene expression data from rat metanephric mesenchymes cultured for 1 day in the presence of LIF Source GEO sample is GSM126194 Last updated (according to GEO): Dec 08 2006 from epididymal fat tissues 21 48 1000 adenoma Wild type inbred mice Source GEO sample is GSM82945 Last updated (according to GEO): Nov 10 2005 cerebellum 7 16 861 Hippocampus Joint Tissue Synovium 4 Normal 901 Cervical sympathetic ganglion Neurodegenerative Disorders 1000 Fibroblasts 1000 of somatomotor cortex 21 41 Tumor__Colorectal_Adeno_HCTN_19339 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Lymphoblastoid Cell Line for Individual 8128.4 log phase 861 Neoplasm 414 /progenitor cells 430 861 Brain Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11261 Last updated (according to GEO): May 28 2005 Osteoblasts 1000 dorsal_root_ganglia_5 Source GEO sample is GSM80629 Last updated (according to GEO): Mar 31 2006 5 0 blood between malignant high-grade astrocytomas 528 568 the blood 393 402 Gene expression data from postmorten brain regions Source GEO sample is GSM145202 Last updated (according to GEO): Nov 20 2006 I_U133Plus_121_CB Category: Cell-line Subcategory: HMEC Scanning Software: unknown Software version: unknown Lot batch = 0183-5k Source GEO sample is GSM1951 Last updated (according to GEO): Nov 21 2005 Cerebral cortex 861 255 234 with HIV encephalitis total RNA extracted from mouse brain Source GEO sample is GSM103424 Last updated (according to GEO): Sep 21 2006 the blood 393 402 HUVEC B on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A T8 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Mouse Liver AIN Diet 8hr Saline Injection, biological replicate E f2#341 versus pool Mouse Brain tissue Gene expression data from postmorten brain regions Source GEO sample is GSM145180 Last updated (according to GEO): Nov 20 2006 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9920.gif Source GEO sample is GSM79887 Last updated (according to GEO): Sep 22 2006 Large-scale analysis of the mouse transcriptome. Adrenal gland C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 213.01 Stdv: 6.47 Min: 202.77 Max: 222.35 Source GEO sample is GSM2953 Last updated (according to GEO): May 27 2005 861 Communicable Diseases Type 1 Diabetes patient and the timepoint 4 months after diagnosis. Source GEO sample is GSM228606 Last updated (according to GEO): Sep 11 2007 TEL-AML1-C44 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A BPH-41 on UMich-10k autism 0 5 73 68 livers Stem cells 1000 CaSki sample 2 stria terminalis 901 of regenerating Dorsal Root Ganglia 21 55 pharyngeal_mucosa_3 Source GEO sample is GSM80749 Last updated (according to GEO): Mar 31 2006 Fetal Occipital cortex cocaine1 119 96 in embryonic stem cells Phenytoin frontal cortex 7 Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53467 Last updated (according to GEO): Jul 06 2005 C57BL/6J Olfactory Bulb B (Ig 215 217 Nasal Epithelium Inhalation Formaldehyde 2ppm 24h ID211 1000 Decapitation 875 Subcutaneous Tissue Measles 861 Disease Source GEO sample is GSM176288 Last updated (according to GEO): Apr 09 2007 placebo 15d, biological rep10 Lymph Node Malignant Neoplasms 861 M7TW01010694 Hippocampus 1000 2869 tumor cells 2880 Epithelium 861 brain_DLPFC_bipolar B_mr648 striatum rattus_norvegicus_strain iP animal_number 3 Gene expression data from postmorten brain regions Source GEO sample is GSM145114 Last updated (according to GEO): Nov 20 2006 B6 day 0, biological rep 2, tech rep 2 Replicate2_Voxel C2 SR hgu95c Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28755 Last updated (according to GEO): May 27 2005 7 cerebral cortex 21 /cByJ Hippocampus A 4 22 Healthy patient. Source GEO sample is GSM228567 Last updated (according to GEO): Sep 11 2007 prostate Source GEO sample is GSM203333 Last updated (according to GEO): Jun 21 2007 1000 frontal lobe NA12751 growth 2, replicate 2 Brain 1000 GBM Treatment, type=remove Source GEO sample is GSM99570 Last updated (according to GEO): Apr 21 2006 Category: Serum-response Subcategory: Fibroblasts Scanning Software: unknown Software version: unknown Lot batch = 419 Source GEO sample is GSM2169 Last updated (according to GEO): Nov 21 2005 Ganglia, Spinal 923 Prefrontal Cortex Source GEO sample is GSM105472 Last updated (according to GEO): Apr 17 2006 20 0 human caudate nucleus onto a collagen 70 84 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with ELC for 120min Source GEO sample is GSM5552 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 To further understand the physiological role of cyclooxygenase (COX), the critical enzyme involved in the production of eicosanoids from arachidonic acid, we performed microarray analysis of gene expression in the cerebral cortex and hippocampus of mice deficient in COX-1 (COX-1-/-) or COX-2 (COX-2-/-). Expression of lipid (ATP citrate lyase, acetyl-CoA acetyltransferase, hydroxyacyl-CoA dehydrogenase) and homocysteine (methionine adenosyltransferase, S-adenosylhomocysteine hydrolase) metabolism genes was increased in the cerebral cortex of COX-2 -/- mice. Further, expression of GABAergic neurotransmission genes (GABA transporter 3, GABA-A receptor subunit ?1) was altered in the cerebral cortex and hippocampus of COX-2 -/- mice. A COX isoform specific effect was observed in the expression of Janus Kinase (JAK) 1 and 2. COX-1 -/- mice exhibited an increase in JAK1 expression while COX-2 -/- mice exhibited a decrease in JAK2 expression, an observation consistent with a previously demonstrated COX isoform specific effect on the expression of NF-kB. In summary, this study demonstrates the wide ranging effects of genetic deletion of COX isoforms in the mouse brain and suggests that inhibition of COX activity may alter the profile of gene expression in specific areas of the brain. We used nylon cDNA microarrays to detail the global programme of gene expression in the Cerebral Cortex and Hippocampus of COX-1 and COX-2 null (knockout) mice Last Updated (by provider): Jan 31 2007 Contributers: Robert Langenbach Kevin G Becker Francesca Bosetti Vinaykumar V Prabhu Christopher D Toscano C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P18 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25126 Last updated (according to GEO): May 27 2005 1059 1025 due to dysfunctional hair follicles Cerebral cortex 861 D04 0h Media spinal cord, spinal cord: RNA450_e1_le1 Laser capture lung cancer cells Source GEO sample is GSM191026 Last updated (according to GEO): May 25 2007 Skeletal muscle structure 1000 mRNA was isolated after 24 hours of incubation from IMR-90 cells seeded onto a collagen/chondroitin sulfate tissue engineering scaffold mesh material. Cells were seeded at a density of 1 x 10^6 cells/ mesh, and this chip represents a pooling of cells from 4 meshes. Keywords = tissue engineering mesh, collagen, chondroitin sulfate, biomaterials design Source GEO sample is GSM6047 Last updated (according to GEO): May 27 2005 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68183 Last updated (according to GEO): Jul 07 2006 7 cerebral cortex 21 14 7 amygdala 901 Neurodegenerative Disorders Infection 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Dimaprit for 60min Source GEO sample is GSM5537 Last updated (according to GEO): May 27 2005 LPS plus IL-10, 10 min, Rep_3 Seminoma 1000 osteoblast 630 640 Disease Source GEO sample is GSM176449 Last updated (according to GEO): Apr 09 2007 1000 Amygdaloid structure Human Sural Nerve Schwann Cell Donor 317 Passage 1 Treatment, type=add, description=growth factors heregulin and forskolin added Source GEO sample is GSM92237 Last updated (according to GEO): Jan 13 2006 7 cerebral cortex 21 liver 0 5 brain, cerebral cortex: 14994_e2_le1 861 Retina 1000 Hippocampus rat kidney at embryonic day 13, rep3 human cerebellum Source GEO sample is GSM87144 Last updated (according to GEO): Feb 08 2006 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47517 Last updated (according to GEO): May 29 2005 HapMap JPT Female Source GEO sample is GSM159658 Last updated (according to GEO): Feb 01 2007 Coronary artery 901 901 frontal lobe GSE77 gene expression of undifferentiated ESCs Source GEO sample is GSM181938 Last updated (according to GEO): Apr 12 2007 BC808A-BE Cerebral cortex 1000 220-97_node plasma cells 50 61 Nervous system structure 901 901 Epithelial Cells Skeletal muscle biopsy was obtained after a 3-hour hyperinsulinemic (infusion rate 40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172154 Last updated (according to GEO): Feb 28 2007 mouse brain 478 489 brain, Left frontal Lobe: Extract12_le2 of diaphram muscle 93 110 M_U133Plus_36_CB Macrophages and dendritic cells exposed to phylogenetically distinct parasites Normal Source GEO sample is GSM176155 Last updated (according to GEO): Apr 09 2007 958 Metastatic melanoma 398 377 pluripotent stem cells Expression profiling of spinal cord section (T8) extracted from rats 30m following laminectomy (sham) Source GEO sample is GSM31404 Last updated (according to GEO): May 27 2005 bronchial epithelia 224 243 Organ 861 no additional Source GEO sample is GSM199417 Last updated (according to GEO): Jun 08 2007 /3T3 fibroblasts 478 493 Testis 1000 of the colon 28 39 DRG006_c Liver 0 4 Brain 861 Nicotine-neocortex, biological rep6 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Interferon-beta (IFN beta) labeled with Cy5- time course with repeats. Date GSE383 Last Updated: May 29 2005 Contributers: Joella Grossoehme Sun Young Lee Angela Alexander Sangdun Choi Jong-Woo Kim Mi Sook Chang Yun Anna Cao Robert Hsueh Rebecca Hart Zhen Yan Includes GDS304. Update date: Nov 18 2003. Dataset description GDS304: Temporal analysis of effects induced by 1.2 nM interferon beta in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. Cochlea_D257A_9mo_2 1000 Ischemia blood, adrenal medulla: Ctx +/- replicate 2_e1_le1 Liver Test (Blinded) Sample Source GEO sample is GSM130117 Last updated (according to GEO): Sep 18 2007 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120679 Last updated (according to GEO): May 14 2007 DLBC26 on Affymetrix GeneChip Human Full Length Array HuGeneFL Bone structure of tibia 1000 Treatment of pediatric acute lymphoblastic leukemia (ALL) is based on the concept of tailoring the intensity of therapy to a patient's risk of relapse. To determine whether gene expression profiling could enhance risk assignment, we used oligonucleotide microarrays to analyze the pattern of genes expressed in leukemic blasts from 360 pediatric ALL patients. Distinct expression profiles identified each of the prognostically important leukemia subtypes, including T-ALL, E2A-PBX1, BCR-ABL, TEL-AML1, MLL rearrangement, and hyperdiploid >50 chromosomes. In addition, another ALL subgroup was identified based on its unique expression profile. Examination of the genes comprising the expression signatures provided important insights into the biology of these leukemia subgroups. Further, within some genetic subgroups, expression profiles identified those patients that would eventually fail therapy. Thus, the single platform of expression profiling should enhance the accurate risk stratification of pediatric ALL patients. Richard Almon-12-1138200269758 7 cerebral cortex 21 processed in batch 2 Source GEO sample is GSM90451 Last updated (according to GEO): Mar 20 2006 WT_PBS_2 PC-3 hgu95a Nasal Epithelium 901 4-cell embryo replication 2 Keywords = preimplantation Keywords = development Source GEO sample is GSM14680 Last updated (according to GEO): May 28 2005 Spleen vs Leukotriene B4 (LTB4)Treated B cell 240min (set1) Wild type 8 wk old male C3H/HeJ mouse periaqueductal gray Source GEO sample is GSM107035 Last updated (according to GEO): Mar 05 2007 of the heart 842 854 D3_TP-72_I Rat vestibular ganglia stained with calretinin. Tissue is LCM captured, calretinin positive cells Source GEO sample is GSM100184 Last updated (according to GEO): Mar 13 2006 from brain 21 30 brain, frontal cortex: ADX PM LC b_e1_le1 Expression data from transgenic mice (3 mo) inducibly expresssing human alpha1-antitrypsin in the liver 4wkB Germ free Jejenum 2 We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples. Source GEO sample is GSM201793 Last updated (according to GEO): Jun 20 2007 "Sample 55, <5 yr survival(18 months) age 41 erp yes" on vantveer-oligo adipose_tissue_omental_4 Source GEO sample is GSM80564 Last updated (according to GEO): Mar 31 2006 /3T3 fibroblasts 478 493 795 783 in the rectum GM07349_technical_rep_1 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13144.gif Source GEO sample is GSM79684 Last updated (according to GEO): Sep 22 2006 Transplant Series 25 Right, Transplant # 4 5 0 brain DRG Source GEO sample is GSM18851 Last updated (according to GEO): Sep 25 2006 brain, hippocampus: Ctr-72h-P15-III_e1_le1 cytoplasm 203 212 Universal Mouse Reference RNA Source GEO sample is GSM93433 Last updated (according to GEO): Jan 23 2006 CNS-SC_InjB14d-3C-s2 GBM Treatment, type=remove Source GEO sample is GSM99491 Last updated (according to GEO): Apr 21 2006 7 0 prostate 861 Blood Mouse Liver AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate F NA18603 This is the fifth replicate for the VTA neurons which were captured using LCM. Source GEO sample is GSM19337 Last updated (according to GEO): May 27 2005 Liver Test (Blinded) Sample Source GEO sample is GSM130136 Last updated (according to GEO): Sep 18 2007 ALLB-cell68 on Affymetrix GeneChip Human Full Length Array HuGeneFL The aged mouse was injected intraperitoneal (ip) with Escherichia coli lipopolysaccharide (LPS, 0.33mg/kg body weight (BW), ~10ug/mouse; serotype O127:B8, Sigma) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use. Source GEO sample is GSM73000 Last updated (according to GEO): Sep 07 2005 861 Alzheimer's Disease 1000 Intestines, Small 1000 Communicable Diseases Performed by UCI Microarray Facility. Source GEO sample is GSM203445 Last updated (according to GEO): Jun 22 2007 131 99 from Huntingtons disease model R6 091236 OVR29 on Affymetrix GeneChip Human Full Length Array HuGeneFL 861 Cerebral cortex Mammary Gland @ Preg19, biological rep2 umbilical cord; E18 embryos Source GEO sample is GSM18657 Last updated (according to GEO): May 27 2005 OA 2 no additional Source GEO sample is GSM199109 Last updated (according to GEO): Jun 08 2007 RNA sample 3 from motor neurons of SOD1 mice Treatment, type=double_round_amplification, description=T7-based two round of RNA amplification Source GEO sample is GSM92523 Last updated (according to GEO): Jan 13 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with fMLP for 60min Source GEO sample is GSM5572 Last updated (according to GEO): May 27 2005 Malignant Neoplasms 861 861 Malignant Neoplasms brain, Left Temporal Lobe: Extract45_le1 Liver Source GEO sample is GSM18794 Last updated (according to GEO): Sep 25 2006 1000 Brain Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11590 Last updated (according to GEO): May 28 2005 C15 on NCI-7.6k LPS-PVH_2 19 0 human frontal cortex from ventral prostate 21 41 021301_HF_357FL 43 0 Chorionic mesoderm-derived mesenchymal cells Simple annotation: Reference verification, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9989.gif Source GEO sample is GSM78473 Last updated (according to GEO): Sep 22 2006 1000 Brain total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Lysophosphatidic Acid for 30min Source GEO sample is GSM5649 Last updated (according to GEO): May 27 2005 B6 16-2-2 Spleen total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Tumor necrosis factor-alpha for 60min Source GEO sample is GSM5803 Last updated (according to GEO): May 27 2005 from the right forebrain 21 44 Whole Brain 62 72 Communicable Diseases 1000 kidney sprague2 of Parkinson's disease 450 471 Parkinson Disease 1000 Male 75.1 yr after antibody enrichment scan 2 (U133B) MCF7_II_CL5001_Breast on Affymetrix GeneChip Human Full Length Array HuGeneFL vestibular_nuclei_superior_4 Source GEO sample is GSM80881 Last updated (according to GEO): Mar 31 2006 "Sample 14,>5 yr survival(99 months) age 48 erp yes" on vantveer-oligo 1000 Prosencephalon Two 90 minute exposures (3 hr recovery in between) to 0.8% halothane every day for 5 days, for a total of 10 exposures Keywords = Eckenhoff, anesthetics Source GEO sample is GSM5109 Last updated (according to GEO): Mar 17 2006 C3H 4-2 Adrenal from a primary branch 21 41 BC402B-AF Accumbens P7 Normal brain 0 5 dentate granule cells Source GEO sample is GSM35826 Last updated (according to GEO): May 27 2005 Diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin's lymphoma, is clinically heterogeneous: 40% of patients respond well to current therapy and have prolonged survival, whereas the remainder succumb to the disease. We proposed that this variability in natural history reflects unrecognized molecular heterogeneity in the tumours. Using DNA microarrays, we have conducted a systematic characterization of gene expression in B-cell malignancies. Here we show that there is diversity in gene expression among the tumours of DLBCL patients, apparently reflecting the variation in tumour proliferation rate, host response and differentiation state of the tumour. We identified two molecularly distinct forms of DLBCL which had gene expression patterns indicative of different stages of B-cell differentiation. One type expressed genes characteristic of germinal centre B cells ('germinal centre B-like DLBCL'); the second type expressed genes normally induced during in vitro activation of peripheral blood B cells ('activated B-like DLBCL'). Patients with germinal centre B-like DLBCL had a significantly better overall survival than those with activated B-like DLBCL. The molecular classification of tumours on the basis of gene expression can thus identify previously undetected and clinically significant subtypes of cancer. Seminoma of testis 1000 the frontal cortex 108 125 Simple annotation: Drug_treatment, Normal tissue Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/9019.gif Source GEO sample is GSM78477 Last updated (according to GEO): Sep 22 2006 none Source GEO sample is GSM123220 Last updated (according to GEO): Jul 26 2006 lung_3 Myometrium 1 Normal Replicate2_Voxel E8 Brain 861 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18221.gif Source GEO sample is GSM91541 Last updated (according to GEO): Sep 22 2006 Ovarian_Tumor_Mucinous_CHTN-OM-032 1521 1499 in the small intestine LDMTX_MP-3 1000 Brain 5 0 Spleen DRG_sema3A_2h_rep1 PGA-Csx_wt_7a-m4 D_U133Plus_126_Amy Malignant neoplasm of thyroid 901 Pool of 13 vestibular tissues at E11.5 Source GEO sample is GSM182595 Last updated (according to GEO): Aug 14 2007 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169503 Last updated (according to GEO): Feb 21 2007 gene expression of undifferentiated ESCs Source GEO sample is GSM181935 Last updated (according to GEO): Apr 12 2007 1000 Insulin Resistance ATCC number CRL-1502 Source GEO sample is GSM6814 Last updated (according to GEO): May 27 2005 Sham Day 5,# 2 M7TW00121811 5 0 Spleen F4_2, mouse, FVB, control (non-infected), 4 day time matched control_rep 2 adenoma 1000 Brain 1000 Human conjunctival cell lines are useful tools for modeling ocular surface disease and evaluation of ocular drugs. Here we demonstrate that the IOBA-NHC and the ChWK conjunctival epithelial cell lines show, using an unbiased gene microarray approach, unique gene expression signatures that differ from primary conjunctival epithelial cells (PCEC) and conjunctival tissue. Globally, the expression profile obtained with the Affymetrix U133A chip (>22000 genes) from PCEC was clustered more closely to conjunctival tissue than either of the 2 cell lines. However, when restricted to Gene Ontology sub-categories: cellular defense, viral replication/cycling, antigen presentation, anti-oxidant pathways and ubiquitin ligase complex, the cell lines correlated reasonably well to PCEC (r > 0.70). In the category response to inflammation, correlation of cell lines to PCEC was poor (r = -0.012 and ?0.041 for IOBA-NHC and ChWK respectively). In general, the expression profile in IOBA-NHC cells was better correlated to PCEC than the ChWK cells. This was statistically significant (p<0.05) when one considers all the genes on the chip, or for proteins in the extracellular region, response to wounding, stress, lipid, protein and organic acid metabolism, development and differentiation. Our results are useful for the choice of conjunctival cell lines, if necessary, in future experiments, to increase validity of extrapolation to clinical scenarios. Last Updated (by provider): Aug 02 2007 Contributers: Louis Tong Michael E Stern Roger W Beuerman Jan-Peng Gao Margarita Calonge Yolanda Diebold Acetaminophen 3hr Rat 5027 blood vs. Acetaminophen 3hr Rat Pooled Control blood Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 24 h to ambient pressure (CP24) and harvested with cells exposed for 24 h to hydrostatic pressure, pressure experiment # 3 (PE3). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11400 Last updated (according to GEO): Dec 15 2006 19 0 human frontal cortex 1000 Coronary Arteriosclerosis 1000 Brain 471 466 T-ALL SNB-19_CL12002_CNS on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression data from male mice. Source GEO sample is GSM115530 Last updated (according to GEO): Jun 13 2007 the blood 393 402 no additional Source GEO sample is GSM199357 Last updated (according to GEO): Jun 08 2007 TUMOR 30 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Salivary Gland 4 Normal 19 0 human frontal cortex 5 0 brain total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD40 for 240min Source GEO sample is GSM5507 Last updated (according to GEO): May 27 2005 27 7 Medial Temporal Gyrus with myocardial infarction 313 339 43 0 Chorionic mesoderm-derived mesenchymal cells ovarian tumor: serous Source GEO sample is GSM139438 Last updated (according to GEO): Apr 09 2007 Coronary artery 901 healthy subject Source GEO sample is GSM211143 Last updated (according to GEO): Sep 10 2007 Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184773 Last updated (according to GEO): Apr 26 2007 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.98 Subject: 2672 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39004 Last updated (according to GEO): May 27 2005 875 Refractory Carcinoma ovary.3 no additional Source GEO sample is GSM199419 Last updated (according to GEO): Jun 08 2007 M_U133A_70_AnCg Neuroblastic Tumors 77 95 Cervix carcinoma 1000 42 minus the frontal cortex 66 gene expression data from melanoma xenografts following ILI with saline Source GEO sample is GSM213622 Last updated (according to GEO): Jul 27 2007 EOM 28 Day Control rep 3 none Source GEO sample is GSM239919 Last updated (according to GEO): Dec 07 2007 27 0 Leukemia Chronic Myelogenous Neostriatum 1000 660 mesenchymal stem cell 639 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc120 Source GEO sample is GSM1913 Last updated (according to GEO): Nov 21 2005 Gene expression data from DAOY cells stably expressing Bmi1 shRNA Source GEO sample is GSM182007 Last updated (according to GEO): Apr 23 2007 901 Bone Marrow at the Human Brain 744 761 Investigation into murine dermal burn wound. Mouse thermal injury induced, and skin excised at different times post-injury. Source GEO sample is GSM7481 Last updated (according to GEO): May 27 2005 brain, Left frontal Lobe: Extract7_le2 Hippocampus Source GEO sample is GSM53376 Last updated (according to GEO): Jul 06 2005 brain, frontal cortex: ADX PM FC b_e1_le1 Brain 1000 1000 Hippocampus Greene-5P01NS017771-220003 brain, hippocampus: CON-CA1-19_e1_le1 Category: Lymphoma Classification Subcategory: Normal lymphoid subsets Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b095 Source GEO sample is GSM2010 Last updated (according to GEO): Nov 21 2005 of somatomotor cortex 21 41 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68261 Last updated (according to GEO): Jul 07 2006 mesenteric 16 25 Simple annotation: Primary tumor, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11737.gif Source GEO sample is GSM76407 Last updated (according to GEO): Sep 22 2006 C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 2hr after experimental mice received their last shock treatment. Source GEO sample is GSM4494 Last updated (according to GEO): May 27 2005 36 15 from whole bone marrow nasal epithelial cells 28 49 1000 Substantia nigra structure no additional Source GEO sample is GSM199314 Last updated (according to GEO): Jun 08 2007 861 Encephalitis 1000 Eye 884 Structure of horn of uterus The two muscle 1064 1077 Brain_nAChRbeta4SubunitDeficent_MiceNob4424 Parkinson Disease 861 Liver Test (Blinded) Sample Source GEO sample is GSM130105 Last updated (according to GEO): Sep 18 2007 of the lung 47 58 D_U133A_44_Amy subthalamic_nucleus_3 Source GEO sample is GSM80828 Last updated (according to GEO): Mar 31 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145802 Last updated (according to GEO): Nov 20 2006 brain, cerebral cortex: Rat_03-26_NroLep_Lipska_e1_le1 tissue sample collected post mortem from SIV infected rhesus macaques full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44894 Last updated (according to GEO): May 27 2005 Brain 861 mouse hippocampus, cox-1 knockout, rep2 1000 Cerebral cortex HCC (HBV+, HK13) frontal cortex wistar 3922 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12358 Last updated (according to GEO): May 28 2005 1000 Coronary Arteriosclerosis Nrf2 +/+ mice (C57B6/SJL) were crossed with nrf2 -/- mice (C57B6/129SVJ) to generate mice heterozygous for nrf2. Interbreeding these heterozygotes generated the double-knockout mice (nrf2 -/-) as well as the corresponding littermate controls (nrf2 +/+). Mice were housed in plastic cages on a bedding of wood chips and maintained at ~22C, ~60% relative humidity, and a 12 hr light/dark cycle. The animals were fed with mouse diet 5015, which includes 30 IU/g of vitamin A and 35 IU/kg of vitamin E, (LabDiet, Richmond, IN) and drinking water ad libitum. All animal protocols were approved by the Institutional Animal Use and Care Committee at the University of Wisconsin-Madison. Total RNA was extracted from livers and spleens isolated from male and female nrf2 wildtype and knockout mice at 5 months of age (prior to the development of severe autoimmune disease). Keywords = Nrf2 Keywords = liver Source GEO sample is GSM13441 Last updated (according to GEO): May 28 2005 Transcriptional profiling was done in Hoxb1 mutant E10.5 embryos in tissues primarily consisting of rhombomere 4 and surrounding branchial arches. Source GEO sample is GSM115796 Last updated (according to GEO): Aug 28 2006 ER negative human primary breast tumor EA02014_41259_H133A_JA-929 861 Leukemia, Lymphocytic, Acute vestibular_nuclei_superior_10 Source GEO sample is GSM80896 Last updated (according to GEO): Mar 31 2006 Transplant Series 32 , PrimaryTumor no additional Source GEO sample is GSM199119 Last updated (according to GEO): Jun 08 2007 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b057 Source GEO sample is GSM1966 Last updated (according to GEO): Nov 21 2005 Mature B cells 1 KO_sham_med_1 1000 Kidney 57 39 with endometriosis Primary tumor 19 32 Fertilized egg replication 3 M_U133A_15_HC 1000 Brain Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3327 Last updated (according to GEO): Mar 21 2006 na Source GEO sample is GSM181262 Last updated (according to GEO): Apr 10 2007 C57BL/6J Amygdala D no additional Source GEO sample is GSM199045 Last updated (according to GEO): Jun 08 2007 Normal human tissue:Normal Fetal Brain Keywords = Human, Normal Tissue, Normal Fetal Brain Source GEO sample is GSM44691 Last updated (according to GEO): May 27 2005 HDMTX_MP-4 1000 Brain Epithelial Cells 1000 for liver 26 35 Wild type 8 wk old male C57BL/6J mouse hypothalamus Source GEO sample is GSM107021 Last updated (according to GEO): Mar 05 2007 7 0 Pancreas Exp C_4, 5mg/kg CPF Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184756 Last updated (according to GEO): Apr 26 2007 CCAT DTS Rep A2 plasma cells 50 61 861 Brain 88 68 with bicuspid valves Wild type 8 wk old male A/J mouse hippocampus Source GEO sample is GSM107008 Last updated (according to GEO): Mar 05 2007 Breast 861 Schizophrenia 1000 NSCLC_NCI-H332M_CL1017 on Affymetrix GeneChip Human Full Length Array HuGeneFL the blood 393 402 Laser captured visceral sensory neurons. Source GEO sample is GSM63668 Last updated (according to GEO): Dec 21 2005 468 459 the rectum Brain of P10 Gja9 (+/-) C57Bl/6j mouse, replica H2 861 Malignant Neoplasms Epithelium of bronchus 983 Nervous system structure 901 Gene expression data from aneurismal tissues obtained from patients with tricuspid valves. Source GEO sample is GSM116803 Last updated (according to GEO): Jun 28 2006 Olfactory Epithelium 1000 74 55 of hyperinsulinaemic RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above Source GEO sample is GSM160015 Last updated (according to GEO): Feb 05 2007 1239 CP24_12 Liver 1000 Category: Cell-line Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.31 Lot batch = svcc74 Source GEO sample is GSM1920 Last updated (according to GEO): Nov 21 2005 901 frontal lobe CurrentSmoker 99 Cochlear nuclei 0 14 bc-ZT9-2 AD control Treatment, type=dissect Source GEO sample is GSM119641 Last updated (according to GEO): Jul 10 2006 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7600.gif Source GEO sample is GSM79897 Last updated (according to GEO): Sep 22 2006 1000 Descending colon Cortex_Control_rep5 (05SE735) Nasal Epithelium 901 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153356 Last updated (according to GEO): Dec 27 2006 Fluid-percussion head injury 83 110 CNS-SC_InjB4h-4B-s2 CAD_replicate69 It has been found that fat oxidation is reduced in the skeletal muscle of obese humans. This study aims to identify the mRNA of proteins involved in fat oxidation that may be reduced in obese and morbidly obese individuals. Information gathered will help in understanding how obesity contributes to cardiovascular disease via insulin resistance.. Date GSE474 Last Updated: Jul 28 2006 Contributers: J A Houmard Includes GDS268. Update date: Jun 27 2003. Dataset description GDS268: Identification of proteins involved in fatty acid oxidation in skeletal muscle. Fat oxidation may be reduced in morbidly obese individuals. Provides understanding of how obesity contributes to cardiovascular disease via insulin resistance.. 1000 Spleen Pregnant females exposed to ethanol for 5 days, AF03 (Alcohol Fed) corresponds to replicate 3 of the postmortem brains 654 678 NA Source GEO sample is GSM198919 Last updated (according to GEO): Jun 07 2007 Expression profiling of somatomotor cortex extracted from rats at 3 months following moderate injury Source GEO sample is GSM41726 Last updated (according to GEO): May 27 2005 Lymphoblastoid Cell Line for Individual 8042.4 log phase Normal Source GEO sample is GSM176392 Last updated (according to GEO): Apr 09 2007 Caudal 1000 Lmna H222P heterozygous male 4 Large-scale analysis of the human transcriptome. Thyroid Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 172.35 Stdv: 5.64 Min: 160.35 Max: 181.49 Source GEO sample is GSM2836 Last updated (according to GEO): Mar 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145585 Last updated (according to GEO): Nov 20 2006 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13415.gif Source GEO sample is GSM79644 Last updated (according to GEO): Sep 22 2006 Standard Affymetrix Protocol Keywords = microarray Keywords = muscle Source GEO sample is GSM15933 Last updated (according to GEO): May 28 2005 4 0 Heart Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart. Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141323 Last updated (according to GEO): Oct 26 2006 1000 Prostate of mouse brain 9 23 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9909.gif Source GEO sample is GSM79852 Last updated (according to GEO): Sep 22 2006 0029_1247_H95A2_KF0138_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A atrial septal defects 198 218 861 Pancreas A_2 Putamen P3 Disease GSE1482 none Source GEO sample is GSM123200 Last updated (according to GEO): Jul 26 2006 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with NGF (Nerve Growth Factor) labeled with Cy5- time course with repeats. Date GSE392 Last Updated: May 29 2005 Contributers: Yun Anna Cao Robert Hsueh Angela Alexander Rebecca Hart Sun Young Lee Jong-Woo Kim Mi Sook Chang Zhen Yan Joella Grossoehme Sangdun Choi Includes GDS313. Update date: Nov 18 2003. Dataset description GDS313: Temporal analysis of effects induced by 8 nM nerve growth factor in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. 1000 Cerebellum CNS-RM_CtrT0-4B-s2 Human Hypothalamus Male 3 (technical replicate) Arteries 1000 PGA-HMO-Obese-8aUA-s2 2737 tumor cells 2747 10h mitotic selection days nasal epithelium 1126 1147 CAD_replicate108 Whole Brain 62 72 39 21 of substantia nigra 861 Cerebral cortex 5 0 brain Metabotropic gamma-aminobutyric acid receptors 0 45 Cochlear structure 1000 0 Human Cortex 11 Liver Test (Blinded) Sample Source GEO sample is GSM130133 Last updated (according to GEO): Sep 18 2007 Skeletal bone 861 IDC198 on harvard-12k Structure of horn of uterus 884 0029_1213_H95A2_KF0110_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Brain 861 0 Human Cortex 11 R748P01234 9 0 fetal lung 1000 melanoma Malignant neoplasm of stomach 901 Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 72h. Lot batch = Source GEO sample is GSM1249 Last updated (according to GEO): May 28 2005 Cerebral cortex 861 Structure of trigeminal ganglion 1000 Meningiomas 0 10 861 Malignant neoplasm of prostate Primary Neoplasm 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145255 Last updated (according to GEO): Nov 20 2006 10 0 Hippocampus D_U133A_87_DLPFC Y SIT D071 Nervous system structure 901 83 54 of Duchenne muscular dystrophy A61 NES 142Q TG1 F6/13 A61 NES Htt exon 1 142Q Mouse 8 months Cerebellum Male Source GEO sample is GSM73226 Last updated (according to GEO): Sep 06 2005 Proteoglycan 1000 144 114 from a single adult spinal cord Gene expression data from rat metanephric mesenchymes cultured for 2 days in the presence of NGAL Source GEO sample is GSM126207 Last updated (according to GEO): Dec 08 2006 M_U133A_98_AnCg Brain 1000 R537P00446 861 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145914 Last updated (according to GEO): Nov 20 2006 Parkinson Disease 1000 265 260 Spleen 1880 1867 schizophrenia Spleen vs Platelet activating factor Treated B cell 240min (set3) Wild-type striatal cells Source GEO sample is GSM82444 Last updated (according to GEO): Jun 26 2007 861 Cancer of Neck Laser capture lung cancer cells Source GEO sample is GSM191054 Last updated (according to GEO): May 25 2007 of mouse brain 9 23 none Source GEO sample is GSM239890 Last updated (according to GEO): Dec 07 2007 in cocaine addiction 74 93 1000 Brain Stem The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169472 Last updated (according to GEO): Feb 21 2007 V5-P420 Probeset expression data from NA12751 growth 2, replicate 1 Source GEO sample is GSM195208 Last updated (according to GEO): Aug 08 2007 cerebral cortex 7 21 thalamus_4 none Source GEO sample is GSM239889 Last updated (according to GEO): Dec 07 2007 entorhinal cortex layer II stellate island cells Source GEO sample is GSM107524 Last updated (according to GEO): May 01 2006 1000 Spleen 861 Cerebral cortex Heart 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Tumor necrosis factor-alpha for 30min Source GEO sample is GSM5802 Last updated (according to GEO): May 27 2005 medial motoneurons (MMN) 4 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18174.gif Source GEO sample is GSM91500 Last updated (according to GEO): Sep 22 2006 Replicate2_Voxel C4 MGJZ030212055Aepidermis Ventral tegmental area 0 22 Control Acetaminophen 3hr Rat left_liver_lobe Pool vs. Acetaminophen 3hr Rat 1658 left_liver_lobe HapMap CHB Male Source GEO sample is GSM159606 Last updated (according to GEO): Feb 01 2007 Myocardial Infarction 1000 Neoplasm 861 GBM Treatment, type=remove Source GEO sample is GSM99532 Last updated (according to GEO): Apr 21 2006 olfactory epithelium 194 213 experiment I, passage 13, replicate 2 ovary 147 151 HapMap CEU_parent Male Source GEO sample is GSM159538 Last updated (according to GEO): Feb 01 2007 Cerebral cortex 1000 Expression profiling of moderately injured raphe at 24h in rats Source GEO sample is GSM41585 Last updated (according to GEO): May 27 2005 Affymetrix Human Genome U133 Plus 2.0 array Source GEO sample is GSM242052 Last updated (according to GEO): Dec 04 2007 NA12043 38 12 of congenital heart disease 1000 Carcinoma 1000 Coronary Arteriosclerosis WKY rep1 Hypothalamus Source GEO sample is GSM107911 Last updated (according to GEO): Jun 06 2006 Malaria 1000 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with CD27 for 30min Source GEO sample is GSM5487 Last updated (according to GEO): May 27 2005 84 69 by heart failure 861 Cerebral cortex 1904 1886 in sporadic tumors none Source GEO sample is GSM190783 Last updated (according to GEO): Jun 25 2007 f2#145 versus pool Mouse Brain tissue Mammary Gland @ Lac1, biological rep4 V5-P324 913 Coronary heart disease Kidney 1000 Anterior nares 1000 1768 1749 for the hippocampus Plasma 861 Parkinson's disease sample x045 1000 Left Medulla Oblongata 861 Heart 1000 114 101 brains quickly 952 929 of the pituitary gland 1000 Lipids Replicate3_Voxel G9 Spleen 1000 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 1 - Pair 3 - IML Source GEO sample is GSM49885 Last updated (according to GEO): Dec 20 2005 DLCL-0039 || lc4b039 Comparison of neural stem cell lines overexpressing Nurr1 to clonal controls 861 Blood Human retinal sphere RNA-2, chip HG-U133B Neurodegenerative Disorders 1000 Ovarian_Tumor_Serous_KU-OS-012 901 Cerebral cortex Wild type inbred mice Source GEO sample is GSM82902 Last updated (according to GEO): Nov 10 2005 19 0 Head and neck cancer coronary_artery_1 FVB-3wk-m-1 plasma cells 332 344 V5-P280 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11302 Last updated (according to GEO): May 28 2005 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114184 Last updated (according to GEO): Jun 16 2006 239 Parkinson's disease 257 Skeletal bone 861 1000 medulloblastoma Gene expression data from hippocampus of one old SAMP10//Ta mouse Source GEO sample is GSM143747 Last updated (according to GEO): Jan 24 2007 none Source GEO sample is GSM239917 Last updated (according to GEO): Dec 07 2007 Backskin_DN-CLIM_P23_rep1 brain, cerebral cortex: NMDA 180 3_le1 D_U133Plus_88_HC 865 Disorder of artery Categorically distinct acute stressors elicit dissimilar transcriptional profiles in the paraventricular nucleus of the hypothalamus. Occipital lobe 983 ventral spinal cord 13 31 Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14347.gif Source GEO sample is GSM79700 Last updated (according to GEO): Sep 22 2006 GBM Treatment, type=remove Source GEO sample is GSM99528 Last updated (according to GEO): Apr 21 2006 Spleen 0 5 Facial nerve nucleus 1000 Whole Brain 62 72 1283 HP48_11 /3T3 fibroblasts 295 310 Our previous studies on brains and hearts of Cx null mice have revealed that expression level, control and coordination of a very large number of genes are regulated compared to wildtype littermates. This result suggests the possibility that the phenotype of the Cx null animals may include genes not only linked to the intracellular communication that gap junction channels provide but also to genes with very different functions. The question often arises, however, of the degree to which ?compensation? occurs in knockouts such that gene regulation depends on pathways altered to make up for the missing gene rather than reflecting normal gene interlinkage. In order to explore this question in the Cx43 null setting, we have compared gene expression patterns in Cx43 null astrocytes with that in wildtype astrocytes acutely treated (36 hrs) with Cx43 siRNA. In these studies, Cx43 levels determined by Western blot analysis were reduced by at least 70% following siRNA treatment, comparable with the 3.24x downregulation for mRNA. For each group of astrocytes, four independent cultures were compared, using oligonucleotide microarrays printed with the mouse Qiagen library. 8060 well annotated unigenes were identifiable in all 8 arrays; of these, 8.2% were upregulated and 6.0% downregulated in Cx43 null astrocytes and 6.2% upreguated and 7.0 downregulated in siRNA treated astrocytes. Interestingly, regulation of 92.3% unigenes significantly regulated in both Cx43 deficient astrocytes had the same orientation, representing a highly significant overlap of gene expression alteration. These experiments thus indicate that the gene regulation in Cx43 null astrocytes is largely due to direct interlinkage rather than to developmental compensation for the missing gene. Last Updated (by provider): Jun 19 2007 Contributers: Dumitru A Iacobas Sanda Iacobas Eliana Scemes David C Spray Whole Brain 73 83 Plasma 861 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with NGF (Nerve Growth Factor) for 240min Source GEO sample is GSM5707 Last updated (according to GEO): May 27 2005 Sample 108 on vantveer-oligo 1255 1247 * Adenoma BC17 861 Brain Primary Neoplasm 1000 Mesenchymal Stem Cells 1000 5 0 Spleen 861 Cerebral cortex at the Human Brain 744 761 1000 Hippocampus Replicate1_Voxel G8 p53 -/-, 0 hour, replicate b Source GEO sample is GSM2547 Last updated (according to GEO): May 27 2005 C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 1 hour after the last shock treatment. Source GEO sample is GSM4519 Last updated (according to GEO): May 27 2005 plasma cells 50 61 Brain 1000 Plasma 861 bronchial epithelia 224 243 Spleen vs CpG-oligodeoxynucleotide Treated B cell 60min (set3) Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184722 Last updated (according to GEO): Apr 26 2007 Nasal Epithelium 865 temporal_lobe_1 Source GEO sample is GSM80834 Last updated (according to GEO): Mar 31 2006 1000 Spinal Cord mouse brain 478 489 19 0 human frontal cortex 7112_Lung did not develop PGD C57BL10 gastroc sample 1 Septum Source GEO sample is GSM107902 Last updated (according to GEO): Jun 06 2006 Parkinson Disease 1000 Transitional epithelium 1000 Breast Carcinoma 901 olfactory epithelium wild type mouse 8 hpO Source GEO sample is GSM80189 Last updated (according to GEO): Oct 26 2005 861 Cerebral cortex 2N-2-MGU74B 1000 Cerebral cortex Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19196 Last updated (according to GEO): May 27 2005 1032 1006 of peripheral blood B cells /SvEvTac periaqueductal gray rep2 5 37 Myocardial Infarction 1000 MGMH030212040Btrigeminal B6_SleepDep_ZT 12_3 against ALS 290 301 Dorsal Raphe Source GEO sample is GSM107930 Last updated (according to GEO): Jun 06 2006 Whole blood 0 10 DBA 7-3-2 Spleen CT-2 861 Cecum 421 412 infection Bone Marrow 1000 Cnr1-/-/Cnr2-/- female number 1, untreated control ear (#7_Ko-C-4) 6 week mutant OMN rep 3 HMEC X BC4 : 0088-5k no additional Source GEO sample is GSM199371 Last updated (according to GEO): Jun 08 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145431 Last updated (according to GEO): Nov 20 2006 A2780_cis_IC90_16h_1 1BJZ02081484a_TemporalLobe 901 frontal lobe 255 235 dilated heart failure 7 Entorhinal Cortex 23 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92373 Last updated (according to GEO): Jan 13 2006 40 21 from the hippocampus Whole blood 0 10 in the adult heart 44 61 3AJZ02081479b_Medulla_Oblongata Nose 1000 NCI60.56_LABEL60EXTRACT59SUB3 Source GEO sample is GSM134278 Last updated (according to GEO): Aug 06 2007 5_cerebral_cortex_6hrs_sleep_#64 HC52 FC BA4 B GBM Treatment, type=remove Source GEO sample is GSM99484 Last updated (according to GEO): Apr 21 2006 Hypothalamic structure 1000 Chemosensitivity prediction by transcriptional profiling. Structure of entorhinal cortex 1000 Parkinson Disease 861 Parkinson Disease 861 of 4 collagen 79 91 gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134653 Last updated (according to GEO): Jul 09 2007 PGA_PA-N_249 normal testis 54 66 medulla_5 1000 Mammary gland Biopsy of a colorectal adenoma from patient #14 12 0 yeoh-leukemia Frontal Cortex Source GEO sample is GSM107941 Last updated (according to GEO): Jun 06 2006 Heart failure 1000 A-J_male_hypothalamus 901 Coronary artery Healthy patient. Source GEO sample is GSM228574 Last updated (according to GEO): Sep 11 2007 Normal Source GEO sample is GSM176412 Last updated (according to GEO): Apr 09 2007 Epithelium of bronchus 983 115 cortex 121 from colorectal adenoma 21 44 of somatomotor cortex 21 41 osteoblast 627 637 Malignant Peripheral Nerve Sheath Tumor 947 861 Muscle Brain 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145334 Last updated (according to GEO): Nov 20 2006 50 41 mouse lung Ganglia, Spinal 923 1263 1249 to group tumors B6 day 3, biological rep 4, tech rep 1 ER+/LN-/Nevins21 on Affymetrix GeneChip Human Full Length Array HuGeneFL hippocampal glutamatergic CA3 pyramidal neurons Source GEO sample is GSM35825 Last updated (according to GEO): May 27 2005 the thalamus 1925 1936 bronchial epithelia 224 243 M_U133A_1_HC kidney_medulla_4 Medulla 861 healthy subject Source GEO sample is GSM211146 Last updated (according to GEO): Sep 10 2007 T2+ gr3 tumour Source GEO sample is GSM2526 Last updated (according to GEO): Mar 21 2006 Diaphragm 112 Day control rep 3 heart sprague2 whole tissue, individual animal, 10 weeks old, male Sprague Dawley heart file:R3JW02103012 Source GEO sample is GSM15210 Last updated (according to GEO): May 28 2005 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11508 Last updated (according to GEO): May 28 2005 Gene expression data from the hippocampus of wild-type mouse Source GEO sample is GSM172961 Last updated (according to GEO): Mar 08 2007 AKR/J Cingulate Cortex F Ovarian_Tumor_Endometrioid_CHTN-OE-019 brain, cortex: 7dsham3_e1_le1 subthalamic_nucleus_4 The nose 94 101 Parkinson Disease 1000 Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide. Source GEO sample is GSM225649 Last updated (according to GEO): Aug 31 2007 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy, pathological hypertrophy, rat, heart failure, cardiomyopathy Source GEO sample is GSM12320 Last updated (according to GEO): May 28 2005 B6 9:1-3 CA3 S46 NLS 142Q TG2 F5/9 S46 NLS Htt exon 1 142Q Mouse 3.5 months Cerebellum Female Source GEO sample is GSM73225 Last updated (according to GEO): Sep 06 2005 striatum 25 33 MGMH030402094Bpreoptic Neoplasm 861 Nasal Epithelium Inhalation Formaldehyde 6ppm 5d ID293 1000 Coronary Arteriosclerosis Large-scale analysis of the human transcriptome. Salivary gland Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 146.86 Stdv: 8.51 Min: 131.54 Max: 162.87 Source GEO sample is GSM2847 Last updated (according to GEO): Mar 20 2006 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118329 Last updated (according to GEO): Jul 11 2006 M-16-31-UN on UMich-10k 424 415 infection aging of cultured human myotubes 1000 Rectum PGA-HMO-MObese-5aUA-s2 Control hippocampus 6 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53452 Last updated (according to GEO): Jul 06 2005 DRG015_c Wild type 8 wk old male C57BL/6J mouse bed nucleus of the stria terminalis Source GEO sample is GSM74931 Last updated (according to GEO): Feb 27 2007 Spleen 1000 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16250.gif Source GEO sample is GSM91512 Last updated (according to GEO): Sep 22 2006 wild type fundus replicate 3 EWSR1-POU5F1 chimera, 5azaC, Undifferentiated bone tumor - extra to drug addiction 1479 1496 182 157 induced status epilepticus brain 162 167 I_U133A_35_AnCg no additional Source GEO sample is GSM199347 Last updated (according to GEO): Jun 08 2007 Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181973 Last updated (according to GEO): Apr 13 2007 Interatrial septum 865 adenocarcinoma 3200 0 18 Parkinson's model voxel C1 932 920 in the brain Prosencephalon 861 T2+ gr 3 tumour Source GEO sample is GSM2510 Last updated (according to GEO): Mar 21 2006 1000 Muscular Dystrophy, Duchenne Blood Test (Blinded) Sample Source GEO sample is GSM130035 Last updated (according to GEO): Sep 18 2007 Dosage-dependent over-expression of genes in the trisomic region of Ts1Cje mouse model for Down syndrome. Epithelium of bronchus 983 7 frontal cortex 20 579 endothelial cells 595 Endometrium/Ovary-Disease 3 Transitional epithelium 1000 Lymphoblastoid Cell Line for Individual 8139.4 log phase cirrhotic liver tissue from patients without HCC Source GEO sample is GSM155952 Last updated (according to GEO): Jun 21 2007 1000 Structure of superior frontal gyrus Spinal Cord 1000 Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation. Source GEO sample is GSM228468 Last updated (according to GEO): Sep 10 2007 no additional Source GEO sample is GSM199181 Last updated (according to GEO): Jun 08 2007 AD-239t1-A158-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 195 with coxsackievirus B3 174 329 306 valvular cardiomyopathy WGACON-151 GBM Treatment, type=remove Source GEO sample is GSM99553 Last updated (according to GEO): Apr 21 2006 660 mesenchymal stem cell 639 Neoplasm 861 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156592 Last updated (according to GEO): Jan 22 2007 Epithelium 861 78 73 rectum organs 426 432 HCT-116 hgu95b Expression profiling of spinal cord section (T10) extracted from rats 4h following severe injury Source GEO sample is GSM31380 Last updated (according to GEO): May 27 2005 Richard Almon-22-1133800609448 Intraabdominal isolated adipocytes, rep1 Comparison of RNA levels in the neocortex of normal mice versus synaptically silent munc18-1 null mutants. Source GEO sample is GSM84368 Last updated (according to GEO): Aug 01 2006 N25__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Malignant Neoplasms 861 Brain 861 Alzheimer's Disease 1000 Brain 1000 for Marfan syndrome 233 251 Peripheral Nerve Sheath Neoplasm 861 D_U133A_49_DLPFC 40 21 from dorsal pancreas 1000 Brain ventral_tegmental_area_2 Source GEO sample is GSM80871 Last updated (according to GEO): Mar 31 2006 41 29 Control blood Bone Marrow 1000 901 Nervous system structure Transcriptional profiling was conducted on RNA from 59 human colon tumor tissue samples to identify genes whose expression level correlates VEGFR-2 Last Updated (by provider): Apr 20 2007 Contributers: Mark Ayers Spleen 0 5 Nose 1000 NB-C-TEST-8 on NHGRI-6.5k_b 257 242 of uterine horns Epithelial Cells 901 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 16 hours after lights on. Original RNA code = LC49A. Source GEO sample is GSM227379 Last updated (according to GEO): Sep 10 2007 Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153414 Last updated (according to GEO): Jan 11 2007 Whole Brain 62 72 brain, Left frontal Lobe: Extract25_le1 Five different human MPNST cell lines, mock treated or infected with G207. Source GEO sample is GSM215820 Last updated (according to GEO): Aug 07 2007 30 0 Adult occipital cortex cocaine5 Standard Affymetrix Protocol Source GEO sample is GSM16477 Last updated (according to GEO): May 28 2005 865 Disorder of artery 861 Cochlear structure Neonatal (P0) whole brain mRNA from 40,XX female In(X)/C3H x C57BL/6J Source GEO sample is GSM27458 Last updated (according to GEO): May 27 2005 Organ 966 Heart 861 with Parkinson's disease 27 50 brain, cerebellum: Lh+/+_Crb2_e1_le1 C57 whole brain 3A intestine_PPARa-knockout_treated_rep2 1000 frontal lobe 28 7 Superior Frontal Gyrus S1P3-KO-hippocampus, biological rep3 (female) Prefrontal Cortex Source GEO sample is GSM105452 Last updated (according to GEO): Apr 17 2006 Here we show that oral creatine (Cr) supplementation leads to increased life span in mice. Treated mice showed improved neurobehavioral performance, decreased accumulation of the aging pigment lipofuscin and upregulation of ?anti-aging? genes in brain. As Cr is virtually free of adverse effects, it may be a promising food supplement for healthy aging in man. Last Updated (by provider): Jun 13 2007 Contributers: Andreas Bender Helmut Fuchs Sabine M Hölter Dan Rujescu Daniela M Vogt Weisenhorn Lore Becker Ilka Schneider Valérie Gailus-Durner Martin Irmler Wolfgang Wurst Martin Hrabé de Angelis Just Genius Michael Mader Tomek Mijalski Jörg Schmidt Thomas Klopstock Johannes Beckers Leticia Quintanilla-Martinez Tobias Haack Tanja Ruthsatz brain, unknown: 00SI_e1_le1 Spleen vs Sphingosine-1-phosphate Treated B cell 30min (set1) Effects of SOCS3 on transcriptional response of macrophages to IL-6. Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Replicate 3 after stimulation for 100 minutes with 10 ng/ml IL-6. Source GEO sample is GSM6084 Last updated (according to GEO): Mar 17 2006 Posterior root of spinal nerve 861 Nasal Epithelium 901 Acetaminophen 6hr Rat 4178 blood vs. Acetaminophen 6hr Rat Pooled Control blood Gene expression data Source GEO sample is GSM230356 Last updated (according to GEO): Sep 19 2007 Brain 861 NHF3-hTERT_G1_C3_26554 n/a Source GEO sample is GSM178041 Last updated (according to GEO): Jun 11 2007 CS 251101A Cerebellum 1000 striatum 31 39 Pooled soleus RNA samples from five 8 wk old male mdx5cv mice Source GEO sample is GSM13741 Last updated (according to GEO): May 28 2005 Exp B, Animal #3, 0.5mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 0.5mg/kg of CPF for 96 hours Source GEO sample is GSM246151 Last updated (according to GEO): Dec 03 2007 1000 Prostate carcinoma 1000 Skin Gene expression data from postmorten brain regions Source GEO sample is GSM146032 Last updated (according to GEO): Nov 20 2006 Bone Marrow SG Normal 1000 Brain 352 340 encephalitis Brain 1000 5 0 brain Heart failure 1000 861 Retina B6:2M-2 retina 1000 ovarian neoplasm GBM Treatment, type=remove Source GEO sample is GSM99559 Last updated (according to GEO): Apr 21 2006 RMS-C4 on NHGRI-6.5k_b Medulla Oblongata 861 48 29 of bladder carcinoma 861 Brain 2 hrs Post-clamp sample 2 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2837 Source GEO sample is GSM2123 Last updated (according to GEO): Nov 21 2005 from brain 21 30 Heart failure 1000 884 Glomerular Basement Membrane M_U133Plus_83_nAcc Caudate P1 Disease 901 Caudate nucleus structure no additional Source GEO sample is GSM199337 Last updated (according to GEO): Jun 08 2007 Brain 1000 0029_1437_H95A2_T97-0090_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A CNS-SC_InjA30m-4B-s2 1000 Tricuspid valve structure Brain Injuries 861 Mental Retardation 1000 Heart 861 1000 frontal lobe Olfactory Epithelium 1000 B_D2_Control_ZT 6_1 D_U133A_50_HC Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15562.gif Source GEO sample is GSM84150 Last updated (according to GEO): Sep 22 2006 comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247379 Last updated (according to GEO): Dec 11 2007 Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Source GEO sample is GSM15953 Last updated (according to GEO): May 28 2005 Keywords = Heart 505 521 The most common congenital cardiac abnormalities 50 97 1000 ovarian neoplasm 1000 Brain Adenoma (HK73) C57 whole brain 2 brain, hippocampus: PR-CA3-1_e1_le1 91 from the bone marrow 72 Wild type 8 wk old male FVB/NJ mouse cingulate cortex Source GEO sample is GSM74953 Last updated (according to GEO): Feb 27 2007 74 49 dorsal root ganglion C57BL Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68262 Last updated (according to GEO): Jul 07 2006 no additional Source GEO sample is GSM199284 Last updated (according to GEO): Jun 08 2007 Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. Source GEO sample is GSM79036 Last updated (according to GEO): Oct 24 2005 A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37 C in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically. Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the ex- perimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained con- stant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic mea- surements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed. The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60 ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42 ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65 ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.). The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism Source GEO sample is GSM5977 Last updated (according to GEO): Nov 21 2005 Lymphoblastoid Cell Line for Individual 8079.3 log phase 1000 Hypertrophic Cardiomyopathy Date 3/16/2001 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : headfold Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 2.5 mg/kg Time : 4.5 hrs post-injection Intervention : 4.0 mg/kg PK11195 co-administered Risk: remediated Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 16-20 headfolds pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : fluorescein-12-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-FL with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = 2-chlorodeoxyadenosine Keywords = PK11195 Keywords = embryo Keywords = microphthalmia Lot batch = AN996 Source GEO sample is GSM12204 Last updated (according to GEO): May 28 2005 Sample Type: human total RNA Sample User: dpatel Experiment User: jmorris Algorithm: Statistical Corner+ Avg:279, Count:32 Corner- Avg:39991, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:6.675019,SFGene:All Background:Avg:404.51,Stdev:3.70,Max:415.5,Min:396.6 Noise:Avg:9.59,Stdev:0.26,Max:10.5,Min:8.7 RawQ:13.42 Keywords = ALL Source GEO sample is GSM3485 Last updated (according to GEO): May 27 2005 Communicable Diseases 901 Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 24h. Lot batch = Source GEO sample is GSM1241 Last updated (according to GEO): May 28 2005 Heart Septal Defects 884 Duchenne muscular dystrophy 0 26 70 40 without coronary artery disease 861 HIV Infections 3 days, repeat 3 861 Encephalitis 861 Malignant Neoplasms 901 Spinal Cord from ventral prostate 21 41 Gene expression data from postmorten brain regions Source GEO sample is GSM144909 Last updated (according to GEO): Nov 20 2006 Transitional epithelium 1000 Dendritic Cells, Exposed to Mycobacterium tuberculosis - Repeat #2 1000 Neoplasm 2 hrs Pre-clamp sample 3 ScN2a_7 Heart failure 1000 Lymphoblastoid Cell Line for Individual 8002.4 log phase 861 Colon M7TW00121472 1000 Spleen VDXRHU_410 CNS-SpinalCmod-Adult-7d-2B-s2 NCI60.31_LABEL35EXTRACT34SUB3 Source GEO sample is GSM134148 Last updated (according to GEO): Aug 06 2007 brain, cerebral cortex: NMDA 30 4_le1 in the brain 150 162 30 month spinal cord rep 3 Fibroblasts 861 DLBC41 on Affymetrix GeneChip Human Full Length Array HuGeneFL 0 Human Cortex 11 Analysis of prefrontal cortex from 3 biological replicates of C57BL/6J mice at four Zeitgeber Times (ZT 3, 9, 15, and 21). Source GEO sample is GSM240426 Last updated (according to GEO): Oct 30 2007 11_0027_Control_Day1_31 ventral tegmental area 24 46 Corpus Callosum 3 Normal M_U133A_3_nAcc Liver 1000 1037 of transitional epithelium 1012 10 weeks Source GEO sample is GSM147512 Last updated (according to GEO): Dec 01 2006 n/a Source GEO sample is GSM177949 Last updated (according to GEO): Jun 11 2007 217 these ganglia 205 plasma cells 332 344 Category: Cell-line Subcategory: Breast This experiment was an out file converted from rana. The original files were not provided to load this experiment in Oracle. Category and Subcategories were made by curators. Scanning Software: unknown Software version: unknown Lot batch = dtp3684 Source GEO sample is GSM2150 Last updated (according to GEO): Nov 21 2005 Examining the effects of tTA expression in mouse hearts Source GEO sample is GSM15062 Last updated (according to GEO): May 28 2005 Small cell carcinoma of lung 867 Primary tumor 19 32 289 280 infection 1000 Structure of locus ceruleus 861 Acquired Immunodeficiency Syndrome Neoplasm 861 Gene expression data from the hippocampus of S1P3-knockout mouse Source GEO sample is GSM172975 Last updated (according to GEO): Mar 08 2007 VDXIGRU_272219 infection 433 442 human caudate nucleus Source GEO sample is GSM86817 Last updated (according to GEO): Feb 08 2006 Gene expression data from a hippocampus from mouse injected 15 mg/kg kainate Source GEO sample is GSM147420 Last updated (according to GEO): Jan 03 2007 with some respiratory epithelium. 1039 1072 Liver (HBV+, SF1) Neoplasm 1000 the vestibular 235 248 Nervous system structure 901 Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589?595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164?169.) Source GEO sample is GSM159484 Last updated (according to GEO): Jun 21 2007 AD control Treatment, type=dissect Source GEO sample is GSM119680 Last updated (according to GEO): Jul 10 2006 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc63 Source GEO sample is GSM1851 Last updated (according to GEO): Nov 21 2005 901 Coronary artery The nose 94 101 Cortex Treatment, type=pharmacogenomic_treatment, description=Chronic Immobilization Stress Source GEO sample is GSM53312 Last updated (according to GEO): Jul 06 2005 Bic Gene expression data from postmorten brain regions Source GEO sample is GSM145168 Last updated (according to GEO): Nov 20 2006 861 Brain HTI-286 in docetaxel-refractory prostate cancer Source GEO sample is GSM206361 Last updated (according to GEO): Jun 29 2007 15 0 human cerebellum Autistic Disorder 877 AMM_0_0_Male3_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats Source GEO sample is GSM111847 Last updated (according to GEO): Nov 21 2006 Infection 1000 Coronary artery 901 DRG_control_5h_rep1 midbrain_8 FC 3144146A Salivary Gland [JunctionChip 2 of 5] human prostate PC3 tumors grown S.C. in nude mice Source GEO sample is GSM195348 Last updated (according to GEO): Jun 04 2007 SCG explant cultured for 65 hours in vitro Source GEO sample is GSM246025 Last updated (according to GEO): Dec 03 2007 858 Prostatic Neoplasms Neostriatum 1000 Epithelium 865 Expression profiling of moderately injured raphe at 7d in rats Source GEO sample is GSM41623 Last updated (according to GEO): May 27 2005 rat cortex Treatment, type=time_course, measurement=14.0 d Source GEO sample is GSM53224 Last updated (according to GEO): Jul 06 2005 Small cell carcinoma of lung 867 101057 Epithelium 861 none Source GEO sample is GSM244638 Last updated (according to GEO): Nov 23 2007 Epithelial Cells 1000 RR216_unifected_Skin_biopsy brain, cerebral cortex: NIC + NMDA 1_le1 H9RGV00102610 180minplus.1 Basal 861 129Cortex(1)subA.txt on Affymetrix GeneChip Murine 11K SubB Array Mu11K-B WGACON-156 GM18522 Gene expression data from colorectal adenoma. Source GEO sample is GSM215109 Last updated (according to GEO): Aug 02 2007 E8.0a_rep1 Affymetrix protocol Source GEO sample is GSM213811 Last updated (according to GEO): Aug 02 2007 adenocarcinoma 972 986 117 112 Lipids putamen_1 Source GEO sample is GSM80569 Last updated (according to GEO): Mar 31 2006 brain, hippocampus: CON-CA1-26_e1_le1 Experimental Autoimmune Encephalomyelitis 901 Expression profiling of moderately injured raphe at 3 months in rats Source GEO sample is GSM41604 Last updated (according to GEO): May 27 2005 n/a Source GEO sample is GSM178034 Last updated (according to GEO): Jun 11 2007 Bladder sample 709_1 Neocortical astrocyte chip 2. CHIP ID 10487 Source GEO sample is GSM130340 Last updated (according to GEO): Mar 14 2007 salivary_gland_3 BPH-205 on UMich-10k mouse brain 478 489 1000 Coronary Arteriosclerosis 133T The aged mouse was injected intraperitoneal (ip) with Escherichia coli lipopolysaccharide (LPS, 0.33mg/kg body weight (BW), ~10ug/mouse; serotype O127:B8, Sigma) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use. Source GEO sample is GSM73341 Last updated (according to GEO): Sep 07 2005 mouse brain contralateral RU486 Source GEO sample is GSM149758 Last updated (according to GEO): Mar 15 2007 Category: Cell-line Subcategory: HMEC Scanning Software: ScanAlyze Software version: 2.44 Lot batch = 0083-5k Source GEO sample is GSM1932 Last updated (according to GEO): Nov 21 2005 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225680 Last updated (according to GEO): Nov 05 2007 Gene expression data from a placenta without malaria Source GEO sample is GSM183607 Last updated (according to GEO): Apr 23 2007 Laser captured visceral sensory neurons. Source GEO sample is GSM63657 Last updated (according to GEO): Dec 21 2005 amygdala_9 Source GEO sample is GSM80592 Last updated (according to GEO): Mar 31 2006 with experimental autoimmune encephalomyelitis 12 57 CNS-SC_InjA24h-2A-s2 no additional Source GEO sample is GSM199356 Last updated (according to GEO): Jun 08 2007 Neurosphere cultures were established from individually isolated E 14.5 forebrains of mouse embryos that carry a bcl2 transgene. Single-cell suspensions were prepared, seeded at 1x105 cells/ml and treated for two days with 150 nM Trichostatin A (TSA), 500 nM 5-Aza-2?-deoxycytidine (AzaC) or both compounds, or left untreated. Two independent experiments were performed. Source GEO sample is GSM8904 Last updated (according to GEO): Oct 28 2005 32h-AC replication 3 Keywords = preimplantation Keywords = development Source GEO sample is GSM14718 Last updated (according to GEO): May 28 2005 NMDA360 (Experiment shortNMDA: Run 19222) Treatment, type=time_course, description=primary cortical neurons were treated with 1 mM NMDA for increasing periods of time (10 to 360 min)., measurement=360.0 m Source GEO sample is GSM96771 Last updated (according to GEO): Feb 14 2006 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215081 Last updated (according to GEO): Aug 02 2007 Lymphoblastoid Cell Line for Individual 8201.5 log phase brain, Left frontal Lobe: Extract28_le2 Bone Marrow 1000 ER-/LN-/Nevins43 on Affymetrix GeneChip Human Full Length Array HuGeneFL 721_Blymphoblasts Source GEO sample is GSM18730 Last updated (according to GEO): Sep 25 2006 Normal Source GEO sample is GSM176251 Last updated (according to GEO): Apr 09 2007 861 frontal lobe Sample represents the Neurointermediate lobe of the Pituitary from 5 dehydrated animals (3 Days) Source GEO sample is GSM69783 Last updated (according to GEO): Dec 15 2005 Multiple sclerosis 0 17 human caudate nucleus Source GEO sample is GSM86789 Last updated (according to GEO): Feb 08 2006 Chromosomes 861 Keywords = Heart 505 521 1000 Malaria 861 Brain Total RNA from iPS clone was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations. Source GEO sample is GSM239966 Last updated (according to GEO): Nov 22 2007 1000 Basal Ganglia 1000 Liver Blood 1000 Fibroblasts 861 NA18522 SN:Human Glioblastoma Biopsy 06730 Subject code A11 91 from the bone marrow 72 in blood 16 23 1BMH02030601_Prostate Myeloid Leukemia 901 AT1-hTERT_1.5Gy_24h_C5_21393 Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d Source GEO sample is GSM153328 Last updated (according to GEO): Dec 27 2006 Site: University of California, Davis Cohort: Male/Female Control Set Diagnosis: Control pH: 6.86 Subject: 2822 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39012 Last updated (according to GEO): May 27 2005 n/a Source GEO sample is GSM177950 Last updated (according to GEO): Jun 11 2007 V5-P213 1000 Cerebral cortex Substantia Nigra 8 Normal of the atrial 647 659 Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19197 Last updated (according to GEO): May 27 2005 38 21 from a hippocampus Heart 861 1000 Coronary Arteriosclerosis 1000 Mammary gland nucleus accumbens_shell sprague2 Biopsy of the normal mucosa of the colon from patient #4 1000 jejunum 0 hr Hela Double Thymidine, exp2 HapMap YRI_parent Male Source GEO sample is GSM159685 Last updated (according to GEO): Feb 01 2007 Tonsil [JunctionChip 1 of 5] GC (HKG15T) ER+/LN-/Nevins36 on Affymetrix GeneChip Human Full Length Array HuGeneFL To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229 Keywords = human, idiopathic, ischemic, cardiac, hypertrophy Source GEO sample is GSM18487 Last updated (according to GEO): May 27 2005 Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 8066 blood post HCMV infection 65 83 Expression profiling of spinal cord section (T10) extracted from rats 14d following laminectomy (sham) Source GEO sample is GSM31278 Last updated (according to GEO): May 27 2005 BTBR T+ tf/tf Amygdala B Substantia Nigra 5 Normal Colon (descending) [JunctionChip 2 of 5] brain, hippocampus: pADX PM Hip_e1_le1 405602 1000 Spleen cortex 7 12 D_U133A_3_DLPFC Simple annotation: Chronic Lymphocytic Leukemia, ARA-G in vivo chemotherapy Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/3031.gif Source GEO sample is GSM72145 Last updated (according to GEO): Sep 22 2006 M_U133Plus_94_AnCg that this gaseous neurotransmitter 1484 1517 RMS-T5 on NHGRI-6.5k_b Bone Marrow 1000 Five different human MPNST cell lines, mock treated or infected with G207. Source GEO sample is GSM215801 Last updated (according to GEO): Aug 07 2007 1112 on whole ganglia 1097 861 Neoplasm 67 40 with coronary artery disease 5 0 Spleen Epithelium 861 mouse brain contralateral control Source GEO sample is GSM149749 Last updated (according to GEO): Mar 15 2007 spinal cord Source GEO sample is GSM18943 Last updated (according to GEO): Sep 25 2006 MDA-MB-231/ATCC hgu95c Epithelium 861 atrial septal defects 198 218 Laser capture lung cancer cells Source GEO sample is GSM191044 Last updated (according to GEO): May 25 2007 ARMS-T-TEST-17 on NHGRI-6.5k_b BTBR T+ tf/tf Olfactory Bulb B 4 0 Liver Squamous epithelial cell 861 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11534 Last updated (according to GEO): May 28 2005 41 29 Control blood JMR-RatSham4h-2aA-s2 from the Superior Frontal Gyrus 21 51 861 Hippocampus liver damage 134 145 the ventricular 1094 1108 Gene expression data from postmorten brain regions Source GEO sample is GSM145918 Last updated (according to GEO): Nov 20 2006 Prosencephalon 1000 Gene expression data from aneurismal tissues obtained from patients with tricuspid valves. Source GEO sample is GSM116798 Last updated (according to GEO): Jun 28 2006 Cochlea 0 6 D_U133A_9_Amy 67 40 with coronary artery disease GSE9006 901 Caudate nucleus structure 861 Nicotinic Receptors Molecular correlates of sleep deprivation in the brain of three inbred mouse strains in an around-the-clock experiment of underlying brain 174 193 861 Mammary gland none Source GEO sample is GSM210302 Last updated (according to GEO): Jul 16 2007 Nose 1000 placenta-0606-uninflamed-uninfected-rep1 PGA-MCR-CR-96h-1bAv2-s1 1000 Communicable Diseases 861 Blood Femur 1000 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11229 Last updated (according to GEO): May 28 2005 17 7 hippocampi 16 7 cerebellum 1000 Carcinoma of lung Heart 1000 1000 Caudate nucleus structure Normal Adrenal Gland (AN15) EWS-C11 on NHGRI-6.5k_b NA Source GEO sample is GSM198894 Last updated (according to GEO): Jun 07 2007 Uterus (corpus) [JunctionChip 5 of 5] 40 21 from the hippocampus 28 0 frontal cortex wistar ky 3929 high gestational age Source GEO sample is GSM213079 Last updated (according to GEO): Jul 25 2007 Control rat 1 ventral tegmental area Source GEO sample is GSM32158 Last updated (according to GEO): May 27 2005 male C57BL6, double amplification Source GEO sample is GSM5430 Last updated (according to GEO): Mar 17 2006 rickman-glioma Acetaminophen 24hr Rat 5924 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool NA Source GEO sample is GSM84313 Last updated (according to GEO): Dec 01 2005 Gene expression data from ER negative human primary breast tumor Source GEO sample is GSM120690 Last updated (according to GEO): May 14 2007 861 HIV Infections umbilical cord_nobpd: 8D WGACON-94 861 Alzheimer's Disease Brain 861 1000 Brain E2A-PBX1-C7 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 melanoma 901 frontal lobe nodose_nucleus_3 T-ALL-#5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A GSE387 Neoplasm 861 861 Prostate 865 Disorder of artery WT 2 Neoplasm 861 organs 28 33 n/a Source GEO sample is GSM177917 Last updated (according to GEO): Jun 11 2007 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy, pathological hypertrophy, rat, heart failure, cardiomyopathy Source GEO sample is GSM12319 Last updated (according to GEO): May 28 2005 OltactoryEpithelium_mutant_biolrepli2 PBMCs-Type 1 Diabetes-IDDM42_T1D_4MO 1000 Coronary Arteriosclerosis CNS-SMTC_Ctr24h-2C-s2 1000 Mammary gland Jejunum [JunctionChip 5 of 5] CAD_replicate39 Gene expression data from liver Source GEO sample is GSM243388 Last updated (according to GEO): Nov 16 2007 Vulva 9 Normal PBMCs-Type 1 Diabetes-IDDM54_T1D_New Nasal Epithelium 901 V5-P566 processed in batch 5 Source GEO sample is GSM90417 Last updated (according to GEO): Mar 20 2006 Epithelium 865 human frontal cortex Source GEO sample is GSM86997 Last updated (according to GEO): Feb 08 2006 Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Keywords = estrogen, uterus, mouse, ovariectomized, gavage Source GEO sample is GSM3890 Last updated (according to GEO): May 27 2005 Heart 1000 228 219 Hippocampi cerebral cortex wistar ky 3911 NB-C6 on NHGRI-6.5k_b MelJuSo, no treatment 901 Connective Tissue Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181223 Last updated (according to GEO): Jul 12 2007 Neostriatum 928 none Source GEO sample is GSM210315 Last updated (according to GEO): Jul 16 2007 Pool Ts1Cje_P15_hyb2 IDC121 on harvard-12k Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141284 Last updated (according to GEO): Oct 26 2006 p53 -/-, 12 hour, replicate b Source GEO sample is GSM2549 Last updated (according to GEO): May 27 2005 0 Human Cortex 11 Heart Septal Defects, Atrial 1000 Leg 112 Day control rep 3 T46__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 Communicable Diseases 10 Bone marrow 0 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141331 Last updated (according to GEO): Oct 26 2006 SN:Human Glioblastoma Biopsy 10517 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68126 Last updated (according to GEO): Jul 07 2006 K-562 hgu95e Gene expression data from postmorten brain regions Source GEO sample is GSM145985 Last updated (according to GEO): Nov 20 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145506 Last updated (according to GEO): Nov 20 2006 from brain 21 30 Mk12: Hippocampus_21PT-AU_rep5 Muscular Dystrophies 1000 SN:Human Glioblastoma Biopsy 10408 SCG explant cultured for 65 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246031 Last updated (according to GEO): Dec 03 2007 GSE4523 AML_23 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A MP-4 clone 42 is a Nurr1 stable c17.2 neural stem cell line with similar proliferation rate as puroB and therefore both were matched for subsequent analysis. Source GEO sample is GSM82224 Last updated (according to GEO): Nov 07 2005 Mouse Alt-Splice Tissue Panel (Brain vs Non-Brain) 39 21 from mammary glands Cerebral cortex 861 prostate Source GEO sample is GSM203329 Last updated (according to GEO): Jun 21 2007 aortic biopsy medium Keywords = pulse wave velocity, arterial stiffness Source GEO sample is GSM6183 Last updated (according to GEO): May 27 2005 101046 with Parkinson's disease 27 50 901 Bone Marrow Lymphoblastoid Cell Line for Individual 8047.4 log phase 861 Retina PCA-402 on UMich-10k 1000 Malignant Neoplasms mdx TA sample 1 Standard affymetrix protocol Source GEO sample is GSM119732 Last updated (according to GEO): Jul 31 2007 Control 1 PBMCs-Type 1 Diabetes-IDDM56_T1D_1MO ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes_C_5549 Source GEO sample is GSM161570 Last updated (according to GEO): Apr 23 2007 n/a Source GEO sample is GSM178036 Last updated (according to GEO): Jun 11 2007 corpus_callosum_2 GC (HKG63T) brain 164 169 Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A61_8 months_replicate 4 brain, cerebellum: Stg-/-_Crb1_e1_le1 by the dorsal root ganglia 140 165 HDMTX_MP-DX-3 C57BL/6 benchmark dataset: Embryonic day 18.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25185 Last updated (according to GEO): May 27 2005 T59__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Blood brain, cortex: Sample9_e1_le1 Liver 0 4 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114233 Last updated (according to GEO): Jun 16 2006 at the Human Brain 735 752 adenocarcinoma 3420 Fluid-percussion head injury 83 110 CNS-SMTC_CtrT0-4C-s2 f2#159 versus pool Mouse Brain tissue C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P28 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25123 Last updated (according to GEO): May 27 2005 adenocarcinoma 3447 PBMCs-Healthy-H37_Healthy 1000 Brain Large-scale analysis of the mouse transcriptome. Hippocampus C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 238.83 Stdv: 11.64 Min: 221.25 Max: 263.09 Source GEO sample is GSM2928 Last updated (according to GEO): May 27 2005 Utricle 0 6 from the cerebellum 20 38 We used the default settings of GCOS software to scan the chips. Source GEO sample is GSM146917 Last updated (according to GEO): Apr 16 2007 901 Caudate nucleus structure 861 HIV Infections from mouse colon 21 36 Sample16, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53267 Last updated (according to GEO): Jul 06 2005 Gene expression data for comparing calorie restricted-fed 30-month-old to control-fed 30-month-old for investigating effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7453 Last updated (according to GEO): May 27 2005 NCI60.10_LABEL13EXTRACT12SUB3 Source GEO sample is GSM134043 Last updated (according to GEO): Aug 06 2007 PGA-MPF-BALB-saline-24h-3aAv2-s2 From naive male Sprague-Dawley rats (400Ã?±25 g), a 7 mm disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane and then stored at -80C. Cortical tissue from one rat provided sufficient RNA without the need for pooling. Source GEO sample is GSM44478 Last updated (according to GEO): Oct 28 2005 EpiHd_022PACI2_114a.txt Spleen vs Dimaprit Treated B cell 30min (set3) from mouse brain 20 35 PBMCs-Type 1 Diabetes-IDDM25_T1D_New 091252 MOLT-4 on Affymetrix GeneChip Human Full Length Array HuGeneFL N6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1st 6hr C+S-CA1 Malignant neoplasm of breast 1000 amygdala_8 Source GEO sample is GSM80591 Last updated (according to GEO): Mar 31 2006 of lung carcinoma 39 56 Adrenal Gland Cortex 1 Normal 16 0 Human cerebellum 20 CN A atrial septal defects 198 218 HMEC -EGF then refed EGF for 1.5hrs SN:Human Glioblastoma Biopsy 07093 366 354 encephalitis adenoma 861 Whole brain was obtained from five 10 week old naive C57BL/2 male mice and four 10 week old naive DBA/2J mice. Total RNA was extracted using a Quiagen RNeasy kit midi kits for lipid rich tissues. Target cRNA were produced using standard Affymetrix procedures from 5 ug of total RNA. This sample is also known as C57 1. Keywords = Mus musculus, inbred strains, whole brain gene expression pattern Source GEO sample is GSM47518 Last updated (according to GEO): May 29 2005 861 Skeletal bone 896 Ovarian adenocarcinoma Skeletal bone 861 Transitional epithelium 1000 Disease Source GEO sample is GSM175803 Last updated (according to GEO): Apr 09 2007 PMN_LB_180min_Patient3 Patient3F in seminoma 28 38 EWSR1-POU5F1 chimera, Undifferentiated bone tumor GST6-extra ALS 216 218 861 Brain Lymphoblastic Leukemia 901 Nasal Epithelium 901 GC (HKG49T) Osteoblasts 1000 Fibroblasts 861 19 0 Head and neck cancer 9 0 Blood Test prostate Source GEO sample is GSM203263 Last updated (according to GEO): Jun 21 2007 861 Bladder Mouse Liver AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate D Mesenchymal Stem Cells 1000 108T PBMCs-Type 1 Diabetes-IDDM15_T1D_New Gene expression data from postmorten brain regions Source GEO sample is GSM145450 Last updated (according to GEO): Nov 20 2006 41 29 Control blood Tumor__CNS_Glioblastoma_GlioB_3 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 430A2_2045_31_KO_neuropath_medulla Source GEO sample is GSM242694 Last updated (according to GEO): Nov 15 2007 ND017 NSCLC_NCI-H23(2)_CL1001 on Affymetrix GeneChip Human Full Length Array HuGeneFL spinal cord, spinal cord: G4B_le1 iFA50clone8+ Brain 861 Gene expressions affected by TNF alpha Source GEO sample is GSM189806 Last updated (according to GEO): May 21 2007 861 Brain Brain 1000 901 Mammary gland Spleen vs Sphingosine-1-phosphate Treated B cell 120min (set1) 1000 Heart EGFP infected SH-SY5Y/TrkA cells: infection (at t=-18 hours), NGF treatment (at t=0 hours), harvest for total RNA extraction (at t=3 hours). Replicate 3 Treatment, type=add Source GEO sample is GSM53387 Last updated (according to GEO): Jul 06 2005 CNS-RM_Mod3mo-4B-s2 "19 hr Hela Double Thymidine, exp3" Bacterial Infections 1000 (cortex 19 25 brain 0 5 CNS-SCsev_InjA14d-1A-s2 none Source GEO sample is GSM149636 Last updated (according to GEO): Jan 03 2007 3AMH02082809_721_BLymphoblasts Neurodegenerative Disorders 901 Prostate 861 Bone Marrow 1000 normal 1144 brain, Left frontal Lobe: Extract33_le2 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68344 Last updated (according to GEO): Jul 07 2006 n/a Source GEO sample is GSM177924 Last updated (according to GEO): Jun 11 2007 NCI60.24_LABEL28EXTRACT27SUB3 Source GEO sample is GSM134111 Last updated (according to GEO): Aug 06 2007 861 Brain Malignant tumor of colon 1000 Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. M_U133A_9_AnCg very early HCC Source GEO sample is GSM155993 Last updated (according to GEO): Jun 21 2007 SR-A mutant olfactory epithelium 48 hpO replicate1 The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76948 Last updated (according to GEO): Oct 11 2005 Blood Platelets 1000 Skeletal muscle structure 1000 NA12741 growth 1 Job's patient Source GEO sample is GSM211093 Last updated (according to GEO): Sep 10 2007 MCF7_I_CL5001_Breast on Affymetrix GeneChip Human Full Length Array HuGeneFL The epithelial cells 962 981 low gestational age Source GEO sample is GSM213122 Last updated (according to GEO): Jul 25 2007 brain, cerebellum: Stg-/-_Crb2_e1_le1 PGA-MPF-BALB-saline-24h-3bAv2-s2 D_U133A_48_Amy 861 HIV Infections Biopsy of the normal mucosa of the colon from patient #17 11 Bone marrow 0 Primary Neoplasm 1000 spinal_cord_9 Source GEO sample is GSM80799 Last updated (according to GEO): Mar 31 2006 f2#258 versus pool Mouse Brain tissue (cortex 19 25 NHE1 null mutation cerebellum-DS1 Expression profiling of spinal cord section (T10) extracted from rats 24h following mild injury Source GEO sample is GSM31318 Last updated (according to GEO): May 27 2005 n/a Source GEO sample is GSM178056 Last updated (according to GEO): Jun 11 2007 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10173.gif Source GEO sample is GSM79715 Last updated (according to GEO): Sep 22 2006 901 Bone Marrow 5 0 brain 6 month spinal cord rep 3 Structure of hemidiaphragm 861 Benign prostatic hypertrophy 884 CNS-SCsev_InjB24h-2B-s2 612 596 of Organ of Corti 901 Cell Nucleus Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28726 Last updated (according to GEO): May 27 2005 1hr time point after 3 Gy of IR exposure Source GEO sample is GSM10967 Last updated (according to GEO): May 28 2005 +_5985_batch2 on NHGRI-6.7k ovarian tumor: endometrioid Source GEO sample is GSM139390 Last updated (according to GEO): Apr 09 2007 861 Brain of the adult forebrain 140 162 Myocardium 861 PC 12Hr rat 4126 blood vs. 2500mg/kg APAP 12Hr rat 4135 blood 1000 Brain Gene expression data from liver Source GEO sample is GSM243391 Last updated (according to GEO): Nov 16 2007 Epithelium 861 360 in the frontal lobe 378 TNFTg-40w-f-3 Brain 1000 861 Ovary total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with ELC for 30min Source GEO sample is GSM5545 Last updated (according to GEO): May 27 2005 Lymphoblastoid Cell Line for Individual 8214.4 log phase GM10830 SN:1030145 Source GEO sample is GSM115418 Last updated (according to GEO): Jun 20 2006 osteoblast 627 637 78 66 Control blood Cerebellum_nontransgenic control A39_4 months_replicate 2 219 210 of stroke 1000 Brain Stem Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184699 Last updated (according to GEO): Apr 26 2007 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/13128.gif Source GEO sample is GSM79639 Last updated (according to GEO): Sep 22 2006 Liver Test (Blinded) Sample Source GEO sample is GSM130079 Last updated (according to GEO): Sep 18 2007 C57_HF_2 Gene expression data from brain of adult rats Source GEO sample is GSM101014 Last updated (according to GEO): Feb 20 2007 1000 Liver HOXB4 const_+10nM TMX, 1hour, biological rep1 seminoma specimen, pT1, patient age: 38y; W99 063 Job's Syndrome 1000 Epithelium of bronchus 983 5 0 Spleen The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM169475 Last updated (according to GEO): Feb 21 2007 861 Cerebral cortex Arteries 861 Brain_MD_14_Medulloblastoma_Desmoplastic_D on Affymetrix GeneChip Human Full Length Array HuGeneFL Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225704 Last updated (according to GEO): Nov 05 2007 Malignant tumor of colon 1000 Abdominal aorta structure 865 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225707 Last updated (according to GEO): Nov 05 2007 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68209 Last updated (according to GEO): Jul 07 2006 C3H 11-1 WAT CH2125 high-grade dysplastic liver tissue Source GEO sample is GSM155975 Last updated (according to GEO): Jun 21 2007 H124 CB B 1000 Kidney NCI60.43_LABEL47EXTRACT46SUB3 Source GEO sample is GSM134213 Last updated (according to GEO): Aug 06 2007 31 0 Cerebellum Alzheimer's disease 5 Barcode:251316210243 Source GEO sample is GSM159384 Last updated (according to GEO): Jul 17 2007 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211312 Last updated (according to GEO): Jul 18 2007 These studies adress differential changes in gene expression between sleep deprived and control mice. We profiled gene expression at four time points across the 24H Light/Dark cycle to take into account circadian influences and used three different inbred strains to understand the influence of genetic background. Last Updated (by provider): Dec 07 2007 Contributers: Paul Franken Mehdi Tafti Sylvain Pradervand Stéphane Dorsaz Brice Petit Spleen vs Tumor necrosis factor-alpha Treated B cell 240min (set2) Diaphragm-skeletal muscle 0 25 46 36 endometrium 1907 1879 of adhering connective tissue collagen 302 310 pooled RNA of the kidney of 36 day old rats Source GEO sample is GSM86646 Last updated (according to GEO): Jun 12 2006 placebo 15d, biological rep1 Olfactory Epithelium 1000 Olfactory Epithelium 1000 BXD6_M7SS02042202 RNA from muscle biopsy specimen Source GEO sample is GSM3719 Last updated (according to GEO): Feb 27 2007 testes_1 747 tumor cells 757 7 0 prostate SCG explant cultured for 2 hours in vitro, in the presence of Sema3A Source GEO sample is GSM246038 Last updated (according to GEO): Dec 03 2007 1st 2hr C+S-CA1 CA99-43B HepG2 + SDF 6h 1 Treated hrs nasal epithelium 1127 1147 1000 Spleen of the heart 842 854 PGA-lv_1h_512 Neoplasm 861 Interatrial septum 865 858 Prostatic Neoplasms Mesenchymal Stem Cells 1000 861 Oocytes 12 0 Uterus_Corpus 70 40 without coronary artery disease Brain (cerebral cortex) [JunctionChip 5 of 5] Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hour time point Source GEO sample is GSM159728 Last updated (according to GEO): Apr 23 2007 HapMap YRI_parent Female Source GEO sample is GSM159713 Last updated (according to GEO): Feb 01 2007 913 Coronary heart disease 1000 Pancreas NA Source GEO sample is GSM84336 Last updated (according to GEO): Dec 01 2005 630 620 cerebellum Individual LCL vs Pooled control LCLs Source GEO sample is GSM3253 Last updated (according to GEO): May 27 2005 460_2 HIGK cells infected with Fusobacterium nucleatum, biological rep2 Expression profiling of spinal cord section (T8) extracted from rats 24h following moderate injury Source GEO sample is GSM31453 Last updated (according to GEO): May 27 2005 osteoblast 627 637 Bone Marrow 1000 1896 1886 for livers mouse brain 478 489 plasma cells 50 61 to the nose 599 609 861 Malignant Neoplasms 232-97_SCC CNS-SpinalCsev-Adult-7d-2C-s2 Salivary Gland 2 Normal A control group consisting of nine C57/BL/6J mice was maintained on a normal diet consisting of Purina Rodent Chow (Harlan Teklad, catalog #5008, 6.5% fat, 49% carbohydrate, 23% protein, 3.5 kcal/ g). The experimental group consisted of nine mice grown on a specialty high-fat diet (Harlan Teklad, catalog #TD88137, 42.16% fat, 42.81% carbohydrate, 15.02% protein, 4.53 kcal/ g). Mice were maintained for ten weeks on their respective diets in a controlled environment with standard light and feeding schedule. Two days before tissue harvest, the experimental group on the high-fat diet was divided into one group of five and one group of four mice. The first group continued on the high-fat diet for the final two days, while the second group fasted. Mouse weights were recorded two days prior, and the day of tissue harvest. At the end of the fasting period liver tissue samples were harvested from each mouse. RNA was purified from the liver tissue samples. Each tissue was homogenized in 1 mL of STAT-60 (Tel-Test, Inc., Friendswood, TX) and the homogenate was mixed with 200 uL of chloroform. The aqueous phase was removed, and mixed with 500 uL of isopropanol to precipitate the RNA. The resulting RNA pellet was washed with 500 uL of 70% ethanol and allowed to air dry. The pellet was dissolved in RNase free water (Ambion, TX), quantified by UV spectroscopy, and stored at -80C. Total RNA control samples (Universal Mouse Reference RNA, catalog # 740100, Stratagene) were labeled using Cy3 dCTP (Perkin-Elmer), and liver total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). The control RNA samples were additionally mixed with 2 uL of random hexamers. The reaction mixtures were incubated at 42 C for two hours. After the reverse transcription reactions, the RNA templates were degraded by addition of 2 uL of 1 N NaOH and incubation at 65 C for 10 minutes. The alkaline conditions were neutralized by addition of 2 uL of 1 N HCl. Liver cDNA samples were then mixed with a control cDNA sample, and the mixtures were cleaned using a QIAquick Nucleotide Removal kit (Qiagen) as described by the manufacturer's instructions. The cleaned samples were concentrated in a speed vacufuge (Eppendorf) for 20 minutes at 65 C, and were dissolved in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), quantified, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 C using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), then in 1X SSC, and finally in 0.1X SSC. The arrays were dried by centrifugation and scanned using a GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and analyzed using Matlab (The MathWorks, Inc.). Microarrays were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). Arrays contained 16,847 features, printed from a synthesized oligonucleotide mouse library (Operon). The library was suspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed at approximately 50% humidity. Once printed, the probes were crosslinked using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride (Fluka AG), 239 mL 1-methyl-2-pyrrolidinone (EM Science), and 10.7 mL of 1 M boric acid (Fisher), pH 8.0. They were cleaned by rinsing twice in 250 mL of milli-Q water, followed by 250 mL of 95% ethanol (Pharmco Products). After blocking, they were dried using filtered air and stored in the dark at room temperature. Keywords = mouse, liver, energy homeostasis, gene expression, microarrays Source GEO sample is GSM6602 Last updated (according to GEO): Nov 21 2005 C3H/HeJ hypothalamus rep1 Neoplasm 861 901 Hepatocyte hrs nasal epithelium 1126 1146 Identification of genes and quantitative trait loci (QTL) that control hematopoietic stem cell functioning Dendritic Cells, CD8- CD4- subset - Expt #2 Cochlear nucleus structure 1000 Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. All patients were considered sporadic cases on the basis that no clinical antecedents of familial adenomatous polyposis were reported, and those that met the clinical criteria for hereditary non-polyposis colon cancer (Amsterdam criteria) were excluded. Source GEO sample is GSM112307 Last updated (according to GEO): Jun 06 2006 zhao-hippocampus Acetylcholine 861 Gene expressions affected by TNF alpha Source GEO sample is GSM189818 Last updated (according to GEO): May 21 2007 Plasma 861 1049 1035 that tenascin-C Cultured in DMEM with 10% FBS and penicillin (100U/ml)/streptomycin (100ug/ml). Media changed every other day. 37ºC, 5% CO2. Cells plated on sample surfaces. Source GEO sample is GSM15795 Last updated (according to GEO): Oct 28 2005 Gene expression data from human colon tumor tissue Source GEO sample is GSM173334 Last updated (according to GEO): Apr 20 2007 Cerebral cortex 861 Oocytes 1000 Parkinson Disease 861 Mouse Testis 2 (technical replicate) 32h-DMSO replication 1 Keywords = preimplantation Keywords = development Source GEO sample is GSM14722 Last updated (according to GEO): May 28 2005 Blood 861 Tumor__CNS_Glioblastoma_GlioB_8 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Primary small cell lung carcinoma 3105 Source GEO sample is GSM17343 Last updated (according to GEO): May 28 2005 Thalamus Lateral Nuclei 1 Disease Fibroblasts 1000 brain, frontal cortex: Sample49_e1_le1 /Ovary 7 Disease 11 26 Nicotine-hippocampus, biological rep3 Cerebral cortex 1000 hrs nasal epithelium 1126 1146 Myometrium 14 Normal M_U133Plus_119_CB This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195236 Last updated (according to GEO): Sep 13 2007 Expression profiling of moderately injured raphe at 7d in rats Source GEO sample is GSM41624 Last updated (according to GEO): May 27 2005 no additional Source GEO sample is GSM199266 Last updated (according to GEO): Jun 08 2007 10 7 Left Normal Source GEO sample is GSM175824 Last updated (according to GEO): Apr 09 2007 SWR/J Saline treated, striatum, biological replicate 3 Source GEO sample is GSM187994 Last updated (according to GEO): Jun 14 2007 2.5 mg/kg 2CdA headfold at 6.0h Contribution of polycomb homologues Bmi-1 and Mel-18 to medulloblastoma pathogenesis. HIGK cells infected with Streptococcus gordonii, biological rep3 Macrophage smi42 nasal epithelial cells 28 49 NA Source GEO sample is GSM109463 Last updated (according to GEO): May 22 2006 brain, brainstem: cRNA-WT2 Neuraxis 1000 adenocarcinoma 3216 0 18 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 5 day time point Source GEO sample is GSM159756 Last updated (according to GEO): Apr 23 2007 Heart 861 861 Malignant Neoplasms MLL_20 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A NCI60.5_LABEL8EXTRACT7SUB3 Source GEO sample is GSM134019 Last updated (according to GEO): Aug 06 2007 I_U133Plus_120_AnCg 84 69 by heart failure VDXGUYU_4096 Adipose tissue 884 36 0 Inflammatory myopathy specimen GEIM16 78 66 Control blood Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology Source GEO sample is GSM22564 Last updated (according to GEO): May 27 2005 R532P00648 204 194 of retinal Macrophage 14smi036 whole brain from nicotinic acetylcholine receptor beta4 subunit null mutant mouse Source GEO sample is GSM120583 Last updated (according to GEO): Sep 22 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145041 Last updated (according to GEO): Nov 20 2006 141 115 of parieto-occipital cortex 861 Cerebral cortex Skeletal bone 861 Normal Source GEO sample is GSM175950 Last updated (according to GEO): Apr 09 2007 Normal Source GEO sample is GSM176079 Last updated (according to GEO): Apr 09 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM146036 Last updated (according to GEO): Nov 20 2006 female MhmBN chip 45 Nose 1000 Spleen vs Bombesin Treated B cell 60min (set1) 1965 1955 for livers 861 Brain Fibroid_2525A Ovary 1000 none Source GEO sample is GSM123185 Last updated (according to GEO): Jul 26 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145106 Last updated (according to GEO): Nov 20 2006 Spleen vs Sphingosine-1-phosphate Treated B cell 60min (set2) V5-P296 (generalized epilepsy 2234 2254 1000 Cerebral cortex The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure. In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time Source GEO sample is GSM76950 Last updated (according to GEO): Oct 11 2005 Brain 1000 Expression profiling of spinal cord section (T8) extracted from rats 14d following mild injury Source GEO sample is GSM31425 Last updated (according to GEO): May 27 2005 Saccule structure 861 1_cerebral_cortex_3hrs_sleep_deprivation_#41 Epithelial Cells 901 Brain 1000 20 0 human caudate nucleus Mouse Liver LRD Diet 5wk 10ppb As Food Exposure, biological replicate E LDMTX_MP-15 Liver 1000 NA12751 growth 1 Myocardial Infarction 1000 Lmna H222P heterozygous male 7 Gene expression data from postmorten brain regions Source GEO sample is GSM145111 Last updated (according to GEO): Nov 20 2006 brain 0 5 skin 80 83 brain, cerebral cortex: Rat_02-41_VHL_Lipska_e1_le1 Normal__Kidney_PAN_1 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Brain 861 Pituitary Gland 861 MCF7-NCI 7 0 prostate Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68199 Last updated (according to GEO): Jul 07 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145937 Last updated (according to GEO): Nov 20 2006 1BJZ02051710_Testi_Intersitial Replicate2_Voxel E10 This dataset contains the gene expression profile of a CD11c high, CD4 positive splenic dendritic cell population. The cells were processed following 2 hour incubation in tissue culture medium at 37 C. Global scaling was applied to Avg Difference intensity values. Keywords = mouse, dendritic cells, spleen Source GEO sample is GSM4758 Last updated (according to GEO): May 27 2005 in the preimplantation uterus 105 134 Lungs 153 157 43 0 Chorionic mesoderm-derived mesenchymal cells Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep8 Spinal Cord 1000 tongue_main_corpus_1 Source GEO sample is GSM80843 Last updated (according to GEO): Mar 31 2006 CNS-SpinalCsev-Adult-14d-2B-s2 bronchial epithelia 224 243 in the PS cDKO cerebral cortex 818 847 GM07345 Gonadectomized Dahl-Iwai Male LowSalt OuterMedulla rat7 gdahl_medullar_k_GX_7om_rh_051402 Job's patient Source GEO sample is GSM211091 Last updated (according to GEO): Sep 10 2007 solid tumors 1284 1296 occipital regions 163 179 mdx diaphragm sample 1 Expression profiling of spinal cord section (T10) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM6652 Last updated (according to GEO): May 28 2005 SkinP2_022WACIW_037.txt in seminoma 28 38 Female 67.3 yr after antibody enrichment scan 2 (U133A) Occipital Lobe 9 Normal Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68330 Last updated (according to GEO): Jul 07 2006 Alzheimer's Disease 1000 embryo_at_day1.5_rep2 19 0 human frontal cortex Hippocampus 1000 no doxycycline, no AAT Source GEO sample is GSM213373 Last updated (according to GEO): Jul 26 2007 N21__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 5 0 Kidney 3_cerebral_cortex_time_0_#40 "Sample 33,>5 yr survival(138 months) age 52 erp no" on vantveer-oligo Gene expression data from postmorten brain regions Source GEO sample is GSM145970 Last updated (according to GEO): Nov 20 2006 1493 1471 These engineered tumors Treated Source GEO sample is GSM176473 Last updated (according to GEO): Apr 09 2007 1000 Hypothalamic structure V5-P255 861 Cerebral cortex leukemia 861 Placenta, primary Murine Rat Brain Injury - Rattus norvegicus mouse brain ipsilateral LPS.RU486, biological rep1 none Source GEO sample is GSM123242 Last updated (according to GEO): Jul 26 2006 26 15 endometrioid 5 0 Spleen A2780_control_16h_1 1000 Infection Exp 1 Time point 4 1000 Malignant Neoplasms Malignant melanoma is a common and frequently lethal disease. Current therapeutic interventions have little effect on survival, emphasizing the need for a better understanding of the genetic, epigenetic, and phenotypic changes in melanoma formation and progression. We identified genes that were not previously known to be silenced by methylation in melanoma using a microarray-based screen following treatment of melanoma cell lines with the DNA methylation inhibitor 5-Aza-2'-deoxycytidine. Last Updated (by provider): Sep 20 2007 Contributers: Matthew Bradbury Sekhar Duraisamy David Curley Betsy Nelson Marcus Bosenberg Cara Hobbs Viswanathan Muthusamy Primary Carcinoma 876 1000 Retina Cerebral cortex 861 GM19103 926 901 in the trigeminal ganglion 5 0 brain placenta-0687-inflamed-infected-rep1 1000 Left Mucous Membrane 861 Wild type (untreated) 5241 Bone Marrow 1000 Large cell carcinoma of lung 937 brain_OFC_bipolar B_mr351 Standard Affymetrix Protocol Source GEO sample is GSM16459 Last updated (according to GEO): May 28 2005 Myocardium 861 Nose 1000 Meningioma Primary Grade 1 Treatment, type=harvest, description=There was no treatment. Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal. Source GEO sample is GSM107992 Last updated (according to GEO): Jun 06 2006 1000 Prostate 14 0 Large Intestine 05_0010_SepticShock_Day1_95 5 0 brain 861 Lung 660 mesenchymal stem cell 639 Brain 861 angiogenesis 1000 frontal lobe Coronary Artery 4 Normal Large-scale analysis of the mouse transcriptome. Small intestine, duodenum C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 241.08 Stdv: 6.20 Min: 230.91 Max: 251.39 Source GEO sample is GSM2904 Last updated (according to GEO): May 27 2005 Embryo_E11.5_Foxo3 Null_Female olfactory epithelium 194 213 HMVEC-L stimulated without LPS for 4 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114567 Last updated (according to GEO): Sep 20 2006 5 0 brain 296 259 the most common malignant brain tumour Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68186 Last updated (according to GEO): Jul 07 2006 Placenta [JunctionChip 1 of 5] 1000 ovarian neoplasm 861 Malignant Neoplasms Medulla 861 HDMTX-9 Spleen 1000 Nanog-iPS MEF 20D16 none Source GEO sample is GSM246014 Last updated (according to GEO): Dec 03 2007 Small Pre-BII cells 3 D_U133Plus_46_HC Gene expression data from brain of adult rats Source GEO sample is GSM101024 Last updated (according to GEO): Feb 20 2007 1000 Prostate MF-21 Trachea 3 Normal /3T3 fibroblasts 295 310 Epithelium 861 Cerebellum 1000 861 Spinal Cord the diaphragm 753 765 3AJZ02051002_AdrenalCortex 901 Coronary artery Expression profile of genes in normal and Down syndrome mouse brains Expression profiling of spinal cord section (T8) extracted from rats 24h following mild injury Source GEO sample is GSM31434 Last updated (according to GEO): May 27 2005 1393 1383 to vascular 1000 Kidney CNS-SCsev_InjA14d-2A-s2 Primary small cell lung carcinoma 2760 Source GEO sample is GSM17341 Last updated (according to GEO): May 28 2005 Mesenchymal Stem Cells 1000 CHIPEXP_NAME: 230_2_050531tpj_33h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Isoproterenol TREAT_TOX_MECHANISM1: Heart_Cardiotoxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0.5 SAMPLING_TIME: 1 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197607 Last updated (according to GEO): Jun 01 2007 B220+CD25+sIg- Large Pre BII cells sorted out of mouse bone marrow, sort no. 10 Source GEO sample is GSM643 Last updated (according to GEO): Mar 20 2006 Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM152012 Last updated (according to GEO): Feb 06 2007 Kidney; FVB/N Folic Acid toxic injury Keywords = mouse gene expression database Source GEO sample is GSM29365 Last updated (according to GEO): May 27 2005 brain, cerebral cortex: Rat_03-42_NroLep_Lipska_e1_le1 1000 Prostate Blood 861 amygdala_2 Source GEO sample is GSM80566 Last updated (according to GEO): Mar 31 2006 Pancreas [JunctionChip 2 of 5] Backskin_DN-CLIM_P14_rep2 Sample3, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53254 Last updated (according to GEO): Jul 06 2005 Blood 861 of the most anterior dorsal root ganglia 23 62 Tumor__Breast_Adeno_95_I_029 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A 861 Cardiomyopathies of coronary artery disease 317 342 CX43 KO vs WT cortical astrocytes 1000 Spleen a_NY18 861 Neoplasm Standard Affymetrix Protocol Source GEO sample is GSM15865 Last updated (according to GEO): May 28 2005 AML cDNA hybridization-ID09-L Coronary Arteriosclerosis 1000 1000 Pancreas 952 937 to an epidermis- Prosencephalon 1000 the blood 393 402 corpus_callosum_3 Source GEO sample is GSM80622 Last updated (according to GEO): Mar 31 2006 with advanced bladder cancer 71 98 Normal Source GEO sample is GSM176161 Last updated (according to GEO): Apr 09 2007 Prostate 861 SP-WT-Nrf2-Female-2 Cerebral cortex 861 N/A Source GEO sample is GSM96297 Last updated (according to GEO): Feb 13 2006 Large cell neuroendocrine carcinoma 901 Infection 1000 human cerebellum Source GEO sample is GSM87176 Last updated (according to GEO): Feb 08 2006 CAD_replicate78 n/a Source GEO sample is GSM178012 Last updated (according to GEO): Jun 11 2007 12 0 ovarian tumor from nose 100 108 PBMCs-Type 1 Diabetes-IDDM41_T1D_1MO Lung 861 CNS-SC_Inj7d-2C-s2c Parkinson Disease 861 in human gastric cancers 37 60 Neostriatum 1000 Primary Neoplasm 1000 1037 of transitional epithelium 1012 Male2, Respiratory RNA_Nasal respiratory epithleium_Tissue was preserved in RNA later and collected from nose Mesenchymal Stem Cells 1000 1000 Uterus stomach_pyloric_2 Source GEO sample is GSM80814 Last updated (according to GEO): Mar 31 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with BLC for 240min Source GEO sample is GSM5472 Last updated (according to GEO): May 27 2005 Meningioma Primary Grade 1 Source GEO sample is GSM108024 Last updated (according to GEO): Jun 06 2006 Control rat 2 substantia nigra Source GEO sample is GSM32159 Last updated (according to GEO): May 27 2005 Cortex_Control_rep3 (05SE1757) Chronic leukemia NOS 913 The gene expression level was presented as ratio of sample intensity against reference intensity. Source GEO sample is GSM159964 Last updated (according to GEO): Feb 01 2007 861 Cerebral cortex Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118343 Last updated (according to GEO): Jul 11 2006 Supranuclear Palsy, Progressive 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145472 Last updated (according to GEO): Nov 20 2006 256 235 with HIV encephalitis Whole blood from a patient with essential tremor Source GEO sample is GSM153466 Last updated (according to GEO): Jan 11 2007 228 219 Hippocampi 24 19 (Renal Nicotinic Receptors 1000 Infertility 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145113 Last updated (according to GEO): Nov 20 2006 91 from the bone marrow 72 77 66 Normal Heart Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184788 Last updated (according to GEO): Apr 26 2007 ER negative human primary breast tumor EA02014_41285_H133A_JA-1821 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12379 Last updated (according to GEO): May 28 2005 BXD33_M7SS02042212 GM18859 CNS-SC_InjA7d-2A-s2 MET-302 on UMich-10k NA12746 growth 1 brain, cerebral cortex: NMDA 2_le1 prostate Source GEO sample is GSM203268 Last updated (according to GEO): Jun 21 2007 1000 Descending colon Category: Serum-response Subcategory: Fibroblasts Scanning Software: unknown Software version: unknown Lot batch = 322 Source GEO sample is GSM2156 Last updated (according to GEO): Nov 21 2005 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215075 Last updated (according to GEO): Aug 02 2007 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12365 Last updated (according to GEO): May 28 2005 R703P01230 Epithelial Cells 1000 7 Entorhinal Cortex 23 Parkinson Disease 861 H9LMS99081601 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc64 Source GEO sample is GSM1890 Last updated (according to GEO): Nov 21 2005 The nose 94 101 Autistic Disorder 1000 1000 frontal lobe Wild type olfactory epithlium 2 hpO replicate2 Gene expression data for comparing control-fed 30-month-old to 5-month-old mice to investigate effect of aging and comparing calorie restricted-fed 30-month-old to control-fed 30-month-old to investigate effect of calorie restriction. Keywords = kidney, aging, calorie restriction Source GEO sample is GSM7463 Last updated (according to GEO): May 27 2005 861 Brain Study of in vitro granulocyte differentiation Source GEO sample is GSM137438 Last updated (according to GEO): Jun 06 2007 Two prognostically significant subtypes of high-grade lung neuroendocrine tumors independent of small-cell and large-cell neuroendocrine carcinomas identified by gene expression profiles. BACKGROUND: Classification of high-grade neuroendocrine tumors (HGNT) of the lung currently recognises large-cell neuroendocrine carcinoma (LCNEC) and small-cell lung carcinoma (SCLC) as distinct groups. However, a similarity in histology for these two carcinomas and uncertain clinical course have led to suggestions that a single HGNT classification would be more appropriate. Gene expression profiling, which can reproduce histopathological classification, and often defines new subclasses with prognostic significance, can be used to resolve HGNT classification. METHODS: We used cDNA microarrays with 40386 elements to analyze the gene expression profiles of 38 surgically resected samples of lung neuroendocrine tumors and 11 SCLC cell lines. Samples of large-cell carcinoma, adenocarcinoma, and normal lung were also included to give a total of 105 samples analyzed. The data were subjected to filtering to yield informative genes before unsupervised hierarchical clustering that identified relatedness of tumor samples. FINDINGS: Distinct groups for carcinoids, large-cell carcinoma, adenocarcinoma, and normal lung were readily identified. However, we were unable to distinguish LCNEC from SCLC by gene expression profiling. Three independent rounds of unsupervised hierarchical clustering consistently divided SCLC samples into two main groups with LCNEC samples largely integrated with these groups. Furthermore, patients in one of the groups identified by clustering had a significantly better clinical outcome than the other (83% vs 12% survived for 5 years; p=0.0094. None of the highly proliferative SCLC cell lines subsequently analyzed clustered with this good-prognosis group. INTERPRETATION: Our findings show that HGNT of the lung can be classified into two groups independent of SCLC and LCNEC. To this end, we have identified many genes, some of which encode well-characterized markers of cancer that distinguish the HGNT groups. These results have implications for the diagnosis, classification, and treatment of lung neuroendocrine tumors, and provide important insights into their underlying biology.. Date GSE1037 Last Updated: May 29 2005 Contributers: Virtanen Carl Ishikawa Yuichi Jones Michael Yuichi Ishikawa Daisuke Ishikawa Carl Virtanen Michael H Jones Includes GDS619. Update date: Jul 12 2004. Dataset description GDS619: Molecular classification of lung high-grade neuroendocrine tumor (HGNT) groups. Carcinoids, large-cell carcinoma, adenocarcinoma, small-cell lung carcinoma cell lines, and normal lung examined.. Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 2 hours after lights on. Original RNA code = LC21A. Source GEO sample is GSM227399 Last updated (according to GEO): Sep 10 2007 ovarian tumor: endometrioid Source GEO sample is GSM139404 Last updated (according to GEO): Apr 09 2007 Spleen 1000 150 mg/kg X 12 hr Source GEO sample is GSM129894 Last updated (according to GEO): Sep 18 2007 1500 mg/kg X 12 hr Source GEO sample is GSM129880 Last updated (according to GEO): Sep 18 2007 brain, hippocampus: KA24-III_e1_le1 1000 Spleen 861 Cerebral cortex n/a Source GEO sample is GSM178016 Last updated (according to GEO): Jun 11 2007 1000 Endometriosis, site unspecified 868 850 of medulloblastoma pooled RNA of the kidney of 36 day old rats Source GEO sample is GSM86658 Last updated (according to GEO): Jun 12 2006 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Dimaprit for 120min Source GEO sample is GSM5538 Last updated (according to GEO): May 27 2005 M_95A_3076_CB_1_GS Probeset expression data from NA12741 growth 1 Source GEO sample is GSM201526 Last updated (according to GEO): Aug 08 2007 Mek exp2 PD98059 901 Bone Marrow 983 Secondary Glioblastoma from the cerebellum 20 38 Simple annotation: Lymph node metastasis, Lung Cancer Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10569.gif Source GEO sample is GSM76458 Last updated (according to GEO): Sep 22 2006 brain, unknown: UTC_e1_le1 A VIS D032 frontal lobe 861 NHF10-hTERT_1.5Gy_2h_C5_21706 Cortex Source GEO sample is GSM53366 Last updated (according to GEO): Jul 06 2005 CNS-SC_InjA24h-2C-s2 Acetaminophen 24hr Rat 2483 left_liver_lobe vs. Control Acetaminophen 24hr Rat left_liver_lobe Pool 1000 Brain Gene expression data from purified granule neuron precursors. Source GEO sample is GSM148579 Last updated (according to GEO): Mar 14 2007 Pooled Total Prefrontal cortex RNA from 4 female FVB/N mice. Source GEO sample is GSM14620 Last updated (according to GEO): May 28 2005 AML_13 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Wild type inbred mice Source GEO sample is GSM83015 Last updated (according to GEO): Nov 10 2005 Hereditary Malignant Neoplasm 876 AD control Treatment, type=dissect Source GEO sample is GSM119674 Last updated (according to GEO): Jul 10 2006 1000 Brain Nasal Epithelium 865 1000 Neoplasm LCM Somatic_3wk. ovary_FVB C57L/J Cingulate Cortex C PGA_MI_nilv_1h_395 1000 ovarian neoplasm CAKI-1 (CL9015) RENAL 861 Mammary gland Melanoma xenograft, SM_Sub_A (LeiFidler) umbilical cord_bpd: 6H Structure of entorhinal cortex 1000 cerebral_cortex_10 660 mesenchymal stem cell 639 861 Carcinoma 861 Autosome 868 849 in the hypothalamus Gene expression data from a placenta with chronic malaria Source GEO sample is GSM183615 Last updated (according to GEO): Apr 23 2007 861 Encephalitis GSE374 1000 Brain Leg 112 Day control rep 1 Mammary; Involution Keywords = mouse gene expression database Source GEO sample is GSM29398 Last updated (according to GEO): May 27 2005 ventral striatum wistar ky 3960 freehand block dissections, removed only cortex, individual animal, 10 weeks old, male Wistar Kyoto ventral striatum file:p3960w Source GEO sample is GSM15182 Last updated (according to GEO): Oct 28 2005 T27__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A PGA_PA-N_118 Brain 861 CNS-RM_Mod7d-3A-s2 between the LAD artery 266 287 prostate-ca-C-TEST-11 on NHGRI-6.5k_b Replicate3_Voxel F5 comparison of corticosterone-treated and control rats with depressive-like behaviour Source GEO sample is GSM247389 Last updated (according to GEO): Dec 11 2007 M7TW00121356 G3 Temp. Retina from ventral prostate 21 41 1000 frontal lobe GC (HKG10T) 73 54 of hyperinsulinaemic 12 CN A Gene expression data from postmorten brain regions Source GEO sample is GSM145034 Last updated (according to GEO): Nov 20 2006 Brain 861 This is a wildtype littermate at postnatal day 1 pool of 5 animals Lot batch = Source GEO sample is GSM4055 Last updated (according to GEO): May 28 2005 1140 1134 in ALS General Paralysis 885 Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 5886 left_liver_lobe 1000 Kidney brain, cerebral cortex: Control_le1 Wild type 8 wk old male 129S6/SvEvTac mouse pituitary gland Source GEO sample is GSM74998 Last updated (according to GEO): Feb 27 2007 Solid tumor 983 that mesenchimal stem cells 360 386 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114237 Last updated (according to GEO): Jun 16 2006 1000 Brain B2-5 on NCI-7.6k Control 2 plasma cells 50 61 875 Common Neoplasm Adipose tissue 901 Bone Marrow 1000 Organ 966 Communicable Diseases 861 V5-P122 901 Alzheimer's Disease in gastric adenocarcinoma 38 62 108 FC BA9 A A2780_cis_IC90_2h_2 from the cerebellum 20 38 861 medulloblastoma Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2776 Source GEO sample is GSM2095 Last updated (according to GEO): Nov 21 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145858 Last updated (according to GEO): Nov 20 2006 1037 of transitional epithelium 1012 D_U133Plus_109_nAcc 1000 Brain 708 661 (cytoskeletal-cell membrane-extracellular matrix heart 1169 1173 Hippocampus_WildType_rep1 CNS-SMTC_Ctr3mo-2B-s2 eye, retina: 1 Retina at ZT 6_e1_le1 Gene expression data from postmorten brain regions Source GEO sample is GSM145479 Last updated (according to GEO): Nov 20 2006 1BMH02022803_Uterus none Source GEO sample is GSM123192 Last updated (according to GEO): Jul 26 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145754 Last updated (according to GEO): Nov 20 2006 Expression profiling of moderately injured raphe at 3 months in rats Source GEO sample is GSM41606 Last updated (according to GEO): May 27 2005 Brain 861 from brain 21 30 B6:23-11-20 choroid plexus Spleen 0 5 plasma cells 332 344 Disease Source GEO sample is GSM175802 Last updated (according to GEO): Apr 09 2007 mouse hippocampus 0 17 Hippocampal cultures at DIV 12 were infected with either As-aCaN or Ad-LacZ, or were uninfected Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Source GEO sample is GSM35389 Last updated (according to GEO): May 27 2005 f2#306 versus pool Mouse Brain tissue Male 23.4 yr before antibody enrichment scan 1 (U133B) esophagus_2 Medulla Oblongata 861 Communicable Diseases 1000 none Source GEO sample is GSM210331 Last updated (according to GEO): Jul 16 2007 Expression data from rat mammary tumors with varying invasive phenotyes none Source GEO sample is GSM244596 Last updated (according to GEO): Nov 23 2007 Wild type 8 wk old male 129S6/SvEvTac mouse hypothalamus Source GEO sample is GSM107018 Last updated (according to GEO): Mar 05 2007 LPS, 20 min, Rep_2 nasal epithelial cells 28 49 plasma cells 50 61 A39 WT4 F25/17 A39 wild type Mouse 4 months Cerebellum Female Source GEO sample is GSM73200 Last updated (according to GEO): Sep 06 2005 SN:Human Glioblastoma Biopsy 10393 861 HIV Infections osteoblast 630 640 mouse cerebral cortex 0 20 Testes 1 Normal mild cognitive impairment - primary visual cortex 1 biopsy sample obtained from a 3-year-old male Duchenne Muscular Dystrophy patient Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15836 Last updated (according to GEO): Sep 08 2006 Epithelium of bronchus 983 MF-34 861 Kidney Diseases RR200_unifected_Skin_biopsy Cerebral cortex 861 3 0 Lung Control total RNA, pooled from the kidney of five normal BALB/c mice, was used as a reference against total RNA extracted from the kidney of BALB/c mice injected with anti-GBM antibody for 1, 3, 7, 11 and 16 days. This SuperSeries is composed of the following subset Series: GSE954: Day 1 anti-GBM mouse GSE955: Day 3 anti-GBM mouse GSE956: Day 7 anti-GBM mouse GSE957: Day 11 anti-GBM mouse GSE958: Day 16 anti-GBM mouse. Date GSE969 Last Updated: Apr 25 2006 Contributers: Ju-Han Kim Dong-Sup Lee Seung-Hee Yang Yun-Anna Cao Ji-Hoon Kim Sangdun Choi Yon-Su Kim Chang-Il Hwang Woong-Yang Park Young-Ju Lee Il-Soo Ha Includes GDS580. Update date: May 10 2004. Dataset description GDS580: Gene expression profiling of anti-glomerular basement membrane (GBM) glomerulonephropathy model. Analysis of kidney tissue of BALB/c mice injected with anti-GBM antibody for 1, 3, 7, 11 or 16 days.. 865 Disorder of artery Expression profiling of mRNA abundance in the adult mouse olfactory epithelium during replacement of OSNs forced by the bilateral ablation of the olfactory bulbs. The experiment was done on 6 week old male C57Bl/6 mice. Olfactory epithelium tissue samples were collected on days 1, 5, and 7 after bulbectomy. The cellular processes activated by bulbectomy include apoptosis of mature olfactory sensory neurons, infiltration of macrophages and dendritic cells, stimulation of proliferation of basal cell progenitors, and differentation of new sensory neurons. Last Updated (by provider): Dec 13 2005 Contributers: Soma C Bose Timothy S McClintock Andrew M Harris Debra H Hardin Jeremy C McIntyre Melissa D Nickell Ranjit S Shetty Includes GDS1431. Update date: Apr 06 2006. Dataset description GDS1431: Analysis of the olfactory epithelium at various time points up to 5 days following olfactory bulbectomy. Olfactory bulbectomy performed to force the replacement of olfactory sensory neurons. Results provide insight into the cellular events involved in olfactory neurogenesis.. cd4+Tcell Source GEO sample is GSM18672 Last updated (according to GEO): May 27 2005 1000 Pancreas cerebral cortex 7 21 Alternative pre-messenger RNA (pre-mRNA) splicing plays important roles in development, physiology, and disease, and more than half of human genes are alternatively spliced. To understand the biological roles and regulation of alternative splicing across different tissues and stages of development, systematic methods are needed. Here, we demonstrate the use of microarrays to monitor splicing at every exon-exon junction in more than 10,000 multi-exon human genes in 52 tissues and cell lines. These genome-wide data provide experimental evidence and tissue distributions for thousands of known and novel alternative splicing events. Adding to previous studies, the results indicate that at least 74% of human multi-exon genes are alternatively spliced. Normal Source GEO sample is GSM175886 Last updated (according to GEO): Apr 09 2007 The objective of this study was to test the hypothesis that innate differences in gene expression in the brain could contribute to the differences in alcohol drinking or response to alcohol between adult male inbred alcohol-preferring (iP) and -non-preferring (iNP) rats. Gene expression was determined in the nucleus accumbens (ACB), amygdala (AMYG), frontal cortex (FC), caudate-putamen (CPU) and hippocampus (HIP) of alcohol-naïve adult male iP and iNP rats, using Affymetrix Rat Genome U34A microarrays (n = 6/strain). Significant differences between the two strains for each region were determined using Statistical Analysis of Microarrays (SAM). Using a false discovery rate threshold of 0.2, there were 46 genes with higher expression in iP rats and 61 genes with lower expression in the ACB, 111 genes with higher and 56 genes with lower expression in the AMYG, 61 genes with higher and 25 genes with lower expression in the FC, 39 genes with higher and 42 genes with lower expression in the CPU, and 35 genes with higher and 51 genes with lower expression in the HIP. In the AMYG, iP rats had higher expression of genes that are involved in neuronal growth and neurogenesis, e.g., brain derived neurotrophic factor, neuritin, etc. In contrast, in the ACB, iP rats had lower expression of genes involved in neurogenesis or cellular plasticity, e.g. cyclin E, vascular endothelial growth factor A. Many of the differences were in genes involved in intracellular signaling, cell membranes, extracellular matrix, and metabolism. These regional gene differences between the iP and iNP rat lines may contribute to the divergent alcohol drinking phenotypes of these rats. Last Updated (by provider): Feb 20 2007 Contributers: William J McBride Mark W Kimpel Howard J Edenberg Lucinda G Carr Jeanette N McClintick Wendy N Strother 5 0 brain Parkinson Disease 861 Wild type inbred mice Source GEO sample is GSM82905 Last updated (according to GEO): Nov 10 2005 Prefrontal Cortex 0 16 Parkinson's disease sample x185 CS-B cell unirradiated replicate 3 U133B in bronchial epithelia 311 332 Sample represents the supraoptic nucleus from 5 dehydrated animals (3 Days) Source GEO sample is GSM69458 Last updated (according to GEO): Dec 15 2005 Epithelium 861 Disorder of artery 865 in the brain 150 162 from the femurs 95 109 human caudate nucleus Source GEO sample is GSM86883 Last updated (according to GEO): Feb 08 2006 1000 Epilepsy 40 21 from skeletal muscle Tissue transferred into RNAlater within 30 minutes of removal, and frozen at -20C Source GEO sample is GSM9095 Last updated (according to GEO): May 28 2005 Spleen 260 265 5 0 brain WGACON-256 CNS-RM_Ctr28d-1C-s2 low gestational age Source GEO sample is GSM213077 Last updated (according to GEO): Jul 25 2007 861 Cardiomyopathies Femur 1000 Head and neck cancer Source GEO sample is GSM155665 Last updated (according to GEO): Apr 24 2007 Knockout 8 months old, female Source GEO sample is GSM154344 Last updated (according to GEO): Jan 09 2007 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 5 day time point Source GEO sample is GSM159767 Last updated (according to GEO): Apr 23 2007 1000 Temporal Lobe in breast tumors 1075 1090 at the Human Brain 743 760 Coronary heart disease 913 MGJZ030212069Aumbilicalcord TUMOR 8 0 6 of Parkinson's disease 450 471 Ganglia, Spinal 923 43 29 from the kidney RNA from Lymphoblastoid Cell Line from this individual Source GEO sample is GSM213297 Last updated (according to GEO): Jul 26 2007 with acute measles 20 37 at the Human Brain 726 743 1500mg/kg APAP 12Hr rat 4132 blood vs. PC 12Hr rat 4126 blood CNS-SC_CtrB7d-2B-s2 901 Caudate nucleus structure of gut neurospheres 39 57 Ganglia, Spinal 923 1000 Spleen Gene expression data of substantia nigra from postmortem brain of PD patients Source GEO sample is GSM184378 Last updated (according to GEO): May 29 2007 of 12 saccules 5 18 78 73 rectum B396 on Affymetrix GeneChip Human Full Length Array HuGeneFL N37__normal on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Liver (HBV+, HK84) 320 291 of human oral epithelial cells 402 392 of diabetes 5 0 brain PBMCs-Type 1 Diabetes-IDDM50_T1D_4MO Skeletal muscle structure 1000 Richard Almon-27-1133800609589 1000 Ciliary Body 43 0 Chorionic mesoderm-derived mesenchymal cells 861 Blood T-ALL-2M#1 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A To screen for output signals that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared relative to SCN2.2 cells in vitro and the rat SCN in vivo. Similar to the circadian profiling of the SCN2.2 and rat SCN transcriptomes, NIH/3T3 fibroblasts exhibited rhythmic fluctuations in the expression of the core clock genes, Per2, Bmal1, and Cry1 and 323 functionally-diverse transcripts (2.6%), many of which regulate cellular communication. Overlap in rhythmically-expressed transcripts among NIH/3T3 fibroblasts, SCN2.2 cells and the rat SCN was limited to these clock genes and four other genes that mediate fatty acid and lipid metabolism or function as nuclear factors. Compared to NIH/3T3 cells, circadian gene expression in SCN oscillators was more prevalent among genes mediating glucose metabolism and neurotransmission. Coupled with evidence for the rhythmic regulation of the inducible isoform of nitric oxide synthase (Nos) in SCN2.2 cells and the rat SCN but not in fibroblasts, studies examining the effects of a NOS inhibitor on metabolic rhythms in co-cultures containing SCN2.2 cells and untreated NIH/3T3 cells suggest that the gaseous neurotransmitter nitric oxide may play a key role in SCN pacemaker function. Thus, comparative analysis of circadian gene expression in SCN and non-SCN cells may have important implications in the selective analysis of circadian signals involved in the coupling of SCN oscillators and regulation of rhythmicity in downstream cells. Source GEO sample is GSM132987 Last updated (according to GEO): Sep 12 2006 Osteoblasts 1000 Acetaminophen 6hr Rat 4145 blood vs. Acetaminophen 6hr Rat Pooled Control blood GM06995_technical_rep_2 urethra_1 Source GEO sample is GSM80911 Last updated (according to GEO): Mar 31 2006 cerebral cortex wistar ky 3912 LymphomaRaji Source GEO sample is GSM18892 Last updated (according to GEO): Sep 25 2006 Gene expression data from embryos at day 2.5. Source GEO sample is GSM176485 Last updated (according to GEO): Mar 19 2007 913 Coronary heart disease Leukemia, Prolymphocytic 1000 1000 Adipocytes Murine NK cell were purified from wild type C57Bl/6 mice (>99% NK1.1+CD3-) and immediately lysed in Trizol and assessed for gene expression on Affy MOE430_2 microarray Source GEO sample is GSM188001 Last updated (according to GEO): May 09 2007 of lipid 317 324 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113899 Last updated (according to GEO): Jun 16 2006 T45__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Expression profiling of moderately injured raphe at 24h in rats Source GEO sample is GSM41579 Last updated (according to GEO): May 27 2005 Gene expression data from postmorten brain regions Source GEO sample is GSM145931 Last updated (according to GEO): Nov 20 2006 brain, ipsi Cortex: Trizol Extraction8_le1 Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 3482 blood NCI60.25_LABEL29EXTRACT28SUB3 Source GEO sample is GSM134115 Last updated (according to GEO): Aug 06 2007 913 Coronary heart disease Spleen vs Lipopolysaccharide (LPS) Treated B cell 120min (set2) Normal Source GEO sample is GSM175984 Last updated (according to GEO): Apr 09 2007 Otic placode at E9, replicate2 Gene expression data from purified granule neuron precursors. Source GEO sample is GSM148575 Last updated (according to GEO): Mar 14 2007 Renal Cell Carcinoma - Papillary types 1 0 40 1000 Synapses GBM Treatment, type=remove Source GEO sample is GSM99547 Last updated (according to GEO): Apr 21 2006 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211249 Last updated (according to GEO): Jul 18 2007 Gene expression data from postmorten brain regions Source GEO sample is GSM145253 Last updated (according to GEO): Nov 20 2006 20 0 Lymph Node || lc4b007 MuscleRegen-ctx20d-2RLbAv2-s2 Hyperdip>50-#11 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A NO_KIDNEY_7 HCC (HBV+, SF35, 3) brain, Right Frontal Lobe: Extract62_le2 PriG_5%O2_Expt3_Day14_rep1 Seminoma 1000 6 stomach 0 Lateral Sclerosis 901 928 Endometrium 861 Muscle Caudal thirds 21 33 in cervical cancer 58 75 ileum 1000 tissue sample collected post mortem from control rhesus macaques (not SIV infected) full description of sample found in Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS. (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol. Jun;162(6):2041-57. Keywords = HIV, NeuroAIDS, brain, encephalitis, AIDS, rhesus macaques, SIV Source GEO sample is GSM44898 Last updated (according to GEO): May 27 2005 67 40 with coronary artery disease Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210415 Last updated (according to GEO): Jul 16 2007 1000 Encephalitis C57BL/6J Basal Ganglia D ileum 1000 1000 Kidney Failure in the brain 150 162 Parkinson Disease 1000 human frontal cortex Source GEO sample is GSM86949 Last updated (according to GEO): Feb 08 2006 nostrils 156 164 from brain 21 30 SCN2.2 Sample 24 (Exp#3-24 hr) 507 498 antibodies Blood 1000 Temporal Cortex Alzheimer's disease 8 (1 utricle 11 20 Normal Source GEO sample is GSM176268 Last updated (according to GEO): Apr 09 2007 brain 0 5 tibiae 115 120 D_U133Plus_117_nAcc From naive male C57BL/6 mice (20-25 g), a 4 mm diameter disk of parieto-occipital cortex was removed and immediately frozen in chilled 2-methylbutane then stored at -80C. 3 mouse cortex disks were pooled prior to RNA extraction. Source GEO sample is GSM44469 Last updated (according to GEO): May 27 2005 CHIPEXP_NAME: 230_2_050531tpj_41h LIMS_SITE: Nutley_3 CHIP_TYPE: RAT230_2 TREATMENT: Isoproterenol TREAT_TOX_MECHANISM1: Heart_Cardiotoxic TISSUE_OR_CELL_TYPE: Heart DOSE_AMOUNT: 0.5 SAMPLING_TIME: 3 PROJECT: ISO_TG STUDY_NO: 9143 Source GEO sample is GSM197618 Last updated (according to GEO): Jun 01 2007 865 Disorder of artery 875 Blood Cells Cerebral cortex 861 Sample User: jmorris Description: ALL-post patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:222, Count:32 Corner- Avg:39136, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:8.201396,SFGene:All Background:Avg:442.52,Stdev:39.36,Max:494.3,Min:339.0 Noise:Avg:9.21,Stdev:0.52,Max:11.0,Min:8.1 RawQ:13.25 Keywords = ALL Source GEO sample is GSM3413 Last updated (according to GEO): May 27 2005 NCI60.38_LABEL42EXTRACT41SUB3 Source GEO sample is GSM134181 Last updated (according to GEO): Aug 06 2007 Cerebral cortex 1000 1000 Liver 1433 from the epithelial cells 1458 hypothalamus_1 91 from the bone marrow 72 Transitional epithelium 1000 Nicotine-hippocampus, biological rep5 Bone Marrow 1000 4535 4527 hepatoma brain, amygdala: Amygdala 6_le1 V5-P597 cerebral cortex 7 21 NA18517 Normal Source GEO sample is GSM175983 Last updated (according to GEO): Apr 09 2007 Macrophage 14smi111 853 Refractory Carcinoma "Sample 23,>5 yr survival(62 months) age 41 erp yes" on vantveer-oligo Myocardial Infarction 1000 ileum 861 Coronary artery 901 VDXIGRU_171558 22-oct-2002-liverE-Mu11KsubAsc proteoglycans 309 321 Standard Affymetrix Protocol Source GEO sample is GSM16462 Last updated (according to GEO): May 28 2005 Substantia nigra PD rep14 brain_DLPFC_bipolar C_mr546 Spleen vs Anti-IgM Treated B cell 60min (set1) Expression profiling of somatomotor cortex extracted from rats at 24h following sham surgery Source GEO sample is GSM41640 Last updated (according to GEO): May 27 2005 Macrophage smi97 GSE6678 1000 Cerebellum Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225965 Last updated (according to GEO): Nov 02 2007 from colonic normal mucosa 21 47 Expression profiling of spinal cord section (T9) extracted from rats 24h following mild injury Lot batch = Source GEO sample is GSM4468 Last updated (according to GEO): May 28 2005 913 Coronary heart disease Structure of horn of uterus 884 Spleen vs CGS Treated B cell 240min (set2) salivary Source GEO sample is GSM67245 Last updated (according to GEO): Jan 19 2006 884 Malignant neoplasm of brain Primary Neoplasm 1000 19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip. Keywords = Heart, Cardiac, Assist Device, LVAD, GATA-4, Sprouty1, microarray, heart failure Source GEO sample is GSM14948 Last updated (according to GEO): Oct 28 2005 Spleen 1000 5 0 brain 15 0 human cerebellum 94 61 after human immunodeficiency virus Testis 1000 Recurrent Squamous cell carcinoma 6 Gene expression data from postmorten brain regions Source GEO sample is GSM145026 Last updated (according to GEO): Nov 20 2006 Skeletal bone 861 Nose 1000 Expression profiling of moderately injured raphe at 14d in rats Source GEO sample is GSM41564 Last updated (according to GEO): May 27 2005 Brain 861 brain, hindbrain and spinal cord: P0WT2_e1_le1 Levitiracetam brainstem 7 Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53432 Last updated (according to GEO): Jul 06 2005 0029_1264_H95A2_KF145_v5p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Parkinson Disease 861 brain, cerebral cortex: Rat_02-127_TTX_Lipska_e1_le1 brain, frontal cortex: ADX PM DR_e1_le1 78 66 Control blood 20 15 liver with some respiratory epithelium. 1039 1072 Replicate2_Voxel B7 Brain 861 152 117 Keywords = congenital heart disease 1000 Prostate Gene expression in eukaryotes is tightly linked to the methylation state of specific lysine residues within the N-terminal region of the core histone proteins. While the mechanisms connecting histone lysine methylation to effector protein recruitment and control of gene activity are increasingly well understood, it remains unknown whether non-histone chromatin proteins are targets for similar modification-recognition systems. Here we show that histone H3 and the H3 methyltransferase G9a share a conserved methylation motif that is both necessary and sufficient to mediate in vivo interaction with the potent epigenetic regulator Heterochromatin Protein 1 (HP1). As with H3, G9a-HP1 interaction is dependent on lysine methylation and can be reversed by adjacent phosphorylation. NMR analysis demonstrates that the HP1 chromodomain recognizes methyl-G9a through a binding mode similar to that used in recognition of methyl-H3, and that adjacent phosphorylation directly antagonizes G9a-HP1 interaction. In addition to uncovering the chromodomain as a generalized methyl-lysine binding module, these data identify histone-like modification cassettes (or ?histone mimics?) as an entirely new class of non-histone methylation targets, and directly demonstrate the relevance of the principles underlying the histone code to the regulation of non-histone proteins. Last Updated (by provider): Jul 16 2007 Contributers: Alexander Tarakhovsky Srihari C Sampath PGA-MCR-ctr-4h-1aAv2-s1 of Parkinson's disease 450 471 Gene expression data from the neocortex of S1P2-knockout mouse Source GEO sample is GSM172940 Last updated (according to GEO): Mar 08 2007 Expression profiling of spinal cord section (T9) extracted from rats 4h following mild injury Lot batch = Source GEO sample is GSM6664 Last updated (according to GEO): May 28 2005 Expression profiling of spinal cord section (T9) extracted from rats 72h following moderate injury Source GEO sample is GSM31574 Last updated (according to GEO): May 27 2005 67 52 descending colon Activated Source GEO sample is GSM176286 Last updated (according to GEO): Apr 09 2007 Head and neck cancer Source GEO sample is GSM155713 Last updated (according to GEO): Apr 24 2007 9 0 Blood Test Coronary artery 901 no doxycycline, mutant Source GEO sample is GSM213386 Last updated (according to GEO): Jul 26 2007 C57BL/6J_female_hypothalamus Source GEO sample is GSM138568 Last updated (according to GEO): Apr 18 2007 861 medulloblastoma 4525 4520 liver Alk shRNA, biological rep1 Simple annotation: Primary tumor, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18169.gif Source GEO sample is GSM91599 Last updated (according to GEO): Sep 22 2006 none Source GEO sample is GSM161909 Last updated (according to GEO): Feb 16 2007 in retinal 153 162 858 Mesodermal cell ovarian tumor: endometrioid Source GEO sample is GSM139403 Last updated (according to GEO): Apr 09 2007 D15 12h TLR2/1L Lung Source GEO sample is GSM18950 Last updated (according to GEO): Sep 25 2006 from colonic normal mucosa 21 47 VDXGUYU_4014 861 Acquired Immunodeficiency Syndrome Plasma 861 Control Acetaminophen 6hr Rat left_liver_lobe Pool vs. Acetaminophen 6hr Rat 1376 left_liver_lobe Biopsy of a colorectal adenoma from patient #29 1000 Rectum 1000 Hippocampus Lung 861 cortex from B6 mice at ZT21 rep1 Source GEO sample is GSM160461 Last updated (according to GEO): Feb 05 2007 brain, hippocampi, left: Sham AM Hypo_e1_le1 1000 Primary carcinoma of the liver cells brainstem 7 15 Plasma 861 Medial #1 none Source GEO sample is GSM123247 Last updated (according to GEO): Jul 26 2006 39 21 from mammary glands 1000 Cerebrum Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211285 Last updated (according to GEO): Jul 18 2007 913 Coronary heart disease Lymphoblastic Leukemia 901 861 Brain Primary combined SCLC-AD 1870 PGA-Csx_het_4b-m4 T20__tumor on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A GSE6306 Nose 1000 by trauma 73 81 17 7 hippocampus PGA-E18.5_2A Disorder of artery 865 Ta gr2 tumour Source GEO sample is GSM2476 Last updated (according to GEO): May 27 2005 hrs nasal epithelium 1127 1147 1000 Brain Cerebellum 1000 Nasal Epithelium Inhalation Formaldehyde 0ppm 5d ID63 1000 Brain Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184767 Last updated (according to GEO): Apr 26 2007 861 Oocytes Exp A, Animal #3, 50mg/kg CPF Gene expression data from male F344 rats treated with a single dose of 50mg/kg of CPF for 96 hours Source GEO sample is GSM246143 Last updated (according to GEO): Dec 03 2007 Brain 1000 Mouse old brain C30-Br-4 Hippocampus 1000 1000 Infection nic + nmda2 (Experiment Neuroprotection4- Run 21823) Treatment, type=timepoint, description=Same sample used for Experiment Neuroprotection4-Run 14985, samples were rerun due to oven failure, measurement=0.0 h Source GEO sample is GSM96699 Last updated (according to GEO): Feb 14 2006 1000 Skin ANIMALS Patched heterozygous mice (Goodrich et al., 1997) were obtained from Matthew Scott?s lab at Stanford, and maintained by breeding with 129X1/SvJ mice from Jackson Laboratories. Math1-GFP transgenic mice (Lumpkin et al., 2003) were provided by Jane Johnson at UT Southwestern Medical Center. Math1-GFP/patched+/- mice were generated by crossing patched heterozygotes with Math1-GFP mice, and then backcrossing to Math1-GFP mice three times before further analysis. All mice were maintained in the Cancer Center Isolation Facility at Duke University Medical Center. ISOLATION OF CELLS Granule cell precursors (GCPs) were isolated from 7-day-old (P7) patched+/- mice; preneoplastic cells were obtained from 6 week-old patched mutants; and tumor cells were obtained from 10-25-week old patched mutants displaying physical and behavioral signs of medulloblastoma. Cells were isolated from each source using a protocol described in (Wechsler- Reya and Scott, 1999). Briefly, cerebella were digested in solution containing 10 U/ml papain Oliver et al. Pre-Neoplastic Stage of Medulloblastoma - 8 - (Worthington, Lakewood, NJ) and 250 U/ml DNase (Sigma) and triturated to obtain a cell suspension. This suspension was centrifuged through a step gradient of 35% and 65% Percoll (Amersham Biosciences, Piscataway, NJ), and cells were harvested from the 35%-65% interface. Cells were resuspended in serum-free culture medium consisting of Neurobasal containing B27 supplement, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen, Carlsbad, California) and counted on a hemacytometer. Cells used for RNA isolation were centrifuged and flash frozen in liquid nitrogen. For proliferation assays or immunostaining, cells were plated on poly-D-lysine (PDL)-coated tissue culture vessels and incubated in serum-free culture medium. MICROARRAY HYBRIDIZATION AND ANALYSIS RNA from GCPs, pre-neoplastic cells and tumor cells (isolated as described above, but not FACS-sorted) and from normal adult cerebellum (not dissociated) was converted to cDNA using the Superscript Choice cDNA kit (Invitrogen) and a T7-dT(24) primer (Genset/Proligo, Boulder, CO). cRNA was generated using a T7-transcription/labeling kit from Enzo Life Sciences and hybridized to Affymetrix U74Av2 chips (Affymetrix, Santa Clara, CA). Chips were scanned, and hybridization data were acquired using Affymetrix Suite 5.0 software. Affymetrix CEL files were normalized and quantified using Bioconductor software with the gcRMA model to quantify gene expression levels (Gentleman and Carey, 2002). Unsupervised principal components analysis (PCA) was used to identify the relationships among normal adult cerebellum, GCPs, pre-neoplastic cells and tumor cells based on expression profiles. To identify genes that were differentially expressed among GCPs, pre-neoplastic cells and tumor cells, supervised analysis was carried out. A gene-by-gene ANOVA model with three groups (GCP, pre-neoplastic, tumor) was used to fit the log2-transformed intensities. To correct for multiple comparisons, the nominal p-value was adjusted using the false discovery rate (Benjamini and Hochberg, 1995). Genes were considered to be differentially expressed if they satisfied all of the following criteria: a difference in expression greater than 1.9-fold between any two groups, a maximum absolute intensity difference larger than 32 units, and an adjusted pvalue < 0.01. There were 118 genes that met these criteria. The identities of differentially expressed genes were verified by integrating data from the Affymetrix and Unigene databases. Gene functions were determined using information from Gene Ontology, Unigene, LocusLink and PubMed databases. Clustering was performed with Cluster and Treeview (Eisen et al., 1998). All statistical analysis was performed using R-1.7 software (Dalgaard, 2002). Results were visualized with Spotfire 6.0 (Somerville, MA). CORRESPONDING AUTHOR Robert J. Wechsler-Reya* Dept. of Pharmacology & Cancer Biology, Duke University Medical Center Box 3813, Durham, NC 27710 Phone: 919-613-8754. Fax: 919-668-3556. Email: rw.reya@duke.edu Keywords = medulloblastoma Keywords = brain tumor Source GEO sample is GSM45624 Last updated (according to GEO): Oct 28 2005 in blood 16 23 Sample13, Post Injury 4 hours Treatment, type=wait Source GEO sample is GSM53264 Last updated (according to GEO): Jul 06 2005 Recurrent Carcinoma 875 Substantia Nigra 10 Normal I_U133A_114_Amy 1000 Pituitary Gland Tumor__Lung_Adeno_009_C on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Control brainstem 1 Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days. Source GEO sample is GSM53440 Last updated (according to GEO): Jul 06 2005 901 Mammary gland Brain 1000 spinal_cord_1 Central gray substance of midbrain 861 1000 Optic Nerve Collagen 1000 Nucleus accumbens, male 10.5 week old c57bl/6J mouse, NON-DEFEATED control Source GEO sample is GSM224737 Last updated (according to GEO): Aug 31 2007 Epithelium 861 861 Oocytes of infection 110 121 70 40 without coronary artery disease 861 Muscle 5 0 brain Cortex_Control_rep1 (05SE731) Expression profiling of moderately injured raphe at 3 months in rats Source GEO sample is GSM41601 Last updated (according to GEO): May 27 2005 Muscle 861 affy original enzo kit processing Source GEO sample is GSM120461 Last updated (according to GEO): Jul 17 2006 5 0 brain 1000 Hippocampus Mouse_E13.5_Front_Middle_Back_12 plasma cells 332 344 11 0 Hypothalamus Huntington Disease 861 Spleen 1000 Epithelial Cells 1000 Liver Test (Blinded) Sample Source GEO sample is GSM130161 Last updated (according to GEO): Sep 18 2007 Pressure-overload induced hypertrophy model. Mouse was sacrificed 48 hours after aortic banding. Keywords = Cardiac hypertrophy Source GEO sample is GSM2242 Last updated (according to GEO): May 27 2005 7 cerebral cortex 21 HUVEC isolate 36 low serum media VEGF-A 4hours cf. #11 Source GEO sample is GSM12905 Last updated (according to GEO): May 28 2005 430A2_2045_44_KO_sham_midbrain Source GEO sample is GSM242700 Last updated (according to GEO): Nov 15 2007 WGACON-131 Nose 1000 Kidney 861 M_U133A_5_DLPFC_R 901 Coronary artery Muscle Source GEO sample is GSM4287 Last updated (according to GEO): May 27 2005 901 Coronary artery Transitional epithelium 1000 353 338 (rostral, caudal NA18545 40 21 from the hippocampus Primary tumor 19 32 861 Colon total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Platelet activating factor for 30min Source GEO sample is GSM5721 Last updated (according to GEO): May 27 2005 5 0 brain Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211410 Last updated (according to GEO): Jul 18 2007 Sample is skeletal muscle from obese patient undergoing elective abdominal surgery Source GEO sample is GSM3999 Last updated (according to GEO): May 28 2005 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225756 Last updated (according to GEO): Nov 02 2007 gfp neg. sorted cells from 3 disected e14.5 cortecies Treatment, type=wait Source GEO sample is GSM135779 Last updated (according to GEO): Sep 12 2006 Muscle 884 NA18942 875 Blood Cells PrEC on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 12 frontal Lobe 23 n/a Source GEO sample is GSM177923 Last updated (according to GEO): Jun 11 2007 Disease Source GEO sample is GSM175794 Last updated (according to GEO): Apr 09 2007 861 Lung Wnt signaling plays a key role in development and adult tissues via effects on cell proliferation, motility, and differentiation. The cellular response to Wnt ligands largely depends on their ability to stabilize beta-catenin and the ability of beta-catenin to bind and activate T-cell factor (TCF) transcription factors. Roughly 40% of ovarian endometrioid adenocarcinomas (OEA) have constitutive activation of Wnt signaling as a result of oncogenic mutations in the beta-catenin protein or inactivating mutations in key negative regulators of beta-catenin, such as the adenomatous polyposis coli and Axin tumor suppressor proteins. We used oligonucleotide microarrays to identify genes of which expression was activated in OEAs with beta-catenin dysregulation compared with OEAs lacking Wnt/beta-catenin pathway defects. Using microarray and quantitative PCR-based approaches, we found that fibroblast growth factor (FGF9) expression was increased >6-fold in primary OEAs with Wnt/beta-catenin pathway defects compared with OEAs lacking such defects. Evidence that beta-catenin and TCFs regulate FGF9 expression in several epithelial cell lines was obtained. We found FGF9 was mitogenic for epithelial cells and fibroblasts and FGF9 could stimulate invasion of epithelial and endothelial cells through Matrigel in transwell assays. Furthermore, FGF9 could promote neoplastic transformation of the E1A-immortalized RK3E epithelial cell line, and short hairpin RNA-mediated inhibition of endogenous FGF9 expression in the OEA cell line TOV112D, which carries a beta-catenin mutation, inhibited neoplastic growth properties of the cells. Our findings support the notion that FGF9 is a key factor contributing to the cancer phenotype of OEAs carrying Wnt/beta-catenin pathway defects. Epithelium 861 MSS-Spa-sev-3moM-1aAv2-s2 1000 Hippocampus Normal Source GEO sample is GSM175897 Last updated (according to GEO): Apr 09 2007 Gene expression data from mouse bone marrow macrophages Source GEO sample is GSM211407 Last updated (according to GEO): Jul 18 2007 none Source GEO sample is GSM123248 Last updated (according to GEO): Jul 26 2006 Plasma 861 Fibroblasts 861 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28740 Last updated (according to GEO): May 27 2005 plasma cells 332 344 testis 52 58 5 0 brain Parkinson Disease 1000 Sun208_TAV12 group Acetaminophen 3hr Rat 3482 blood vs. Acetaminophen 3hr Rat Pooled Control blood Epithelial Cells 901 NoCAD_replicate16 heart failure 583 595 Cerebral cortex 861 17 7 hippocampi NCI-H522 hgu95d Nose 1000 861 Cancer of Neck Primary Neoplasm 1000 CA01-103B (high density lipoprotein 522 546 352 347 brain PGA-MPF-C57-bleo-72h-1bAv2-s2 f2#347 versus pool Mouse Brain tissue park_1152_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A MuscleRegen-ctx12h-2LLAv2-s2 Blood 861 human caudate nucleus Source GEO sample is GSM86919 Last updated (according to GEO): Feb 08 2006 Melanoma metastatic cell line A375, biological rep5 (LeiATCC) NICM pool 4 (n=4) Huntington Disease 861 Leukemia, Lymphocytic, Chronic 1000 Intestines 1000 1000 Infection no additional Source GEO sample is GSM199138 Last updated (according to GEO): Jun 08 2007 1000 Spleen Brain 861 Brain_Melanotransferrin Knockout_affs275-1097 /SvEvTac cingulate cortex rep2 5 34 861 Communicable Diseases no additional Source GEO sample is GSM199130 Last updated (according to GEO): Jun 08 2007 1000 Muscle Epithelium 861 901 frontal lobe Lymphoblastoid Cell Line for Individual 8213.5 log phase Analysis of chromosome copy number in leukemic cells by different microarray platforms. 861 Cardiomyopathies Gene expression data from postmorten brain regions Source GEO sample is GSM145083 Last updated (according to GEO): Nov 20 2006 (Breast 77 84 Brain 861 labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156589 Last updated (according to GEO): Jan 22 2007 861 Skeletal bone 1180 1163 other chromosomes Tumor__Mesothelioma_300_T on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Large Pre-BII cells 1_2 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy Keywords = pathological hypertrophy Keywords = rat Keywords = heart failure Keywords = cardiomyopathy Source GEO sample is GSM11883 Last updated (according to GEO): May 28 2005 Epithelium 861 861 Neoplasm Standard Affymetrix Protocol Source GEO sample is GSM15853 Last updated (according to GEO): May 28 2005 serotonin receptor 901 Ovarian_Tumor_Mucinous_UM-OM-01 Coronary Arteriosclerosis 1000 Wnt (32 h) B on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A Myocardium 861 1000 Brain Post-mordem human hypothalamus total RNA samples were obtained from Ambion (Austin, TX). All total RNA samples has an agilent ratio greater than 1 indicating there had been no degredation. The causes of death varied as well as the age at death, but averaged aproximately 70 years of age. The total RNA samples were labeled for hybridization onto the microarray according to affymetrix protocols listed at: http://keck.med.yale.edu/affymetrix/protocols Keywords = Sex Specific Transcription, Human, Affymetrix, Healthy Mammalian Tissue Source GEO sample is GSM19199 Last updated (according to GEO): May 27 2005 861 Pancreas post HCMV infection 72 90 1BJZ02081480b_Pons 32 12 frontal temporal lobe Cerebral cortex 1000 1000 Spleen brain, forebrain: Sample9_e1_le1 10 Bone marrow 0 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12363 Last updated (according to GEO): May 28 2005 861 Brain C17 on NCI-7.6k Hippocampus of HuD overexpressor mice. Perrone-Bizzozero-5R01NS030255-12 osteoblast 627 637 FACS purified cortical projection neurons Whole Brain 73 83 Left hemidiaphragm 884 bone marrow; flushed from femur Source GEO sample is GSM18663 Last updated (according to GEO): May 27 2005 brain, amygdala: Sham AM A_e1_le1 Ta gr2 tumour Source GEO sample is GSM2504 Last updated (according to GEO): May 27 2005 Parkinson's model voxel D3 Primary Neoplasm 1000 Muscle 1000 CS-B cell UVC-irradiated (2hour) replicate 2 U133A frontal lobe 901 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the lv samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12338 Last updated (according to GEO): May 28 2005 Muscle 51 56 Layer 6 pyramidal neurons in cigulate cortex which project to medial dorsal thalamus. Source GEO sample is GSM63034 Last updated (according to GEO): Dec 01 2005 24h1 Synaptic activity-regulated gene expression_embryonic day 14 Neuroblastoma 1000 861 Duodenum 861 Chondrocytes 1000 Cerebrovascular accident WGACON-274 NA18561 12mo APPSw #2 Seminoma 1000 5 0 Spleen Cerebral cortex 861 /tf Olfactory Bulb A 10 29 forebrain 7 15 HapMap YRI_parent Female Source GEO sample is GSM159704 Last updated (according to GEO): Feb 01 2007 brain, unknown: 00PX_e1_le1 Spinal cord [JunctionChip 5 of 5] Disease Source GEO sample is GSM176441 Last updated (according to GEO): Apr 09 2007 91 from the bone marrow 72 with autism spectrum disorder 37 65 no additional Source GEO sample is GSM199400 Last updated (according to GEO): Jun 08 2007 none Source GEO sample is GSM244570 Last updated (according to GEO): Nov 23 2007 Heart 1000 Skeletal bone 861 PMN_LB_180min_Patient17 DNA Damage 1000 858 Mesodermal cell 1506 1497 IV gliomas SCLC cell line DMS53 Source GEO sample is GSM17307 Last updated (according to GEO): May 28 2005 901 Cerebral cortex Germ free Rectum 2 901 frontal lobe Spleen 1000 Gene expression changes induced by alpha-secretase cleaved amyloid precursor protein (sAPPalpha) in organotypic hippocampal slice cultures of male, postnatal day 15 mice (C57B6/SJL). Hippocampal slice cultures were treated with phosphate buffered saline (GSM26700, GSM26701, GSM26702) or 1 nM sAPPalpha (GSM26703, GSM26704, GSM26705) for 24 h. Each sample consists of total RNA isolated from 8-12 slices from 4 mice. Data were analyzed with MAS 5.0 and scaled to 2500. sAPPalpha induces the amyloid sequestration protein transthyretin, insulin-like growth factor 2, insulin-like growth factor binding protein 2, and other genes involved in protective pathways such as apoptosis inhibition, detoxification, and retinol transport. See Stein, TD, Anders, NJ, DeCarli, C, Chan, SL, Mattson, MP, and Johnson JA. Neutralization of transthyretin reverses the neuroprotective effects of secreted APP in APPSw mice resulting in tau phosphorylation and loss of hippocampal neurons: support for the amyloid hypothesis. J Neurosci. in press. Last Updated (by provider): Oct 28 2005 Contributers: Jeffrey A Johnson Thor D Stein Includes GDS809. Update date: Nov 15 2004. Dataset description GDS809: Expression profiling of hippocampal slice cultures treated with 1 nM alpha-secretase cleaved amyloid precursor protein (sAPPalpha) for 24 hours. Hippocampi obtained from 15 day postnatal C57B6/SJL males. Results provide insight into the neuroprotective activity of sAPPalpha.. Gene expression profile of the cell line UB/OC-1 grown at 33C (undifferentiated, day 0). This data set is a replica experiment of sample GSM1533. Genome Research 12(7):1091-1099, 2002. Source GEO sample is GSM1545 Last updated (according to GEO): May 27 2005 brain, cerebral cortex: Rat_03-59_NroLep_Lipska_e1_le1 Myocardial Infarction 1000 Mesenchymal Stem Cells 1000 ACHN hgu95d M-22-12-UN on UMich-10k beta-thymosin 707 720 267 250 the growth plates Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11485 Last updated (according to GEO): May 28 2005 861 Longitudinal 247 233 cerebral palsy 9 0 Blood Test Tumor__Bladder_TCC_B_0001 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Nose 1000 Timepoint6 brain, Right Frontal Temporal: Extract67_le2 human Duchenne muscular dystrophy 525 557 Nasal Epithelium Inhalation Formaldehyde 07ppm 6h ID127 Expression profiling of spinal cord section (T9) extracted from rats 14d following severe injury Source GEO sample is GSM31599 Last updated (according to GEO): May 27 2005 Substantia nigra structure 1000 Gene expression data from postmorten brain regions Source GEO sample is GSM145595 Last updated (according to GEO): Nov 20 2006 tongue_main_corpus_2 cortex from B6 mice at ZT3 rep1 Source GEO sample is GSM160452 Last updated (according to GEO): Feb 05 2007 Otic vesicle at E9.5, replicate1 Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141307 Last updated (according to GEO): Oct 26 2006 Kidney; Day 2 postnatal Keywords = mouse gene expression database Source GEO sample is GSM29360 Last updated (according to GEO): May 27 2005 no additional Source GEO sample is GSM199388 Last updated (according to GEO): Jun 08 2007 1BMH02022801_Whole Brain with some respiratory epithelium. 1039 1072 B10.PL mice with severe (stage 2.5-3) experimental autoimmune encephalomyelitis were treated with placebo or 200 ng 1,25(OH)2D3. Six hours later, the spinal cords were harvested and mRNA was extracted for microarray analysis. Naive mice serve as controls. Individual samples were hybridized to individual microarrays.. Date GSE842 Last Updated: May 29 2005 Contributers: Tsuyoshi Kayo Faye E Nashold Karen M Spach Brian S Yandell Colleen E Hayes Tomas A Prolla Laura B Pedersen Includes GDS510. Update date: Mar 18 2004. Dataset description GDS510: Examination of effect of 200 ng 1,25-dihydroxyvitamin D3 (1alpha,25-(OH)2D3) on B10.PL mice with severe (stage 2.5-3) experimental autoimmune encephalomyelitis (EAE), a model of multiple sclerosis (MS). Spinal cord tissue examined.. GC (HKG7T) Endometrium 6 Normal Blood B cells;anti-IgM 24h midbrain_2 567 548 the descending colon 320 306 Keywords = HIV Endometrium 1000 Nerve 861 of chromosome 16 61 76 between the LAD artery 266 287 Melanoma xenograft, MC2_Sub_A (LeiATCC) n/a Source GEO sample is GSM178001 Last updated (according to GEO): Jun 11 2007 none Source GEO sample is GSM149555 Last updated (according to GEO): Jan 03 2007 NZW/LacJ_male_hypothalamus Recommended Affymetrix protocols were followed. Source GEO sample is GSM148467 Last updated (according to GEO): May 01 2007 Hep2_40_rep1 Expression profiling of spinal cord section (T9) extracted from rats 30m following laminectomy (sham) Lot batch = Source GEO sample is GSM1332 Last updated (according to GEO): May 28 2005 Heart 861 H131 CB A ALL-B-cell-15 on Affymetrix GeneChip Human Full Length Array HuGeneFL 42 30 Control blood Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD). Source GEO sample is GSM151982 Last updated (according to GEO): Feb 06 2007 of the normal mucosa 7 26 of the postmortem brains 676 700 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181190 Last updated (according to GEO): Jul 12 2007 GM18507_technical_rep_1 HOP-62_CL1026_NSCLC 246-97_SCC_p Gene expression data from human colon tumor tissue Source GEO sample is GSM173365 Last updated (according to GEO): Apr 20 2007 Expression profiling of spinal cord section (T9) extracted from rats 7d following mild injury Lot batch = Source GEO sample is GSM6668 Last updated (according to GEO): May 28 2005 1BJZ02052113_TestiSeminiferousTubule Alzheimer's Disease 861 CNS-SC_Inj24h-3B-s2b HOXB4ERT-LSK+ cells_ 4 hours after TMX withdrawal Source GEO sample is GSM228747 Last updated (according to GEO): Sep 13 2007 Epithelium of bronchus 983 E9 91 from the bone marrow 72 FormerSmoker 72 1000 Organ of Corti Mental Retardation 1000 n/a Source GEO sample is GSM177936 Last updated (according to GEO): Jun 11 2007 brain, hippocampi, left: pADX AM Hypo_e1_le1 1000 Coronary Arteriosclerosis Standard Affymetrix Protocol Source GEO sample is GSM16454 Last updated (according to GEO): May 28 2005 PBMCs-Healthy-H149_Healthy neurological disease control sample x150 MGMH030212058Aspinalcordupper labeling, hybridization, and data extraction performed by ExonHit Therapeutics Source GEO sample is GSM156715 Last updated (according to GEO): Jan 22 2007 861 Liver 1000 Prostate brain 0 5 89 70 isolated theca cells Day 1 Mouse #12 - 2nd replicate 32h-AC replication 1 Keywords = preimplantation Keywords = development Source GEO sample is GSM14716 Last updated (according to GEO): May 28 2005 Brain 861 Ovary_PD1_Foxo3 Null_Replica 1 Cochlear structure 1000 DCIS30 on harvard-12k Primary Carcinoma 876 SN:1022994;Fetal Cartilage, biological rep2 validation Normal Source GEO sample is GSM176213 Last updated (according to GEO): Apr 09 2007 PMN_LB_360min_Patient2 1000 Heart Brain 861 CC8 sample 1 Whole blood from a patient with Alzheimer's disease Source GEO sample is GSM153474 Last updated (according to GEO): Jan 11 2007 861 Neoplasm Brain 861 Barcode: 251316210184 Source GEO sample is GSM159386 Last updated (according to GEO): Jul 17 2007 Expression profiling of somatomotor cortex extracted from rats at 3 months following sham surgery Source GEO sample is GSM41658 Last updated (according to GEO): May 27 2005 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215067 Last updated (according to GEO): Aug 02 2007 Spleen 1000 Heart 1000 1000 frontal lobe kidney Source GEO sample is GSM18688 Last updated (according to GEO): May 27 2005 from the femurs 95 109 2hr time point after 3 Gy of IR exposure Source GEO sample is GSM10968 Last updated (according to GEO): May 28 2005 858 Mesodermal cell of 9 saccules 5 17 CNS-RM_Ctr4h-1B-s2 Breast 1000 brain, cerebral cortex: Rat_03-21_NroLep_Lipska_e1_le1 G9a-WT Expression profiling of spinal cord section (T8) extracted from rats 30m following mild injury Source GEO sample is GSM31443 Last updated (according to GEO): May 27 2005 5 0 Uterus hippocampus: Sample #2_e1_le2 Mc1: Hippocampus_5T-Y_rep2 1000 Brain 1000 Hippocampus mouse brain 478 489 1000 Rett Syndrome 1000 Brain Thymus_022EACHK_t1b.txt 21 0 Heart failure sample 1 Brain 861 89 70 isolated theca cells 36 21 from whole brain 1000 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145159 Last updated (according to GEO): Nov 20 2006 SCLC cell line Lu-134a Source GEO sample is GSM17310 Last updated (according to GEO): May 28 2005 1000 Structure of entorhinal cortex 901 Coronary artery KidE185_0221ACJ8_109.txt of the colon 28 39 Gene expression data from liver Source GEO sample is GSM243355 Last updated (according to GEO): Nov 16 2007 mouse brains 187 198 Branch 861 f2#299 versus pool Mouse Brain tissue AO Treatment, type=remove Source GEO sample is GSM99521 Last updated (according to GEO): Apr 21 2006 Date : 1/21/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 9 d.p.c., Theiler stage 14 Tissue : forebrain & surrounding tissue Treatments applied Agent : methylmercury Route : single i.p. injection Dose : 5.0 mg/kg Time : 4.5 hrs post-injection Intervention : none Risk: estimated 20% increased risk for encephalopathy Conditional biomarker: no p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 10-12 forebrains pooled from two litters Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots Keywords = methylmercury Keywords = forebrain Keywords = embryo Keywords = Fetal Minamata Disease Lot batch = AD605 Source GEO sample is GSM12248 Last updated (according to GEO): May 28 2005 of parieto-occipital cortex 120 146 Expression profiling of spinal cord section (T8) extracted from rats 7d following mild injury Source GEO sample is GSM31454 Last updated (according to GEO): May 27 2005 Job's patient Source GEO sample is GSM211100 Last updated (according to GEO): Sep 10 2007 Hippocamp0227AC38_003.txt 861 Oocytes Primary Carcinoma 876 67 40 with coronary artery disease Rats (3 per time point) were housed in a tightly controlled environment with light:dark cycles of 12 hours each and were sacrificed at 18 times within the 24 hour.This animal was sacrificed at 23 hours after lights on.Original sample code = CM53A Source GEO sample is GSM227315 Last updated (according to GEO): Sep 10 2007 Carcinoma 861 PCA33_localized prostate cancer Brain 1000 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114252 Last updated (according to GEO): Jun 16 2006 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11315 Last updated (according to GEO): May 28 2005 901 frontal lobe 28 0 Fetal frontal cortex cocaine4 Affymetrix GeneChip® Mouse Genome 430 2.0 Array Source GEO sample is GSM197125 Last updated (according to GEO): May 31 2007 58 41 with endometriosis 211 202 Ta tumors 861 Blood (No additional Information) Source GEO sample is GSM114397 Last updated (according to GEO): Jun 19 2006 for liver 26 35 Carcinoma 861 1216 1208 Carcinoma Leukemia, Myelocytic, Acute 861 861 Colon Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes Source GEO sample is GSM141280 Last updated (according to GEO): Oct 26 2006 D_U133A_72_DLPFC brain 0 5 Although dystrophin mutations are the proximate cause of Duchenne muscular dystrophy (DMD), interactions among heterogeneous downstream mechanisms may be key phenotypic determinants. Temporal gene expression profiling was used to identify and correlate diverse transcriptional patterns to one another and to the disease course, for both affected and spared muscle groups, in postnatal day 7-112 dystrophin-deficient (mdx) mice. While 719 transcripts were differentially expressed at one or more ages in leg muscle, only 56 genes were altered in the spared extraocular muscles (EOM). Contrasting molecular signatures of affected versus spared muscles provide compelling evidence that the absence of dystrophin alone is necessary but not sufficient to cause the patterned fibrosis, inflammation and failure of muscle regeneration characteristic of dystrophinopathy. Dystrophic and adaptive changes in the microarray profiles were further quantified using an aggregate disease load index (DLI) to measure stage-dependent transcriptional impact in both muscles. DLI analysis highlighted the divergent responses of EOM and leg muscle groups. Cellular process-specific DLIs in leg muscle identified positively correlated temporal expression profiles for some gene classes, and the independence of others, that are linked to major disease components. Data also showed a previously unrecognized transient and selective developmental delay in pre-necrotic mdx skeletal muscle that was confirmed by qPCR. Taken together, validation and targeting of signaling pathways responsible for the coordination of the fibrotic, proteolytic and inflammatory mechanisms shown here for mdx muscle may yield new therapeutic means of mitigating the devastating consequences of DMD. the frontal cortex 107 124 Biopsy of a colorectal adenoma from patient #24 tTA 7308 HapMap YRI_parent Female Source GEO sample is GSM159702 Last updated (according to GEO): Feb 01 2007 21 0 Temporal lobe epilepsy Whole neuroblastoma tumor_2259 Liver Test (Blinded) Sample Source GEO sample is GSM130141 Last updated (according to GEO): Sep 18 2007 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12962.gif Source GEO sample is GSM79970 Last updated (according to GEO): Sep 22 2006 brain, hippocampus: PR-CA3-4_e1_le1 Osteoblasts 1000 Gene expression data from brain of adult rats Source GEO sample is GSM101036 Last updated (according to GEO): Feb 20 2007 1000 Brain 24 skeletal muscle 10 1000 Solid tumor M_U133A_13_DLPFC Frontal Lobe 8 Normal Communicable Diseases 1000 VDXOXFU_869 43 0 Chorionic mesoderm-derived mesenchymal cells no additional Source GEO sample is GSM199355 Last updated (according to GEO): Jun 08 2007 1000 Descending colon Day 5_L_-LIF_Achip CNS-SCsev_InjA28d-3B-s2 3AJZ02022867_Pituitary 1368 1353 by brain injury Cisplatin, a platinating agent commonly used in treating several cancers is associated with nephrotoxicity, neurotoxicity and ototoxicity that have hindered its utility. To gain a better understanding of the genetic variants associated with cisplatin induced toxicity, we present a step-wise approach integrating genotypes, gene expression and sensitivity of HapMap cell lines to cisplatin. Cell lines derived from 30 trios of European descent (CEU) and 30 trios of African descent (YRI) were utilized to develop a preclinical model to identify genetic variants and gene expression that contribute to cisplatin induced cytotoxicity in two different populations. Cytotoxicity was determined as cell growth inhibition at increasing concentrations of cisplatin for 48 h. Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip® Human Exon 1.0 ST Array. We identified 6, 2 and 9 representative SNPs that contribute to cisplatin-induced cytotoxicity through their effects on 8, 2 and 16 gene expressions in the combined, CEPH and Yoruban populations, respectively. These genetic variants contribute to 27, 29 and 45% of the overall variation in cell sensitivity to cisplatin in the combined, CEPH and Yoruban populations, respectively. Our whole genome approach can be used to elucidate expression quantitative trait loci contributing to a wide range of cellular phenotypes. Last Updated (by provider): Jun 06 2007 Contributers: John E Blume Emily O Kistner R S Huang Sunita J Shukla Tyson A Clark Shiwei Duan Tina X Chen M E Dolan Anthony C Schweitzer lg_NY10 nostrils 156 164 HUMANCULTUREDADIPOCYTE Source GEO sample is GSM18817 Last updated (according to GEO): Sep 25 2006 SCG_sema3A_5h_rep1 None Source GEO sample is GSM198095 Last updated (according to GEO): Jul 16 2007 PGA-E18.5_1 861 Brain 1000 Cytoskeleton 1000 ovarian neoplasm Spinal Cord 1000 Lymphoblastic Leukemia 901 ko mouse number 2 Source GEO sample is GSM187137 Last updated (according to GEO): Jun 11 2007 Fibroblasts 861 mouse brain 478 489 Skeletal bone 861 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy, pathological hypertrophy, rat, heart failure, cardiomyopathy Source GEO sample is GSM12308 Last updated (according to GEO): May 28 2005 Nasal Epithelium 901 901 Stem cells brain, hippocampus: CON-DG-A8_e1_le1 brain, hippocampus: Sample24_e1_le1 070302_HF_301MB with progressive supranuclear palsy 27 61 CNS-SpinalCmod-Adult-28d-1B-s2 MLL-C6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 861 Cerebral cortex -_test-3_batch5 on NHGRI-6.7k 36 21 from whole brain 5 0 Spleen Brain 861 352 347 brain Fibroblasts 861 5 0 brain Lymphoblastoid Cell Line for Individual 8153.3 log phase 43 0 Chorionic mesoderm-derived mesenchymal cells Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 3 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10960 Last updated (according to GEO): May 27 2005 Mesenchymal Stem Cells 1000 Collagen 1000 V5-P502 Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132485 Last updated (according to GEO): Feb 26 2007 Ova C3H 1 vs control C3H pool Whole genome expression profiling reveals a significant role for immune function in human abdominal aortic aneurysms. 928 Endometrium Large-scale analysis of the mouse transcriptome. Striatum C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 239.34 Stdv: 8.95 Min: 229.80 Max: 259.97 Source GEO sample is GSM2923 Last updated (according to GEO): Mar 20 2006 Whole ganglioneuroma tumor_1377 na Source GEO sample is GSM181286 Last updated (according to GEO): Apr 10 2007 Coronary heart disease 913 Gene expression data from human colon tumor tissue Source GEO sample is GSM173346 Last updated (according to GEO): Apr 20 2007 Integumentary system 1000 Z1 juvenile biol repl 2 Squamous epithelial cell 861 Macrophage 14smi096 Brain 50 55 861 Cerebral cortex Prostate 15 Disease 0 18 HMVEC-L stimulated without LPS for 24 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114573 Last updated (according to GEO): Sep 20 2006 D_U133Plus_116_nAcc C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 6 hour after the last shock treatment. Source GEO sample is GSM4523 Last updated (according to GEO): May 27 2005 10 0 Endometrium Human infertility 0 16 testis 52 58 mammarygland.3 Brain 1000 Male 13-week-old ddY mice (Japan SLC Co., Hamamatsu, Japan) weighing 38-43 g were used. Dose of 25 mg/kg thioridazine HCl (Sigma-Aldrich Co) was used in the study. The drug was dissolved in acetic anhydride and diluted with 0.9% saline, resulting in a final concentration of acetic acid of 0.5%. The drugs were injected intraperitoneally once daily for 28 consecutive days in a volume of 0.1 ml/10 g body weight. Microarray experiments were performed using an Agilent G4121A Mouse Oligo Microarray Kit as per the manufacturer?s instructions. The frontal cortex was immediately removed and the RNA was stabilized in RNAlater RNA Stabilization Reagent (Qiagen, Valencia, CA) and stored at -80°C until use. Total RNA was extracted using the RNeasy Mini Kit (Qiagen). The RNA was amplified and labeled by the Low RNA Input Fluorescent Linear Amplification Kit (Agilent). To synthesize cDNA, 200 ng total RNA was used. Vehicle-injected controls were labeled by cyanine 3 (PerkinElmer Life Sciences, Inc., Boston, MA) and drug-injected mice were labeled by cyanine 5. Hybridizations to the microarray were performed using the In situ Hybridization Kit Plus (Agilent). Doses of 750 ng cyanine 3-labeled cRNA, 750 ng cyanine 5-labeled cRNA, and control targets were mixed and fragmented in the kit?s fragmentation buffer, and then hybridized to the microarrays for 17 hours at 60°C in a hybridization rotator (Agilent) set to rotate at 4 rpm. Microarrays were washed in 6×SSC with 0.005% Triton X-102 at RT for 10 min, followed by 0.1×SSC with 0.005% Triton X-102 at 4°C for 5 min. The slides were dried, and then scanned by the Agilent G2565BA Microarray Scanner System. Data were analyzed using the Agilent Feature Extraction Software version 7.1. A rank consistency filter and LOWESS were used for dye normalization. Control mice and drug-injected mice were processed in parallel. Keywords = thioridazine Lot batch = US22502606_16011978017256 Source GEO sample is GSM25983 Last updated (according to GEO): Oct 28 2005 5 0 Spleen Normal Source GEO sample is GSM175951 Last updated (according to GEO): Apr 09 2007 HC65 FC BA4 A Blood Test (Blinded) Sample Source GEO sample is GSM130047 Last updated (according to GEO): Sep 18 2007 Uterus (corpus) [JunctionChip 3 of 5] Plasma 861 the most common mesenchymal tumors 41 74 Wild type 8 wk old male C3H/HeJ mouse pituitary gland Source GEO sample is GSM107047 Last updated (according to GEO): Mar 05 2007 Human Cell Line, adrenal medulla: RNA617_le1 Rats were housed in a tightly controlled environment with light:dark periods of 12h each. 3 animals per time point were sacrificed at 18 different times within the 24h. This animal was sacrificed at 12.25 hours after lights on. Original RNA code = LC46A. Source GEO sample is GSM227369 Last updated (according to GEO): Sep 10 2007 (cortex 19 25 H9LMS00102611 901 frontal lobe Spleen vs Platelet activating factor Treated B cell 60min (set1) Pool of total RNA from 3 Ts1Cje cerebella (segmental trisomy of chromosome 16) at P30 postnatal stage Keywords = Down syndrome Keywords = Chromosome 21 Keywords = Transcriptome Keywords = Microarray Keywords = Brain Keywords = Cerebellum Keywords = Development Source GEO sample is GSM27482 Last updated (according to GEO): May 27 2005 Mouse_E13.5_Front_Middle_Back_5 1000 Brain Heart 1000 I + P T-Cell 06.00 hr. Mesenchymal Stem Cells 1000 861 Bone neoplasms 2_hypothalamus_9hrs_sleep_deprivation_#82 whole blood_100315 Small cell carcinoma of lung 901 1000 Brain SN:Human Glioblastoma Biopsy 06486 Nervous system structure 901 Primary Neoplasm 1000 pull-downC_4, ZT6 ovarian tumor: endometrioid Source GEO sample is GSM139414 Last updated (according to GEO): Apr 09 2007 Ovarian_Tumor_Endometrioid_UM-OE-1T Amygdala 10 Normal 3AJZ02021915_ LIVER 901 Caudate nucleus structure Spleen 1000 Primary tumor 19 32 in prostate cancer 85 103 UO-31_CL9004_Renal on Affymetrix GeneChip Human Full Length Array HuGeneFL Cell Culture: Hippocampal cells from E18 rat embryos were plated at a density of 500,000 cells per 60 mm poly-L-lysine (1mg/ml; Sigma) coated dish. Cultures were maintained at 37 C in 5% CO2 humidified incubator and used for experiments at 21 day in vitro (DIV). Control and experimental group cultures were incubated with 10 micro M TTX for 15 min followed by addition of 100 micro M baclofen or vehicle. Total RNA preparation: Each experimental group was compared as replicates of three. For each replicate cultured hippocampal neurones were harvested after 2 hours incubation +/- baclofen and total RNA was isolated using RNeasy Mini kit (Qiagen, UK) according to the manufacturer's protocol. Microarray Target Labelling and Hybridisation: Targets for cDNA microarrays were generated using 5 micro g of total RNA in a standard reverse transcription (RT) reaction. RNA was annealed, in 16 micro l water, with 1 micro g of 24-mer poly(dT) primer (Invitrogen, UK), by heating at 65oC for 10 min and cooling on ice for 2 min. The RT reaction was performed by adding 8 micro l of 5X first strand RT buffer (Life technologies, MD), 4 micro l of 20mM dNTPs minus dCTP (Pharmacia, UK), 4 micro l of 0.1M DTT, 40U of RNAse OUT (Life Technologies, MD), 6 micro l of 3000 Ci/mmol 33P-dCTP (ICN Biomedicals, UK) to the RNA/primer mixture to a final volume of 40 micro l. Two micro l (400 U) of Superscript II reverse transcriptase (Life Technologies, MD) was then added and the sample incubated for 30 min at 42oC followed by additional 2 micro l of Superscript II reverse transcriptase and another 30 min incubation. The reaction was stopped by addition of 5 micro l 0.5 M EDTA. Samples were incubated at 65oC for 30 min after addition of 10 micro l of 0.1M NaOH to hydrolyse and remove RNA. Samples were pH neutralized with 45 micro l 0.5M Tris, pH 8.0 and purified using Bio-Rad 6 purification columns (BioRad, UK). The NIA NeuroArray consists of 1152 cDNAs printed on nylon membrane in duplicate. The arrays were hybridised with alpha-33P-dCTP labelled cDNA probes overnight at 50oC in 4ml of hybridisation solution. Hybridised arrays were rinsed in 50ml of 2XSSC and 1%SDS twice at 55oC followed by two washes in 2X SSC and 1% SDS at 55oC for 15 min each. The microarrays were exposed to phosphorimager screens for 1-3 days. The screens were then scanned with Molecular Dynamics STORM PhosphorImager (Sunnyvale, CA) at 25 micro m resolution. Source GEO sample is GSM28536 Last updated (according to GEO): May 27 2005 Hereditary Diseases 901 861 Skeletal muscle structure tongue_superior_part_w/_papillae_4 Source GEO sample is GSM80885 Last updated (according to GEO): Mar 31 2006 SN:Human Glioblastoma Biopsy 10456 Primary Neoplasm 1000 Parkinson's disease (PD) progresses relentlessly and affects five million people worldwide. Laboratory tests for PD are critically needed for developing treatments designed to slow or prevent progression of the disease. We performed a transcriptome-wide scan in 105 individuals to interrogate the molecular processes perturbed in cellular blood of patients with early-stage PD. The molecular multigene marker here identified is associated with risk of PD in 66 samples of the training set comprising healthy and disease controls [third tertile cross-validated odds ratio of 5.7 (P for trend 0.005)]. It is further validated in 39 independent test samples [third tertile odds ratio of 5.1 (P for trend 0.04)]. Insights into disease-linked processes detectable in peripheral blood are offered by 22 unique genes differentially expressed in patients with PD versus healthy individuals. These include the co-chaperone ST13, which stabilizes heat-shock protein 70, a modifier of alpha-synuclein misfolding and toxicity. ST13 messenger RNA copies are lower in patients with PD (mean +/- SE 0.59 +/- 0.05) than in controls (0.96 +/- 0.09) (P = 0.002) in two independent populations. Thus, gene expression signals measured in blood can facilitate the development of biomarkers for PD. MuscleRegen-ctx30d-1LLAv2-s2 Large-scale analysis of the human transcriptome Normal Source GEO sample is GSM175848 Last updated (according to GEO): Apr 09 2007 2500 mg/kg X 24 hr Source GEO sample is GSM129850 Last updated (according to GEO): Sep 18 2007 Parkinson Disease 861 Macrophage smi88 Squamous cell carcinoma 923 Post Natally excised CCAM 3 1000 Mitral Valve Primary tumor 19 32 Epithelium 861 Head and neck cancer Source GEO sample is GSM155685 Last updated (according to GEO): Apr 24 2007 Data was scanned using Genechip scanner 3000 using the manufacturer?s protocol. Source GEO sample is GSM181974 Last updated (according to GEO): Apr 13 2007 Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks. Source GEO sample is GSM118355 Last updated (according to GEO): Jul 11 2006 cerebellum.1 Liver Test (Blinded) Sample Source GEO sample is GSM130128 Last updated (according to GEO): Sep 18 2007 Gene expression data from mouse colon Source GEO sample is GSM198103 Last updated (according to GEO): Aug 22 2007 Adipose tissue 884 Spleen vs MIP3-alpha Treated B cell 901 Epithelial Cells globus_pallidus Source GEO sample is GSM18913 Last updated (according to GEO): Sep 25 2006 Chronic leukemia NOS 913 Brain 861 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2835 Source GEO sample is GSM2122 Last updated (according to GEO): Nov 21 2005 Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: dpatel Algorithm: Statistical Corner+ Avg:239, Count:32 Corner- Avg:38822, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:7.316926,SFGene:All Background:Avg:371.14,Stdev:5.69,Max:385.0,Min:359.1 Noise:Avg:10.15,Stdev:0.33,Max:11.2,Min:9.4 RawQ:12.76 Keywords = ALL Source GEO sample is GSM3493 Last updated (according to GEO): May 28 2005 574 542 in the spared extraocular muscles 15 0 human cerebellum 1000 Lung GSE2270 PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls. All samples were normalized with quantile normalization and summarized using RMA. Source GEO sample is GSM135583 Last updated (according to GEO): Dec 19 2006 Gene expression data from whole brain infected mouse, day 6 Source GEO sample is GSM189656 Last updated (according to GEO): May 16 2007 Brain 861 nasal epithelial cells 28 49 Aortic Aneurysm 901 no additional Source GEO sample is GSM199365 Last updated (according to GEO): Jun 08 2007 0 Frontal Cortex 13 osteoblast 630 640 Gene expression data from hippocampus of one old SAMP10//Ta mouse Source GEO sample is GSM143746 Last updated (according to GEO): Jan 24 2007 bc-ZT3-1 Carcinoma, Large Cell 867 7 0 prostate 21 0 acute myeloid leukemia 10 Bone marrow 0 of the normal mucosa 7 26 Breast 2 Disease Recurrent Carcinoma 875 Biological replicate 3 of 3. Voxel labeled with Cy3, Control Whole Brain Labeled with Cy5. Source GEO sample is GSM181237 Last updated (according to GEO): Jul 12 2007 wild type fundus replicate 2 861 Epithelial Cells HMEC X NB2 brain_DLPFC_bipolar B_mr446 Colon 861 Epithelium 861 RNA8 Exp2 AzaC/TSA treated to the nose 599 609 Seminoma 861 114 of diabetes 104 EGFR Gene Amplification 1000 to the central nervous system 60 88 1000 Immunoglobulins Parkinson Disease 1000 High Freezing Source GEO sample is GSM92415 Last updated (according to GEO): Jan 13 2006 Bone Marrow 1000 YFPH-SomatosensoryCortex-replicate2 Tumor__Leukemia_ALL-T_ALL_(92_571)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A GSE6942 1000 Structure of parenchyma of lung Blood 1000 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225746 Last updated (according to GEO): Nov 02 2007 Brain 1000 861 Alzheimer's Disease 99 86 of spinal cord 91 FC BA9 B 1500 mg/kg X 24 hr Source GEO sample is GSM129892 Last updated (according to GEO): Sep 18 2007 Neurotoxicity Syndromes 1000 04_0004_SepticShock_Day1_10 1000 Odontoblasts Neoplasm 861 osteoblast 627 637 M-14_CL10014_MELANOMA Brain 1000 901 Caudate nucleus structure Pituitary Gland 861 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68300 Last updated (according to GEO): Jul 07 2006 from whole tumor 21 36 5 0 Spleen 1000 Brain Lymphoblastoid Cell Line for Individual 8060.5 log phase Hypothalamus Source GEO sample is GSM18933 Last updated (according to GEO): Sep 25 2006 outer medulla 31 43 9 0 Blood Test 861 Brain none Source GEO sample is GSM239928 Last updated (according to GEO): Dec 07 2007 913 Coronary heart disease Prostatic hypertrophy 901 no additional Source GEO sample is GSM199123 Last updated (according to GEO): Jun 08 2007 861 Stem cells Bone Marrow 1000 Mislabeled (was labeled Heart (interventricular septum)) [JunctionChip 3 of 5] 0 Human Cortex 11 861 Nerve outer medulla 31 43 Primary large cell carcinoma 2081 0 32 861 Malaria ct-2 Sham 19 Treatment, type=incubate, description=Sham (normoxic) preconditioning Source GEO sample is GSM107508 Last updated (according to GEO): May 01 2006 Gene expression data from male mice. Source GEO sample is GSM115526 Last updated (according to GEO): Jun 13 2007 L_B6_Control_ZT 6_1 861 Substantia nigra structure HapMap YRI_parent Male Source GEO sample is GSM159666 Last updated (according to GEO): Feb 01 2007 1000 Brain 195 with coxsackievirus B3 174 none Source GEO sample is GSM239946 Last updated (according to GEO): Dec 07 2007 Serum stimulation of fibroblasts 245 227 Embryonic forebrain Simple annotation: Non-tumor tissue, Stomach cancer Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18372.gif Source GEO sample is GSM91553 Last updated (according to GEO): Sep 22 2006 I_U133A_97_AnCg Kainate-hippocampus, biological rep3 After 2 week acclimation to 12 hr/12 hr light/dark regimen, c57/Bl6 mice were subjected to a 36 hour period of constant darkness. Aortae were subsequently harvested at 4 hour intervals to 48 hours. Duplicate microarrays were hybridized with biotin-labeled probes derived from aorta tissue (6 pooled aortae/timepoint).. Date GSE414 Last Updated: Jun 15 2005 Contributers: John Hogenesch Radu D Rudic Peter McNamara Garret FitzGerald Satchidananda Panda Includes GDS404. Update date: Oct 30 2003. Dataset description GDS404: Examination of molecular basis of circadian oscillation system in aorta. After 2 week acclimation to 12/12 hour light/dark regimen, C57Bl6 mice subjected to 36 hours constant darkness. Aortae subsequently harvested at 4 hour intervals to 48 hours.. 861 Medulla Oblongata Brain 861 H117 CB A in human liver cancers 25 46 213 203 bone marrow Expression profiling of spinal cord section (T9) extracted from rats 12h following moderate injury Source GEO sample is GSM31513 Last updated (according to GEO): May 27 2005 Mouse Liver AIN Diet 8hr Saline Injection, biological replicate C no additional Source GEO sample is GSM199335 Last updated (according to GEO): Jun 08 2007 - Source GEO sample is GSM216548 Last updated (according to GEO): Aug 09 2007 Gene expression data from skeletal muscle following 240 minutes of a insulin infusion (80 mU clamp) Source GEO sample is GSM230458 Last updated (according to GEO): Sep 19 2007 Human Hypothalamus Male 6 Liver 1000 18 Trigeminal Ganglion 0 in the adult olfactory epithelium 62 94 119 96 in embryonic stem cells D_U133Plus_84_HC Muscular Dystrophy, Duchenne 913 1000 Ischemia P7CN1 Simple annotation: T-cell, Costimulation Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15563.gif Source GEO sample is GSM84153 Last updated (according to GEO): Sep 22 2006 Mouse old brain w/ a-tocopherol aT-Br-3 30 19 Solid tumor Parkinson Disease 1000 CF knockout HMCF CHN539 healthy subject Source GEO sample is GSM211019 Last updated (according to GEO): Sep 10 2007 660 mesenchymal stem cell 639 testis 52 58 Large Intestine; Cecum Keywords = mouse gene expression database Source GEO sample is GSM29288 Last updated (according to GEO): May 27 2005 HUVEC isolate C rich media control for #6 Source GEO sample is GSM12898 Last updated (according to GEO): May 28 2005 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181157 Last updated (according to GEO): Jul 12 2007 na Source GEO sample is GSM181264 Last updated (according to GEO): Apr 10 2007 AD-253t1-A168-4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data Source GEO sample is GSM183185 Last updated (according to GEO): Jul 30 2007 with some respiratory epithelium. 1039 1072 /2J periaqueductal gray rep2 3 30 Communicable Diseases 1000 Heart Septal Defects 884 adACN8 Malignant Childhood Neoplasm 983 park_1158_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A SK-MEL-5 hgu95a 7 frontal cortex 20 PGA-E14.5_3 Gene expression data from postmorten brain regions Source GEO sample is GSM144932 Last updated (according to GEO): Nov 20 2006 7 0 prostate Glutamic Acid Surface 6 hours mouse brains 187 198 901 Stem cells Mesenchymal Stem Cells 1000 at the Human Brain 744 761 7108_Lung did not develop PGD Large-scale analysis of the mouse transcriptome. Thyroid C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 325.24 Stdv: 8.85 Min: 311.13 Max: 340.74 Source GEO sample is GSM2958 Last updated (according to GEO): Mar 20 2006 Primary large cell neuroendocrine carcinoma 571 0 46 Liver (fetal) [JunctionChip 1 of 5] in the brain 150 162 Affymetrix protocol Source GEO sample is GSM213813 Last updated (according to GEO): Aug 02 2007 861 Heart Keywords = kidney 113 130 brain_OFC_bipolar B_mr94 7 0 prostate (No additional Information) Source GEO sample is GSM114410 Last updated (according to GEO): Jun 19 2006 #30 (isolate 8 low serum media PlGF 24hours) G5 macula 10 0 Endometrium osteoblast 630 640 VDXOXFU_1006 cerebral cortex 7 21 Nose 1000 Large-scale analysis of the human transcriptome. Lung Source: Contech Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 133.75 Stdv: 7.22 Min: 122.85 Max: 148.29 Source GEO sample is GSM2822 Last updated (according to GEO): Mar 20 2006 Keywords = Heart 505 521 Lymphoblastoid Cell Line for Individual 8067.3 log phase 1_cerebral_cortex_9hrs_sleep_deprivation_#2 above anterior commisure 17 41 Femur 1000 SMCL-SMCL9t1-A357-6 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68150 Last updated (according to GEO): Jul 07 2006 globus_pallidus Source GEO sample is GSM18755 Last updated (according to GEO): Sep 25 2006 32h-AC replication 3 1000 Hypertrophic Cardiomyopathy 180minplus.2 /3T3 fibroblasts 478 493 5 0 brain Kidney 1000 Melanoma xenograft, MA2_Lung_A (LeiATCC) 43h-DMSO replication 2 Keywords = preimplantation Keywords = development Source GEO sample is GSM14726 Last updated (according to GEO): May 28 2005 SF-539 hgu95b Cockayne syndrome B cell Source GEO sample is GSM225387 Last updated (according to GEO): Sep 04 2007 brain, cerebral cortex: Rat_02-133_TTX_Lipska_e1_le1 in prostate epithelial cells 91 119 861 Cancer of Neck Pool Eu_P0_hyb2 Informed consent was obtained from all participants following an explanation of the nature of the study, as approved by the research ethics board of our hospital. All patients were considered sporadic cases on the basis that no clinical antecedents of familial adenomatous polyposis were reported, and those that met the clinical criteria for hereditary non-polyposis colon cancer (Amsterdam criteria) were excluded. Source GEO sample is GSM112303 Last updated (according to GEO): Jun 06 2006 Epithelial Cells 901 healthy subject Source GEO sample is GSM211030 Last updated (according to GEO): Sep 10 2007 1113 1097 in breast cancer Total RNA from cultured stria vascularis, pool from 12 cochleas. Source GEO sample is GSM124848 Last updated (according to GEO): Aug 04 2006 1000 Hippocampus Untreated,# 1 1000 Brain Liver 1000 Rett Syndrome 861 CO_NP_mid_4 1000 ovarian neoplasm 1000 Skeletal muscle structure 901 Coronary artery 3AJZ02030476_pituitary Human prostate cancer cells in different conditions Source GEO sample is GSM13091 Last updated (according to GEO): May 28 2005 5 0 brain 1000 Malignant Neoplasms Little is known about the genetic regulation of medulloblastoma dissemination, but metastatic medulloblastoma is highly associated with poor outcome. We obtained expression profiles of 23 primary medulloblastomas clinically designated as either metastatic (M+) or non-metastatic (M0) and identified 85 genes whose expression differed significantly between classes. Using a class prediction algorithm based on these genes and a leave-one-out approach, we assigned sample class to these tumors (M+ or M0) with 72% accuracy and to four additional independent tumors with 100% accuracy. We also assigned the metastatic medulloblastoma cell line Daoy to the metastatic class. Notably, platelet-derived growth factor receptor alpha (PDGFRA) and members of the downstream RAS/mitogen-activated protein kinase (MAPK) signal transduction pathway are upregulated in M+ tumors. Immunohistochemical validation on an independent set of tumors shows significant overexpression of PDGFRA in M+ tumors compared to M0 tumors. Using in vitro assays, we show that platelet-derived growth factor alpha (PDGFA) enhances medulloblastoma migration and increases downstream MAP2K1 (MEK1), MAP2K2 (MEK2), MAPK1 (p42 MAPK) and MAPK3 (p44 MAPK) phosphorylation in a dose-dependent manner. Neutralizing antibodies to PDGFRA blocks MAP2K1, MAP2K2 and MAPK1/3 phosphorylation, whereas U0126, a highly specific inhibitor of MAP2K1 and MAP2K2, also blocks MAPK1/3. Both inhibit migration and prevent PDGFA-stimulated migration. These results provide the first insight into the genetic regulation of medulloblastoma metastasis and are the first to suggest a role for PDGFRA and the RAS/MAPK signaling pathway in medulloblastoma metastasis. Inhibitors of PDGFRA and RAS proteins should therefore be considered for investigation as possible novel therapeutic strategies against medulloblastoma. burde-affy-arabi-64764 901 Heart failure Gene expression data from human colon tumor tissue Source GEO sample is GSM173326 Last updated (according to GEO): Apr 20 2007 Endometrium-Normal 4 861 Neoplasm Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68042.gif Source GEO sample is GSM137405 Last updated (according to GEO): Sep 26 2006 E6, E7, hTERT, endometrial cell +2 NA18605 861 Immediate hypersensitivity urethra_2 Source GEO sample is GSM80912 Last updated (according to GEO): Mar 31 2006 Replicate3_Voxel G6 prostate Source GEO sample is GSM203386 Last updated (according to GEO): Jun 21 2007 M7TW01013108 Heart 1000 31 0 Cerebellum Alzheimer's disease 9 (cortex 19 25 MDA-MB-435 hgu95b Site: University of California, Davis Cohort: Male/Female Control Set Diagnosis: Control pH: 6.13 Subject: 1871 Gender: Female Chip: Affymetrix GeneChip Human Genome U95A We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM38991 Last updated (according to GEO): May 27 2005 Uterus_Corpus Source GEO sample is GSM19016 Last updated (according to GEO): Sep 25 2006 Cerebellar Hemisphere AB Normal 114 101 brains quickly Parkinson's model voxel E1 Mesenchymal Stem Cells 1000 Gene expression data from colonic normal mucosa. Source GEO sample is GSM215061 Last updated (according to GEO): Aug 02 2007 4_cerebral_cortex_time_0_#50 913 Myeloid Leukemia DLBC46 on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184795 Last updated (according to GEO): Apr 26 2007 Brain 861 HapMap CEU_parent Female Source GEO sample is GSM159531 Last updated (according to GEO): Feb 01 2007 osteoblast 627 637 Pressure-overload induced hypertrophy model. Mouse was sacrificed 1 hour after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2248 Last updated (according to GEO): May 27 2005 Pool of 10 otic vesicles at E9.5 Source GEO sample is GSM182567 Last updated (according to GEO): Aug 14 2007 of the human frontal cortex 26 52 Gene expression data from dorsal pancreas at e14.5, MG-U74B version2 Source GEO sample is GSM199458 Last updated (according to GEO): Jun 08 2007 861 Kidney Cerebral cortex 861 430A2_1945_13_KO_neuropath_medulla Source GEO sample is GSM242680 Last updated (according to GEO): Nov 15 2007 Epithelial Cells 1000 114 101 brains quickly Expression profiling of somatomotor cortex extracted from rats at 28d following moderate injury Source GEO sample is GSM41713 Last updated (according to GEO): May 27 2005 in seminoma 28 38 the blood 393 402 20 0 human caudate nucleus Gene expression data from the right forebrain of C57BL mouse received no treatment for twelve weeks. Source GEO sample is GSM148682 Last updated (according to GEO): Dec 12 2006 78 66 Control blood 10 7 Left in cervical cancer 152 170 61 41 in extraocular muscle MuscleRegen-ctx13d-1LLAv2-s2 1343 1321 in primary human tumors Ovarian Diseases 877 861 Malignant Neoplasms the spinal cords 144 159 Cerebellum 7 Normal Samp10 Retina Young Sample 2 Lymphoblastoid Cell Line for Individual 8099.4 log phase 1000 Female infertility of anovulatory origin NOS Gene expression data from postmorten brain regions Source GEO sample is GSM145875 Last updated (according to GEO): Nov 20 2006 Bladder sample 1161-1 901 Coronary artery 61 41 from postmortem brain Comparison between NHE1 null mutation and wild-type. RNA has been amplified. Dye-swap. Source GEO sample is GSM15964 Last updated (according to GEO): May 28 2005 Cerebral cortex 861 blood 0 5 Rat frontal cortex RNA - Neuroleptic Experiment Source GEO sample is GSM92372 Last updated (according to GEO): Jan 13 2006 CNS-SC_CtrBT0-1A-s2 rat hippocampus Treatment, type=time_course, measurement=1.0 h Source GEO sample is GSM32124 Last updated (according to GEO): May 27 2005 Neuronal Differentiation of Primary Myoblast Sphere Cultures CNS-SMTC_Mod14d-3A-s2 MGJZ030207007Acerebellum brain, cerebral cortex: Rat_02-135_TTX_Lipska_e1_le1 R6/1 27 week wildtype_B9F2 CNS-RM_Mod14d-3A-s2 MuscleRegen-ctx5d-2LLAv2-s2 5 0 Spleen in the hippocampus 644 661 healthy subject Source GEO sample is GSM211080 Last updated (according to GEO): Sep 10 2007 brain, caudate nucleus Source GEO sample is GSM18920 Last updated (according to GEO): Sep 25 2006 144 133 metastasize of the stria terminalis 49 71 DBA whole brain 2A NCI60.1_LABEL124EXTRACT63SUB3 Source GEO sample is GSM133995 Last updated (according to GEO): Aug 06 2007 NCI60.36_LABEL40EXTRACT39SUB3 Source GEO sample is GSM134171 Last updated (according to GEO): Aug 06 2007 Recurrent Squamous cell carcinoma 4 0 34 C57BL/6 benchmark dataset: Embryonic day 13.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25162 Last updated (according to GEO): May 27 2005 1000 Skeletal muscle structure Hypothalamus Source GEO sample is GSM107952 Last updated (according to GEO): Jun 06 2006 CNS-SpinalC-30mAdult-3A-s2 pharyngeal_mucosa_4 ovary 45 50 Primary tumor 19 32 bronchial epithelia 224 243 ventral striatum sprague 3962 Normal Source GEO sample is GSM176395 Last updated (according to GEO): Apr 09 2007 of regenerating Dorsal Root Ganglia 21 55 liver 0 5 901 Epithelial Cells 3AJZ02022111_ fetal brain Parkinson Disease 1000 frontal cortex wistar 3920 Gene expression data from liver Source GEO sample is GSM243363 Last updated (according to GEO): Nov 16 2007 Neoplasm 861 /NJ periaqueductal gray rep1 3 30 Congenital Abnormality 853 1000 Prostate Stria 861 Lung tissue from C57BL/6 mice that were always fed by 2/3 and sacrificed. Lot batch = Source GEO sample is GSM4037 Last updated (according to GEO): May 28 2005 Testis 1000 n/a Source GEO sample is GSM177976 Last updated (according to GEO): Jun 11 2007 Brain 861 1000 Skeletal muscle structure Colorectal cancer patient SC3_vs_Pool rat kidney at embryonic day 18, rep1 1000 Spleen Prostate Gland 5 Normal -uninjured cortex 103 119 Plasma 861 CNS-SC_InjB24h-4A-s2 32 21 from retinas from whole tumor 21 36 none Source GEO sample is GSM246008 Last updated (according to GEO): Dec 03 2007 165 159 Muscles 5 0 brain 57 31 -induced status epilepticus Migraine Disorders 1000 1226 1206 of metastatic tumors 116 95 middle temporal gyrus 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114447 Last updated (according to GEO): Jun 16 2006 138 133 heart of Parkinson's disease 450 471 atrial septal defects 198 218 Skeletal bone 861 brain, Posterior Singulate: Sample47_e1_le1 19 0 human frontal cortex 1000 Immunoglobulins from colonic normal mucosa 21 47 14 NT control Source GEO sample is GSM92488 Last updated (according to GEO): Jan 13 2006 Untreated Control 12weeks AffyGC RMA rep1 200 in the frontal cortex 220 S1P2-KO-hippocampus, biological rep2 (male) Brain 861 substantia_nigra_3 Source GEO sample is GSM80832 Last updated (according to GEO): Mar 31 2006 Gene expression data from whole brain infected mouse, day 6 Source GEO sample is GSM189657 Last updated (according to GEO): May 16 2007 Nasal Epithelium 865 Gene expression data from older male during 1 week of adequate protein intake Source GEO sample is GSM209811 Last updated (according to GEO): Jul 11 2007 Haloperidol treated 12weeks AffyGC RMA rep2 GSE4780 Barcode: 251316210198 Source GEO sample is GSM159381 Last updated (according to GEO): Jul 17 2007 none Source GEO sample is GSM241961 Last updated (according to GEO): Nov 29 2007 2523 CP0_32 861 Prostate Normal Caudate Nucleus of the normal mucosa 7 26 Uterus Source GEO sample is GSM18801 Last updated (according to GEO): Sep 25 2006 Gene expression data from postmorten brain regions Source GEO sample is GSM145541 Last updated (according to GEO): Nov 20 2006 CF knockout LFCF CHN532 171 diabetes 163 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Neuropeptide Y for 240min Source GEO sample is GSM5718 Last updated (according to GEO): May 27 2005 265 260 Spleen 1000 Brain HS-578T_CL5006_Breast on Affymetrix GeneChip Human Full Length Array HuGeneFL Oculomotor nucleus 1000 osteoblast 627 637 Nasal Epithelium Inhalation Formaldehyde 6ppm 19d ID312 Glioblastoma multiforme (GBM) is the most common form of malignant glioma, characterized by genetic instability, intratumoral histopathological variability, and unpredictable clinical behavior. We investigated global gene expression in surgical samples of brain tumors. Gene expression profiling revealed large differences between normal brain samples and tumor tissues and between GBMs and lower-grade oligodendroglial tumors. Extensive differences in gene expression were found among GBMs, particularly in genes involved in angiogenesis, immune cell infiltration, and extracellular matrix remodeling. We found that the gene expression patterns in paired specimens from the same GBM invariably were more closely related to each other than to any other tumor, even when the paired specimens had strikingly divergent histologies. Survival analyses revealed a set of approximately 70 genes more highly expressed in rapidly progressing tumors that stratified GBMs into two groups that differed by >4-fold in median duration of survival. We further investigated one gene from the group, FABP7, and confirmed its association with survival in two unrelated cohorts totaling 105 patients. Expression of FABP7 enhanced the motility of glioma-derived cells in vitro. Our analyses thus identify and validate a prognostic marker of both biologic and clinical significance and provide a series of putative markers for additional evaluation. Expression profiling of spinal cord section (T9) extracted from rats 7d following moderate injury Source GEO sample is GSM31588 Last updated (according to GEO): May 27 2005 5 0 Muscle Liver 1000 00291004H95A2-T01194v2p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A GBM Treatment, type=remove Source GEO sample is GSM99589 Last updated (according to GEO): Apr 21 2006 1000 Spleen none Source GEO sample is GSM149635 Last updated (according to GEO): Jan 03 2007 from liver 21 30 R650P01104 1000 Glioblastoma Gene expression data from postmorten brain regions Source GEO sample is GSM145522 Last updated (according to GEO): Nov 20 2006 7 0 prostate Thalamus Lateral Nuclei 3 Normal 861 Heart A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke. White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by 6 hours of reperfusion; third replicate; pooled mRNA from 6 brains. Source GEO sample is GSM2212 Last updated (according to GEO): May 27 2005 Expression profiling of spinal cord section (T8) extracted from rats 4h following severe injury Source GEO sample is GSM31504 Last updated (according to GEO): May 27 2005 no additional Source GEO sample is GSM199367 Last updated (according to GEO): Jun 08 2007 Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 0 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays. Source GEO sample is GSM10942 Last updated (according to GEO): May 27 2005 Cerebral cortex 861 Transcriptional responses to UV irradiation in CS-B cells 1000 Atherosclerosis Tumor__Ovary_Adeno_93_I_081 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A HNC2686 Central gray substance of midbrain 861 PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls. All samples were normalized with quantile normalization and summarized using RMA. Source GEO sample is GSM135581 Last updated (according to GEO): Dec 19 2006 Arteries 861 Replicate3_Voxel B8 DMN-NF1Hippo28d-1bAv2-s2 14 NT B4 Treatment, type=add, description=10ng/mL Bonemorphogentic Protein, 4d Source GEO sample is GSM92495 Last updated (according to GEO): Jan 13 2006 HapMap CHB Female Source GEO sample is GSM159598 Last updated (according to GEO): Feb 01 2007 Leprosy presents as a clinical and immunological spectrum of disease. With the use of gene expression profiling, we observed that a distinction in gene expression correlates with and accurately classifies the clinical form of the disease. Genes belonging to the leukocyte immunoglobulin-like receptor (LIR) family were significantly up-regulated in lesions of lepromatous patients suffering from the disseminated form of the infection. In functional studies, LIR-7 suppressed innate host defense mechanisms by shifting monocyte production from interleukin-12 toward interleukin-10 and by blocking antimicrobial activity triggered by Toll-like receptors. Gene expression profiles may be useful in defining clinical forms of disease and providing insights into the regulation of immune responses to pathogens.. Date GSE443 Last Updated: May 29 2005 Includes GDS358. Update date: Jun 24 2003. Dataset description GDS358: Molecular characterization of lepromatous leprosy (LL) and borderline tuberculoid (BT) leprosy skin lesions.. Cerebral cortex 1000 Gene expression data from brain of adult rats Source GEO sample is GSM101037 Last updated (according to GEO): Feb 20 2007 1000 Aorta 5 0 brain Bone Marrow 1000 Baseline comparison of global gene expression in ILS and ISS cerebellum to find differences in the naive state. Source GEO sample is GSM69567 Last updated (according to GEO): Oct 28 2005 hip_1046_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Disease Source GEO sample is GSM176261 Last updated (according to GEO): Apr 09 2007 Cultured_osteoblast-like_shear-stressed_MC3T3-E1_cells_rep3 1000 Coronary Arteriosclerosis Bone Marrow 1000 The identification of molecular differences in the endometrium of women with endometriosis is an important step toward understanding the pathogenesis of this condition and toward developing novel strategies for the treatment of associated infertility and pain. In this study, we conducted global gene expression analysis of endometrium from women with and without moderate/severe stage endometriosis and compared the gene expression signatures across various phases of the menstrual cycle. The transciptome analysis revealed molecular dysregulation of the proliferative-to-secretory transition in endometrium of women with endometriosis. Paralleled gene expression analysis of endometrial specimens obtained during the early secretory phase demonstrated a signature of enhanced cellular survival and persistent expression of genes involved in DNA synthesis and cellular mitosis in the setting of endometriosis. Comparative gene expression analysis of progesterone-regulated genes in secretory phase endometrium confirmed the observation of attenuated progesterone response. Additionally, interesting candidate susceptibility genes were identified that may be associated with this disorder, including FOXO1A, MIG6, and CYP26A1. Collectively, these findings provide a framework for further investigations on causality and mechanisms underlying attenuated progesterone response in endometrium of women with endometriosis. Gene expression data from liver Source GEO sample is GSM243368 Last updated (according to GEO): Nov 16 2007 25 0 frontal cortex wistar 3920 Gene expression data from liver Source GEO sample is GSM243403 Last updated (according to GEO): Nov 16 2007 0 Human Cortex 11 861 Acquired Immunodeficiency Syndrome /HeJ periaqueductal gray rep1 3 31 3 Retina 15 22 Brain 861 atrial septal defects 198 218 GSE740 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with CpG-oligodeoxynucleotide labeled with Cy5- time course with repeats. Date GSE378 Last Updated: May 29 2005 Contributers: Rebecca Hart Sangdun Choi Zhen Yan Sun Young Lee Angela Alexander Jong-Woo Kim Robert Hsueh Yun Anna Cao Joella Grossoehme Mi Sook Chang Includes GDS299. Update date: Nov 18 2003. Dataset description GDS299: Temporal analysis of effects induced by 30 uM CpG-containing oligodeoxynucleotide in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. Utricle structure 1000 adenocarcinoma 3200 normal human skeletal muscle sample 12 lymph_nodes_1 Source GEO sample is GSM80735 Last updated (according to GEO): Mar 31 2006 1000 Spinal Cord Spleen vs CGS Treated B cell 19 0 human frontal cortex 40 12 Amyotrophic lateral sclerosis 1000 Cerebral cortex Five different human MPNST cell lines, mock treated or infected with G207. Source GEO sample is GSM215817 Last updated (according to GEO): Aug 07 2007 B6:17-1,2,3 superior colliculi 17 7 hippocampi Wild type olfactory epithlium 0 h replicate3 5 0 brain gene expression data of regenerating Dorsal Root Ganglia Source GEO sample is GSM134616 Last updated (according to GEO): Jul 09 2007 endothelial cells sprague2 MO_control_0min_Patient17 91 from the bone marrow 72 Primary large cell neuroendocrine carcinoma 571 Gene expression data from an individual without coronary artery disease Source GEO sample is GSM184738 Last updated (according to GEO): Apr 26 2007 none Source GEO sample is GSM149568 Last updated (according to GEO): Jan 03 2007 biopsy sample obtained from 10-year-old male individual Keywords = gene expression profile of normal human skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15826 Last updated (according to GEO): May 28 2005 D06 6h TLR2/1L 091230 OVR23 on Affymetrix GeneChip Human Full Length Array HuGeneFL Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions. Source GEO sample is GSM174513 Last updated (according to GEO): Mar 14 2007 in the brain 150 162 Plasma 861 none Source GEO sample is GSM123207 Last updated (according to GEO): Jul 26 2006 Brain 1000 Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10160.gif Source GEO sample is GSM79670 Last updated (according to GEO): Sep 22 2006 Brain 1000 Gene expression data from skeletal muscle at baseline Source GEO sample is GSM230456 Last updated (according to GEO): Sep 19 2007 858 Mesodermal cell Uterus (corpus) [JunctionChip 1 of 5] 861 Brain NCI60.58_LABEL62EXTRACT61SUB3 Source GEO sample is GSM134287 Last updated (according to GEO): Aug 06 2007 adipose_tissue_subcutaneous_5 Source GEO sample is GSM80589 Last updated (according to GEO): Mar 31 2006 Control_mid-term S25 WT2 F41/390 S25 wild type Mouse 2.5 months Cerebellum Female Source GEO sample is GSM73208 Last updated (according to GEO): Sep 06 2005 22 19 left Gene expression profiling of isogenic cells with different TP53 gene dosage reveals numerous genes that are affected by TP53 dosage and identifies CSPG2 as a direct target of p53. from intraabdominal adipose tissue 25 58 Nose 1000 [prefrontal cortex 812 830 1000 Lung Control 6 Category: Lymphoma Classification Subcategory: Diffuse Large B-Cell Lymphoma Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc4b036 Source GEO sample is GSM1969 Last updated (according to GEO): Nov 21 2005 1000 Communicable Diseases Five different human MPNST cell lines, mock treated or infected with G207. Source GEO sample is GSM215818 Last updated (according to GEO): Aug 07 2007 no additional Source GEO sample is GSM199182 Last updated (according to GEO): Jun 08 2007 Simple annotation: Solid tumor, Brain Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3521.gif Source GEO sample is GSM93133 Last updated (according to GEO): Sep 22 2006 Frontal Cortex AB Normal the blood 393 402 Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow. Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html Keywords = physiological hypertrophy Keywords = pathological hypertrophy Keywords = rat Keywords = heart failure Keywords = cardiomyopathy Source GEO sample is GSM11887 Last updated (according to GEO): May 28 2005 Macrophage 14smi064 C57BL/6 mice were bred with mice heterozygous for Nf1. Their male pups were euthanized at P20 and brains quickly dissected and flash-frozen. Their livers were also removed and frozen for the purpose of genotyping. Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling. Lot batch = Source GEO sample is GSM25124 Last updated (according to GEO): May 27 2005 Plasma 861 Simple annotation: Development, Fibroblasts Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16874.gif Source GEO sample is GSM81572 Last updated (according to GEO): Sep 22 2006 (No additional Information) Source GEO sample is GSM114434 Last updated (according to GEO): Jun 19 2006 MGMH030212057Bspinalcordlower Gene expression regulated by DACH1-3 Murine NK cell were purified from wild type C57Bl/6 mice (>99% NK1.1+CD3-), stimulated with rmIL-15 for 24 hours, and then lysed in Trizol and assessed for gene expression on Affy MOE430_2 microarray Source GEO sample is GSM188005 Last updated (according to GEO): May 09 2007 D_U133Plus_55_Amy ovarian tumor: mucinous Source GEO sample is GSM139431 Last updated (according to GEO): Apr 09 2007 142T Epithelium of bronchus 983 RMS-T7 on NHGRI-6.5k_b Neoplasm 861 Heart Septal Defects, Atrial 1000 Medulla Oblongata 861 WHOLEBLOOD Source GEO sample is GSM18867 Last updated (according to GEO): Sep 25 2006 whole blood_101700 1000 Infection 31 in the frontal cortex 51 Hyperdip>50-#14 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A plasma cells 50 61 with some respiratory epithelium. 1039 1072 CNS-SC_CtrA24h-2C-s2 Leukemic fractions of ID59 AML patient have been hybridized. Source GEO sample is GSM154052 Last updated (according to GEO): Feb 26 2007 Mouse Liver AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate A R525P00604 WGACON-244 This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html Keywords = acute myocardial infarction, AMI, cardiac Source GEO sample is GSM12350 Last updated (according to GEO): May 28 2005 Large-scale analysis of the mouse transcriptome. Adrenal gland C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 382.21 Stdv: 20.34 Min: 352.54 Max: 418.36 Source GEO sample is GSM2968 Last updated (according to GEO): Mar 20 2006 Thalamic Diseases 862 D_U133A_66_CB PGA_PA-N_326 Squamous cell carcinoma 2 1000 Brain MO_control_180min_Patient13 Nervous system structure 901 McLean Parkinson 0 15 Whole neuroblastoma tumor_1547 861 Cecum 901 Brain Injuries none Source GEO sample is GSM244580 Last updated (according to GEO): Nov 23 2007 Healthy patient. Source GEO sample is GSM228664 Last updated (according to GEO): Sep 11 2007 1000 Maxilla 67 52 descending colon 901 Bone Marrow 1000 Tonsil 278 255 ischemic cardiomyopathy PGA-Csx_null_9b-m4 Human prostate cancer cells in different conditions Source GEO sample is GSM13092 Last updated (according to GEO): May 28 2005 TEL-AML1-C5 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Cervix 9 Normal Sensitized on days 0 and 3 with PBS, challenged intratrecheally on days 10 and 17 with PBS and sacrificed after 72h. Lot batch = Source GEO sample is GSM1250 Last updated (according to GEO): May 28 2005 Mesenchymal Stem Cells 1000 1000 Brain Stem Gene expression data from postmorten brain regions Source GEO sample is GSM145851 Last updated (according to GEO): Nov 20 2006 861 Blood Spinal Cord 901 Bipolar affective disorder 0 25 from mouse colon 21 36 Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9970.gif Source GEO sample is GSM79823 Last updated (according to GEO): Sep 22 2006 M_U133A_83_AnCg none Source GEO sample is GSM210307 Last updated (according to GEO): Jul 16 2007 NG023_a The function of melanotransferrin: a role in melanoma cell proliferation and tumorigenesis. 861 Cardiomyopathies PMN_LB_360min_Patient14 1000 Carcinoma GC (HKG93T) Simple annotation: Primary tumor, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9966.gif Source GEO sample is GSM79807 Last updated (according to GEO): Sep 22 2006 2528 HP6_33 1160 with degenerative diseases 1185 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114403 Last updated (according to GEO): Jun 16 2006 biopsy sample obtained from 4-year-old male individual Keywords = gene expression profile of normal human skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15825 Last updated (according to GEO): May 28 2005 Indicative oligodendrocyte dysfunction in spinal cords of human fetuses suffering from a lethal motoneuron disease. Control, biological rep1 CHB Con-1 901 theca cell Bone structure of tibia 1000 Brain 861 The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals. Keywords = human brain aging Source GEO sample is GSM27041 Last updated (according to GEO): May 27 2005 865 Disorder of artery Heart 861 Simple annotation: Non-tumor tissue, Liver Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10021.gif Source GEO sample is GSM79866 Last updated (according to GEO): Sep 22 2006 Liver 1000 Flow cytometry sorted double negative thymocytes from Egr1/Egr3 double knockout animal #1. Treatment, type=fractionate Source GEO sample is GSM130404 Last updated (according to GEO): Aug 24 2006 Heart 1000 ovary 45 50 brain, Left frontal Lobe: Extract23_le2 Malignant Neoplasms 861 SkinP2_022MACIA_037.txt Stem cells 913 12 0 ovarian tumor 1000 Colon 0 Human Cortex 11 HMVEC-L stimulated without LPS for 24 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures. Source GEO sample is GSM114575 Last updated (according to GEO): Sep 20 2006 Expression in Superior Frontal Gyrus of normal individuals or females of different ages affected by Rett syndrome brain, hippocampus: PH6_e1_le1 BAL_25_A0B0 Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225931 Last updated (according to GEO): Nov 02 2007 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68157 Last updated (according to GEO): Jul 07 2006 C57BL/6 benchmark dataset: Embryonic day 12.5. The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development. Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults. To address this question it is imperative to get insight into the genes expressed during normal heart development. Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5. These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract. Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart. At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis. From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers. Keywords = cardiac development, heart Source GEO sample is GSM25159 Last updated (according to GEO): May 27 2005 ISR13-Fv2E-PERK UT1 RNA from an Fv2E-PERK expressing mouse fibroblast cell line in an eIF2 alpha SS (wildtype), PERK-/- background. The PERK-/- background was used in order to obtain a cell line that expressed high levels of the Fv2E-PERK transgene. (We were unable to obtain clones with high levels of expression in wildtype cells.) The data are part of 24 chip experiment comparing genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules. Keywords = ATF4 Keywords = PERK Keywords = ISR eIF2alpha Source GEO sample is GSM10896 Last updated (according to GEO): May 28 2005 Endometrium 1000 R6/1 27 week wildtype_1338 Gene expression data from B6xBALB F2 mouse lung Source GEO sample is GSM133477 Last updated (according to GEO): Apr 05 2007 1000 Kidney Otic placode at E9, replicate1 Hepatocyte 861 no additional Source GEO sample is GSM199044 Last updated (according to GEO): Jun 08 2007 Infantile neuronal ceroid lipofuscinosis (aka infantile Batten disease) is a severe neurodegenerative disorder of early childhood characterized by cortical atrophy, blindness and seizures, leading to premature death in the first decade. The disorder is caused by deficiency in a soluble lysosomal enzyme, palmitoyl protein thioesterase-1 (PPT1). PPT1 knockout mice faithfully reproduce the features of the human disease, with motor deterioration, blindness, seizures, and death before 10 months of age. The progression of events leading from enzyme deficiency to organ failure is poorly defined. The neuronal ceroid lipofuscinoses are of particular interest because of the similarities between the accumulated material and lipofuscin that is associated with normal aging. We will determine changes in gene expression that occur during the course of neurodegeneration in PPT1 knockout as compared to control mice. Gene expression profiling of brain tissue from PPT1 knockout mice as compared to normal controls will provide insights into the mechanism of neurodegeneration. Comparison of this profile with gene expression profiles associated with normal aging may provide insights into the contribution of lipofuscin to aging and neurodegeneration. PPT1 knockout mice on a C57BL/6 background will be sacrificed under CO2 and whole brains removed and frozen under liquid nitrogen. Three mice will be used for each time point. Data points will be collected at 3 months, 5 months and 8 months of age. Normal age- and sex-matched C57BL/6 mice will be used as controls. Last Updated (by provider): Jan 09 2007 Contributers: Sandra L Hofmann AD-277t1-A97-3 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 901 frontal lobe Wild type 8 wk old male FVB/NJ mouse cingulate cortex Source GEO sample is GSM74952 Last updated (according to GEO): Feb 27 2007 Cerebral cortex 861 endometrium_8 Source GEO sample is GSM80672 Last updated (according to GEO): Mar 31 2006 Nasal Epithelium 865 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated withTerbutaline for 60min Source GEO sample is GSM5783 Last updated (according to GEO): May 27 2005 Compare the transcriptomes of Cx43 null and Cx43 siRNA treated cortical astrocytes with the transcriptome of the wildtype cortical astrocytes Source GEO sample is GSM202239 Last updated (according to GEO): Jun 19 2007 Anterior nares 1000 141 106 Keywords = Congestive heart failure Control pool 2 (n=5) from brain 21 30 Gene expression data from mouse primary visual cortex Source GEO sample is GSM101716 Last updated (according to GEO): Mar 27 2006 advanced HCC Source GEO sample is GSM155990 Last updated (according to GEO): Jun 21 2007 Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2818 Source GEO sample is GSM2128 Last updated (according to GEO): Nov 21 2005 CNS-SpinalCmod-Adult-12h-4C-s2 12 4 of Kidney 1000 Descending colon Primary Neoplasm 1000 ci_NY43 Chlorpyrifos is an organophosphorus insecticide that despite imposed restricitions on its use by the EPA, is one of the most commonly used insecticides. Although CPF is so widely used little is known about its effect on overall gene expression in vivo. DNA microarray technology was used to determine differential gene expression resulting from chlorpyrifos (CPF) exposure. Last Updated (by provider): Dec 03 2007 Contributers: Victor T Chan Andrea R Stapleton Testis 1000 Nasal Epithelium 865 PGA-HBE-CtrAir18h-1aA-S2 cocaine naive, septum, 0 hrs/day access to cocaine Source GEO sample is GSM93849 Last updated (according to GEO): Jan 26 2006 12237 on TGRI-6.5k SCG_control_12h_rep1 Identification of potential KLF7 target genes in olfactory sensory neurons D11 24h Media 901 Mental disorders Analysis of prefrontal cortex from 3 biological replicates of C57BL/6J mice at four Zeitgeber Times (ZT 3, 9, 15, and 21). Source GEO sample is GSM240417 Last updated (according to GEO): Oct 30 2007 64 47 that whole ovaries prostate_gland_1 861 Blood CurrentSmoker 102 Chorionic mesoderm-derived mesenchymal cells Source GEO sample is GSM210372 Last updated (according to GEO): Jul 16 2007 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11286 Last updated (according to GEO): May 28 2005 Pituitary Gland 861 9 0 rat kidney Blood B cells;anti-IgM+IL-4 24h PGA-Pi3k_ntg_2819v2 plasma cells 50 61 Calcineurin triggers reactive/inflammatory processes in astrocytes and is upregulated in aging and Alzheimer's models. 913 Coronary heart disease DLBC21 on Affymetrix GeneChip Human Full Length Array HuGeneFL Medulla Oblongata 861 UACC-257 hgu95b Utricle 0 6 22-oct-2002-BrainEsubB-ab150 Lung 861 after traumatic brain injury 81 109 cardiac 763 769 hindbrain 1000 Structure of olfactory bulb 1000 Whole Brain 73 83 861 Neoplasm To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at ?80C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at ?80°C before routine processing for GeneChip analysis. Source GEO sample is GSM28666 Last updated (according to GEO): Oct 28 2005 901 lymph nodes brain, unknown: 2292-99_e1_le1 AD control Treatment, type=dissect Source GEO sample is GSM119681 Last updated (according to GEO): Jul 10 2006 3AJZ02040823_salivarygland mdx5cv EDL sample 1 983 Malignant neoplasm of cervix uteri SCG explant cultured for 48 hours in vitro Source GEO sample is GSM246024 Last updated (according to GEO): Dec 03 2007 Cortex_Bulbectomized_rep1 1000 Descending colon GSE8596 Neoplasm 1000 NSCLC_HOP-92_CL1029_Colon on Affymetrix GeneChip Human Full Length Array HuGeneFL Low-density CCg progenitors Source GEO sample is GSM47547 Last updated (according to GEO): Jun 10 2005 PE_N_598 of the postmortem brains 676 700 861 Blood Effects of Phenylethyl Isothiocyanate on N-Nitrosomethylbenzylamine-induced Cytotoxicity in Rat Esophagus 913 Hereditary Malignant Neoplasm Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225668 Last updated (according to GEO): Nov 02 2007 Proteoglycan 1000 GC (HKG80T) Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep3 AdLacz-2 Wild-type striatal cells treated with 3NP Source GEO sample is GSM82443 Last updated (according to GEO): Jun 26 2007 HCC (HBV+, HK66, T5) 17 7 hippocampus Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153418 Last updated (according to GEO): Jan 11 2007 Ventral Tegmental Area 4 Normal Polyamide 1 treated LNCaP cells not stimulated with DHT, biological replicate 2 Source GEO sample is GSM187378 Last updated (according to GEO): May 04 2007 striatum_wt_3m_467 39 27 the maxillary 70 40 without coronary artery disease 10 0 Hippocampus bladder_T1GH_pool-2 901 Coronary artery Fetal occipital cortex cocaine1 NA12740 growth 3 Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. This sample is also known as sham mice. Set 1 - Pair 4 - MMN Source GEO sample is GSM49889 Last updated (according to GEO): Dec 20 2005 Replicate1_Voxel G4 Gene expression data from postmorten brain regions Source GEO sample is GSM145884 Last updated (according to GEO): Nov 20 2006 ADH-1 ip LPAM ILI 4hrs post ILI sample A 861 Chromosomes of regenerating Dorsal Root Ganglia 21 55 "Sample 47, <5 yr survival(26 months) age 43 erp no" on vantveer-oligo 53 year old male 861 Heart Richard Almon-1-1138200269274 of Parkinson's disease 450 471 FormerSmoker 28 13 0 G2 Optic Nerve Pool of 10 saccules at E13 Source GEO sample is GSM182612 Last updated (according to GEO): Aug 14 2007 GSE1000 Site: University of California, Irvine Cohort: Male/Female Control Set Diagnosis: Control pH: 6.86 Subject: 2822 Gender: Male Chip: Affymetrix GeneChip Human Genome U95A Version 2 We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Source GEO sample is GSM39017 Last updated (according to GEO): May 27 2005 Gene expression of stria vascularis of newborn rats inner ear 1000 Eye 091255 StromaMix on Affymetrix GeneChip Human Full Length Array HuGeneFL 7 frontal cortex 20 none Source GEO sample is GSM149633 Last updated (according to GEO): Jan 03 2007 NCI60.45_LABEL49EXTRACT48SUB3 Source GEO sample is GSM134219 Last updated (according to GEO): Aug 06 2007 Brain 861 kidney.1 M_U133Plus_109_nAcc Mid secretory endometrium from normal patient Source GEO sample is GSM150220 Last updated (according to GEO): Dec 14 2006 CNS-RM_CtrT0-3C-s2 Liver 1000 NA18524 ovarian tumor: serous Source GEO sample is GSM139456 Last updated (according to GEO): Apr 09 2007 Heart 1000 Normal Fetal Brain BAL_12_A1B0 Prostate 861 Dahl Salt Sensitive Rat Lung- Hypoxia, SU-5416, and Sorafenib rep3 Whole brain 0 10 Brain 861 total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Terbutaline labeled with Cy5- time course with repeats. Date GSE399 Last Updated: May 29 2005 Contributers: Sun Young Lee Yun Anna Cao Mi Sook Chang Zhen Yan Robert Hsueh Joella Grossoehme Rebecca Hart Sangdun Choi Jong-Woo Kim Angela Alexander Includes GDS320. Update date: Nov 18 2003. Dataset description GDS320: Temporal analysis of effects induced by 10 uM terbutaline in male c57BL/6 B cells. Cells incubated in culture with ligand and samples removed at several time points up to 4 hours. Spleen from male c57BL/6 used as reference.. none Source GEO sample is GSM241964 Last updated (according to GEO): Nov 29 2007 24 0 human prostate PC3 tumors V5-P465 Neoplasm 861 Parkinson 0 8 lung 0 3 D_U133Plus_124_nAcc 20 0 human caudate nucleus 861 Blood High Freezing Source GEO sample is GSM92417 Last updated (according to GEO): Jan 13 2006 861 Ganglia Human Cortex from neurologically normal control, Caucasian, male. Source GEO sample is GSM225729 Last updated (according to GEO): Nov 02 2007 5 0 Spleen Structure of trigeminal ganglion 1000 in the brain 150 162 liver, PPARa-null mice, control conditions Source GEO sample is GSM205777 Last updated (according to GEO): Jul 24 2007 Gene expression data from human colon tumor tissue Source GEO sample is GSM173358 Last updated (according to GEO): Apr 20 2007 HapMap JPT Female Source GEO sample is GSM159643 Last updated (according to GEO): Feb 01 2007 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11496 Last updated (according to GEO): May 28 2005 SWR/J CHR, Rep1 861 Blood fetalThyroid Source GEO sample is GSM18805 Last updated (according to GEO): Sep 25 2006 /3T3 fibroblasts 743 759 134 115 by CO2 asphyxiation Replicate2_Voxel E11 DCIS180 on harvard-12k blood, Blood: 2285_0102_le1 Stem cells 1000 Coronary heart disease 913 Voxel I4 of mouse brain. Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age. Source GEO sample is GSM1451 Last updated (according to GEO): Nov 21 2005 Category: Primary tumor Subcategory: Breast Scanning Software: ScanAlyze Software version: 2.44 Lot batch = svcc84 Source GEO sample is GSM1845 Last updated (according to GEO): Nov 21 2005 A/J_female_hypothalamus Source GEO sample is GSM138563 Last updated (according to GEO): Apr 18 2007 Circadian Profiling of the Transcriptome in Immortalized Rat SCN Cells Muscle 1000 NA18971 Double KO 2 Thymus, Whole thymus: Amplified mRNA_le1 I_U133A_107_CB IMR90 from the ES(IMR90)-1 sample 23 0 Substantia nigra PD rep5 Muscle_inadequate protein_female_rep6 f2#194 versus pool Mouse Brain tissue Bladder sample 861-1 Liver Test (Blinded) Sample Source GEO sample is GSM130075 Last updated (according to GEO): Sep 18 2007 PGA-HMO-MObese-2aUA-s2a 861 Cerebral cortex Lung 14 0 Normal Amygdala Gene expression data from postmorten brain regions Source GEO sample is GSM144984 Last updated (according to GEO): Nov 20 2006 Large-scale analysis of the human transcriptome. Brain, corpus callosum Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 217.04 Stdv: 11.39 Min: 194.61 Max: 236.17 Source GEO sample is GSM2887 Last updated (according to GEO): Mar 20 2006 Normal epithelial cells were removed by dissection and digestion from bronchi of donor long tissue from normal subject. Source GEO sample is GSM3919 Last updated (according to GEO): May 27 2005 Epithelium 861 Nasal Epithelium 901 858 Mesodermal cell Blood 1000 Cerebral cortex 1000 Neoplasm 861 none Source GEO sample is GSM210305 Last updated (according to GEO): Jul 16 2007 Cytomegalovirus Infections 901 2 hr Hela Double Thymidine, exp2 Vestibular Nuclei Superior 10 Normal olfactory epithelium 194 213 bronchial epithelia 224 243 Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 8 day time point Source GEO sample is GSM159779 Last updated (according to GEO): Apr 23 2007 Retina 1000 MGJZ030207135Btestis Acetaminophen 3hr Rat 7415 left_liver_lobe vs. Control Acetaminophen 3hr Rat left_liver_lobe Pool Whole blood 0 10 Spleen 0 5 861 Eminence This is the mutant littermate at postnatal day 1 pooled 4 animals Lot batch = Source GEO sample is GSM4073 Last updated (according to GEO): May 28 2005 PGA-lv_48h_518 heart_atrium_4 of the tumors 155 167 861 Occipital lobe BC711B-BE 983 Occipital region Autistic Disorder 877 43 0 Chorionic mesoderm-derived mesenchymal cells Mesenchymal Stem Cells 1000 Blood 861 G2 Optic Nerve Gene expression data from postmorten brain regions Source GEO sample is GSM145582 Last updated (according to GEO): Nov 20 2006 Human breast tumours are diverse in their natural history and in their responsiveness to treatments. Variation in transcriptional programs accounts for much of the biological diversity of human cells and tumours. In each cell, signal transduction and regulatory systems transduce information from the cell's identity to its environmental status, thereby controlling the level of expression of every gene in the genome. Here we have characterized variation in gene expression patterns in a set of 65 surgical specimens of human breast tumours from 42 different individuals, using complementary DNA microarrays representing 8,102 human genes. These patterns provided a distinctive molecular portrait of each tumour. Twenty of the tumours were sampled twice, before and after a 16-week course of doxorubicin chemotherapy, and two tumours were paired with a lymph node metastasis from the same patient. Gene expression patterns in two tumour samples from the same individual were almost always more similar to each other than either was to any other sample. Sets of co-expressed genes were identified for which variation in messenger RNA levels could be related to specific features of physiological variation. The tumours could be classified into subtypes distinguished by pervasive differences in their gene expression patterns. Sample # 1385-1 7 0 prostate Small Intestine; d14 small intestine Keywords = mouse gene expression database Source GEO sample is GSM29295 Last updated (according to GEO): May 27 2005 Wild type replicate #1 Source GEO sample is GSM107464 Last updated (according to GEO): May 01 2006 substantia_nigra_8 Source GEO sample is GSM80858 Last updated (according to GEO): Mar 31 2006 00291126H95A2-T010310v2p on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Striatal sample from a 12-month-old Hdh4/Q80 mouse. Source GEO sample is GSM238691 Last updated (according to GEO): Oct 19 2007 861 Muscle Coronary heart disease 913 Normal__Ovary_OV_4 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Tissue Source GEO sample is GSM67232 Last updated (according to GEO): Jan 19 2006 Spinal Cord 901 Brain 1000 brain, hippocampus: Aldh5a1-/- #3403 Cereb_e1_le1 330 324 uterus 1000 Left Expression profiling of somatomotor cortex extracted from rats at T0 naive Source GEO sample is GSM41685 Last updated (according to GEO): May 27 2005 Parkinson Disease 861 Liver (HBV+, SF18) SN:1029154 Source GEO sample is GSM115417 Last updated (according to GEO): Jun 20 2006 Adenocarcinoma 861 Coronary heart disease 913 2671 in somatosensory cortex 2693 f2#316 versus pool Mouse Brain tissue Epithelium of bronchus 983 1000 Skin Burkitt Lymphoma 1000 osteoblast 627 637 none Source GEO sample is GSM244554 Last updated (according to GEO): Nov 23 2007 Prefrontal Cortex 0 16 156 145 Their livers Wild type P18 mouse visual cortex contralateral to monocular enucleation Source GEO sample is GSM97200 Last updated (according to GEO): Feb 17 2006 Colon 1000 ER+/LN-/Marks211 on Affymetrix GeneChip Human Full Length Array HuGeneFL Keywords = Heart 505 521 SNU182 cells Spleen 1000 Brain 1000 CNS-SC_InjB30m-4bA-s2 in seminoma 28 38 Expression profiling of spinal cord section (T9) extracted from rats 24h following moderate injury Source GEO sample is GSM31532 Last updated (according to GEO): May 27 2005 Ventral Tegmental Area 1 Normal CNS-SC_InjA4h-4C-s2 in fibroblasts 1222 1236 brain, cerebral cortex: PC3_e1_le1 861 Carcinoma HapMap CHB Male Source GEO sample is GSM159587 Last updated (according to GEO): Feb 01 2007 of the urothelium 147 164 Anterior nares 1000 HCT-116 hgu95d adenoma 1000 1000 Structure of trigeminal ganglion GSE2890 WT-Nrf2-Female-2 Parkinson Disease 1000 brain, cerebral cortex: NMDA1H 5/7_le1 1BJZ02051611_CerebellumPeduncles HUVEC isolate 22 low serum media control for #16 Source GEO sample is GSM12908 Last updated (according to GEO): May 28 2005 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201296 Last updated (according to GEO): Jun 14 2007 during mouse inner ear 68 89 GSE4753 gene expression of 1 day RA differentiated ESCs Source GEO sample is GSM181961 Last updated (according to GEO): Apr 12 2007 PGA-swim_4w_n901 Blastocyst replication 2 Keywords = preimplantation Keywords = development Source GEO sample is GSM14692 Last updated (according to GEO): May 28 2005 Parkinson Disease 861 Tissue Source GEO sample is GSM67223 Last updated (according to GEO): Jan 19 2006 R721P00481 T-ALL-#4 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from postmorten brain regions Source GEO sample is GSM145804 Last updated (according to GEO): Nov 20 2006 Infection 1000 human caudate nucleus Source GEO sample is GSM86838 Last updated (according to GEO): Feb 08 2006 pfc_1029_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A healthy subject Source GEO sample is GSM211039 Last updated (according to GEO): Sep 10 2007 in fibroblasts 1222 1236 of fibroblasts 18 31 no additional Source GEO sample is GSM199374 Last updated (according to GEO): Jun 08 2007 schizophrenia 559 572 Communicable Diseases 861 Placenta [JunctionChip 3 of 5] R490P00325 Transitional epithelium 1000 5 0 brain Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM226051 Last updated (according to GEO): Nov 02 2007 5 0 brain Cerebral cortex 1000 A2780_cis_IC90_pre_2 1000 Neoplasm 607 597 the rectum 425_1 0 cortex 5 Expression profiling of somatomotor cortex extracted from rats at 4h following moderate injury Source GEO sample is GSM44408 Last updated (according to GEO): May 27 2005 Type 1 Diabetes patient and the timepoint 4 months after diagnosis. Source GEO sample is GSM228648 Last updated (according to GEO): Sep 11 2007 266 257 infection CA97-14A Pressure-overload induced hypertrophy model. Mouse was sacrificed 8 weeks after aortic banding. Keywords = cardiac hypertrophy Source GEO sample is GSM2247 Last updated (according to GEO): May 27 2005 40 21 from dorsal pancreas Gene expression data from postmorten brain regions Source GEO sample is GSM144900 Last updated (according to GEO): Nov 20 2006 Nasal Epithelium 865 901 Nervous system structure 33 18 bone marrow cell 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201280 Last updated (according to GEO): Jun 14 2007 Brain 1000 Wild type 8 wk old male C3H/HeJ mouse hippocampus Source GEO sample is GSM74962 Last updated (according to GEO): Feb 27 2007 7111_Lung did not develop PGD Nerve 1000 hip_1042_03 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Gene expression data from whole brain infected mouse, day 6 Source GEO sample is GSM189626 Last updated (according to GEO): May 16 2007 Gene expression regulated by DACH1-4 Macrophage 14smi113 15 7 hindbrain Activation of neurons is one of the fundamental events for the functioning of nervous system. Neuronal activation relays information to next neurons. On the other hand, the activated neurons themselves are also influenced by neuronal activation. Depending on the type and condition of neuronal activation, these activated neurons change their gene expressions, thereby being able to process information more or less efficiently. We applied the microarray technology to identify hither-to-uncharacterized as activity-dependent genes. Especially, we screened the transcription factors, because early changes in the transcription factors should result in alterations of gene expression profiles and subsequent neuronal properties. Last Updated (by provider): Mar 15 2006 Contributers: Sang-Hyun Choi Soon-Jung Kim Woong Sun Eun-Hae Kim Hyun Kim Hyun-Ju Kim Soon-Kwon Park Blood 1000 Cerebral cortex 861 10 Bone marrow 0 Myocardial Infarction 1000 1033 to the pyramidal cells 1055 0 Human Cortex 11 Gene expression data from mammary glands of lactating mice Source GEO sample is GSM202697 Last updated (according to GEO): Jun 20 2007 TUMOR 13 B on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A 1000 ovarian neoplasm GSE7146 858 Prostatic Neoplasms 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM113914 Last updated (according to GEO): Jun 16 2006 901 frontal lobe Category: Cell-line Subcategory: Pharmacogenomics Scanning Software: ScanAlyze Software version: 2.44 Lot batch = dtp2778 Source GEO sample is GSM2097 Last updated (according to GEO): Nov 21 2005 Head and neck cancer Source GEO sample is GSM155646 Last updated (according to GEO): Apr 24 2007 0 Human Cortex 11 Standard Affymetrix Protocol Source GEO sample is GSM16455 Last updated (according to GEO): May 28 2005 Pituitary Gland 861 Human Cortex from neurologically normal control, Caucasian, female. Source GEO sample is GSM225915 Last updated (according to GEO): Nov 02 2007 1000 Cerebral cortex of the postmortem brains 675 699 M_U133A_18_DLPFC 36 21 from whole brain R6/1 wildtype, brain hemisphere Source GEO sample is GSM83874 Last updated (according to GEO): Apr 20 2007 0.2hr Hela Double Thymidine Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68134 Last updated (according to GEO): Jul 07 2006 861 Neoplasm Nanog-iPS cells Source GEO sample is GSM190229 Last updated (according to GEO): May 18 2007 SCG_sema3A_12h_rep2 Examining the effects of tTA expression in mouse hearts Source GEO sample is GSM15067 Last updated (according to GEO): May 28 2005 Primary typical carcinoid 1753 Source GEO sample is GSM17318 Last updated (according to GEO): May 28 2005 Simple annotation: Cell-cycle, thymidine-nocodazole Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14348.gif Source GEO sample is GSM79702 Last updated (according to GEO): Sep 22 2006 Sample Type: cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs nasal epithelium, formaldehyde instilation exposure, vehicle control, single exposure, 6 h time point Source GEO sample is GSM159791 Last updated (according to GEO): Apr 23 2007 N2_d1 #2(16012165010074) n/a Source GEO sample is GSM177935 Last updated (according to GEO): Jun 11 2007 255 235 dilated heart failure Transitional epithelium 1000 M_U133A_111_AnCg at the Human Brain 743 760 large intestine; cecum Source GEO sample is GSM18660 Last updated (according to GEO): May 27 2005 861 Blood 1000 Cerebellum Cerebral cortex 861 Anterior interpositus nucleus-centered deep cerebellar nuclei were sampled using syringe needles Source GEO sample is GSM84983 Last updated (according to GEO): Mar 29 2006 Human prostate cancer cells in different conditions Source GEO sample is GSM13096 Last updated (according to GEO): May 28 2005 nostrils 156 164 Small cell carcinoma of lung 867 861 Blood Primary adenocarcinoma 0 21 861 Spinal Cord 1840 1822 in the PCOS oocyte seminoma specimen, pT3, patient age: 48y; W00 023 brain, frontal cortex: Sample54_e1_le1 67 40 with coronary artery disease collagen 302 310 0 Human Cortex 11 Coronary heart disease 913 G1E_14_A 1000 Hippocampus human cerebellum Source GEO sample is GSM87080 Last updated (according to GEO): Feb 08 2006 control wild-type prostate epithelial cell line maintained in RPMI-1640 medium without fetal bovine serum for 48 hours Keywords = prostate Keywords = epithelial Source GEO sample is GSM14672 Last updated (according to GEO): May 28 2005 Chronic Lymphocytic Leukemia 19 47 cDNAs were generated from 5ug of total RNA per sample by reverse transcription (RT) for two hours at 42oC using the 3DNA SubmicroTM Oligo Expression Array Detection Kit (Genisphere, Hatfield, PA) and Superscript II (Invitrogen, Carlsbad, CA). For each microarray chip two consecutive hybridizations were performed with cDNAs and the fluorescent probes following the manufacture?s specifications. Briefly, in the first hybridization reaction the solution containing the mixture of cDNAs obtained from control and treated cells was loaded onto the CAG Human 19K array and incubated overnight at 55oC in a hybridization chamber (Genemachines, San Carlos, CA). The human 19K array (www.cag.icph.org/microarray_facility.htm) contains 60-mer oligonucleotides (Compugen, San Jose, CA) representing 18,861 human genes spotted onto poly-l-lysine coated glass microscope slides. In the second hybridization reaction Cy3 (green) and Cy5 (red) fluorescent probes were used to label the cDNAs from control and PGJ2-treated cells, respectively. The second hybridization was carried out for 3 hours at 65oC in the hybridization chambers. The arrays were scanned using an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) with laser intensities adjusted to bring the brightest spot just below saturation and the data extracted with the Axon GenePix Pro software. Source GEO sample is GSM98763 Last updated (according to GEO): May 31 2006 GSE3790 1000 Descending colon Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11311 Last updated (according to GEO): May 28 2005 1000 Blood human cerebellum Source GEO sample is GSM87107 Last updated (according to GEO): Feb 08 2006 in the breast tumors also 1133 1157 195 180 atherosclerosis 14 7 amygdala 129S6/SvEvTac amygdala rep3 1000 Muscle Category: Lymphoma Classification Subcategory: Chronic Lymphocytic Leukemia Scanning Software: ScanAlyze Software version: 2.30 Lot batch = lc7b048 Source GEO sample is GSM2019 Last updated (according to GEO): Nov 21 2005 NA19099 Normal Source GEO sample is GSM175870 Last updated (according to GEO): Apr 09 2007 M_U133A_105_DLPFC Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP) and harvested at the beginning (0 h) of pressure experiment #4 (PE4). Keywords = astrocytes Keywords = optic nerve Keywords = hydrostatic pressure Source GEO sample is GSM11378 Last updated (according to GEO): Dec 15 2006 660 mesenchymal stem cell 639 152 117 Keywords = congenital heart disease Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68218 Last updated (according to GEO): Jul 07 2006 Excerpt from a larger study which characterized the transcriptional effects of a spinal cord contusion injury in rats. This is the data from the almost chronic contusion state (35 days) at the injury site (Thoracic 8) - where we saw significant changes in several areas, including cholesterol metabolism genes. Other spinal cord areas (rostral, caudal) and time-points (3 hours, 24 hours, 7 days and 35 days) were analyzed as well and are discussed in our paper and at www.crpf.org/microarray. Note: [] samples from this series, which appear in other Expression Experiments in Gemma, were not imported from the GEO source. The following samples were removed: Last Updated (by provider): May 29 2005 Contributers: Leigh J Leasure Victoria M Perreau Michaela Thallmair James B Aimone Includes GDS1238. Update date: Aug 31 2005. Dataset description GDS1238: Expression profiling of contused spinal cords of Fischer animals. Spinal cords examined 35 days following contusion at the thoracic 8 segment. Results identify potential targets for therapeutic intervention following spinal cord injury.. 913 Coronary heart disease of Parkinson's disease 450 471 1000 Brain 0 Human Cortex 11 Tumor__Breast_Adeno_93_I_192 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A SN:Human Glioblastoma Biopsy 10382 human caudate nucleus Source GEO sample is GSM86845 Last updated (according to GEO): Feb 08 2006 CNS-SCsev_InjA7d-1B-s2 Expression profiling of spinal cord section (T9) extracted from rats 30min following mild injury Source GEO sample is GSM31804 Last updated (according to GEO): May 27 2005 Acetaminophen 6 hr Rat 8960 Blood vs. Acetaminophen 6hr Rat Pooled Control blood Replicate2_Voxel D2 7 0 Pancreas Transplant Series 32 , Transplant # 2 R6/1 27 week transgenic_75F3 NMDA 10 (7/8 RC) (Experiment NMDA1-Run 13384) Treatment, type=time_course, description=samples are treated for 10, 30 or 60 min with NMDA 1mM, the agonist is then washed out and the cells are harvested 24h later, measurement=10.0 m Source GEO sample is GSM96715 Last updated (according to GEO): Feb 14 2006 Subject code A31 Normal Source GEO sample is GSM176334 Last updated (according to GEO): Apr 09 2007 at the Human Brain 724 741 D_U133Plus_16_Amy Large-scale analysis of the human transcriptome. Spleen Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 109.21 Stdv: 5.08 Min: 99.51 Max: 116.91 Source GEO sample is GSM2858 Last updated (according to GEO): May 27 2005 Gene expression data from wild type DAOY cells Source GEO sample is GSM182019 Last updated (according to GEO): Apr 23 2007 Mesenchymal Stem Cells 1000 901 frontal lobe 1000 Left Prostate 861 32 12 frontal temporal lobe Gene expression data from epididymal fat tissues. Source GEO sample is GSM215584 Last updated (according to GEO): Aug 07 2007 Individual LCL vs Pooled Control LCLs Source GEO sample is GSM3333 Last updated (according to GEO): Mar 21 2006 Mesenchymal Stem Cells 1000 10 7 Left R6/1 brain hemisphere time series gene expression Molecular profiles (HG-U95A) of dystrophin-deficient and normal human muscle 1000 Retina Brain 1000 Large-scale analysis of the mouse transcriptome. salivary gland C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 349.62 Stdv: 10.58 Min: 332.63 Max: 369.11 Source GEO sample is GSM2950 Last updated (according to GEO): Mar 20 2006 r7 Gene expression data from postmorten brain regions Source GEO sample is GSM145771 Last updated (according to GEO): Nov 20 2006 HDMTX-13 Accumbens P8 Normal This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system. Source GEO sample is GSM195233 Last updated (according to GEO): Sep 13 2007 Collagen 1000 ventral spinal cord 13 31 17 7 hippocampus 1000 melanoma 86 70 Fetal liver cells Control male 4 901 frontal lobe heart failure 583 595 pfc_1014_01 on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A brain 0 5 Blood Cells 853 861 Heart Gap Junction and Purinergic P2 Receptor Proteins as a Functional Unit: Insights from Transcriptomics. Total RNA from cultured stria vascularis, pool from 12 cochleas. Source GEO sample is GSM124849 Last updated (according to GEO): Aug 04 2006 3_hypothalamus_time_0_#119 GSE7955 1000 Amygdaloid structure mouse brains 187 198 AdACN-1 861 Encephalitis 1000 Brain Gene expression data from postmorten brain regions Source GEO sample is GSM145484 Last updated (according to GEO): Nov 20 2006 5 0 brain Gene-expression variation within and among human populations. Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM11288 Last updated (according to GEO): May 28 2005 brain, unknown: C1B_e1_le1 Posterior root of spinal nerve 901 47 40 modiolus of coronary artery disease 258 284 172 in the cerebral cortex 193 Gene expression data from postmorten brain regions Source GEO sample is GSM144880 Last updated (according to GEO): Nov 20 2006 170 134 with familial combined hyperlipidemia Identif. of oscillatory genes in somitogenesis from functional genomic analysis of C2C12 myoblast line brain, hippocampus: C1-II_e1_le1 1000 Hippocampus Blood 1000 Plasma 861 1000 frontal lobe M14 hgu95e none Source GEO sample is GSM244603 Last updated (according to GEO): Nov 23 2007 1000 Brain Cerebellum 1000 Whole Brain 62 72 MSE_D_G73A Tumor__Leukemia_AML_AML_(13,PK)_BM on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Skeletal bone 861 4 0 Heart Myocardial Infarction 1000 Skeletal muscle structure 901 861 Hippocampus 1082 1062 with medulloblastomas Cerebellum 1000 liver 0 5 070302_HF_301CB 1000 Structure of superior frontal gyrus DBA/2J periaqueductal gray rep1 Parkinson Disease 1000 Chronic Lymphocytic Leukemia 19 47 Prostatic Diseases 913 Gene expression data from postmorten brain regions Source GEO sample is GSM145489 Last updated (according to GEO): Nov 20 2006 1000 Brain f2#68 versus pool Mouse Brain tissue 1000 Liver gene expression from allergen stimulated mouse lung Source GEO sample is GSM158146 Last updated (according to GEO): Jan 25 2007 490 476 to these tumors Gene expression data from Young and Aged behaviorally characterized F344 rats Source GEO sample is GSM132543 Last updated (according to GEO): Feb 26 2007 Hippocampus 861 Autocrine platelet-derived growth factor-dependent gene expression in glioblastoma cells is mediated largely by activation of the transcription factor sterol regulatory element binding protein and is associated with altered genotype and patient survival in human brain tumors. Whole blood from a patient with Parkinson's disease Source GEO sample is GSM153432 Last updated (according to GEO): Jan 11 2007 ES cell line, RNA 73 5 0 brain Mammary Gland @ Invo2, biological rep3 1000 Hippocampus VDXKIU_27B8 brain, Left frontal Lobe: Extract35_le2 1000 Cerebrum with autism spectrum disorder 37 65 D3_TP-72_C Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184680 Last updated (according to GEO): Apr 26 2007 861 Epidermis nostrils 156 164 1000 Brain Skeletal bone 861 KT1027_AR3 HT29_I_CL4001_Colon on Affymetrix GeneChip Human Full Length Array HuGeneFL Simple annotation: Cell-cycle, Dbl thymidine Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13413.gif Source GEO sample is GSM79642 Last updated (according to GEO): Sep 22 2006 1BMH02022101_Colorectal Adenocarc Liver 861 in the cerebral cortex 580 601 Kidney 861 DBA 1-1-3 Testes Brain 861 31 0 Cerebellum Alzheimer's disease 2 Meningioma Primary Grade 1 Source GEO sample is GSM108021 Last updated (according to GEO): Jun 06 2006 1000 Malaria 5 0 Muscle Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68295 Last updated (according to GEO): Jul 07 2006 FL-9;CD19+ Lymphoblastoid Cell Line for Individual 8171.3 log phase heart sprague1 whole tissue, individual animal, 10 weeks old, male Sprague Dawley heart file:R3JW02103011 Source GEO sample is GSM15209 Last updated (according to GEO): May 28 2005 Lymphoblastic Leukemia 901 D3_TP-24_I Brain 861 Gene expression data from postmorten brain regions Source GEO sample is GSM145035 Last updated (according to GEO): Nov 20 2006 Pressure-overload induced hypertrophy model. Mouse was sacrificed 4 hours after sham operation. Keywords = cardiac hypertrophy Source GEO sample is GSM2251 Last updated (according to GEO): May 27 2005 V5-P427 1000 Hyperinsulinism Epithelial ovarian cancer 1000 medulla_4 ESE_N_650 Carcinoma of lung 1000 biopsy sample obtained from a 6-year-old male Duchenne Muscular Dystrophy patient Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle Keywords = Affymetrix HG-U95A array Source GEO sample is GSM15840 Last updated (according to GEO): Sep 08 2006 Hypothalamus RYGB- 0 17 1000 Hippocampus 1000 Hippocampus primary prostate cancer 178 200 Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. FormerSmoker 76 1000 Brain testes_5 mouse brain 452 463 861 Cerebral cortex 861 Pancreas 1000 Malignant neoplasm of breast of the heart 842 854 Total RNA from cultured modiolus, pool from 12 cochleas; used as control for hypoxia. Source GEO sample is GSM124572 Last updated (according to GEO): Aug 04 2006 1000 Liver Astrocytoma 861 Brain 861 "46 hr Hela Double Thymidine, exp3" brain, cerebral cortex: Rat_03-20_NroLep_Lipska_e1_le1 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1). Source GEO sample is GSM201248 Last updated (according to GEO): Jun 14 2007 Heart failure 1000 1000 Rectum Gene expression data from colonic normal mucosa. Source GEO sample is GSM215074 Last updated (according to GEO): Aug 02 2007 CD14+ peripheral blood-derived monocytes were isolated from leukopacks from healthy donors by counterflow centrifugal elutriation. Fresh monocytes were cultured in 6-well tissue culture plates at 2-3 ´ 106/ml in complete RPMI 1640 supplemented with 20 mM glutamine, 2% heat-inactivated human AB serum, 100 ug/ml penicillin, and 100 g/ml streptomycin. For generation of DC, recombinant human (rh) IL-4 and rhGMCSF were added to the culture at 50 ng/ml on days 1, 3, and 5 of culture. Cells were exposed to the pathogens on day 8 of culture, and 16 hours later were harvested and used for RNA preparation. Because of donor-to-donor differences, human experimental systems can be prone to considerable variability. Therefore cells from a total of 7 donors were prepared and infected independently. The RNA from all 7 donors was extracted separately; equivalent amount of RNA from each donor was pooled, and used for subsequent labeling and hybridization. We assessed the variability associated with the preparation of targets and processing of microarrays by replicating this procedure with another set of RNA from the same donors. Keywords = Infectious diseases, Parasites, Infection, Innate immunity Source GEO sample is GSM5139 Last updated (according to GEO): Mar 21 2006 21 adrenal medulla 7 Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds. All sample were compared to a common pool created from equal portions of RNA from each of the samples. Source GEO sample is GSM68143 Last updated (according to GEO): Jul 07 2006 PGA_MI_nilv_24h_360 Skeletal muscle biopsy was obtained before a 3-hour hyperinsulinemic (infusion rate 40 mU/m2/min) euglycemic clamp Source GEO sample is GSM172159 Last updated (according to GEO): Feb 28 2007 861 Cerebral cortex Epithelium 861 MuscleRegen-ctx9d-1RLAv2-s2 Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. MRI-no-lytic-lesion sample Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1 Source GEO sample is GSM11447 Last updated (according to GEO): May 28 2005 T-ALL-C19 on Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A Stromo vascular fraction from subcutaneous adipose tissue Source GEO sample is GSM210987 Last updated (according to GEO): Jul 17 2007 BXD31_M7SS02042209 Tissue homogenate from cingulate cortex from GIN mouse (Gad1 inhibitory ref. (pubmed id:10777798) ). Source GEO sample is GSM64187 Last updated (according to GEO): Dec 01 2005 Neoplasm 861 901 Epithelial Cells none Source GEO sample is GSM149617 Last updated (according to GEO): Jan 03 2007 84 69 by heart failure Vastus lateralis muscle biopsy from 69 year old healthy male. Analysis done with Affymetrix Microarray Suite 5.0 software. Source GEO sample is GSM2396 Last updated (according to GEO): May 27 2005 contralateral Cortex 7 27 Small cell carcinoma of lung 901 2 day !Sample_source_name_ch1 = Post Natally excised Human lung tissue Source GEO sample is GSM107834 Last updated (according to GEO): May 04 2006 Nose 1000 Mesenchymal Stem Cells 1000 Biological replicate 2 of 3. (Dye Swap) Voxel labeled with Cy5, Control Whole Brain Labeled with Cy3. Source GEO sample is GSM181106 Last updated (according to GEO): Jul 12 2007 1000 Amygdaloid structure Gene expression data from postmorten brain regions Source GEO sample is GSM145226 Last updated (according to GEO): Nov 20 2006 Primary typical carcinoid 134 Source GEO sample is GSM17315 Last updated (according to GEO): May 28 2005 Cerebral cortex 861 861 Blood Gene expression data from an individual with coronary artery disease Source GEO sample is GSM184763 Last updated (according to GEO): Apr 26 2007 Large-scale analysis of the human transcriptome. Brain, amygdala Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf Analyzed using the Affymetrix MAS4 algorithm. Background: Avg: 257.57 Stdv: 8.51 Min: 243.99 Max: 269.74 Source GEO sample is GSM2874 Last updated (according to GEO): May 27 2005 Myocardium 861 Trigeminal_Ganglion Source GEO sample is GSM18847 Last updated (according to GEO): Sep 25 2006 Kidney Medulla 4 Normal 1000 Muscle Sample Type: human total RNA Sample User: jmorris Description: ALL-pre patient study Comments: Experiment User: jmorris Algorithm: Statistical Corner+ Avg:344, Count:32 Corner- Avg:44606, Count:32 BF: Alpha1:0.04,Alpha2:0.06,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000,SF:12.605693,SFGene:All Background:Avg:445.13,Stdev:15.80,Max:478.5,Min:410.7 Noise:Avg:13.13,Stdev:0.52,Max:14.7,Min:11.6 RawQ:18.16 Keywords = ALL Source GEO sample is GSM3512 Last updated (according to GEO): May 28 2005 Laser captured visceral sensory neurons. Source GEO sample is GSM63667 Last updated (according to GEO): Dec 21 2005 C57L/J Hippocampus B D_U133Plus_92_Amy Spleen 0 5 very advanced HCC Source GEO sample is GSM155954 Last updated (according to GEO): Jun 21 2007 5 0 Muscle 406 395 whose hearts Normal__Kidney_KT_5 on Affymetrix GeneChip Human 35K SubA Array Hu35k-A Liver; Regeneration 24 hrs Keywords = mouse gene expression database Source GEO sample is GSM29371 Last updated (according to GEO): May 27 2005 861 Intestines 67 40 with coronary artery disease mouse brains 187 198 Cerebral cortex 861 ventral spinal cord 13 31 total RNA from mouse (male c57BL/6) spleen total RNA from mouse (male c57BL/6) B cells treated with Bombesin for 120min Source GEO sample is GSM5480 Last updated (according to GEO): May 27 2005 R534P00429 brain 0 5 Spleen vs Platelet activating factor Treated B cell 30min (set1) 901 Epithelial Cells Nervous System; Hypothalamus Keywords = mouse gene expression database Source GEO sample is GSM29421 Last updated (according to GEO): May 27 2005 clone 42 replicate 1 WGACON-217 901 Skeletal muscle structure Myocardial Infarction 1000 Neoplasm 861 SN:1006730 Source GEO sample is GSM115355 Last updated (according to GEO): Jun 20 2006 3x3 pooling strategy, see Nadler et al., 2006 Source GEO sample is GSM114257 Last updated (according to GEO): Jun 16 2006 Pool of 6 saccules at E14.5 Source GEO sample is GSM182619 Last updated (according to GEO): Aug 14 2007 plus_720_2 brain, cerebral cortex: Rat_03-54_NroLep_Lipska_e1_le1 mouse brain contralateral LPS.Dmso, biological rep3 Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg). Source GEO sample is GSM231045 Last updated (according to GEO): Sep 26 2007 na Source GEO sample is GSM181272 Last updated (according to GEO): Apr 10 2007 Small cell carcinoma of lung 901 Epithelium 861 Skeletal_Muscle_Psoas Source GEO sample is GSM19013 Last updated (according to GEO): Sep 25 2006 1000 Brain 430A2_1245_54_control_sham_midbrain Source GEO sample is GSM242679 Last updated (according to GEO): Nov 15 2007 PMN_control_0min_Patient6 Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, LINK_PRE:"http://genomebiology.com/2003/4/10/R66", Roberts CJ et al., Science 2000, 287:873-880, and Johnson et al., submitted to Science, 2003. Keywords = junction alternate splicing oligonucleotide Source GEO sample is GSM28780 Last updated (according to GEO): May 27 2005 Dahl-Iwai (DI) salt-sensitive rats were studied using microarrays to identify gender-specific differences in the kidney, both basal differences and responses to a high salt diet. In DI rat kidneys, gene expression profiles demonstrated inflammatory and fibrotic responses selectively in females. Gonadectomy of DI rats abrogated gender differences in gene expression. Gonadectomized female and gonadectomized male DI rats both responded to high salt with the same spectrum of gene expression changes as intact female DI rats. Androgens dominated the gender selective responses to salt. Several androgen-responsive genes were identified with roles potentiating the differential responses to salt including increased male expression of Angiotensin-Vasopressin