title: thoraric aorta, SCD, biological repl. 3


title: abdominal aorta, HPD, biological repl. 3

status: Public on May 26 2014

type: RNA

city: Graz

first: Birgit

last: Gallé

address: Stiftingtalstr. 24

country: Austria

institute: ZMF

description: Gene expression data from abdominal aortic tissue from mice fed a high phosphate diet

hyb_protocol: Affymetrix Mouse Gene 2.0 ST arrays; Affymetrix GeneChip HT Hybridization, Wash and Staining Kit; Affymetrix Fluidics station 450: protocol FS_450_0007 for Cartridge Arrays

scan_protocol: Affymetrix scanner: GCS3000

data_processing:
Affymetrix Geneexpression Console (1.3.1) using Affymetrix default analysis settings for generating CEL.files
Data pre-processing and filtering (Partek Genomic Suite Software v 6.6): RMA (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summerization), ANOVA

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: abdominal aorta, HPD

label_protocol: NuGen Applause WT Amp Plus ST System and NuGen Biocore Biotin Module

growth_protocol: DBA/2NCrl mice were 8 weeks old at the start of the experiment.

extract_protocol: For RNA isolation the aorts were disrupted and homogenized in RLT-buffer (Qiagen)using MagNA lyzer green beads and MagNa lyzer tissue disrupter. Total RNA was isolated using Rneasy Mini Kit (Qiagen) according to the manufacturer´s protocol.

treatment_protocol: DBA/2NCrl mice were fed either a high-phosphate diet (HPD) containing 20.2 g phosphorus per kg or a standard chow diet (SCD) containing 7.0 g phosphorus per kg.for 5 days, respectively.

tag: tissue

value: abdominal aorta

tag: strain


title: thoraric aorta, SCD, biological repl. 1

description: Gene expression data from thoracic aortic tissue from mice fed a standard chow diet

source_name: thoraric aorta, SCD

value: thoracic aorta


title: abdominal aorta, HPD, biological repl. 4


title: thoaric aorta, HPD, biological repl. 1

description: Gene expression data from thoracic aortic tissue from mice fed a high phosphate diet

source_name: thoaric aorta, HPD


title: thoraric aorta, SCD, biological repl. 2


title: thoaric aorta, HPD, biological repl. 3


title: abdominal aorta, SCD, bioloogical repl. 3

description: Gene expression data from abdominal aortic tissue from mice fed a standard chow diet

source_name: abdominal aorta, SCD


title: abdominal aorta, SCD, bioloogical repl. 2


title: abdominal aorta, SCD, bioloogical repl. 1


title: Rheumatoid arthritis_patient24

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

country: Spain

institute: Vall d'Hebron Hospital Research Institute

description: CD4+ T cell RNA from rheumatoid arthritis patient

hyb_protocol: Biotin labeled cRNA (1.5ug) was hybridized to Sentrix(r) whole genome bead chips 6 x 2 (Illumina, San Diego, CA, USA)

scan_protocol: Scanning was performed on the Illumina(r) BeadStation 500x.

data_processing: Log2 transformation of BeadStudio raw data, gene filtering of BeadChip version1 RefSeq valid probes, quantile normalization using the preprocessCore R package.

label: Biotin

organism: Homo sapiens

source_name: Rheumatoid arthritis patient, at 8:30-9:30 morning

label_protocol: Biotin labeled cRNA preparation for the Illumina platform was performed using the Ambion(r) Illumina RNA amplification kit (Ambion Europe, Huntington, Cambridgeshire, UK).

extract_protocol: CD4+ T lymphocytes were isolated from whole blood using the RossetteSep negative selection kit (Stem Cell Technologies, Canada), were immediately preserved in RNA stabilization reagent RNAlater (Qiagen, Hilden, Germany) and frozen at -80ºC. RNA extraction from CD4+ T cells was performed with the RNeasy extraction kit (Qiagen, Hilden, Germany).

tag: gender

value: female

value: CD4+ T cell


title: Huh7 Sph LDZ G3 replicate 1

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

country: USA

institute: Psomagen Inc

description:
replicate 1
Sample 22

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed by using Gene Expression Module v 1.9.0 in Genome Studio V2011.1 from illumina, Inc. The background noise was substrated and quantile normalization was applied.

source_name: Sphare Low Density ZEB treated 3rd Generation

label_protocol: Biotinylated cRNA were prepared with the Ambion Totalprep RNA Amplification kit for Illumina arrays

growth_protocol: All experiments were conducted according to the National Institutes of Health (NIH) guidelines for animal care and following a study protocol approved by the National Cancer Institute (NCI) Animal Care and Use Committee. Mice had free access to food and water.

extract_protocol: Total RNA was extracted with Quiagen Rneasy Kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

treatment_protocol: Liver samples from male animals were collected at various time-points ranging from 0 weeks to 3 weeks. Tissue samples were divided into two parts; one was fixed in 10% formalin for histological evaluation and the other was used for RNA analysis.

tag: cell line

value: Huh7 Liver Cancer Cell Line

tag: treatment

value: Zebularine (ZEB)


title: Huh7 Mono HDZ G1 replicate 2

description:
replicate 2
Sample 20

source_name: Monolayer High Density ZEB treated 1st Generation


title: Rheumatoid arthritis_patient23


title: Yap, rep3

city: Boston

first: Fei

last: Gu

state: MA

address: 320 Longwood Ave.

department: Cardiology

institute: Childrens hospital boston, Harvard Medical School

hyb_protocol: Following fragmentation, the samples were hybridized on Mouse Gene 2.0 ST arrays at 45C with rotation set at 60 RPM for 16 hours using the GeneChip Hybridization Oven 640. The fluidics stations used for washing and staining are the Genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The software we use is Affy's Expression Console, version 1.3.1.187. We use the software default setting for the RMA analysis. It's RMA background corrected and sketch-quantile normalized.

source_name: Heart Apex, 5 Days after MI and AAV9:YAP injection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were kept in a standard mouse room. All animal procedures were approved by the Institutional Animal Care and Use Committee.

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

treatment_protocol: CFW Mice aged 10–12 weeks were subjected to myocardium infarction surgery. Briefly, mice were anesthetized (isoflorin), intubated, and ventilated. Left thoracotomy was performed and left anterior descending artery (LAD) permanently ligated with 7-0 silk. Immediately after LAD ligation, AAV9:Luci and AAV9:hYAP were injected into the myocardium seperately. 5 Days after MI and AAV9 injection, heart apexes were collected and placed on ice in the Trizol solution (Invitrogen).

value: Heart Apex

value: CFW


title: Rheumatoid arthritis_patient25


title: Rheumatoid arthritis_patient26


title: abdominal aorta, HPD, biological repl. 1


title: Huh7 Mono HDZ G1 replicate 3

description:
replicate 3
Sample 21


title: Rheumatoid arthritis_patient22


title: Rheumatoid arthritis_patient18

value: male


title: Rheumatoid arthritis_patient21


title: Rheumatoid arthritis_patient20


title: Rheumatoid arthritis_patient17


title: Huh7 Mono HDU G1 replicate 2

description:
replicate 2
Sample 17

source_name: Monolayer High Density ZEB untreated 1st Generation


title: abdominal aorta, HPD, biological repl. 2


title: Rheumatoid arthritis_patient16


title: Rheumatoid arthritis_patient13


title: Huh7 Mono HDZ G1 replicate 1

description:
replicate 1
Sample 19


title: Huh7 Mono HDU G1 replicate 1

description:
replicate 1
Sample 16


title: Rheumatoid arthritis_patient11


title: Sham, rep3

source_name: Heart apex, no MI and AAV9 injection


title: Rheumatoid arthritis_patient15


title: Rheumatoid arthritis_patient19


title: Sham, rep2


title: Rheumatoid arthritis_patient12


title: Yap, rep2


title: Yap, rep1


title: Rheumatoid arthritis_patient14


title: Huh7 Mono HDU G1 replicate 3

description:
replicate 3
Sample 18


title: Rheumatoid arthritis_patient9


title: Huh7 Mono LDZ G1 replicate 3

description:
replicate 3
Sample 15

source_name: Monolayer Low Density ZEB treated 1st Generation


title: Rheumatoid arthritis_patient10


title: Rheumatoid arthritis_patient8


title: Sham, rep1


title: Rheumatoid arthritis_patient7


title: Huh7 Mono LDZ G1 replicate 2

description:
replicate 2
Sample 14


title: L, rep2

source_name: Heart Apex, 5 Days after MI and AAV9:Luci injection


title: Huh7 Mono LDZ G1 replicate 1

description:
replicate 1
Sample 13


title: Rheumatoid arthritis_patient4


title: Rheumatoid arthritis_patient3


title: Rheumatoid arthritis_patient6


title: E. coli 5.5% NaCl

type: mixed

city: Norwich

first: Aline

last: Metris

state: Norfolk

address: Norwich research Park

department: GHFS

country: United Kingdom

institute: Institute of Food Research

hyb_protocol: A 0.5 µg aliquot of Cy3-labelled Escherichia coli K12, MG1655 DNA was added to the Cy5-labelled cDNA in a hybridisation buffer containing Agilent Hi-RPM Hybridisation buffer plus blocking agent (both Agilent Technologies) , the mix was boiled, 5 minutes, and kept at 37°C before adding to the microarray and hybridisation on a microarray slide overnight at 64°C.

scan_protocol: Microarrays were scanned using an Axon 4000B laser scanner (Axon Instruments, CA, USA). The data from detected features were initially processed using the GenePix Pro v.6.0 software supplied with the scanner.

data_processing:
The data were normalised manually in Excel. For each spot, the median of the spot intensity minus the background were considered. Because we wanted to compare different environmental conditions, the cDNA signal in each condition was normalised to that of gDNA with M=ln(cDNA/gDNA). To ensure that the fluorescence measurements were independent of the overall signal intensity of the spot, the values of M were made independent of A=(lncDNA+lngDNA)/2 with a linear shift. Spots where the A values were less than 5.5 were not considered. Finally the experiments were aligned so that the median of M=0 and their deviation was normalised.
The analysis of the data is based on cross validation with datasets generated by Monte-Carlo simulation. The null hypothesis was that the gene expression changes monotonously as a function of NaCl concentration. The existence of a deviation from monotony was tested by F-tests for each gene probe. By comparing the number of probes with the lowest p(F) values for each NaCl concentrations with analogous results generated from Monte-Carlo sampling of the null hypothesis, we show that it is very unlikely that a switch between 4.5 and 5% NaCl could have happened by chance (in fact p<<0.01).

organism: Escherichia coli K-12

source_name: E. coli, stressed by NaCl, in presence of glycine betaine

label_protocol: Aliquots (2 µg) of total RNA were labelled with Cy5-dUTP (GE Healthcare, UK) after reverse transcription to cDNA. Genomic DNA (gDNA) was labelled with fluorescent nucleotides with Cy3-dUTP.

growth_protocol: E. coli was grown to exponential phase in glucose minimal medium in the presence of the osmoprotectant glycine beatine with a range of salt concentrations at 2, 3.5 (2 repeats), 4.5, 5 and 5.5% NaCl.  E. coli were inoculated at 104 cfu/ml and cultures incubated to reach 107 cfu/ml, an ODs of about 0.03 (cultures entered stationary phase at 108 cfu/ml)  before harvesting.

extract_protocol: Genomic DNA was purified from exponentially growing cells by lysis in lysozyme/mutanolysin, incubation in proteinase K/SDS, followed by a standard phenol/chloroform extraction procedure. Final pellets were dissolved in TE (10 mM Tris-HCl at pH 8.0, 1 mM EDTA). Genomic DNA was digested to completion with Sau3A1 (Promega) and purified by phenol/chloroform extraction. Synthesis and degradation of RNA were stopped by adding 1/4 volume of stop-solution (95% ethanol/5% phenol). Cells were harvested by centrifugation (4,000 rpm, 20 min) at 4°C and resuspended in 0.5 mL of  lysis buffer (0.5 mg/mL lysozyme, 10% SDS, Tris-EDTA buffer,  3 M sodium acetate, pH 5.2). Phenol (0.5 ml, pH 4.5) was added, and the samples were vortexed vigorously before incubation at 64 °C for 6 min. After placing the samples on ice, the aqueous layer was extracted with 1:1 phenol:chloroform and with chloroform, and the RNA was precipitated with ethanol at -80°C. After resuspension, RNA concentration and purity was assessed by NanoDrop ND-1000 UV spectrophotometer (Nanodrop Technologies, Wilmingon, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively.

tag: growth phase

value: Exponential

molecule: genomic DNA

value: exponential


title: Huh7 Mono LDU G1 replicate 3

description:
replicate 3
Sample 12

source_name: Monolayer Low Density ZEB untreated 1st Generation


title: E. coli 4.5% NaCl


title: Rheumatoid arthritis_patient5


title: L, rep3


title: Huh7 Mono LDU G1 replicate 2

description:
replicate 2
Sample 11


title: E. coli 5% NaCl


title: Rheumatoid arthritis_patient1


title: L, rep1


title: Rheumatoid arthritis_patient2


title: E. coli 3.5% NaCl, replicate 2


title: Huh7 Mono LDU G1 replicate 1

description:
replicate 1
Sample 10


title: aged satellite cells, replicate 3

city: Ottawa

first: Hang

last: Yin

state: Ontario

address: 501 Smyth Road, CCW 5113

department: Sprott Centre for Stem Cell Research

country: Canada

institute: Ottawa Hospital Research Institute

description: Gene expression data for aged satellite cells

hyb_protocol: Labeled DNA was hybridized for 17 hr at 45'C on GeneChip® Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned by GeneChip® Scanner 3000 High-Resolution Scanning.

data_processing: Cell intensity files were loaded into Affymetrix Expression Console (ver 1.2.1.20) and analyzed with default RMA-Sketch method at gene level.

source_name: sorted ZsGreen+ satellite cells

label_protocol: 100 ng total RNA was processed by WT Expression Kit (Ambion) and 5.5 ug single strand DNA was fragmentated and terminal labeled by WT Terminal Labeling Kit (Affymetrix).

growth_protocol: All mice were housed under standard conditions and allowed free access to food and water ad libitum.

extract_protocol: Total RNA was extracted from each replicate using the Picopure RNA isolation kit (Applied Biosystems) and concentrated using the RNA Clean and Concentrator-5 kit (Zymo Research) according to the manucfacturer’s instructions.

treatment_protocol: Skeletal muscles from heterozygous Pax7-ZsGreen mice were aseptically dissected. Muscles were minced and digested in a dispase/collagenase solution (1 mg/ml collagenase, 4 mg/ml Dispase II, Roche) for 25 minutes at 37°C. The digested muscle slurry was briefly triturated after 15 min of incubation and returned to the incubator. The slurry was subsequently diluted with PBS containing 10% fetal bovine serum and 2 mM EDTA (FACS sorting medium), filtered through 70 um Netwell cell strainers (Costar), and pelleted at 1700 rpm for 5 min (Thermo IEC Centra CL2). Cell pellets were gently resuspended in FACS buffer filtered through 30 uM filters (Miltenyi Biotech) prior to FACS sorting. Cells were separated on a MoFlo cytometer (DakoCytomation) equipped with 3 lasers. Sorting gates were strictly defined based on age of sample or in the case of a negative control for Pax7zsgreen, wild type SV129 mice.

value: sorted ZsGreen+ satellite cells from hindlimb muscles

tag: age

value: postnatal >1 year old


title: E. coli 3.5% NaCl, replicate 1


title: aged satellite cells, replicate 1


title: Huh7 Sph HDZ G1 replicate 2

description:
replicate 2
Sample 8

source_name: Sphare High Density ZEB treated 1st Generation


title: aged satellite cells, replicate 2


title: ALK5CA mouse3, rep.1

status: Public on May 25 2014

city: Stanford

first: Yingbo

last: He

address: Stanford University

institute: Stanford University

description: replicate 1

data_processing:
The data were processed with Illumina's BeadStudio and Significance Analysis of Microarrays  (SAM) 3.0
Normalized values are simple median centering of the arrays (processsed by SAM)

source_name: Hippocampus

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Nanodrop Bioanalyser.

tag: background strain

value: FVB/N

value: 3 months

value: Hippocampus


title: ALK5CA mouse2, rep.1

description: replicate 1


title: ALK5CA mouse1, rep.1

description: replicate 1


title: ALK5Ctrl mouse2, rep.1

description: replicate 1


title: ALK5Ctrl mouse1, rep.1

description: replicate 1


title: ALK5Ctrl mouse3, rep.1

description: replicate 1


title: Huh7 Sph HDZ G1 replicate 1

description:
replicate 1
Sample 7


title: Huh7 Sph HDU G1 replicate 1

description:
replicate 1
Sample 4

source_name: Sphare High Density ZEB untreated 1st Generation


title: adult satellite cells, replicate 2

description: Gene expression data for adult satellite cells

value: postnatal 2-3 months


title: Huh7 Sph LDZ G1 replicate 1

description:
replicate 1
Sample 1

source_name: Sphare Low Density ZEB treated 1st Generation


title: adult satellite cells, replicate 1


title: Leafminer locally damaged Arabidopsis thaliana seedlings, biological rep2

city: Beijing

first: Sufang

last: Zhang

address: No.2 Dong Xiao Fu, Wan Shou Shan, Haidian District

country: China

institute: Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry

description: Gene expression data from leafminer locally damaged Arabidopsis leaves.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

organism: Arabidopsis thaliana

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

growth_protocol: The seeds were surface-sterilized for 15 min in 10% bleach, washed five times with sterile water, and plated on half-strength Murashige and Skoog medium. Plants were stratified at 4℃ for 2 days in darkness and then transferred to an environmental chamber set at 22℃ with a 16-h-light/8-h-dark cycle (light intensity 120 mmol m-2 s-1). After 2 to 3 weeks, seedlings were also potted in a mixed potting medium of peat and vermiculite (1:2), and placed in a growth room at 22℃ with a 16-h-light/8-h-dark cycle (light intensity 120 mmol m-2 s-1).

extract_protocol: Total RNAs were isolated using the RNeasy® Plant Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.

treatment_protocol: Mated L. huidobrensis adults were released on four-week-old Arabidopsis thaliana leaves for oviposition. The adults were removed within 4 h. When the leafminer grew to second instar larvae , the damaged leaves of Arabidopsis thaliana for local damage analysis and the intact leaves on the same plant for systemic damage analysis were separately frozen by liquid nitrogen.

tag: ecotype

value: leaves

value: four weeks

value: locally damaged by leafminer


title: Undamaged Arabidopsis thaliana seedlings, biological rep1

description: Gene expression data from control undamaged Arabidopsis leaves.

value: undamaged


title: Leafminer locally damaged Arabidopsis thaliana seedlings, biological rep3


title: fetal satellite cells, replicate 2

description: Gene expression data for fetal satellite cells

value: sorted ZsGreen+ satellite cells from whole forelimb and hindlimb

value: fetal E17.5


title: Undamaged Arabidopsis thaliana seedlings, biological rep2


title: Leafminer systemically damaged Arabidopsis thaliana seedlings, biological rep2

description: Gene expression data from leafminer systemically damaged Arabidopsis leaves.

value: systemically damaged by leafminer


title: fetal satellite cells, replicate 3


title: Huh7 Sph LDZ G1 replicate 3

description:
replicate 3
Sample 3

value: Huh7 Liver Cancer Cell Line

value: Zebularine (ZEB)


title: adolescent satellite cells, replicate 3

description: Gene expression data for adolescent satellite cells

value: postnatal P21


title: E. coli 2% NaCl

value: Exponential

value: exponential


title: 5B_HeCo

city: Evry Cedex

first: Robert

last: Olaso

address: 2 rue Gaston Cremieux

department: CNRGH

country: France

institute: CEA-DRF

description: SAMPLE 15

data_processing: The data were normalized using quantile normalization with GenomeStudio

source_name: Mouse brain

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: Total RNA were extracted using the Qiagen RNeasy Protect mini kit

tag: genotype/variation

value: HeCo mutant

value: Brain

value: Embryonic day 18


title: Leafminer locally damaged Arabidopsis thaliana seedlings, biological rep1


title: fetal satellite cells, replicate 1


title: Leafminer systemically damaged Arabidopsis thaliana seedlings, biological rep3


title: Leafminer systemically damaged Arabidopsis thaliana seedlings, biological rep1


title: 15B_HeCo

description: SAMPLE 16


title: 13B_HeCo

description: SAMPLE 14


title: Huh7 Sph HDU G1 replicate 2

description:
replicate 2
Sample 5


title: 10B_wt

description: SAMPLE 13

value: control


title: Sucrose_300mM,60min vs control - 3000188434R

city: Seattle

first: Tie

last: Koide

state: WA

address: 1441 N 34th street

institute: Institute for Systems Biology

description: Fluorescence mean intensity and surrounding median background from each spot were obtained with ArrayVision v6.0 (Imaging Research, Inc). Unreliable spots, having intensities too similar to local background or saturated were filtered out. Spots presenting mean intensity below 2 times the standard deviation of its background in Cy3 and Cy5 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless,. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the heat shock time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((cy3+cy5)/2)]

hyb_protocol: Cy3 and Cy5 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were shrinked? in water for 10s and dried with nitrogen gas.

scan_protocol: Microarray slides were scanned with a Generation III DNA Scanner (Amersham Biosciences).

data_processing: filtering low intensity spots, LOWESS normalization

organism: Xylella fastidiosa

source_name: Sucrose_300mM,60min (cy3)

label_protocol: 20ug of total RNA was reverse transcribed and labeled using Superscript cDNA Post-labeling kit (Invitrogen). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in speed vac.

growth_protocol: Xylella fastidiosa strain 9a5c was grown in Periwinkle wilt broth plus 0.5% glucose(PWG) at 29oC for 7 days.

extract_protocol: Total RNA was isolated with Trizol and residual DNA was removed by treatment with 10U of RQ1 RNAse-free DNAse I (Promega) and 40U RNAse inhibitor RNAsin (Promega). The integrity of the RNA was checked by agarose gel electrophoresis and the lack of residual DNA was checked by PCR.

treatment_protocol: Osmotic stress was applied to 7 days old cultures by adding sucrose to a final concentration of 300mM, in a water bath incubator at 29oC with rotatory agitation of 150 rpm. 50ml aliquots of cell cultures were taken at time point 60 minutes and immediately harvested for RNA extraction.

tag: Sucrose_300mM,60min (cy3)

source_name: control (cy5)

tag: control (cy5)


title: Huh7 Sph HDZ G1 replicate 3

description:
replicate 3
Sample 9


title: Sucrose_300mM,30min vs control - 3000188433L

source_name: Sucrose_300mM,30min (cy3)

treatment_protocol: Osmotic stress was applied to 7 days old cultures by adding sucrose to a final concentration of 300mM, in a water bath incubator at 29oC with rotatory agitation of 150 rpm. 50ml aliquots of cell cultures were taken at time point 30 minutes and immediately harvested for RNA extraction.

tag: Sucrose_300mM,30min (cy3)


title: 7B_HeCo

description: SAMPLE 11


title: Sucrose_300mM,07min vs control - 3000137028R

source_name: Sucrose_300mM,07min (cy3)

treatment_protocol: Osmotic stress was applied to 7 days old cultures by adding sucrose to a final concentration of 300mM, in a water bath incubator at 29oC with rotatory agitation of 150 rpm. 50ml aliquots of cell cultures were taken at time point 07 minutes and immediately harvested for RNA extraction.

tag: Sucrose_300mM,07min (cy3)


title: adult satellite cells, replicate 3

value: sorted ZsGreen+ satellite cells from hindlimb muscles

value: postnatal 2-3 months


title: 3B_wt

description: SAMPLE 10


title: adolescent satellite cells, replicate 1


title: 1B_wt

description: SAMPLE 9


title: Huh7 Sph HDU G1 replicate 3

description:
replicate 3
Sample 6


title: Sucrose_300mM,60min vs control - 3000188434L


title: Undamaged Arabidopsis thaliana seedlings, biological rep3

value: leaves

value: four weeks


title: adolescent satellite cells, replicate 2


title: 4B_wt

description: SAMPLE 12


title: 12B_wt

description: SAMPLE 8


title: 9B_wt

description: SAMPLE 7


title: Huh7 Sph LDZ G1 replicate 2

description:
replicate 2
Sample 2


title: Sucrose_300mM,30min vs control - 3000188433R


title: Sucrose_300mM,15min vs control - 3000137029R

source_name: Sucrose_300mM,15min (cy3)

treatment_protocol: Osmotic stress was applied to 7 days old cultures by adding sucrose to a final concentration of 300mM, in a water bath incubator at 29oC with rotatory agitation of 150 rpm. 50ml aliquots of cell cultures were taken at time point 15 minutes and immediately harvested for RNA extraction.

tag: Sucrose_300mM,15min (cy3)


title: Sucrose_300mM,15min vs control - 3000137029L


title: 16B_HeCo

description: SAMPLE 6


title: 2B_wt

description: SAMPLE 3


title: Sucrose_300mM,07min vs control - 3000137028L


title: 8B_HeCo

description: SAMPLE 5


title: Sucrose_300mM,07min vs control - 3000137026R

source_name: control (cy3)

tag: control (cy3)

source_name: Sucrose_300mM,07min (cy5)

tag: Sucrose_300mM,07min (cy5)


title: Sucrose_300mM,15min vs control - 3000137027R

source_name: Sucrose_300mM,15min (cy5)

tag: Sucrose_300mM,15min (cy5)


title: 14B_HeCo

description: SAMPLE 2

tag: tissue

tag: strain


title: 6B_HeCo

description: SAMPLE 1


title: Sucrose_300mM,15min vs control - 3000137027L


title: Sucrose_300mM,15min vs control - 3000137025L


title: 11B_wt

description: SAMPLE 4


title: Sucrose_300mM,07min vs control - 3000137026L


title: Sucrose_300mM,60min vs control - 3000115663R


title: Sucrose_300mM,07min vs control - 3000137024R


title: Sucrose_300mM,15min vs control - 3000137025R


title: Sucrose_300mM,07min vs control - 3000137024L


title: Sucrose_300mM,60min vs control - 3000115663L


title: Sucrose_300mM,30min vs control - 3000115662L


title: Liver CREMKO 12h batch 5 [LiKOh12.38]

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: Gene expression data from liver Crem-/- sample taken at 12h

hyb_protocol: 100 ng of total RNA was used for hybridization of Affymetrix Gene Chip Mouse 1.0 ST Arrays according to manufacturer’s instructions (Genechip® Whole Transcript (wt) Sense Ttarget Labeling Assay Manual – P/N 701880 Rev 4). Labled samples were injected into Affymetrix arrays and hybridized at 45°C and 60 rpm for 16 h in an Affymetrix Hybridization Oven. Arrays were stained and washed in the Affymetrix GeneChip Fluidic Station 450.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000 7G.

data_processing:
GeneChip data was processed and analyzed using R/Bioconductor packages. Data were summarized (w.r.t. core meta-probeset annotations and AFFX control probes, probes grouped to the level of transcripts) and quantile-normalized (background computed from antigenomic probes) using RMA algorithm from XPS package.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: Whole liver RNA from Crem-/- mouse #109 at 12h

label_protocol: Total RNA was used to synthesize double-stranded cDNA with random hexamer primers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA and dUTP was incorporated to produce single-stranded DNA. This single-stranded DNA sample were then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognized the unnatural dUTP residues and broke the DNA strand. DNA was labeled by terminal eoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: WT and Crem-/- animals of the mixed strain (129Pas x C57Bl/J ) [Nantel F, Monaco L, Foulkes NS, Masquilier D, LeMeur M, Henriksén K, Dierich A, Parvinen M, Sassone-Corsi P: Spermiogenesis deficiency and germ-cell apoptosis in CREM-mutant mice. Nature 1996, 380:159-162] were maintained in a temperature and humidity controlled room under a 12:12 h light:dark cycle (light on at 7:00 am, light off at 7:00 pm) with free access to food (Harland Tekland 2916) and water.

extract_protocol: 8 weeks old mice were sacrificed with cervical dislocation at 7 am (0h circadian time) or 7 pm (12h circadian time) and tissue samples from liver, were excised, snap frozen in liquid nitrogen and stored at -80°C for subsequent analysis. Samples were first pulverized and then homogenized in 1000 μl of TRI Reagent (Sigma) and total RNA was isolated according to the manufacturer’s instructions. RNA quantity and quality were assessed with NanoDrop and Agilent 2100 Bioanalyzer instruments, all samples isolated fulfilled the minimum requirements (OD260/280 and OD230/280 > 1.8) for microarray hybridization.

treatment_protocol: Mice were not treated.

value: Liver

value: 129Pas x C57Bl/J

value: CREMKO

tag: animal

tag: time

tag: batch


title: Liver WT 12h batch 5 [LiWTh12.35]

description: Gene expression data from liver WT sample taken at 12h

source_name: Whole liver RNA from WT mouse #170 at 12h

value: WT


title: Sucrose_300mM,30min vs control - 3000115662R


title: Liver CREMKO 12h batch 5 [LiKOh12.39]

source_name: Whole liver RNA from Crem-/- mouse #110 at 12h


title: Liver CREMKO 12h batch 5 [LiKOh12.40]

source_name: Whole liver RNA from Crem-/- mouse #166 at 12h


title: Sucrose_300mM,60min vs control - 3000115661R

source_name: Sucrose_300mM,60min (cy5)

tag: Sucrose_300mM,60min (cy5)


title: Sucrose_300mM,60min vs control - 3000115661L


title: Liver CREMKO 12h batch 5 [LiKOh12.37]

source_name: Whole liver RNA from Crem-/- mouse #55 at 12h


title: Liver CREMKO 12h batch 5 [LiKOh12.36]

source_name: Whole liver RNA from Crem-/- mouse #18 at 12h


title: NaCl_250mM,30min vs control - 3000188431L

source_name: NaCl_250mM,30min (cy3)

treatment_protocol: Salt stress was applied to 7 days old cultures by adding NaCl to a final concentration of 250mM, in a water bath incubator at 29oC with rotatory agitation of 150 rpm. 50ml aliquots of cell cultures were taken at time point 30 minutes and immediately harvested for RNA extraction.

tag: NaCl_250mM,30min (cy3)


title: Liver WT 12h batch 5 [LiWTh12.32]

source_name: Whole liver RNA from WT mouse #167 at 12h


title: Liver WT 0h batch 3 [LiWTh00.24]

description: Gene expression data from liver WT sample taken at 0h

source_name: Whole liver RNA from WT mouse #80 at 0h


title: NaCl_250mM,30min vs control - 3000188431R

source_name: control (cy5)


title: Liver WT 12h batch 5 [LiWTh12.33]

source_name: Whole liver RNA from WT mouse #168 at 12h


title: Sucrose_300mM,30min vs control - 3000115660L

source_name: Sucrose_300mM,30min (cy5)

tag: Sucrose_300mM,30min (cy5)


title: Liver WT 12h batch 5 [LiWTh12.31]

source_name: Whole liver RNA from WT mouse #111 at 12h

tag: genotype/variation


title: NaCl_250mM,60min vs control - 3000188432R

source_name: NaCl_250mM,60min (cy3)

treatment_protocol: Salt stress was applied to 7 days old cultures by adding NaCl to a final concentration of 250mM, in a water bath incubator at 29oC with rotatory agitation of 150 rpm. 50ml aliquots of cell cultures were taken at time point 60 minutes and immediately harvested for RNA extraction

tag: NaCl_250mM,60min (cy3)


title: NaCl_250mM,15min vs control - 3000167023L

source_name: NaCl_250mM,15min (cy3)

treatment_protocol: Salt stress was applied to 7 days old cultures by adding NaCl to a final concentration of 250mM, in a water bath incubator at 29oC with rotatory agitation of 150 rpm. 50ml aliquots of cell cultures were taken at time point 15 minutes and immediately harvested for RNA extraction.

tag: NaCl_250mM,15min (cy3)

tag: control (cy5)


title: Liver WT 0h batch 4 [LiWTh00.30]

source_name: Whole liver RNA from WT mouse #147 at 0h


title: Liver WT 12h batch 5 [LiWTh12.34]

source_name: Whole liver RNA from WT mouse #169 at 12h


title: Sucrose_300mM,30min vs control - 3000115660R

source_name: control (cy3)


title: Liver WT 0h batch 3 [LiWTh00.21]

source_name: Whole liver RNA from WT mouse #145 at 0h


title: Liver CREMKO 0h batch 3 [LiKOh00.17]

description: Gene expression data from liver Crem-/- sample taken at 0h

source_name: Whole liver RNA from Crem-/- mouse #144 at 0h


title: NaCl_250mM,60min vs control - 3000188432L


title: NaCl_250mM,07min vs control - 3000167022R

source_name: NaCl_250mM,07min (cy3)

treatment_protocol: Salt stress was applied to 7 days old cultures by adding NaCl to a final concentration of 250mM, in a water bath incubator at 29oC with rotatory agitation of 150 rpm. 50ml aliquots of cell cultures were taken at time point 07 minutes and immediately harvested for RNA extraction.

tag: NaCl_250mM,07min (cy3)


title: Liver CREMKO 0h batch 4 [LiKOh00.27]

source_name: Whole liver RNA from Crem-/- mouse #76 at 0h


title: Liver CREMKO 0h batch 2 [LiKOh00.10]

source_name: Whole liver RNA from Crem-/- mouse #1 at 0h


title: Liver WT 0h batch 2 [LiWTh00.14]

source_name: Whole liver RNA from WT mouse #78 at 0h


title: NaCl_250mM,15min vs control - 3000167023R


title: NaCl_250mM,07min vs control - 3000167022L


title: NaCl_250mM,15min vs control - 3000167021L

source_name: NaCl_250mM,15min (cy5)

tag: NaCl_250mM,15min (cy5)


title: Liver WT 0h batch 1 [LiWTh00.7]

source_name: Whole liver RNA from WT mouse #146 at 0h


title: NaCl_250mM,07min vs control - 3000167020L

tag: control (cy3)

source_name: NaCl_250mM,07min (cy5)

tag: NaCl_250mM,07min (cy5)


title: NaCl_250mM,07min vs control - 3000167020R


title: NaCl_250mM,15min vs control - 3000167021R


title: Liver CREMKO 0h batch 1 [LiKOh00.3]

source_name: Whole liver RNA from Crem-/- mouse #143 at 0h


title: Liver CREMKO 0h batch 1 [LiKOh00.2]

source_name: Whole liver RNA from Crem-/- mouse #77 at 0h


title: NaCl_250mM,15min vs control - 3000167019R


title: NaCl_250mM,15min vs control - 3000167019L


title: Adipocyte_unstimulated_3

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

institute: bioMérieux

description: Unstimulated adipocytes

hyb_protocol: RNA was analyzed using microarray chips including 45,000 probes (4x44K Whole Mouse Genome, Agilent Technologies, G4122F) and One-color Microarray Based Gene Expression Analysis. Hybridization was performed at 65°C using the in situ Hybridization Plus kit (Agilent Technologies) for 17 hours.

scan_protocol: Arrays were scanned with a pixel size of 5 µm with the DNA Microarray Scanner G2505C. Image analysis and correction of intra-array signals were performed with the Feature Extraction Software A.9.1.3 (Agilent Technologies).

data_processing: Microarray data analysis was performed using the R and the Bioconductor software suite. Raw data were filtered and normalized using the Agi4x44PreProcess library. In this dataset, > 10,000 probes did not exhibit a signal above BG in > 75% of the samples were filtered out. Unsupervised and supervised analyses were done using hierarchical clustering, correspondence analysis (COA) (made4 library) and Significance Analysis of Microarray (SAM) algorithm (siggenes library). Supervised analysis was performed using SAM. Genes were considered to be differentially expressed when the false discovery rate was below 5% and absolute log2 fold change (FC) was above 1.5. The preprocessing script and the output from R can be found in the readme.txt.

source_name: Unstimulated adipocytes

label_protocol: In brief, 300 ng RNA were labeled with cyanine-3-CTP using the Low RNA Input Fluorescent Amplification Kit from Agilent Technologies.

growth_protocol: 3T3-L1 cells (from ATCC) were differentiated into adipocytes using 100 mM 3-isobutyl-1-methylxanthine, 250 nM dexamethasone and 1µg/mL insulin. After 2 weeks, differentiation was checked by red oil and bodipy 493/503 staining of the lipid droplets.

extract_protocol: RNA was extracted using an RNeasy Mini kit (Qiagen, Courtaboeuf, France). The quantity and quality of total RNA were assessed using the Nanodrop (Thermo Scientific, Illkirch, France) and a 2100 Bioanalyzer (Agilent Technologies, Massy, France). The RNA was eluted in 30 µl of water and stored at -20°C.

treatment_protocol: Differentiated adipocytes were either stimulated with Coxiella burnetii (NMI) at a ratio of 50 bacteria per cell for eight hours, or left unstimulated.

tag: stimulation

value: NO

value: NS

value: Adipocytes


title: Adipocyte_stimulated_4

description: Stimulated adipocytes

source_name: Stimulated adipocytes

value: YES

value: Coxiella burnetii


title: Adrenal WT 0h batch 4 [AdWTh00.26]

description: Gene expression data from adrenal WT sample taken at 0h

source_name: Whole adrenal RNA from WT mouse #147 at 0h

extract_protocol: 8 weeks old mice were sacrificed with cervical dislocation at 7 am (0h circadian time). Tissue samples from adrenal glands were excised, snap frozen in liquid nitrogen and stored at -80°C for subsequent analysis. Samples were homogenized in 500 μl of TRI Reagent (Sigma) and total RNA was isolated according to the manufacturer’s instructions. RNA quantity and quality were assessed with NanoDrop and Agilent 2100 Bioanalyzer instruments, all samples isolated fulfilled the minimum requirements (OD260/280 and OD230/280 > 1.8) for microarray hybridization.

tag: tissue

value: Adrenal gland


title: Adrenal CREMKO 0h batch 3 [AdKOh00.18]

description: Gene expression data from adrenal Crem-/- sample taken at 0h

source_name: Whole adrenal RNA from Crem-/- mouse #143 at 0h

tag: strain


title: Adrenal WT 0h batch 3 [AdWTh00.19]

source_name: Whole adrenal RNA from WT mouse #146 at 0h

tag: animal


title: Adrenal CREMKO 0h batch 2 [AdKOh00.15]

source_name: Whole adrenal RNA from Crem-/- mouse #2 at 0h

tag: time


title: Adipocyte_stimulated_1

description: Stimulated adipocytes


title: Adipocyte_unstimulated_2

description: Unstimulated adipocytes


title: NaCl_250mM,60min vs control - 3000115666R

source_name: NaCl_250mM,60min (cy3)

source_name: control (cy5)


title: NaCl_250mM,07min vs control - 3000167018L

source_name: control (cy3)


title: Adipocyte_unstimulated_1

description: Unstimulated adipocytes


title: Adipocyte_stimulated_3

description: Stimulated adipocytes


title: Adrenal WT 0h batch 3 [AdWTh00.23]

source_name: Whole adrenal RNA from WT mouse #145 at 0h

tag: batch


title: NaCl_250mM,30min vs control - 3000115665L

source_name: NaCl_250mM,30min (cy3)


title: NaCl_250mM,07min vs control - 3000167018R


title: Adrenal WT 0h batch 3 [AdWTh00.22]

source_name: Whole adrenal RNA from WT mouse #80 at 0h


title: NaCl_250mM,60min vs control - 3000115666L


title: Adipocyte_stimulated_2

description: Stimulated adipocytes


title: NaCl_250mM,60min vs control - 3000115659R

source_name: NaCl_250mM,60min (cy5)

treatment_protocol: Salt stress was applied to 7 days old cultures by adding NaCl to a final concentration of 250mM, in a water bath incubator at 29oC with rotatory agitation of 150 rpm. 50ml aliquots of cell cultures were taken at time point 60 minutes and immediately harvested for RNA extraction.

tag: NaCl_250mM,60min (cy5)


title: Adrenal CREMKO 0h batch 1 [AdKOh00.8]

source_name: Whole adrenal RNA from Crem-/- mouse #144 at 0h


title: NaCl_250mM,30min vs control - 3000115665R

tag: NaCl_250mM,30min (cy3)


title: Adrenal CREMKO 0h batch 2 [AdKOh00.16]

source_name: Whole adrenal RNA from Crem-/- mouse #77 at 0h


title: NaCl_250mM,30min vs control - 3000115658L

source_name: NaCl_250mM,30min (cy5)

tag: NaCl_250mM,30min (cy5)


title: Adrenal CREMKO 0h batch 1 [AdKOh00.1]

source_name: Whole adrenal RNA from Crem-/- mouse #1 at 0h

tag: genotype/variation


title: 2.5 uM DAPT, day 4

city: Los Angeles

first: Justin

last: Ichida

state: CA

address: 1425 San Pablo St. Bcc 307

institute: University of Southern California

description: keratinocytes isolated from neonatal mice

data_processing: The data were normalized using cubic spine with Illumina BeadStudio

source_name: primary keratinocytes

growth_protocol: Keratinocytes were grown in SFM media from Invitrogen at 30 degrees Celsius and 10% CO2

extract_protocol: RNA was extracted with Trizol LS reagent and extracted according to the Trizol LS protocol from Invitrogen.

treatment_protocol: Cells were treated with 2.5 uM DAPT for 4 days or 7 days before RNA was harvested

value: day 4

tag: cell type

value: primary keratinocyte

tag: treatment

value: DAPT

tag: genotype

value: 129, with Pou5f1::GFP transgene

tag: genetic background


title: Adrenal WT 0h batch 1 [AdWTh00.4]

source_name: Whole adrenal RNA from WT mouse #78 at 0h


title: NaCl_250mM,60min vs control - 3000115659L


title: 2.5 uM DAPT, day 7

value: day 7


title: no DAPT, day 7


title: no DAPT, day 4


title: NaCl_250mM,30min vs control - 3000115658R


title: Aerobic growth, H37Rv vs. lsr2 mutant, replicate 1

status: Public on May 24 2014

city: Aurora

first: Martin

last: Voskuil

state: CO

address: 12800 E. 19th Ave. Mail Stop 8333 RC1-North Room P18-9115

department: Microbiology

institute: CU-AMC

description: Biological replicate 1 of 4.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Microarrays were scanned using a GenePix 4000b scanner (Axon Instruments). The intensities of the two dyes at each spot were quantified using GenePix Pro 6.0 (Molecular Devices).

data_processing: ArrayStar software was used for microarray analysis. Experiments performed in triplicate or quadruplicate were loaded into ArrayStar and normalized using RMA. Statistical significance was determined using the Students t-test.

organism: Mycobacterium tuberculosis

source_name: Wild type H37Rv, settled aerobic growth

label_protocol: 1.5 ug of RNA was primed with N6 primers, heated for 10 minutes at 65 C, then incubated 10 minutes at 25 C followed by 90 minutes at 42 C. 5mM A,G,C and 0.2mM T dNTP mix was used.

growth_protocol: Samples were grown in 50 mL volumes in 125 mL flasks. Samples for Rach models were grown in 16 mL cultures at an OD600 of 0.15 were started in glass tubes (16 mm X 125 mm) containing stir bars (12 mm X 4.5 mm). Minimal head space remained in the tubes (~1 mL). The tubes were sealed with caps containing butyl rubber septa and stirred at 60% of maximum speed using a rotary magnetic tumble stirrer from V & P Scientific (San Diego, CA).

extract_protocol: Cell pellets were flash frozen on dry ice, resuspended in Trizol, and bead-beaten 3 x 30 seconds. Resulting cell lysate was added to chloroform and nucleic acids were then precipitated in isopropanol, rehydrated in 75% ethanol, then DNase treated. Fur further purification, Qiagen RNeasy kit was used according to the manufacturer's instructions.

treatment_protocol: For H2O2 experiments, 3mM H2O2 was added either to the aerobic samples or Rach model samples, and samples were harvested after 1h of treatment.

tag: strain/background

value: wild type

tag: growth condition

value: settled aerobic growth

source_name: H37Rv Δlsr2, settled aerobic growth


title: Aerobic growth, H37Rv vs. lsr2 mutant, replicate 2

description: Biological replicate 2 of 4.


title: Aerobic growth, H37Rv vs. lsr2 mutant, replicate 3

description: Biological replicate 3 of 4.


title: 48h Rach model, 3mM H2O2 added, H37Rv vs. lsr2 mutant, replicate 3

description: Biological replicate 3 of 3.

source_name: Wild type H37Rv, 48h Rach dormancy model, 3mM H2O2 added

value: 48h Rach dormancy model, 3mM H2O2 added

source_name: H37Rv Δlsr2, 48h Rach dormancy model, 3mM H2O2 added


title: 48h Rach model, 3mM H2O2 added, H37Rv vs. lsr2 mutant, replicate 2

description: Biological replicate 2 of 3.


title: 48h Rach model, 3mM H2O2 added, H37Rv vs. lsr2 mutant, replicate 1

description: Biological replicate 1 of 3.


title: Aerobic growth, 3mM H2O2 added, H37Rv vs. lsr2 mutant, replicate 3

description: Biological replicate 3 of 3.

source_name: Wild type H37Rv, aerobic growth, 3mM H2O2 added

value: aerobic growth, 3mM H2O2 added

source_name: H37Rv Δlsr2, aerobic growth, 3mM H2O2 added


title: 24h Rach model, H37Rv vs. lsr2 mutant, replicate 3

description: Biological replicate 3 of 3.

source_name: Wild type H37Rv, 24h Rach dormancy model

value: 24h Rach dormancy model

source_name: H37Rv Δlsr2, 24h Rach dormancy model


title: 48h Rach model, H37Rv vs. lsr2 mutant, replicate 2

description: Biological replicate 2 of 3.

source_name: Wild type H37Rv, 48h Rach dormancy model

value: 48h Rach dormancy model

source_name: H37Rv Δlsr2, 48h Rach dormancy model


title: 48h Rach model, H37Rv vs. lsr2 mutant, replicate 1

description: Biological replicate 1 of 3.


title: Aerobic growth, 3mM H2O2 added, H37Rv vs. lsr2 mutant, replicate 1

description: Biological replicate 1 of 3.


title: 48h Rach model, H37Rv vs. lsr2 mutant, replicate 3

description: Biological replicate 3 of 3.


title: Aerobic growth, 3mM H2O2 added, H37Rv vs. lsr2 mutant, replicate 2

description: Biological replicate 2 of 3.


title: 24h Rach model, H37Rv vs. lsr2 mutant, replicate 1

description: Biological replicate 1 of 3.


title: Aerobic growth, H37Rv vs. lsr2 mutant, replicate 4

description: Biological replicate 4 of 4.


title: 24h Rach model, H37Rv vs. lsr2 mutant, replicate 2

description: Biological replicate 2 of 3.


title: CD8SP cells derived from control OT-l 16-8-W8O

city: Chiba

first: ATSUSHI

last: IWAMA

address: 1-8-1 Inohana, Chuo-ku

department: Department of Cellular and Molecular Medicine

country: Japan

institute: Graduate School of Medicine, Chiba University

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ng total RNA (One-Color Microarray-Based Gene Expression Analysis: Low Input Quick Amp Labeling, ve6.0, December2009).

scan_protocol: GeneChips were scanned using the DNA Microarray Scanner (Agilent).

data_processing: The data were analyzed with GeneSpring GX 11.5.1(Agilent) using recommended analysis settings and global scaling as normalization method.

source_name: CD8SP cells derived from control OT-l

label_protocol: Biotinylated cRNA were prepared  from the purified total RNA equivalent to 30,000 cells according to the standard Affymetrix protocol.

value: Brd1+/+, Tie2-Cre, OT-l

value: Thymocyte

tag: surface marker

tag: age


title: CD4SP(TCRβ-) cells derived from Brd1 CKO 5-6-F4N2

value: Brd1flox/flox, Tie2-Cre


title: CD8SP cells derived from Brd1 CKO OT-l 17-9-F8O

source_name: CD8SP cells derived from Brd1 CKO OT-l

value: Brd1flox/flox, Tie2-Cre, OT-l


title: CD8SP cells derived from Brd1 CKO 6-7-F82

source_name: CD8SP cells derived from Brd1 CKO


title: case_3

type: genomic

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Agilent Scanner protocol for a full slide

data_processing: Agilent Feature Extraction Software (v 9.1.1) was used for background subtraction and LOWESS normalization.

source_name: Hepatosplenic T-cell Lymphoma

label_protocol: Agilent lable protocol

growth_protocol: natural tumor

extract_protocol: standard DNA extraction protocol

treatment_protocol: no treatment

tag: tissue

value: Hepatosplenic T-cell Lymphoma

tag: karyotype

source_name: control

tag: sample type

value: Normal DAN sample from Agilent


title: CD4+CD8+DP cells derived from Brd1 CKO 3-4-FD2

source_name: CD4+CD8+DP cells derived from Brd1 CKO

tag: strain


title: CD4SP cells derived from Brd1 CKO 4-5-4P2

source_name: CD4SP cells derived from Brd1 CKO


title: DERL-2


title: case_5


title: case_2


title: SC5314 with DMSO, biological rep1 [re-analysis]

city: Memphis

first: Erin

last: Vasicek

state: TN

address: 881 Madison Ave

institute: University of Tennessee Health Science Center

hyb_protocol: The cRNA pellet was suspended in 10 µl of RNase-free water and 10 µg was fragmented by ion-mediated hydrolysis at 95 °C for 35 min in 200 mM Tris-acetate (pH 8.1), 500 mM potassium acetate, 150 mM magnesium acetate. The fragmented cRNA was hybridized for 16 h at 45 °C to the C. albicans NimbleExpress GeneChip arrays. Arrays were washed at 25 °C with 6 × SSPE, 0.01% Tween 20 followed by a stringent wash at 50 °C with 100 mM MES, 0.1 M NaCl, 0.01% Tween 20. Hybridizations and washes employed the Affymetrix Fluidics Station 450 using their standard EukGE-WS2v5 protocol. The arrays were then stained with phycoerythrein-conjugated streptavidin (Molecular Probes).

scan_protocol: The fluorescence intensities were determined using the GCS 3000 high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using software resident in GeneChip Operating System v2.0 (Affymetrix).

data_processing: The scaled gene expression values from GeneChip Operating System v2.0 software were imported into GeneSpring 7.2 software (Agilent Technologies) for preprocessing and data analysis. Probe sets were deleted from subsequent analysis if they were called absent by the Affymetrix criterion and displayed an absolute value below 20 in all experiments. The expression value of each gene was normalized to the median expression of all genes in each chip as well as the median expression for that gene across all chips in the study. Pairwise comparison of gene expression was performed for each matched experiment.

organism: Candida albicans

source_name: 8 hr SC5314 culture grown with DMSO

label_protocol: Immediately prior to cDNA synthesis, the purity and concentration of RNA samples were determined from A260/A280 readings, and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Laboratory-on-a-Chip kit and Bioanalyzer 2100 (Agilent Technologies) as per the manufacturer's instructions. First and second strand cDNA was synthesized from 15 μg total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and oligo-dT24-T7 primer (PrOligo) according to the manufacturer's instructions. cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double-stranded cDNA as template and the Bioarray HighYield RNA Transcript Labeling Kit (ENZO Diagnostics). Double-stranded cDNA synthesized from the previous steps was washed twice with 70% ethanol and suspended in 22 μl of RNase-free water. The cDNA was incubated as recommended with reaction buffer, biotin-labeled ribonucleotides, dithtiothreitol, RNase inhibitor mix, and T7 RNA polymerase for 5 h at 37 °C. The labeled cRNA was separated from unincorporated ribonucleotides by passing through a CHROMA SPIN-100 column (Clontech) and ethanol precipitated at −20°C overnight.

growth_protocol: Cells were grown overnight at 30°C in YPD (1% yeast extract, 2% peptone, and 1% dextrose) with agitation, and these saturated cultures were used to seed 100 ml YPD cultures (OD600=0.005) which were then grown with agitation at 30°C for an additional 8 hours to an OD600 of 1.0.

extract_protocol: Total RNA was isolated using a large-scale version of the hot phenol method of RNA isolation (Schmitt, M. E., T. A. Brown, and B. L. Trumpower. 1990. Nucleic Acids Res. 18:3091-3092.). Briefly, Cell pellets were resuspended in 12 ml of AE buffer (50 mM sodium acetate [pH 5.3], 10 mM EDTA [pH 8.0]) and were then transferred to 50-ml Oak Ridge tubes treated with RNase Away (Molecular BioProducts) containing 12 ml acid phenol (pH 4.3) with 1% SDS. Cells were incubated at 65°C for 10 min; then lysates were clarified by centrifugation. The supernatant was then transferred to a new tube containing 15 ml of chloroform, and the contents of the tube were mixed. The sample was then subjected to centrifugation again, and the top aqueous layer was transferred to a new tube containing 1 volume of isopropanol and 0.1 volume of 2 M sodium acetate. The RNA pellet was subsequently washed with 10 ml of 70% ethanol and was collected by centrifugation. The RNA pellet was resuspended in DNase/RNase-free H2O and was stored at -80°C until needed. Quantity and purity were determined spectrophotometrically by A260 and A280.

treatment_protocol: Cultures were diluted again to an OD600 of 0.025 in 100 ml fresh YPD, incubated at 30°C with agitation for one doubling, inoculated with or without 10 µg/ml FLC, and then grown at 30°C with agitation for 6 hours. Cells were collected by centrifugation and were stored at -80°C.

tag: strain background

value: wild-type

tag: treated with

value: DMSO


title: cas5Δ/Δ with DMSO, biological rep2

source_name: 8 hr cas5Δ/Δculture grown with DMSO

value: homozygous CAS5 mutant (cas5Δ/Δ)


title: cas5Δ/Δ with FLC, biological rep1

source_name: 8 hr cas5Δ/Δ culture grown with 10 µg/ml FLC

value: 10 µg/ml FLC in DMSO


title: CD4+CD8+DP cells derived from control 9-1-WD

source_name: CD4+CD8+DP cells derived from control

value: Brd1+/+, Tie2-Cre


title: SC5314 with FLC, biological rep1 [re-analysis]

source_name: 8 hr SC5314 culture grown with 10 µg/ml FLC


title: SC5314 with DMSO, biological rep2 [re-analysis]


title: cas5Δ/Δ with DMSO, biological rep1

source_name: 8 hr cas5Δ/Δ culture grown with DMSO


title: case_1


title: CD4SP cells derived from control 10-2-W4

source_name: CD4SP cells derived from control


title: SC5314 with FLC, biological rep2 [re-analysis]


title: PAPD5 knockdown, first replicate

city: Yokohama-shi, Tsurumi-ku

first: Michiel

last: de Hoon

state: Kanagawa-ken

address: Suehiro-cho 1-7-22

department: Center for Life Science Technologies

institute: RIKEN

description: Lot 3 out of 4 cell lots

hyb_protocol: cRNA was hybridized to Illumina Human Sentrix-6 bead chips Ver. 3 according to standard Illumina protocols (http://www.illumina.com).

scan_protocol: Chips were scanned using the Illumina BeadScan and BeadStudio software packages and summarized data was generated in BeadStudio (version 3.4.0).

data_processing: Data were processed using the lumi and limma packages. First the background signal was subtracted from the raw data, then the data were quantile normalized, and then transformed using the base-2 logarithm.

label_protocol: 500 ng RNA was labeled using the Illumina® TotalPrepTM RNA Amplification Kit (Ambion), according to manufacturer's instructions.

growth_protocol: THP-1 cells were cultured in RPMI1640 (Invitrogen), 10% FBS, penicillin/streptomycin (Invitrogen), 10 mM HEPES (Invitrogen), 1 mM sodium pyruvate (Invitrogen), and 50 μM 2-mercaptoethanol (Invitrogen).

extract_protocol: Total RNA was extracted 72 h after transfection with TRIzol (Invitrogen) and FastPure RNA kit (TaKaRa BIO) according to the modified manufacturer's instructions. After phase separation of TRIzol, aqueous phase was mixed with the same amount of 100% ethanol and flowed through a filter cartridge. After RNA binding to the filter cartridge, each bound total RNA was washed three times with 700 μL of treble ethanol diluted wash buffer and eluted with elution buffer.

treatment_protocol: Reverse transfection of 10e6 cells in 60-mm cell culture dish was performed with 20 nM (final concentration) of each siRNA, Opti-MEM (Invitrogen), and 1.6 μg/mL (final concentration) of Lipofectamine 2000 (Invitrogen) according to manufacturer's instructions.

value: PAPD5 knockdown

tag: cell line

value: Peripheral blood

tag: gender

value: Male

value: Monocyte

tag: developmental stage

value: 1 year old infant


title: CD8SP cells derived from control 11-3-W8

source_name: CD8SP cells derived from control

tag: cell type


title: cas5Δ/Δ with FLC, biological rep2

source_name: 8 hr cas5Δ/Δculture grown with 10 µg/ml FLC

tag: genotype/variation


title: Negative control, first replicate

description: Lot 3 out of 4 cell lots

tag: treatment

value: Negative control


title: GLD2 knockdown, first replicate

description: Lot 3 out of 4 cell lots

value: GLD2 knockdown


title: PAPD5 knockdown, second replicate

description: Lot 4 out of 4 cell lots


title: Negative control, second replicate

description: Lot 4 out of 4 cell lots


title: GLD2 knockdown, second replicate

description: Lot 4 out of 4 cell lots


title: upc2Δ/Δ with FLC, biological rep2

source_name: 8 hr upc2Δ/Δculture grown with 10 µg/ml FLC

value: homozygous UPC2 mutant (upc2Δ/Δ)


title: SC5314 with DMSO, biological rep2


title: SC5314 with FLC, biological rep2


title: upc2Δ/Δ with DMSO, biological rep2

source_name: 8 hr upc2Δ/Δculture grown with DMSO


title: SC5314 with DMSO, biological rep1


title: SC5314 with FLC, biological rep1


title: leaf at T1, biological rep2

city: Bjing

first: Liu

last: Juanjuan

address: XiangShan Road, HaiDian District

department: Research Institute of Forestry

institute: Chinese Academy of Forestry

description: Gene expression data from leaves under elevated CO2 concentration (550 ppm)

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: (Populus tomentosa x Populus bolleana) x Populus tomentosa

source_name: Poplar leaves under elevated CO2 concentration (550 ppm)

label_protocol: biotin

growth_protocol: Homogeneous 20 cm long, woody-stem cuttings of triploid white poplar were planted in 20 cm*26 cm*34 cm plastic pots. After growth for about three months, twenty randomly selected pots were moved into three controlled environment chambers (Beijing, China).Ten days later, they were subjected to different CO2 concentrations treatments three months.

extract_protocol: total RNA

treatment_protocol: The three different CO2 concentration treatments were: T0 treatment (385 ppm, day 25˚C/night 20˚C), T1 treatment (550 ppm, day 28˚C/night 23˚C) and T2 treatment (720 ppm, day 31˚C/night 26˚C).

value: elevated CO2 concentration (550 ppm)

value: leaf


title: leaf at T1, biological rep3


title: upc2Δ/Δ with DMSO, biological rep1

source_name: 8 hr upc2Δ/Δ culture grown with DMSO


title: leaf at T1, biological rep1


title: leaf at T2, biological rep2

description: Gene expression data from leaves under elevated CO2 concentration (720 ppm)

source_name: Poplar leaves under elevated CO2 concentration (720 ppm)

value: elevated CO2 concentration (720 ppm)


title: upc2Δ/Δ with FLC, biological rep1

source_name: 8 hr upc2Δ/Δ culture grown with 10 µg/ml FLC


title: leaf at T2, biological rep3


title: leaf at T2, biological rep1


title: leaf at T0, biological rep3

description: Gene expression data from leaves under normal CO2 concentration

source_name: Poplar leaves under normal CO2 concentration

value: normal CO2 concentration


title: leaf at T0, biological rep1


title: leaf at T0, biological rep2


title: CSBwt 24h post AM rep_1

status: Public on May 23 2014

city: Illkirch

first: Egly

last: Jean-Marc

address: 1 rue Laurent Fries

institute: IGBMC

description: 10 micrograms/ml

hyb_protocol: Hybridization User manual for use with the Ambion Expression Kit : Part Number 702808 Rev.1

scan_protocol: Affymetrix GeneChip Expression Wash, Stain and Scan User Manual for Cartridge Arrays : Part Number 702731 Rev.3

data_processing: After chip scanning, a raw image file (.DAT) was generated by Affymetrix Command Console (AGCC v 4.0). After alignment of a grid (.GRD file), a smoothened image file (.CEL) was automatically created. This later file was then used to calculate the signal intensity for each probeset on the chip using RMA algorithms with the Affymetrix Software Expression Console v 1.1

source_name: Immortalized human fibroblasts representing trancated CSB (ERCC6) protein and restored by stable transfection of pcDNA3 CSB wt vector

label_protocol: Affymetrix GeneChip WT Terminal Labeling

growth_protocol: Dulbecco/HamF10 medium containing 10% FCS and 40 mg/mL gentamycin

extract_protocol: GenElute Mammalian Total RNA Miniprep Kit

treatment_protocol: UV-C 10 J/m2, alpha-amanitin 10 micrograms/ml

value: Dermal fibroblasts

tag: genotype

value: CSB taged by:HA N-term, His C-term

value: alpha-amanitin 10 micrograms/ml


title: CSBmut 24h post UV rep_2

description: UV-C 10 J/m2

source_name: Immortalized human fibroblasts representing trancated CSB (ERCC6) protein

value: endogeneous CBS is trancated

value: UV-C 10 J/m2


title: CSBmut 24h post UV rep_1

description: UV-C 10 J/m2


title: CSBmut control rep_1

description: control


title: CSBwt 24h post AM rep_2

description: 10 micrograms/ml


title: CSBwt control rep_1

description: control


title: CSBwt control rep_2

description: control


title: LD8_GW501516

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).

source_name: Myotubes from musculus obliquus internus after 7 days of differentiation

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Human skeletal muscle cells (myotubes) grown from satellite cells were isolated from the M. obliquus internus abdominis of 4 healthy female donors. Body mass index, fasting glucose, insulin, plasma lipids and blood pressure of donors were within normal range. The biopsies were obtained with informed consent and the procedure was approved by the National Committee for Research Ethics (Oslo, Norway). The cells were cultured in DMEM-Glutamax (5.5 mM glucose), 2 % FCS, 2 % Ultroser G, P/S, and amphotericin B. At 70-80 % confluence the growth medium was replaced by DMEM-Glutamax™ supplemented with 2 % FCS, P/S, 1.25 µg/ml amphotericin B, and 25 pM insulin to induce differentiation. The cells were cultured in humidified 5 % CO2 atmosphere at 37 °C, and the medium was changed every 2–3 days.

extract_protocol: Total RNA was prepared using the Agilent Total RNA isolation kit. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Experiments were performed after 7 days of differentiation. Cells were pretreated for 96 h with 0.1% DMSO (vehicle, control) or the PPARδ agonist GW501516 (10 nmol/l) prior to harvesting.

value: cells were pretreated with the PPARδ agonist GW501516 (10 nmol/l) for 96h prior to harvesting.

tag: background

value: caucasian

value: female

value: 43 years

value: muscle


title: LD31_ctrl

value: cells were pretreated with 0.1% DMSO (vehicle, control) for 96h prior to harvesting.

value: 50 years


title: CSBmut control rep_2

description: control


title: CSBwt 24h post UV rep_1

description: UV-C 10 J/m2


title: LD31_GW501516


title: CSBwt 24h post UV rep_2

description: UV-C 10 J/m2


title: LD8_ctrl


title: LD12_GW501516

value: 51 years


title: LD15_GW501516

value: 55 years


title: SCL008_NSP16_72h_3

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.

growth_protocol: Calu-3 2B-4 cells, a clonal derivative of a human lung adenocarcinoma cell line, were maintained in a 1:1 mixture of Dulbecco’s modified Eagle’s medium and Ham’s F12 nutrient medium (DF12; Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum.  All cells were grown at 37°C in an atmosphere of 5% CO2, with an antibiotic/antimycotic mixture (Invitrogen).

extract_protocol: At indicated time points triplicate wells of Mock-infected or virus-infected Calu-3 2B-4 monolayers were washed with 5 ml cold phosphate buffered saline (PBS) and lysed directly with 1 ml of TRIzol (Invitrogen) according to the manufacturer’s recommendation, and resulting lysates were stored at -80°C until further processing.  All Trizol lysates were processed simultaneously:  they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA).  RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for quantitative real-time PCR (qPCR) and microarray analyses.

treatment_protocol: For RNA isolation, Calu-3 2B-4 cells were seeded in 6-well plates (1 x 10^6 cells/well) two days prior to infection.  Immediately preceding infection, monolayers were washed twice with DMEM/F12 supplemented with 0.3% bovine serum albumin (DF12-BSA), and inoculated with virus at an MOI of 1 in DF12-BSA for 50 minutes at 37°C.  Mock-infected controls were inoculated with DF12-BSA only.  Following inoculation, monolayers were washed once with DF12-BSA and incubated in DF12-BSA containing 0.5 μg/ml of TPCK-treated trypsin (Worthington Biochemical Corporation, Lakewood, NJ).

value: 2B-4 cells (clonal derivatives of Calu-3 cells)

tag: infection code

tag: sample material

value: Cells

tag: timepoint

tag: biological replicate


title: LD15_ctrl

tag: age

tag: tissue


title: LD12_ctrl


title: SCL008_NSP16_72h_2

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.


title: SCL008_NSP16_60h_3


title: SCL008_NSP16_72h_1


title: SCL008_NSP16_48h_3


title: SCL008_NSP16_24h_3


title: SCL008_NSP16_48h_2


title: SCL008_NSP16_48h_1


title: SCL008_NSP16_60h_1


title: SCL008_NSP16_12h_2


title: SCL008_NSP16_12h_1


title: SCL008_NSP16_36h_3


title: SCL008_NSP16_36h_1


title: SCL008_NSP16_24h_1


title: SCL008_NSP16_24h_2


title: with 110 mg/L pyrimethanil (IC50)_biological rep3

city: Lisboa

first: Cristina

middle: Anjinho

last: Viegas

address: Av Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Técnico

description: Gene expression data from cells incubated with the IC50 of pyrimethanil

hyb_protocol: 5 µg of fragmented aRNA was used in a 100-µl hybridization cocktail containing added hybridization controls. 80 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0003; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Scanned arrays were analyzed first with Affymetrix Expression Console software for quality control. Subsequent analysis was carried out with DNA-Chip Analyzer (dChip) 2010 (http://www.dchip.org, Wong Lab, Harvard) applying a probeset mask file excluding all probes on the array representing Schizosaccharomyces pombe transcripts. The arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method (Li and Wong, 2001). Normalized CEL intensities of the 9 arrays were used to obtain model-based gene expression indices based on a PM (Perfect Match)-only model (Li and Hung Wong, 2001). Replicate data for the same sample type were weighted gene-wise by using inverse squared standard error as weights. All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.2 .

organism: Saccharomyces cerevisiae

source_name: Cell population incubated with 110 mg/L pyrimethanil (IC50)

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Yeast Genome 2.0 Arrays, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in a 16h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix). Size distribution of the aRNA and fragmented aRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Exponential cell populations (OD640nm = 0.25 ± 0.05) of S. cerevisiae BY4741 were incubated in minimal growth medium (pH 6.5), at 30ºC, with orgital agitation (250 RPM) in each of the exposure conditions indicated above.

extract_protocol: Total RNA isolation was performed using the hot-phenol method (Koher & Domdey, 1991, Methods in Enzimology 194:398-405).

treatment_protocol: Cells were harvested by centrifugation (10000 rpm, 5 min, 0ºC) and immediately frozen in liquid nitrogen and stored at -80ºC until RNA extraction.

tag: strain

tag: cell population

value: Exponential cells (O.D.640nm = 0.25 ± 0.05)

value: with 110 mg/L pyrimethanil (IC50)


title: with 20 mg/L pyrimethanil (IC20)_biological rep3

description: Gene expression data from cells incubated with the IC20 of pyrimethanil

data_processing: Scanned arrays were analyzed first with Affymetrix Expression Console software for quality control. Subsequent analysis was carried out with DNA-Chip Analyzer (dChip) 2010 (http://www.dchip.org, Wong Lab, Harvard) applying a probeset mask file excluding all probes on the array representing Schizosaccharomyces pombe transcripts. The arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method (Li and Wong, 2001). Normalized CEL intensities of the 36 arrays were used to obtain model-based gene expression indices based on a PM (Perfect Match)-only model (Li and Hung Wong, 2001). Replicate data for the same sample type were weighted gene-wise by using inverse squared standard error as weights. All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.2 .

source_name: Cell population incubated with 20 mg/L pyrimethanil (IC20PYR)

treatment_protocol: Cells were harvested by centrifugation (10000 rpm, 3 min, 0ºC) and immediately frozen in liquid nitrogen and stored at -80ºC until RNA extraction.

value: with 20 mg/L pyrimethanil (IC20)


title: with 110 mg/L pyrimethanil (IC50)_biological rep2


title: with 110 mg/L pyrimethanil (IC50)_biological rep1


title: SCL008_NSP16_7h_2_B


title: SCL008_NSP16_7h_1_B


title: SCL008_Mock_72h_1_B

value: Mock


title: SCL008_Mock_60h_3


title: SCL008_NSP16_0h_2


title: SCL008_Mock_72h_2


title: SCL008_NSP16_36h_2


title: SCL008_NSP16_7h_3


title: SCL008_NSP16_12h_3


title: SCL008_NSP16_0h_3


title: SCL008_NSP16_0h_1


title: Hepatosplenic T-cell lymphoma case 4

description: Hybridized to Affymetrix CytoscanHD Array

hyb_protocol: DNA was purified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
CEL files generated by Affymetrix Command Console and CYCHP files generated byAffymetrix Chromosome Analysis Suite software (ChAS).  DNA copy number and allele analysis were performed using Affymetrix ChAS, which compares all hybridization intensities against a built-in reference data set
Hybridized to Affymetrix CytoscanHD array

source_name: tumor DNA

label_protocol: Biotin, affymetrix protocol for the  CytoScanHD

growth_protocol: No culture-just DNA from frozen tissue

extract_protocol: Qiagen kit for DNA extraction

treatment_protocol: no previous treatment

value: Hepatosplenic T-cell Lymphoma

tag: karyotype


title: Hepatosplenic T-cell lymphoma case 6


title: Hepatosplenic T-cell lymphoma case 8


title: Hepatosplenic T-cell lymphoma case 7


title: with 20 mg/L pyrimethanil (IC20)_biological rep2


title: without pyrimethanil (CT02 exp)_biological rep3

description: Gene expression data from cells incubated without pyrimethanil

source_name: Cell population incubated without pyrimethanil

value: without pyrimethanil (CT02 exp)


title: with 20 mg/L pyrimethanil (IC20)_biological rep1


title: without pyrimethanil (CT02 exp)_biological rep2


title: without pyrimethanil (CT02 exp)_biological rep1


title: SCL008_Mock_48h_2


title: SCL008_Mock_36h_3


title: SCL008_Mock_48h_1


title: SCL008_Mock_48h_3


title: SCL008_Mock_36h_2


title: SCL008_Mock_60h_1


title: SCL008_Mock_12h_2


title: SCL008_Mock_24h_2


title: SCL008_Mock_36h_1


title: SCL008_Mock_12h_3


title: SCL008_Mock_24h_1_B


title: SCL008_Mock_12h_1


title: ASC MB-Z

city: Chapel Hill

first: Mohanish

last: Deshmukh

state: NC

address: 7109E Neuroscience Research Building, 105 Mason Farm Road

department: Cell Biology and Physiology

institute: University of North Carolina

description: Pycard wild-type, SmoA1 (medulloblastoma strain) P20 cerebellum; Z

hyb_protocol: Overnight hybridization of two-color whole mouse genome 4x44K microarrays (Agilent Technologies) according to manufacturer recommendations.

scan_protocol: Agilent G2505C microarray scanner according to manufacturer recommendations.

data_processing: Raw data was processed and analyzed by Feature Extraction Software (Agilent Technologies).

source_name: Reference: pooled P16 wildtype cerebella

label_protocol: 1000 ng RNA per sample was labeled using the Quick Amp Labeling Kit (Agilent Technologies) per manufacturer instructions, 2 color amplification method

extract_protocol: Total RNA extracted by Trizol Reagent (Invitrogen)

tag: reference

value: pool of P16 wildtype cerebella

source_name: ASC WT-3

value: Pycard wild-type

value: SmoA1 (medulloblastoma strain)

value: P20 cerebellum


title: ASC MB-24

description: Pycard wild-type, SmoA1 (medulloblastoma strain) P20 cerebellum; 24

source_name: ASC WT-4


title: SCL008_Mock_7h_3


title: ASC MB-Q

description: Pycard knockout, SmoA1 (medulloblastoma strain) P20 cerebellum; Q

source_name: ASC KO-2

value: Pycard knockout


title: ASC MB-V

description: Pycard wild-type, SmoA1 (medulloblastoma strain) P20 cerebellum; V

source_name: ASC WT-2


title: SCL008_Mock_24h_3


title: SCL008_Mock_7h_1


title: skin_48h_susceptible_animal09

city: Bagé

last: Domingues

state: Rio Grande do Sul

address: Av. General Osório 1737/302

department: Animal health

country: Brazil

institute: Embrapa

description: Animal of the susceptible group

hyb_protocol: About 12.5ug of purified and fragmented aRNA were hybridized in Genechip Bovine Genome Array (Affymetrix) using GeneChip Hybridization Oven.

scan_protocol: After washed in GeneChip Fluidics Station 450 according to the manufactere's instructions, the GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Bos taurus

source_name: skin, 48 hous after infestation, tick susceptible animal

label_protocol: 3' IVT Express kit (Affymetrix) was used to the amplification and labeling from 50 ng of total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. After, the total RNA was purified using RNeasy mini kit (Qiagen) according to the manufacterer's instructions.

treatment_protocol: Skin biopsies were kept in RNAlater (Ambion) until the RNA extraction.

value: F2 population of Gyr (Bos indicus) X Holstein (Bos taurus)

tag: time

value: 48 hours after infestation

tag: phenotype

value: susceptible

value: skin


title: ASC MB-50

description: Pycard wild-type, SmoA1 (medulloblastoma strain) P20 cerebellum; 50

source_name: ASC WT-5


title: skin_48h_susceptible_animal11

description: Animal of the susceptible group


title: ASC MB-L

description: Pycard knockout, SmoA1 (medulloblastoma strain) P20 cerebellum; L

source_name: ASC KO-3


title: skin_48h_susceptible_animal10

description: Animal of the susceptible group


title: ASC MB-N

description: Pycard wild-type, SmoA1 (medulloblastoma strain) P20 cerebellum; N

source_name: ASC WT-1


title: ASC MB-39

description: Pycard knockout, SmoA1 (medulloblastoma strain) P20 cerebellum; 39

source_name: ASC KO-4


title: skin_48h_resistant_animal06

description: Animal of the resistant group

source_name: skin, 48 hous after infestation, tick resistant animal

value: resistant


title: SCL008_Mock_0h_3_B

tag: cell type

value: 2B-4 cells (clonal derivatives of Calu-3 cells)

value: Cells


title: ASC MB-P

description: Pycard knockout, SmoA1 (medulloblastoma strain) P20 cerebellum; P

source_name: ASC KO-1


title: skin_48h_susceptible_animal13

description: Animal of the susceptible group


title: SCL008_Mock_0h_2


title: skin_48h_susceptible_animal07

description: Animal of the susceptible group


title: skin_48h_resistant_animal05

description: Animal of the resistant group


title: SCL008_Mock_0h_1


title: SCL008_icSARS_60h_3

value: icSARS


title: SCL008_icSARS_48h_3


title: SCL008_icSARS_60h_2


title: skin_48h_resistant_animal03

description: Animal of the resistant group


title: skin_48h_resistant_animal02

description: Animal of the resistant group


title: skin_24h_susceptible_animal12

description: Animal of the susceptible group

source_name: skin, 24 hous after infestation, tick susceptible animal

value: 24 hours after infestation


title: SCL008_icSARS_72h_3


title: skin_24h_susceptible_animal08

description: Animal of the susceptible group


title: SCL008_icSARS_60h_1


title: SCL008_icSARS_72h_1


title: skin_24h_susceptible_animal11

description: Animal of the susceptible group


title: SCL008_icSARS_72h_2


title: skin_48h_resistant_animal01

description: Animal of the resistant group


title: SCL008_icSARS_48h_2


title: skin_24h_resistant_animal06

description: Animal of the resistant group

source_name: skin, 24 hous after infestation, tick resistant animal


title: skin_24h_susceptible_animal10

description: Animal of the susceptible group


title: skin_24h_susceptible_animal09

description: Animal of the susceptible group


title: skin_24h_resistant_animal04

description: Animal of the resistant group


title: skin_24h_resistant_animal05

description: Animal of the resistant group


title: SCL008_icSARS_48h_1


title: SCL008_icSARS_36h_3_B


title: SCL008_icSARS_36h_1


title: SCL008_Mock_60h_2

value: Mock


title: skin_24h_resistant_animal03

description: Animal of the resistant group


title: SCL008_icSARS_36h_2


title: SCL008_icSARS_12h_1


title: SCL008_icSARS_7h_3


title: SCL008_icSARS_12h_2


title: skin_24h_resistant_animal01

description: Animal of the resistant group


title: skin_24h_resistant_animal02

description: Animal of the resistant group


title: SCL008_icSARS_7h_1


title: SCL008_icSARS_24h_2


title: SCL008_icSARS_24h_1


title: SCL008_icSARS_24h_3


title: skin_0h_susceptible_animal11

description: Animal of the susceptible group

source_name: skin, before infestation, tick susceptible animal

value: before infestation


title: SCL008_icSARS_7h_2


title: SCL008_icSARS_12h_3


title: skin_0h_susceptible_animal10

description: Animal of the susceptible group


title: skin_0h_resistant_animal02

description: Animal of the resistant group

source_name: skin, before infestation, tick resistant animal


title: skin_0h_resistant_animal03

description: Animal of the resistant group


title: skin_0h_susceptible_animal09

description: Animal of the susceptible group


title: SCL008_ExoNI_48h_2

value: ExoNI


title: SCL008_ExoNI_7h_3_B


title: SCL008_icSARS_0h_3


title: SCL008_ExoNI_24h_1


title: SCL008_ExoNI_72h_2


title: SCL008_ExoNI_60h_1


title: SCL008_ExoNI_7h_1_B


title: SCL008_ExoNI_36h_2


title: SCL008_ExoNI_60h_3


title: SCL008_icSARS_0h_1


title: skin_24h_susceptible_animal13

description: Animal of the susceptible group


title: skin_0h_resistant_animal04

description: Animal of the resistant group


title: SCL008_ExoNI_12h_2


title: SCL008_ExoNI_48h_3


title: SCL008_ExoNI_12h_1


title: SCL008_ExoNI_72h_1


title: skin_0h_resistant_animal05

description: Animal of the resistant group


title: SCL008_ExoNI_24h_3


title: SCL008_ExoNI_48h_1


title: skin_0h_resistant_animal01

description: Animal of the resistant group


title: SCL008_ExoNI_7h_2


title: SCL008_ExoNI_24h_2


title: SCL008_ExoNI_36h_3


title: SCL008_ExoNI_12h_3


title: SCL008_icSARS_0h_2


title: SCL008_ExoNI_60h_2


title: SCL008_ExoNI_72h_3


title: SCL008_ExoNI_36h_1


title: SCL008_ExoNI_0h_1


title: SCL008_ExoNI_0h_3


title: BCR-ABL1-control rep 2

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

institute: University of Cambridge

description:
BCR-ABL1-1074-2
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: LIN-CB

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

growth_protocol: Transduced lineage depleted cord blood cells were grown in liquide culture (M9 media)

extract_protocol: RNA was extracted with the Arcturus® Picopure RNA® isolation kit followed by DNase I treatment. Quality control was performed with Agilent Bioanalyser

value: lineage depleted cord blood cells

tag: culture

value: liquid culture day 11

tag: transduction 1

tag: transduction 2

value: control


title: BCR-ABL1-Ik6 rep 4

description:
BCR-ABL1-1074-Ik6-4
replicate 4


title: BCR-ABL1-control rep 4

description:
BCR-ABL1-1074-4
replicate 4


title: control-Ik6 rep 4

description:
MiG-1074-Ik6-4
replicate 4


title: control-Ik6 rep 2

description:
MiG-1074-Ik6-2
replicate 2


title: control-Ik6 rep 1

description:
MiG-1074-Ik6-1
replicate 1


title: BCR-ABL1-Ik6 rep 3

description:
BCR-ABL1-1074-Ik6-3
replicate 3


title: control-control rep 2

description:
MiG-1074-2
replicate 2


title: BCR-ABL1-Ik6 rep 2

description:
BCR-ABL1-1074-Ik6-2
replicate 2


title: control-control rep 4

description:
MiG-1074-4
replicate 4


title: SCL008_ExoNI_0h_2


title: BCR-ABL1-control rep 3

description:
BCR-ABL1-1074-3
replicate 3


title: control-Ik6 rep 3

description:
MiG-1074-Ik6-3
replicate 3


title: BCR-ABL1-Ik6 rep 1

description:
BCR-ABL1-1074-Ik6-1
replicate 1


title: 2nd_63_hours

city: Heidelberg

first: Anton

last: Shostak

address: Im Neuenheimer Feld 328

department: Circadian Rhythms and Molecular Clocks

country: Germany

institute: Heidelberg University Biochemistry Center (BZH)

hyb_protocol: Hybridization, blocking, and washing was performed following the Agilent instructions

scan_protocol: Scanning of arrays was eprformed using Agilent DNA Microarray Scanner and Agilent Scan control software (v A.8.4.1.)

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) Protocol: GE2_107_Sep09 with modifications; Background Substraction Method - Local Background; Detrend on Replicates Only - False; Robust Neg Ctrl Stats? - True; Choose universal error, or the most conservative - Use Universal Error Model; Dye Normalization Probe Selection Method/Variable Rank Tolerance - True; Max Number Ranked Probes - -1; Normalization Correction Method - Lowess Only; Spikein Target Used - False

source_name: U2OS cells

label_protocol: Samples were labeled with the Two-Color Low Input Quick Labeling kit (Agilent) according to the provided protocol. Samples were labeled in two colors to allow a comparison of RNA amounts from each of the 16 time points (labeled individually with Cyanine-5 (Cy5)) to the average of all time points (labeled together with Cy3).

growth_protocol: U2OS cells were temperature entrained at alternating 12 h, 33°C and 12 h, 37°C cycles. Medium changes were carried out at the transition from 33°C to 37°C.

extract_protocol: Cell pellets were harvested every 3 hours.  RNA was isolated using the RNeasy kit (Qiagen) following the manufacturers instructions.

treatment_protocol: For the1st time course, cells were pre-incubated under temperature entrainment for 4 days. On day 5, 160,000 cells/well were seeded in 35 mm dishes and grown for 5 more days under temperature entrainment until they reached confluence. Growth medium was exchanged directly before the cells were released to constant 37°C. 24 h and 48 h after medium change cells were harvested at 3 h intervals for 24 h. The 2nd time course was carried out similarly, with the exception that cells were incubated in two incubators with opposite temperature rhythms and harvested for 12 h on two days.

tag: cell line

value: epithelial

value: bone

source_name: pooled RNA of all time points of experiment 2


title: 2nd_60_hours


title: 2nd_66_hours


title: BCR-ABL1-control rep 1

description:
BCR-ABL1-1074-1
replicate 1


title: 2nd_69_hours


title: control-control rep 3

description:
MiG-1074-3
replicate 3


title: 2nd_45_hours


title: 2nd_57_hours


title: 2nd_51_hours


title: control-control rep 1

description:
MiG-1074-1
replicate 1


title: 2nd_39_hours


title: 2nd_27_hours


title: 2nd_48_hours


title: 2nd_54_hours


title: 1st_66_hours

source_name: pooled RNA of all time points of experiment 1


title: 2nd_36_hours


title: 2nd_24_hours


title: LowResponderSoleus3

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

institute: University of Stirling

hyb_protocol: The arrays were incubated at 60°C for 16 hours in a hybridisation oven.

scan_protocol: After hybridisation the slides were washed briefly at 60oC using buffer A, rinsed in buffer B, followed by a 2 minute wash in buffer B, a 2 minute wash in buffer C with a final brief fixing rinse in 99% ethanol. The arrays were dried by centrifugation (1000rpm for 5 minutes) followed by immediate scanning using a GenePix 4200A microarray scanner. Raw scan data were analysed using GenePix Pro 6® software.

data_processing: Raw data from the array scanner (gpr) files were loaded in the limma suite in R for background subtraction and quantile normalisation.

organism: Rattus norvegicus

source_name: Soleus muscle from exercise low responder rat

label_protocol: Samples were labelled using Exiqon’s miRCURY LNA array labelling kit (Vedbæk, Denmark): After treatment with calf alkaline phosphatase, 1μg of total RNA was incubated with the Hy3 dye, labelling enzyme and spike-in microRNAs, in a total volume of 12.5μl for 1 hour at 16oC. The enzyme was then heat-inactivated at 65oC for 15 minutes. The samples were incubated at 95oC for 2 minutes protected from light. Labelled samples were made up to 50μl by addition of 37.5μl of hybridization buffer. The samples were briefly spun down and then loaded onto a MAUI hybridization station (BioMicro Inc. Salt Lake City, USA).

growth_protocol: Soleus or left ventricle muscle was taken from high responder (HRT) or low responder (LRT) rats.

extract_protocol: RNA was extracted using QIAzol lysis reagent (Qiagen, USA) and purified using RNeasy cleanup kit (Qiagen, USA).

treatment_protocol: After extraction muscle was snap frozen in liquid nitrogen and stored at -80oC prior to further processing and analysis.

value: soleus muscle

value: low responder


title: 2nd_42_hours


title: HighResponderSoleus3

source_name: Soleus muscle from exercise high responder rat

value: high responder


title: LowResponderSoleus1


title: LowResponderLeftVentricle2

source_name: Left ventricle muscle from exercise low responder rat

value: left ventricle muscle


title: LowResponderLeftVentricle1


title: HighResponderSoleus2


title: 1st_69_hours


title: LowResponderLeftVentricle3


title: 1st_63_hours


title: 2nd_30_hours


title: 2nd_33_hours


title: HighResponderSoleus1


title: HighResponderLeftVentricle1

source_name: Left ventricle muscle from exercise high responder rat


title: HighResponderLeftVentricle3


title: LowResponderSoleus2


title: HighResponderLeftVentricle2


title: 1st_54_hours


title: 1st_51_hours


title: 1st_57_hours


title: 1st_60_hours


title: 1st_48_hours


title: BI-3

city: Hangzhou

first: Yun

last: Xiao

address: Yuhangtang Road

institute: Zhejiang University

description: HepG2 cells

hyb_protocol: Labeled cDNA was hybridized to Affymetrix：GeneChip® PrimeView™ Human Gene Expression Array. Array hybridization and wash were performed using GeneChip Hybridization, Wash and Stain Kit (Affymetrix) in Hybridization Oven 645 (Affymetrix) and Fluidics Station (Affymetrix) by following the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000.

data_processing: Slides were scanned by GeneChip® Scanner 3000 and Command Console Software 3.1 with default settings. Spike-in control transcripts were monitored to verify hybridization integrity.

source_name: hepatoma

label_protocol: Total RNA were amplified, labeled, and purified using GeneChip® 3’IVT Express Kit (Affymetrix) according to the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: R-HepG2 cells were cultured on tissue culture dishes in DMEM supplemented with 10% FCS, 50 mg/mL penicillin and 50 mg/mL streptomycin at 37 °C with 5% CO2.

extract_protocol: Total RNA was extracted using TRIZol Reagent (Life technologies) and purified using RNeasy Mini kit (QIAGEN), following manufacturers’ protocols.

treatment_protocol: R-HepG2 cells were treated with 1 ml serum-free DMEM overnight, after which the cell culture medium was replaced with 1mL DMEM, 1 ml insulin or BI solution (total insulin concentration was identical, 40 ug/ml). The cells were incubated at 37 °C and 5% CO2 for 4 h and washed using phosphate-buffered saline (PBS, pH = 7.4) and 0.03% ethylene diamine tetraacetic acid (EDTA) to remove any residual complexes.

value: hepatoma carcinoma cell

value: liver