title: Mouse E10.5 urogenital epithelium -/- #3

status: Public on Jan 30 2008

city: Okazaki

first: Ken-ichirou

last: Morohashi

state: Aichi

address: 5-1 Higashiyama, Myodaiji

department: Developmental biology

institute: National institute for basic biology

description: Fluidics Station: Fluidics Script were used FS450_0004

hyb_protocol: The labeled aRNA was fragmented and hybridized to the GeneChip Mouse Genome 430 2.0 array (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: The chips were washed, and stained,with Fluidics Station 450 (Affymetrix) and then scanned with the GeneChip Scanner 3000 (Affymetrix) in accordance with the manufacturer's standard protocols.

data_processing: The scaled values were then analyzed by GeneSpring software (Silicon Genetics, Redwood City, CA). To identify differentially expressed transcripts, pairwise comparison analyses were carried out with Affymetrix GCOS 1.2. Each of the experimental samples (n=3) was compared with each of the reference samples (n=3), resulting in nine pairwise comparisons. This approach based on Mann-Whitney pairwise comparison test allows ranking of the differentially expressed genes as well as calculation of significance (P value <0.05) of each identified change.

source_name: urogenital ridge epithelium, E10.5, -/-

label_protocol: Total RNA was prepared from three groups of wild-type and Emx2 KO specimens, and an aliquot (15 ng) was subjected to two-cycle amplification using MessageAmp™ II aRNA Amplification Kit (Ambion), and thereafter biotin labeling using MessageAmp™ II-Biotin Enhanced Kit (Ambion).

extract_protocol: Wild-type and Emx2 KO fetuses at E10.5 were frozen in OCT compound without fixation. They were sectioned (30 m), stained with heamatoxylin, and air-dried. Some of them were used for GATA4 immunostaining to locate gonadal primordium. The epithelial cells of the gonadal primordium were obtained by Laser Microdissection System (Leica). The specimens prepared from three individuals of wild-type or Emx2 KO were mixed as one group.

tag: Emx2 KO mouse


title: Mouse E10.5 urogenital epithelium +/+ #2

type: RNA

country: Japan

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: urogenital ridge epithelium, E10.5, +/+


title: MCF10A_Monolayer_3

status: Public on Jan 31 2008

city: Cincinnati

first: Nelson

middle: D

last: Horseman

state: OH

address: 231 Albert Sabin Way; MSB 3160

department: Molec & Cell Physiology

country: USA

institute: University of Cincinnati

description:
MCF10A_Monolayer_3
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

hyb_protocol: The hybridization, staining, and washing are carried out using the Affymetrix GeneChip Hybridization Wash and Stain Kit following the manufacturer’s protocols, and the arrays were hybridized for 16 hr at 45oC.   FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

scan_protocol: The GeneChips are scanned with Affymetrix GeneChip Scanner 3000 7G using GCOS and software and Affymetrix preset settings.

data_processing: Analysis was performed using R statistical software and the limma Bioconductor package 39.  All steps of data preprocessing, including background correction, normalization, and expression set summaries, were performed using RMA (Robust Multi-chip Average).  Estimated fold changes at each time point were calculated using ANOVA, and resulting t-statistics from each comparison were modified using an intensity-based empirical Bayes method (IBMT) 40 to obtain accurate significance levels.  P-values were adjusted using the False Discovery Rate (FDR) method.

organism: Homo sapiens

source_name: monolayer

label_protocol: Quality of total RNA was first analyzed by Agilent Bioanalyzer 2100, and RNA samples with RIN (RNA Integrity Number) greater than 7.0 are acceptable for microarray analysis.  Total RNA samples were amplified one round, and the amplified RNA (aRNA) biotinylated using Ambion Biotin-Enhanced Message Amp II kit (#1791, Ambion, Austin, Texas), following the manufacturer’s protocols.

growth_protocol: Normal growth media for MCF10As is DMEM:F12 (Cellgro) w/ 2mM glutamine, containing 5% horse serum, insulin (10 µg ml-1) (Gibco), hydrocortisone (0.5 µg ml-1) (Sigma), EGF (20 ng ml-1) (Upstate) and 1 I.U. ml-1 penicillin, 0.1 µg ml-1 streptomysin, 0.25 µg ml-1 amphotericin B (Cellgro).

extract_protocol: Total RNA from cells grown in monolayer and Transwell® cultures were extracted using Tri reagent (MRC, Cincinnati, OH) and cleaned using DNaseI (Promega, Madison, WI) followed by standard phenol/chloroform precipitation and extraction method.

tag: MCF10A cells grown to confluency on sterile plastic from Corning Inc


title: MCF10A_Monolayer_1

description:
MCF10A_Monolayer_1
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).


title: Mouse E10.5 urogenital epithelium +/+ #3


title: Mouse E10.5 urogenital epithelium -/- #1


title: liver_PPARa-knockout_C18:3_6h_rep5

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: liver, PPARα-null mice, C18:3 bolus

hyb_protocol: According to standard Affymetrix protocols.

data_processing: GCRMA version 2.20, empirical Bayes

extract_protocol: TRIzol reagent (Invitrogen), according to manufacturer's instructions

tag: Strain

value: 129S4/SvJae (PPARα-null)

tag: Gender

value: male

tag: Age

value: 8-24 weeks

tag: Tissue

value: liver


title: liver_PPARa-knockout_C18:3_6h_rep3

description: liver, PPARα-null mice, C18:3 bolus

scan_protocol: According to standard Affymetrix protocols.


title: liver_PPARa-knockout_C18:2_6h_rep5

description: liver, PPARα-null mice, C18:2 bolus

label_protocol: According to standard Affymetrix protocols.


title: liver_wildtype_C18:3_6h_rep4

description: liver, wild type mice, C18:3 bolus

value: 129S1/SvImJ (wildtype)


title: Mouse E10.5 urogenital epithelium +/+ #1


title: liver_wildtype_C18:3_6h_rep3

description: liver, wild type mice, C18:3 bolus


title: liver_wildtype_C18:3_6h_rep5

description: liver, wild type mice, C18:3 bolus


title: liver_wildtype_C18:3_6h_rep2

description: liver, wild type mice, C18:3 bolus


title: liver_PPARa-knockout_C18:3_6h_rep1

description: liver, PPARα-null mice, C18:3 bolus


title: liver_PPARa-knockout_C18:3_6h_rep2

description: liver, PPARα-null mice, C18:3 bolus


title: liver_wildtype_C18:3_6h_rep1

description: liver, wild type mice, C18:3 bolus


title: Mouse E10.5 urogenital epithelium -/- #2


title: liver_PPARa-knockout_C18:3_6h_rep4

description: liver, PPARα-null mice, C18:3 bolus


title: liver_PPARa-knockout_C18:2_6h_rep3

description: liver, PPARα-null mice, C18:2 bolus


title: liver_wildtype_C18:2_6h_rep1

description: liver, wild type mice, C18:2 bolus


title: liver_PPARa-knockout_C18:2_6h_rep2

description: liver, PPARα-null mice, C18:2 bolus


title: liver_wildtype_C18:2_6h_rep2

description: liver, wild type mice, C18:2 bolus


title: liver_PPARa-knockout_C18:2_6h_rep4

description: liver, PPARα-null mice, C18:2 bolus


title: liver_wildtype_C18:2_6h_rep4

description: liver, wild type mice, C18:2 bolus


title: liver_PPARa-knockout_C10:0_6h_rep2

description: liver, PPARα-null mice, C10:0 bolus


title: liver_PPARa-knockout_C10:0_6h_rep4

description: liver, PPARα-null mice, C10:0 bolus


title: liver_PPARa-knockout_C18:2_6h_rep1

description: liver, PPARα-null mice, C18:2 bolus


title: liver_wildtype_C18:2_6h_rep3

description: liver, wild type mice, C18:2 bolus


title: liver_wildtype_C10:0_6h_rep5

description: liver, wild type mice, C10:0 bolus


title: liver_PPARa-knockout_C10:0_6h_rep5

description: liver, PPARα-null mice, C10:0 bolus


title: liver_PPARa-knockout_C10:0_6h_rep3

description: liver, PPARα-null mice, C10:0 bolus


title: liver_wildtype_C10:0_6h_rep3

description: liver, wild type mice, C10:0 bolus


title: liver_wildtype_C10:0_6h_rep2

description: liver, wild type mice, C10:0 bolus


title: liver_PPARa-knockout_C10:0_6h_rep1

description: liver, PPARα-null mice, C10:0 bolus


title: human BM MSC TGFb3 stimulated day 7 rep 2

city: Berlin

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

country: Germany

institute: Charité

description: gene expression data of human bone marrow mesenchymal stem cells induced by TGFb3 for chondrogenic differentiation: day 7

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database SiPaGene (www.bioretis.de).

source_name: donor 5, stimulated with TGFb3 for 7 days

label_protocol: 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)

growth_protocol: MSC were isolated from human bone marrow aspirates of healthy donors by adherence to culture dishes. Mononuclear cells were plated at the density of 5x104 cells/cm2 in α-MEM, supplemented with 10% fetal bovine serum (FBS), 1ng/ml basic fibroblast growth factor, 100U/ml penicillin and 100μg/ml streptomycin. When cultures reached 80-90% confluence, cells were detached with 0.05 % trypsin and 0.53 mM EDTA and subsequently plated at the density of 1000cells/cm2 for expansion. Cells from 3 donors were used at passage 3.

extract_protocol: MSC cultured in monolayer were harvested by treatment with trypsin and EDTA, washed with phosphate buffered saline (PBS) and pelleted at 300 X g for 5 min at 4°C to extract RNA on day 0. At day 1, 3, 7 and 21 of chondrogenesis, micropellets were recovered, washed in PBS and mechanically dissociated. The lysis buffer was added on top of the cells and total RNA (3 µg) was extracted using the RNeasy Kit (Qiagen) according to the recommendations of the supplier.

treatment_protocol: Chondrogenic differentiation was induced by a 21 days culture in micropellets. Cells were suspended in 15ml polypropylene conical tubes at the density of 2.5 X 105 cells, after spun down for 5min at 600 X g. The resulting pellets were cultured in 500 µl DMEM supplemented with 0.1 μM dexamethasone, 0.17 mM ascorbate-2 phosphate, 1% insulin-transferrin-sodium selenite supplement and 10 or 100ng/ml of recombinant TGFβ3 or BMP-2, respectively. Media were changed every 2-3 days.

tag: human BM-MSC cultured in α-MEM, supplemented with 10% fetal bovine serum (FBS), 1ng/ml basic fibroblast growth factor, 100U/ml penicillin and 100μg/ml streptomycin at passage 3; thereafter cells were pelleted and cultured in 500 µl DMEM supplemented with 0.1 μM dexamethasone, 0.17 mM ascorbate-2 phosphate, 1% insulin-transferrin-sodium selenite supplement and 100ng/ml of recombinant TGFb3 for 7 days


title: human BM MSC TGFb3 stimulated day 7 rep 3

source_name: donor 6, stimulated with TGFb3 for 7 days


title: human BM MSC TGFb3 stimulated day 3 rep 3

description: gene expression data of human bone marrow mesenchymal stem cells induced by TGFb3 for chondrogenic differentiation: day 3

source_name: donor 6, stimulated with TGFb3 for 3 days

tag: human BM-MSC cultured in α-MEM, supplemented with 10% fetal bovine serum (FBS), 1ng/ml basic fibroblast growth factor, 100U/ml penicillin and 100μg/ml streptomycin at passage 3; thereafter cells were pelleted and cultured in 500 µl DMEM supplemented with 0.1 μM dexamethasone, 0.17 mM ascorbate-2 phosphate, 1% insulin-transferrin-sodium selenite supplement and 100ng/ml of recombinant TGFb3 for 3 days


title: human BM MSC TGFb3 stimulated day 7 rep 1

source_name: donor 4, stimulated with TGFb3 for 7 days


title: human BM MSC TGFb3 stimulated day 1 rep 3

description: gene expression data of human bone marrow mesenchymal stem cells induced by TGFb3 for chondrogenic differentiation: day 1

source_name: donor 6, stimulated with TGFb3 for 1 day

tag: human BM-MSC cultured in α-MEM, supplemented with 10% fetal bovine serum (FBS), 1ng/ml basic fibroblast growth factor, 100U/ml penicillin and 100μg/ml streptomycin at passage 3; thereafter cells were pelleted and cultured in 500 µl DMEM supplemented with 0.1 μM dexamethasone, 0.17 mM ascorbate-2 phosphate, 1% insulin-transferrin-sodium selenite supplement and 100ng/ml of recombinant TGFb3 for 1 day


title: human BM MSC TGFb3 stimulated day 21 rep 3

description: gene expression data of human bone marrow mesenchymal stem cells induced by TGFb3 for chondrogenic differentiation: day 21

source_name: donor 6, stimulated with TGFb3 for 21 days

tag: human BM-MSC cultured in α-MEM, supplemented with 10% fetal bovine serum (FBS), 1ng/ml basic fibroblast growth factor, 100U/ml penicillin and 100μg/ml streptomycin at passage 3; thereafter cells were pelleted and cultured in 500 µl DMEM supplemented with 0.1 μM dexamethasone, 0.17 mM ascorbate-2 phosphate, 1% insulin-transferrin-sodium selenite supplement and 100ng/ml of recombinant TGFb3 for 21 days


title: liver_wildtype_C10:0_6h_rep1

description: liver, wild type mice, C10:0 bolus


title: liver_wildtype_C10:0_6h_rep4

description: liver, wild type mice, C10:0 bolus


title: human BM MSC TGFb3 stimulated day 21 rep 1

source_name: donor 4, stimulated with TGFb3 for 21 days


title: human BM MSC TGFb3 stimulated day 3 rep 2

source_name: donor 5, stimulated with TGFb3 for 3 days


title: human BM MSC TGFb3 stimulated day 1 rep 2

source_name: donor 5, stimulated with TGFb3 for 1 day


title: liver_PPARa-knockout_control2_6h_rep4

description: liver, PPARα-null mice, control condition


title: liver_PPARa-knockout_control2_6h_rep1


title: liver_PPARa-knockout_control2_6h_rep2


title: liver_wildtype_control2_6h_rep3

description: liver, wild type mice, control condition


title: liver_wildtype_control2_6h_rep2


title: liver_PPARa-knockout_control2_6h_rep3


title: liver_wildtype_control2_6h_rep4


title: human BM MSC TGFb3 stimulated day 3 rep 1

source_name: donor 4, stimulated with TGFb3 for 3 days


title: human BM MSC TGFb3 stimulated day 1 rep 1

source_name: donor 4, stimulated with TGFb3 for 1 day


title: human BM MSC BMP2 stimulated day 21 rep 2

description: gene expression data of human bone marrow mesenchymal stem cells induced by BMP2 for chondrogenic differentiation: day 21

source_name: donor 2, stimulated with BMP2 for 21 days

tag: human BM-MSC cultured in α-MEM, supplemented with 10% fetal bovine serum (FBS), 1ng/ml basic fibroblast growth factor, 100U/ml penicillin and 100μg/ml streptomycin at passage 3; thereafter cells were pelleted and cultured in 500 µl DMEM supplemented with 0.1 μM dexamethasone, 0.17 mM ascorbate-2 phosphate, 1% insulin-transferrin-sodium selenite supplement and 100ng/ml of recombinant BMP-2 for 21 days


title: liver_wildtype_control2_6h_rep1


title: human BM MSC BMP2 stimulated day 7 rep 3

description: gene expression data of human bone marrow mesenchymal stem cells induced by BMP2 for chondrogenic differentiation: day 7

source_name: donor 3, stimulated with BMP2 for 7 days

tag: human BM-MSC cultured in α-MEM, supplemented with 10% fetal bovine serum (FBS), 1ng/ml basic fibroblast growth factor, 100U/ml penicillin and 100μg/ml streptomycin at passage 3; thereafter cells were pelleted and cultured in 500 µl DMEM supplemented with 0.1 μM dexamethasone, 0.17 mM ascorbate-2 phosphate, 1% insulin-transferrin-sodium selenite supplement and 100ng/ml of recombinant BMP-2 for 7 days


title: human BM MSC BMP2 stimulated day 7 rep 2

source_name: donor 2, stimulated with BMP2 for 7 days


title: liver_PPARa-knockout_fenofibrate_6h_rep5

description: liver, PPARα-null mice, fenofibrate treatment


title: human BM MSC BMP2 stimulated day 7 rep 1

source_name: donor 1, stimulated with BMP2 for 7 days


title: liver_PPARa-knockout_fenofibrate_6h_rep1


title: human BM MSC BMP2 stimulated day 21 rep 1

source_name: donor 1, stimulated with BMP2 for 21 days


title: liver_wildtype_fenofibrate_6h_rep5

description: liver, wild type mice, fenofibrate treatment


title: liver_PPARa-knockout_fenofibrate_6h_rep3


title: human BM MSC BMP2 stimulated day 1 rep 3

description: gene expression data of human bone marrow mesenchymal stem cells induced by BMP2 for chondrogenic differentiation: day 1

source_name: donor 3, stimulated with BMP2 for 1 day

tag: human BM-MSC cultured in α-MEM, supplemented with 10% fetal bovine serum (FBS), 1ng/ml basic fibroblast growth factor, 100U/ml penicillin and 100μg/ml streptomycin at passage 3; thereafter cells were pelleted and cultured in 500 µl DMEM supplemented with 0.1 μM dexamethasone, 0.17 mM ascorbate-2 phosphate, 1% insulin-transferrin-sodium selenite supplement and 100ng/ml of recombinant BMP-2 for 1 day


title: human BM MSC BMP2 stimulated day 1 rep 1

source_name: donor 1, stimulated with BMP2 for 1 day


title: human BM MSC BMP2 stimulated day 21 rep 3

source_name: donor 3, stimulated with BMP2 for 21 days


title: human BM MSC unstimulated rep 5

description: gene expression data of unstimulated human bone marrow mesenchymal stem cells

source_name: donor 5, unstimulated

tag: human BM-MSC cultured in α-MEM, supplemented with 10% fetal bovine serum (FBS), 1ng/ml basic fibroblast growth factor, 100U/ml penicillin and 100μg/ml streptomycin at passage 3


title: liver_PPARa-knockout_fenofibrate_6h_rep4


title: liver_wildtype_fenofibrate_6h_rep3


title: liver_wildtype_fenofibrate_6h_rep2


title: human BM MSC BMP2 stimulated day 3 rep 3

description: gene expression data of human bone marrow mesenchymal stem cells induced by BMP2 for chondrogenic differentiation: day 3

source_name: donor 3, stimulated with BMP2 for 3 days

tag: human BM-MSC cultured in α-MEM, supplemented with 10% fetal bovine serum (FBS), 1ng/ml basic fibroblast growth factor, 100U/ml penicillin and 100μg/ml streptomycin at passage 3; thereafter cells were pelleted and cultured in 500 µl DMEM supplemented with 0.1 μM dexamethasone, 0.17 mM ascorbate-2 phosphate, 1% insulin-transferrin-sodium selenite supplement and 100ng/ml of recombinant BMP-2 for 3 days


title: liver_wildtype_fenofibrate_6h_rep4


title: human BM MSC BMP2 stimulated day 3 rep 1

source_name: donor 1, stimulated with BMP2 for 3 days


title: liver_wildtype_fenofibrate_6h_rep1


title: liver_PPARa-knockout_fenofibrate_6h_rep2


title: human BM MSC BMP2 stimulated day 3 rep 2

source_name: donor 2, stimulated with BMP2 for 3 days


title: human BM MSC unstimulated rep 4

source_name: donor 4, unstimulated


title: human BM MSC BMP2 stimulated day 1 rep 2

source_name: donor 2, stimulated with BMP2 for 1 day


title: human BM MSC unstimulated rep 6

source_name: donor 6, unstimulated


title: liver_PPARa-knockout_C226_6h_rep5

description: liver, PPARα-null mice, C22:6 bolus


title: human BM MSC unstimulated rep 2

source_name: donor 2, unstimulated


title: liver_PPARa-knockout_C226_6h_rep2

description: liver, PPARα-null mice, C22:6 bolus


title: liver_PPARa-knockout_C226_6h_rep4

description: liver, PPARα-null mice, C22:6 bolus


title: liver_PPARa-knockout_C226_6h_rep1

description: liver, PPARα-null mice, C22:6 bolus


title: liver_PPARa-knockout_C226_6h_rep3

description: liver, PPARα-null mice, C22:6 bolus


title: human BM MSC unstimulated rep 3

source_name: donor 3, unstimulated


title: liver_wildtype_C22:6_6h_rep4

description: liver, wild type mice, C22:6 bolus


title: human BM MSC unstimulated rep 1

source_name: donor 1, unstimulated


title: liver_wildtype_C22:6_6h_rep2

description: liver, wild type mice, C22:6 bolus


title: liver_wildtype_C22:6_6h_rep5

description: liver, wild type mice, C22:6 bolus


title: liver_wildtype_C22:6_6h_rep3

description: liver, wild type mice, C22:6 bolus


title: liver_wildtype_C22:6_6h_rep1

description: liver, wild type mice, C22:6 bolus


title: liver_PPARa-knockout_C205_6h_rep3

description: liver, PPARα-null mice, C20:5 bolus


title: Partially reprogrammed clone Clone100

city: Los Angeles

first: William

last: Lowry

state: CA

address: 621 Charles Young Drive

department: MCDB

institute: UCLA

description: standard protocol

hyb_protocol: Affy Hyb Kit

scan_protocol: Affy Scan Kit

data_processing: GCOS software

label_protocol: Affy Kit

extract_protocol: Stratagene kit

tag: partially reprogrammed clone


title: liver_PPARa-knockout_C205_6h_rep4

description: liver, PPARα-null mice, C20:5 bolus


title: liver_wildtype_C20:5_6h_rep5

description: liver, wild type mice, C20:5 bolus


title: Partially reprogrammed clone Hips29

description: standard protocols applied

hyb_protocol: Affy Eukaryotic Hyb Kit

scan_protocol: Gene Chip scanner 3000

data_processing: GCOS operating software

label_protocol: affy HT IVT kit

extract_protocol: Stratagene


title: Human embryonic stem cell line H9

description: standard protocol

tag: human embryonic stem cell line


title: Partially reprogrammed clone 54

description: standard protocol

tag: partially reprogrammed clone 54


title: liver_PPARa-knockout_C205_6h_rep2

description: liver, PPARα-null mice, C20:5 bolus


title: liver_PPARa-knockout_C205_6h_rep1

description: liver, PPARα-null mice, C20:5 bolus


title: Reprogrammed clone 7 Hips7

description: standard protocols applied

tag: reprogrammed clone 7


title: liver_wildtype_C20:5_6h_rep4

description: liver, wild type mice, C20:5 bolus

tag: Strain


title: liver_wildtype_C20:5_6h_rep2

description: liver, wild type mice, C20:5 bolus

tag: Gender


title: Partially reprgrammed clone Hips24

description: standard protocols applied


title: Reprogrammed clone 2 Hips2

description: standard protocol

tag: reprogrammed clone 2


title: Reprogrammed clone Hips1

description: standard protocol

tag: reprogrammed clone


title: Reprogrammed clone 5 hips5

description: standard protocols applied

tag: reprogrammed clone 5


title: human BM MSC TGFb3 stimulated day 21 rep 2

source_name: donor 5, stimulated with TGFb3 for 21 days


title: Human Embryonic Stem Cells passage 49 HSF1

description: standard protocols applied

source_name: Human Embryonic Stem Cells

tag: passage 49


title: Fibroblasts NHDF1

description: standard protocol

source_name: NHDF

tag: fibroblasts


title: Fibroblasts and 5 factors after 18 days NHDF1 +5V

description: standard protocols applied

tag: NHDF1 + 5 factors after 18 days


title: Fibroblasts with GFP virus NHDF1 + GFP

description: standard protocols applied

tag: fibroblasts with GFP virus


city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

description: Transcriptome analyses of HeLa cells treated by hScc1 RNAi(1). hScc1 RNAi sample was compared with non-treated control sample (Control RNAi(1)).

hyb_protocol: Samples were denatured at 99C for 5 minutes, and then put at 45C for 5min. before being hybridized for 16 hours at 45C in an hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).

scan_protocol: Arrays were scanned using the Genechip Scanner3000 7G following the library array description.

data_processing: Chip data was analyzed by MAS (Microarray Analysis Suit) 5 software provided by Affymetrix using default setting.

source_name: HeLa cells treated by hScc1 RNAi

label_protocol: IVT labelling was performed using GeneChip Expression 3'-Amplification Reagents (P/N900449)

extract_protocol: The siRNA oligos were annealed according to manufacturer’s instruction and used at a final concentration of 100-200 nM. The siRNA transfection was performed using oligofectamine (Invitrogen) and the cells were synchronized in G2 phase by double thymidine block before harvesting. For the preparation of total RNA from mammalian cells, Trizol extraction protocol was used, followed by a clean up step using the RNeasy Total RNA Isolation Mini Kit (Qiagen 74104).To minimize the possibility of artifacts by RNAi treatment, experiment was performed twice, using two different oligos for the knock down of hScc1 and CTCF, respectively.

tag: HeLa cells treated by hScc1 RNAi was used.


title: liver_wildtype_C20:5_6h_rep3

description: liver, wild type mice, C20:5 bolus

tag: Age

tag: Tissue


title: liver_wildtype_C20:5_6h_rep1

description: liver, wild type mice, C20:5 bolus


description: Transcriptome analyses of HeLa cells treated by Control RNAi(1). Used for normalization of hScc1RNAi(1) and CTCFRNAi(1) samples.

source_name: HeLa cells treated by Control RNAi

tag: HeLa cells treated by control RNAi was used.


description: Transcriptome analyses of HeLa cells treated by Control RNAi(2). Used for normalization of hScc1RNAi(2) and CTCFRNAi(2) samples.


title: liver_PPARa-knockout_C181_6h_rep5

description: liver, PPARα-null mice, C18:1 bolus


title: liver_PPARa-knockout_C181_6h_rep4

description: liver, PPARα-null mice, C18:1 bolus


title: liver_PPARa-knockout_C181_6h_rep1

description: liver, PPARα-null mice, C18:1 bolus


title: liver_PPARa-knockout_C181_6h_rep2

description: liver, PPARα-null mice, C18:1 bolus


title: liver_PPARa-knockout_C181_6h_rep3

description: liver, PPARα-null mice, C18:1 bolus


title: liver_wildtype_C18:1_6h_rep5

description: liver, wild type mice, C18:1 bolus


title: liver_wildtype_C18:1_6h_rep3

description: liver, wild type mice, C18:1 bolus


title: liver_wildtype_C18:1_6h_rep4

description: liver, wild type mice, C18:1 bolus


title: liver_wildtype_C18:1_6h_rep2

description: liver, wild type mice, C18:1 bolus


title: liver_PPARa-knockout_WY14643_6h_rep1

description: liver, PPARa-null mice, treatment with WY14643 for 6h

value: 12-20 weeks


title: liver_wildtype_C18:1_6h_rep1

description: liver, wild type mice, C18:1 bolus


description: Transcriptome analyses of HeLa cells treated by CTCF RNAi(1). CTCF RNAi sample was compared with non-treated control RNAi sample(ControlRNAi(1)).

source_name: HeLa cells treated by CTCF RNAi

tag: HeLa cells treated by CTCF RNAi was used.


description: Transcriptome analyses of HeLa cells treated by CTCF RNAi(2). CTCF RNAi sample was compared with non-treated control sample.


title: liver_PPARa-knockout_WY14643_6h_rep2


title: liver_PPARa-knockout_WY14643_6h_rep3


title: liver_PPARa-knockout_WY14643_6h_rep5


title: liver_PPARa-knockout_WY14643_6h_rep4


title: liver_PPARa-knockout_control_6h_rep5

description: liver, PPARa-null mice, control conditions


title: liver_wildtype_WY14643_6h_rep2

description: liver, wild type mice, treatment with WY14643 for 6h


description: Transcriptome analyses of HeLa cells treated by hScc1 RNAi(2). hScc1 RNAi sample was compared with non-treated control sample (ControlRNAi(2)).


title: liver_PPARa-knockout_control_6h_rep3


title: liver_PPARa-knockout_control_6h_rep4


title: liver_PPARa-knockout_control_6h_rep1


title: liver_wildtype_WY14643_6h_rep3


title: liver_PPARa-knockout_control_6h_rep2


title: liver_wildtype_WY14643_6h_rep4


title: liver_wildtype_WY14643_6h_rep1


title: liver_wildtype_control_6h_rep1

description: liver, wild type mice, control conditions


title: liver_wildtype_control_6h_rep2


title: IRF4,8 null_+IRF4_rep3

status: Public on Jan 26 2008

city: Chicago

first: Harinder

last: Singh

state: IL

department: Molecular Genetics and Cell Biology

institute: Howard Hughes Medical Institute/ University of Chicago

description: IRF4,8 null_+IRF4_rep3, gene expression data

hyb_protocol: According to standard Affymetrix protocols

data_processing: dChip analysis

source_name: IRF4,8 null pre-B cells, IRF4 reintroduced to cells and cultured in 5ng/ul IL-7

growth_protocol: OptiMEM, 5% FCS, 37 degrees celsius, 5%CO2, 5ng/ml recombinant IL-7

extract_protocol: Trizol, phenol chloroform, column prurified

treatment_protocol: Cells were cultured in high Il-7 (5ng/ml), low IL-7 (0.25ng/ul) or in high IL-7 + IRF4

tag: Genotype


title: IRF4,8 null_IL7hi_rep3

description: IRF4,8 null_IL7hi_rep3, gene expression data

scan_protocol: According to standard Affymetrix protocols

source_name: IRF4,8 null pre-B cells, cultured in 5ng/ul IL-7

tag: cultured in 5ng/ul IL-7


title: IRF4,8 null_IL7hi_rep2

description: IRF4,8 null_IL7hi_rep2, gene expression data

label_protocol: According to standard Affymetrix protocols


title: IRF4,8 null_+IRF4_rep2

description: IRF4,8 null_+IRF4_rep2, gene expression data

tag: IRF4 reintroduced to cells and cultured in 5ng/ul IL-7


title: IRF4,8 null_IL7lo_rep3

description: IRF4,8 null_IL7lo_rep3, gene expression data

source_name: IRF4,8 null pre-B cells, cultured in 0.25ng/ul IL-7

tag: cultured in 0.25ng/ul IL-7


title: IRF4,8 null_+IRF4_rep1

description: IRF4,8 null_+IRF4_rep1, gene expression data


title: F7; PATIENT_ID: PA19; CONDITION: co-cultured, E2, PG

city: Stanford

first: Junhee

last: Seok

address: 318 Campus Drive W310 - Davis Lab

institute: Stanford University

description: Breast epithelial cells from contralateral breast tissue of patients diagnosed with a primary breast lesion

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing: dChip

source_name: Breast

label_protocol: cRNA synthesis was performed with 2 µg of total cellular RNA, and labelled based on the protocol outlined by Affymetrix Inc. (Santa Clara, CA), with few modifications

extract_protocol: total epithelial cell RNA was directly extracted from duplicate wells of each treatment using the Rneasy kit (Qiagen)

tag: CONDITION

value: co-cultured, 17-beta estradiol (E2), progesterone (PG)


title: G4; PATIENT_ID: PA20; CONDITION: co-cultured, E2, PG


title: IRF4,8 null_IL7hi_rep1

description: IRF4,8 null_IL7hi_rep1, gene expression data


title: G5; PATIENT_ID: PA20; CONDITION: co-cultured, E2, PG, BPA

value: co-cultured, 17-beta estradiol (E2), progesterone (PG), bisphenol A (BPA)


title: IRF4,8 null_IL7lo_rep2

description: IRF4,8 null_IL7lo_rep2, gene expression data


title: C1; PATIENT_ID: PA12; CONDITION: co-cultured, E2, PG, BPA


title: G3; PATIENT_ID: PA20; CONDITION: co-cultured, E2

value: co-cultured, 17-beta estradiol (E2)


title: IRF4,8 null_IL7lo_rep1

description: IRF4,8 null_IL7lo_rep1, gene expression data


title: F8; PATIENT_ID: PA19; CONDITION: co-cultured, E2, PG, BPA


title: E1; PATIENT_ID: PA16; CONDITION: co-cultured, E2, PG


title: F6; PATIENT_ID: PA19; CONDITION: co-cultured, E2


title: B9; PATIENT_ID: PA12; CONDITION: co-cultured, E2, PG


title: E2; PATIENT_ID: PA16; CONDITION: co-cultured, E2, PG, BPA


title: C5; PATIENT_ID: PA13; CONDITION: co-cultured, E2


title: C8; PATIENT_ID: PA13; CONDITION: co-cultured, E2, PG, BPA


title: D9; PATIENT_ID: PA16; CONDITION: co-cultured, E2


title: F2; PATIENT_ID: PA18; CONDITION: co-cultured, E2, PG, BPA


title: B4; PATIENT_ID: PA7; CONDITION: co-cultured, E2, PG, BPA


title: liver_wildtype_control_6h_rep3

tag: Strain

tag: Gender


title: B8; PATIENT_ID: PA12; CONDITION: co-cultured, E2


title: C7; PATIENT_ID: PA13; CONDITION: co-cultured, E2, PG


title: B3; PATIENT_ID: PA7; CONDITION: co-cultured, E2, PG


title: F1; PATIENT_ID: PA18; CONDITION: co-cultured, E2, PG


title: striatum_wt_22m_200

status: Public on Jan 24 2008

city: Bethesda

first: Alexandre

last: Kuhn

state: MD

address: 35 Convent Dr

department: NIA

institute: NIH

description: Affymetrix GeneChip® Mouse Genome 430 2.0 Array

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol for 100 Format midi arrays (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5)

scan_protocol: Affymetrix® GeneChip® Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5)

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

label: Biotin

source_name: Striatum (brain) wild-type, 22 months, 200

label_protocol: Affymetrix GeneChip® IVT Labeling Kit, according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5)

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturer's protocols

tag: strain

value: C57BL/6 X CBA F1 hybrid

tag: gender

tag: age

value: 22 months

tag: tissue

value: striatum (brain)

tag: mouse model

value: wild-type


title: striatum_CHL2_22m_154

source_name: Striatum (brain) CHL2 mutant, 22 months, 154

value: female

value: CHL2 knock-in mice carrying 150 CAG repeats derived from exon 1 of human HD gene knocked in to the endogenous mouse gene (Lin, C-H. et al. Neurological abnormalities in a knock-in mouse model of Huntington's disease. Hum. Mol. Genet. 10, 137-144 (2001))


title: B2; PATIENT_ID: PA7; CONDITION: co-cultured, E2


title: striatum_wt_22m_180

source_name: Striatum (brain) wild-type, 22 months, 180


title: E9; PATIENT_ID: PA18; CONDITION: co-cultured, E2


title: striatum_wt_22m_170

source_name: Striatum (brain) wild-type, 22 months, 170


title: A7; PATIENT_ID: PA4; CONDITION: co-cultured, E2, PG


title: A8; PATIENT_ID: PA4; CONDITION: co-cultured, E2, PG, BPA


title: striatum_CHL2_22m_153

source_name: Striatum (brain) CHL2 mutant, 22 months, 153


title: CD8 T lymphocytes, replicate 1

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

description: Gene expression data from purified splenic CD8 T lymphocytes from 1 WT C57BL6 mouse

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOE-430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 with the EukGE_WS2v5 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Raw data were transformed with the Mas5 algorithm, which yields a normalized expression value, and "absent" and "present" calls. Target intensity was set to 100 for all chips.

label_protocol: 100 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from between 7.5x10E5 and 1.5x10E6 cells for each leukocyte subset with the Qiagen micro RNAeasy kit, with on column DNase digestion, according to the manufacturer protocol, yielding between 200 and 700 ng of total RNA for each sample.

treatment_protocol: Isolated spleen were digested with collagenase (Liberase CI), erythrocytes were lysed with NH(4)Cl, and leukocytes were resuspended in PBS EDTA 5mM before magnetic separation

tag: Spleen CD8 T cells, sorted as CD8 (pos), CD4 (neg), and CD3 (pos)

tag: Strain:C57BL/6 mice, Gender

value: Female, Age:6-8 weeks, Tissue:spleen


title: A6; PATIENT_ID: PA4; CONDITION: co-cultured, E2


title: B lymphocytes, replicate 3

description: Gene expression data from purified splenic follicular B lymphocytes from 1 WT C57BL6 mouse

tag: Spleen Follicular B lymphocytes from WT mice, sorted as B220 (positive), CD23 (positive), and CD21 (lo/med)

value: Male, Age:6 weeks, Tissue:spleen


title: striatum_CHL2_22m_191

source_name: Striatum (brain) CHL2 mutant, 22 months, 191


title: CD8 T lymphocytes, replicate 2


title: B lymphocytes, replicate 1

description: Gene expression data from purified splenic B lymphocytes from 3 WT C57BL6 mice

tag: Spleen B lymphocytes from WT mice, FACS sorted as CD19(positive) and low in autofluorescence


title: B lymphocytes, replicate 2

description: Gene expression data from purified splenic follicular B lymphocytes from 2 WT C57BL6 mice

tag: Spleen Follicular B lymphocytes from WT mice, sorted as B220 (pos), CD23 (pos), and CD21 (lo/med)


title: striatum_CHL2_22m_141

source_name: Striatum (brain) CHL2 mutant, 22 months, 141


title: CD11b cDCs, replicate 2

description: Gene expression data from purified splenic DCs from 10-15 WT C57BL6 mice

tag: Spleen dendritic cells from WT mice, positively enriched with a cocktail of anti-CD11c- and PDCA1-conjugated magnetic beads (Miltenyi Biotec), and FACS sorted as CD19(neg), CD3(neg), NK1.1(neg), 120G8(neg/low), CD11c(high), CD11b(positive)


title: NK cells, replicate 1

description: Gene expression data from purified splenic NK cells from 6-10 WT C57BL6 mice

tag: Spleen Natural Killer (NK) Cells from WT mice, positively enriched with anti-DX5-conjugated magnetic beads (Miltenyi Biotec), and FACS sorted as TCRbeta(neg), NK1.1(positive)


title: pDCs, replicate 2

tag: Spleen plasmacytoid dendritic cells from WT mice, positively enriched with a cocktail of anti-CD11c- and PDCA1-conjugated magnetic beads (Miltenyi Biotec), and FACS sorted as CD19(neg), CD3(neg), NK1.1(neg), 120G8(high), CD11c(intermediate)


title: striatum_wt_22m_161

source_name: Striatum (brain) wild-type, 22 months, 161


title: NK cells, replicate 2


title: CD8alpha cDCs, replicate 2

tag: Spleen dendritic cells from WT mice, positively enriched with a cocktail of anti-CD11c- and PDCA1-conjugated magnetic beads (Miltenyi Biotec), and FACS sorted as CD19(neg), CD3(neg), NK1.1(neg), 120G8(neg/low), CD11c(high), CD8alpha(positive)


title: placenta_WT_rep#2

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

description: Comparison of gene expression between G9a-/- and wildtype placentae.

hyb_protocol: 15µg of labeled probe was hybridised to the array, washed and stained on the Affymetrix fluidics station 450. Standard protocol. Standard protocol.

scan_protocol: An Affymetrix Scanner 3000 was used to quantify the signal. Standard protocol.

data_processing: MAS5/GCOS: TGT=500, otherwise default values.

source_name: pooled placentae, 9.5 dpc, wildtype, biological replicate

label_protocol: RNA was quantified on an Agilent Bioanalyser and 3µg were used to prepare biotin-labeled cRNA target, as prescribed in the Affymetrix expression manual (Affymetrix, 2004). The biotinylated cRNA target was purified using cRNA Cleanup spin columns (Affymetrix), fragmented with 5x fragmentation buffer (Affymetrix), and quantified prior to hybridization on an Agilent Bioanalyser.

extract_protocol: Total RNAs were extracted using Trizol reagent (Invitrogen).

tag: Age

tag: Tissue

value: placenta.


title: CD8alpha cDCs, replicate 1


title: CD11b cDCs, replicate 1


title: pDCs, replicate 1


title: placenta_G9aKO_rep#2

source_name: pooled placentae, 9.5 dpc, G9a-/-, biological replicate

tag: Strain

value: The G9a gene was trapped by insertion of a beta-galactosidase-neomycin phosphotransferase (beta-geo) construct comprising a splice acceptor (Sutherland et al. 2001). We used a G9a-trapped ES cell line, ES62, to generate chimaeric mice by blastocyst injection. Germ line transmission was obtained from these chimaeras. The obtained transgenic line was maintained in a hemizygous state and was crossed for four generations to C57BL/6 mice. Concomitantly, a second line was derived by back-crossing to a (M. spretus) congenic mouse line, SDP711. G9a-/- embryos and placentas were obtained by inter-crossing these two lines.


title: CD8 P14 Memory cells-1

status: Public on Jan 23 2008

city: Atlanta

first: Shruti

last: Subramaniam

state: GA

address: G211 RRC, Emory University School of Medicine

department: Emory University School of Medicine

institute: Emory University

description: This sample is called Memory-1

hyb_protocol: Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples

data_processing: The array used was GeneChip Mouse Genome 430 2.0 Array. There are 4 groups Naïve, Memory, KLRG-1 Int and KLRG-1 Hi . Each group has 3 biological replicates. The biological replicates are numbered 1 to 3.The data was analyzed using Genespring software.

source_name: Mouse Spleen CD8 T cells

label_protocol: Standard Affymetrix labeling

growth_protocol: Day 60-120 post infection P14 CD8 T-cells were FACS sorted and mRNA isolated for microarray analysis

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: RNA was isolated from cells in Trizol (GIBCO/BRL Life Technologies, Rockville, MD) according to manufacture’s protocol. cDNA was synthesized using SuperScript Choice cDNA synthesis kit (GIBCO/BRL) and an oligo (dT) primer containing a T7 promoter. The MEGAscript T7 kit (Ambion, Austin, TX) was used to amplify cRNA from the cDNA. The cRNA was reverse transcribed with biotinylated nucleotides using Enzo BioArray High Yield RNA Transcript Labeling Kit in the second round of cRNAsynthesis, fragmented, and hybridized on mouse 430.2 Affymetrix microarray chips

tag: LCMV armstrong infection induced FACS sorted CD P14 Memory cells


title: CD8 P14 day 4.5 post-infection KLRG-1 Hi sorted cells-2

description: This sample is called KLRG-1 Hi -2

hyb_protocol: Standard Affymetrix hybridization protocols for eukaryotic total RNA were used for the samples.All samples were hybed at 45C,16 hours,60 RPM in 640 Affymetrix Hyb oven. Affymetrix fludics program EUKGEWS2v4_450 was used for washing and staining

growth_protocol: Day 4.5 post infection P14 CD8 T-cells were FACS sorted for KLRG-1 Hi cells and mRNA isolated for microarray analysis

tag: LCMV armstrong day 4.5 post-infection induced  CD8 P14 FACS sorted KLRG-1 Hi cells


title: CD8 P14 day 4.5 post-infection KLRG-1 Int sorted cells-2

description: This sample is called KLRG-1 Int - 2

growth_protocol: Day 4.5 post infection P14 CD8 T-cells were FACS sorted for KLRG-1 Int cells and mRNA isolated for microarray analysis

tag: LCMV armstrong day 4.5 post-infection induced  CD8 P14 FACS sorted KLRG-1 Int cells


title: CD8 P14 Memory cells-3

description: This sample is called Memory-3


title: CD8 P14 day 4.5 post-infection KLRG-1 Hi sorted cells-1

description: This sample is called KLRG-1 Hi -1


title: CD8 P14 day 4.5 post-infection KLRG-1 Int sorted cells-3

description: This sample is called KLRG-1 Int - 3


title: CD8 P14 Naive cells-1

description: This sample is called Naïve-1

growth_protocol: Naïve P14 CD8 T-cells were FACS sorted and mRNA isolated for microarray analysis

tag: FACS sorted CD8 P14 Naive cells


title: CD8 P14 day 4.5 post-infection KLRG-1 Hi sorted cells-3

description: This sample is called KLRG-1 Hi -3


title: CD8 P14 Naive cells-3

description: This sample is called Naïve-3


title: CD8 P14 Memory cells-2

description: This sample is called Memory-2


title: F1 hybrid (musculus mother x domesticus father) 1, biological rep1, testis

status: Public on Jan 19 2008

city: Cologne

first: Ruth

last: Rottscheidt

address: Zuelpicher Strasse 47

department: Institute for Genetics

institute: University of Cologne

description: Gene expression data from M. m. musculus mother x M. m. domesticus father F1 hybrids,  testis

hyb_protocol: Following fragmentation, 12ug of cRNA were hybridized for 16-18 hr at 45 °C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Bioconductor default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 660 for brain and testis and to 800 for liver.

organism: Mus musculus musculus x M. m. domesticus

source_name: testis

label_protocol: Biotinylated cRNA was prepared according to the Ambion MessageAmp™ II aRNA Amplification Kit from 1ug total RNA.

tag: Gender

value: male, age:53 days, tissue:testis


title: CD8 P14 Naive cells-2

description: This sample is called Naïve-2


title: domesticus male 1, biological rep1, testis

description: Gene expression data from M. m. domesticus testis

organism: Mus musculus domesticus

value: male, age:45 days, tissue:testis


title: F1 hybrid (musculus mother x domesticus father) 2, biological rep2, testis


title: F1 hybrid (castaneus mother x musculus father ) 2, biological rep2, liver

description: Gene expression data from M. m. musculus father x M. m. castaneus mother  F1 hybrids,  liver

organism: Mus musculus musculus x Mus musculus castaneus

source_name: liver

value: male, age:54 days, tissue:liver


title: F1 hybrid (castaneus mother x musculus father ) 2, biological rep2, testis

description: Gene expression data from M. m. musculus father x M. m. castaneus mother  F1 hybrids,  testis

value: male, age:54 days, tissue:testis


title: musculus male 2, biological rep2, testis

description: Gene expression data from M. m. musculus testis

organism: Mus musculus musculus

value: male, age:47 days, tissue:testis


title: musculus male 1, biological rep1, testis


title: F1 hybrid (castaneus mother x musculus father ) 1, biological rep1, liver


title: castaneus male 1, biological rep1, testis

description: Gene expression data from M. m. castaneus testis

organism: Mus musculus castaneus


title: F1 hybrid (musculus mother x castaneus father) 1, biological rep1, testis

description: Gene expression data from M. m. musculus mother x M. m. castaneus father F1 hybrids,  testis


title: castaneus male 2, biological rep2, testis


title: F1 hybrid (castaneus mother x musculus father ) 1, biological rep1, testis


title: domesticus male 2, biological rep2, testis


title: F1 hybrid (musculus mother x castaneus father) 2, biological rep2, liver

description: Gene expression data from M. m. musculus mother x M. m. castaneus father F1 hybrids,  liver

value: male, age:53 days, tissue:liver


title: F1 hybrid (domesticus mother x musculus father) 1, biological rep1, testis

description: Gene expression data from M. m. musculus father x M. m. domesticus mother F1 hybrids,  testis

value: male, age:50 days, tissue:testis


title: F1 hybrid (musculus mother x castaneus father) 2, biological rep2, testis


title: F1 hybrid (domesticus mother x musculus father) 2, biological rep2, testis


title: CD8 P14 day 4.5 post-infection KLRG-1 Int sorted cells-1

description: This sample is called KLRG-1 Int - 1


title: castaneus male 2, biological rep2, liver

description: Gene expression data from M. m. castaneus liver

value: male, age:47 days, tissue:liver


title: musculus male 2, biological rep2, liver

description: Gene expression data from M. m. musculus liver


title: F1 hybrid (domesticus mother x musculus father) 1, biological rep1, liver

description: Gene expression data from M. m. musculus father x M. m. domesticus motherF1 hybrids,  liver

value: male, age:50 days, tissue:liver


title: F1 hybrid (domesticus mother x musculus father) 2, biological rep2, liver


title: F1 hybrid (musculus mother x domesticus father) 2, biological rep2, liver

description: Gene expression data from M. m. musculus mother x M. m. domesticus father F1 hybrids,  liver


title: musculus male 1, biological rep1, liver


title: F1 hybrid (castaneus mother x musculus father ) 1, biological rep1, brain

description: Gene expression data from M. m. musculus father x M. m. castaneus mother  F1 hybrids,  brain

source_name: brain

value: male, age:54 days, tissue:brain


title: domesticus male 2, biological rep2, liver

description: Gene expression data from M. m. domesticus liver

value: male, age:45 days, tissue:liver


title: castaneus male 1, biological rep1, liver


title: F1 hybrid (castaneus mother x musculus father ) 2, biological rep2, brain


title: domesticus male 1, biological rep1, brain

description: Gene expression data from M. m. domesticus brain

value: male, age:45 days, tissue:brain


title: F1 hybrid (musculus mother x domesticus father) 1, biological rep1, brain

description: Gene expression data from M. m. musculus mother x M. m. domesticus father F1 hybrids,  brain

value: male, age:53 days, tissue:brain


title: F1 hybrid (musculus mother x castaneus father) 1, biological rep1, brain

description: Gene expression data from M. m. musculus mother x M. m. castaneus father F1 hybrids,  brain


title: F1 hybrid (musculus mother x castaneus father) 2, biological rep2, brain


title: F1 hybrid (domesticus mother x musculus father) 2, biological rep2, brain

description: Gene expression data from M. m. musculus father x M. m. domesticus mother F1 hybrids,  brain

value: male, age:50 days, tissue:brain


title: musculus male 1, biological rep1, brain

description: Gene expression data from M. m. musculus brain

value: male, age:47 days, tissue:brain


title: F1 hybrid (musculus mother x domesticus father) 2, biological rep2, brain


title: domesticus male 1, biological rep1, liver


title: musculus male 2, biological rep2, brain


title: F1 hybrid (musculus mother x domesticus father) 1, biological rep1, liver


title: castaneus male 2, biological rep2, brain

description: Gene expression data from M. m. castaneus brain


title: F1 hybrid (domesticus mother x musculus father) 1, biological rep1, brain


title: domesticus male 2, biological rep2, brain


title: F1 hybrid (musculus mother x castaneus father) 1, biological rep1, liver


title: castaneus male 1, biological rep1, brain


title: IP Staufen2 59kDa

status: Public on Jan 18 2008

type: other

city: Montréal

first: Luc

last: DesGroseillers

state: Québec

address: 2900 Edouard Montpetit

department: Biochimie

country: Canada

institute: Université de Montréal

description: HEK293 cells transiently transfected with a plasmid coding for Staufen2-HA

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

molecule: other

label_protocol: Standard Affymetrix procedures

growth_protocol: Human HEK293 cells were propagated in DMEM medium (GIBCO-BRL) containing 10% fetal bovine serum. 2 X 106 HEK293 cells were transiently transfected with a plasmmid coding for Staufen2-HA.

extract_protocol: TriZol reagent

treatment_protocol: Cells extracts were immunoprecipitated with anti-HA antibody and co-IPed mRNAs were purified.


title: IP control duplicate

description: Mock transfected HEK293 cells

source_name: Mock transfected HEK293 cells

growth_protocol: Human HEK293 cells were propagated in DMEM medium (GIBCO-BRL) containing 10% fetal bovine serum. 2 X 106 HEK293 cells were mock transfected.

tag: Mock transfected HEK293 cells


title: IP Staufen2 62kDa

source_name: HEK293 cells transiently transfected with a plasmid coding for Staufen2-HA


title: IP Staufen1

description: HEK293 cells transiently transfected with a plasmid coding for Staufen1-HA

growth_protocol: Human HEK293 cells were propagated in DMEM medium (GIBCO-BRL) containing 10% fetal bovine serum. 2 X 106 HEK293 cells were transiently transfected with a plasmmid coding for Staufen1-HA.


title: IP Staufen1 duplicate 3

source_name: HEK293 cells transiently transfected with a plasmid coding for Staufen1-HA


title: IP control(2) duplicate

description: HEK293 cells were mock transfected .


title: IP control(1)

description: Mock transfected HEK293 cells


title: Exp 2876_CLA

status: Public on Jan 17 2008

city: Santa Monica

first: Margaret

last: Flowers

address: 2200 Santa Monica Blvd.

department: Dept of Experimental Therapeutics

institute: John Wayne Cancer Institute

description: Mammary gland, virgin, 8 wk.

hyb_protocol: Affymetrix standard protocols

scan_protocol: Scanning Hardware: Affymetrix 3000 scanner Software: GCOS, manufacturer's recommended settings

data_processing: MAS 5.0 standard processing protocols and settings.

source_name: mouse fed 1% CLA

label_protocol: Affymetrix standard protocols

extract_protocol: Mammary glands were collected according to standard necropsis procedures. Tissue was stored in RNAlater (Sigma, St. Louis, MO) until processing. RNA was obtained using Qiagen RNeasy (Valencia CA) and stored in -80 degrees Celsius.

treatment_protocol: PyV-MT expressing female mice were fed a diet supplemented with 1% conjugated linoleic acid or control chow for 4 weeks. Animals were euthanized at 8 weeks of age and mammary glands were collected for RNA processing.

value: FVB/PyV-Mt

value: 8 weeks

tag: Sex

value: Female

tag: Parity

value: No

value: Mammary gland


title: IP Staufen1 duplicate 1

tag: HEK293 cells transiently transfected with a plasmid coding for Staufen1-HA


title: IP Staufen1 duplicate 2


title: IP Staufen2 59kDa duplicate

description: HEK293 cells were transiently transfected with a plasmmid coding for Staufen2-HA.

tag: HEK293 cells transiently transfected with a plasmid coding for Staufen2-HA


title: Exp 2878_CLA

description: Mammary gland, virgin, 8 wk.


title: Exp 2879_control

description: Mammary gland, virgin, 8 wk.

source_name: mouse fed control chow


title: Exp 2877_CLA

description: Mammary gland, virgin, 8 wk.


title: Exp 2775_CLA

description: Mammary gland, virgin, 8 wk.


title: clone M, tethered, replicate 3

status: Public on Jan 16 2008

description: gene expression data from cultured cells

source_name: NIH3T3 cells carrying multiple lacO insertions (clone M)

growth_protocol: DMEM, 10% FCS, 37 degrees celsius, 5%CO2

extract_protocol: Trizol, phenol chloroform

treatment_protocol: Cells were plated on 10cm dishes and allowed to grow to ~80% confluency

tag: gene position

value: genomic insertion at nuclear periphery


title: clone M, tethered, replicate 1


title: clone M, untethered, replicate 1

value: genomic insertion centrally disposed


title: clone M, tethered, replicate 2


title: Skin_Control E16.5_rep2

city: Logan

first: Jill

last: Guttormsen

state: UT

address: 5600 Old Main Hill

department: ADVS

institute: Utah State University

description: Mouse Skin from embryonic stage E16.5 with Tcfap2c mutation

hyb_protocol: Affymetrix protocols

scan_protocol: Affymetrix Scanner

source_name: mouse skin

label_protocol: Affymetrix kits/protocol

extract_protocol: Qiagen RNeasy kit using manufacturer's instructions

tag: Skin removed from back region of embryonic day 16.5 mouse


title: Skin_Tcfap2c Mutant E16.5_rep3

source_name: mouse skin, Tcfap2c mutant

tag: Skin removed from back region of embryonic day 16.5 mouse, Tcfap2c mutation


title: clone M, untethered, replicate 2


title: Skin_Control E16.5_rep1


title: Skin_Tcfap2c Mutant E16.5_rep2


title: Exp 2773_control

description: Mammary gland, virgin, 8 wk.


title: Mut, biological rep3

status: Public on Jan 15 2008

city: Kansas City

first: Gaye

last: Hattem

state: MO

address: 1000 E. 50th Street

department: Bioinformatics

institute: Stowers Institute for Medical Research

description: Mut, biological rep3

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hrs at 45C on Mouse Genome 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with GCOS (GeneChip Operating Software Version 1.2.0.037) using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: Mus musculus embryo E8.5 Tcof1+/-

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix Two-Cycle Target Labeling Protocol from 100 ng total RNA (Expression Analysis Technical Manual, November 2004 update, Affymetrix).

extract_protocol: Total RNA was extracted using the RNeasy Mini Protocol for Isolation of Total RNA from Animal Tissues (Qiagen).

tag: E.8 DBA-C57BL/6 whole embryo


title: Exp 2880_control

description: Mammary gland, virgin, 8 wk.

tag: Age


title: IP control(1) duplicate 1

description: Mock transfected HEK293 cells


title: IP Staufen2 62kDa duplicate


title: Skin_Control E16.5_rep3


title: Mut, biological rep2

description: Mut, biological rep2


title: Wt, biological rep1

description: Wt, biological rep1

source_name: Mus musculus embryo E8.5 wild-type


title: Skin_Tcfap2c Mutant E16.5_rep1

source_name: mouse skin, Tcfap2 mutant


title: clone M, untethered, replicate 3


title: Wt, biological rep3

description: Wt, biological rep3


title: Mut, biological rep1

description: Mut, biological rep1


title: Wt, biological rep2

description: Wt, biological rep2


title: Activated_CD8+_T_cells

first: Jason

last: Lee

address: 675 Charles E. Young Dr. South

description: Differential gene expression screening between naive and activated CD8+ T cells.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Absolute calls describing whether a probe set is present (P), marginally present (M), or absent (A) were generated using the Affymetrix GeneChip Operating Software v1.3 (GCOS) and expression values were calculated using the PM/MM difference model of DNA-Chip (dChip). Expression values across samples were normalized using dChip’s invariant set method. A gene was considered differentially expressed if the corresponding probe set fit the following criteria: absolute call was P in at least half of the samples, fold change >1.4 between baseline (naïve CD8+ T cells) and experimental (activated CD8+ T cells) using the lower 90% confidence bound of fold change as defined in dChip, and expression difference between the baseline and experimental samples was >100.

source_name: activated CD8+ T cells

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was purified from tissues using the Qiagen RNeasy Mini kit.  Pooled RNA from 4 independent experiments was hybridized.

tag: pmel-1 TCR transgenic mice


title: Liver from Nrf2 wt mice, biological replicate 2

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

description: mRNA pooled from 3 individuals

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.4 software (Affymetrix); Probability scores and fold changes were calculated using the Rosetta Resolver software (Rosetta Biosoftware, Seattle, WA).

source_name: Liver, wt control

label_protocol: Biotinylation; IVT Labeling Kit (Affymetrix Inc., Santa Clara, CA)

extract_protocol: Phenol/Chloroform extraction; RNeasy MinElute kit

tag: mouse strain

tag: genotype

value: Nrf2 wt

tag: tissue

value: mouse liver, 10 weeks


title: Naive_CD8+_T_cells

source_name: naive CD8+ T cells

tag: Pooled RNA from 4 independent experiments was hybridized.


title: Liver from Nrf2 k.o. mice, biological replicate 3

description: mRNA pooled from 3 individuals

source_name: Liver, Nrf2 deficient

value: Nrf2 ko


title: Liver from Nrf2 k.o. mice, biological replicate 1

description: mRNA pooled from 3 individuals


title: Liver from Nrf2 wt mice, biological replicate 1

description: mRNA pooled from 3 individuals


title: Mouse_Liver_PelletDiet__Batch_1__replicate_3

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

description: Gene expression data from Liver of a laboratory mouse fed a Pellet diet for two weeks.

hyb_protocol: Hybridization to Affymetrix® GeneChip® Mouse Genome 430 2.0 arrays was carried out following standard Affymetrix® protocols.

scan_protocol: GeneChips® were scanned using GeneChip Scanner 3000

data_processing: Affymetrix® microarray image data were collected with Affymetrix® GeneChip® Operating Software version 1.1 using default parameters. We used the Bioconductor 'affy' software package for further data analysis. Signal intensities were calculated with the 'rma' function using default parameters, including quantile normalization and log2 transformation. Detection p-values were calculated with the 'mas5calls' function using default parameters.

source_name: Dissected Mouse Liver

label_protocol: Biotinylated cRNA were prepared from 5 microg. total RNA following standard Affymetrix® protocols

growth_protocol: Laboratory mice were fed a Pellet diet for two weeks.

treatment_protocol: Mice were euthanized by cervical dislocation and liver tissue was dissected. RNA was extracted from the 24 samples as per established lab protocols (Franz et al, 2005, PMID: 16420671) and processed in two batches (containing equal numbers of individuals from all treatment groups).

tag: Strain

value: Female.

value: 8 weeks at the experiment start.


title: Mouse_Liver_PelletDiet__Batch_2__replicate_1

tag: Gender


title: Mouse_Liver_PelletDiet__Batch_2__replicate_3


title: Mouse_Liver_PelletDiet__Batch_2__replicate_2


title: Mouse_Liver_ChimpanzeeDiet__Batch_2__replicate_3

description: Gene expression data from Liver of a laboratory mouse fed a Chimpanzee diet for two weeks.

growth_protocol: Laboratory mice were fed a Chimpanzee diet for two weeks.


title: Mouse_Liver_HumanCafeDiet__Batch_2__replicate_3

description: Gene expression data from Liver of a laboratory mouse fed a HumanCafe diet for two weeks.

growth_protocol: Laboratory mice were fed a HumanCafe diet for two weeks.


title: Mouse_Liver_FastFoodDiet__Batch_1__replicate_1

description: Gene expression data from Liver of a laboratory mouse fed a FastFood diet for two weeks.

growth_protocol: Laboratory mice were fed a FastFood diet for two weeks.


title: Mouse_Liver_PelletDiet__Batch_1__replicate_1


title: Mouse_Liver_HumanCafeDiet__Batch_2__replicate_2


title: Mouse_Liver_HumanCafeDiet__Batch_1__replicate_2


title: Liver from Nrf2 wt mice, biological replicate 3

description: mRNA pooled from 3 individuals


title: Mouse_Liver_HumanCafeDiet__Batch_2__replicate_1


title: Mouse_Liver_FastFoodDiet__Batch_2__replicate_3


title: Mouse_Liver_HumanCafeDiet__Batch_1__replicate_3


title: Mouse_Liver_FastFoodDiet__Batch_1__replicate_2


title: Mouse_Liver_FastFoodDiet__Batch_2__replicate_1


title: Mouse_Liver_HumanCafeDiet__Batch_1__replicate_1


title: Mouse_Liver_FastFoodDiet__Batch_2__replicate_2


title: Mouse_Liver_ChimpanzeeDiet__Batch_2__replicate_2


title: Mouse_Liver_FastFoodDiet__Batch_1__replicate_3


title: Mouse_Liver_ChimpanzeeDiet__Batch_2__replicate_1


title: Mouse_Liver_ChimpanzeeDiet__Batch_1__replicate_3


title: Mouse_Liver_PelletDiet__Batch_1__replicate_2


title: Mouse_Liver_ChimpanzeeDiet__Batch_1__replicate_2


title: Mouse_Liver_ChimpanzeeDiet__Batch_1__replicate_1


title: Low_Mo_seg_pool_Ler_col_F2

type: genomic

city: St. Louis

first: Ivan

last: Baxter

address: 975 North Warson Rd

department: PLant Genetics Research Unit

institute: USDA-ARS

description: DNA sample for Bulk Segregant analysis

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaves

label_protocol: Invitrogen Bioprime labelling kit

extract_protocol: Qiagen DNeasy kit

tag: Age:~6 weeks Tissue:Leaves


title: High_Mo_seg_pool_Ler_col_F2

description: DNA sample for Bulk Segregant analysis


title: Mouse_Brain_HumanCafeDiet__Batch_2__replicate_3

description: Gene expression data from Brain of a laboratory mouse fed a HumanCafe diet for two weeks.

source_name: Dissected Mouse Brain

treatment_protocol: Mice were euthanized by cervical dislocation and brain (right cerebral hemisphere) tissue was dissected. RNA was extracted from the 24 samples as per established lab protocols (Franz et al, 2005, PMID: 16420671) and processed in two batches (containing equal numbers of individuals from all treatment groups).


title: Mouse_Brain_PelletDiet__Batch_1__replicate_1

description: Gene expression data from Brain of a laboratory mouse fed a Pellet diet for two weeks.


title: Mouse_Brain_HumanCafeDiet__Batch_1__replicate_1


title: Mouse_Brain_PelletDiet__Batch_1__replicate_3


title: Mouse_Brain_FastFoodDiet__Batch_2__replicate_3

description: Gene expression data from Brain of a laboratory mouse fed a FastFood diet for two weeks.


title: Mouse_Brain_FastFoodDiet__Batch_2__replicate_1


title: Mouse_Brain_HumanCafeDiet__Batch_1__replicate_3


title: Mouse_Brain_ChimpanzeeDiet__Batch_2__replicate_2

description: Gene expression data from Brain of a laboratory mouse fed a Chimpanzee diet for two weeks.


title: Mouse_Brain_PelletDiet__Batch_2__replicate_2


title: Mouse_Brain_FastFoodDiet__Batch_2__replicate_2


title: Mouse_Brain_FastFoodDiet__Batch_1__replicate_2


title: Mouse_Brain_ChimpanzeeDiet__Batch_2__replicate_3


title: Mouse_Brain_FastFoodDiet__Batch_1__replicate_1


title: Mouse_Brain_HumanCafeDiet__Batch_1__replicate_2


title: Mouse_Brain_ChimpanzeeDiet__Batch_2__replicate_1


title: Mouse_Brain_FastFoodDiet__Batch_1__replicate_3


title: Mouse_Brain_HumanCafeDiet__Batch_2__replicate_1


title: Mouse_Brain_ChimpanzeeDiet__Batch_1__replicate_3


title: Mouse_Brain_HumanCafeDiet__Batch_2__replicate_2


title: Mouse_Brain_ChimpanzeeDiet__Batch_1__replicate_2


title: Mouse_Brain_PelletDiet__Batch_2__replicate_3


title: Mouse_Brain_PelletDiet__Batch_1__replicate_2


title: Mouse_Brain_PelletDiet__Batch_2__replicate_1


title: Mouse_Brain_ChimpanzeeDiet__Batch_1__replicate_1


title: SMARTA_Lmgp61_d7_#2

status: Public on Jan 11 2008

city: Salt Lake City

first: Matthew

last: Williams

address: 15 N. Medical Dr. E.

department: Pathology

institute: University of Utah

description: SMARTA cells responding to LCMV expand dramatically and go on to form a long-lived memory population.  Following Lm-gp61 infection, the same cells again expand but fail to form memory.  This experiment analyzes differences in gene expression at the peak of expansion.

hyb_protocol: Standard hybridization to Affymetrix 430_2.0 arrays.

scan_protocol: Standard scanning of Affymetrix 430_2.0 arrays.

data_processing: GCRMA, Bioconductor

source_name: SMARTA TCR transgenic T cells

label_protocol: Two rounds of in vitro transcription using the MessageAmp II kit provided by Ambion (Austin, TX) according to the manufacturer's instructions.  The second round of IVT was performed with added biotin-labled UTP.  RNA was fragmented prior to hybridization.

extract_protocol: Trizol lysis (Invitrogen), chloroform extraction, isopropanol precipitation.

treatment_protocol: SMARTA TCR transgenic T cells were transferred into C57BL/6 mice.  One day later mice were infected with Lm-gp61.  At day 7 post-infection, SMARTA cells were FACS-sorted twice (>99% final purity) using a FACSAria on the basis of expression of the congenic marker Thy1.1.

tag: C57BL/6, female, 10 weeks


title: SMARTA_Lmgp61_d7_#1


title: 3T3-L1 preadipocyte tissue culture, CLA treated, T3, biological rep1

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: 3T3-L1 mouse tissue (preadipocytes) treated with CLA and control samples

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm

data_processing: The data was analysed using Rosetta Resolver 6.0, creating ratio-experiments  for each timepoint using control reps as one pool, and treatment reps as the other pool.  Resulting logratios and p-values are calculated using Rosetta's proprietary ratio error model.

source_name: 3T3-L1 preadipocyte tissue culture, CLA, 12 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

tag: cell line:3T3-L1


title: 3T3-L1 adipocyte tissue culture, c9t11 CLA treated, T2, biological rep1

description: 3T3-L1 RNA treated with cis-9,trans-11 CLA and control samples at different time points

source_name: 3T3-L1 adipocyte tissue culture, c9t11 CLA, 12 hours


title: SMARTA_LCMV_d7_#1

treatment_protocol: SMARTA TCR transgenic T cells were transferred into C57BL/6 mice.  One day later mice were infected with LCMV.  At day 7 post-infection, SMARTA cells were FACS-sorted twice (>99% final purity) using a FACSAria on the basis of expression of the congenic marker Thy1.1.


title: 3T3-L1 preadipocyte tissue culture, CLA treated, T3, biological rep2


title: Liver from Nrf2 k.o. mice, biological replicate 2

description: mRNA pooled from 3 individuals


title: 3T3-L1 adipocyte tissue culture, c9t11 CLA treated, T1, biological rep1

source_name: 3T3-L1 adipocyte tissue culture, c9t11 CLA, 8 hours


title: 3T3-L1 adipocyte tissue culture, LA treated, T1, biological rep2

source_name: 3T3-L1 adipocyte tissue culture, LA, 8 hours


title: 3T3-L1 preadipocyte tissue culture, CLA treated, T2, biological rep1

source_name: 3T3-L1 preadipocyte tissue culture, CLA, 8 hours


title: 3T3-L1 preadipocyte tissue culture, LA treated, T3, biological rep2

source_name: 3T3-L1 preadipocyte tissue culture, LA, 12 hours


title: 3T3-L1 adipocyte tissue culture, LA treated, T1, biological rep4


title: SMARTA_LCMV_d7_#2


title: 3T3-L1 preadipocyte tissue culture, LA treated, T2, biological rep2

source_name: 3T3-L1 preadipocyte tissue culture, LA, 8 hours


title: 3T3-L1 adipocyte tissue culture, LA treated, T1, biological rep3


title: 3T3-L1 preadipocyte tissue culture, LA treated, T3, biological rep1


title: 3T3-L1 preadipocyte tissue culture, CLA treated, T2, biological rep2


title: 3T3-L1 preadipocyte tissue culture, LA treated, T1, biological rep1

source_name: 3T3-L1 preadipocyte tissue culture, LA, 4 hours


title: 3T3-L1 preadipocyte tissue culture, CLA treated, T1, biological rep1

source_name: 3T3-L1 preadipocyte tissue culture, CLA, 4 hours


title: 3T3-L1 adipocyte tissue culture, LA treated, T2, biological rep2

source_name: 3T3-L1 adipocyte tissue culture, LA, 12 hours


title: 3T3-L1 preadipocyte tissue culture, CLA treated, T1, biological rep2


title: 3T3-L1 preadipocyte tissue culture, LA treated, T2, biological rep1


title: 3T3-L1 adipocyte tissue culture, control, T2, biological rep1

description: mouse 3T3-L1 RNA was isolated from tunicamycin exposed and control tissues at 4,8, and 12 hours

source_name: 3T3-L1 adipocyte tissue culture, control, 8 hours


title: 3T3-L1 adipocyte tissue culture, tunicamycin exposed, T2, biological rep1

source_name: 3T3-L1 adipocyte tissue culture, tunicamycin exposed, 8 hours


title: 3T3-L1 adipocyte tissue culture, tunicamycin exposed, T3, biological rep2

source_name: 3T3-L1 adipocyte tissue culture, tunicamycin exposed, 12 hours


title: 3T3-L1 adipocyte tissue culture, control, T3, biological rep1

source_name: 3T3-L1 adipocyte tissue culture, control, 12 hours


title: 3T3-L1 adipocyte tissue culture, tunicamycin exposed, T1, biological rep1

source_name: 3T3-L1 adipocyte tissue culture, tunicamycin exposed, 4 hours


title: 3T3-L1 adipocyte tissue culture, control, T1, biological rep1

source_name: 3T3-L1 adipocyte tissue culture, control, 4 hours


title: 3T3-L1 adipocyte tissue culture, tunicamycin exposed, T3, biological rep1


title: 3T3-L1 adipocyte tissue culture, control, T2, biological rep2


title: 3T3-L1 adipocyte tissue culture, CLA fed, T4, biological rep1

description: mouse 3T3-L1 RNA for each time point was isolated from control (LA) and treatment (CLA) samples

source_name: 3T3-L1 adipocyte tissue culture, CLA, 24 hours


title: 3T3-L1 adipocyte tissue culture, CLA fed, T4, biological rep3


title: 3T3-L1 adipocyte tissue culture, CLA fed, T4, biological rep2


title: 3T3-L1 adipocyte tissue culture, LA fed, T4, biological rep3

source_name: 3T3-L1 adipocyte tissue culture, LA, 24 hours


title: 3T3-L1 adipocyte tissue culture, CLA fed, T3, biological rep3

source_name: 3T3-L1 adipocyte tissue culture, CLA, 12 hours


title: 3T3-L1 adipocyte tissue culture, LA fed, T4, biological rep1


title: 3T3-L1 adipocyte tissue culture, LA fed, T3, biological rep1


title: 3T3-L1 adipocyte tissue culture, LA fed, T4, biological rep2


title: 3T3-L1 adipocyte tissue culture, CLA fed, T3, biological rep1


title: 3T3-L1 adipocyte tissue culture, CLA fed, T3, biological rep2


title: 3T3-L1 adipocyte tissue culture, LA fed, T3, biological rep4


title: 3T3-L1 adipocyte tissue culture, LA fed, T2, biological rep3


title: 3T3-L1 adipocyte tissue culture, CLA fed, T3, biological rep4


title: 3T3-L1 adipocyte tissue culture, LA fed, T3, biological rep2


title: 3T3-L1 adipocyte tissue culture, CLA fed, T2, biological rep2

source_name: 3T3-L1 adipocyte tissue culture, CLA, 8 hours


title: 3T3-L1 adipocyte tissue culture, CLA fed, T2, biological rep1


title: 3T3-L1 adipocyte tissue culture, CLA fed, T2, biological rep3


title: 3T3-L1 adipocyte tissue culture, CLA fed, T1, biological rep2

source_name: 3T3-L1 adipocyte tissue culture, CLA, 4 hours


title: 3T3-L1 adipocyte tissue culture, CLA fed, T1, biological rep1


title: 3T3-L1 adipocyte tissue culture, LA fed, T1, biological rep2

source_name: 3T3-L1 adipocyte tissue culture, LA, 4 hours


title: mouse white adipose tissue, LA fed (control), T2, biological rep1

description: five pooled mice for each Sample

source_name: RP tissue, LA, 12 hours

tag: Tissue:RP fatpad


title: mouse white adipose tissue, LA fed (control), T2, biological rep2

description: five pooled mice for each Sample


title: 3T3-L1 adipocyte tissue culture, LA fed, T1, biological rep1


title: 3T3-L1 adipocyte tissue culture, LA fed, T1, biological rep3


title: mouse white adipose tissue, CLA fed, T2, biological rep2

description: five pooled mice for each Sample

source_name: RP tissue, CLA, 12 hours


title: mouse white adipose tissue, LA fed (control), T3, biological rep2

description: five pooled mice for each Sample

source_name: RP tissue, LA, 24 hours


title: mouse white adipose tissue, LA fed (control), T3, biological rep1

description: five pooled mice for each Sample


title: mouse white adipose tissue, CLA fed, T3, biological rep1

description: five pooled mice for each Sample

source_name: RP tissue, CLA, 24 hours


title: mouse white adipose tissue, CLA fed, T2, biological rep1

description: five pooled mice for each Sample


title: mouse white adipose tissue, CLA fed, T3, biological rep2

description: five pooled mice for each Sample


title: mouse white adipose tissue, CLA fed, T1, biological rep1

description: five pooled mice for each Sample

source_name: RP tissue, CLA, 4 hours


title: mouse white adipose tissue, LA fed (control), T1, biological rep2

description: five pooled mice for each Sample

source_name: RP tissue, LA, 4 hours


title: mouse white adipose tissue, LA fed (control), T1, biological rep1

description: five pooled mice for each Sample


title: mouse white adipose tissue, CLA fed, T1, biological rep2

description: five pooled mice for each Sample


title: T cell_No IL-2_8 hour_rep3

city: Livermore

first: Zhaoduo

last: Zhang

address: 7011 East Ave

department: Biosystems

institute: Sandia National Labs

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by additional IL-2 starvation for 8 hours

hyb_protocol: Following fragmentation, 10 ?g of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix Gene-Chip scanner 3000.

data_processing: The data were analyzed with Affymetric GeneChip Operating Software (GCOS, version 1.3) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: T cells, IL-2 starved for 14 hours followed by additional IL-2 starvation for 8 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ?g total RNA (GeneChip Expression Analysis, Technical Manual (701021 Rev. 5), 2005, Affymetrix).

growth_protocol: Mouse CTLL-2 cells was maintained in an incubator with 5% CO2 at 37oC in D10 medium (D10 = ATCC modified RPMI-1640 medium (10 mM HEPES, 2 mM L-glutamine, 1 mM Sodium pyruvate, 4.5 g/L glucose, 1.5 g/L sodium bicarbonate), supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 50 U/mL penicillin, 50 mg/mL streptomycin, 1 mM sodium pyruvate, 45 µM ?-mercaptoethanol), and 50 U/mL human rIL-2 (Chiron).

extract_protocol: Cells was collected and washed with PBS, resuspended in PBS before adding RNAlater RNA stabilization solution (Qiagen). Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by additional IL-2 starvation for 8 hours at 37oC with 5% CO2.

tag: Cytotoxic T lymphocyte cell line CTLL-2, derived from a C57BL/6 mouse, dependent upon IL-2 for growth


title: T cell_No IL-2_4 hour_rep4

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by additional IL-2 starvation for 4 hours

source_name: T cells, IL-2 starved for 14 hours followed by additional IL-2 starvation for 4 hours

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by additional IL-2 starvation for 4 hours at 37oC with 5% CO2.


title: T cell_No IL-2_8 hour_rep2


title: T cell_No IL-2_4 hour_rep3


title: T cell_No IL-2_8 hour_rep1


title: T cell_No IL-2_4 hour_rep1


title: T cell_IL-2_16 hour_rep2

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by IL-2 stimulation for 16 hours

source_name: T cells, IL-2 starved for 14 hours followed by IL-2 stimulation for 16 hours

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by human rIL-2 (100 U/mL, Chiron) stimulation for 16 hours at 37oC with 5% CO2.


title: T cell_IL-2_24 hour_rep1

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by IL-2 stimulation for 24 hours

source_name: T cells, IL-2 starved for 14 hours followed by IL-2 stimulation for 24 hours

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by human rIL-2 (100 U/mL, Chiron) stimulation for 24 hours at 37oC with 5% CO2.


title: T cell_IL-2_24 hour_rep3


title: T cell_No IL-2_4 hour_rep2


title: T cell_IL-2_12 hour_rep2

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by IL-2 stimulation for 12 hours

source_name: T cells, IL-2 starved for 14 hours followed by IL-2 stimulation for 12 hours

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by human rIL-2 (100 U/mL, Chiron) stimulation for 12 hours at 37oC with 5% CO2.


title: T cell_IL-2_24 hour_rep2


title: T cell_IL-2_16 hour_rep1


title: T cell_IL-2_16 hour_rep3


title: T cell_IL-2_12 hour_rep3


title: T cell_IL-2_12 hour_rep1


title: T cell_IL-2_6 hour_rep3

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by IL-2 stimulation for 6 hours

source_name: T cells, IL-2 starved for 14 hours followed by IL-2 stimulation for 6 hours

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by human rIL-2 (100 U/mL, Chiron) stimulation for 6 hours at 37oC with 5% CO2.


title: T cell_IL-2_10 hour_rep3

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by IL-2 stimulation for 10 hours

source_name: T cells, IL-2 starved for 14 hours followed by IL-2 stimulation for 10 hours

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by human rIL-2 (100 U/mL, Chiron) stimulation for 10 hours at 37oC with 5% CO2.


title: T cell_IL-2_8 hour_rep1

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by IL-2 stimulation for 8 hours

source_name: T cells, IL-2 starved for 14 hours followed by IL-2 stimulation for 8 hours

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by human rIL-2 (100 U/mL, Chiron) stimulation for 8 hours at 37oC with 5% CO2.


title: T cell_IL-2_10 hour_rep2


title: T cell_IL-2_8 hour_rep2


title: T cell_IL-2_8 hour_rep3


title: T cell_IL-2_10 hour_rep1


title: T cell_IL-2_2 hour_rep2

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by IL-2 stimulation for 2 hours

source_name: T cells, IL-2 starved for 14 hours followed by IL-2 stimulation for 2 hours

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by human rIL-2 (100 U/mL, Chiron) stimulation for 2 hours at 37oC with 5% CO2.


title: T cell_IL-2_2 hour_rep3


title: T cell_IL-2_6 hour_rep1


title: T cell_IL-2_1 hour_rep3

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by IL-2 stimulation for 1 hour

source_name: T cells, IL-2 starved for 14 hours followed by IL-2 stimulation for 1 hour

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by human rIL-2 (100 U/mL, Chiron) stimulation for 1 hour at 37oC with 5% CO2.


title: T cell_IL-2_6 hour_rep2


title: T cell_IL-2_2 hour_rep1


title: T cell_IL-2_4 hour_rep4

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by IL-2 stimulation for 4 hours

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software (GCOS, version 1.3) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: T cells, IL-2 starved for 14 hours followed by IL-2 stimulation for 4 hours

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by human rIL-2 (100 U/mL, Chiron) stimulation for 4 hours at 37oC with 5% CO2.


title: T cell_IL-2_1 hour_rep2


title: T cell_IL-2_0.5 hour_rep3

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by IL-2 stimulation for 0.5 hour

source_name: T cells, IL-2 starved for 14 hours followed by IL-2 stimulation for 0.5 hour

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by human rIL-2 (100 U/mL, Chiron) stimulation for 0.5 hour at 37oC with 5% CO2.


title: T cell_IL-2_0.5 hour_rep1


title: T cell_IL-2_1 hour_rep1


title: T cell_IL-2_0.5 hour_rep2


title: T cell_IL-2_4 hour_rep3


title: T cell_IL-2_0hour_rep4

description: Gene expression data from T cells cultured without IL-2, i.e. before IL-2 stimulation.

source_name: T cells, IL-2 starved for 14 hours

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2.


title: T cell_IL-2_4 hour_rep1


title: T cell_IL-2_0hour_rep1


title: T cell_IL-2_4 hour_rep2


title: T cell_IL-2_0hour_rep5


title: T cell_IL-2_0hour_rep2


title: T cell_IL-2_0hour_rep3


title: Sample from retroviral MSCV-D1b infected cyclin D1 knockout 3T3 cells (Line 7).

status: Public on Jan 07 2008

city: Philadelphia

first: Mathew

last: Casimiro

state: PA

address: 1035 BLSB, 233 South 10th street

department: Cancer Biology

institute: Thomas Jefferson University

description: Gene expression data from cyclin D1 knockout 3T3s (cell line 7) infected with cyclin D1 splice variant (variant D1b) using Murine Stem Cell Virus (MSCV) system.

hyb_protocol: The hybridization protocol was followed for single probe array 49 format (standard)/64 format array outlined in genechip expression analysis technical manual provided by Affymetrix. This was also true for washing, staining and scanning procedures.

scan_protocol: Mouse 430 2.0 chips scanned using Gene chip scanner 3000 with autoloader following Affymetrix guidelines. Image aquired using Gene Chip Operating Sofware version 1.4.

data_processing: The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm.

source_name: 3T3 cells from cyclin D1KO mice infected with MSCV-D1b

label_protocol: Total RNA (5µg of RNeasy purified) was reverse transcribed using Superscript III First-Strand Synthesis System (Invitrogen) using a HPLC purified T7-dT24 primer (Sigma Genosys) which contains the T7 polymerase promoter sequence. The single stranded cDNA was converted to double stranded cDNA using DNA polymerase I (promega) and purified by cDNA spin column purification using GeneChip Sample Cleanup Module (Affymetrix). The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix). 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module.

growth_protocol: Cells maintained in DMEM supplemented with 10% fetal bovine serum/ 100u/ml of Penicillin-Streptomycin and cultured at 37oC in 5% carbon dioxide.

extract_protocol: Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.

treatment_protocol: Cell strain 7 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV murine stem cell virus expressing cyclin D1b.

tag: Retrovirus


title: Sample from retroviral MSCV-GFP control infected cyclin D1 knockout 3T3 cells (line 7).

description: Gene expression data from cyclin D1 knockout 3T3s (cell line 7) infected with MSCV-GFP control using Murine Stem Cell Virus (MSCV) system.

source_name: 3T3 cells from cyclin D1KO mice infected with MSCV-GFP control.

treatment_protocol: Cell strain 7 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV-GFP murine stem cell virus.

value: MSCV-GFP


title: Timepoint1b_CP_rep1

city: Rochester

first: Atta

last: Behfar

state: MN

address: 200 First Street SW

institute: Mayo Clinic

description: Gene expression data from stem cells following combinatorial growth factor stimulation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Murine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Stem cells following combinatorial growth factor stimulation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cell culture derived from inner cell mass of murine blastocysts.

extract_protocol: Extraction of total RNA using the Invitrogen Micro-to-Midi kit, performed according to the manufacturer's instructions.

tag: cell type

value: cardopoietic cell (CP)


title: Control_ES-LIF(+)_rep2

description: Gene expression data from naïve stem cells

source_name: Naïve murine stem cells

value: ES-LIF(+)


title: Sample from retroviral MSCV-GFP control infected cyclin D1 knockout 3T3 cells (line 1).

description: Gene expression data from cyclin D1 knockout 3T3s (cell line 1) infected with control retrovirus using Murine Stem Cell Virus (MSCV) system.

treatment_protocol: Cell strain 1 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV-GFP control murine stem cell virus.


title: Sample from retroviral MSCV-D1a infected cyclin D1 knockout 3T3 cells (line 12).

description: Gene expression data from cyclin D1 knockout 3T3s (cell line 12) infected with full length cyclin D1 (variant D1a) using Murine Stem Cell Virus (MSCV) system.

source_name: 3T3 cells from cyclin D1KO mice infected with MSCV-D1a.

treatment_protocol: Cell strain 12 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV-D1a murine stem cell virus.


title: Timepoint2_CM_rep2

value: cardiomyocyte (CM)


title: Sample from retroviral MSCV-D1b infected cyclin D1 knockout 3T3 cells (line 1).

description: Gene expression data from cyclin D1 knockout 3T3s (cell line 1) infected with a splice variant of cyclin D1 (variant D1b) using Murine Stem Cell Virus (MSCV) system.

treatment_protocol: Cell strain 1 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV murine stem cell virus expressing cyclin D1b.


title: Sample from retroviral MSCV-GFP control infected cyclin D1 knockout 3T3 cells (line 12).

description: Gene expression data from cyclin D1 knockout 3T3s (cell line 12) infected with MSCV-GFP control using Murine Stem Cell Virus (MSCV) system.

treatment_protocol: Cell strain 12 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV-GFP control Murine Stem Cell Virus.

value: MSCV-GFP control


title: Sample from retroviral MSCV-D1a infected cyclin D1 knockout 3T3 cells (line 7).

description: Gene expression data from cyclin D1 knockout 3T3s (cell line 7) infected with full length cyclin D1 (variant D1a) using Murine Stem Cell Virus (MSCV) system.

source_name: 3T3 cells from cyclin D1KO mice infected with MSCV-D1a

treatment_protocol: Cell strain 7 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV murine stem cell virus expressing cyclin D1a.


title: Timepoint1_ES-LIF(-)_rep2

description: Gene expression data from stem cells following growth factor withdrawal

source_name: Stem cells following growth factor withdrawal

value: ES-LIF(-)


title: Control_ES-LIF(+)_rep1


title: Timepoint1_ES-LIF(-)_rep1


title: Sample from retroviral MSCV-D1a infected cyclin D1 knockout 3T3 cells (line 1).

description: Gene expression data from cyclin D1 knockout 3T3s (cell line 1) infected with full length cyclin D1 (variant D1a) using Murine Stem Cell Virus (MSCV) system.

treatment_protocol: Cell strain 1 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV murine stem cell virus expressing cyclin D1a.


title: Timepoint2_CM_rep1


title: CP35CA_subject 35

status: Public on Jan 03 2008

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: Gene expression data from subject at time 0h exposed to 200ug diesel exhaust

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133plus2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 scanner

data_processing: The data were analyzed with BioConductor GCRMA using the gcrma package.

source_name: healthy human subject

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle protocol from 50ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Residual phenol were removed using Qiagen's spin columns.


title: CP29BA_subject 29

description: Gene expression data from subject at time 0h exposed to filtered air


title: CP35CC_subject 35

description: Gene expression data from subject at time 4h exposed to 200ug diesel exhaust

source_name: healthy human subject 4h exposed to 200ug diesel exhaust


title: CP29AA_subject 29


title: CP29BC_subject 29

description: Gene expression data from subject at time 4h exposed to filtered air

source_name: healthy human subject 4h exposed to filtered air


title: CP18AA_subject 18


title: CP35BA_subject 35


title: CP29AC_subject 29


title: CP18AD_subject 18

description: Gene expression data from subject at time 22h exposed to 200ug diesel exhaust

source_name: healthy human subject 22h exposed to 200ug diesel exhaust


title: CP16BD_subject 16

description: Gene expression data from subject at time 22h exposed to filtered air

source_name: healthy human subject 22h exposed to filtered air


title: CP29AD_subject 29


title: CP16BC_subject 16


title: CP18AC_subject 18


title: CP35BC_subject 35


title: CP29BD_subject 29


title: CP16AD_subject 16


title: CP16BA_subject 16


title: CP10BC_subject 10


title: CP16AC_subject 16


title: CP10CC_subject 10


title: CP10CA_subject 10


title: Reselected MA low line D2 (2490.VD2-3)

status: Public on Jan 02 2008

city: San Diego

first: Ralph

middle: J

last: Greenspan

address: 10640 John Jay Hopkins Dr.

institute: The Neurosciences Institute

description: Gene expression data from wing discs.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 2500.

organism: Drosophila melanogaster

source_name: Wing discs MA D2 line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Lines H and L were derived from a wild Massachusetts population sample by 20 generations of divergent selection, then isogenized.  H and L were then crossed to make hybrid populations A-D.  After 34 generations of genomic mingling, hybrid lines were divergently selected for 25 generations, then inbred for 10.  The California lines were selected from a separate population.  Flies were cultured at 20ºC on cornmeal agar medium.

treatment_protocol: Larvae were dissected in 30 μl drops of cold PBS on siliconized slides, with needle-tip tweezers where wing disks were rapidly excised and cleaned with tungsten wire needles.  Each pair of disks was then transferred from the needle tip to the bottom of a 0.5 ml microcentrifuge tube in dry ice, where 100 disks were collected in single microcentrifuge tubes.

tag: Reselected Massachussetts low angular offset

value: 3rd instar larvae median age 6.2 hr prior to pupariation.


title: High selected line CA (2531.CF1-1)

description: Gene expression data from wing discs.

source_name: Wing discs CA high line

tag: California high angular offset


title: High selected line CA (2532.CF1-2)

description: Gene expression data from wing discs.

tag: Age


title: Low selected line CA (2535.CF2-2)

description: Gene expression data from wing discs.

source_name: Wing discs CA low line

tag: California low angular offset