title: Maize_Control_Root_14d_BioRep2

source_name: LCM of maize control root cells, 14 days

treatment_protocol: Two-week-old Zea mays seedlings planted on a 2:1 sand:turface mixture were inoculated with 1,000 M. incognita stage 2 juveniles near the root. Fourteen days after inoculation, the non-infested portions of the roots were harvested and frozen in cryomatrix. An area of approximately 13,000,000 um2 (~75-150 cells) was captured from non-infested regions of the infested root. Control root cells were catapulted using the AutoLPC method directly to P.A.L.M. Adhesive caps.


title: Maize_Control_Root_14d_BioRep3

status: Public on Apr 28 2012

type: RNA

city: Gainesville

first: Lauren

last: McIntyre

state: FL

address: 2033 Mowry Rd

department: Department of Molecular Genetics and Microbiology

country: USA

institute: University of Florida

description: cDNA amplified from total RNA isolated from control root cells.

hyb_protocol: The hybridization mixture was prepared according to NuGEN and Affymetrix procedures and hybridized to GeneChip© Maize Genome Arrays.

scan_protocol: GeneChips were scanned at the University of Pennsylvania School of Medicine Microarray Facility according to standard manufacturer protocols.

data_processing: Data were quantified with the Expression Console (Affymetrix) software application using the MAS5 algorithm.

label: biotin

molecule: total RNA

organism: Zea mays

label_protocol: NuGEN FL module.

growth_protocol: Zea mays seeds were sown in a 2:1 sand:turface mix and grown in a greenhouse for 2 weeks prior to infestation with stage 2 Meloidogyne incognita juveniles.

extract_protocol: Total RNA samples were isolated using the PicoPure RNA Isolation Kit (Arcturus, Mountain View, USA). RNA was amplified according to NuGEN WT-Ovation Pico kit instructions.

tag: treatment

value: Meloidogyne incognita infestation

tag: time

value: 14 days post challenge with M. incognita

tag: tissue

value: laser-captured control root cells

tag: genotype

value: IS A A188 C B73 Cross

tag: sample size


title: Australian Twin Registry monozygotic twin6b depression white blood cells12

type: genomic

city: Toronto

first: Art

last: Petronis

state: Ontario

address: 250 College St

department: Campbell Family Mental Health Research Institute

country: Canada

institute: Centre for Addiction and Mental Health

description: Australian Twin Registry monozygotic twin6b vs. common reference pool

hyb_protocol: The enriched PCR products were hybridized overnight at 48°C onto the 8.1k human CpG island microarray (Microarray Facility, University Health Network, Toronto) as previously described (Schumacher, A., et al. (2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic acids research 34, 528-542.) .

scan_protocol: The arrays were scanned using the Genepix 4000B scanner and Genepix Pro 6.0 (Axon Instruments). The automated photomultiplier (PMT) function of the scanner was used to optimize signal intensity and channel balances.

data_processing: Linear Models for Microarray Data (LIMMA) package (Bioconductor) for R was used for background correction, normalization, and to extract the signal intensities. Briefly, normexp was used for background correction, print-tip loess was used for within-array normalization, and Gquantile was used for between-array normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: white blood cells, depression

label_protocol: 1 μg of purified enriched PCR products were fluorescently labelled with Cy3 (Roche) for the reference and with Cy5 (Roche) for the sample, as previously described (Schumacher, A., et al. (2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic acids research 34, 528-542.) .

extract_protocol: The samples were first digested using proteinase K (20mg/ml) and lysis buffer mixture at 55°C overnight.  A mixture of phenol, chloroform, and iso-amyl alcohol (in ratios of 25:24:1) was used to remove the proteins, followed by two times chloroform wash, precipitation of DNA using cold isopropanol, and a final wash using 70% ethanol.  After the extraction, the DNA samples were suspended in 0.1M Tris-EDTA buffer and were kept in -80°C for storage prior to use.  The purity and the concentrations of DNA were checked using a UV spectrophotometer (Nanodrop ND1000).

tag: cell type

value: white blood cells

tag: disease status

value: depression

tag: individual

tag: twin pair

source_name: white blood cells, common reference pool

tag: sample type

value: common reference pool


title: Australian Twin Registry monozygotic twin4b control white blood cells8

description: Australian Twin Registry monozygotic twin4b vs. common reference pool

source_name: white blood cells, control

value: control


title: Maize_Control_Root_14d_BioRep1


title: Australian Twin Registry monozygotic twin2b depression white blood cells4

description: Australian Twin Registry monozygotic twin2b vs. common reference pool


title: Australian Twin Registry monozygotic twin5b control white blood cells10

description: Australian Twin Registry monozygotic twin5b vs. common reference pool


title: Control, Biological Replicate 1 [Exosc9i]

city: San Diego

first: Devendra

middle: S

last: Mistry

state: CA

address: 9500 Gilman Drive MC#0869

department: Medicine

institute: University of California-San Diego

description: Cell transduced with Control shRNA and then nucleofected with control siRNA

hyb_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)

scan_protocol: Affymetrix HG-U133 2.0 plus arrays were performed at the UCSD Genechip Microarray Core Facility.

data_processing:
For gene expression analysis, arrays were RMA normalized and differential expression was defined using the following filters: Significance Analysis of Microarrays 3.0(Tusher et al., 2001) with a false discovery rate less than 5%, an average fold change ≥ 1.5 at any time point, and an average raw expression intensity ≥ 100 at any time point. Hierarchical clustering and heat map generation were performed as previously described(Sen et al., 2010). For future analyses, Affymetrix probe IDs were converted to unique Unigene IDs. GO term enrichment was performed using DAVID analysis(Huang da et al., 2009) with the total set of genes on the appropriate microarray as the background.
The two Control samples, although represent two CEL files, are submitted as 4 Samples since they were normalized twice - once with the Exosc9i Samples, and also with the Exosc9i+GRHL3i Samples.

label: Biotin

source_name: Control Cells

growth_protocol: Human Primary Keratinocytes were grown in self-renewing condition using KSF-M (GIBCO-BRL) supplemented with epidermal growth factor (EGF) and bovine pituitary extract (BPE).

extract_protocol: Total RNA from cells was extracted using the RNeasy mini kit according to manufacturer's protocol.

treatment_protocol: EXOSC9 gene was knocked down using retroviral delivery of shRNA in indicated samples. GRHL3 was knocked down through nucleofaction of siRNA in indicated samples.

value: Human Primary Keratinocytes


title: Australian Twin Registry monozygotic twin5a depression white blood cells9

description: Australian Twin Registry monozygotic twin5a vs. common reference pool


title: Control, Biological Replicate 2 [Exosc9i]

label_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)


title: Australian Twin Registry monozygotic twin3a depression white blood cells5

description: Australian Twin Registry monozygotic twin3a vs. common reference pool


title: Australian Twin Registry monozygotic twin2a control white blood cells3

description: Australian Twin Registry monozygotic twin2a vs. common reference pool


title: Australian Twin Registry monozygotic twin6a control white blood cells11

description: Australian Twin Registry monozygotic twin6a vs. common reference pool


title: Exosc9i Biological Replicate 1

description: Cell transduced with EXOSC9 shRNA and then nucleofected with control siRNA

source_name: EXOSC9 knocked down cells


title: Australian Twin Registry monozygotic twin1a control white blood cells1

description: Australian Twin Registry monozygotic twin1a vs. common reference pool


title: HTR 8 (rep1)

status: Public on Apr 27 2012

city: Jena

first: Udo

middle: R.

last: Markert

address: Bachstraße 18

department: Department of Obstetrics

country: Germany

institute: Universitätsklinikum Jena

description: Test

data_processing:
SDS software (Applied Biosystems) was used to collect data. Data were processed using DataAssist v3.0 (Applied Biosystems).
Fold Change was calculated against First trimester Trophoblasts [linked as supplementary file on Series record].

label: FAM

source_name: Cell line

label_protocol: 100 ng total RNA per sample was reverse-transcribed using Megaplex primers, sets A and B (Applied Biosystems). cDNA was pre-amplified for 12 cycles with Megaplex Pre-Amp primers. Sets A and B (Applied Biosystems) then diluted to 100 ul. Manufacturer´s protocol was followed throughout.

growth_protocol:
Cells cultures were performed at 10^6 cells/175 cm2 flask, and maintained under standard conditions (37ºC, 5% CO2, humid atmosphere) in Ham’s F-12 Nutrient Mixture with L-glutamine (GIBCO, Paisley, UK) or RPMI Medium (GIBCO) (HTR-8 cells) supplemented with 10 % heat-inactivated fetal calf serum (FCS; GIBCO) and 1 % penicillin/streptomycin antibiotic solution (GIBCO).
Isolation protocol: Trophoblast isolation was performed using a modified Kliman method that is detailed described by Stenqvist. Am J Reprod Immunol, 2008. 60(1): p. 33-42.

extract_protocol: Cells were seeded in 12-well plates, allowed to attach overnight and serum deprived for at least two hours. Total RNA was isolated by mirVana isolation kit (Life Technologies, Darmstadt, Germany), according to the manufacturer's protocol.

tag: cell line

value: HTR 8

tag: type of cells

value: Immortalized cell line


title: HTR 8 (rep2)

description: Test


title: Australian Twin Registry monozygotic twin4a depression white blood cells7

description: Australian Twin Registry monozygotic twin4a vs. common reference pool


title: Control, Biological Replicate 2 [Exosc9i+GRHL3i]


title: Australian Twin Registry monozygotic twin3b control white blood cells6

description: Australian Twin Registry monozygotic twin3b vs. common reference pool


title: RWh11_Week12postSIV_PBMCs

city: Atlanta

first: RAVI

last: DYAVAR SHETTY

state: Georgia

address: 954 Gatewood RD NE

department: Microbiology and Immunology

institute: emory university

hyb_protocol: The biotinylated cRNAs were cleaned up, fragmented, and hybridized to the rhesus macaque expression arrays at 45°C for 16 h with constant rotation at 60 rpm. The gene chips were then washed and stained with Affymetrix fluidics stations 450.

scan_protocol: The gene chips were scanned on Affymetrix scanner 3000

data_processing:
The images are processed to collect raw data with GeneChip Operating Software (GCOS) 1.4.
.CEL files were loaded in to Genespring GX10 software, data was preprocessed with RMA (Robost Multichip Analaysis) and  per gene normaization was performed by setting measurements to median.Only those transcripts that were called present or marginal in at least one of the same condition were taken into account. Genes with statistically significant differences between the SIV infected, PD-1 antibody treated versus SIV infected, Control antibody treated group of Rhesus macaques were classified(One way ANOVA, p-value cutoff 0.05) with minimum of 1.5 fold change difference.

organism: Macaca mulatta

source_name: SIV infected, PD-1 antibody treated Rhesus macaque PBMCs

label_protocol: Biotinylated complementary RNAs (cRNAs) were synthesized in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix by in vitro transcription (IVT) reaction.

extract_protocol: RNA was extracted with Rneasy mini kit (Qiagen)

treatment_protocol: Rhesus macaques were infected intravenously with 200 TCID50 of SIVmac251 strain. The SIV-negative animals used here were sacrificed due to neurological and mental problems but were checked to ensure no history of bowel problems.

tag: disease state

value: week 12 post SIV infected

value: day 14 post PD-1 antibody

value: PBMCs


title: Australian Twin Registry monozygotic twin1b depression white blood cells2

description: Australian Twin Registry monozygotic twin1b vs. common reference pool


title: RDb11_Week12postSIV_PBMCs


title: RBm11_Week12postSIV_PBMCs

source_name: SIV infected, Control (un treated) Rhesus macaque PBMCs

value: day 14 post untreated


title: RJi_Week12postSIV_PBMCs

source_name: SIV infected, Control antibody treated Rhesus macaque PBMCs

value: day 14 post Control antibody


title: RIg11_Week12postSIV_PBMCs


title: AC1-M59 (rep 2)

description: Test

value: Hybridome


title: RFe11_Week12postSIV_PBMCs


title: ACH-3P (rep2)

description: Test


title: AC1-M59 (rep 1)

description: Test


title: RIg11_SIVnegative_PBMCs

source_name: SIV negative Rhesus macaque PBMCs

value: SIV negative


title: ACH-3P (rep1)

description: Test


title: RBm11_SIVnegative_PBMCs


title: RGj11_SIVnegative_PBMCs


title: RJM11_SIVnegative_PBMCs


title: Third Trimester Trophoblast 3

description: Test

source_name: Placenta tissue

value: placenta

value: Isolated trophoblasts from third trimester placenta


title: JEG-3 cells (rep2)

description: Test

value: Choriocarcinoma cell line


title: Third Trimester Trophoblast 2

description: Test


title: JEG-3 cells (rep3)

description: Test


title: JEG-3 cells (rep1)

description: Test


title: Third Trimester Trophoblast 1

description: Test


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 9 wk of age, replicate 4

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

description: Sample 20

hyb_protocol: A cDNA spotted glass slide (Del-Mar 14K Chicken Integrated Systems microarray) was pre-treated for 45 min at 42 degrees Celsius in pre-hybridization solution containing 5x SSC, 0.1 % SDS and 1 % BSA and followed by dipping for 5 min in deionized water and dry spinning for 5 min at 1,000 x g. The labeled cDNA was dried down (Speed Vac) and reconstituted prior to hybridization in a 30 microliter volume of pre-warm DIG Easy Hyb solution (Roche Diagnostics; Indianapolis, IN). The two target samples (Alexa 555 and Alexa 647 labeled) were pooled and mixed with 2.5 microliter of 10 mg/ml Yeast tRNA, 2.5 microliter of 10 mg/ml salmon testes DNA (Sigma, Louis, MO) and 2.5 microliter of 1 microgram/microliter of pSport 6.1(Invitrogen) vector (PCR amplified product from “empty” pSport 6.1 vector sequence). The target mixture was denatured for 2 min at 94 degrees Celsius, cooled at room temperature, carefully loaded onto the middle of a pre-treated mircoarray slide held in a hybridization chamber (Corning #2551, Lowell, MA) and overlaid with a 22 x 65 mm LifterSlip (Erie Scientific, Portsmouth, NH). The sealed hybridization chamber was incubated overnight (approximately 16 hours) at 42 degrees Celsius in a water bath under a light-tight box. On the following day, slides were sequentially washed with 1 x SSC, 0.2% SDS, and 0.5% DTT at 50 degrees C for 10 min, then 0.1 x SSC, 0.2% SDS, and 0.5% DTT for 5 min at room temperature, and finally 0.1 x SSC and 0.5% DTT for 1 min at room temperature, with nitrogen gas bubbled through each of the washes to prevent interference from ozone. The slides were subsequently rinsed in dH2O and dried by centrifugation. Slides were stored until scanning in individual 50 ml tubes covered in aluminum foil and filled with nitrogen gas.

scan_protocol: Each microarray slide was scanned using a GenePix 4000B microarray scanner (Molecular Devices; Sunnyvale, CA) set at 635 nm for Alexa647 and 532 nm for Alexa555 after adjustment of the PMT count ratio (635/532) to 1. Two high-resolution TIFF images (embedded in a single file) were generated for each slide.

data_processing: Image analysis was performed on high-resolution TIFF images using GenePix Pro 4.1 (Molecular Devices, Sunnyvale, CA). The results of image analysis [GenePix Report (GPR) files] were automatically merged with Excel files containing the clone identification number/plate address and gene name/function (from the highest BLAST score). Fluorescence intensities were analyzed in LIMMA (version 3.4.5) package R (R version 2.11.1) [Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3] producing M-values (log-2 expression ratios) and A-values (average log-2 expression values). Values in the sample data table are the loess-normalized log2 ratio of (Alexa 647 loess adjusted median/Alexa 555 loess adjusted median). The values are based on median intensity values (not background corrected) for Alexa 555 and Alexa 647.

label: Alexa Flour 647

organism: Gallus gallus

label_protocol: Twenty micrograms of total RNA were indirectly labeled using SuperScript Plus Indirect cDNA Labeling System (Invitrogen, Carlsbad, CA). Briefly, the first strand cDNA synthesis was performed in a 30 microliter final volume containing 1x first-strand buffer, 5 micrograms of anchored oligo(dT)20, DTT, dNTP mix (including aminoallyl- and aminohexyl-modified nucleotides), 40 U of RNaseOUT and 800 U of SuperScript III reverse transcriptase with an incubation at 46 degrees Celsius for 3 hours. The original RNA was destroyed by NaOH hydrolysis and followed by neutralization with HCl. The cDNAs were purified using a low-elution volume spin cartridge (Invitrogen; Carlsbad, CA) and labeled with either Alexa Fluor 555 or Alexa Fluor 647 succinimidyl ester in the dark at room temperature for 2 hours. After purification of labeled cDNAs with a low-elution-volume spin cartridge, the efficiency of dye incorporation was determined using the Microarray Module on the NanoDrop ND-1000 spectrophotometer and the Base:Dye Ratio Calculator on the Invitrogen website.

growth_protocol: Standard broiler chicken growth protocol

extract_protocol: Total RNA was extracted using a RNeasy Midi kit according to the manufacturer’s protocol (Qiagen; Valencia, CA). The RNA concentration was determined with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies; Wilmington, DE). RNA integrity was examined using a RNA 6000 Nano Assay kit and the Model 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA).

treatment_protocol: Divergently selected on abdominal fat weight (FL genotype) for seven generations.

tag: line

value: Adipose FL cockerel

tag: age

value: 9 week

value: abdominal adipose

label: Alexa Flour 555

value: Adipose LL cockerel


title: rpfF mutant vs. wild type strain at 25 h

city: Lake Alfred

first: Yinping

last: Guo

address: 700 Experiment station road

department: Microbiology and cell science; Citrus research and education center

institute: Xanthomonas axonopodis pv. citri

description:
rpfF25/W25
This Sample represent 4 biological replicates, including 2 dye swaps.

Raw data files:
Cy3=wild type, Cy5=mutant: *_2_1.txt, *_2_3.txt
Cy5=wild type, Cy3=mutant: *_2_2.txt, *_2_4.txt

hyb_protocol: The microarray analysis was performed using the Agilent 8x15k XAC genome array.  Four independent biological replicates were performed for two time-point comparisons with a dye-swap design.  A total of 300 ng of labeled cDNA per sample was used for the hybridization. A dye swap was performed to remove any bias from the labeling dyes. Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies, Santa Clara, CA) according to the user’s manual and was done at hybridization oven for 17.5hr at 65°C.  The arrays were washed according to the manufacturer’s recommended protocols. Briefly, arrays were washed with Gene Expression Wash Buffer 1/0.005% Triton-102 for 1min at room temperature and then washed with 37°C warmed Gene Expression Wash Buffer 2/0.005% Triton-102  for 1 min and dried by Agilent Stabilization and Dying Solution.

scan_protocol: The arrays were scanned using a dual-laser DNA microarray scanner (Model G2505C) (Agilent Technologies, Santa Clara, CA). The data were extracted from scanned images using Feature Extraction 10.1.1.1 software (Agilent Technologies, Santa Clara, CA).

data_processing: The raw data were imported into the R environment and statistical tests were performed using BioConductor statistical software. Data preprocessing and normalization were performed using the Linear Models for Microarray Data (LIMMA) package. Raw mean signal intensities from all microarray spots were background corrected and normalized using within-array lowess approach.  Log2-transformed values were used for statistical analysis. Histograms, box plots and pair-wise scatter plots were generated to examine data quality and comparability. A linear modeling approach and the empirical Bayes statistics as implemented in the limma package were then employed for differential expression analysis.  The p-values were adjusted using the Benjamini and Hochberg method, designated as FDR.

organism: Xanthomonas citri pv. citri str. 306

source_name: wild type strain growing in XVM2 medium at 25 h

label_protocol: Labeled cDNA was generated using the Fairplay III microarray labeling kit (Agilent Technologies, Santa Clara, CA). Five ug of total RNA input was used to generate labeled cDNA according to the manufacturer’s protocol. Briefly, cDNA was synthesized from 5ug of the total RNA with AffinityScript HC and random primer, and then modified cDNA was labeled with either Cy3 or Cy5. Labeled cDNA was purified following the manufacturer's instructions.

growth_protocol: The rpfG, rpfC and rpfF deletion mutants were constructed by standard cloning and double cross-over homologous recombination. The mutants and wild type strain 306 were grown in XVM2 medium with shaking at 200 rpm at 28°and samples of culture were collected at 11 h and 25 h according to the growth curve in XVM2. RNA was stabilized immediately by mixing bacterial culture with two volumes of RNAprotect bacterial reagent (Qiagen, Valencia, CA) and incubated at room temperature for 5 min. Bacterial cells were centrifuged at 5000×g for 10 min and cell pellets were used for RNA extraction.

extract_protocol: Cell pellets were treated with proteinase K and lysozyme, and RNA extractions were performed using the RNeasy mini kit (Qiagen, Valencia, CA). Contaminating genomic DNA was removed from the RNA by treatment with the TURBO-DNA free kit (Ambion, Austin, TX). RNA quantity was initially determined on a ND-8000 Nanodrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: strain/background

value: wild type

tag: sampling time

organism: Xanthomonas citri

source_name: rpfF mutant growing in XVM2 medium at 25 h

value: rpfF deletion mutant


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 11 wk of age, replicate 2

description: Sample 22

value: 11 week


title: rpfF mutant vs. wild type strain at 11 h

description:
rpfF11/W11
This Sample represent 4 biological replicates, including 2 dye swaps.

Raw data files:
Cy3=wild type, Cy5=mutant: *_1_1.txt, *_1_3.txt
Cy5=wild type, Cy3=mutant: *_1_2.txt, *_1_4.txt

source_name: wild type strain growing in XVM2 medium at 11 h

source_name: rpfF mutant growing in XVM2 medium at 11 h


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 9 wk of age, replicate 2

description: Sample 18


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 11 wk of age, replicate 1

description: Sample 21


title: First Trimester Trophoblast, placenta3

description: Normalizer

value: Isolated trophoblasts from first trimester placenta


title: First Trimester Trophoblast, placenta2

description: Normalizer


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 11 wk of age, replicate 4

description: Sample 24


title: First Trimester Trophoblast, placenta1

description: Normalizer


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 9 wk of age, replicate 1

description: Sample 17


title: rpfC mutant vs. wild type strain at 11 h

description:
rpfC11/W11
This Sample represent 4 biological replicates, including 2 dye swaps.

Raw data files:
Cy3=wild type, Cy5=mutant: *_1_1.txt, *_1_3.txt
Cy5=wild type, Cy3=mutant: *_1_2.txt, *_1_4.txt

source_name: rpfC mutant growing in XVM2 medium at 11 h

value: rpfC deletion mutant


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 11 wk of age, replicate 3

description: Sample 23


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 9 wk of age, replicate 3

description: Sample 19


title: rpfG mutant vs. wild type strain at 25 h

description:
rpfG25/W25
This Sample represent 4 biological replicates, including 2 dye swaps.

Raw data files:
Cy3=wild type, Cy5=mutant: *_2_1.txt, *_2_3.txt
Cy5=wild type, Cy3=mutant: *_2_2.txt, *_2_4.txt

source_name: rpfG mutant growing in XVM2 medium at 25 h

value: rpfG deletion mutant


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 7 wk of age, replicate 1

description: Sample 13

value: 7 week


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 7 wk of age, replicate 3

description: Sample 15


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 5 wk of age, replicate 4

description: Sample 12

value: 5 week


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 3 wk of age, replicate 3

description: Sample 7

value: 3 week


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 3 wk of age, replicate 1

description: Sample 5


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 7 wk of age, replicate 4

description: Sample 16


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 5 wk of age, replicate 3

description: Sample 11


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 5 wk of age, replicate 2

description: Sample 10


title: rpfC mutant vs. wild type strain at 25 h

description:
rpfC25/W25
This Sample represent 4 biological replicates, including 2 dye swaps.

Raw data files:
Cy3=wild type, Cy5=mutant: *_2_1.txt, *_2_3.txt
Cy5=wild type, Cy3=mutant: *_2_2.txt, *_2_4.txt

source_name: rpfC mutant growing in XVM2 medium at 25 h


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 3 wk of age, replicate 4

description: Sample 8


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 7 wk of age, replicate 2

description: Sample 14


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 3 wk of age, replicate 2

description: Sample 6


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 5 wk of age, replicate 1

description: Sample 9


title: 581T_Macro [PICO WTA]

city: Bronx

first: Miao

last: Shi

state: NY

address: 1301 Morris Park ave

institute: Albert einstein College of Medicine

description: Macro Samples amplified with PICO WTA system

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the CHP files.

label_protocol: 100ng total RNA was amplified using Ambion WT Expression Kit following the manufacturer’s instructions. 5.5 µg of amplification products were labeled with Affymetrix WT Terminal Labeling Kit hybridized to Affymetrix HG Gene 1.0ST chips using Affymetrix Hybridization Control Kit and washed and stained using Affymetrix Wash and Stain Kit. All steps were done following the manufacturer’s instructions.

extract_protocol: 50mg of snap frozen lung tissue was added to a tube containing 1 ml of ice cold trizol and homogenized until tissue was totally homogenized. After incubation for 5 min at room temperature, 0.2ml of chloroform was added; tube was shaked vigorously by hand for 15 sec and then incubated for 3 min at room temperature. Then samples were centrifuged for 20 min at 12000g at 4C. Aqueous phase was transfered to a clean 1.5-ml tube and 1 x volume of 70% ethanol was added into the aqueous phase. Sample was applied to the Rneasy column and centrifuged at 8000g for 30 sec. Further procedure was done using Rneasy mini kit according to the manufactures suggestions including an optional 30 min DNase I treatment.

value: tumor

value: squamous-cell carcinoma


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 1 wk of age, replicate 1

description: Sample 1

value: 1 week


title: 607T_Macro [PICO WTA]


title: 581NT_Macro [PICO WTA]

value: non-tumor


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 1 wk of age, replicate 4

description: Sample 4

value: Adipose FL cockerel


title: 566NT_Macro [PICO WTA]


title: Maize_GiantCell_Root_14d_BioRep1

description: cDNA amplified from total RNA isolated from giant cells.

source_name: LCM of maize giant cells, 14 days

treatment_protocol: Two-week-old Zea mays seedlings planted on a 2:1 sand:turface mixture were inoculated with 1,000 M. incognita stage 2 juveniles near the root. Fourteen days after inoculation, the infested portions of the roots were harvested and frozen in cryomatrix. An area of approximately 5,000,000 um2 (~40-60 cells) was captured from infested regions of the root. Giant cells were catapulted using the AutoLPC method directly to P.A.L.M. Adhesive caps.

tag: treatment

value: Meloidogyne incognita infestation

value: 14 days post challenge with M. incognita

value: laser-captured giant cells

value: IS A A188 C B73 Cross


title: 561T_Macro [PICO WTA]


title: 566T_Macro [PICO WTA]


title: Late Secretory Myometrium, biological rep5

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: Late Secretory Myometrium5, biological rep5

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: The image data were compiled into a project using  Beadstudio software gene expression module version 3.2.7.  No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format. The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.

source_name: Late Secretory Myometrium

label_protocol: According to Illumina protocol.

extract_protocol: Total RNA was isolated from flash-frozen tissue specimens using the mirVANA Kit (Ambion, Austin, TX). Transcriptional profiles were generated by the Genomics and Proteomics Core Laboratory at Texas Children's Hospital using Human WG-6 (v3) BeadChip (Illumina, San Diego, CA). Prior to profiling, RNA integrity was determined using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).

value: Late Secretory Myometrium


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 1 wk of age, replicate 3

description: Sample 3

value: Adipose LL cockerel

value: abdominal adipose


title: 561NT_Macro [PICO WTA]


title: Late Secretory Myometrium, biological rep2


title: 607NT_Macro [PICO WTA]


title: 558NT_Macro [PICO WTA]

value: adenocarcinoma


title: Late Secretory Myometrium, biological rep3


title: Late Secretory Myometrium, biological rep4


title: 552T_Macro [PICO WTA]


title: 552NT_Macro [PICO WTA]


title: ULMS, biological rep11

description: ULMS, biological rep11

source_name: ULMS

value: Uterine leiomyosarcoma


title: ULMS, biological rep12

description: ULMS, biological rep12


title: 558T_Macro [PICO WTA]


title: Late Secretory Myometrium, biological rep1


title: ULMS, biological rep10

description: ULMS, biological rep10


title: Wild-type strain_2

city: Shanghai Municipality

first: Kehe

last: Fu

address: Rd.800 Dongchuan,Minhang district, shanghai municipality,China

country: China

institute: Shanghai Jiao Tong University

description:
F01_2
gene expression after 5 d in YPD medium, conatining 1 mM copper sulfate

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl of 10× blocking agent and 2.2 μl of 25× fragmentation buffer and then heated at 60 °C for 30 min. Finally, 55 μl of 2x GE hybridization buffer was added to dilute the labeled cRNA. Hybridization solution (100 μl) was dispensed into the gasket slide and assembled into the gene expression microarray slide. The slides were incubated for 17 h at 65 °C in an Agilent hybridization oven.

scan_protocol: The hybridized arrays were washed, fixed, and scanned with an Agilent DNA Microarray Scanner (part number G2505B)

data_processing: Agilent Feature Extraction software (version 10.5.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies) After Quantile normalization of the raw data, genes that at least 1 out of 4 samples have flags in Present ('All Targets Value) were chosen for further data analysis.

organism: Trichoderma reesei QM6a

source_name: WT_mycelium_1mM CuSO4_5d

label_protocol: 1 μg of the total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNA were purified with an RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured with a NanoDrop ND-1000.

growth_protocol: Strains were cultured in YPD medium containing 1 mM copper Sulfate, 25 °C for 5 d.

extract_protocol: Total RNA was extracted by the Trizol method (Invitrogen). The integrity of RNA can be assessed by electrophoresis on a denaturing agarose gel. Intact total RNA run on a denaturing gel will have sharp 28S and 18S rRNA bands (eukaryotic samples)

treatment_protocol: Mycelium of the strains were collected by filter in short time, and stored in -70°C

tag: genotype/variation

value: wild type

value: mycelium


title: 539T_Macro [PICO WTA]


title: Mutant strain AT01_1

description:
F02_1
gene expression after 5 d in YPD medium, conatining 1 mM copper sulfate

source_name: AT01_mycelium_1mM CuSO4_5d

value: AT01 mutant (with high ability of copper accumulation)

tag: tissue


title: 551NT_Macro [PICO WTA]


title: Wild-type strain_1

description:
F01_1
gene expression after 5 d in YPD medium, conatining 1 mM copper sulfate


title: 551T_Macro [PICO WTA]

value: tumor


title: Mutant strain AT01_2

description:
F02_2
gene expression after 5 d in YPD medium, conatining 1 mM copper sulfate


title: 539NT_Macro [PICO WTA]


title: 538T_Macro [PICO WTA]


title: ULMS, biological rep6

description: ULMS, biological rep6


title: ULMS, biological rep9

description: ULMS, biological rep9


title: ULMS, biological rep7

description: ULMS, biological rep7


title: ULMS, biological rep5

description: ULMS, biological rep5


title: ULMS, biological rep8

description: ULMS, biological rep8


title: 538NT_Macro [PICO WTA]


title: ULMS, biological rep4

description: ULMS, biological rep4


title: 507NT_Macro [PICO WTA]


title: rpfG mutant vs. wild type strain at 11 h

description:
rpfG11/W11
This Sample represent 4 biological replicates, including 2 dye swaps.

Raw data files:
Cy3=wild type, Cy5=mutant: *_1_1.txt, *_1_3.txt
Cy5=wild type, Cy3=mutant: *_1_2.txt, *_1_4.txt

tag: genotype

source_name: rpfG mutant growing in XVM2 medium at 11 h

value: rpfG deletion mutant


title: ULMS, biological rep3

description: ULMS, biological rep3


title: Day29_Control

city: tsukuba

first: Sone

last: Hideko

state: ibaraki

department: Center for Environmental Risk Research

country: Japan

institute: National Institute for Environmental Studies

description: Expose 0.1% Ethanol for 4days between Day2 and Day6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GeneSpring GX11(Agilent technologies)

organism: Mus musculus

source_name: Mouse embryonic stem cell (G6B-2)

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

growth_protocol: Embryoid bodies formed from nouse ES cells and differentiated into Neural cells by differentiation-inducing medium.

extract_protocol: RNA was extracted with the QIAGEN RLT buffer, 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 Bioanalyser.

treatment_protocol: Retinoic acid were treated into the culture media at the iniciated stage after forming embryonic body

value: Mouse blastocyst

value: Mouse embryonic stem cell (G6B-2)

tag: treatment/growth condition


title: Chicken Abdominal fat, fat (FL) vs. lean (LL) lines, 1 wk of age, replicate 2

description: Sample 2

value: Adipose FL cockerel

value: 1 week


title: Day8_RA10-7M

description: Expose 10-7M Retinoic acid for 4days between Day2 and Day6

tag: cell type


title: testis_ko_4

city: Edinburgh

first: Ian

last: Adams

address: Crewe Road

department: Genome Regulation

country: United Kingdom

institute: MRC Human Genetics Unit

description:
Knockout animal 4.
Biological replicate 4 of 4.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Background subtracted using Illumina BeadStudio, then log-transformed, quantile-normalized using lumi in R.

source_name: 16 dpp testis, knockout

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen), and then treated with DNase I. Quality control was performed with Agilent Bioanalyser.

tag: strain

tag: gender

value: male

value: testis

tag: developmental stage

value: 16 days post partum


title: ULMS, biological rep1

description: ULMS, biological rep1


title: Day29_RA10-7M

value: Expose 10-7M Retinoic acid for 4days between Day2 and Day6


title: ULMS, biological rep2

description: ULMS, biological rep2


title: Day8_RA10-8M

description: Expose 10-8M Retinoic acid for 4days between Day2 and Day6


title: testis_ko_3

description:
Knockout animal 3.
Biological replicate 3 of 4.


title: testis_ko_1

description:
Knockout animal 1.
Biological replicate 1 of 4.


title: testis_ko_2

description:
Knockout animal 2.
Biological replicate 2 of 4.


title: Day8_Control

value: Expose 0.1% Ethanol for 4days between Day2 and Day6


title: Proliferative Myometrium, biological rep4

source_name: Proliferative Myometrium

value: Proliferative Myometrium


title: Proliferative Myometrium, biological rep3


title: Day2_EB

description: Second day from the formation of Embryonic body


title: Proliferative Myometrium, biological rep5


title: ES

description: ES cells

value: control ES cells


title: Day29_RA10-8M

value: Expose 10-8M Retinoic acid for 4days between Day2 and Day6


title: testis_het_4

description:
Heterozygote animal 4.
Biological replicate 4 of 4.

source_name: 16 dpp testis, heterozygote


title: Proliferative Myometrium, biological rep2


title: AGH-OG-2 vs kidney

city: Shanghai

first: Linyu

address: 320 Yueyang Road

institute: Institute of Biochemistry and Cell Biology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences

description: CNV analysis of AGH-OG-2 vs male kidney

hyb_protocol: Hybridization was processing overnight at 42°C in Roche-NimbleGen hybridization system12.

scan_protocol: Arrays were scanned on an Roche-NimbleGen MS200 scanner.

data_processing: Arrays were processed using NimbleScan,which transformed image signal to digital signal, following using segMNT algorithm to analyse the normalized signal ratio.

label_protocol: The sample labelling was using NimbleGen Dual-Color DNA Labeling Kit (05223547001).

growth_protocol: ES cells were cultured on feeder in 2i medium

extract_protocol: The genomic DNA was extracted using Promega Genomic DNA Purification Kit (A1620).

treatment_protocol: ES cells were collected without feeder.

value: Oct4-EGFP transgene

tag: dna source

value: androgenetic haploid stem cells

source_name: male mouse kidney

growth_protocol: C57BL/6J male mouse

treatment_protocol: Kidneys were directly dissected from male mouse.

value: wild type

value: male mouse kidney


title: Day8_RA10-9M

description: Expose 10-9M Retinoic acid for 4days between Day2 and Day6


title: testis_het_3

description:
Heterozygote animal 3.
Biological replicate 3 of 4.


title: HepG2 DDX20 knockdown

city: Tokyo

first: Motoyuki

last: Otsuka

address: 7-3-1 Hongo Bunkyo-ku

institute: The University of Tokyo

description: Hepatocellular carcinoma cell line with DDX20 knockdown

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol

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

data_processing: Average Beta normalized

label: Cy5 and Cy3

source_name: HepG2 DDX20 knockdown

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

tag: cell line

value: DDX20 knockdown


title: TRIGFP NOD #2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Affymetrix GeneChip WT cDNA Synthesis and Amplification Kits

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: spleen

label_protocol: Affymetrix GeneChip WT Sense Target Labeling and Control Reagents

extract_protocol: TriZol

value: 6 Week

value: CD4+ Treg

tag: genetic background

value: NOD

tag: genetic variation

tag: phenotype markers

value: CD3+, CD4+, GFP+

tag: separation method

value: MoFlo

tag: Sex

value: Male


title: TRIGFP NOD #1

tag: age


title: Short-term water deficit treatment, D2

city: Beijing

first: Jin

middle: Hui

last: Chen

state: Beijing

address: No. 35, Qinghua East Road

department: College of Biological Sciences and Biotechnology, Beijing Forestry University

institute: Beijing Forestry University

description: Expression data from one-year-old leaves of Populus simonii treated with short-term water deficit.

hyb_protocol: Array hybridization and washing were performed using the 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 the MAS 5.0 algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Populus simonii

source_name: leaves from short-term water-deficit-treated plants

label_protocol: Total RNA were amplified, labeled and purified by using the GeneChip 3' IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions to obtain biotin-labeled cRNA.

growth_protocol: The cuttings were planted in basins (15 cm diameter × 10 cm depth) that contained sand, organic matter and vermiculite (3:1:1,v/v/v) in the greenhouse of Beijing Forestry University in March 2010. After sprouting and growth for about one year, healthy cuttings with approximately the same crown size and equal height were chosen and moved into growth chambers at the laboratory of Beijing Forestry University.

extract_protocol: Total RNA was extracted by the procedure of Chang et al. 1993. mRNA was isolated from total RNA (~0.5 ug for each treatment) using the PolyATract mRNA Isolation System (Promega). Double-stranded cDNA was then synthesized from mRNA with the Universal RiboClone cDNA Synthesis System (Promega) following the manufacturer’s protocol. The synthesized cDNA was dissolved in 50 μl TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by the RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The water deficit treatments were carried out by limiting the watering for 3 days until the leaves showed primary wilting. The controls were watered once a day as normal.

value: leaves

value: 1 year

tag: treatment

value: short-term water deficit


title: kidney vs kidney

description: CNV analysis of male kidney vs male kidney


title: Proliferative Myometrium, biological rep1

value: Proliferative Myometrium


title: S. mitis KCTC 3556T

city: Seoul

first: Heekuk

last: Park

address: Heukseok-dong

department: Department of Medical Microbiology

country: South Korea

institute: Chung-Ang University College of Medicine

description: This sample is of type strain S. mitis KCTC 3556T.

hyb_protocol: Hybridization were carried out according to NimbleGen protocols.

scan_protocol: Arrays were scanned using the NimbleGen MS 200 Microarray Scanner

data_processing: Array data export processing and analysis was performed using NimbleScan v2.5 (RMA algorithm) correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Streptococcus mitis

source_name: S. mitis KCTC 3556T

label_protocol: cDNA were prepared from 10 ug total RNA using the SuperScript double-stranded cDNA synthesis kit(Invitrogen). Labeling were carried out according to NimbleGen protocols.

growth_protocol: S. pneumoniae KCTC 5080T, S. pseudopneumoniae CCUG 49455 T, S. mitis KCTC 3556T, and S. oralis KCTC 13048T strains were grown on Brain Heart Infusion (BHI) agar (Difco., Detroit, MI, U.S.A.) at 37°C for 18 hours.

extract_protocol: Total RNA was extracted using RiboPure Bacteria Kit (Ambion, UK) following manufacturer’s instructions. RNA quality and concentration was determined by analysis with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

value: KCTC 3556T

tag: phenotype

value: normal


title: S. oralis KCTC 13048T

description: This sample is of type strain S. oralis KCTC 13048T .

organism: Streptococcus oralis

source_name: S. oralis KCTC 13048T

value: KCTC 13048T


title: Control, CK2

description: Expression data from one-year-old leaves of control Populus simonii.

source_name: leaves from control plants

tag: tissue

value: control


title: testis_het_1

description:
Heterozygote animal 1.
Biological replicate 1 of 4.

tag: genotype

value: male

value: testis

value: 16 days post partum


title: S. pneumoniae KCTC 5080T

description: This sample is of type strain S. pneumoniae KCTC 5080T.

organism: Streptococcus pneumoniae

source_name: S. pneumoniae KCTC 5080T

value: KCTC 5080T


title: testis_het_2

description:
Heterozygote animal 2.
Biological replicate 2 of 4.


title: AGH-OG-3 vs kidney

description: CNV analysis of AGH-OG-3 vs male kidney

value: Oct4-EGFP transgene

value: androgenetic haploid stem cells

value: wild type

value: male mouse kidney


title: Short-term water deficit treatment, D1


title: AGH-EG-1 vs kidney

description: CNV analysis of AGH-EG-1 vs male kidney

value: Actin-EGFP transgene


title: TRIGFP B6 #1

value: 6 Week

value: CD4+ Treg

value: CD3+, CD4+, GFP+

value: MoFlo

value: Male


title: Epicardial cells_Transforming Growth Factor-beta1_rep3

city: Odense

first: Hasse

middle: B.

last: Jensen

address: Winsløwparken 21, 3.

country: Denmark

institute: University of Southern Denmark

description: Sample name: 2.TG.5

hyb_protocol: Hybridization was performed on 2x250 ng total RNA for 16h and subsequently washed according to the recommendations of the manufacturer (Exiqon).

scan_protocol: Scanned on an Agilent Microarray Scanner (G2565CA) and analyzed by GenePix 6.0 software.

data_processing: Normalization and background correction was performed in R (Bioconductor) using the vsn package. Using the limma package differential microRNA expression was computed by fitting to a eBayes linear model and contrasting individual treatments with untreated controls.

organism: Rattus norvegicus

source_name: [test] epicardial cells, Transforming Growth Factor-beta1

label_protocol: Samples were labelled with Hy3 and a pool of samples constituting the common reference was labelled with Hy5 by using miRCURY LNA microRNA Array Power labelling kit (Exiqon) acoording to the instructions of the manufacturer.

growth_protocol: Primary rat epicardial mesothelial cells were isolated from the epicardium by sequential trypsinization. Emerging clones of mesothelial cells were isolated by cloning tubes and expanded for up to five passages in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA extracted using TriReagent following manufacturer's instructions

treatment_protocol: Epicardial mesothelial cells were incubated for 48h with 10 ng/mL recombinant human Interleukin-1beta, Tumor Necrosis Factor-alpha, or Transforming Growth Factor-beta1 (all R&D Biosystems). A treatment control was included containing only the background medium (DMEM with 2% Fetal Bovine Serum).

value: Sprague Dawley

tag: cell origin

value: epicardial mesothelium

value: epicardial cell

tag: passage

tag: agent

value: Transforming Growth Factor-beta1

source_name: [common reference] epicardial cells, pool of all samples

tag: reference composition

value: a pool of all 13 samples


title: Epicardial cells_Transforming Growth Factor-beta1_rep2

description: Sample name: 2.TG.6

tag: strain

tag: gender

value: male

tag: cell type


title: Epicardial cells_Transforming Growth Factor-beta1_rep1

description: Sample name: 2.TG.1


title: Epicardial cells_Tumor Necrosis Factor-alpha_rep2

description: Sample name: 2.TN.6

source_name: [test] epicardial cells, Tumor Necrosis Factor-alpha treatment

value: Tumor Necrosis Factor-alpha


title: TRGFP NOD #1

tag: genetic background

value: NOD


title: TRGFP B6 #1

tag: genetic variation


title: HepG2 control

description: Hepatocellular carcinoma cell line

source_name: HepG2 control

tag: cell line

tag: genotype/variation


title: Epicardial cells_Tumor Necrosis Factor-alpha_rep1

description: Sample name: 2.TN.1


title: TRGFP B6 #2

tag: phenotype markers

tag: separation method

tag: Sex


title: Arab_Control_Root_14d_BioRep3

city: Gainesville

first: Lauren

last: McIntyre

address: 2033 Mowry Rd

institute: University of Florida

description: cDNA amplified from total RNA isolated from control root cells.

hyb_protocol: The hybridization mixture was prepared according to NuGEN and Affymetrix procedures and hybridized to GeneChip© Arabidopsis ATH1 Arrays.

scan_protocol: GeneChips were scanned at the University of Pennsylvania School of Medicine Microarray Facility according to standard manufacturer protocols.

data_processing: Data were quantified with the Expression Console (Affymetrix) software application using the MAS5 algorithm.

organism: Arabidopsis thaliana

source_name: LCM of Arabidopsis control root cells, 14 days

label_protocol: NuGEN FL module.

growth_protocol: Arabidopsis seedlings were grown for infestation with Meloidogyne incognita nematodes according to (Hammes et al. Plant J. 2006 48:414-426). Briefly, Arabidopsis seeds were sterilized and sown, five seeds per plate, 30 plates total, in a medium containing 2% sucrose, 0.3% Gamborg’s basal salts, and 0.6 % Phytagel, pH 6.1. Plates were placed at a 45o angle in a short-day chamber.

extract_protocol: Total RNA was isolated using the PicoPure RNA isolation kit (Arcturus, Mountain View, CA, USA) with the optional DNase treatment, according to the manufacturer's instructions. RNA was amplified according to NuGEN WT-Ovation Pico kit instructions.

treatment_protocol: Arabidopsis seedlings were infested with Meloidogyne incognita nematodes according to (Hammes et al. Plant J. 2006 48:414-426). Briefly, 3-week-old Arabidopsis seedlings, 5 per plate, were inoculated with 1,000 M. incognita stage 2 juveniles and placed at an angle in a clear acrylic humid box in a short-day chamber. Fourteen days after inoculation, control root cells not undergoing giant cell formation (~13,000,000 um2 area, ~150 cells) were captured from non-infested regions of the infested root. Control root cells were catapulted using the AutoLPC method directly to P.A.L.M. Adhesive caps.

tag: treatment

value: Meloidogyne incognita infestation

tag: time

value: 14 days post challenge with M. incognita

value: laser-captured control root cells

tag: ecotype

value: Columbia

tag: sample size


title: Arab_GiantCell_Root_14d_BioRep3

description: cDNA amplified from total RNA isolated from giant cells.

source_name: LCM of Arabidopsis giant cells, 14 days

treatment_protocol: Arabidopsis seedlings were infested with Meloidogyne incognita nematodes according to (Hammes et al. Plant J. 2006 48:414-426). Briefly, 3-week-old Arabidopsis seedlings, 5 per plate, were inoculated with 1,000 M. incognita stage 2 juveniles and placed at an angle in a clear acrylic humid box in a short-day chamber. Fourteen days after inoculation, root cells undergoing giant cell formation (~5,000,000 um2 area, ~80 cells) were captured from infested regions of the root. Giant cells were catapulted using the AutoLPC method directly to P.A.L.M. Adhesive caps.

tag: tissue

value: laser-captured giant cells


title: Epicardial cells_Tumor Necrosis Factor-alpha_rep3

description: Sample name: 2.TN.5

tag: cell origin

tag: passage

tag: agent


title: TCIGFP NOD #2

tag: age

value: 6 Week

value: CD4+ Tconv

value: CD3+, CD4+, GFP-


title: Epicardial cells_Interleukin-1beta_rep3

description: Sample name: 2.I.5

source_name: [test] epicardial cells, Interleukin-1beta treatment

tag: strain

tag: gender

tag: cell type

tag: reference composition


title: Arab_GiantCell_Root_14d_BioRep2


title: TCIGFP NOD #1

tag: genetic background

tag: genetic variation

value: MoFlo

value: Male


title: Arab_Control_Root_14d_BioRep2


title: MEF,biological rep2

description: Gene expression data from MEF derived from male d13.5 embyos

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.

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

source_name: MEFs isolated from a male d13.5 embryo

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Androgeneic haploid embryonic stem cells (AG-haESCs) were cultured on feeder in ES medium supplemented with CHIR99021 and PD0325901.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit(Cat#74106, QIAGEN, GmBH,Germany) according to the manufacturer's instructions.

treatment_protocol: To sort haploid cells, ES cells were trypsinized, washed by DPBS (GIBCO), and then incubated with 15 μg/ml Hoechst 33342 in 37°C water bath. Subsequently, the haploid 1n peak was purified using BD FACS AriaII for microarry analysis. For E14 and MEF, the diploid 2n peak was purified. All the cells were preserved in -80°C.

tag: karotype

value: diploid

value: somatic cells

tag: genotype

value: wild type


title: Arab_Control_Root_14d_BioRep1

tag: treatment


title: E14, biological rep3

description: Gene expression data from E14

source_name: diploid male embryonic stem cells

value: embryonic stem cells


title: VCAP, 24h ETOH

city: Singapore

first: Kern Rei

last: Chng

address: 60 Biopolis Street #02-01 Genome

department: Cancer Biology and Pharmacology 3

country: Singapore

institute: GIS

description:
This Sample represents triplicates.

Raw data IDs: 4671881007_B, 4671881104_B, 4671881105_B

hyb_protocol: 750ng of cRNA were hybridized to the Sentrix HumanRef-8 v3 Expression BeadChip Kit (Illumina) according to the manufacturer's protocol.

scan_protocol: BeadChips were scanned using the BeadArray Reader.

data_processing: Raw data was analyzed using GeneSpring GX 11.0 software. The dataset was normalized using percentile shift normalization and baseline-transformed to the median of control samples. Analyses were performed using the average of the triplicates (after normalization).

source_name: VCaP prostate cancer cells, 24h ETOH

label_protocol: Biotinylated cRNA were prepared from 500ng total RNA using the Illumina TotalPrep-96 RNA Amplification Kit (Ambion).

growth_protocol: The human prostate cancer VCaP cells (American Type Culture Collection) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution at 37˚C under 5% CO2.

extract_protocol: RNA was harvested using Trizol reagent (Sigma) and purified according to the manufacturer's protocol in the PureLink RNA Mini Kit (Invitrogen).

treatment_protocol: VCaP cells were seeded in DMEM supplemented with 10% fetal bovine serum (FBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution for 3 days. Prior to ETOH/DHT stimulation, VCaP cells were washed and the medium was replaced with phenol red free DMEM supplemented with 10% charcoal stripped fetal bovine serum (CDFBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution to starve the cells for 24 hours. Hormone-deprived VCaP cells were treated with ETOH/10nM DHT for different times.

tag: cell line

value: VCaP

value: prostate cancer cells

value: ETOH

tag: treatment duration


title: Arab_GiantCell_Root_14d_BioRep1

value: Meloidogyne incognita infestation

tag: time

tag: ecotype

tag: sample size


title: E14, biological rep2

description: Gene expression data from E14

tag: passage


title: Epicardial cells_Interleukin-1beta_rep2

description: Sample name: 2.I.3

value: Sprague Dawley

value: male

tag: cell origin

value: epicardial mesothelium

value: epicardial cell

tag: agent

value: a pool of all 13 samples


title: Epicardial cells_Interleukin-1beta_rep1

description: Sample name: 2.I.1

tag: strain


title: TCIGFP B6 #2

tag: age

value: 6 Week

value: CD4+ Tconv

tag: phenotype markers

tag: separation method

tag: Sex


title: E14, biological rep1

description: Gene expression data from E14

tag: cell type


title: VCAP, 24h 10nM DHT

description:
This Sample represents triplicates.

Raw data IDs: 4671881007_A, 4671881104_A, 4671881105_A

source_name: VCaP prostate cancer cells, 24h DHT

value: 10nM dihydrotestosterone (DHT)


title: Epicardial cells_control_rep4

description: Sample name: 2.0.6

source_name: [test] epicardial cells, control treatment

tag: gender

value: control

tag: reference composition


title: TCIGFP B6 #1

source_name: spleen

tag: genetic background

tag: genetic variation

value: CD3+, CD4+, GFP-

value: MoFlo

value: Male


title: TCGFP NOD #2

value: NOD


title: TCGFP NOD #1


title: VCAP, 12h ETOH

description:
This Sample represents triplicates.

Raw data IDs: 4671881007_D, 4671881104_D, 4671881105_D

source_name: VCaP prostate cancer cells, 12h ETOH

tag: cell line

value: VCaP

tag: treatment

tag: treatment duration


title: VCAP, 12h 10nM DHT

description:
This Sample represents triplicates.

Raw data IDs: 4671881007_C, 4671881104_C, 4671881105_C

source_name: VCaP prostate cancer cells, 12h DHT

value: prostate cancer cells


title: TRIGFP B6 #2

value: CD4+ Treg

value: CD3+, CD4+, GFP+


title: 507T_Macro [PICO WTA]

description: Macro Samples amplified with PICO WTA system

tag: disease state

value: tumor

value: adenocarcinoma


title: VCAP, 6h 10nM DHT

description:
This Sample represents triplicates.

Raw data IDs: 4671881007_E, 4671881104_E, 4671881105_E

source_name: VCaP prostate cancer cells, 6h DHT


title: AGH-OG-4

description: Gene expression data from androgenetic haploid embryonic stem cells

source_name: haploid embryonic stem cells derived from androgenetic blastocyst

tag: karotype

value: haploid

value: embryonic stem cells

tag: genotype

value: Oct4-EGFP transgene

tag: passage


title: Epicardial cells_control_rep1

description: Sample name: 2.0.1

tag: strain

value: Sprague Dawley

value: male

tag: cell origin

value: epicardial mesothelium

value: epicardial cell

tag: agent

value: a pool of all 13 samples


title: TCGFP B6 #2

tag: age

value: 6 Week

value: CD4+ Tconv

tag: phenotype markers

value: CD3+, CD4+, GFP-

tag: separation method

value: MoFlo


title: Epicardial cells_control_rep3

description: Sample name: 2.0.5

tag: gender

tag: cell type

value: control


title: Epicardial cells_control_rep2

description: Sample name: 2.0.3

tag: reference composition


title: AGH-OG-3


title: AGH-EG-1

value: Actin-EGFP transgene


title: TCGFP B6 #1

tag: genetic background

tag: genetic variation

tag: Sex

value: Male


title: AGH-OG-2


title: VCAP, 6h ETOH

description:
This Sample represents triplicates.

Raw data IDs: 4671881007_F, 4671881104_F, 4671881105_F

source_name: VCaP prostate cancer cells, 6h ETOH

tag: cell line

value: VCaP

value: prostate cancer cells

tag: treatment

value: ETOH

tag: treatment duration


title: 103538_IgM_0_HR_#15

status: Public on Apr 26 2012

city: Dallas

first: Igor

last: Dozmorov

address: 5323 Harry Hines Boulevard

department: Immunology

institute: UT Southwestern Medical Center

description: ebvBcells from Rep_Norm donor 3 0hr_BCRFCR

hyb_protocol: hybridization to Affymetrix Mouse Genome 430 2.0 arrays.

scan_protocol: scanned on an Affymetrix GeneChip Analysis System GC3000 7G.

data_processing:
Two-step normalization procedure. The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”. All data analyses were based on the use of “internal standards” as presented elsewhere (1,2).
1. Dozmorov IM, Lefkovits I. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucleic Acids Res., 2009 Aug 31. [Epub ahead of print] PMID:19720734
2. Igor M Dozmorov, James Jarvis, Ricardo Saban, Doris Benbrook, Edward Wakeland, Ivona Aksentijevich , John Ryan, Nickolas Chiorazzi, Joel Guthridge, Elizabeth Drew, Patrick J Tighe, Michael Centola, and Ivan Lefkovits  Internal standard-based analysis of microarray data. 2. Analysis of functional associations between HVE-genes, Nucleic Acids Res., 2011 Oct, 39(18): 7881-99. Epub 2011 Jun 28

label_protocol: cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)

growth_protocol: CD4+ T cells from 5 mo old female B6 and B6.Sle1a.1 mice (N = 4 per strain) were isolated by negative selection with the SpinSep enrichment protocol.  recombinants obtained from a backcross with C57BL6/J (B6) were identified and fine-mapped with a panel of microsatellite markers and SNPs that are polymorphic between NZB and B6 (Fig. 2). These recombinants were then expanded in out-crosses to B6 and bred to homozygozity to generate three Sle2c1 recombinant strains.  B6, NZM2410, NZB and NZW mice were originally obtained from the Jackson Laboratories.  B6.Sle2c1 and recombinant phenotypes were analyzed in both males and females at the age indicated. (NZB X B6.Sle2c1)F1 (NxSle2c1) and (NZB X B6)F1 (NxB) females were aged to 12 mo of age.

extract_protocol: RNA was extracted with the Qiagen RNeasy Micro Kit.

value: Epstein-Barr virus (EBV) transformed B cells

tag: diagnosis

value: Normal


title: VCAP, 0h 10nM DHT

description:
This Sample represents triplicates.

Raw data IDs: 4671881007_G, 4671881104_G, 4671881105_G

source_name: VCaP prostate cancer cells, 0h DHT

value: 10nM dihydrotestosterone (DHT)


title: 103538_SC_0.5_HR_#14

description: ebvBcells from Rep_Norm donor 3 .5hr_serum control


title: 103538_SC_0_HR_#13

description: ebvBcells from Rep_Norm donor 3 0hr_serum control


title: AGH-OG-1

tag: karotype

value: haploid

value: embryonic stem cells

tag: genotype

value: Oct4-EGFP transgene

tag: passage


title: 301965_SC_0.5_HR_#02

description: ebvBcells from Rep_Norm donor 1 .5hr_serum control


title: 301965_IgM_0_HR_#03

description: ebvBcells from Rep_Norm donor 1 0hr_BCRFCR


title: 301965_SC_0_HR_#01

description: ebvBcells from Rep_Norm donor 1 0hr_serum control


title: VCAP, 0h ETOH

description:
This Sample represents triplicates.

Raw data IDs: 4671881007_H, 4671881104_H, 4671881105_H

source_name: VCaP prostate cancer cells, 0h ETOH


title: 301965_IgM_0.5_HR_#04

description: ebvBcells from Rep_Norm donor 1 .5hr_BCRFCR


title: 103391_SC_0_HR_#25

description: ebvBcells from Rep_Norm donor 4 0hr_serum control


title: 103391_SC_0.5_HR_#26

description: ebvBcells from Rep_Norm donor 4 .5hr_serum control


title: 103391_IgM_0.5_HR_#28

description: ebvBcells from Rep_Norm donor 4 .5hr_BCRFCR


title: 103391_IgM_0_HR_#27

description: ebvBcells from Rep_Norm donor 4 0hr_BCRFCR


title: 100680_IgM_0_HR_#07

description: ebvBcells from Rep_Norm donor 2 0hr_BCRFCR


title: 100680_SC_0.5_HR_#06

description: ebvBcells from Rep_Norm donor 2 .5hr_serum control


title: 100850_IgM_0.5_HR_#24

description: ebvBcells from Rep_Lupus patient 3 .5hr_BCRFCR

value: Systemic Lupus Erythematosus (SLE)


title: 100680_IgM_0.5_HR_#08

description: ebvBcells from Rep_Norm donor 2 .5hr_BCRFCR


title: 100680_SC_0_HR_#05

description: ebvBcells from Rep_Norm donor 2 0hr_serum control


title: 100450_SC_0_HR_#17

description: ebvBcells from Rep_Lupus patient 2 0hr_serum control


title: 100450_SC_0.5_HR_#18

description: ebvBcells from Rep_Lupus patient 2 .5hr_serum control


title: 100450_IgM_0.5_HR_#20

description: ebvBcells from Rep_Lupus patient 2 .5hr_BCRFCR


title: 349_SC_0_HR_#09

description: ebvBcells from Rep_Lupus patient 1 0hr_serum control


title: 100850_SC_0_HR_#21

description: ebvBcells from Rep_Lupus patient 3 0hr_serum control


title: 100850_IgM_0_HR_#23

description: ebvBcells from Rep_Lupus patient 3 0hr_BCRFCR


title: 100423_SC_0.5_HR_#34

description: ebvBcells from Rep_Lupus patient 5 .5hr_serum control


title: S. pseudopneumoniae CCUG 49455 T

description: This sample is of type strain S. pseudopneumoniae CCUG 49455 T.

organism: Streptococcus pseudopneumoniae ATCC BAA-960 = CCUG 49455

source_name: S. pseudopneumoniae CCUG 49455 T

tag: strain

value: CCUG 49455 T

tag: phenotype

value: normal


title: 100423_IgM_0_HR_#35

description: ebvBcells from Rep_Lupus patient 5 0hr_BCRFCR


title: 100850_SC_0.5_HR_#22

description: ebvBcells from Rep_Lupus patient 3 .5hr_serum control


title: 100450_IgM_0_HR_#19

description: ebvBcells from Rep_Lupus patient 2 0hr_BCRFCR


title: 100423_IgM_0.5_HR_#36

description: ebvBcells from Rep_Lupus patient 5 .5hr_BCRFCR


title: Control, CK1

description: Expression data from one-year-old leaves of control Populus simonii.

source_name: leaves from control plants

tag: tissue

value: leaves

tag: age

value: 1 year


title: 45_SC_0_HR_#37

description: ebvBcells from Rep_Lupus patient 6 0hr_serum control


title: 349_SC_0.5_HR_#10

description: ebvBcells from Rep_Lupus patient 1 .5hr_serum control


title: 349_IgM_0_HR_#11

description: ebvBcells from Rep_Lupus patient 1 0hr_BCRFCR


title: 100423_SC_0_HR_#33

description: ebvBcells from Rep_Lupus patient 5 0hr_serum control


title: 45_SC_0.5_HR_#38

description: ebvBcells from Rep_Lupus patient 6 .5hr_serum control


title: 45_IgM_0.5_HR_#40

description: ebvBcells from Rep_Lupus patient 6 .5hr_BCRFCR


title: TRGFP NOD #2

value: 6 Week

value: CD4+ Treg

value: NOD

tag: phenotype markers

value: CD3+, CD4+, GFP+

tag: separation method

value: MoFlo


title: 349_IgM_0.5_HR_#12

description: ebvBcells from Rep_Lupus patient 1 .5hr_BCRFCR

tag: cell type


title: 45_IgM_0_HR_#39

description: ebvBcells from Rep_Lupus patient 6 0hr_BCRFCR


title: 103538_IgM_0.5_HR_#16

description: ebvBcells from Rep_Norm donor 3 .5hr_BCRFCR


title: 96_301948_24hr_BCRFCR

description: ebvBcells from Lupus patient2 24hr_BCRFCR


title: 95_301948_16hr_BCRFCR

description: ebvBcells from Lupus patient2 16hr_BCRFCR


title: 32_IgM_0.5_HR_#32

description: ebvBcells from Rep_Lupus patient 4 .5hr_BCRFCR


title: 32_SC_0.5_HR_#30

description: ebvBcells from Rep_Lupus patient 4 .5hr_serum control


title: 32_SC_0_HR_#29

description: ebvBcells from Rep_Lupus patient 4 0hr_serum control


title: 94_301948_8hr_BCRFCR

description: ebvBcells from Lupus patient2 8hr_BCRFCR


title: 32_IgM_0_HR_#31

description: ebvBcells from Rep_Lupus patient 4 0hr_BCRFCR


title: 93_301948_4hr_BCRFCR

description: ebvBcells from Lupus patient2 4hr_BCRFCR


title: 91_301948_1hr_BCRFCR

description: ebvBcells from Lupus patient2 1hr_BCRFCR


title: 88_101884_24hr_BCRFCR

description: ebvBcells from Lupus patient1 24hr_BCRFCR


title: 90_301948_0.5hr_BCRFCR

description: ebvBcells from Lupus patient2 .5hr_BCRFCR


title: 89_301948_0hr_BCRFCR

description: ebvBcells from Lupus patient2 0hr_BCRFCR


title: MEF,biological rep1

description: Gene expression data from MEF derived from male d13.5 embyos

value: diploid

value: somatic cells

value: wild type


title: 86_101884_8hr_BCRFCR

description: ebvBcells from Lupus patient1 8hr_BCRFCR

value: Epstein-Barr virus (EBV) transformed B cells


title: 85_101884_4hr_BCRFCR

description: ebvBcells from Lupus patient1 4hr_BCRFCR


title: 84_101884_2hr_BCRFCR

description: ebvBcells from Lupus patient1 2hr_BCRFCR


title: 87_101884_16hr_BCRFCR

description: ebvBcells from Lupus patient1 16hr_BCRFCR


title: 92_301948_2hr_BCRFCR

description: ebvBcells from Lupus patient2 2hr_BCRFCR


title: 83_101884_1hr_BCRFCR

description: ebvBcells from Lupus patient1 1hr_BCRFCR


title: 79_100688_16hr_BCRFCR

description: ebvBcells from Lupus patient2 16hr_BCRFCR


title: 82_101884_0.5hr_BCRFCR

description: ebvBcells from Lupus patient1 .5hr_BCRFCR


title: 78_100688_8hr_BCRFCR

source_name: ebvBcells from Lupus patient2 8hr_BCRFCR


title: mono_1

city: New York

first: Matthew

middle: M

last: Meredith

state: New York

address: 1230 York Ave

institute: The Rockefeller University

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Genespring (v.10), using default RMA normalization. The normalized values are log2 scaled, where the median is set as zero.

source_name: bone marrow mono

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

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

treatment_protocol: naive, wildtype mice

tag: gender

value: male

tag: tissue source

value: bone marrow

value: Ly6Chi monocytes


title: CDP_1

source_name: bone marrow CDP

treatment_protocol: Mice were treated with Flt3L in vivo to expand DCs and DC progenitors

value: female

value: Common Dendritic cell Progenitors (CDPs)


title: 81_101884_0hr_BCRFCR

description: ebvBcells from Lupus patient1 0hr_BCRFCR

value: Systemic Lupus Erythematosus (SLE)


title: preDC_2

source_name: bone marrow preDC

value: committed dendritic cell precursors (pre-DCs)


title: preDC_3


title: 77_100688_4hr_BCRFCR

source_name: ebvBcells from Lupus patient2 4hr_BCRFCR


title: MDP_2

source_name: bone marrow MDP

value: Macrophage & Dendritic cell Progenitors (MDPs)


title: CDP_2


title: mono_2


title: mono_3


title: preDC_1


title: MDP_1


title: CDP_3


title: MDP_3


title: 80_100688_24hr_BCRFCR

description: ebvBcells from Lupus patient2 24hr_BCRFCR


title: 76_100688_2hr_BCRFCR

source_name: ebvBcells from Lupus patient2 2hr_BCRFCR


title: MCAD + LPS 5

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

hyb_protocol: Standard Affymetrix protocols where used

data_processing: The data where normalised using gcRMA normalisation protocols using MADMAX analysis pipeline pmid: 21778530

source_name: Liver

extract_protocol: TRI -reagent was used to isolate RNA, and Qiagen Rneasy columns where used to purify the RNA

treatment_protocol: Wild type and mcad-/- mice where injected with vehicle or lps and subsequently fasted for 12 hrs , liver was isolated and RNA was extracted

value: mcad -/-

value: Male

tag: genetic background

value: BL6/SV129 mixed

value: 50-60 days of age

tag: diet

value: 12 hrs fasted

value: LPS

value: liver


title: 72_316_24hr_BCRFCR

source_name: ebvBcells from Lupus patient1 24hr_BCRFCR


title: 73_100688_0hr_BCRFCR

source_name: ebvBcells from Lupus patient2 0hr_BCRFCR


title: 74_100688_1hr_BCRFCR

source_name: ebvBcells from Lupus patient2 1hr_BCRFCR


title: 71_316_16hr_BCRFCR

source_name: ebvBcells from Lupus patient1 16hr_BCRFCR


title: 75_100688_0.5hr_BCRFCR

source_name: ebvBcells from Lupus patient2 .5hr_BCRFCR


title: MCAD + LPS 4

scan_protocol: Standard Affymetrix protocols where used

tag: treatment


title: 70_316_8hr_BCRFCR

source_name: ebvBcells from Lupus patient1 8hr_BCRFCR


title: 69_316_4hr_BCRFCR

source_name: ebvBcells from Lupus patient1 4hr_BCRFCR


title: MCAD + LPS 2

label_protocol: Standard Affymetrix protocols where used


title: MCAD 4

value: vehicle


title: 68_316_2hr_BCRFCR

source_name: ebvBcells from Lupus patient1 2hr_BCRFCR

value: Epstein-Barr virus (EBV) transformed B cells


title: 67_316_1hr_BCRFCR

source_name: ebvBcells from Lupus patient1 1hr_BCRFCR


title: MCAD 5


title: 66_316_0.5hr_BCRFCR

source_name: ebvBcells from Lupus patient1 .5hr_BCRFCR


title: MCAD + LPS 3


title: 65_316_0hr_BCRFCR

source_name: ebvBcells from Lupus patient1 0hr_BCRFCR


title: MCAD + LPS 1


title: MCAD 2


title: Control + LPS 4

value: wild type


title: MCAD 3


title: 63_301948_16hr_Serum

description: ebvBcells from Norm donor2 16hr_serum control

value: Normal


title: MCAD 1


title: Control + LPS 1


title: Control + LPS 3


title: 62_301948_8hr_Serum

description: ebvBcells from Norm donor2 8hr_serum control


title: 61_301948_4hr_Serum

description: ebvBcells from Norm donor2 4hr_serum control


title: Control + LPS 2


title: Control + LPS 5


title: Control 5


title: 64_301948_24hr_Serum

description: ebvBcells from Norm donor2 24hr_serum control


title: 56_101884_24hr_Serum

description: ebvBcells from Norm donor1 24hr_serum control


title: Control 4


title: 60_301948_2hr_Serum

description: ebvBcells from Norm donor2 2hr_serum control


title: 55_101884_16hr_Serum

description: ebvBcells from Norm donor1 16hr_serum control


title: 57_301948_0hr_Serum

description: ebvBcells from Norm donor2 0hr_serum control


title: 58_301948_0.5hr_Serum

description: ebvBcells from Norm donor2 .5hr_serum control


title: 59_301948_1hr_Serum

description: ebvBcells from Norm donor2 1hr_serum control


title: Control 3


title: 52_101884_2hr_Serum

description: ebvBcells from Norm donor1 2hr_serum control


title: 51_101884_1hr_Serum

description: ebvBcells from Norm donor1 1hr_serum control


title: Control 2


title: NHM_light_NT_control_rep2

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

institute: Unilever

description: Untreated cells

hyb_protocol: The Agilent Hybridisation Kit (catalogue number 5188-5242) was used in conjunction with Agilent human whole genome Oligo Arrays (catalogue number G4112F).  2μg of the labelled sample RNA were used for hybridisation according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol. The hybridisation was performed for 17 h at 65 ºC with 10 rpm rotation. Slides were then washed for 1 min at 22 ºC in Wash Solution 1 (catalogue number 5188-5325), followed by 1 min in Wash Solution 2 that was pre-warmed to 37 ºC (catalogue number 5188-5326) as described in the manufacturer’s manual. Slides were then washed in acetonitrile (Fisher cat# A/0630/PB15) for 1 min followed by 30s in Agilent Stabilisation and Drying Solution (catalogue number 5185-5979).

scan_protocol: The slides were scanned with the Agilent G2565BA Microarray Scanner System.

data_processing: For data extraction and quality control, the Agilent G2567AA Feature Extraction Software (v.9.1) was used.

source_name: Cultured melanocytes

label_protocol: 300ng RNA and 3µl (1:5000 dilution) Agilent One-Color RNA Spike-In RNA were labelled with reagents supplied in the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to Manufacturer’s instructions as follows:  Primers were annealed to template by mixing 1.2 µl T7 Promoter Primer, 200ng RNA and 2µl spike in control (in a volume of 11.5µl), denatured at 65ºC for 10min followed by incubation at 4ºC for 5min. First Strand Buffer (to 1X), DTT (to 10mM), dNTP (to 0.5mM), MMLV (1µl) and RNaseOut (0.5 µl) were then added to make up the cDNA synthesis reaction (20µl), which was incubated for 2h at 40 ºC. After 15 min denaturation at 65ºC, the reaction was made up to 80µl with the addition of Cyanine 3-CTP (to 0.3mM), Transcription Buffer (to 1X), DTT (to 10mM), NTP (8µl), PEG (to 4%), RNaseOUT (0.5µl), Inorganic Phosphatase (0.6µl), and T7 RNA Polymerase (0.8µl) and incubated for 2h at 40 ºC to synthesise the fluorescent labelled cRNA.  The labelled cRNA was purified with the RNeasy Mini Kit (Qiagen Ltd, Crawley, UK) according to Manufacturer’s protocol.

growth_protocol: Melanocytes from lightly and darkly pigmented donors were plated in 6-well plates at 100000 cells per well (2ml volume) and cultured for 24h in Medium 254 + HMGS1 supplement (Invitrogen Ltd) at 9% CO2, 37ºC.

extract_protocol: Total RNA was isolated using Qiagen RNeasy kit, as per the manufacturers instructions. The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyser using the RNA 6000 nano LabChip kit.

treatment_protocol: Cells were incubated with transfection reagents for 6h; 2μl/ml Lipofectamine 2000 in Opti-MEM medium (Invitrogen Ltd, Paisley, UK), plus siRNA duplex at a final concentration of 50nM. Cells were returned to the normal culture medium for 5d. siRNA treatments comprised; Stealth™ RNA-mediated interference duplexes (Invitrogen Ltd, Paisley, UK) targeting nucleotides 185-210 (termed 185) and 492-517 (termed 492) of SLC24A5. A negative control siRNA duplex treatment comprised comprised Allstars (termed All*) non-targeting siRNA (Qiagen Ltd, Crawley, UK).Additional negative control treatments comprised lipofectamine alone and and unchallenged melanocytes, cultured alongside the cellular treatments. All treatments and controls were conducted in triplicate in both cell lines.

tag: treatment type

value: Untreated

tag: pigmentation level

value: Lightly pigmented


title: NHM_light_NT_control_rep3

description: Untreated cells


title: NHM_light_LF_control_rep3

description: Transfection reagent only treatment

value: Lipofectamine only


title: 54_101884_8hr_Serum

description: ebvBcells from Norm donor1 8hr_serum control

tag: diagnosis


title: 50_101884_0.5hr_Serum

description: ebvBcells from Norm donor1 .5hr_serum control


title: 49_101884_0hr_Serum

description: ebvBcells from Norm donor1 0hr_serum control


title: Control 1

tag: genotype


title: NHM_light_LF_control_rep2

description: Transfection reagent only treatment


title: NHM_light_NT_control_rep1

description: Untreated cells


title: NHM_light_LF_control_rep1

description: Transfection reagent only treatment


title: 16_316_24hr_Serum

source_name: ebvBcells from Norm donor2 24hr_serum control


title: 15_316_16hr_Serum

source_name: ebvBcells from Norm donor2 16hr_serum control


title: NHM_light_d185_treat_rep3

description: SLC24A5 knockdown treatment

value: siRNA 185 to SLC24A5


title: NHM_light_d492_treat_rep3

description: SLC24A5 knockdown treatment

value: siRNA 492 to SLC24A5


title: 53_101884_4hr_Serum

description: ebvBcells from Norm donor1 4hr_serum control


title: 14_316_8hr_Serum

source_name: ebvBcells from Norm donor2 8hr_serum control


title: NHM_light_d492_treat_rep2

description: SLC24A5 knockdown treatment


title: 11_316_1hr_Serum

source_name: ebvBcells from Norm donor2 1hr_serum control


title: 7_100688_16hr_Serum

source_name: ebvBcells from Norm donor1 16hr_serum control


title: NHM_light_d492_treat_rep1

description: SLC24A5 knockdown treatment


title: NHM_light_d185_treat_rep2

description: SLC24A5 knockdown treatment


title: 9_316_0hr_Serum

source_name: ebvBcells from Norm donor2 0hr_serum control


title: NHM_light_All*_control_rep2

description: Control siRNA knockdown

value: Allstars negative control siRNA


title: NHM_light_All*_control_rep3

description: Control siRNA knockdown


title: 12_316_2hr_Serum

source_name: ebvBcells from Norm donor2 2hr_serum control


title: 6_100688_8hr_Serum

source_name: ebvBcells from Norm donor1 8hr_serum control


title: 5_100688_4hr_Serum

source_name: ebvBcells from Norm donor1 4hr_serum control


title: NHM_dark_NT_control_rep2

description: Untreated cells

value: Darkly pigmented


title: NHM_light_All*_control_rep1

description: Control siRNA knockdown


title: NHM_light_d185_treat_rep1

description: SLC24A5 knockdown treatment


title: NHM_dark_NT_control_rep3

description: Untreated cells


title: NHM_dark_LF_control_rep2

description: Transfection reagent only treatment


title: 4_100688_2hr_Serum

source_name: ebvBcells from Norm donor1 2hr_serum control


title: 10_316_0.5hr_Serum

source_name: ebvBcells from Norm donor2 .5hr_serum control


title: NHM_dark_NT_control_rep1

description: Untreated cells


title: NHM_dark_LF_control_rep3

description: Transfection reagent only treatment


title: 13_316_4hr_Serum

source_name: ebvBcells from Norm donor2 4hr_serum control


title: 3_100688_0.5hr_Serum

source_name: ebvBcells from Norm donor1 .5hr_serum control


title: 8_100688_24hr_Serum

source_name: ebvBcells from Norm donor1 24hr_serum control


title: 2_100688_1hr_Serum

source_name: ebvBcells from Norm donor1 1hr_serum control


title: 1_100688_0hr_Serum

source_name: ebvBcells from Norm donor1 0hr_serum control


title: S.cerevisiae Pool_Oleato0.1_72h

city: Segrate, Milano

first: Clelia

last: Peano

address: Via Fratelli Cervi 93

department: Institute of Biomedical Technologies

country: Italy

institute: National Research Council

description:
DNA amplicons.
Biological replicates 1 and 2.

hyb_protocol: Amplified upTAG and downTAG sequences were combined in equal amounts and used to probe high-density oligonucleotide arrays (Affymetrix GeneChip_DNA_Tag3) in 150µl of 1x Hybridization Buffer (100mM MES, 1M NaCl, 20mM EDTA, 0.01%Tween20, 1x Denhardt’s, 0.6fM Control-oligo-B2, and 1µM of U1, U2, D1 and D2 oligonucleotides and their complementary sequences). Samples were incubated at 99°C for 5’, chilled on ice for 1’, kept at 42°C for 1’ and hybridized at 42° for 16h with 60rpm rotation in the Hybridization oven 640 (Affymetrix). Washing and Staining were performed in the GeneChip Fluidic Station 450 (Affymetrix) according to the MIDI_DNAARRAY_WS2_450 protocol.

scan_protocol: Chips were scanned through GeneArray Scanner 3000 7G (Affymetrix) at an emission wavelength of 560nm.

data_processing:
GeneChips were primarily analyzed with GTYPE software 4.0 for quantification of raw signal intensities and production of a report file. Data analysis was performed as previously described (Pierce et al., 2007: PMID 18007632). In order to adapt this data analysis protocol to our experimental design and to the use of  GeneChip_DNA_Tag3 arrays, some changes to the procedure have been improved. Genes whose background filter was different form 0 and NC were considered valid. Among these we considered differentially represented genes those having p-val<0.01 and fold change <0.67 and >1.5 (List 1).  In the text we refer to the hybridization experiments as: fitness ole 0.1% 24h, fitness ole 5% 24h, fitness ole 0.1% 72h, fitness ole 5% 72h. All the data are referred to growth on 2% glucose as control.
To retrieve list of genes present in YPD, we calculated for each gene the mean value of up/downtag signals and the corresponding background signals in all replicates. We considered as “present” all the genes showing a tag intensity/background ratio >3. We thus identified a list of 3985 genes. After crossing this list with that of valid genes in oleate experimental conditions, we excluded all the ORFs valid in all four oleate experiments, identifying genes “present” in YPD and “absent” in YPO.

organism: Saccharomyces cerevisiae

source_name: Yeast Homozygous Diploid Deletion Pool, 0.1% oleic acid, 72h

label_protocol: The upTAG and downTAG regions were amplified separately in PCR reactions, one for each experimental condition, using specific Biotinylated primers.

growth_protocol: An aliquot of the Yeast Homozygous Diploid Deletion Pool (95401.H1Pool, Invitrogen), containing equal amounts of each barcoded viable knock-out mutant from the Saccharomyces Genome Deletion project (http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html), was grown in the presence of G418 (200µg/ml - GIBCO) in YPD medium for 24h, then aliquots of 5x10^7 cells were harvested, washed with sterile water, frozen in liquid nitrogen and stored at -80°C.

extract_protocol: We collected samples of 5x10^7cells 24h and 72h after carbon source metabolic shift. From frozen samples, genomic DNA was extracted using the DNeasy Blood and Tissue Kits (Qiagen) following manufacturer's instructions.

treatment_protocol: From the same pooled culture, equal amounts of cells were washed and transferred to YP medium added with oleic acid 0.1% or 5%.

tag: condition

value: 0.1% oleic acid

tag: time

tag: sample type

value: experimental


title: NHM_dark_LF_control_rep1

description: Transfection reagent only treatment

source_name: Cultured melanocytes


title: S.cerevisiae Pool_Oleato5_24h

source_name: Yeast Homozygous Diploid Deletion Pool, 5% oleic acid, 24h

value: 5% oleic acid


title: S.cerevisiae Pool_Oleato5_72h

source_name: Yeast Homozygous Diploid Deletion Pool, 5% oleic acid, 72h


title: S.cerevisiae Pool_Oleato0.1_24h

source_name: Yeast Homozygous Diploid Deletion Pool, 0.1% oleic acid, 24h


title: ZR-75-1-24h_10nMORG2058_Replicate2

city: Westmead

first: J

middle: Dinny

last: Graham

state: NSW

address: 176 Hawkesbury Rd

department: Westmead Institute for Medical Research

country: Australia

institute: University of Sydney

description: Replicate 2

hyb_protocol: 750ng biotin-labeled sample was hybridized to each HT-12 array using Illumina reagents and standard procedure

scan_protocol: The standard Illumina scanning protocol was used

data_processing: The data were background subtracted and normalized using the cubic spline normalization method using Illumina Genome Studio software

source_name: ZR-75-1 breast cancer cells grown in monolayer culture, treated 24h with 10nM ORG2058

label_protocol: 500ng total RNA per sample was amplified and biotin labeled using Invitrogen Illumina total Prep reagents, following the standard protocol

growth_protocol: Cells were grown in standard recommended media in monolayer cultures at 37C and 5% CO2 to 70% confluent prior to treatment

extract_protocol: Total RNA was isolated using Invitrogen RNaqueous reagents and following the standard protocol

treatment_protocol: Cells were treated with 10nM ORG2058 or ethanol vehicle (0.1% final in growth medium) for the times indicated, followed by harvesting by trypsinization and centrifugation.


title: NHM_dark_d492_treat_rep2

description: SLC24A5 knockdown treatment


title: NHM_dark_d185_treat_rep2

description: SLC24A5 knockdown treatment


title: NHM_dark_d492_treat_rep3

description: SLC24A5 knockdown treatment


title: S.cerevisiae Pool YPD_glu2%_B

description:
DNA amplicons.
Biological replicate 2 of 6.

source_name: Yeast Homozygous Diploid Deletion Pool, 2% glucose

value: 2% glucose

value: control


title: S.cerevisiae Pool YPD_glu2%_E

description:
DNA amplicons.
Biological replicate 5 of 6.


title: S.cerevisiae Pool YPD_glu2%_F

description:
DNA amplicons.
Biological replicate 6 of 6.


title: ZR-75-1-24h_10nMORG2058_Replicate3

description: Replicate 3


title: ZR-75-1-6h_10nMORG2058_Replicate3

description: Replicate 3

source_name: ZR-75-1 breast cancer cells grown in monolayer culture, treated 6h with 10nM ORG2058


title: S.cerevisiae Pool YPD_glu2%_A

description:
DNA amplicons.
Biological replicate 1 of 6.


title: ZR-75-1-6h_10nMORG2058_Replicate1

description: Replicate 1


title: ZR-75-1-24h_10nMORG2058_Replicate1

description: Replicate 1


title: ZR-75-1-2h_10nMORG2058_Replicate2

description: Replicate 2

source_name: ZR-75-1 breast cancer cells grown in monolayer culture, treated 2h with 10nM ORG2058


title: S.cerevisiae Pool YPD_glu2%_D

description:
DNA amplicons.
Biological replicate 4 of 6.


title: NHM_dark_d185_treat_rep1

description: SLC24A5 knockdown treatment


title: NHM_dark_d185_treat_rep3

description: SLC24A5 knockdown treatment


title: S.cerevisiae Pool YPD_glu2%_C

description:
DNA amplicons.
Biological replicate 3 of 6.


title: ZR-75-1-2h_10nMORG2058_Replicate1

description: Replicate 1


title: ZR-75-1-Vehicle_control_Replicate2

description: Replicate 2

source_name: ZR-75-1 breast cancer cells grown in monolayer culture, treated 24h with ethanol vehicle


title: ZR-75-1-2h_10nMORG2058_Replicate3

description: Replicate 3


title: ZR-75-1-Vehicle_control_Replicate1

description: Replicate 1


title: ZR-75-1-6h_10nMORG2058_Replicate2

description: Replicate 2


title: NHM_dark_All*_control_rep3

description: Control siRNA knockdown


title: AB9-24h_10nMORG2058_Replicate2

description: Replicate 2

source_name: MCF-10A clone AB9 grown in monolayer culture, treated 24h with 10nM ORG2058


title: NHM_dark_All*_control_rep2

description: Control siRNA knockdown


title: ZR-75-1-Vehicle_control_Replicate3

description: Replicate 3


title: AB9-24h_10nMORG2058_Replicate3

description: Replicate 3


title: AB32-24h_10nMORG2058_Replicate3

description: Replicate 3

source_name: MCF-10A clone AB32 grown in monolayer culture, treated 24h with 10nM ORG2058

tag: tissue

value: breast

tag: cell line


title: AB9-24h_10nMORG2058_Replicate1

description: Replicate 1


title: NHM_dark_All*_control_rep1

description: Control siRNA knockdown


title: AB9-6h_10nMORG2058_Replicate2

description: Replicate 2

source_name: MCF-10A clone AB9 grown in monolayer culture, treated 6h with 10nM ORG2058


title: AB9-2h_10nMORG2058_Replicate3

description: Replicate 3

source_name: MCF-10A clone AB9 grown in monolayer culture, treated 2h with 10nM ORG2058


title: AB9-2h_10nMORG2058_Replicate1

description: Replicate 1


title: AB9-6h_10nMORG2058_Replicate3

description: Replicate 3


title: AB9-6h_10nMORG2058_Replicate1

description: Replicate 1


title: AB32_FOXA1_overexpression_6hORG2

description: Replicate 2

source_name: MCF-10A clone AB32 cells grown in monolayer culture, transduced 48h with pCDH-CMV-FOXA1-EF1-copGFP virus then treated 6h with 10nM ORG2058

growth_protocol: Cells were grown in standard recommended media in monolayer cultures at 37C and 5% CO2 for 24h prior to viral transduction and treatment

treatment_protocol: Cells were transduced with empty vector (pCDH) or FOXA1 expression viral particles 48h, then treated with 10nM ORG2058 or ethanol vehicle (0.1% final in growth medium) for the indicated times, followed by harvesting by trypsinization and centrifugation.

tag: transduced virus


title: AB9-2h_10nMORG2058_Replicate2

description: Replicate 2


title: zebrafish at ZT36, DD condition

first: Haifang

last: Wang

address: 320 yueyang road

department: CAS-MPG Partner institute for Computational Biology

institute: Shanghai institute for biology science

hyb_protocol: Cy3-labeled cRNA (800ng each) were hybridized to the zebrafish microarray (G5219F, Agilent) for 17 h at 65°C.

scan_protocol: The hybridized microarrays were then washed according to the manufacturer’s protocol. Microarray results were extracted using Agilent G2565BA Scanner and Feature Extraction software (v10.5.1, Agilent), and subsequently analyzed by Gene-Spring GX software (v11.0.1, Agilent).

data_processing: Data were extracted using Feature Extraction software (v10.5.1, Agilent) and Gene-Spring GX software (v11.0.1, Agilent).

organism: Danio rerio

source_name: whole body

label_protocol: Purified total RNA of each sample was amplified and labeled with a fluorescent dye Cyanine 3 (Cy3) using a low-RNA input linear amplification kit following the manufacturer's protocol (5184-3523, Agilent).

extract_protocol: Total RNA of larval sample was extracted using Trizol (Invitrogen) according to the manufacturer’s instruction. The quantity and quality of the RNA samples were assessed with a NanoDrop ND-1000 spectrometer (NanoDrop Technologies) and an Agilent 2100 bioanalyzer (Agilent).

value: larva

value: male

value: DD condition


title: AB32_FOXA1_overexpression_24hORG2

description: Replicate 2

source_name: MCF-10A clone AB32 cells grown in monolayer culture, transduced 48h with pCDH-CMV-FOXA1-EF1-copGFP virus then treated 24h with 10nM ORG2058


title: AB32-2h_10nMORG2058_Replicate3

description: Replicate 3

source_name: MCF-10A clone AB32 grown in monolayer culture, treated 2h with 10nM ORG2058


title: zebrafish at ZT40, DD condition


title: zebrafish at ZT44, DD condition


title: AB32-24h_10nMORG2058_Replicate1

description: Replicate 1


title: AB9-Vehicle_control_Replicate2

description: Replicate 2

source_name: MCF-10A clone AB9 grown in monolayer culture, treated 24h with ethanol vehicle


title: zebrafish at ZT24, DD condition


title: AB32_FOXA1_overexpression_24hORG1

description: Replicate 1


title: zebrafish at ZT32, DD condition


title: zebrafish at ZT28, DD condition


title: AB32-6h_10nMORG2058_Replicate2

description: Replicate 2

source_name: MCF-10A clone AB32 grown in monolayer culture, treated 6h with 10nM ORG2058


title: AB32_FOXA1_overexpression_6hORG1

description: Replicate 1


title: AB9-Vehicle_control_Replicate3

description: Replicate 3


title: AB32-24h_10nMORG2058_Replicate2

description: Replicate 2


title: AB9-Vehicle_control_Replicate1

description: Replicate 1


title: AB32-2h_10nMORG2058_Replicate1

description: Replicate 1


title: AB32-6h_10nMORG2058_Replicate1

description: Replicate 1


title: AB32-2h_10nMORG2058_Replicate2

description: Replicate 2


title: AB32_FOXA1_overexpression_Vehicle2

description: Replicate 2

source_name: MCF-10A clone AB32 cells grown in monolayer culture, transduced 48h with pCDH-CMV-FOXA1-EF1-copGFP virus then treated 24h with ethanol vehicle (0.1%)


title: AB32-6h_10nMORG2058_Replicate3

description: Replicate 3


title: AB32_pCDH_vectorControl_24hORG2

description: Replicate 2

source_name: MCF-10A clone AB32 cells grown in monolayer culture, transduced 48h with pCDH empty vector virus then treated 24h with 10nM ORG2058


title: zebrafish at ZT16, DD condition


title: AB32-Vehicle_control_Replicate2

description: Replicate 2

source_name: MCF-10A clone AB32 grown in monolayer culture, treated 24h with ethanol vehicle


title: AB32_pCDH_vectorControl_6hORG1

description: Replicate 1

source_name: MCF-10A clone AB32 cells grown in monolayer culture, transduced 48h with pCDH empty vector virus then treated 6h with 10nM ORG2058


title: T-47D-24h_10nMORG2058_Replicate3

description: Replicate 3

source_name: T-47D breast cancer cells grown in monolayer culture, treated 24h with 10nM ORG2058


title: zebrafish at ZT44, LD condition

value: LD condition


title: AB32_pCDH_vectorControl_6hORG2

description: Replicate 2


title: AB32_pCDH_vectorControl_Vehicle1

description: Replicate 1

source_name: MCF-10A clone AB32 cells grown in monolayer culture, transduced 48h with pCDH empty vector virus then treated 24h with ethanol vehicle (0.1%)


title: AB32-Vehicle_control_Replicate3

description: Replicate 3


title: zebrafish at ZT0, DD condition


title: AB32_pCDH_vectorControl_24hORG1

description: Replicate 1