title: Colorectal cancer tissue Replicate 3

description: Biological replicate 3 of 3,cancer tissue,colorectal cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,cancer tissue,colorectal cancer patient 3

source_name: nput，cancer tissue,colorectal cancer patient 3


title: Endometrial biopsy_ETB60_CD146+/PDGFRB+

status: Public on Nov 14 2011

type: RNA

city: San Francisco

first: Linda

last: Giudice

state: CA

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

country: USA

institute: University of California, San Francisco

hyb_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

scan_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

data_processing: GeneSpringGX 8.0, Microarray Technology: Affymetrix.ExonExprChip.HuGene-1_0-st-v1, Summarization Algorithm: ExonRMA16, Normalization: Quantile, Baseline Transformation: median of all samples

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Endometrial biopsy_ETB60

label_protocol: RNA was reverse transcribed/amplified into cDNA using the NuGEN FFPE kit, and sense-strand cDNA targets were created using the NuGEN WT-Ovation Exon Module, followed by fragmentation and labeling using NuGEN Encore Biotin Module for hybridization to Affymetrix Human Gene 1.0 ST arrays.

extract_protocol: FACS analyzed sorted cell populations were subject to RNA isolation and purification, with DNAse treatment, using Pico Pure RNA Isolation Kit

tag: age (years)

tag: tissue

value: endometrium

tag: phase

value: Interval

tag: cycle day

tag: cd146 and pdgfrb expression


title: Endometrial biopsy_ETB60_CD146-/PDGFRB+


title: Endometrial biopsy_ETB60_CD146+/PDGFRB-


title: Colorectal cancer tissue Replicate 1

type: genomic

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

description: Biological replicate 1 of 3,cancer tissue,colorectal cancer patient

hyb_protocol: According to the instructions of Agilent Oligo aCGH  Hybridization Kit

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent GeneSpring GX 11.5 was used for background subtraction and LOWESS normalization. Following global mean normalization, probes with an intensity <300 were discarded from further analysis.

molecule: genomic DNA

source_name: methylated CpG-island recovery assay (MIRA) enriched,cancer tissue,colorectal cancer patient 1

label_protocol: The products of whole genome amplification from the total input DNA without MBD enrichment and from methylation-enriched DNA were purified by using DNA purification kit, respectively. The purified DNA fragments were then labeled with cy3-dCTP or cy5-dCTP with Klenow enzyme (Takara) according to the instruction of the manufacturer.

extract_protocol: DNA was isolated from fresh frozen tissues using standard phenol/chloroform method.

value: colorectal cancer

tag: patient

tag: fraction

value: methylated DNA-enriched

source_name: Input, cancer tissue,colorectal cancer patient 1

tag: sample type

value: Input


title: Rps19_polysomal sample_bilogical replicate 2

city: Rotterdam

first: Erdogan

last: Taskesen

address: dr. molewaterplein 50

country: Netherlands

institute: Erasmus University Medical Center (EMC)

hyb_protocol: Affymetrix protocol.

scan_protocol: Affymetrix protocol.

data_processing: Affymetrix Microarray Suite 5 (MAS5) with global scaling to target value 100. Probe sets with polyribosomal intensity lower than 100 were excluded. Subsequently, the intensity values were normalized per probe set for each sample within the associated class to quantify the mRNA transcript association with polyribosomes. These are computed by taking the polyribosomal intensity value per probe set of each sample with respect to the total intensity value within the sample. This resulted into translational ratios that range between 0 and 1.

organism: Mus musculus

source_name: erythrobalsts

label_protocol: Affymetrix protocol.

growth_protocol: Immortalized erythroblasts were expanded under the Epo/SCF/Dex in serum free media.

extract_protocol: 7 ug of RNA was extracted from collected fractions from sucrose gradients profile such, that polyribosomes up to 80S peak were pooled and designated poly sample and the rest of the fractions were pooled and designated sub fractions.

treatment_protocol: 3 days after shRNA lentiviral delivery the cells were treated with cycloheximide, harvested and frozen on nitrogen.

tag: shRNA

value: poly


title: Ikaros KO thymocyte stage 1, biological rep3

status: Public on Nov 13 2011

city: Cambridge

first: Jiangwen

last: Zhang

state: MA

address: 7 Divinity Ave

department: FAS Center for Systems Biology

institute: Harvard University

description: Gene expression data from mouse DP stage thymocytes.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse430_2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with affy bioconductor package.

source_name: mouse C57BL/6 x129S4/SvJae DP pre-leukemic stage1 thymocytes (CD4+ CD8+ TCRlo) with Ikaros inactivation by null mutation (Iknull).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Ikaros null and dominant negative (IkDN) and WT strains were bred and housed under pathogen-free conditions

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

treatment_protocol: Mice were sacrificed at 16 days, 27 days,  3 weeks, 9 weeks of age (3weeks for wt and pre-leukemic 16d, 27d, 9 weeks for pre-leukemic stage I-II-III, and 3)

tag: source tissue

value: thymus

tag: cell phenotype

value: double positive for Cd4 and Cd8

tag: developmental stage

value: thymocyte stage 1

tag: genotype

value: Ikaros knock-out

tag: cell type

value: DP thymocyte

tag: age

value: 3 weeks

tag: genetic background

value: C57BL/6 x129S4/SvJae


title: Ikaros dominant negative thymocyte stage 2 (27 d), biological rep2

description: Gene expression data from mouse DP stage thymocytes with Ikaros inactivation by dominant negative Ik.

source_name: mouse C57BL/6 x129S4/SvJae DP pre-leukemic stage2 thymocytes (CD4+ CD8+ TCRint)with Ikaros inactivation by dominant negative (IkDN).

value: thymocyte stage 2

value: Ikaros dominant negative

value: 27 days


title: Ikaros KO thymocyte stage 1, biological rep2


title: Ikaros dominant negative thymocyte stage 3, biological rep1

source_name: mouse C57BL/6 x129S4/SvJae DP leukemic stage3 thymocytes (CD4+ CD8+ TCRint ICN+ CD25+) with Ikaros inactivation by dominant negative (IkDN).

value: thymocyte stage 3

value: 9 weeks


title: DP wt thymocyte, biological rep2

source_name: mouse C57BL/6 x129S4/SvJae DP stage thymocytes.

value: wt


title: Ikaros dominant negative thymocyte stage 2 (27 d), biological rep1

source_name: mouse C57BL/6 x129S4/SvJae DP pre-leukemic stage2 thymocytes (CD4+ CD8+ TCRint) with Ikaros inactivation by dominant negative (IkDN).


title: DP wt thymocyte, biological rep3


title: No treatment, replicate 3

city: Boston

first: Steven

last: Mullenbrock

address: 24 Cummington St.

department: Biology

institute: Boston University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Normalized using RMA method. The average expression levels of genes upregulated or downregulated upon NGF treatment are provided as a Series Supplementary file [summary_table.xls]

organism: Rattus norvegicus

source_name: PC12_No treatment

label_protocol: standard Affymetrix protocol

growth_protocol: PC12 rat pheochromocytoma cells were grown in Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal bovine serum and 5% horse serum.  For gene expression studies, PC12 cells were plated at 7.6x105 cells per 60 mm plate and 3.5x105 cells per 35 mm plate and allowed to grow for 24 hrs.  After 24 hrs, cells were washed once in low serum media (DMEM with 0.5% horse serum) and then starved for 24 hrs in this low serum media.

extract_protocol: Total RNA for microarray experiments was extracted with TRIzol reagent (Invitrogen).  Following ethanol precipitation, RNA was applied to an RNeasy column (Qiagen) for further purification as per the manufacturer’s protocol.  The quality of the RNA was determined using an Agilent bioanalyzer prior to analysis on Affymetrix Rat Gene 1.0ST microarrays.

treatment_protocol: PC12 cells were treated with NGF (50ng/mL) or EGF (25ng/mL) for 2 or 4 hrs, or left untreated.

tag: cell line

value: pheochromacytoma cells

tag: growth factor treatment

value: No treatment

tag: timepoint


title: Ikaros dominant negative thymocyte stage 2 (16 d), biological rep1

value: 16 days


title: DP wt thymocyte, biological rep1


title: 4hr EGF, replicate 3

source_name: PC12_4hr EGF

value: 25ng/ml EGF


title: 2hr NGF, replicate 3

source_name: PC12_2hr NGF

value: 50ng/ml NGF


title: 4hr NGF, replicate 3

source_name: PC12_4hr NGF


title: 2hr NGF, replicate 2


title: 2hr EGF, replicate 2

source_name: PC12_2hr EGF


title: 4hr NGF, replicate 1


title: No treatment, replicate 2


title: 2hr EGF, replicate 1


title: Dendritic cell plus TNFa sample 2 (GM-TNFa-DC_2)

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

description: BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).

hyb_protocol: Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: Dendritic cells obtained from GM-MPP with GM-CSF plus TNFa

label_protocol: Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.

extract_protocol: Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

tag: strain

value: dendritic cell

tag: treatment

value: GM-CSF and TNFa


title: 4hr NGF, replicate 2


title: 2hr EGF, replicate 3


title: Dendritic cell sample 2 (GM-DC_2)

source_name: Dendritic cells obtained from GM-MPP with GM-CSF

value: GM-CSF


title: 4hr EGF, replicate 2


title: Dendritic cell sample 1 (GM-DC_1)


title: Ikaros dominant negative thymocyte stage 2 (16 d), biological rep2

value: thymus

value: double positive for Cd4 and Cd8

value: DP thymocyte


title: Multipotent progenitor sample 2 (GM-MPP_2)

source_name: Multipotent progenitor (MPP) from mouse bone marrow obtained with stem cell cytokines plus GM-CSF

value: multipotent progenitor cell


title: Dendritic cell plus TNFa sample 1 (GM-TNFa-DC_1)


title: 4hr EGF, replicate 1


title: Ikaros KO thymocyte stage 1, biological rep1

value: thymocyte stage 1

value: Ikaros knock-out

value: 3 weeks

value: C57BL/6 x129S4/SvJae


title: eIF2B R132H/R132H mutant brain at P18, biological rep3

city: Tel Aviv

first: Liraz

last: Marom

address: Department of Cell Research and Immunology Tel Aviv University

department: Cell Research and Immunology

country: Israel

institute: Tel Aviv University

description:
eIF2Bmut P18_c
Gene expression data from brain at postnatal day 18

scan_protocol: according to the instruction manual, as described in the Affymetrix website.

data_processing: Microarray data were normalized using RMA

source_name: eIF2B R132H/R132H mutant brain at P18

label_protocol: 300ng total RNA underwent first-strand and second strand cDNA synthesis. Complementary RNA was generated and used to produce sense-strand cDNA, which was fragmented and end-labeled with biotin. Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

extract_protocol: Total RNA from brain tissues (without the cerebellum) was isolated using Trizol reagent according to the manufacturer's protocol (Invitrogen). RNA samples for microarray analysis were further cleaned using Phase Lock Gel (Eppendorf). RNA quality was assessed by its absorbance at 260nm and 280nm using a NanoDrop spectrophotometer and its integrity was assessed by agarose gel electrophoresis.

tag: tissue

value: brain, not incuding cerebellum

tag: genotype/variation

value: eIF2B-R132H/R132H mutant

value: postnatal day18


title: An evolved EC9-7 clone from Line1

city: Taipei

first: Jun-Yi

last: Leu

address: 128 Academia Road, Section 2, Nankang

department: Insititute of Molecular Biolody

country: Taiwan

institute: Academia Sinica

hyb_protocol: The hybridization protocol was adapted from Microarray Core Facility, Insititute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html)

scan_protocol: Scanned on an Molecular Device AXON 4000B (version GenePix 6.0) and got .gpr files

data_processing: Subtracted background  (no normalization) . Dividing by ch2 (control) was used to transform data (Agilent GeneSpring 7.3.1 software)

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae haploid evolved cells [test]

label_protocol: The label protocol was adapted from Microarray Core Facility, Insititute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html)

growth_protocol: Yeast cells were grown in YPD medium, at 30 degree.

extract_protocol:
After PFGE, The ChrVIII DNA of evolved EC9-7cells was purified from agarose gel and purified by column. Then the DNA was amplified by GenomePlex Whole Genome Amplification Kit. For control W303 strains, Yeast genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit.
Fragmentation protocol: 4.5 µg total genomic DNA were digested by 1 µl Dnase I (0.05 U) at 37 degree for 5 minutes and at 100 degree, 15 minutes for enzyme inactivation.

tag: extract

value: ChrVIII chromosomal DNA

tag: line

source_name: S. cerevisiae haploid evolved cells [reference]

value: total genomic DNA


title: An evolved EC9-7 clone from Line2


title: No treatment, replicate 1

value: pheochromacytoma cells

value: No treatment


title: Total mRNA TSC2 KO+Rapa(30min)

status: Public on Nov 12 2011

city: Ithaca

first: Shu-Bing

last: Qian

state: NY

address: 301 Biotech Bldg.

department: Division of Nutritional Sciences

institute: Cornell University

description: Total mRNA abundance in TSC2 knock out MEFs treated with rapamycin for 30 minutes.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Total mRNA, TSC2 knock out MEFs, Rapamycin 30 min

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Amino Allyl Message AmpTM Amplication kit (Ambion) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MEFs were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum.The cultures were incubated  at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA from each fraction group sample was prepared by Trizol (Invitrogen) following the manufacturer's recommendations . RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: TSC2 WT MEFs or TSC2 KO MEFs were treated with 20nM rapamysin for 30 minutes or 3 hours.

value: mouse embryonic fibroblast

value: TSC2 knock out

tag: sample type

value: total RNA

value: rapamycin 30min


title: M Group mRNA TSC2 WT+Rapa(3hr)

description: mRNA abundance in fractions with 2-4 ribosomes of TSC2 wild type MEFs treated with rapamycin for 3 hours.

source_name: mRNA in fractions with 2-4 ribosomes, TSC2 wild type MEFs, Rapamycin 3 hours

value: TSC2 wild type

value: fractions with 2-4 ribosomes

value: rapamycin 3hr


title: L Group mRNA TSC2 WT+Rapa(3hr)

description: mRNA abundance in fractions with ≥5 ribosomes of TSC2 wild type MEFs treated with rapamycin for 3 hours.

source_name: mRNA in fractions with ≥5 ribosomes, TSC2 wild type MEFs, Rapamycin 3 hours

value: fractions with ≥5 ribosomes


title: S Group mRNA in TSC2 KO+DMSO

description: mRNA abundance in 1 ribosome fraction of TSC2 knock out MEFs ribosome profiling

source_name: mRNA in 1 ribosome fraction, TSC2 knock out MEFs

growth_protocol: TSC2 KO MEFs were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum.The cultures were incubated  at 37 ºC in a humidified incubator with 5% CO2.

treatment_protocol: DMSO as the control

value: 1 ribosome fraction


title: M Group mRNA in TSC2 WT+Rapa(30min)

description: mRNA abundance in fractions with 2-4 ribosomes of TSC2 wild type MEFs treated with rapamycin for 30 minutes.

source_name: mRNA in fractions with 2-4 ribosomes, TSC2 wild type MEFs, Rapamycin 30 min

growth_protocol: TSC2 WT MEFs were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum.The cultures were incubated  at 37 ºC in a humidified incubator with 5% CO2.

treatment_protocol: TSC2 WT MEFs were treated with 20nM rapamycin for 30 minutes.


title: Total mRNA TSC2 WT

description: Total mRNA abundance in TSC2 wild type MEFs

source_name: Total mRNA, TSC2 wild type MEFs


title: 2hr NGF, replicate 1

value: 50ng/ml NGF


title: S Group mRNA in TSC2 WT+Rapa(30min)

description: mRNA abundance in 1 ribosome fraction in TSC2 wild type MEFs treated with rapamycin for 30 minutes.

source_name: mRNA in 1 ribosome fraction, TSC2 wild type MEFs, Rapamycin 30 min


title: M Group mRNA TSC2 KO

description: mRNA abundance in fractions with 2-4 ribosomes of TSC2 knock out MEFs ribosome profiling

source_name: mRNA in fractions with 2-4 ribosomes, TSC2 knock out MEFs


title: Multipotent progenitor sample 1 (GM-MPP_1)

value: multipotent progenitor cell

value: GM-CSF


title: M Group mRNA TSC2 WT

description: mRNA abundance in fractions with 2-4 ribosomes of TSC2 wild type MEFs ribosome profiling

source_name: mRNA in fractions with 2-4 ribosomes, TSC2 wild type MEFs


title: M Group mRNA in TSC2 KO+DMSO

source_name: mRNA in fractions with 2-4 ribosomes, TSC2  knock out MEFs


title: L Group mRNA TSC2 WT

description: mRNA abundance in fractions with ≥5 ribosomes of TSC2 wild type MEFs ribosome profiling

source_name: mRNA in fractions with ≥5 ribosomes, TSC2 wild type MEFs


title: S Group mRNA TSC2 WT

description: mRNA abundance in 1 ribosome fraction of TSC2 wild type MEFs ribosome profiling

source_name: mRNA in 1 ribosome fraction, TSC2 wild type MEFs


title: L Group mRNA in TSC2 WT+DMSO

source_name: mRNA in fractions with ≥5 ribosomes, TSC2 WT MEFs


title: L Group mRNA in TSC2 WT+Rapa(30min)

description: mRNA abundance in fractions with ≥5 ribosomes of TSC2 wild type MEFs treated with rapamycin for 30 minutes.

source_name: mRNA in fractions with ≥5 ribosomes, TSC2 wild type MEFs, Rapamycin 30 min


title: L Group mRNA in TSC2 KO+DMSO

description: mRNA abundance in fractions with ≥5 ribosomes of TSC2 knock out MEFs ribosome profiling

source_name: mRNA in fractions with ≥5 ribosomes, TSC2 knock out MEFs


title: L Group mRNA TSC2 KO+Rapa(30min)

description: mRNA abundance in fractions with ≥5 ribosomes of TSC2 knock out MEFs treated with rapamycin for 30 minutes.

source_name: mRNA in fractions with ≥5 ribosomes, TSC2 knock out MEFs, Rapamycin 30 min


title: Total mRNA TSC2 KO

description: Total mRNA abundance in TSC2 knock out MEFs

source_name: Total mRNA, TSC2 knock out MEFs


title: S Group mRNA TSC2 WT+Rapa(3hr)

description: mRNA abundance in 1 ribosome fraction in TSC2 wild type MEFs treated with rapamycin for 3 hours.

source_name: mRNA in 1 ribosome fraction, TSC2 wild type MEFs, Rapamycin 3 hours


title: S Group mRNA TSC2 KO+Rapa(30min)

description: mRNA abundance in 1 ribosome fraction in TSC2 knock out MEFs treated with rapamycin for 30 minutes.

source_name: mRNA in 1 ribosome fraction, TSC2 knock out MEFs, Rapamycin 30 min


title: Total mRNA in TSC2 WT+Rapa(30min)

description: Total mRNA abundance in TSC2 wild type MEFs treated with rapamycin for 30 minutes.

source_name: Total mRNA, TSC2 wild type MEFs, Rapamycin 30 min


title: S Group mRNA TSC2 KO

source_name: mRNA in 1 ribosome fraction, TSC2 knock out MEFs


title: Total mRNA TSC2 WT+Rapa(3hr)

description: Total mRNA abundance in TSC2 wild type MEFs treated with rapamycin for 3 hours.

source_name: Total mRNA, TSC2 wild type MEFs, Rapamycin 3 hours


title: M Group mRNA TSC2 KO+Rapa(30min)

description: mRNA abundance in fractions with 2-4 ribosomes of TSC2 knock out MEFs treated with rapamycin for 30 minutes.

source_name: mRNA in fractions with 2-4 ribosomes, TSC2 knock out MEFs, Rapamycin 30 min


title: Total mRNA in TSC2 KO+DMSO

source_name: total mRNA , TSC2 knock out MEFs


title: M Group mRNA in TSC2 WT+DMSO

source_name: mRNA in fractions with 2-4 ribosomes, TSC2 WT MEFs


title: S Group mRNA in TSC2 WT+DMSO


title: L Group mRNA TSC2 KO


title: Total mRNA TSC2 WT+DMSO

source_name: Total mRNA, TSC2 Wild Type MEFs


title: colonic tissue from macrophage-specific PPARgamma-deficient mouse, biological rep2

city: Baltimore

first: Maria

last: Salvato

state: MD

address: 725 W Lombard Street

department: Institute of Human Virology

institute: University of Maryland School of Medicine

description:
mut22
Gene expression data from colon of PPARr-deficient littermate mice.

hyb_protocol: According to Affymetrix standard method.

data_processing: gcRMA normalized by using Bioconductor package 'gcrma' in R 2.8.

source_name: colon from macrophage-specific PPARg-deficient mouse

growth_protocol: Six- to eight-week-old PPAR gamma flfl Cre+ mice, with a Cre recombinase targeted to the LysM promoter, and control Cre- littermates (n=20) were housed at the animal facilities at Virginia Polytechnic Institute and State University in a room maintained at 75 F, with a 12:12 h light-dark cycle starting from 6:00 AM.  All experimental procedures were approved by the Institutional Animal Care and Use Committee of Virginia Polytechnic Institute and State University and met or exceeded requirements of the Public Health Service/National Institutes of Health and the Animal Welfare Act.

extract_protocol: Whole colonic tissue was collected from mice and preserved in RNAlater® (Applied Biosystems/Ambion Foster City, CA). After homogenization, total RNA was extracted and purified using the RNAeasy system according to manufacturer's instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.

treatment_protocol: Colitis was induced with 2.5% dextran sodium sulfate (DSS), 36,000–44,000 mol wt (ICN Biomedicals, Aurora, OH) in the drinking water.  After the DSS challenge mice were weighed on a daily basis and examined for clinical signs of disease associated with colitis (i.e., perianal soiling, rectal bleeding, diarrhea, and piloerection).  For the DSS challenge, the disease activity indices and rectal bleeding scores were calculated using a modification of a previously published compounded clinical score. Briefly, disease activity index consisted of a scoring for diarrhea and lethargy, whereas rectal bleeding consisted of a visual observation of blood in feces and the perianal area.  Mice in the DSS study were euthanized on day 7 of the DSS challenge by CO2 asphyxiation and blood was withdrawn from the heart.  Colons and spleens were scored based on size and macroscopic inflammatory lesions.

value: colon

value: PPAR g fl/fl; Lysozyme M cre+

tag: phenotype

value: PPAR gamma deficient

value: dextran sodium sulfate (DSS)


title: colonic tissue from macrophage-specific PPARgamma-deficient mouse, biological rep3

description:
mut25
Gene expression data from colon of PPARr-deficient littermate mice.

scan_protocol: According to Affymetrix standard method.


title: colonic tissue from macrophage-specific PPARgamma-deficient mouse, biological rep1

description:
mut14
Gene expression data from colon of PPARr-deficient littermate mice.

label_protocol: According to Affymetrix standard method.


title: colonic tissue from floxed mouse, biological rep1

description:
wild4
Gene expression data from colon of control littermate mice.

source_name: colon from floxed mouse, wild-type phenotype

value: PPAR g fl/fl; Lysozyme M cre-

value: wild-type


title: colonic tissue from floxed mouse, biological rep3

description:
wild8
Gene expression data from colon of control littermate mice.


title: colonic tissue from floxed mouse, biological rep2

description:
wild7
Gene expression data from colon of control littermate mice.


title: UUX01-E

city: Farmington

first: Paul

last: Robson

state: CT

address: 10 Discovery Way

institute: The Jackson Laboratory for Genomic Medicine

description: Genomic DNA extracted from embryonic stem cells was genotyped using the Infinium HumanOmni1-Quad BeadChip (Illumina).

hyb_protocol: The DNA resuspended in RA1 was dispensed onto BeadChips arrays. The BeadChips were incubated in the Illumina Hybridization Oven to hybridize  the samples onto the BeadChips for 16-24 hours.

scan_protocol: BeadChip arrays were stained and then coated with XC4/ 100% Ethanol , dried for 55 minutes and scanned on a BeadArray Reader (Illumina). The iScan Reader uses two lasers to excite the fluorphores of the singlebase extension products attached to beads of the BeadChip sections. Light emissions from these fluorphores are then recorded in high resolution  images of the BeadChip sections. Data from these images are analyzed using Illumina’s GenomeStudio Genotyping Module.

data_processing: The initial analysis and the data export was done using Genomestudio by Illumina.

label: C-Bio and A-DNP

source_name: embryonic stem cells

label_protocol: 50ng/µL of genomic DNA was denatured and neutralised using 0.1N NaOH, MA1, MA2, and MSM and then whole-genome amplified for 20-24 hours at 37°C. After incubation the amplified DNA was fragmented using end-point fragmentation with the fragmentation mix (FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Genomic DNA was extracted from 1–2 x 10^6 cell culture lysates using the Qiagen Flexigene DNA kit, cat # 51204.

tag: gender

value: Female

tag: call rate

tag: snp sample id

value: embryonic stem cells


title: UU03-L

tag: cell type


title: VV04-E

value: Male


title: UU03-E


title: XX02-E


title: VV05-E


title: VV03-E


title: VV03-L


title: UUX02-L


title: VV05-L


title: VV04-L


title: U11-E


title: UUX02-E


title: UUX01-L


title: XX02-L


title: UU01-E


title: U11-L


title: U04-L


title: UU02-E


title: U16-E


title: U03-L


title: XX01-L


title: UU02-L


title: U03-E2


title: XX01-E


title: WW01-E


title: U03-L2


title: WW01-L


title: TT19-L


title: TT20-E


title: TT19-E


title: U16-L


title: SS02-L


title: TT20-L


title: U03-E


title: SS02-E


title: UU01-L


title: S04-Man


title: RR09


title: RR07-L


title: RR05-L

source_name: induced pluripotent stem cells

value: induced pluripotent stem cells


title: RR-8


title: SS01-E


title: S04-Mn


title: RR04


title: RR03-E


title: RR10


title: RR06-E


title: S04-L


title: RR07-E


title: S04-E


title: SS01-L


title: RR06-L


title: RR03-L


title: S03004DL


title: RR05-E


title: S03-E


title: RR02-L


title: RR01-L


title: RR01-E


title: R03-L


title: Q04-E


title: R02-E


title: R01-E


title: R01-L


title: Q02-L


title: R04-E


title: Q02-E


title: R04-L


title: R02-L


title: PP70-E


title: PP03-E


title: PP35-L


title: PP35-E


title: R03-E


title: PP137-L


title: PP20-E


title: PP03-L


title: RR02-E


title: PP18-L


title: PP18-E


title: PP10-E


title: PP137-E


title: PP70-L


title: OO02-L


title: PP22-E


title: OO05-E


title: OO06-E


title: PP22-L


title: OO01-E


title: PP20-L


title: Q04-L


title: OO05-L


title: OO01-L


title: PP10-L


title: NN07-L


title: NN06-L


title: NN03-E


title: OO02-E


title: NN05-E


title: NN06-E


title: NN05-L


title: NN02-L


title: NN02-E


title: NN01-L


title: NN01-E


title: MM01-L2


title: MM01-E


title: M01-L


title: MM01-L


title: LL02-L2


title: NN03-L


title: M01-E


title: LL02-L


title: LL01-L2


title: LL01-E


title: LL01-L


title: L02-E


title: K05-E


title: LL01-E2


title: K05-L


title: K07-E


title: LL02-E


title: K04-E


title: K06-E


title: OO06-L


title: K04-L


title: K06-L


title: K03-L


title: LL02-E2


title: K02-L


title: L02-L


title: J02-L


title: J01-E


title: K02-E


title: K01-E


title: J01-L


title: I06-E


title: J02-E


title: K01-L


title: K03-E


title: I06-L


title: HH01-E


title: I02-E


title: I05-L


title: I05-E


title: I04-L


title: I01-L


title: HH01-L


title: K07-L


title: I03-L


title: GG04-E


title: I02-L


title: I03-E


title: I04-E


title: GG04-L


title: GG03-L


title: GG02-L


title: I01-E


title: G04-E


title: G05-L


title: GG03-E


title: GG02-E


title: G04-L


title: G07-L


title: G03-E


title: G03-L


title: G06-E

source_name: fibroblast

value: fibroblast


title: G02-L


title: G07-E


title: G01-E


title: X04-L


title: G05-E


title: G02-E


title: X03-E


title: X02-E


title: FF01-L


title: X04-E


title: G01-L


title: X03-L


title: F04-L


title: FF02-E


title: FF01-E


title: FF02-L


title: X01-L


title: X01-E


title: F03-L


title: X02-L


title: F04-E


title: EE02-E


title: F02-L


title: F01-E


title: F02-E


title: F03-E


title: EE01-L


title: F01-L


title: E01-E


title: E01-L


title: EE01-E


title: D08-L


title: D07-E


title: D05-L


title: D06-E


title: D06-L


title: D07-L


title: D08-E


title: D01-L


title: V12-L

value: CHAS V 12 CHA-hES-12 004-D-L


title: D05-E


title: D04-L


title: D04-E


title: D01-E


title: V11-E

value: CHAS V 11 CHA-hES-11 003-D-E


title: FBA-TPQ-treated OVCAR-3 cell replicate 2

city: Shanghai

first: hui

last: wang

address: Rm 429, No. 41 Building, 320 Yueyang Road, Shanghai

institute: Institute for Nutritional Sciences (INS), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS).

description: Biological replicate 2 of 2. control vehicle-treated OVCAR-3  vs. FBA-TPQ treated-OVCAR-3 cells

hyb_protocol: Please see manufacturer's web site at http://www.agilent.com/

scan_protocol: Scanned on an Agilent G2505C scanner.Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: control vehicle-treated-treated   OVCAR-3-2

growth_protocol: OVCAR-3 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin according to the ATCC‟s instructions

extract_protocol: Total RNA are isolated from cell pellets using TriZol reagent(Invitrogen) followed by Rneasy mini kit (Qiagen) clean-up

treatment_protocol: OVCAR-3 cells were seeded in 10 cm dishes and treated with 1000nM FBA-TPQ or vehicle (DMSO; <0.1% of the final incubation concentration) for 24 hours

value: ovarian cancer cell line OVCAR-3

tag: agent

value: control

source_name: FBA-TPQ treated OVCAR-3-2

value: FBA-TPQ


title: V12-E

value: CHAS V 12 CHA-hES-12 003-D-E


title: FBA-TPQ-treated OVCAR-3 cell replicate 1

description: Biological replicate 1 of 2. control vehicle-treated OVCAR-3  vs. FBA-TPQ treated-OVCAR-3 cells

source_name: control vehicle-treated-treated   OVCAR-3-1

label_protocol: Please see manufacturer's web site at http://www.agilent.com/

source_name: FBA-TPQ treated OVCAR-3-1


title: V10-L

value: CHAS V 10 CHA-hES-10 004-D-L


title: V11-L

value: CHAS V 11 CHA-hES-11 004-D-L


title: NK92 + uRBC (24h, C)

city: Tuebingen

first: Evelyn

last: Boettger

address: Wilhelmstrasse 27

institute: Institute of Tropical Medicine

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: GC-RMA normalization

label: Biotin

source_name: NK92 cells

label_protocol: Standard Affymetrix scanning protocol

growth_protocol: The NK92 cell line was routinely grown in 75% alpha-MEM supplemented with 12.5% fetal bovine serum and 12.5% horse serum, 2 mM L-glutamine, 10ml/l penicillin – streptomycin and 10 ng/ml recombinant human interleukin-2 (rIL-2). Cultures were kept at a concentration of 0.2-0.6x106 cells/ml.

extract_protocol: Total RNA was extracted from 3 x 106 cells with RNeasy MiniKit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with uninfected RBCs in a ratio 1:3 of NK cells to uRBCs. After 24 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse erythrocytes.

tag: co-culture

value: NK92 + uninfected RBC

tag: time


title: V10-E

value: CHAS V 10 CHA-hES-10 003-D-E


title: V03-L

value: CHAS V 03 CHA-hES-3 004-D-L


title: NK92 + uRBC (12h, C)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with uninfected RBCs in a ratio 1:3 of NK cells to uRBCs. After 12 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse erythrocytes.

tag: cell line


title: NK92 + iRBC (24h, C)

growth_protocol:
The NK92 cell line was routinely grown in 75% alpha-MEM supplemented with 12.5% fetal bovine serum and 12.5% horse serum, 2 mM L-glutamine, 10ml/l penicillin – streptomycin and 10 ng/ml recombinant human interleukin-2 (rIL-2). Cultures were kept at a concentration of 0.2-0.6x106 cells/ml.
The P. falciparum laboratory strain 3D7 was maintained in continuous culture as described by Trager and Jensen.

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with 3D7 schizont-infected RBCs in a ratio 1:3 of NK cells to iRBCs. After 24 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse erythrocytes.

value: NK92 + Plasmodium falciparum infected RBC


title: NK92 + iRBC (12h, C)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with 3D7 schizont-infected RBCs in a ratio 1:3 of NK cells to iRBCs. After 12 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse erythrocytes.


title: V09-E

value: Female

value: CHAS V 09 CHA-hES-9 003-D-E


title: NK92 + iRBC (6h, C)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with 3D7 schizont-infected RBCs in a ratio 1:3 of NK cells to iRBCs. After 6 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse erythrocytes.


title: V09-L

value: CHAS V 09 CHA-hES-9 004-D-L

value: embryonic stem cells


title: NK92 + uRBC (6h, C)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with uninfected RBCs in a ratio 1:3 of NK cells to uRBCs. After 6 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse erythrocytes.


title: NK92 before co-culture (0h, C)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight.

value: NK92 before co-culture


title: NK92 + iRBC (24h, B)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with 3D7 schizont-infected erythrocytes in a ratio 1:3 of NK cells to iRBCs. After 24 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse erythrocytes.


title: CC05-E


title: V04-E

value: Male

value: CHAS V 04 CHA-hES-4 003-D-E


title: NK92 + uRBC (24h, B)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with uninfected erythrocytes in a ratio 1:3 of NK cells to uRBCs. After 24 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse erythrocytes.


title: V03-E2

value: CHAS V 03 CHA-hES-3 003-D-E


title: NK92 + iRBC (12h, B)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with 3D7 schizont-infected erythrocytes in a ratio 1:3 of NK cells to iRBCs. After 12 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse the erythrocytes.


title: V04-L

value: CHAS V 04 CHA-hES-4 004-D-L


title: C01-L


title: NK92 + iRBC (6h, B)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with 3D7 schizont-infected erythrocytes in a ratio 1:3 of NK cells to iRBCs. After 6 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added the co-culture to lyse the erythrocytes.


title: NK92 + uRBC (6h, B)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with uninfected erythrocytes in a ratio 1:3 of NK cells to uRBCs. After 6 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added the co-culture to lyse the erythrocytes.


title: C01-E


title: C02-E


title: CC06-L


title: NK92 + iRBC (24h, A)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with 3D7 schizont-infected erythrocytes in a ratio 1:3 of NK cells to iRBC. After 24 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse erythrocytes.


title: NK92 before co-culture (0h, B)


title: NK92 + uRBC (24h, A)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with uninfected erythrocytes in a ratio 1:3 of NK cells to uRBC. After 24 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse erythrocytes.


title: BB09-L


title: BB07E


title: CC05-L


title: BB05-L


title: BB08-L


title: NK92 + iRBC (12h, A)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with 3D7 schizont-infected erythrocytes in a ratio 1:3 of NK cells to iRBC. After 12 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse erythrocytes.


title: BB07-L


title: NK92 + uRBC (12h, A)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with uninfected erythrocytes in a ratio 1:3 of NK cells to uRBC. After  12 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse erythrocytes.


title: Transiently transfected Jurkat_pTax_exp2

city: Doylestown

first: Saifur

last: Rahman

state: PA

address: 3805 Old Easton Rd

department: Microbiology and Immunology

institute: Drexel University

description: Nuclear extract

hyb_protocol: according to manufacturer's protocol

scan_protocol: The hybridized membranes were exposed to the chemiluminescence imaging sytem (Fluorchem Imager, Cell Biosciences).

data_processing: The spots were analyzed using the ImageQuant software (GE Healthcare). The spots from each membrane were normalized to their respective positive controls after background subtraction. Average Fold change (pCMV-Tax / pCMV) data is available on a Series records.

source_name: Transiently transfected Jurkat_pTax

label_protocol: according to manufacturer's protocol

extract_protocol: Nuclear extract was obtained from cells by using Nuclear extract kit (Panomics).

treatment_protocol: The stably integrated Jurkat cells (with HTLV-1 LTR) were transfected with pCMV or pCMV-Tax. The transiently transfected Jurkat cells were co-transfected with pU3R-Luc and the empty vector pCMV or with pCMV-Tax.

value: Jurkat (CD4 T cell)

value: transiently transfected HTLV-1 LTR

tag: time point

value: 24 hrs


title: Transiently transfected Jurkat_pTax_exp1

description: Nuclear extract


title: CC06-E


title: NK92 + iRBC (6h, A)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with 3D7 schizont-infected erythrocytes in a ratio 1:3 of NK cells to iRBC. After  24 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added to the co-culture to lyse erythrocytes.


title: C02-L


title: BB09-E


title: CC01-E


title: Transiently transfected Jurkat_pCMV_exp2

description: Nuclear extract

source_name: Transiently transfected Jurkat_pCMV


title: CC01-L


title: BB08-E


title: Transiently transfected Jurkat_pCMV_exp1

description: Nuclear extract


title: Stably intergated Jurkat_pTax_exp2

description: Nuclear extract

source_name: Stably intergated Jurkat_pTax

value: stably integrated HTLV-1 LTR


title: Stably intergated Jurkat_pTax_exp1

description: Nuclear extract


title: Subject 28 Time 8

city: London

first: Jordan

middle: Eduard

last: Bisanz

state: Ontario

address: 268 Grosvenor Street, Room F2-116

country: Canada

institute: Lawson Health Research Institute

hyb_protocol: Hybridized for 16 hours at 45 C. All liquid handling steps were performed with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Scanning done with a GeneChip Scanner 3000 7G and Command Console v1.1 (Affymetrix)

data_processing: .CEL files were imported into Partel GS 6.4 using RMA processing.

source_name: vaginal epithelium

label_protocol: Labeling was carried out with the Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript WT Expression Arrays and Affymetrix GeneChip WT Terminal Labeling kit as per the manufacturer's instructions.

extract_protocol: TRIzol was used to extract total RNA from samples within 72 hours of collection following the manufacturer’s instructions. An extra step was added after homogenization and before addition of chloroform where excess un-homogenized material was cleared from the TRIzol by centrifugation at 12000g for 10 min.

treatment_protocol: Cytobrushes (Cooper Surgical) were used to collect vaginal samples from ~5cm into the vagina. These were suspended in 700ul RNAlater (Ambion).

value: vaginal epithelium

tag: dryness group

value: control

tag: weeks since first clinic visit


title: Stably intergated Jurkat_pCMV_exp2

description: Nuclear extract

source_name: Stably intergated Jurkat_pCMV


title: BB04-L


title: NK92 + uRBC (12h, B)

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were co-cultured with uninfected erythrocytes in a ratio 1:3 of NK cells to uRBCs. After 12 hours of incubation at 37ºC and 5% CO2, lysis buffer (BD) was added the co-culture to lyse the erythrocytes.

value: NK92 + uninfected RBC


title: NK92 before co-culture (0h, A)

hyb_protocol: standard Affymetrix hybridization protocol

scan_protocol: standard Affymetrix scanning protocol

data_processing: GC-RMA

label_protocol: standard Affymetrix labelling protocol

growth_protocol: Cells were kept in culture at 0.2-0.6x106 cells/ml in alpha-MEM (Sigma-Aldrich) supplemented with FBS (12,5%; Sigma-Aldrich), horse serum (12,5%; Sigma-Aldrich), L-glutamine (2 mM; Sigma-Aldrich), penicillin – streptomycin (10ml/L; Invitrogen) and recombinant human interleukin-2 (rIL-2; 10 ng/ml; Invitrogen).

treatment_protocol: NK92 cells, kept without rhIL-2 overnight


title: Subject 2 Time 10


title: Subject 13 Time 10


title: Stably intergated Jurkat_pCMV_exp1

description: Nuclear extract


title: BB04-E


title: Subject 35 Time 4

value: dry


title: B03-L


title: Subject 12 Time 8


title: Subject 25 Time 8


title: Subject 4 Time 8


title: BB05-E

value: Female


title: Subject 15 Time 8


title: Subject 20 Time 8


title: Biopsy, involved psoriatic skin (PP18)

status: Public on Nov 11 2011

city: St. Louis

first: Elisha

last: Roberson

state: MO

address: 660 South Euclid Ave., CB 8045

department: Internal Medicine & Genetics

institute: Washington University in St. Louis

description: Sample name: PP18

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
R methylumi software. Color channels were normalized by quantile normalization. Simple scaling normalization was used for between array normalization. P-values were calculated using the limma eBayes function to fit linear models to probe intensities for each contrast.
Processed data definitions: Beta and M values based on quantile color channel correct, simple scaling normalized data.

label: Cy3 & Cy5

source_name: skin punch biopsy

label_protocol: Standard Illumina labeling.

extract_protocol: Qiagen Dneasy kit used to isolate DNA. Zymo Research EZ DNA methylation kit for bisulfite conversion

tag: tissue

value: skin

tag: paired with


title: female_H51_rep6 vs male_H51_rep6 (dye-swap)

city: Vienna

first: D

middle: P

last: Kreil

address: Muthgasse 18

department: Dept of Biotechnology

country: Austria

institute: Boku University Vienna

description: male sample contains spikeMixA; female samples contains spikeMixB

hyb_protocol: Labelled sample aliquots were resuspended in Ocimum hybridization buffer (Biosolutions, Cat. No. 1180-200000) with sonicated salmon sperm DNA equivalent to 20 microgram per array (Invitrogen; Cat. No. 15632-011), pooled, and split into aliquots corresponding to the number of arrays to be hybridized. Hybridization was performed in randomly assigned hybridization chambers of an automated GeneTAC Hybridization Station (Genomic Solutions) at the selected temperatures (50, 52, 54, 56; 47, 49, 50, and 51 C) for 16 hours (http://www.flychip.org.uk/protocols/hybridisation/). Hybridization temperature: 51 degree Celsius.

scan_protocol: Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/)

data_processing: Standard settings for BlueFuse data extraction. Non-normalized data. We employ an information theoretic model directly on the raw data to avoid normalization artefacts.

organism: Drosophila melanogaster

label_protocol: 100 microgram of total RNA were labelled by direct incorporation of Cy3-dCTP (Amersham, Cat. No. PA 53021) or Cy5-dCTP (Amersham, Cat. No. PA 55021) in a reverse transcription reaction primed by anchored oligo(dT)23 (Sigma, Cat. No. 04387) using Superscript III

growth_protocol: Flies maintained at 25 degrees C on standard cornmeal agar

extract_protocol: RNA was extracted from male or female tissue using Trizol and multiple extractions were pooled to yield sufficient RNA for the whole experiment (http://www.flychip.org.uk/protocols/gene_expression/)

value: female

tag: strain

value: OregonR

value: whole fly

tag: developmental stage

value: adult, 0-7 days post eclosion

value: male


title: Biopsy, involved psoriatic skin (PP17)

description: Sample name: PP17


title: female_H51_rep4 vs male_H51_rep4 (dye-swap)


title: female_H51_rep3 vs male_H51_rep3


title: female_H51_rep5 vs male_H51_rep5 (dye-swap)


title: NK92 + uRBC (6h, A)

label_protocol: Standard Affymetrix labelling protocol

treatment_protocol: To exclude prior activation, NK92 cells were kept in cell medium without rIL-2 overnight. NK92 cells were either co-cultured with uRBCs in a ratio 1:3 of NK cells to RBCs for 6 hours. After co-culture, RBCs were lysed and RNA was extracted from NK92 cells.


title: Subject 30 Time 0


title: B02-E

value: embryonic stem cells


title: B02-L


title: Biopsy, involved psoriatic skin (PP19)

description: Sample name: PP19


title: Biopsy, involved psoriatic skin (PP16)

description: Sample name: PP16


title: B03-E

value: Male


title: female_H51_rep2 vs male_H51_rep2


title: Biopsy, involved psoriatic skin (PP15)

description: Sample name: PP15


title: Biopsy, involved psoriatic skin (PP14)

description: Sample name: PP14


title: female_H51_rep1 vs male_H51_rep1


title: Biopsy, involved psoriatic skin (PP12)

description: Sample name: PP12


title: Biopsy, involved psoriatic skin (PP13)

description: Sample name: PP13


title: female_H49_rep4 vs male_H49_rep4 (dye-swap)

hyb_protocol: Labelled sample aliquots were resuspended in Ocimum hybridization buffer (Biosolutions, Cat. No. 1180-200000) with sonicated salmon sperm DNA equivalent to 20 microgram per array (Invitrogen; Cat. No. 15632-011), pooled, and split into aliquots corresponding to the number of arrays to be hybridized. Hybridization was performed in randomly assigned hybridization chambers of an automated GeneTAC Hybridization Station (Genomic Solutions) at the selected temperatures (50, 52, 54, 56; 47, 49, 50, and 51 C) for 16 hours (http://www.flychip.org.uk/protocols/hybridisation/). Hybridization temperature: 49 degree Celsius.


title: female_H49_rep3 vs male_H49_rep3


title: Biopsy, involved psoriatic skin (PP11)

description: Sample name: PP11


title: Biopsy, involved psoriatic skin (PP9)

description: Sample name: PP9


title: female_H49_rep5 vs male_H49_rep5 (dye-swap)


title: female_H49_rep2 vs male_H49_rep2


title: Biopsy, involved psoriatic skin (PP8)

description: Sample name: PP8


title: B01-E


title: female_H50_rep12 vs male_H50_rep12 (dye-swap)

hyb_protocol: Labelled sample aliquots were resuspended in Ocimum hybridization buffer (Biosolutions, Cat. No. 1180-200000) with sonicated salmon sperm DNA equivalent to 20 microgram per array (Invitrogen; Cat. No. 15632-011), pooled, and split into aliquots corresponding to the number of arrays to be hybridized. Hybridization was performed in randomly assigned hybridization chambers of an automated GeneTAC Hybridization Station (Genomic Solutions) at the selected temperatures (50, 52, 54, 56; 47, 49, 50, and 51 C) for 16 hours (http://www.flychip.org.uk/protocols/hybridisation/). Hybridization temperature: 50 degree Celsius.


title: AA07-E


title: B01-L


title: female_H49_rep1 vs male_H49_rep1


title: Biopsy, involved psoriatic skin (PP7)

description: Sample name: PP7


title: female_H49_rep6 vs male_H49_rep6 (dye-swap)


title: female_H50_rep11 vs male_H50_rep11 (dye-swap)


title: Biopsy, involved psoriatic skin (PP10)

description: Sample name: PP10


title: Biopsy, involved psoriatic skin (PP6)

description: Sample name: PP6


title: AA04-E


title: Biopsy, involved psoriatic skin (PP5)

description: Sample name: PP5


title: Biopsy, involved psoriatic skin (PP4)

description: Sample name: PP4


title: Biopsy, involved psoriatic skin (PP3)

description: Sample name: PP3


title: female_H50_rep8 vs male_H50_rep8


title: AA05-L


title: AA04-L


title: Biopsy, involved psoriatic skin (PP2)

description: Sample name: PP2


title: female_H50_rep10 vs male_H50_rep10 (dye-swap)


title: female_H47_rep6 vs male_H47_rep6 (dye-swap)

hyb_protocol: Labelled sample aliquots were resuspended in Ocimum hybridization buffer (Biosolutions, Cat. No. 1180-200000) with sonicated salmon sperm DNA equivalent to 20 microgram per array (Invitrogen; Cat. No. 15632-011), pooled, and split into aliquots corresponding to the number of arrays to be hybridized. Hybridization was performed in randomly assigned hybridization chambers of an automated GeneTAC Hybridization Station (Genomic Solutions) at the selected temperatures (50, 52, 54, 56; 47, 49, 50, and 51 C) for 16 hours (http://www.flychip.org.uk/protocols/hybridisation/). Hybridization temperature: 47 degree Celsius.


title: female_H50_rep9 vs male_H50_rep9


title: female_H47_rep3 vs male_H47_rep3


title: female_H47_rep4 vs male_H47_rep4 (dye-swap)


title: female_H50_rep7 vs male_H50_rep7


title: Biopsy, involved psoriatic skin (PP1)

description: Sample name: PP1


title: Biopsy, uninvolved psoriatic skin (PN8)

description: Sample name: PN8


title: female_H47_rep2 vs male_H47_rep2


title: AA05-E


title: Biopsy, uninvolved psoriatic skin (PN5)

description: Sample name: PN5


title: Biopsy, uninvolved psoriatic skin (PN6)

description: Sample name: PN6


title: Biopsy, uninvolved psoriatic skin (PN4)

description: Sample name: PN4


title: Biopsy, uninvolved psoriatic skin (PN7)

description: Sample name: PN7


title: female_H47_rep1 vs male_H47_rep1


title: female_H47_rep5 vs male_H47_rep5 (dye-swap)


title: AA02-L


title: AA07-L


title: A01-E

value: induced pluripotent stem cells


title: female_H56_rep6 vs male_H56_rep6 (dye-swap)

hyb_protocol: Labelled sample aliquots were resuspended in Ocimum hybridization buffer (Biosolutions, Cat. No. 1180-200000) with sonicated salmon sperm DNA equivalent to 20 microgram per array (Invitrogen; Cat. No. 15632-011), pooled, and split into aliquots corresponding to the number of arrays to be hybridized. Hybridization was performed in randomly assigned hybridization chambers of an automated GeneTAC Hybridization Station (Genomic Solutions) at the selected temperatures (50, 52, 54, 56; 47, 49, 50, and 51 C) for 16 hours (http://www.flychip.org.uk/protocols/hybridisation/). Hybridization temperature: 56 degree Celsius.


title: Biopsy, uninvolved psoriatic skin (PN3)

description: Sample name: PN3


title: Biopsy, uninvolved psoriatic skin (PN1)

description: Sample name: PN1


title: A02-L


title: Biopsy, uninvolved psoriatic skin (PN2)

description: Sample name: PN2


title: female_H56_rep5 vs male_H56_rep5 (dye-swap)


title: AA03-L


title: Biopsy, control skin (NN10)

description: Sample name: NN10


title: female_H56_rep4 vs male_H56_rep4 (dye-swap)


title: Biopsy, control skin (NN9)

description: Sample name: NN9


title: AA02-E


title: AA03-E


title: female_H56_rep3 vs male_H56_rep3


title: Biopsy, control skin (NN8)

description: Sample name: NN8


title: female_H56_rep2 vs male_H56_rep2


title: A01-L


title: female_H50_rep4 vs male_H50_rep4 (dye-swap)

hyb_protocol: Labelled sample aliquots were resuspended in Ocimum hybridization buffer (Biosolutions, Cat. No. 1180-200000) with sonicated salmon sperm DNA equivalent to 20 microgram per array (Invitrogen; Cat. No. 15632-011), pooled, and split into aliquots corresponding to the number of arrays to be hybridized. Hybridization was performed in randomly assigned hybridization chambers of an automated GeneTAC Hybridization Station (Genomic Solutions) at the selected temperatures (50, 52, 54, 56; 47, 49, 50, and 51 C) for 16 hours (http://www.flychip.org.uk/protocols/hybridisation/). Hybridization temperature: 50 degree Celsius (first batch).


title: female_H50_rep5 vs male_H50_rep5 (dye-swap)


title: Biopsy, control skin (NN4)

description: Sample name: NN4


title: Biopsy, control skin (NN5)

description: Sample name: NN5


title: female_H50_rep2 vs male_H50_rep2


title: A02-E


title: Biopsy, control skin (NN3)

description: Sample name: NN3


title: Biopsy, control skin (NN7)

description: Sample name: NN7


title: female_H54_rep5 vs male_H54_rep5 (dye-swap)

hyb_protocol: Labelled sample aliquots were resuspended in Ocimum hybridization buffer (Biosolutions, Cat. No. 1180-200000) with sonicated salmon sperm DNA equivalent to 20 microgram per array (Invitrogen; Cat. No. 15632-011), pooled, and split into aliquots corresponding to the number of arrays to be hybridized. Hybridization was performed in randomly assigned hybridization chambers of an automated GeneTAC Hybridization Station (Genomic Solutions) at the selected temperatures (50, 52, 54, 56; 47, 49, 50, and 51 C) for 16 hours (http://www.flychip.org.uk/protocols/hybridisation/). Hybridization temperature: 54 degree Celsius.


title: female_H50_rep3 vs male_H50_rep3


title: Biopsy, control skin (NN2)

description: Sample name: NN2


title: female_H50_rep1 vs male_H50_rep1


title: female_H56_rep1 vs male_H56_rep1


title: female_H54_rep4 vs male_H54_rep4 (dye-swap)


title: Biopsy, control skin (NN6)

description: Sample name: NN6


title: Biopsy, control skin (NN1)

description: Sample name: NN1


title: female_H54_rep2 vs male_H54_rep2


title: female_H54_rep3 vs male_H54_rep3


title: female_H54_rep6 vs male_H54_rep6 (dye-swap)


title: hNHEPS_0.1 μM_6 h_rep4

city: Silver Spring

first: Xiugong

last: Gao

address: 503 Robert Grant Ave

institute: Walter Reed Army Institute of Research

description: gene expression data of hNHEPS human hepatocytes exposed to 0.1 μM VX 6 h after exposure

hyb_protocol: Hybridization was carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit following the manufacturer’s protocols.

scan_protocol: The chips were scanned using an Affymetrix GeneChip Instrument System and the image (.DAT) files were processed using the Affymetrix GeneChip Operating Software (GCOS) to generate cell intensity (.CEL) files.

data_processing: The data were averaged and normalized in Partek Genomics Suite 6.5 (Partek, St. Louis, MO) using the robust multiarray analysis (RMA) algorithm.

label_protocol: ~0.1 μg of total RNA were labeled using the Affymetrix (Santa Clara, CA) GeneChip 3’ IVT Express Kit following the manufacturer’s protocol.

growth_protocol: Human hNHEPS hepatocytes were seeded in 6-well plates in media formulated by the manufacturer (Lonza, Walkersville, MD) and cultured at 37 °C under humidified 5% CO2 for 48 h before VX exposure.

extract_protocol: Total RNA was isolated using the RNeasy Plus Mini Kit from Qiagen (Valencia, CA) following the manufacturer’s protocol, including an on-column DNase digestion.

treatment_protocol: VX was added to cell culture at the specified concentrations and maintained for 1 h. Then VX was removed and the culture was washed 3X with fresh medium. The culture was then maintained at 37 °C with 5% CO2 until the indicated time points.

value: Normal human primary hepatocytes isolated from non-transplantable donor tissue

value: 6 h

tag: dose

value: VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothiolate)


title: hNHEPS_10 μM_6 h_rep3

description: gene expression data of hNHEPS human hepatocytes exposed to 10 μM VX 6 h after exposure

value: 10 μM


title: hNHEPS_10 μM_6 h_rep2

source_name: hNHEPS human hepatocytes exposed to 10 μM VX 6 h after exposure


title: female_H54_rep1 vs male_H54_rep1


title: SC2009-012

city: Tianjin

first: Wei

address: Huan Hu Xi Road

institute: ianjin Medical University Cancer Institute and Hospital

description: Total RNA was spoted in 96 wells of the array, and real-time PCR was performed by SupperArray PH033A

data_processing:
Data Analysis: ΔΔCt Method
1. Calculate the ΔCt for each pathway-focused gene in each treatment group.ΔCt (group 1) = average Ct – average of HK genes’ Ct for group 1 array; ΔCt (group 2) = average Ct – average of HK genes’ Ct for group 2 array

label: SYBR green

label_protocol: 1.5μg total RNA was mixed with 1 μl of 500 ng of oligo(dT) 18 and Heat mixture to 65°C for 5 min. and incubate on ice for at least 1 min. Collect the contents of the tube by brief centrifugation and add 0.1 M DTT 1 μl, RNase Ihibitor 1 μl and SuperScript. III RT 1 μl and incubate at 50°C for 60 min, then Inactivate the reaction by heating at 70°C for 15 min. Add 91 μl of ddH2O to each 20-μl of cDNA synthesis reaction. Mix well. Hold the finished First Strand cDNA Synthesis Reaction on ice until the next step or store overnight at -20 °C. and then perform real-time PCR by 2X SuperArray PCR master mix, and then performing real-time PCR Detection: Cycles Duration Temperature, 10 minutes 95 °C,15 seconds 95 °C, 1 minute2 60 °C for 40cycles

extract_protocol: TRIZOL Reagent (Invitrogen life technologies) Homogenize tissue samples in 1 ml of TRIZOL Reagent per 50-100 mg of tissue using a power homogenizer. The sample volume should not exceed 10% of the volume of TRIZOL Reagent used for homogenization.

treatment_protocol: cells (1×107) were inoculated subcutaneously into the right flanks of 6-week-old BALBc nu/nu male mice. Three or 4 weeks after this subcutaneous inoculation, when the tumor reached about 1 cm in diameter, nonnecrotic tumor tissue was cut into 1 mm3 pieces and orthotopically implanted into the liver. And 2 weeks later when tumor volume reached to about 0.5cm3, mice was divided into 2 groups with of 6 mice in each group; they were treated with vehicle or 30 mg/kg sorafenib for 4 weeks, anesthetized, and then humanely killed. Tumor samples were obtained and analyzed by Cancer PathwayFinder PCR array.

value: hepatocellular carcinoma

tag: treatment

value: treated


title: hNHEPS_10 μM_6 h_rep4


title: hNHEPS_control_0 h_rep4

description: gene expression data of hNHEPS human hepatocytes not exposed to VX at the beginning of experiment


title: hNHEPS_control_6 h_rep4

description: gene expression data of hNHEPS human hepatocytes not exposed to VX at 6 h


title: hNHEPS_0.1 μM_6 h_rep3

source_name: hNHEPS human hepatocytes exposed to 0.1 μM VX 6 h after exposure


title: hNHEPS_10 μM_6 h_rep1


title: SC2009-010


title: female_H52_rep4 vs male_H52_rep4 (dye-swap)

hyb_protocol: Labelled sample aliquots were resuspended in Ocimum hybridization buffer (Biosolutions, Cat. No. 1180-200000) with sonicated salmon sperm DNA equivalent to 20 microgram per array (Invitrogen; Cat. No. 15632-011), pooled, and split into aliquots corresponding to the number of arrays to be hybridized. Hybridization was performed in randomly assigned hybridization chambers of an automated GeneTAC Hybridization Station (Genomic Solutions) at the selected temperatures (50, 52, 54, 56; 47, 49, 50, and 51 C) for 16 hours (http://www.flychip.org.uk/protocols/hybridisation/). Hybridization temperature: 52 degree Celsius.

tag: gender


title: female_H52_rep6 vs male_H52_rep6 (dye-swap)


title: SC2009-011


title: hNHEPS_0.1 μM_6 h_rep1


title: hNHEPS_control_6 h_rep1

source_name: hNHEPS human hepatocytes not exposed to VX at 6 h


title: female_H52_rep5 vs male_H52_rep5 (dye-swap)


title: female_H52_rep3 vs male_H52_rep3


title: hNHEPS_control_0 h_rep3

source_name: hNHEPS human hepatocytes not exposed to VX at the beginning of experiment


title: hNHEPS_control_6 h_rep2


title: hNHEPS_0.1 μM_6 h_rep2


title: hNHEPS_control_0 h_rep1


title: Old HSC 6

city: Stanford

first: Debashis

last: Sahoo

address: 265 Campus Drive, Rm G3101B

department: Pathology

institute: Stanford University

description: Gene expression data from old HSC

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: The data were normalized using RMA.

source_name: Old HSC

label_protocol: All RNA samples were quantified with the RiboGreen RNA Quantitation Kit (Molecular Probes, Eugene, OR), subjected to reverse transcription, 2 consecutive rounds of linear amplification, and production and fragmentation of biotinylated cRNA (Affymetrix, Santa Clara, CA).

growth_protocol: Analyzed/sorted fresh or cryopreserved in 90% FBS, 10% DMSO in liquid nitrogen.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) or Ambion RNA Isolation Kit (Applied Biosystems by Life Technologies, Carlsbad, CA), according to the manufacturer's protocols, and treated with DNaseI (Qiagen, Germany).

treatment_protocol: Mononuclear cells were prepared using Ficoll-Paque Plus (GE Healthcare), and either analyzed/sorted fresh or cryopreserved in 90% FBS, 10% DMSO in liquid nitrogen. Human CD34-positive cells were enriched using magnetic beads (Miltenyi Biotec, Germany; Stemcell Technologies, Vancouver, BC).

value: bone marrow

value: hematopoietic stem cell

tag: age


title: female_H52_rep1 vs male_H52_rep1


title: Old HSC 5

description: Gene expression data from old HSC


title: Old HSC 8

description: Gene expression data from old HSC


title: Old HSC 7

description: Gene expression data from old HSC


title: female_H52_rep2 vs male_H52_rep2


title: SC2009-007


title: SC2009-009


title: SC2009-008


title: SC2009-004

value: control


title: SC2009-006


title: SC2009-002


title: SC2009-001


title: Old HSC 3

description: Gene expression data from old HSC


title: hNHEPS_control_0 h_rep2


title: SC2009-003


title: Middle HSC 4

description: Gene expression data from middle aged HSC

source_name: Middle HSC


title: Old HSC 2

description: Gene expression data from old HSC


title: female_H50_rep6 vs male_H50_rep6 (dye-swap)

value: female


title: Old HSC 4

description: Gene expression data from old HSC


title: Middle HSC 3


title: Old HSC 1

description: Gene expression data from old HSC


title: Middle HSC 5


title: Middle HSC 1


title: Breast non-cancer tissue Replicate 8

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

hyb_protocol: According to the instructions of Agilent Gene Expression Hybridization Kit

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).
Agilent Feature Extraction Software  (version 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: Breast non-cancer tissue

label_protocol: 1μg of total RNA was used to synthesize the double strand cDNA. RNA was amplified by in vitro transcription using Ambion’s MessageAmp™ II aRNA Amplification Kits (Life Technologies, Austin, TX, USA). Then, aRNA was reverse transcribed into cDNA and further labeled with cy3-dCTP with Klenow enzyme.

extract_protocol: Total RNA from fresh breast tumor and non-tumor tissues was extracted using Dr.P Kit (Biochain, Hayward, CA, USA), according to the manufacturer’s instructions.

value: normal breast

value: Female

value: 39 years


title: Young HSC 14

description: Gene expression data from young HSC

source_name: Young HSC


title: Young HSC 13

description: Gene expression data from young HSC


title: Middle HSC 2


title: Breast non-cancer tissue Replicate 5


title: Breast cancer tissue Replicate 8

source_name: Breast cancer tissue

value: breast cancer

value: 49 years


title: Breast cancer tissue Replicate 7

value: 44 years


title: Breast non-cancer tissue Replicate 6


title: Breast non-cancer tissue Replicate 7

value: 51 years


title: Mouse C2C12 cells (96h)

city: Shinagawa

first: Atsushi

last: Yamada

state: Tokyo

address: 1-5-8 Hatanodai

department: School of Dentistry

country: Japan

institute: Showa University

description: Osteoblastgenesis

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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: Mouse C2C12 cells (96h)

label_protocol: Affymetrix protocol

growth_protocol: Mouse C2C12 cells were harvested and cultured in the presence of 15% FBS for culture.

extract_protocol: Rneasy mini kit (Qiagen) extraction of total RNA was performed according to the manufacture's instructions.

treatment_protocol: C2C12 cells were treated with hBMP2 (300 ng/ml) for 96h.

value: skeletal myotubules


title: Mouse C2C12 cells treated with BMP2 (96h)

description: Osteoblastgenesis

value: osteoblasts


title: Young HSC 12

description: Gene expression data from young HSC


title: Breast cancer tissue Replicate 6


title: thymus 10 ml/kg corn oil gavage once daily 14 consecutive days replicate 5

description: Gene expression in thymus from female Wistar rats daily administered with 10 ml/kg of corn oil by gavage for 14 consecutive days

hyb_protocol: Fluorescence dye labeled cRNA was hybridized to Agilent Rat Whole Genome 8×*60K array according to the instructions of Agilent Gene Expression Hybridization Kit.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent GeneSpring GX 11.5 was used for background subtraction and Lowess normalization.

source_name: thymus

label_protocol: RNA was amplified and labeled using Agilent LowInput Quick Amp Labeling Kit.

growth_protocol: Female Wistar rats obtained from Beijing Vital River Laboratory Animal Technology Co., Ltd (licensed by Beijing Administrative Office of Laboratory Animal, China) were used at the age of 7 wks. All animals were bred specific pathogen-free and kept in polycarbonate cages (L×W×H: 460×315×210 mm) under condition of 22±3 ºC, 40-70% relative humidity and 12-h light-dark cycle. Standard rodent diet and water were available ad libitum throughout the study. Rats were housed 3 per cage.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, Gaithersburg, MD) according to the manufacture’s instructions. The quantity of RNA in each sample was assessed spectrophotometerically (NanoDrop Technologies, Wilmington, DE) and RNA integrity was assessed by formaldehyde agarose gel electrophoresis.

treatment_protocol: After being housed in our facilities for one week to acclimate, the rats were randomly divided into four groups (6 animals per group) including one normal saline (NS) control group (dosing volume 10 ml/kg) and three CO groups (dosing volume 2, 5, 10 ml/kg, respectively). All groups were administered NS or CO by gavage once daily for 14 consecutive days.

value: Wistar

value: thymus

value: 7 weeks

value: 10 ml/kg corn oil


title: Young HSC 10

description: Gene expression data from young HSC

value: bone marrow


title: Mouse C2C12 cells (0h)

description: Osteoblastgenesis

source_name: Mouse C2C12 cells (0h)

value: skeletal myoblasts


title: thymus 10 ml/kg corn oil gavage once daily 14 consecutive days replicate 4


title: Breast non-cancer tissue Replicate 3


title: thymus 2 ml/kg corn oil gavage once daily 14 consecutive days replicate 4

description: Gene expression in thymus from female Wistar rats daily administered with 2 ml/kg of corn oil by gavage for 14 consecutive days

value: 2 ml/kg corn oil


title: Young HSC 8

description: Gene expression data from young HSC

value: hematopoietic stem cell


title: Young HSC 7

description: Gene expression data from young HSC


title: Breast non-cancer tissue Replicate 1

value: normal breast

value: 33 years


title: Breast non-cancer tissue Replicate 4

value: Female


title: Breast cancer tissue Replicate 5

value: breast cancer

value: 55 years


title: Young HSC 11

description: Gene expression data from young HSC


title: thymus 2 ml/kg corn oil gavage once daily 14 consecutive days replicate 1


title: Young HSC 9

description: Gene expression data from young HSC


title: thymus 5 ml/kg corn oil gavage once daily 14 consecutive days replicate 2

description: Gene expression in thymus from female Wistar rats daily administered with 5 ml/kg of corn oil by gavage for 14 consecutive days

value: 5 ml/kg corn oil


title: Breast non-cancer tissue Replicate 2

value: 29 years


title: thymus 10 ml/kg saline gavage once daily 14 consecutive days replicate 2

description: Gene expression in thymus from female Wistar rats daily administered with 10 ml/kg of saline by gavage for 14 consecutive days

value: 10 ml/kg saline


title: Breast cancer tissue Replicate 4

value: 57 years


title: Young HSC 6

description: Gene expression data from young HSC


title: SC2009-005

last: Zhang

value: hepatocellular carcinoma

value: control


title: thymus 10 ml/kg saline gavage once daily 14 consecutive days replicate 5

value: Wistar

value: thymus

value: 7 weeks


title: Breast cancer tissue Replicate 1

value: 40 years


title: B16-F10 cells exposed to 200 μM CoCl2, biological replica 2, experiment 3

city: Warsaw

first: Michal

last: Swierniak

address: Banacha 2C

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

description: Gene expression data from B16-F10 cells exposed to 200 μM CoCl2 for 24 hours

hyb_protocol: Following fragmentation, 16 μg of cRNA were hybridized for 16 hr at 45ºC on Mouse Expression Arrays 430A (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned using Hewlett-Packard GeneArray G2500A scanner with MAS5 software (Affymetrix).

data_processing: Data was acquired using GCOS 1.2 software (Affymetrix). The preprocessing was performed by Robust Multiarray Analysis (RMA, Bioconductor).

source_name: B16-F10 cells exposed to hypoxia mimicry

label_protocol: Total RNA (8 μg) was used for synthesis of double stranded cDNA according to manufacturer's instructions. Half of the cDNA volume was used for synthesis of biotynylated cRNA with the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics).

growth_protocol: The mouse melanoma B16-F10 cells were grown in CO2 incubator at 37°C in RPMI medium (Sigma-Aldrich) supplemented with 10% fetal bovine serum (ICN).

extract_protocol: Total RNA was isolated using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Hypoxic cpnditions were introduced by incubating the cells in 1% oxygen using either Billubs-Rothenberg chamber or oxygen flow-regulated incubator for 24 h. Hypoxia-mimicry was performed by treating the cells with either 100 μM or 200 μM CoCl2 for 24 h.

tag: cell origin

value: melanoma

tag: biomaterial provider

value: ATCC CRL-6475T

tag: condition

value: exposed to 200 μM CoCl2


title: thymus 10 ml/kg saline gavage once daily 14 consecutive days replicate 1


title: Breast cancer tissue Replicate 3

value: 43 years


title: thymus 10 ml/kg corn oil gavage once daily 14 consecutive days replicate 1

value: Female

value: 10 ml/kg corn oil


title: thymus 10 ml/kg corn oil gavage once daily 14 consecutive days replicate 3


title: Young HSC 5

description: Gene expression data from young HSC

value: bone marrow

tag: cell type

value: hematopoietic stem cell


title: thymus 10 ml/kg corn oil gavage once daily 14 consecutive days replicate 2


title: Young HSC 3

description: Gene expression data from young HSC


title: thymus 5 ml/kg corn oil gavage once daily 14 consecutive days replicate 4

value: 5 ml/kg corn oil


title: Young HSC 2

description: Gene expression data from young HSC


title: B16-F10 cells exposed to 200 μM CoCl2, biological replica 1, experiment 3


title: hMSCs_21% O2 rep2 (gene expression)

description: Biological replicate 2 of 3,21% O2,subject2

data_processing: Agilent Feature Extraction Software  (version 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: hMSCs_21% O2_rep2

growth_protocol: Human bone marrow was extracted from healthy donors with no known pathologic condition after informed consent was obtained. After washed with phosphate-buffered saline (PBS) twice, total bone marrow were plated and cultivated in Dulbecco’s modified Eagle’s medium-low glucose (DMEM-LG; Invitrogen, Carlsbad, CA, USA) supplemented with 20% FBS (Invitrogen). After 48 hours culture at 37°C and 5% CO2, non adherent cells were removed, and medium was replaced every other day. Once confluent, adherent cells were further passaged and replated into new culture dishes. After 3-5 passages, these cells were resuspended as 5×105 cells/100 μl in PBS containing 1% bovine serum albumin for each antibody, and incubated with human specific monoclonal antibodies CD29-phycoerythrin (PE) (eBioscience), CD34-PE (MACS, Miltenyi Biotec), CD105-PE, CD117-PE and CD166-PE (all from BD Biosciences Pharmingen)， respectively. After 45 min of incubation at 4oC, cells were washed twice in PBS and at least 10,000 events were acquired for each sample using using BD FACSCantoTM II Flow Cytometry System.

extract_protocol: Total RNA from different cultured cells was extracted using Dr.P Kit (Biochain, Hayward, CA, USA), according to the manufacturer’s instructions.

treatment_protocol: hMSCs were plated at 1×105 cells/cm2 in complete culture medium and incubated at 37°C under hypoxia (0.5% O2, 5% CO2) with supplemental nitrogen or normoxia (21% O2, 5% CO2) for 24 hours using a well characterized, finely controlled ProOx-C-chamber system (Biospherix, Redfield, NY).

value: bone marrow-derived mesenchymal stem cells

tag: 02 exposure

tag: subject


title: Young HSC 1

description: Gene expression data from young HSC


title: hMSCs_21% O2 rep3 (gene expression)

description: Biological replicate 3 of 3,21% O2,subject3

source_name: hMSCs_21% O2_rep3


title: K562_2 mM valproate for 12 hours_vs_control_rep1

hyb_protocol: Fluorescent dye-labelled cDNA was hybridised to an Agilent-028004 SurePrint G3 Human GE 8x60K Microarray according to the instructions of Agilent Gene Expression Hybridization Kit

source_name: K562 cells, human cell line of chronic myeloid leukemia

label_protocol: 1 μg of total RNA was used to synthesize the double strand cDNA. RNA was amplified by in vitro transcription using Ambion’s MessageAmp™ II aRNA Amplification Kits (Life Technologies, Austin, TX, USA). Then, aRNA was reverse transcribed into cDNA and further labeled with cy3-dCTP or cy5-dCTP with Klenow enzyme.

growth_protocol: K562, human chronic myelogenic leukemic cell line was obtained from Sun Yat-sen University Cancer Center. K562 cells were grown and maintained in RPMI (Life Technology Corporation, Camarillo, CA) containing 15% FBS, 100 U/mL penicillin, and 1 mg/mL streptomycin in a 5 % C02 incubator at 37°C.

extract_protocol: RNA was extracted from cultured cells using the RNeasy Mini Kit (QIAGen, USA) according to the manufacturer’s instructions. RNA quality was assessed using formaldehyde agarose gel electrophoresis and was quantified via spectrophotometry (Nanodrop, Wilmington, DE).

treatment_protocol: K562 cells were either treated with 2 mM VPA for 12 hours or left untreated as a control.

tag: cell line

tag: agent

value: Treatment with 2 mM valproate for 12 hours


title: B16-F10 cells cultured in control conditions (21% oxygen), biological replica 2, experiment 3

description: Gene expression data from control B16-F10 cells

source_name: control B16-F10 cells


title: Breast cancer tissue Replicate 2

value: breast cancer


title: Young HSC 4

description: Gene expression data from young HSC


title: thymus 5 ml/kg corn oil gavage once daily 14 consecutive days replicate 1


title: thymus 2 ml/kg corn oil gavage once daily 14 consecutive days replicate 5

value: 2 ml/kg corn oil


title: B16-F10 cells cultured in control conditions (21% oxygen), biological replica 1, experiment 3


title: thymus 5 ml/kg corn oil gavage once daily 14 consecutive days replicate 3

value: Wistar


title: hMSCs_0.5% O2 rep3 (gene expression)

description: Biological replicate 3 of 3,0.5% O2,subject3

source_name: hMSCs_0.5% O2_rep3


title: hMSCs_21% O2 rep1 (gene expression)

description: Biological replicate 1 of 3,21% O2,subject1

source_name: hMSCs_21% O2_rep1


title: B16-F10 cells exposed to 100 μM CoCl2, biological replica 2, experiment 3

description: Gene expression data from B16-F10 cells exposed to 100 μM CoCl2 for 24 hours

value: exposed to 100 μM CoCl2


title: B16-F10 cells exposed to experimental hypoxia (1% oxygen) in incubator, biological replica 3, experiment 2

description: Gene expression data from B16-F10 cells exposed to hypoxia (1% oxygen) for 24 hours

source_name: B16-F10 cells exposed to hypoxia


title: hMSCs_0.5% O2 rep1 (gene expression)

description: Biological replicate 1 of 3,0.5% O2,subject1

source_name: hMSCs_0.5% O2_rep1


title: hMSCs_0.5% O2 rep2 (gene expression)

description: Biological replicate 2 of 3,0.5% O2,subject2

source_name: hMSCs_0.5% O2_rep2


title: B16-F10 cells exposed to experimental hypoxia (1% oxygen) in incubator, biological replica 1, experiment 2


title: B16-F10 cells cultured in control conditions (21% oxygen), biological replica 2, experiment 2


title: thymus 10 ml/kg saline gavage once daily 14 consecutive days replicate 3

value: thymus

value: 7 weeks

value: 10 ml/kg saline


title: B16-F10 cells cultured in control conditions (21% oxygen), biological replica 1, experiment 2

value: melanoma

value: ATCC CRL-6475T


title: thymus 2 ml/kg corn oil gavage once daily 14 consecutive days replicate 2


title: Strain O11 during stationary phase (replicate 3)

type: mixed

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: S. aureus gDNA pool

hyb_protocol: A mixture of RNA from specific condition and gDNA (500 ng total) was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven.

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method

label: cyanine 3

organism: Staphylococcus aureus

source_name: Strain O11 during stationary phase

label_protocol: Random Primers with Kleenow fragment (BioPrime, Invitrogen)

growth_protocol: mid-log phase or stationary phase at an optical density at 600 nm of 0.5 or 1.0, respectively

extract_protocol: Ethanol-acetone. Then, washings and centrigugation followed by enzymatic digestion and RNeasy extration using DNAse treatment

label: cyanine 5

source_name: Pool gDNA

growth_protocol: Mueller-Hinton broth 37 degrees C

extract_protocol: DNeasy Kit from Qiagen

value: NCTC 8325

value: COL


title: thymus 10 ml/kg saline gavage once daily 14 consecutive days replicate 4

value: Female


title: Strain O11 during stationary phase (replicate 2)

description: S. aureus gDNA pool


title: thymus 2 ml/kg corn oil gavage once daily 14 consecutive days replicate 3


title: 2800 (Twin Pair 4, unaffected)

first: Christina

middle: A

last: Castellani

address: Biological and Geological Sciences Building

institute: The University of Western Ontario

hyb_protocol: As per manufactuer (Affymetrix)

scan_protocol: Scanning using a gene chip scanner

data_processing: CEL files were processed by Affymetrix Genotyping Console 4.0 and Partek Genotyping Suite

source_name: Whole Blood

label_protocol: As per manufactuer (Affymetrix)

extract_protocol: Genomic DNA was extracted from whole blood using the QIAgen DNA Blood Midi Kit. DNA quality and quantity were assessed using a Nanodrop Spectophotometer and Agarose Gel Electrophoresis.

value: Blood

tag: relationship

value: Twin Pair 4

tag: state

value: unaffected


title: Singh4 (Twin Pair 5, unaffected)

tag: tissue

value: Twin Pair 5


title: hMSCs_21% O2 rep3 (exon array)

label_protocol: RNA was amplified using Agilent’s Low Input Quick Amp WT Labeling Kit with minor modifications. Briefly, 100ng of total RNA was used to synthesize the double strand cDNA. RNA was amplified by in vitro transcription using the WT Primer Mix in the kit that reverse-transcribed throughout 3’ to 5’ end of mRNA, replacing the T7 promoter primer using in mRNA level expression profile, in which only reverse-transcribed at the 3’ end of mRNA. aRNA then was reverse transcribed into cDNA and was further labeled with cy5-dCTP with Klenow enzyme.

value: bone marrow-derived mesenchymal stem cells


title: hMSCs_0.5% O2 rep3 (exon array)


title: 2801 (Twin Pair 4, affected)

value: schizophrenia


title: B16-F10 cells exposed to experimental hypoxia (1% oxygen) in incubator, biological replica 3, experiment 1

tag: strain


title: Strain O11 during stationary phase (replicate 1)

description: S. aureus gDNA pool


title: B16-F10 cells exposed to experimental hypoxia (1% oxygen) in Billups_Rothenberg chamber, biological replica 3


title: Strain O46 during stationary phase (replicate 3)

description: S. aureus gDNA pool

source_name: Strain O46 during stationary phase


title: B16-F10 cells exposed to experimental hypoxia (1% oxygen) in incubator, biological replica 1, experiment 1


title: hMSCs_21% O2 rep1 (exon array)


title: B16-F10 cells exposed to experimental hypoxia (1% oxygen) in incubator, biological replica 2, experiment 1


title: B16-F10 cells cultured in control conditions (21% oxygen), biological replica 2, experiment 1


title: 2590 (Twin Pair 3, unaffected)

value: Twin Pair 3


title: hMSCs_21% O2 rep2 (exon array)


title: Strain O46 during stationary phase (replicate 2)

description: S. aureus gDNA pool


title: B16-F10 cells exposed to experimental hypoxia (1% oxygen) in Billups_Rothenberg chamber, biological replica 2


title: 2588 (Twin Pair 2, unaffected)

value: Twin Pair 2


title: IT02 (Twin Pair 6, unaffected)

value: Twin Pair 6


title: hMSCs_0.5% O2 rep2 (exon array)


title: hMSCs_0.5% O2 rep1 (exon array)


title: B16-F10 cells cultured in control conditions (21% oxygen), biological replica 1, experiment 1


title: Strain O46 during stationary phase (replicate 1)

description: S. aureus gDNA pool


title: Strain O11 during exponential phase (replicate 1)

description: S. aureus gDNA pool

source_name: Strain O11 during exponential phase


title: B16-F10 cells exposed to 100 μM CoCl2, biological replica 1, experiment 3

value: exposed to 100 μM CoCl2


title: Strain O11 during exponential phase (replicate 3)

description: S. aureus gDNA pool


title: B16-F10 cells cultured in control conditions (21% oxygen), biological replica 2

description: Gene expression data from B16-F10 control cells


title: K562_2 mM valproate for 12 hours_vs_control_exon array_rep1

hyb_protocol: Fluorescent dye-labelled cDNA was hybridised to an Agilent Human 4×180K Exon Microarray according to the instructions of Agilent Gene Expression Hybridization Kit

data_processing: Agilent GeneSpring GX 11.5 was used for background subtraction and LOWESS normalization.

label_protocol: RNA was amplified using Agilent’s Low Input Quick Amp WT Labeling Kit according to the manufacturer’s guidelines with a small modification. Briefly, 100 ng of total RNA was used to synthesise double-stranded cDNA. RNA was amplified by in vitro transcription using WT Primer Mix that reverse transcribed throughout the 3’ to 5’ end of mRNA, replacing the T7 promoter primer using in standard expression array, in which only the 3’ end of mRNA was reverse-transcribed. aRNA was then reverse transcribed into cDNA and was labelled with cy3-dCTP or cy5-dCTP using Klenow enzyme.

value: 2 mM valproate for 12 hours


title: Strain O11 during exponential phase (replicate 2)

description: S. aureus gDNA pool


title: Strain O46 during exponential phase (replicate 1)

description: S. aureus gDNA pool

source_name: Strain O46 during exponential phase


title: B16-F10 cells exposed to experimental hypoxia (1% oxygen) in incubator, biological replica 2, experiment 2


title: Strain O46 during exponential phase (replicate 2)

description: S. aureus gDNA pool


title: B104 siRBM3 rep2

status: Public on Nov 10 2011

city: La Jolla

first: Julie

last: Pilotte

address: 10550 North Torrey Pines Rd, Sbr-14

department: Neurobiology

institute: The Scripps Research Institute

description: microRNA expression 48 hours after RBM3 knockdown by siRNA transfection

hyb_protocol: Hybridization was done according to Agilent's specifications.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Microarrays were analyzed with Genespring software. The Agilent Feature Extraction tool was used to obtain the signal values and detection above background for the Agilent chip.  Processing of the data was performed within the Bioconductor project and the R program software (R is available as Free Software under the terms of the Free Software Foundation's GNU General Public License).  The scale normalization method used was proposed by Yang et al [49, 50] and is further elaborated by Smyth and Speed [51]. Log-values were scaled to have the same median-absolute-deviation (MAD) across arrays.  The 578 Human miRNAs were filtered down to 216 by excluding those miRNAs with signals not detected above background for all the samples.

source_name: B104 clonal cell line, transfected, 48 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from total RNA using the microRNA Spike-In Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: B104 cells were cultured in DMEM supplemented with 10% FBS, 200 mM L-glutamine and penicillin/streptomycin.

extract_protocol: The mirVana miRNA isolation kit (Life Technologies) was used to isolate miRNAs according to the manufactor's reccomendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cell lines were transfected with an siRNA duplex against RBM3 at a ratio of 20 nM siRNA per 25 µl Lipofectamine RNAiMax (Life Technologies) to knockdown RBM3, or mock treated as a control; cells were harvested after 48 hrs.

value: neuroblastoma

tag: knockdown


title: 2585 (Twin Pair 1, affected)

value: Twin Pair 1


title: B104 siRBM3 rep1


title: 2587 (Twin Pair 2, affected)


title: IT01 (Twin Pair 6, affected)


title: ES[MC1R(20):tetZmat4(15)]_day2_Dox-_rep2

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description:
Zmat4(15)]_day2_Dox-
Raw data file:
5012-US12302333_251508710865_S01_GE2-v5_95_Feb07_1_4.txt
Represents ch1 in dual channel hybridzation.

hyb_protocol: Slides were hybridized according to the manufacturer's protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol, Product # G4140-90050, Version 5.0.1, August 2006).

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). The data is then combined into a matrix.
(2) in each column estimate 15 quantiles that correspond to ratios: 1/30, 3/30, ... 29/30.
(3) estimate 15 target quantiles as average quantiles across all columns.
(4) transform data using a piece-linear function that converts actual quantiles in each column into target quantiles.
(5) back-transform data with exponent function.
The result is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

label_protocol: Total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit according to the manufacturer's instructions.

extract_protocol: Stratagene Absolute RNA extraction kit

tag: transcription factor

value: Embryonic Stem Cells

value: male

tag: culture condition

value: Dox-

tag: development stage

value: embryo

tag: individual identifier


title: ES[MC1R(20):tetZic1(6)]_day2_Dox-_rep2

description:
Zic1(6)]_day2_Dox-
Raw data file:
4827-US12302333_251508710821_S01_GE2-v5_95_Feb07_1_2.txt
Represents ch1 in dual channel hybridzation.

tag: gender


title: ES[MC1R(20):tetZic1(6)]_day2_Dox-_rep1

description:
Zic1(6)]_day2_Dox-
Raw data file:
4824-US12302333_251508710821_S01_GE2-v5_95_Feb07_1_1.txt
Represents ch1 in dual channel hybridzation.


title: ES[MC1R(20):tetZmat4(15)]_day2_Dox-_rep1

description:
Zmat4(15)]_day2_Dox-
Raw data file:
5010-US12302333_251508710865_S01_GE2-v5_95_Feb07_1_3.txt
Represents ch1 in dual channel hybridzation.


title: ES[MC1R(20):tetZmat4(15)]_day2_Dox+_rep2

description:
Zmat4(15)]_day2_Dox+
Raw data file:
5012-US12302333_251508710865_S01_GE2-v5_95_Feb07_1_4.txt
Represents ch2 in dual channel hybridzation.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). The data is then combined into a matrix.
(2) in each column estimate 15 quantiles that correspond to ratios: 1/30, 3/30, ... 29/30.
(3) estimate 15 target quantiles as average quantiles across all columns.
(4) transform data using a piece-linear function that converts actual quantiles in each column into target quantiles.
(5) back-transform data with exponent function.
The result is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

tag: transcript factor


title: ES[MC1R(20):tetZic1(6)]_day2_Dox+_rep1

description:
Zic1(6)]_day2_Dox+
Raw data file:
4824-US12302333_251508710821_S01_GE2-v5_95_Feb07_1_1.txt
Represents ch2 in dual channel hybridzation.


title: ES[MC1R(20):tetZfp57(22)]_day2_Dox-_rep2

description:
Zfp57(22)]_day2_Dox-
Raw data file:
4972-US12302333_251508710855_S01_GE2-v5_95_Feb07_1_2.txt
Represents ch1 in dual channel hybridzation.


title: 2586 (Twin Pair 1, unaffected)

value: Blood


title: Singh3 (Twin Pair 5, affected)


title: 2589 (Twin Pair 3, affected)


title: ES[MC1R(20):tetZfp57(22)]_day2_Dox+_rep1

description:
Zfp57(22)]_day2_Dox+
Raw data file:
4970-US12302333_251508710855_S01_GE2-v5_95_Feb07_1_1.txt
Represents ch2 in dual channel hybridzation.


title: ES[MC1R(20):tetUgp2(20)]_day2_Dox-_rep1

description:
Ugp2(20)]_day2_Dox-
Raw data file:
4907-US12302333_251508710839_S01_GE2-v5_95_Feb07_1_3.txt
Represents ch1 in dual channel hybridzation.


title: ES[MC1R(20):tetZfp57(22)]_day2_Dox+_rep2

description:
Zfp57(22)]_day2_Dox+
Raw data file:
4972-US12302333_251508710855_S01_GE2-v5_95_Feb07_1_2.txt
Represents ch2 in dual channel hybridzation.


title: ES[MC1R(20):tetZmat4(15)]_day2_Dox+_rep1

description:
Zmat4(15)]_day2_Dox+
Raw data file:
5010-US12302333_251508710865_S01_GE2-v5_95_Feb07_1_3.txt
Represents ch2 in dual channel hybridzation.


title: ES[MC1R(20):tetZfp57(22)]_day2_Dox-_rep1

description:
Zfp57(22)]_day2_Dox-
Raw data file:
4970-US12302333_251508710855_S01_GE2-v5_95_Feb07_1_1.txt
Represents ch1 in dual channel hybridzation.


title: ES[MC1R(20):tetZic1(6)]_day2_Dox+_rep2

description:
Zic1(6)]_day2_Dox+
Raw data file:
4827-US12302333_251508710821_S01_GE2-v5_95_Feb07_1_2.txt
Represents ch2 in dual channel hybridzation.


title: ES[MC1R(20):tetUgp2(20)]_day2_Dox-_rep2

description:
Ugp2(20)]_day2_Dox-
Raw data file:
4909-US12302333_251508710839_S01_GE2-v5_95_Feb07_1_4.txt
Represents ch1 in dual channel hybridzation.


title: ES[MC1R(20):tetTrpv2(9)]_day2_Dox+_rep1

description:
Trpv2(9)]_day2_Dox+
Raw data file:
5011-US12302333_251508710864_S01_GE2-v5_95_Feb07_1_3.txt
Represents ch2 in dual channel hybridzation.


title: ES[MC1R(20):tetTrpv2(9)]_day2_Dox+_rep2

description:
Trpv2(9)]_day2_Dox+
Raw data file:
5013-US12302333_251508710864_S01_GE2-v5_95_Feb07_1_4.txt
Represents ch2 in dual channel hybridzation.


title: ES[MC1R(20):tetTgm2(14)]_day2_Dox-_rep1

description:
Tgm2(14)]_day2_Dox-
Raw data file:
4983-US12302333_251508710858_S01_GE2-v5_95_Feb07_1_3.txt
Represents ch1 in dual channel hybridzation.


title: ES[MC1R(20):tetTrpv2(9)]_day2_Dox-_rep2

description:
Trpv2(9)]_day2_Dox-
Raw data file:
5013-US12302333_251508710864_S01_GE2-v5_95_Feb07_1_4.txt
Represents ch1 in dual channel hybridzation.


title: ES[MC1R(20):tetTgif1(8)]_day2_Dox-_rep1

description:
Tgif1(8)]_day2_Dox-
Raw data file:
4965-US12302333_251508710854_S01_GE2-v5_95_Feb07_1_1.txt
Represents ch1 in dual channel hybridzation.