title: RIN5F Noninfected_Cell_control_72_hour


title: YoungAdult_Rig_I_6hrs YA_8

status: Public on Jan 01 2015

type: RNA

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

country: USA

institute: Case Western Reserve University

description:
Sample ID: E362
Sample name: 8118927047_I
YoungAdult_Rig_I_6hrs

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to HumanHT-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC). The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the limma from the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: PBMC, young adult, Rig I, 6h

label_protocol: Labeling was done with Ambion's Illumina kit as specified by Illumina's direct hybridization protocol.

growth_protocol: Gene expression was analyzed directly ex vivo.

extract_protocol: Cells were washed twice with cold PBS and lysed with 100 µl of cold RLT buffer (QIAGEN, Germany) supplemented with 1% beta-mercaptoethanol (BM) (Sigma, St. Louis, MO USA), and transferred to 1.7 ml tubes with 250 µl of cold RLT/BM buffer and quickly stored at -80oC. The samples underwent nucleic acid isolation in a designated Pre-PCR room using Qiagen’s RNeasy Micro Kit and underwent DNase I treatment. Total RNA concentrations were quantified using a NanoDrop 2000c spectrophotometer and quality was assessed using BioRad’s Experion automated electrophoresis system. With each batch of samples, a 500 ng HeLa RNA control and two water non-template negative controls were included.

treatment_protocol: Total PBMCs isolated from adults and old subjects were plated in triplicate at 100,000 cells/well in 96-well U-bottom plates. TLR and RIG-I agonists were added at the following concentrations: LPS-TLR4 (0.5 µg/ml) or CLO97-TLR7/8 (0.5 µg/ml) or poly I:C/Lyovec-RIGI/MDA5 (2 µg/ml) or 5’-pppRNA/Lyovec-RIG-I (400 ng/ml). PBMCs cultured in medium alone were used as a control for LPS and CLO97. Stimulation by poly I:C and 5’-pppRNA required the use of a cationic transfection agent LyoVec (InvivoGen), so medium plus Lyovec alone was used as a control for these two agonists. PBMCs were cultured for 6 and 24 hrs at 37oC in a 5% CO2-humidified environment.

tag: donor

tag: age class

value: young adult

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: treatment

value: Rig I

tag: time


title: 9020331172_R04C02

type: genomic

city: NEDLANDS

first: David

last: Martino

state: Western Australia

address: Perth Childrens Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute

hyb_protocol: Infinium Methylation Assay according to manufacturers protocol (Illumina)

scan_protocol: iScan system

data_processing: idat files processed in Minfi normalized using the stratified quantile normalization method. Sex probes removed, cross hybridizing probes removed, poor quality probes removed, SNP probes (MAF < 0.05 at extension site) removed

label: Cy5 and Cy3

molecule: genomic DNA

source_name: gDNA from normal PBMC

label_protocol: Cy5 and Cy3

growth_protocol: untouched cells rested for 48 hours in RPMI media (serum free)

extract_protocol: DNA purified using Qiagen All prep column extraction method

tag: gender

value: FEMALE

tag: phenotype

tag: challenge outcome

value: allergic


title: YoungAdult_No_treatment_6hrs YA_7

description:
Sample ID: E325
Sample name: 7018861084_J
YoungAdult_No_treatment_6hrs

source_name: PBMC, young adult, NoTx, 6h

value: NoTx


title: 9020331172_R05C02

value: MALE

value: sensitized


title: YoungAdult_Poly_IC_6hrs YA_7

description:
Sample ID: E319
Sample name: 7018861099_I
YoungAdult_Poly_IC_6hrs

source_name: PBMC, young adult, PolyIC, 6h

value: PolyIC


title: YoungAdult_Poly_IC_24hrs YA_7

description:
Sample ID: E322
Sample name: 6990990031_C
YoungAdult_Poly_IC_24hrs

source_name: PBMC, young adult, PolyIC, 24h


title: 9020331172_R03C02

value: nonallergic


title: INS1E COXB4_infected_72_hour

city: Shatin, New Territories

first: Wai Yip

last: Lam

address: Area 39, Lo Kwee-Seong Integrated Biomedical Sciences Building

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: miRNA expression in pancreatic islet cells after 72 hours of Coxsackie B4 infection.

hyb_protocol: Labeled RNA was purified and hybridized to Agilent miRNA arrays with eight identical arrays per slide, with each array containing probes interrogating 699 rat miRNAs.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent Technologies) using the standard settings for 8x15k array slides (miRBase v16).

data_processing: Fluorescence intensity was calculated using Feature Extraction software (Vsn. 10.5.1.1, Agilent) and analysis performed using Genespring GX (Agilent) and Excel (Microsoft, WA). GeneSpring defaults with the percentile shift to the 50th percentile; hence raw signal to 1.0, normalisation by percentile shift to the 50th percentile, and no baseline transformation.

organism: Rattus norvegicus

source_name: 72 hour COXB4 infected cells

label_protocol: MiRNAs were labeled using the Agilent miRNA labeling reagent and hybridized to Agilent human miRNA arrays according to the manufacturer's protocol. Briefly, total RNA (100 ng) was dephosphorylated and ligated with 3', 5'-cytidine bisphosphate (pCp-Cy3).

growth_protocol: The clonal rat β-cell line INS-1E, derived from parental INS-1 cells was cultured as monolayers in RPMI-1640 medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/mL streptomycin (all from Gibco, Life Technology, Rockville, Md., USA) at 37°C in a 5% CO2 incubator.

extract_protocol: Total RNA was extracted from normal and infected INS-1E cells using Trizol reagent (Invitrogen) following the manufacturer's protocol at time points 48, 72 hours post-infection. RNA pellets were resuspended in RNase-free water. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: INS-1E cells were grown to confluence in sterile T75 tissue culture flasks for the inoculation of virus isolate at a multiplicity of infection (m.o.i.) of one. After 1 hour of absorption, the virus was removed and 2 ml of fresh RPMI-1640 media with 2% FBS, 100 U/ml penicillin, 100 μg/mL streptomycin (all from Gibco, Life Technology) was added, and incubated at 37oC in 5% CO2 humidified air.

tag: cell line

value: pancreatic islet cells


title: YoungAdult_Rig_I_24hrs YA_7

description:
Sample ID: E317
Sample name: 7018861099_B
YoungAdult_Rig_I_24hrs

source_name: PBMC, young adult, Rig I, 24h


title: RIN5F Noninfected_Cell_control_48_hour

description: miRNA expression in pancreatic islet cells after 48 hours of incubation.

source_name: 48 hour cell control

growth_protocol: The RIN-5F cell line (ATCC® CRL-2058, Rockville, MD, USA) was a clone derived from the RIN rat islet cells which is an insulin-secreting rat cell line - was cultured as monolayers in RPMI-1640 medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/mL streptomycin (all from Gibco, Life Technology, Rockville, Md., USA) at 37°C in a 5% CO2 incubator.

extract_protocol: Total RNA was extracted from normal and infected RIN-5F cells using Trizol reagent (Invitrogen) following the manufacturer's protocol at time points 48, 72 hours post-infection. RNA pellets were resuspended in RNase-free water. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: RIN-5F cells were grown to confluence in sterile T75 tissue culture flasks for the inoculation of virus isolate at a multiplicity of infection (m.o.i.) of one. After 1 hour of absorption, the virus was removed and 2 ml of fresh RPMI-1640 media with 2% FBS, 100 U/ml penicillin, 100 μg/mL streptomycin (all from Gibco, Life Technology) was added, and incubated at 37oC in 5% CO2 humidified air.


title: RIN5F COXB4_infected_48_hour

description: miRNA expression in pancreatic islet cells after 48 hours of Coxsackie B4 virus infection.

source_name: 48 hour COXB4 infected cells


title: 9020331172_R06C01


title: 9020331172_R02C02


title: YoungAdult_LPS_24hrs YA_7

description:
Sample ID: E310
Sample name: 7018861087_C
YoungAdult_LPS_24hrs

source_name: PBMC, young adult, LPS, 24h

value: LPS


title: NS vs. LD_2

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

hyb_protocol: Hybridization was performerd according to the Agilent two-color microarray protocol

scan_protocol: Microarays were scanned using the Agilent DNA microarray scanner. Raw data was collected using the Agilent feature extraction software v10.7.

data_processing: Median values of Cy3 and Cy5 channel were processed in the R environment using the limma package. Backround correction was performed using the normexp method, Cy3 and Cy5 channels were loess normalized, Quantil-normalization was used for seperate microarrays.

organism: Dinoroseobacter shibae DFL 12 = DSM 16493

source_name: DFL12T non starved, light-dark cycle

label_protocol: total RNA was labelled using the Universal Linker System (Kreatech) according to the manufacturers  protocol

growth_protocol: DFL12 was grown in a defined minimal medium with succinate as sole carbon source. Growth temperature was 30°C, cells were kept in the dark or light/dark cycles

extract_protocol: Samples were collected in RNAprotect (Qiagen). RNA was extracted using the Rneasy Mini kit (Qiagen) with on column DNA digestion according to the manufacturers protocol followed by a second DNA digestion step in solution using DnaseI (Quiagen) and RNA purification using the RNeasy mini kit.

treatment_protocol: DFL12 ∆luxI1 was supplemented with 500 nM AHL at cultivation start

tag: starved/non-starved

value: non-starved

tag: light-dark cycle/dark

value: light/dark cycle

source_name: DFL12T starved 2 days, light-dark cycle

value: starved 2 days


title: YoungAdult_Rig_I_6hrs YA_7

description:
Sample ID: E314
Sample name: 7018861051_B
YoungAdult_Rig_I_6hrs


title: YoungAdult_CLO_97_24hrs YA_7

description:
Sample ID: E298
Sample name: 6898350039_J
YoungAdult_CLO_97_24hrs

source_name: PBMC, young adult, CLO_97, 24h


title: DD_2 vs. NS

source_name: DFL12T starved 2 days, dark

value: dark


title: 9020331172_R05C01


title: 9020331172_R04C01


title: YoungAdult_LPS_6hrs YA_7

description:
Sample ID: E307
Sample name: 8118927047_D
YoungAdult_LPS_6hrs

source_name: PBMC, young adult, LPS, 6h


title: YoungAdult_CLO_97_6hrs YA_7

description:
Sample ID: E295
Sample name: 7018861084_E
YoungAdult_CLO_97_6hrs

source_name: PBMC, young adult, CLO_97, 6h


title: YoungAdult_LyoVec_only_24hrs YA_6

description:
Sample ID: E286
Sample name: 6898481077_C
YoungAdult_LyoVec_only_24hrs

source_name: PBMC, young adult, LyoVec_only, 24h


title: 9020331172_R03C01


title: YoungAdult_No_treatment_24hrs YA_6

description:
Sample ID: E280
Sample name: 6898481080_C
YoungAdult_No_treatment_24hrs

source_name: PBMC, young adult, NoTx, 24h


title: 9020331172_R01C01

source_name: gDNA from normal PBMC


title: 9020331172_R02C01


title: YoungAdult_No_treatment_6hrs YA_6

description:
Sample ID: E277
Sample name: 6898481077_I
YoungAdult_No_treatment_6hrs

source_name: PBMC, young adult, NoTx, 6h


title: YoungAdult_Poly_IC_24hrs YA_6

description:
Sample ID: E274
Sample name: 6898481080_D
YoungAdult_Poly_IC_24hrs


title: P01105 Non-failing Left Ventricle

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description:
P01105
PolyA mRNA

hyb_protocol: cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to Affymetrix Human Gene 1.1 ST Array GeneChips (Affymetrix Inc., Santa Clara, CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Microarray Processing batch were controlled for using the R package Combat. Differential gene expression was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates.

label: biotin

source_name: heart left ventricle, non-failing

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

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

treatment_protocol: Explanted myocardium snap frozen in liquid nitrogen.

tag: tissue

value: heart left ventricle

tag: heart failure

value: no

tag: disease status

value: non-failing

value: male

tag: age


title: YoungAdult_LyoVec_only_6hrs YA_6

description:
Sample ID: E283
Sample name: 6898481080_J
YoungAdult_LyoVec_only_6hrs

source_name: PBMC, young adult, LyoVec_only, 6h

value: young adult

value: peripheral blood mononuclear cells (PBMCs)


title: YoungAdult_Poly_IC_6hrs YA_6

description:
Sample ID: E271
Sample name: 6991010102_H
YoungAdult_Poly_IC_6hrs

source_name: PBMC, young adult, PolyIC, 6h


title: 9247377111_R06C01

value: allergic


title: 9020331169_R06C02

value: FEMALE


title: 9020331172_R01C02

value: MALE


title: 9020331169_R02C02


title: 9020331169_R01C02


title: YoungAdult_Rig_I_24hrs YA_6

description:
Sample ID: E268
Sample name: 7018861087_H
YoungAdult_Rig_I_24hrs

source_name: PBMC, young adult, Rig I, 24h

value: Rig I


title: P01104 Idiopathic Dilated CMP Left Ventricle

description:
P01104
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP

value: yes

value: idiopathic dilated CMP

value: female


title: P01245 Non-failing Left Ventricle

description:
P01245
PolyA mRNA


title: YoungAdult_Rig_I_6hrs YA_6

description:
Sample ID: E266
Sample name: 7018861099_A
YoungAdult_Rig_I_6hrs

source_name: PBMC, young adult, Rig I, 6h


title: YoungAdult_LPS_24hrs YA_6

description:
Sample ID: E262
Sample name: 7018861087_G
YoungAdult_LPS_24hrs

source_name: PBMC, young adult, LPS, 24h

value: LPS


title: 9020331169_R02C01

value: nonallergic


title: 9020331169_R05C02


title: C02093 Ischemic Left Ventricle

description:
C02093
PolyA mRNA

source_name: heart left ventricle, ischemic

value: ischemic


title: P00205 Ischemic Left Ventricle

description:
P00205
PolyA mRNA


title: YoungAdult_LPS_6hrs YA_6

description:
Sample ID: E259
Sample name: 6898481077_K
YoungAdult_LPS_6hrs


title: P00280 Ischemic Left Ventricle

description:
P00280
PolyA mRNA


title: YoungAdult_CLO_97_24hrs YA_6

description:
Sample ID: E250
Sample name: 6898368101_H
YoungAdult_CLO_97_24hrs


title: P00315 Idiopathic Dilated CMP Left Ventricle

description:
P00315
PolyA mRNA


title: P01270 Non-failing Left Ventricle

description:
P01270
PolyA mRNA


title: 9020331164_R06C02

value: sensitized


title: YoungAdult_LyoVec_only_24hrs YA_5

description:
Sample ID: E238
Sample name: 6991010093_K
YoungAdult_LyoVec_only_24hrs


title: 9020331169_R05C01


title: 9020331164_R04C02


title: LD_2 vs. DD_2

source_name: DFL12T starved 2 days, light-dark cycle

value: starved 2 days

value: light/dark cycle

value: dark


title: 9020331169_R03C02


title: P00278 Ischemic Left Ventricle

description:
P00278
PolyA mRNA

value: heart left ventricle

value: male


title: P00282 Ischemic Left Ventricle

description:
P00282
PolyA mRNA


title: YoungAdult_CLO_97_6hrs YA_6

description:
Sample ID: E247
Sample name: 6991010093_A
YoungAdult_CLO_97_6hrs

value: young adult

value: peripheral blood mononuclear cells (PBMCs)


title: 9020331164_R05C02

value: FEMALE

value: allergic


title: 9020331164_R02C02

value: MALE


title: 9020331169_R01C01


title: 9020331164_R05C01


title: 9020331169_R04C01


title: 9020331164_R03C01


title: 9020331164_R06C01


title: 9020331164_R04C01


title: YoungAdult_No_treatment_24hrs YA_5

description:
Sample ID: E232
Sample name: 7018861084_B
YoungAdult_No_treatment_24hrs

value: NoTx


title: 9020331164_R01C01


title: 9020331164_R02C01


title: YoungAdult_Rig_I_24hrs YA_5

description:
Sample ID: E221
Sample name: 7018861051_H
YoungAdult_Rig_I_24hrs

value: Rig I


title: 9020331131_R06C02


title: P00275 Ischemic Left Ventricle

description:
P00275
PolyA mRNA

value: yes


title: YoungAdult_Poly_IC_24hrs YA_5

description:
Sample ID: E226
Sample name: 7018861084_C
YoungAdult_Poly_IC_24hrs

source_name: PBMC, young adult, PolyIC, 24h

value: PolyIC


title: P00189 Ischemic Left Ventricle

description:
P00189
PolyA mRNA

value: female


title: P00240 Ischemic Left Ventricle

description:
P00240
PolyA mRNA

value: ischemic


title: FT organoids + DBZ vs FT organoids

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: cell culture

hyb_protocol: Whole human genome 44k microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware)

source_name: fallopain tube

label_protocol: RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: Fallopian tube cells were extracted from human and seeded in Matrigel.  Cultures were kept at 37°C, 5% CO2 in a humidified incubator

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol.

treatment_protocol: Treatment of the effect of NOTCH inhibition on the growth and differentiation of tubal organoids was tested by adding - secretase inhibitor (DBZ)

value: 3D organoids

value: + DBZ


title: YoungAdult_Poly_IC_6hrs YA_5

description:
Sample ID: E223
Sample name: 7018879019_G
YoungAdult_Poly_IC_6hrs


title: P00242 Ischemic Left Ventricle

description:
P00242
PolyA mRNA


title: P00182 Ischemic Left Ventricle

description:
P00182
PolyA mRNA


title: YoungAdult_CLO_97_6hrs YA_5

description:
Sample ID: E199
Sample name: 6898350005_J
YoungAdult_CLO_97_6hrs


title: P00239 Ischemic Left Ventricle

description:
P00239
PolyA mRNA


title: 9020331131_R05C02

value: sensitized


title: YoungAdult_Rig_I_6hrs YA_5

description:
Sample ID: E218
Sample name: 7018861098_F
YoungAdult_Rig_I_6hrs


title: P00267 Ischemic Left Ventricle

description:
P00267
PolyA mRNA


title: YoungAdult_LyoVec_only_6hrs YA_5

description:
Sample ID: E235
Sample name: 6898350005_K
YoungAdult_LyoVec_only_6hrs


title: FT organoids vs FT organoids + DBZ

description: cell culture


title: YoungAdult_LyoVec_only_24hrs YA_4

description:
Sample ID: E190
Sample name: 7018879026_J
YoungAdult_LyoVec_only_24hrs


title: P00266 Ischemic Left Ventricle

description:
P00266
PolyA mRNA


title: YoungAdult_LPS_24hrs YA_5

description:
Sample ID: E214
Sample name: 6898481080_F
YoungAdult_LPS_24hrs

value: LPS


title: P00248 Ischemic Left Ventricle

description:
P00248
PolyA mRNA

value: heart left ventricle


title: YoungAdult_LyoVec_only_6hrs YA_4

description:
Sample ID: E187
Sample name: 6990990031_G
YoungAdult_LyoVec_only_6hrs


title: YoungAdult_LPS_6hrs YA_5

description:
Sample ID: E211
Sample name: 6898481080_E
YoungAdult_LPS_6hrs

source_name: PBMC, young adult, LPS, 6h


title: YoungAdult_CLO_97_24hrs YA_5

description:
Sample ID: E202
Sample name: 6991010102_C
YoungAdult_CLO_97_24hrs

source_name: PBMC, young adult, CLO_97, 24h


title: YoungAdult_No_treatment_24hrs YA_4

description:
Sample ID: E184
Sample name: 6898350005_G
YoungAdult_No_treatment_24hrs


title: P00219 Ischemic Left Ventricle

description:
P00219
PolyA mRNA


title: P00347 Idiopathic Dilated CMP Left Ventricle

description:
P00347
PolyA mRNA

value: idiopathic dilated CMP


title: Spermatozoa_NS5_rep1

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

description:
dataNorm_251485046835_1_4
Gene expression alterations in human control spermatozoa

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 Human Genome Oligo Microarrays (G4112A) 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. All data were normalized by quantile normalization.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

extract_protocol: Subsequent to storage, samples were thawed and washed twice in 2 ml of PBS, then suspended in round cell lysis buffer (0.1% SDS, 0.5% Triton X-100 in RNase free H2O). RNA was extracted using the RNeasy mini kit (Qiagen GmbH., Germany) with gentle modifications. Sperm cells were suspended in 600 µl of lysis buffer for 107 cells. This cell suspention was lysed using a Politron as previously described (Saade, et al., 2007), to maximize the recovery of spermatozoal RNA. The lysates were then processed according to the manufacturer’s instructions using the animal cell protocol. After RNase-free DNase treatment (Qiagen GmbH., Germany), the RNA was eluted with 30µl.  RNA concentration was determined using a nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). RNA integrity was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: male

tag: status

value: non-smoker

tag: spermatozoa (m/ml)

tag: round cells (m/ml)

tag: motility (a/b/c/d)

tag: % normal forms

tag: cigarette/day (starting year)


title: P00418 Ischemic Left Ventricle

description:
P00418
PolyA mRNA


title: 9020331131_R04C01


title: 9020331131_R03C02


title: P00389 Ischemic Left Ventricle

description:
P00389
PolyA mRNA


title: YoungAdult_No_treatment_6hrs YA_4

description:
Sample ID: E181
Sample name: 7018861087_K
YoungAdult_No_treatment_6hrs

tag: donor

tag: age class

value: young adult

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: treatment

tag: time


title: Spermatozoa_S4_rep1

description:
dataNorm_251485046834_1_4
Tobacco-induced gene expression alterations in human spermatozoa

tag: gender

value: smoker


title: 9020331131_R02C02

value: MALE

tag: phenotype

tag: challenge outcome

value: allergic


title: P00333 Idiopathic Dilated CMP Left Ventricle

description:
P00333
PolyA mRNA

tag: tissue

tag: heart failure

value: yes


title: Spermatozoa_S5_rep1

description:
dataNorm_251485046835_1_1
Tobacco-induced gene expression alterations in human spermatozoa

tag: age


title: 9020331094_R06C02


title: 9020331131_R01C01


title: 9020331131_R04C02


title: Spermatozoa_S6_rep1

description:
dataNorm_251485046835_1_3
Tobacco-induced gene expression alterations in human spermatozoa

tag: status


title: Spermatozoa_NS3_rep1

description:
dataNorm_251485046834_1_3
Gene expression alterations in human control spermatozoa

tag: spermatozoa (m/ml)


title: YoungAdult_Poly_IC_24hrs YA_4

description:
Sample ID: E178
Sample name: 7018861084_L
YoungAdult_Poly_IC_24hrs

value: PolyIC


title: P00353 Ischemic Left Ventricle

description:
P00353
PolyA mRNA

tag: disease status


title: P00348 Idiopathic Dilated CMP Left Ventricle

description:
P00348
PolyA mRNA


title: YoungAdult_Rig_I_24hrs YA_4

description:
Sample ID: E173
Sample name: 7018861051_L
YoungAdult_Rig_I_24hrs

value: Rig I


title: Spermatozoa_NS4_rep1

description:
dataNorm_251485046835_1_2
Gene expression alterations in human control spermatozoa

tag: round cells (m/ml)

tag: motility (a/b/c/d)


title: YoungAdult_Poly_IC_6hrs YA_4

description:
Sample ID: E175
Sample name: 6991010093_E
YoungAdult_Poly_IC_6hrs


title: P00337 Idiopathic Dilated CMP Left Ventricle

description:
P00337
PolyA mRNA

value: female


title: Spermatozoa_S3_rep1

description:
dataNorm_251485046834_1_2
Tobacco-induced gene expression alterations in human spermatozoa

tag: % normal forms

tag: cigarette/day (starting year)


title: 9020331131_R01C02


title: YoungAdult_Rig_I_6hrs YA_4

description:
Sample ID: E169
Sample name: 8118927047_C
YoungAdult_Rig_I_6hrs

tag: donor

tag: age class


title: 9020331131_R05C01


title: YoungAdult_LPS_24hrs YA_4

description:
Sample ID: E166
Sample name: 6991010102_I
YoungAdult_LPS_24hrs

tag: cell type

tag: treatment


title: P00319 Idiopathic Dilated CMP Left Ventricle

description:
P00319
PolyA mRNA

tag: gender


title: Spermatozoa_S2_rep1

description:
dataNorm_251485046822_1_3
Tobacco-induced gene expression alterations in human spermatozoa


title: 9020331131_R06C01

value: FEMALE

tag: phenotype


title: P00308 Idiopathic Dilated CMP Left Ventricle

description:
P00308
PolyA mRNA


title: P00323 Ischemic Left Ventricle

description:
P00323
PolyA mRNA

value: ischemic


title: Spermatozoa_NS2_rep1

description:
dataNorm_251485046822_1_4
Gene expression alterations in human control spermatozoa


title: 9020331094_R05C02

tag: challenge outcome

value: sensitized


title: Spermatozoa_NS1_rep1

description:
dataNorm_251485046822_1_2
Gene expression alterations in human control spermatozoa


title: YoungAdult_LPS_6hrs YA_4

description:
Sample ID: E163
Sample name: 6898350005_L
YoungAdult_LPS_6hrs

value: LPS

tag: time


title: 9020331094_R02C02

value: nonallergic


title: P00317 Idiopathic Dilated CMP Left Ventricle

description:
P00317
PolyA mRNA

tag: tissue

value: heart left ventricle

tag: heart failure

value: idiopathic dilated CMP


title: YoungAdult_LyoVec_only_24hrs YA_3

description:
Sample ID: E142
Sample name: 6990990031_F
YoungAdult_LyoVec_only_24hrs

source_name: PBMC, young adult, LyoVec_only, 24h


title: YoungAdult_CLO_97_6hrs YA_4

description:
Sample ID: E151
Sample name: 7018861098_I
YoungAdult_CLO_97_6hrs

source_name: PBMC, young adult, CLO_97, 6h


title: P00302 Ischemic Left Ventricle

description:
P00302
PolyA mRNA

value: male

tag: age


title: 9020331094_R04C02

source_name: gDNA from normal PBMC


title: YoungAdult_LyoVec_only_6hrs YA_3

description:
Sample ID: E139
Sample name: 6990990031_J
YoungAdult_LyoVec_only_6hrs

value: young adult


title: 9020331094_R03C02


title: Spermatozoa_S1_rep1

description:
dataNorm_251485046822_1_1
Tobacco-induced gene expression alterations in human spermatozoa

tag: status

tag: spermatozoa (m/ml)


title: YoungAdult_No_treatment_24hrs YA_3

description:
Sample ID: E136
Sample name: 7018861098_H
YoungAdult_No_treatment_24hrs

source_name: PBMC, young adult, NoTx, 24h

value: peripheral blood mononuclear cells (PBMCs)

value: NoTx


title: DISTAL - BIOLOGICAL CONTROL 2

city: HERAKLION

first: ARISTIDES

last: ELIOPOULOS

state: CRETE

address: UNIVERSITY CAMPUS

department: MEDICAL SCHOOL

country: Greece

institute: UNIVERSITY OF CRETE

hyb_protocol: The resultant fragmented and labeled cDNA was added to the hybridization cocktail in accordance with the NuGEN™ guidelines for hybridization onto Affymetrix GeneChip® arrays. Hybridization was performed for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridization Oven 640.

scan_protocol: The array was washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script, before being inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000.

data_processing: The Robust Multichip Algorithm (RMA) in Partek 6.5 with quantile normalisation and median polish was applied to the raw data in order to generate the pre-processed data.

label: BIOTIN

organism: Mus musculus

source_name: UNTREATED

label_protocol: Total RNA was amplified using the NuGEN™ WT-Ovation™ FFPE RNA Amplification System / NuGEN™ Ovation™ RNA Amplification System V2. The appropriate amount of amplified single-stranded cDNA was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2.

extract_protocol: Homogenization in Trizol

value: DISTAL COLON

value: Female

tag: strain


title: DISTAL - BIOLOGICAL CONTROL 1


title: 9020331094_R06C01

value: allergic


title: DISTAL - BIOLOGICAL CONTROL 3


title: P00296 Ischemic Left Ventricle

description:
P00296
PolyA mRNA

value: yes

tag: disease status


title: 9020331094_R02C01


title: YoungAdult_Poly_IC_24hrs YA_3

description:
Sample ID: E130
Sample name: 6991010093_L
YoungAdult_Poly_IC_24hrs

value: PolyIC


title: PROXIMAL - BIOLOGICAL CONTROL 2

value: PROXIMAL COLON


title: YoungAdult_Poly_IC_6hrs YA_3

description:
Sample ID: E127
Sample name: 6991010102_J
YoungAdult_Poly_IC_6hrs


title: P00286 Ischemic Left Ventricle

description:
P00286
PolyA mRNA


title: 9020331094_R04C01

value: MALE


title: P00292 Ischemic Left Ventricle

description:
P00292
PolyA mRNA

value: ischemic


title: YoungAdult_Rig_I_24hrs YA_3

description:
Sample ID: E124
Sample name: 6898368101_I
YoungAdult_Rig_I_24hrs

value: Rig I


title: YoungAdult_Rig_I_6hrs YA_3

description:
Sample ID: E122
Sample name: 7018879026_D
YoungAdult_Rig_I_6hrs


title: PROXIMAL - BIOLOGICAL CONTROL 1


title: P00283 Idiopathic Dilated CMP Left Ventricle

description:
P00283
PolyA mRNA


title: 9020331094_R05C01

value: FEMALE

value: sensitized


title: YoungAdult_LPS_24hrs YA_3

description:
Sample ID: E118
Sample name: 7018861098_D
YoungAdult_LPS_24hrs

value: LPS


title: 9020331094_R03C01

value: nonallergic


title: P00290 Ischemic Left Ventricle

description:
P00290
PolyA mRNA

value: heart left ventricle

value: male


title: P00273 Ischemic Left Ventricle

description:
P00273
PolyA mRNA


title: Methylation in colon mucosa 495

city: Houston

first: R.

middle: Alan

last: Harris

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Ulcerative colitis treated with infliximab and mesalamine colon mucosa sample.

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner settings

data_processing:
GenomeStudio software version 2010.3.0.30128
Average beta values were normalized to internal array controls as implemented in GenomeStudio

source_name: colon mucosa 495, after treatment with infliximab and mesalamine

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted and purified from colon mucosa samples using QIAamp DNA Mini Kit (Qiagen, Valencia, CA) starting at step 5 of the Tissue Protocol following bead beating and Qiagen TissueLyser treatment. All samples were quality tested with PicoGreen prior to proceeding with the microarrays.

value: Male

value: Colon mucosa

tag: disease state

value: Ulcerative colitis

value: infliximab and mesalamine


title: Methylation in colon mucosa 382

description: Crohn's disease colon mucosa sample

source_name: colon mucosa 382

value: Female

value: Crohn's disease


title: PROXIMAL - BIOLOGICAL CONTROL 3


title: P00245 Idiopathic Dilated CMP Left Ventricle

description:
P00245
PolyA mRNA

value: yes

value: idiopathic dilated CMP


title: mouse macrophage at M2+10058F4, biological rep2

city: Singapore

first: Ling

last: Li

address: 8A Biomedical Grove

country: Singapore

institute: Agency for Science Technology and Research, Singapore

description: Gene expression data from mouse macrophages at M2 treated with 10058F4 (MYC inhibitor).

hyb_protocol: Following fragmentation, 15 ug of labeled cRNA per sample was hybridized onto the GeneChip Mouse Genome 430 2.0 array (Affymetrix) for 16-18 hours at 45oC. Arrays were then washed and stained using Fluidics Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 7G.

data_processing: Data were processed using the GeneChip Operating Software following default Robust Multi-array Average (RMA) settings.

source_name: Mouse macrophage at M2 treated with 10058F4

label_protocol: For each sample, double-stranded cDNA was synthesized from 1 ug of total RNA using a T7-oligo(dT) primer. After cleanup, biotin-labeled cRNA was synthesized, then purified and quantified. Quality of the cRNA was additionally checked by spectrophotometric analysis.

growth_protocol: Mouse bone marrow derived macrophages grown in M-CSF for 7 days in culture

extract_protocol: Total RNA was first isolated using TriZOL® reagent (Invitrogen) followed by the RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: M0 - not treated. M1 - polarized with E coli lipopolysacharide (LPS) and INF-g. M2 - polarized with IL4 and IL13.

value: bone marrow derived macrophages

value: polarized with IL4 and IL13.

tag: agent

value: MYC inhibitor (10058F4)


title: Methylation in colon mucosa 433

description: Crohn's disease colon mucosa sample

source_name: colon mucosa 433


title: YoungAdult_LyoVec_only_24hrs YA_2

description:
Sample ID: E094
Sample name: 6990990031_E
YoungAdult_LyoVec_only_24hrs

tag: donor

value: young adult

value: peripheral blood mononuclear cells (PBMCs)


title: P00271 Ischemic Left Ventricle

description:
P00271
PolyA mRNA

value: ischemic


title: YoungAdult_CLO_97_24hrs YA_3

description:
Sample ID: E106
Sample name: 6898481080_L
YoungAdult_CLO_97_24hrs

tag: age class


title: YoungAdult_CLO_97_6hrs YA_3

description:
Sample ID: E103
Sample name: 6898368101_E
YoungAdult_CLO_97_6hrs

tag: cell type


title: mouse macrophage at M2+10058F4, biological rep1

tag: treatment


title: Methylation in colon mucosa 386

description: Crohn's disease colon mucosa sample

source_name: colon mucosa 386

tag: gender


title: P00251 Idiopathic Dilated CMP Left Ventricle

description:
P00251
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP


title: Methylation in colon mucosa 419

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa 419


title: P00268 Idiopathic Dilated CMP Left Ventricle

description:
P00268
PolyA mRNA


title: Methylation in colon mucosa 425

description: Crohn's disease colon mucosa sample

source_name: colon mucosa 425


title: mouse macrophage at M2+nutlin, biological rep3

description: Gene expression data from mouse macrophages at M2 treated with nutlin-3a.

source_name: Mouse macrophage at M2 treated with nutlin-3a


title: mouse macrophage at M2+nutlin, biological rep1


title: YoungAdult_No_treatment_24hrs YA_2

description:
Sample ID: E088
Sample name: 7018879026_E
YoungAdult_No_treatment_24hrs

value: NoTx


title: Methylation in colon mucosa 432

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa 432


title: YoungAdult_LyoVec_only_6hrs YA_2

description:
Sample ID: E091
Sample name: 7018879026_C
YoungAdult_LyoVec_only_6hrs

source_name: PBMC, young adult, LyoVec_only, 6h


title: mouse macrophage at M2+10058F4, biological rep3


title: Methylation in colon mucosa 399

description: Crohn's disease colon mucosa sample

source_name: colon mucosa 399


title: YoungAdult_No_treatment_6hrs YA_2

description:
Sample ID: E085
Sample name: 6898350039_A
YoungAdult_No_treatment_6hrs

source_name: PBMC, young adult, NoTx, 6h


title: mouse macrophage at M2, biological rep3

description: Gene expression data from mouse macrophages at M2.

source_name: Mouse macrophage at M2


title: Methylation in colon mucosa 395

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa 395


title: Methylation in colon mucosa 416

description: Ulcerative colitis before treatment with infliximab and mesalamine colon mucosa sample.

source_name: colon mucosa 416, before treatment with infliximab and mesalamine


title: P00229 Idiopathic Dilated CMP Left Ventricle

description:
P00229
PolyA mRNA

value: heart left ventricle


title: mouse macrophage at M2, biological rep1


title: P00227 Idiopathic Dilated CMP Left Ventricle

description:
P00227
PolyA mRNA

value: male


title: P00123 Ischemic Left Ventricle

description:
P00123
PolyA mRNA

source_name: heart left ventricle, ischemic


title: YoungAdult_Poly_IC_24hrs YA_2

description:
Sample ID: E082
Sample name: 7018879019_I
YoungAdult_Poly_IC_24hrs

source_name: PBMC, young adult, PolyIC, 24h

value: PolyIC


title: mouse macrophage at M2, biological rep2


title: YoungAdult_Poly_IC_6hrs YA_2

description:
Sample ID: E079
Sample name: 7018861084_G
YoungAdult_Poly_IC_6hrs

source_name: PBMC, young adult, PolyIC, 6h


title: mouse macrophage at M2+nutlin, biological rep2


title: P00228 Ischemic Left Ventricle

description:
P00228
PolyA mRNA


title: YoungAdult_Rig_I_6hrs YA_2

description:
Sample ID: E074
Sample name: 6991010093_H
YoungAdult_Rig_I_6hrs

source_name: PBMC, young adult, Rig I, 6h

value: Rig I


title: P00215 Idiopathic Dilated CMP Left Ventricle

description:
P00215
PolyA mRNA


title: mouse macrophage at M1, biological rep3

description: Gene expression data from mouse macrophages at M1.

source_name: Mouse macrophage at M1

value: polarized with E coli lipopolysacharide (LPS) and INF-g.


title: YoungAdult_LPS_6hrs YA_2

description:
Sample ID: E067
Sample name: 6898350039_G
YoungAdult_LPS_6hrs

source_name: PBMC, young adult, LPS, 6h

value: LPS


title: YoungAdult_LPS_24hrs YA_2

description:
Sample ID: E070
Sample name: 6991010093_F
YoungAdult_LPS_24hrs

source_name: PBMC, young adult, LPS, 24h


title: YoungAdult_Rig_I_24hrs YA_2

description:
Sample ID: E077
Sample name: 6991010093_G
YoungAdult_Rig_I_24hrs

source_name: PBMC, young adult, Rig I, 24h


title: mouse macrophage at M1, biological rep2


title: mouse macrophage at M1, biological rep1


title: Methylation in colon mucosa 397

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa 397

value: Male

value: Colon mucosa

value: Ulcerative colitis


title: P00208 Idiopathic Dilated CMP Left Ventricle

description:
P00208
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP

value: yes

value: idiopathic dilated CMP


title: P00265 Idiopathic Dilated CMP Left Ventricle

description:
P00265
PolyA mRNA


title: Methylation in colon mucosa 356

description: Normal colon mucosa sample

source_name: colon mucosa 356

value: Female

value: normal


title: mouse macrophage at M0, biological rep3

description: Gene expression data from mouse macrophages at M0.

source_name: Mouse macrophage at M0

value: bone marrow derived macrophages

value: not treated


title: Methylation in colon mucosa 398

description: Normal colon mucosa sample

source_name: colon mucosa 398


title: Methylation in colon mucosa 206

description: Normal colon mucosa sample

source_name: colon mucosa 206


title: P00206 Idiopathic Dilated CMP Left Ventricle

description:
P00206
PolyA mRNA


title: Methylation in colon mucosa 394

description: Normal colon mucosa sample

source_name: colon mucosa 394


title: Methylation in colon mucosa 266

description: Normal colon mucosa sample

source_name: colon mucosa 266


title: mouse_lungEC_WT_2

city: Tokyo

first: Shogo

last: Yamamoto

address: 4-6-1 Komaba, Megro-ku

department: Research Center for Advanced Science and Technology

country: Japan

institute: The University of Tokyo

description: mouse lungEC_WT

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45 degree Celsius, 16 hours). Hybridization was controlled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: GeneChip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm with target intensity=100.

source_name: WT lung

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

tag: strain/background

tag: genotype/variation

value: wildtype

value: whole lung


title: P00204 Idiopathic Dilated CMP Left Ventricle

description:
P00204
PolyA mRNA

value: heart left ventricle

value: female


title: mouse_lungEC_DSCR-KO_1

description: mouse lungEC_DSCR-1KO

source_name: DSCR-1-/- lung

value: DSCR1 knockout


title: P00187 Ischemic Left Ventricle

description:
P00187
PolyA mRNA

source_name: heart left ventricle, ischemic

value: ischemic

value: male


title: P00207 Ischemic Left Ventricle

description:
P00207
PolyA mRNA


title: Gr1Mac, 2

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

description: Gene expression data from Gr1+/CD11b+ bone marrow cells

hyb_protocol: amplified, fragmented, biotin labeled aRNA was hybridized for 18 hr at 45C on Affymetrix GeneChip Mouse 430 2.0. Chips were washed and stained in the Affymetrix Fluidics Station 450 according to manufacturers instructions

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA (Robust Multichip Average; Bioconductor)

source_name: Gr1+/CD11b+ bone marrow cells

label_protocol: Affymetrix GeneChip 3' IVT Express Kit according to manufacturers instructions

growth_protocol: C57BL/6J  bone marrow cells were harvested from mice treated for 4 days with 150 mg 5-fluorouracil/kg  and stimulated for 48 hours in DMEM supplemented with 15% FBS, 10 ng/mL hIL6, 6ng/mL mIL3, and 20ng/mL mSCF

extract_protocol: TRIZOL  according to manufacturers instructions

treatment_protocol: Transduction with gammaretroviral supernatants 48h after isolation; transplantation into syngenic mice. FACS-isolation 4 weeks after transplantation


title: P00201 Ischemic Left Ventricle

description:
P00201
PolyA mRNA


title: YoungAdult_No_treatment_6hrs YA_1

description:
Sample ID: E037
Sample name: 6898350005_A
YoungAdult_No_treatment_6hrs

source_name: PBMC, young adult, NoTx, 6h

value: young adult

value: peripheral blood mononuclear cells (PBMCs)

value: NoTx

tag: time


title: YoungAdult_No_treatment_24hrs YA_1

description:
Sample ID: E040
Sample name: 7018879026_K
YoungAdult_No_treatment_24hrs

source_name: PBMC, young adult, NoTx, 24h


title: YoungAdult_CLO_97_6hrs YA_2

description:
Sample ID: E055
Sample name: 6898481077_B
YoungAdult_CLO_97_6hrs

source_name: PBMC, young adult, CLO_97, 6h


title: YoungAdult_CLO_97_24hrs YA_2

description:
Sample ID: E058
Sample name: 8118927047_F
YoungAdult_CLO_97_24hrs

source_name: PBMC, young adult, CLO_97, 24h


title: P00234 Ischemic Left Ventricle

description:
P00234
PolyA mRNA

tag: tissue


title: YoungAdult_LyoVec_only_6hrs YA_1

description:
Sample ID: E043
Sample name: 7018861087_I
YoungAdult_LyoVec_only_6hrs

source_name: PBMC, young adult, LyoVec_only, 6h


title: mouse macrophage at M0, biological rep1


title: mouse_lungEC_DSCR-KO_2

description: mouse lungEC_DSCR-1KO


title: mouse_lungEC_WT_1

description: mouse lungEC_WT


title: YoungAdult_LyoVec_only_24hrs YA_1

description:
Sample ID: E046
Sample name: 7018879019_D
YoungAdult_LyoVec_only_24hrs

source_name: PBMC, young adult, LyoVec_only, 24h


title: Methylation in colon mucosa 429

description: Normal colon mucosa sample

source_name: colon mucosa 429

value: Male

value: Colon mucosa


title: mouse macrophage at M0, biological rep2


title: P00202 Ischemic Left Ventricle

description:
P00202
PolyA mRNA

tag: heart failure

value: yes


title: Methylation in colon mucosa 422

description: Normal colon mucosa sample

source_name: colon mucosa 422

tag: age


title: YoungAdult_Poly_IC_24hrs YA_1

description:
Sample ID: E034
Sample name: 7018861098_L
YoungAdult_Poly_IC_24hrs

source_name: PBMC, young adult, PolyIC, 24h

value: PolyIC


title: P00177 Idiopathic Dilated CMP Left Ventricle

description:
P00177
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP

value: idiopathic dilated CMP


title: P00153 Ischemic Left Ventricle

description:
P00153
PolyA mRNA


title: P00158 Ischemic Left Ventricle

description:
P00158
PolyA mRNA


title: Methylation in colon mucosa 421

description: Normal colon mucosa sample

source_name: colon mucosa 421

value: Female

value: normal


title: Gr1Mac, 1


title: YoungAdult_LPS_24hrs YA_1

description:
Sample ID: E022
Sample name: 7018879019_H
YoungAdult_LPS_24hrs

source_name: PBMC, young adult, LPS, 24h

value: LPS


title: Gironde - A717

city: Arcachon

first: lucie

last: baillon

address: place du docteur Peyneau

institute: université de Bordeaux UMR ePOC

hyb_protocol: For cDNA hybridization, microarray was pre-hybridized in 5X SSC buffer; 0.1% SDS; 0.1 g.L-1 BSA during 45 min at 55°C. Microarray was washed twice 5 min in 0.1X SSC at RT followed by 30s in purified water under continuous agitation. Microarray was then centrifuged 2 min for drying.   800ng of cDNA sample was pooled with 800ng of cDNA reference and hybridized on microarray in 2X hybridization buffer (8X SSC; 0.4% SDS; 0.1g.L-1 calf thymus DNA) and incubated at 55°C in Agilent chamber overnight. Hybridized microarray was washed at 55°C in 2X SSC; 0.1% SDS buffer, washed, twice 5 min in 2X SSC; 0.1% SDS buffer under agitation at RT; twice 5 min in 0.1X SSC; 0.1% SDS buffer and finally 4 times in 0.1X SSC buffer and dried by centrifugation (2 min).

scan_protocol: Microarray data were generated by the Innoscan 710 microarray scanner using Mapix software.

data_processing:
the filtering of raw data was done for both green and red channels. The median foreground (F635median and F532median) and median background (B635median and B532median) was chosen for the data normalization. If the ratio Fmedian/Bmedian was lower than 1.5, data were removed from the analysis. For each channel, the background was removed of the foreground data and the mean of triplicates (three spots for each gene) was then calculated and both green and red channels were used for data normalization. Normalization and statistical analysis was done by using the BRB-arrayTools version 4.4.0 software package (http://linus.nci.nih.gov/BRB-ArrayTools.html). Each array was median normalized over entire arrays and genes were excluded if 50% of values were missing in the complete set of arrays.
Data normalized by median-centering log-ratios in each array,  based on the average of the red and green log-intensities

organism: Anguilla anguilla

source_name: Fish from Gironde natural site

label_protocol: For the first step of reverse-transcription procedure, 10µg of RNA was mixed with 3µg of random primer and 2µg of oligodT. Water was added for 20µl qs. Mix was incubated 5 min at 70°C followed by10 min at 18°C and finally stored at 4°C. 20µl of the RT mix (GoScript™ 5X Reaction Buffer: 8µl; DTT [0.1M]: 4µl; MgCl2 [25mM]: 4.8µl; 50X aa-dNTP mix (25mM each): 1µl; dUTP: 1µl; GoScript™ RT: 2µl) was added to the RNA mix. The mix was incubated during 12h at 42°C followed by 5 min at 18 °C and stored at 4°C. RNAs were then hydrolyzed with 4µl of EDTA [0.2M] pH 8 and 6µl of NaOH [1M] during 10 min at 70°C.  To re-adjust the pH, 6µl of HCL [1M] was then added. cDNA purification was carried out with the Qiagen PCR purification kit following the manufacturer’s protocol. cDNA was eluted in 60µl of sodium bicarbonate [0.1M] pH 9 and placed at -20°C before labeling.   In order to normalize microarray data, we used a common reference design. This was composed by a pool of gonads from 30 wild eels (Anguilla anguilla) from Certes our reference site(15 fishes collected in 2011 and 15 in 2012). This reference was combined in equal amounts with each sample before to be hybridized on the microarray slide. Reference and sample cDNAs were labeled with CyDye™ Post-Labelling Reactive Dye Pack (Amersham). Each cDNA sample and reference was mix with 1 vial of CyDye (Cy3 for sample and Cy5 for reference) and incubated at RT in the dark during 90 min. Reaction was stopped by adding 15µl of hydroxylamine hydrochloride [4M] and incubated during 15 min in the dark. Purification of labeled cDNA was carried out with the Qiagen PCR purification kit following the manufacturer’s protocol and eluted in 60µl of water. Amount of labeled cDNA  as well as the frequency of incorporation (FOI) were determined spectrophotometrically (Epoch, Biotek).

extract_protocol: RNA extraction was carried out by means of the SV total RNA islotaion Kit, promega). Sampleswere placed in 450 µl of RNA lysis (Promega) buffer in sterile microtube and were homogenized by means of two metal beads and tissue homogenizer (Retsch). After 2 min of centrifugation at 10,000 rpm, 400 µl of the lysate was recovered.  One volume of Phenol:Chloroform:Isoamyl Alcohol 25:24:1 was then added. The homogenate was vortexed 10s and centrifuged 10 min at RT. The upper phase was recovered. One volume of 75% EtOH was adeed. After homogenization by vortexing, the mix was transferred to a spin column and the standard manufacturer’s procedures were followed (including DNAseI treatment).. Quality and integrity of the total RNA were controlled by electrophoresis on a 1% agarose gel.

value: Gonad

tag: collection site

value: Gironde

source_name: reference pool

value: gonad

value: Certes


title: Gironde - A715


title: MN1, 2

description: Gene expression data from GFP+ BM cells overexpressing MN1

source_name: GFP+ one marrow cells transduced with pSF91-MN1-IRES-GFP 4  weeks after Tx


title: MN1VP16, 1

description: Gene expression data from GFP+ BM cells overexpressing MN1VP16

source_name: GFP+ one marrow cells transduced with pSF91-MN1VP16-IRES-GFP 4  weeks after Tx


title: P00162 Ischemic Left Ventricle

description:
P00162
PolyA mRNA

source_name: heart left ventricle, ischemic

value: heart left ventricle

value: ischemic


title: Methylation in colon mucosa 434

description: Normal colon mucosa sample

source_name: colon mucosa 434


title: YoungAdult_LPS_6hrs YA_1

description:
Sample ID: E019
Sample name: 6990990031_H
YoungAdult_LPS_6hrs

source_name: PBMC, young adult, LPS, 6h

value: young adult


title: MN1VP16, 2


title: Gironde - A713


title: P00150 Ischemic Left Ventricle

description:
P00150
PolyA mRNA

value: male


title: YoungAdult_Rig_I_24hrs YA_1

description:
Sample ID: E028
Sample name: 6898350005_F
YoungAdult_Rig_I_24hrs

source_name: PBMC, young adult, Rig I, 24h

value: peripheral blood mononuclear cells (PBMCs)

value: Rig I


title: YoungAdult_Poly_IC_6hrs YA_1

description:
Sample ID: E031
Sample name: 6898350039_B
YoungAdult_Poly_IC_6hrs

source_name: PBMC, young adult, PolyIC, 6h


title: YoungAdult_CLO_97_24hrs YA_1

description:
Sample ID: E010
Sample name: 7018861098_E
YoungAdult_CLO_97_24hrs

source_name: PBMC, young adult, CLO_97, 24h


title: P00149 Ischemic Left Ventricle

description:
P00149
PolyA mRNA


title: YoungAdult_CLO_97_6hrs YA_1

description:
Sample ID: E007
Sample name: 6990990031_B
YoungAdult_CLO_97_6hrs

source_name: PBMC, young adult, CLO_97, 6h


title: P00147 Idiopathic Dilated CMP Left Ventricle

description:
P00147
PolyA mRNA


title: Gironde - A714


title: Gironde - A711


title: Gironde - A712


title: MN1, 1


title: Gironde - A709


title: SclKO_Flk+Scl-_rep2

city: Tartu

first: Tõnis

last: Org

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: The R package Limma (Gentleman, 2005) provided through the open source project Bioconductor (Gentleman et al., 2004) was used for assessing differential expression. To calculate absolute mRNA expression levels, the RMA (Robust Multiarray Averaging (Bolstad et al., 2003)) method (provided through R library affy) was used to obtain background adjusted, quantile normalized and probe level data summarized values for all probe sets. The Affymetrix Mouse Genome 430 2.0 Array GeneChip platform was used for the analysis. Official gene symbols for probe sets were obtained using the Bioconductor annotation database mouse4302.db. The mas5calls algorithm (Liu et al., 2006) through the R package affy was used for calculating PMA detection calls for each array sample. The algorithm employs a signed rank test to consider the significance of the difference between the PM and MM values for each probeset and returns a detection p-value that is used to flag a transcript as 'Present', 'Marginal' or 'Absent' (P/M/A). Probes that were 'Absent' for all samples analyzes were excluded from further analysis. Differentially expressed genes were uploaded into the DAVID (Huang et al., 2007) interface to identify significantly over-represented functional GO biological process categories.

label_protocol: Affymetrix standard labeling kit

growth_protocol: Standard ES cell culture media with DMEM (Cellgro), 15% serum (Hyclone or Omega) and 10ng/ml LIF (Millipore) and gelatin coated dishes were used to maintain SclhCD4 knock-in (Chung et al., 2002), SclKO (Porcher et al., 1996) and WT ES cells.

extract_protocol: Day 4 EB cells were sorted on a BD FACS Aria II (BD Biosciences) using Flk1-PE and hCD4 (clone S3.5, Invitrogen) antibodies to collect WT Flk1+hCD4+(Scl+), WT Flk1+hCD4-(Scl-) and SclKO Flk1+ cell polulations.

treatment_protocol: ES cells were differentiated into Flk1+ cells by 2 days of culture in pre-EB media (IMDM with the addition of L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M monothiolglycerol (MTG), 15% of FBS and 10ng/ml LIF; followed by plateing 100 000 cells per well to low attachment 6-well plates (Costar) in EB media ((IMDM with the addition of 15% of FBS, L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M MTG, 3mg/ml human transferrin (Roche) and 2.5mg/ml ascorbic acid (Sigma) and clulturing the cells for 4 days. Cells were digested enzymatically and FACS sorted for desired populations.

tag: strain that es cell-line is derived from

tag: original mes cell line

tag: cell-line

value: SclKO mESC

value: ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells

tag: treatment/cell subtype

value: EB formation, FACS sorting for Flk1+ mesodermal cells


title: Certes - A616

source_name: Fish from Certes natural site


title: P00143 Idiopathic Dilated CMP Left Ventricle

description:
P00143
PolyA mRNA

value: yes

tag: disease status

value: idiopathic dilated CMP


title: Certes - A615


title: WT_Flk+Scl-_rep2

value: (129/Sv x 129/Sv-CP)F1 3.5-day blastocyst

value: WT hCD4 Scl reporter mESC

value: EB formation, FACS sorting for Flk1+hCD4-(Scl-) mesodermal cells


title: WT_Flk+Scl-_rep1


title: Ventricles- Human fetal heart rep4

city: Leiden

first: Harsha

middle: D

last: Devalla

address: Einthovenweg 20

department: Anatomy & Embryology

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Standard Illumina protocol: Whole-Genome Gene Expression Direct Hybridization Assay.

scan_protocol: Samples were scanned with illumina iscan array scanner using standard Illumina protocol

data_processing: The data was normalized using quantile normalization in Genespring GX  v12.5.

source_name: Human Heart

label_protocol: Biotin-labeled (Biotin-16-UTP) amplified cRNA was generated using Illumina Totalprep-96 RNA Amplification Kit

growth_protocol: Differentiation of hESCs to cardiac lineage was performed by Spin EB method. Cytokine cocktail is added on day 0 to the cells and refreshed on day 3. Beating EBs are observed on day 10.

extract_protocol: RNA extraction was performed with Macherey-Nagel Nucleospin Kit. DNAse treatment was performed on the column and quality of samples was asessed on Agilent bioanalyzer.

treatment_protocol: hESCs differentiations were treated with 1 uM Retinoic Acid (Sigma) from day 4 to day 7. Control differentiations were treated with DMSO from day 4 to day 7.

value: ventricles

value: Fetal


title: Atria- Human fetal heart rep4

value: atria


title: P00136 Idiopathic Dilated CMP Left Ventricle

description:
P00136
PolyA mRNA

value: heart left ventricle


title: P00146 Ischemic Left Ventricle

description:
P00146
PolyA mRNA

value: ischemic


title: Certes - A614

value: Gonad

value: Certes

value: gonad


title: Ventricles- Human fetal heart rep2


title: Certes - A613


title: Atria- Human fetal heart rep3


title: P00134 Ischemic Left Ventricle

description:
P00134
PolyA mRNA

value: female


title: Atria- Human fetal heart rep2


title: MN1del7, rep2

description: Gene expression data from BM cells transduced with MN1 del 7.

hyb_protocol: Amplified, fragmented, biotin labeled aRNA was hybridized for 18 hr at 45C on Affymetrix GeneChip Mouse 430 2.0. Chips were washed and stained in the Affymetrix Fluidics Station 450 according to manufacturer's instructions.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing: RMA (Robust Multichip Average; Bioconductor).

source_name: bone marrow cells transduced with MN1del7, 4 weeks after Tx

label_protocol: Affymetrix GeneChip 3' IVT Express Kit according to manufacturer's instructions.

growth_protocol: C57BL/6J bone marrow cells were harvested from mice treated for 4 days with 150 mg 5-fluorouracil/kg and stimulated for 48 hours in DMEM supplemented with 15% FBS, 10 ng/mL hIL6, 6ng/mL mIL3, and 20ng/mL mSCF.

extract_protocol: TRIZOL according to manufacturer's instructions.

treatment_protocol: Transduction with retroviral supernatants 48h after isolation; transplantation into syngenic mice. FACS-isolation 4 weeks after transplantation.

value: bone marrow cells

tag: transduction

tag: time after transplantation

value: 4 weeks


title: Ventricles- Human fetal heart rep3


title: Certes - A612


title: P00130 Ischemic Left Ventricle

description:
P00130
PolyA mRNA

value: male


title: WT_Flk+Scl+_rep2

tag: cell type

value: ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells

value: EB formation, FACS sorting for Flk1+hCD4+(Scl+) mesodermal cells


title: P00140 Ischemic Left Ventricle

description:
P00140
PolyA mRNA

value: yes


title: MN1del7, rep1


title: Certes - A611


title: P00141 Idiopathic Dilated CMP Left Ventricle

description:
P00141
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP

value: idiopathic dilated CMP


title: P00127 Idiopathic Dilated CMP Left Ventricle

description:
P00127
PolyA mRNA


title: Certes - A609


title: Certes - A610


title: WT_Flk+Scl+_rep1

value: (129/Sv x 129/Sv-CP)F1 3.5-day blastocyst

value: WT hCD4 Scl reporter mESC


title: Atria- Human fetal heart rep1

value: Fetal


title: Day31- GFP+ rep5

source_name: Human embryonic stem cells

value: Human embryonic stem cells

tag: treatment

value: RA-treated


title: GrMac, rep2

description: Gene expression data from Gr1+/CD11b+ bone marrow cells.

source_name: Gr1+/CD11b+ bone marrow cells

value: Gr1+/CD11b+ bone marrow cells


title: P00116 Ischemic Left Ventricle

description:
P00116
PolyA mRNA

value: heart left ventricle

value: ischemic

tag: gender


title: Day31- GFP- rep4


title: GrMac, rep1

tag: strain/background


title: Garonne - A365, liver

description: SAMPLE 84

source_name: Fish from Garrone natural site (France)

label_protocol: For the first step of reverse-transcription procedure, 10µg of RNA was mixed with 3µg of random primer and 2µg of oligodT. Water was added for 20µl qs. Mix was incubated 5 min at 70°C followed by10 min at 18°C and finally stored at 4°C. 20µl of the RT mix (GoScript™ 5X Reaction Buffer: 8µl; DTT [0.1M]: 4µl; MgCl2 [25mM]: 4.8µl; 50X aa-dNTP mix (25mM each): 1µl; dUTP: 1µl; GoScript™ RT: 2µl) was added to the RNA mix. The mix was incubated during 12h at 42°C followed by 5 min at 18 °C and stored at 4°C. RNAs were then hydrolyzed with 4µl of EDTA [0.2M] pH 8 and 6µl of NaOH [1M] during 10 min at 70°C.  To re-adjust the pH, 6µl of HCL [1M] was then added. cDNA purification was carried out with the Qiagen PCR purification kit following the manufacturer’s protocol. cDNA was eluted in 60µl of sodium bicarbonate [0.1M] pH 9 and placed at -20°C before labeling.   In order to normalize microarray data, we used a common reference design. This was composed by a pool of 30 wild eels of Certes (15 fishes collected in 2011 and 15 in 2012). This reference was combined in equal amounts with each sample before to be hybridized on the microarray slide. . Reference and sample cDNAs were labeled with CyDye™ Post-Labelling Reactive Dye Pack (Amersham). Each cDNA sample and reference was mix with 1 vial of CyDye (Cy3 for sample and Cy5 for reference) and incubated at RT in the dark during 90 min. Reaction was stopped by adding 15µl of hydroxylamine hydrochloride [4M] and incubated during 15 min in the dark. Purification of labeled cDNA was carried out with the Qiagen PCR purification kit following the manufacturer’s protocol and eluted in 60µl of water. Amount of labeled cDNA  as well as the frequency of incorporation (FOI) were determined spectrophotometrically (Epoch, Biotek).

value: Liver

value: Garonne river (France)

tag: reference composition

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: P00115 Ischemic Left Ventricle

description:
P00115
PolyA mRNA

value: male


title: MN1del1, rep2

description: Gene expression data from BM cells transduced with MN1 del 1.

source_name: bone marrow cells transduced with MN1del1, 4 weeks after Tx

value: bone marrow cells

value: 4 weeks


title: MN1del1, rep1


title: Ventricles- Human fetal heart rep1

value: ventricles


title: Day31- GFP+ rep3


title: Garonne - A360, liver

description: SAMPLE 82

source_name: reference pool


title: Garonne - A362, liver

description: SAMPLE 83


title: Day31- GFP- rep3

value: Control


title: P00090 Idiopathic Dilated CMP Left Ventricle

description:
P00090
PolyA mRNA

value: yes

value: idiopathic dilated CMP


title: P00093 Idiopathic Dilated CMP Left Ventricle

description:
P00093
PolyA mRNA


title: Garonne - A359, liver

description: SAMPLE 81


title: Day31- GFP+ rep4


title: MN1, rep2

description: Gene expression data from BM cells transduced with MN1.

source_name: bone marrow cells transduced with MN1, 4 weeks after Tx


title: P00092 Ischemic Left Ventricle

description:
P00092
PolyA mRNA

source_name: heart left ventricle, ischemic


title: Day31- GFP+ rep2


title: Garonne - A353, liver

description: SAMPLE 80


title: P00086 Ischemic Left Ventricle

description:
P00086
PolyA mRNA


title: P00082 Idiopathic Dilated CMP Left Ventricle

description:
P00082
PolyA mRNA


title: MN1, rep1


title: P00080 Ischemic Left Ventricle

description:
P00080
PolyA mRNA


title: Gironde - A312, liver

description: SAMPLE 78

source_name: Fish from Gironde natural site (France)

value: Gironde estuary (France)


title: Gironde - A314, liver

description: SAMPLE 79


title: Day31- GFP- rep2

value: Human embryonic stem cells


title: Gironde - A311, liver

description: SAMPLE 77


title: P00073 Ischemic Left Ventricle

description:
P00073
PolyA mRNA


title: Gironde - A304, liver

description: SAMPLE 76


title: P00069 Ischemic Left Ventricle

description:
P00069
PolyA mRNA


title: Day4 cells with DMSO,Rspo, Noggin, biological rep2

city: ILLKIRCH

first: philippe

last: moncuquet

address: 1 rue laurent fries

institute: IGBMC

description: Transcriptomic landscape of ES Cells

hyb_protocol: Following fragmentation, cRNAs were hybridized for 16 hours at 45oC on GeneChip® Chicken Genome arrays.  Each microarray was then washed and stained on a GeneChip® fluidics station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G. Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.1.

data_processing: MAS 5.0

source_name: ES cell lines E14 129P2/OlaHsd

label_protocol: Biotinylated cRNA targets were prepared from total RNA using a double amplification protocol according to the GeneChip® Expression Analysis Technical Manual: Two-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).

growth_protocol: Mouse embryonic stem cells (Msgn1RepV) were maintained on gelatin-coated dishes in DMEM supplemented with 15% fetal bovine serum (FBS; from PAA), penicillin, streptomycin, 2mM L-Glutamine, 0.1mM non essential amino acids, 0.2% β-mercaptoethanol, at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted from ES cell cultures using Trizol (Invitrogen) or with the Rnaeasy plus mini-kit (Qiagen).

treatment_protocol: Mouse embryonic stem cells (Msgn1RepV) were seeded on gelatin-coated plate, and differentiated in a DMEM based medium containing 15% fetal bovine serum,0.5% DMSO, recombinant R-spondin3 (10ng/mL) and recombinant Noggin (200ng/mL). Msgn1-Venus positive cells were sorted for RNA extraction after 3 and 4 days of differentiation.

tag: cell line

tag: time

tag: genetic background

tag: growth condition


title: SclKO_Flk+Scl-_rep1

value: SclKO mESC

value: ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells

value: EB formation, FACS sorting for Flk1+ mesodermal cells


title: Day4 cells with DMSO,Rspo, Noggin, biological rep3

description: Transcriptomic landscape of ES Cells

value: 0.5% DMSO, recombinant R-spondin3 (10ng/mL) and recombinant Noggin (200ng/mL)


title: Day31- GFP- rep1

tag: age


title: TET21_siCONTROL_NT_C

city: Seattle

first: Lisa

last: McFerrin

state: WA

address: 1100 Fairview Ave

institute: FHCRC

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data were normalized using quantile normalization with lumi R package from Bioconductor and log2 transformed. Ten of the probes were excluded from the analysis due to missing bead types.

source_name: Tet21N, Myc-on, siControl

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: DMEM, 10% FBS, pen/strep, Fungizone.

extract_protocol: RNA was purified using Qiagen RNeasy Plus columns.

treatment_protocol: Cells were cultured in standard condition, transfected with either siControl or siMondoA, and doxycycline was added (1 microgram/ml) or not for 3 days.

tag: sirna

value: non-specific


title: Day4 cells with DMSO,Rspo, Noggin, biological rep1

description: Transcriptomic landscape of ES Cells


title: P00059 Ischemic Left Ventricle

description:
P00059
PolyA mRNA

tag: tissue

value: heart left ventricle

tag: heart failure

value: ischemic


title: TET21_siCONTROL_DOXY_C

description: Replicate 3

source_name: Tet21N, Myc-off, siControl

value: doxycycline


title: Day3 cells with DMSO,Rspo, Noggin, biological rep2

description: Transcriptomic landscape of ES Cells


title: TET21_siMONDOA_DOXY_A

description: Replicate 1

source_name: Tet21N, Myc-off, siMONDOA

value: MondoA


title: Pre Somitic Mesoderm part7, biological rep3

description: Transcriptomic landscape of developping PSM from Tailbud to somite in E8.5 mouse embryo

source_name: Mouse embryos PSM at stage E8.5

treatment_protocol: CD-1 mouse embryos (9.0 days post-coitus [dpc]) were dissected in cold PBS prepared in RNAse-free conditions. Embryo is treated by Pancreatin (2mg/ml) at 1 min. The PSM and Neural tube were dissected using tungsten needles to remove the surrounding structures (e.g., the ectoderm, endoderm and lateral plate), then dissected PSM were divided into 7 pieces and Neural tube were divided into 6 pieces, finally stored in Trizol (Invitrogen) at -80C for RNA extraction.

value: Pre-Somitic Mesoderm

tag: developmental stage

tag: sample type


title: Day3 cells with DMSO,Rspo, Noggin, biological rep3

description: Transcriptomic landscape of ES Cells


title: Day3 cells with DMSO,Rspo, Noggin, biological rep1

description: Transcriptomic landscape of ES Cells


title: P00145 Ischemic Left Ventricle

description:
P00145
PolyA mRNA

tag: disease status

value: male


title: Gironde - A301, liver

description: SAMPLE 75

value: Liver

tag: collection site

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: P00062 Ischemic Left Ventricle

description:
P00062
PolyA mRNA

value: yes

value: female


title: Pre Somitic Mesoderm part7, biological rep1


title: Dordogne - A262, liver

description: SAMPLE 74

source_name: Fish from Dordogne natural site (France)

value: Dordogne river (France)


title: Pre Somitic Mesoderm part7, biological rep2


title: TET21_siCONTROL_DOXY_A

description: Replicate 1


title: TET21_siMONDOA_NT_C

description: Replicate 3

source_name: Tet21N, Myc-on, siMONDOA


title: Dordogne - A255, liver

description: SAMPLE 72


title: Dordogne - A258, liver

description: SAMPLE 73


title: P00043 Ischemic Left Ventricle

description:
P00043
PolyA mRNA


title: Dordogne - A253, liver

description: SAMPLE 71


title: P01055 Idiopathic Dilated CMP Left Ventricle

description:
P01055
PolyA mRNA

value: idiopathic dilated CMP


title: P01179 Idiopathic Dilated CMP Left Ventricle

description:
P01179
PolyA mRNA


title: TET21_siMONDOA_NT_B

description: Replicate 2


title: TET21_siCONTROL_NT_B

description: Replicate 2


title: P01019 Idiopathic Dilated CMP Left Ventricle

description:
P01019
PolyA mRNA


title: Dordogne - A252, liver

description: SAMPLE 70


title: TET21_siCONTROL_DOXY_B

description: Replicate 2


title: Pre Somitic Mesoderm part6, biological rep1


title: Pre Somitic Mesoderm part6, biological rep2


title: TET21_siMONDOA_NT_A

description: Replicate 1


title: Pre Somitic Mesoderm part6, biological rep3


title: TET21_siCONTROL_NT_A

description: Replicate 1


title: Stfrançois - A162, liver

description: SAMPLE 69

organism: Anguilla rostrata

source_name: Fish from St François natural site (Quebec)

value: St François lake (Quebec)


title: Stfrançois - A161, liver

description: SAMPLE 68


title: Stfrançois - A160, liver

description: SAMPLE 67


title: Pre Somitic Mesoderm part5, biological rep3


title: Pre Somitic Mesoderm part5, biological rep2


title: TET21_siMONDOA_DOXY_B

description: Replicate 2


title: Stfrançois - A157, liver

description: SAMPLE 66


title: P01108 Idiopathic Dilated CMP Left Ventricle

description:
P01108
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP


title: P01072 Idiopathic Dilated CMP Left Ventricle

description:
P01072
PolyA mRNA


title: Pre Somitic Mesoderm part5, biological rep1


title: TET21_siMONDOA_DOXY_C

description: Replicate 3


title: Stfrançois - A156, liver

description: SAMPLE 65


title: Pre Somitic Mesoderm part4, biological rep2


title: Stpierre - A110, liver

description: SAMPLE 63

source_name: Fish from St Pierre natural site (Quebec)

value: St Pierre lake (Quebec)


title: P01141 Idiopathic Dilated CMP Left Ventricle

description:
P01141
PolyA mRNA


title: P01118 Idiopathic Dilated CMP Left Ventricle

description:
P01118
PolyA mRNA


title: P01194 Idiopathic Dilated CMP Left Ventricle

description:
P01194
PolyA mRNA


title: PANC-1 antimir-10b 3

city: indianapolis

first: Haoxu

last: Ouyang

state: in

address: 980 w walnut street

department: Medicine

institute: IUPUI

hyb_protocol: biotin-labeled cRNA samples were hybridized to Illumina HumanHT-12 BeadChips (Version 4.00), using protocol provided by the manufacturer

scan_protocol: BeadChips were imaged using the Illumina BeadArray Reader

data_processing: Array data analysis was performed using BRB-Array Tools (Version 3.8.1) and the Database for Annotation, Visualization and Integrated Discovery (DAVID, version 6.7)

source_name: Human PDAC cell line

label_protocol: Illumina TotalPrep Kit

growth_protocol: PANC-1 cells were grown in DMEM, supplemented with 5% FBS, 100 units/ml penicillin, and 100 µg/ml streptomycin

extract_protocol: Trizol

treatment_protocol: PANC-1 cells were transfected with premir control, premir miR-10b, antimir control, or antimir-10b for 20hr


title: PANC-1 antimir-10b 2


title: Pre Somitic Mesoderm part3, biological rep3


title: P01075 Idiopathic Dilated CMP Left Ventricle

description:
P01075
PolyA mRNA


title: P01064 Ischemic Left Ventricle

description:
P01064
PolyA mRNA


title: Pre Somitic Mesoderm part4, biological rep1


title: Pre Somitic Mesoderm part3, biological rep2


title: Pre Somitic Mesoderm part4, biological rep3


title: PANC-1 antimir-10b 1


title: P01012 Idiopathic Dilated CMP Left Ventricle

description:
P01012
PolyA mRNA


title: Stpierre - A111, liver

description: SAMPLE 64


title: PANC-1 antimir control 2

value: antimir control


title: Pre Somitic Mesoderm part3, biological rep1


title: Stpierre - A108, liver

description: SAMPLE 62


title: PANC-1 antimir control 3


title: Stpierre - A107, liver

description: SAMPLE 61


title: Stpierre - A106, liver

description: SAMPLE 60


title: Sudouest - A63, liver

description: SAMPLE 59

source_name: Fish from Sud-Ouest natural site (Quebec)

value: Sud-ouest river (Quebec)


title: Sudouest - A62, liver

description: SAMPLE 58


title: Sudouest - A61, liver

description: SAMPLE 57


title: PANC-1 premir miR-10b 3

value: premir miR-10b


title: PANC-1 premir miR-10b 2


title: PANC-1 antimir control 1


title: Sudouest - A59, liver

description: SAMPLE 56


title: Pre Somitic Mesoderm part2, biological rep2


title: Pre Somitic Mesoderm part2, biological rep1


title: Pre Somitic Mesoderm part1, biological rep3


title: P01050 Idiopathic Dilated CMP Left Ventricle

description:
P01050
PolyA mRNA

value: heart left ventricle


title: C02440 Ischemic Left Ventricle

description:
C02440
PolyA mRNA

value: ischemic


title: P01081 Idiopathic Dilated CMP Left Ventricle

description:
P01081
PolyA mRNA


title: PANC-1 premir control 3

value: premir control


title: C02038 Idiopathic Dilated CMP Left Ventricle

description:
C02038
PolyA mRNA


title: Pre Somitic Mesoderm part1, biological rep2

value: Pre-Somitic Mesoderm


title: C02454 Idiopathic Dilated CMP Left Ventricle

description:
C02454
PolyA mRNA

value: male


title: P01121 Non-failing Left Ventricle

description:
P01121
PolyA mRNA

source_name: heart left ventricle, non-failing

value: no

value: non-failing


title: Pre Somitic Mesoderm part2, biological rep3


title: Pre Somitic Mesoderm part1, biological rep1


title: PANC-1 premir miR-10b 1


title: PANC-1 premir control 2


title: C02190 Idiopathic Dilated CMP Left Ventricle

description:
C02190
PolyA mRNA


title: Sudouest - A58, liver

description: SAMPLE 55

value: Liver

source_name: reference pool

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: Stjean - A15, liver

description: SAMPLE 54

source_name: Fish from St Jean natural site (Quebec)

value: St Jean river (Quebec)


title: P00322 Non-failing Left Ventricle

description:
P00322
PolyA mRNA


title: Stjean - A14, liver

description: SAMPLE 53


title: Stjean - A13, liver

description: SAMPLE 52


title: male KO, replicate 3 [exon]

city: Freiburg im Breisgau

first: Thomas

last: Manke

address: Stuebeweg 51

department: Bioinformatics and Deep-Sequencing Unit

institute: Max-Planck-Institute for Immunobiology and Epigenetics

hyb_protocol: according to manufacturer's instructions

data_processing: We performed exon- (probeset-) and gene-level analysis using the Affymetrix Power Tools (version=1.14.3.1). The rma-sketch algorithm was used to normalize the intensities in CEL files and detection p-values were generated for each probeset using the “detection above background” (DABG) method.

source_name: Male MEFs, CAGG-Cre-ER T/+, 4OHT treated

growth_protocol: DMEM supplemented with 10% FCS, pen/strep

extract_protocol: QIAGEN Rneasy

treatment_protocol: 200nM 4-Hydroxytamoxifen for 4 days. Ethanol represents vehicle control.

tag: genotype/variation

value: KO

value: 200nM 4-Hydroxytamoxifen for 4 days


title: PANC-1 premir control 1

tag: treatment


title: male KO, replicate 2 [exon]

scan_protocol: according to manufacturer's instructions

tag: gender


title: Stjean - A11, liver

description: SAMPLE 50


title: Stjean - A12, liver

description: SAMPLE 51


title: C01957 Idiopathic Dilated CMP Left Ventricle

description:
C01957
PolyA mRNA

value: yes

value: idiopathic dilated CMP


title: C02037 Ischemic Left Ventricle

description:
C02037
PolyA mRNA

source_name: heart left ventricle, ischemic


title: P00307 Idiopathic Dilated CMP Left Ventricle

description:
P00307
PolyA mRNA


title: male WT, replicate 3 [exon]

source_name: Male MEFs, CAGG-Cre-ER T/+

label_protocol: according to manufacturer's instructions

value: WT

value: vehicle control


title: male KO, replicate 1 [exon]


title: C02193 Ischemic Left Ventricle

description:
C02193
PolyA mRNA

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

value: heart left ventricle


title: male WT, replicate 2 [exon]


title: P00003 Idiopathic Dilated CMP Left Ventricle

description:
P00003
PolyA mRNA


title: Brain_FK5_FK-506

city: San Francisco

first: Derek

last: Pappas

state: CA

address: 675 Nelson Rising Lane, RM 240

department: Neurology

institute: University of California, San Francisco

description:
4060001052_C
FK5
Non-control single sample.

data_processing: The data were background subtracted and normalized (cubic spline) using the Illumina BeadStudio Gene Expression module v3.1.

source_name: Cortical neurons, FK-506, NMDA

label_protocol: Standard Illumina labeling protocol.

growth_protocol: Dissociated cortical neurons were cultured on poly-ornithine/poly-lysine coated plates in neurobasal A medium supplemented with B-27 and penicillin/streptomycin. Neurons were cultured for seven days before experimental conditions were introduced.

extract_protocol: RNA was extracted with clean-up using the QIAGEN RNeasy mini kit in accordance with the manufacturer's protocol.

treatment_protocol: Media was replaced with fresh media containing neuroprotective molecules or controls and incubated for one hour. Neurons were then exposed to NDMA in excitotoxic media (hypotonic salt solution) for one hour. Media was replaced with fresh media containing molecule or controls, respectively, and incubated for a further 16hr.

tag: cell type

value: cortical neurons from whole brain

tag: neuroprotective molecule

tag: solvent

value: DMSO

tag: mechanism

value: immunomodulator

tag: ratio protection

tag: class

value: not used


title: Brain_CAR_Carbenoxolone

description:
4060001052_B
CAR
Non-control single sample.

source_name: Cortical neurons, Carbenoxolone, NMDA

value: Carbenoxolone

value: water

value: multi-target

value: protective


title: female KO, replicate 3 [exon]

source_name: Female MEFs, CAGG-Cre-ER T/+, 4OHT treated

value: female


title: Brain_CON:ND3_Vehicle

description:
4060001052_A
CON_ND3
Vehicle control replicate 3 of 5.

source_name: Cortical neurons, vehicle, NMDA

value: vehicle

value: control

value: non-protective


title: Temperature - Aa80, liver

description: SAMPLE 49

source_name: Fish from laboratory low temperature experiment

value: Liver

value: Low temperature [13°C]

tag: reference composition

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: Brain_MIF_Mifepristone

description:
4060001052_D
MIF
Non-control single sample.

source_name: Cortical neurons, Mifepristone, NMDA

value: Mifepristone

value: ethanol

value: receptor agonist


title: male WT, replicate 1 [exon]

value: male

value: WT

value: vehicle control


title: Brain_ZVFrep1_Z-VAD-FMK

description:
4060001046_F
ZVFrep1
Non-control single sample.

source_name: Cortical neurons, Z-VAD-FMK, NMDA

value: cortical neurons from whole brain

value: Z-VAD-FMK

value: DMSO

value: enzyme inhibitor

value: not used


title: Brain_ZVFrep2_Z-VAD-FMK

description:
4060001052_F
ZVFrep2
Non-control single sample.


title: Brain_NIM_Nimodipine

description:
4060001052_E
NIM
Non-control single sample.

source_name: Cortical neurons, Nimodipine, NMDA

value: Nimodipine

value: ion channel blocker


title: P00497 Non-failing Left Ventricle

description:
P00497
PolyA mRNA

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Microarray Processing batch were controlled for using the R package Combat. Differential gene expression was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates.

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

value: heart left ventricle

value: no

value: non-failing

value: female

tag: age


title: Temperature - Aa79, liver

description: SAMPLE 48

tag: tissue

value: Liver

value: Low temperature [13°C]

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: Temperature - Aa76, liver

description: SAMPLE 45


title: Temperature - Aa78, liver

description: SAMPLE 47


title: Temperature - Aa77, liver

description: SAMPLE 46


title: P00477 Non-failing Left Ventricle

description:
P00477
PolyA mRNA

tag: heart failure


title: OCP - Aa75, liver

description: SAMPLE 44

source_name: Fish from laboratory mix of organochlorinated pesticides experiment

value: OCP [13 ng.g-1 dw]_trophic_route


title: Brain_NEC_Necrostatin-1

description:
4060001046_E
NEC
Non-control single sample.

source_name: Cortical neurons, Necrostatin-1, NMDA

value: ethanol

value: anti-apoptotic

value: protective


title: P00325 Non-failing Left Ventricle

description:
P00325
PolyA mRNA

value: male


title: P00381 Non-failing Left Ventricle

description:
P00381
PolyA mRNA


title: Brain_MEM_Memantine

description:
4060001046_D
MEM
Non-control single sample.

source_name: Cortical neurons, Memantine, NMDA

value: cortical neurons from whole brain

value: Memantine

value: water

value: NMDAR antagonist


title: P00490 Non-failing Left Ventricle

description:
P00490
PolyA mRNA

source_name: heart left ventricle, non-failing

value: heart left ventricle


title: female WT, replicate 1 [exon]

source_name: Female MEFs, CAGG-Cre-ER T/+

value: WT

value: vehicle control


title: female KO, replicate 1 [exon]

value: female

value: KO

value: 200nM 4-Hydroxytamoxifen for 4 days


title: P00226 Idiopathic Dilated CMP Left Ventricle

description:
P00226
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP

value: yes

value: idiopathic dilated CMP


title: Brain_BEN_Benzamide

description:
4060001046_B
BEN
Non-control single sample.

source_name: Cortical neurons, Benzamide, NMDA

value: Benzamide

value: DMSO

value: enzyme inhibitor


title: female KO, replicate 2 [exon]


title: P00365 Non-failing Left Ventricle

description:
P00365
PolyA mRNA

value: no

value: non-failing


title: OCP - Aa74, liver

description: SAMPLE 43

value: Liver

value: OCP [13 ng.g-1 dw]_trophic_route

source_name: reference pool

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: Brain_SIM_Simvastatin

description:
4060001036_F
SIM
Non-control single sample.

source_name: Cortical neurons, Simvastatin, NMDA

value: cortical neurons from whole brain

value: Simvastatin

value: ethanol

value: not used


title: female WT, replicate 2 [exon]

value: female

value: WT

value: vehicle control


title: OCP - Aa73, liver

description: SAMPLE 42


title: Brain_ETF_Ethyl Ferulate

description:
4060001046_C
ETF
Non-control single sample.

source_name: Cortical neurons, Ethyl Ferulate, NMDA

value: Ethyl Ferulate

value: non-protective


title: P00331 Non-failing Left Ventricle

description:
P00331
PolyA mRNA

value: heart left ventricle


title: OCP - Aa72, liver

description: SAMPLE 41


title: C02174 Ischemic Left Ventricle

description:
C02174
PolyA mRNA

source_name: heart left ventricle, ischemic

value: yes

value: ischemic

value: male


title: Brain_LIO_Liothyronine

description:
4060001036_D
LIO
Non-control single sample.

source_name: Cortical neurons, Liothyronine, NMDA

value: Liothyronine

value: water

value: hormone

value: protective


title: Brain_CON:ND2_Vehicle

description:
4060001046_A
CON_ND2
Vehicle control replicate 2 of 5.

source_name: Cortical neurons, vehicle, NMDA

value: cortical neurons from whole brain

value: vehicle

value: DMSO

value: control


title: C02172 Idiopathic Dilated CMP Left Ventricle

description:
C02172
PolyA mRNA

value: idiopathic dilated CMP


title: Brain_ERP_Erythropoietin

description:
4060001036_C
ERP
Non-control single sample.

source_name: Cortical neurons, Erythropoietin, NMDA

value: Erythropoietin

value: not used


title: Mercury - Aa68, liver

description: SAMPLE 39

source_name: Fish from laboratory methylmercury experiment

value: Liver

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: C02157 Ischemic Left Ventricle

description:
C02157
PolyA mRNA

value: heart left ventricle

value: yes


title: Brain_BAC_Baclofen

description:
4060001036_B
BAC
Non-control single sample.

source_name: Cortical neurons, Baclofen, NMDA

value: Baclofen

value: receptor agonist

value: non-protective


title: Mercury - Aa66, liver

description: SAMPLE 37


title: Cd_4 - Aa50, liver

description: SAMPLE 34

source_name: Fish from laboratory cadmium experiment

value: Cd [4µg/L]_water_route


title: Mercury - Aa63, liver

description: SAMPLE 35


title: Cd_4 - Aa49, liver

description: SAMPLE 33


title: female WT, replicate 3 [exon]

value: female

value: WT

value: vehicle control


title: C02170 Ischemic Left Ventricle

description:
C02170
PolyA mRNA

value: ischemic

value: male


title: OCP - Aa71, liver

description: SAMPLE 40

source_name: Fish from laboratory mix of organochlorinated pesticides experiment

value: OCP [13 ng.g-1 dw]_trophic_route


title: Mercury - Aa67, liver

description: SAMPLE 38


title: Mercury - Aa65, liver

description: SAMPLE 36


title: C02158 Idiopathic Dilated CMP Left Ventricle

description:
C02158
PolyA mRNA

value: idiopathic dilated CMP


title: Brain_CON:ND1_Vehicle

description:
4060001036_A
CON_ND1
Vehicle control replicate 1 of 5.

value: cortical neurons from whole brain

value: vehicle

value: DMSO

value: control


title: Brain_ROL_Rolipram

description:
4060001032_F
ROL
Non-control single sample.

source_name: Cortical neurons, Rolipram, NMDA

value: Rolipram

value: enzyme inhibitor

value: protective


title: Brain_INB_Interferon-b1a

description:
4060001032_D
INB
Non-control single sample.

source_name: Cortical neurons, Interferon-b1a, NMDA

value: water

value: immunomodulator

value: not used


title: C02152 Ischemic Left Ventricle

description:
C02152
PolyA mRNA

value: heart left ventricle

value: yes


title: Brain_DEP_Deprenyl

description:
4060001032_C
DEP
Non-control single sample.

source_name: Cortical neurons, Deprenyl, NMDA

value: Deprenyl

value: anti-apoptotic


title: C02168 Ischemic Left Ventricle

description:
C02168
PolyA mRNA

value: ischemic

value: male


title: Brain_MTX_Methotrexate

description:
4060001036_E
MTX
Non-control single sample.

source_name: Cortical neurons, Methotrexate, NMDA

value: Methotrexate


title: Brain_MOX_Moxalactam

description:
4060001032_E
MOX
Non-control single sample.

source_name: Cortical neurons, Moxalactam, NMDA

value: cortical neurons from whole brain

value: Moxalactam

value: antibiotic


title: Brain_AZA_Azathioprine

description:
4060001032_B
AZA
Non-control single sample.

source_name: Cortical neurons, Azathioprine, NMDA

value: Azathioprine


title: C02156 Ischemic Left Ventricle

description:
C02156
PolyA mRNA


title: Brain_CON:NT4_None

description:
4060001032_A
CON_NT4
Mock control replicate 4 of 5.

source_name: Cortical neurons, none, NMDA

value: control

value: non-protective


title: Cd_4 - Aa48, liver

description: SAMPLE 32

value: Liver

value: Cd [4µg/L]_water_route

source_name: reference pool

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: C02154 Ischemic Left Ventricle

description:
C02154
PolyA mRNA

value: heart left ventricle


title: Cd_4 - Aa45, liver

description: SAMPLE 30


title: Cd_4 - Aa47, liver

description: SAMPLE 31


title: Cd_0.4 - Aa42, liver

description: SAMPLE 27

value: Cd [0.4µg/L]_water_route


title: Cd_0.4 - Aa41, liver

description: SAMPLE 26


title: C02150 Ischemic Left Ventricle

description:
C02150
PolyA mRNA

value: yes


title: Brain_RIL_Riluzole

description:
4060001024_F
RIL
Non-control single sample.

source_name: Cortical neurons, Riluzole, NMDA

value: Riluzole

value: DMSO

value: NMDAR antagonist

value: protective


title: Cd_0.4 - Aa44, liver

description: SAMPLE 29


title: Cd_0.4 - Aa43, liver

description: SAMPLE 28


title: Brain_MK8_MK-801

description:
4060001024_E
MK8
Non-control single sample.

source_name: Cortical neurons, MK-801, NMDA

value: cortical neurons from whole brain


title: C02101 Idiopathic Dilated CMP Left Ventricle

description:
C02101
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP

value: idiopathic dilated CMP

value: female


title: C02104 Idiopathic Dilated CMP Left Ventricle

description:
C02104
PolyA mRNA


title: Brain_CON:NT3_None

description:
4060001024_A
CON_NT3
Mock control replicate 3 of 5.

value: water


title: Cd_0.4 - Aa37, liver

description: SAMPLE 25


title: C02100 Idiopathic Dilated CMP Left Ventricle

description:
C02100
PolyA mRNA

value: male


title: PCB_300 - Aa35, liver

description: SAMPLE 24

source_name: Fish from laboratory PCBs experiment

value: PCB [300ng/g dw]_trophic_route


title: Brain_MPBrep2_MitoPBN2

description:
4060001023_E
MPBrep2
Non-control single sample.

source_name: Cortical neurons, MitoPBN2, NMDA

value: free radical scavenger

value: not used


title: C02107 Ischemic Left Ventricle

description:
C02107
PolyA mRNA

source_name: heart left ventricle, ischemic

value: ischemic


title: C02099 Idiopathic Dilated CMP Left Ventricle

description:
C02099
PolyA mRNA


title: PCB_300 - Aa34, liver

description: SAMPLE 23

value: Liver

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: C02064 Ischemic Left Ventricle

description:
C02064
PolyA mRNA

value: heart left ventricle

value: yes


title: PCB_300 - Aa33, liver

description: SAMPLE 22


title: Brain_INA_Interferon-a2b

description:
4060001024_D
INA
Non-control single sample.

source_name: Cortical neurons, Interferon-a2b, NMDA

value: immunomodulator


title: Brain_AGM_Agmatine

description:
4060001024_B
AGM
Non-control single sample.

source_name: Cortical neurons, Agmatine, NMDA

value: Agmatine

value: receptor agonist

value: non-protective


title: C00149 Non-failing Left Ventricle

description:
C00149
PolyA mRNA

source_name: heart left ventricle, non-failing

value: no

value: non-failing


title: Brain_IFD_Ifenprodil

description:
4060001023_D
IFD
Non-control single sample.

source_name: Cortical neurons, Ifenprodil, NMDA

value: cortical neurons from whole brain

value: Ifenprodil

value: water

value: NMDAR antagonist

value: protective


title: Brain_RES_Resveratrol

description:
4060001023_F
RES
Non-control single sample.

source_name: Cortical neurons, Resveratrol, NMDA

value: Resveratrol

value: DMSO

value: enzyme inhibitor


title: Brain_DCY_Decyclubiquinone

description:
4060001024_C
DCY
Non-control single sample.

source_name: Cortical neurons, Decyclubiquinone, NMDA

value: Decyclubiquinone

value: anti-apoptotic

value: not used


title: C00100 Non-failing Left Ventricle

description:
C00100
PolyA mRNA

value: heart left ventricle

value: male


title: C00140 Non-failing Left Ventricle

description:
C00140
PolyA mRNA


title: PCB_300 - Aa32, liver

description: SAMPLE 21

value: Liver

value: PCB [300ng/g dw]_trophic_route

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: C00136 Non-failing Left Ventricle

description:
C00136
PolyA mRNA

value: no

value: non-failing


title: PCB_50 - Aa29, liver

description: SAMPLE 20

value: PCB [50ng/g dw]_trophic_route


title: L_ANEU_4.6N

city: Scottsdale

first: Mitesh

last: Borad

state: AZ

address: 13400 E Shea Blvd

institute: Mayo Clinic in Arizona

hyb_protocol: Labeled DNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol

scan_protocol: The arrays were scanned using an Agilent Technologies G2656C Scanner and default setting according to manufacturer's recommendation.

data_processing: Data was extracted from the TIFF files using default settings in Agilent FE 7.5.  The data quality was assessed using the QC reports in FE 7.5.

source_name: liposarcoma

label_protocol: DNA was digested with DNaseI then labeled with Cy-5 dUTP and Cy-3 dUTP respectively, using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to manufacturer's protocol.

growth_protocol: Tumor sample from a liposarcoma was flash frozen and stored at -80 C until processed for flow sorting

extract_protocol: Tumor was chipped from flash frozen samples. Nuclei were extracted then resuspended in the presence of 10mg/ml DAPI in NST buffer prior to sorting with an Influx flow cytometer equipped with a UV laser. The DNA from each flow sorted sample was extracted with QIAGEN QIAamp DNA Micro Kit according to the manufacturer's protocol.

tag: disease state

value: Well differentiated liposarcoma

source_name: Reference pooled 46XX

value: Normal female genome