title: YCC-22 [SNP]

value: Gastric cancer cell line

value: Adenocarcinoma


title: RPMI_CPI 0.01uM

status: Public on Sep 28 2016

type: RNA

city: Barcelona

first: Patricia

last: Pérez-Galán

state: Barcelona

address: Centre Esther Koplowitz, Hemato-oncology dept, Rosello 149-153, 2nd floor

department: Hemato-oncology

country: Spain

institute: IDIBAPS

description:
RPMI_CPI
Gene expression data in treated RPMI-8226 cells.

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the GeneTitan instrument.

data_processing:
Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).
Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm implemented in the Expression Console Software v1.1 (Affymetrix).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: RPMI-8226 multiple myeloma cell line, CPI

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150ng total RNA.

growth_protocol: MM cells at exponential phase were set at 5x10^5 cells/ml for the experiment.

extract_protocol: Total RNA was extracted using the Trizol reagent.

treatment_protocol: MM cells were treated with 0.01uM CPI203 +/- 5uM LENA and 0.05uM Dexa for 6h.

tag: cell line

tag: cell type

value: multiple myeloma cell line

tag: treatment


title: RPMI_LENA 5uM/Dexa 0.05uM 6h

description:
RPMI_LENA_DEXA
Gene expression data in treated RPMI-8226 cells.

source_name: RPMI-8226 multiple myeloma cell line, LENA/DEXA

value: lenalidomide plus dexamethasone


title: RPMI_C 6h

description:
RPMI_CONTROL
Gene expression data in control RPMI-8226 cells.

source_name: RPMI-8226 multiple myeloma cell line, control

value: control


title: placenta_standard_infected, IM67

city: Durham

first: Cody

middle: Shaw

last: Nelson

state: NC

address: 2 Genome Ct

department: MGM

country: USA

institute: Duke University

hyb_protocol: Targets were hybridized to Affymetrix GeneChip® Rhesus Macaque Genome arrays in Affymetrix GeneChip® Hybridization Oven 645, then washed in Affymetrix GeneChip® Fluidics Station 450 according to standard Affymetrix GeneChip® Hybridization and Wash protocols.

scan_protocol: Chip was scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® protocols.

data_processing: Affymetrix microarray data was initially processed, underwent QC, and was normalized with the robust multi-array average method using the affy Bioconductor package from the R statistical programming environment (R studio version 0.99.902). Differential expression was carried out using a moderated t-statistic from the limma package. The false discovery rate was used to control for multiple hypothesis testing.

label: Biotin

organism: Macaca mulatta

source_name: fetal placenta from standard HIG group, CMV-infected

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion) from total RNA. Biotin labeling.

extract_protocol: Tissue sections weighing approximately 30mg were obtained from flash frozen rhesus placenta, lysed using a TissueLyser LT (Qiagen), then total RNA extracted using an RNeasy Mini Kit (Qiagen). RNA was assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies) and NanoDrop 8000 spectrophotometer (Thermo Scientific/NanoDrop) and confirmed to have: A260/A280>1.8, A260/A230>1.0, and RIN>7.0.

treatment_protocol: Placentas were flash frozen upon fetal abortion or fetal harvest, then stored at -80C.

tag: tissue

value: Fetal placenta

tag: rhcmv infection

value: Infected

tag: hig tx

value: Standard


title: Healthy Control 1

city: Rotterdam

first: Arne

last: IJpma

address: Dr. Molewaterplein 50

department: Bioinformatics

country: Netherlands

institute: Erasmus MC

hyb_protocol: After fragmentation the chips were hybridized for 18h at 45°C. 5ug biotinylated cDNA was hybridized on Human Genome U133 plus 2.0 Array Gene Chips (Affymetrix, High Wycombe, UK) according to the manufacturer's protocols.

scan_protocol: Chips were scanned on a Affymetrix GeneChip Scanner 3000 7G according to the manufacturers protocol using the GeneChip® Command Console® Software (AGCC) v3.2.4

data_processing: The data were analyzed with Partek Genomics Suite version 6.6 using GCRMA with default settings and quantile normalization method. The data is log2 transformed.

source_name: Healthy Control

label_protocol: The RNA (RIN≥8) was reverse transcribed, amplified, biotinylated and fragmented with the Ovation® Pico WTA system and EncoreTM Biotin Module (NuGEN Technologies, Leek, The Netherlands)

growth_protocol: Plasmacytoid dendritic cells were obtained from peripheral blood using ficoll peripheral blood mononuclear cell isolation.  FACS sorting was used to select BDCA4+CD123+ pDCs.

extract_protocol: Total RNA was isolated from purified CD123+BDCA4+ sorted cell-populations with the PicoPure RNA isolation kit (Arcturus®, Applied Biosystem, CA, USA) according to the manufacturers protocol, including a DNase I treatment (Qiagen, Venlo, The Netherlands) to remove genomic DNA contamination.

treatment_protocol: Steady-state (no treatment)

tag: disease state

tag: gender

value: female

tag: age at inclusion

value: purified CD123+BDCA4+ plasmacytoid dendritic sorted cell-population


title: N2000639

type: genomic

city: Singapore

first: Aditi

last: Qamra

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: GIS

scan_protocol: BeadChips were scanned using the iScan system

data_processing:
Methylation β-values were calculated and background corrected using the methylumi R BioConductor package.
Normalization was performed using the BMIQ method (watermelon package in R).

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Gastric Primary Tissue

label_protocol: Standard Illumina protocol - Infinium HD Methylation protocol  Hybridization Protocol: Standard Illumina protocol - Infinium HD Methylation protocol

extract_protocol: Genomic DNA was isolated using Qiagen Blood & Cell Culture DNA Mini Kit according to the manufacturer's protocol

tag: tissue subtype

value: Gastric primary non-malignant tissue


title: N2000721

hyb_protocol: Hybridization Protocol: Standard Illumina protocol - Infinium HD Methylation protocol


title: JJN3_CPI 0.01uM + LENA 5uM/Dexa 0.05uM 6h

description:
JJN3_COMBO
Gene expression data in treated JJN3 cells.

source_name: JJN3 multiple myeloma cell line, COMBO

value: CPI203 plus lenalidomide plus dexamethasone


title: placenta_high_uninfected, HD82

source_name: fetal placenta from high-potency HIG group, not CMV-infected

value: Not infected

value: High-potency


title: JJN3_CPI 0.01uM

description:
JJN3_CPI
Gene expression data in treated JJN3 cells.

source_name: JJN3 multiple myeloma cell line, CPI


title: placenta_control_infected, HD79

source_name: fetal placenta from control group, CMV-infected

value: Control


title: JJN3_LENA 5uM/Dexa 0.05uM 6h

description:
JJN3_LENA_DEXA
Gene expression data in treated JJN3 cells.

source_name: JJN3 multiple myeloma cell line, LENA/DEXA


title: N980097


title: T2000639

value: Gastric primary tumor tissue


title: IFN pos signature 1

source_name: IFN pos signature

value: IFNpos pSS


title: T2000721


title: JJN3_C 6h

description:
JJN3_CONTROL
Gene expression data in control JJN3 cells.

source_name: JJN3 multiple myeloma cell line, control


title: placenta_standard_infected, GI73


title: N2000986


title: ARP1_LENA 5uM/Dexa 0.05uM 6h

description:
ARP1_LENA_DEXA
Gene expression data in treated ARP1 cells.

source_name: ARP1 multiple myeloma cell line, LENA/DEXA


title: placenta_control_infected, GM04


title: ARP1_CPI 0.01uM

description:
ARP1_CPI
Gene expression data in treated ARP1 cells.

source_name: ARP1 multiple myeloma cell line, CPI


title: ARP1_CPI 0.01uM + LENA 5uM/Dexa 0.05uM 6h

description:
ARP1_COMBO
Gene expression data in treated ARP1 cells.

source_name: ARP1 multiple myeloma cell line, COMBO


title: ARP1_C 6h

description:
ARP1_C
Gene expression data in control ARP1 cells.

source_name: ARP1 multiple myeloma cell line, control


title: MDS5q-10269

status: Public on Sep 27 2016

city: Salamanca

first: Beatriz

middle: Roson

last: Burgo

address: Campus Miguel de Unamuno

department: Cancer Research Centre

institute: Consejo Superior de Investigaciones Científicas & Universidad de Salamanca

description:
MDS
MYELODYSPLASTIC SYNDROME 5q-

data_processing:
The raw Ct values were normalized using the array endogenous control features: the RNU48 and the four replicates of RNU6B, by the formula:
 ΔCtmiRNA = CtmiRNA - mean (Ct RNU6B, RNU48).

label: FAM

source_name: MSCs Microvesicles (MSC-MVs)_MDS5q-

label_protocol: RNA from microvesicles was retrotranscribed with Megaplex™ RT Primers pool, following manufacturer instructions of Taqman Human miRNA Array card A (Applied Biosystems)

growth_protocol: BM-MSCs were isolated from mononuclear cell fraction by Ficoll-Paque, plated and expanded in DMEM (10%FCS, 1%Penicillin/Streptomycin) until passage 3 (incubated at 37ºC and 5% CO2)

extract_protocol: Total RNA from microvesicle fraction was extracted using TRIzol reagent according to the manufactures’s instructions (Invitrogen).

treatment_protocol: For microvesicle production: MSC cultures were cultured in DMEM deprived of FCS, and the supernatants were collected either 6 or 24 hours after. Purification of microvesicles was performed by ExoQuick-TC exosome precipitation solution (ExoQuick; System Biosiences)

value: Bone Marrow

value: MSC (Mesenchymal Stem/Stromal Cell)


title: MDS-N11

description:
MDS
LOW RISK MYELODYSPLASTIC SYNDROME

source_name: MSCs Microvesicles (MSC-MVs)_MDS

value: low risk MDS


title: MDS5q-10185

description:
MDS
MYELODYSPLASTIC SYNDROME 5q-


title: MDS-N10

description:
MDS
LOW RISK MYELODYSPLASTIC SYNDROME


title: MDS5q-10370

description:
MDS
MYELODYSPLASTIC SYNDROME 5q-


title: MDS-N9

description:
MDS
LOW RISK MYELODYSPLASTIC SYNDROME


title: MDS5q-10277

description:
MDS
MYELODYSPLASTIC SYNDROME 5q-


title: placenta_high_uninfected, JM52


title: T2000986


title: KOp3C_31

type: SRA

city: La Jolla

first: Kun

last: Zhang

state: California

address: 9500 Gilman Drive

institute: UCSD

description: No raw data available for this sample

library_source: transcriptomic

data_processing:
50bp single-end reads (or first 50bp of 100bp reads using parameter "--clip3pNbases 50") were mapped to the mouse genome using STAR (v2.3.0): STAR --readFilesCommand zcat --runThreadN 8  --outSAMstrandField intronMotif --genomeDir "genome dir" --readFilesIn "fastq files" --outFileNamePrefix "sample name"
Gene read counts were calculated based on exon mapping using HTSeq (v0.6.1): htseq-count -q -t exon - "gtf file" > "readCount file"
Transcripts per million mapped reads (TPM) values were calculated
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for each Sample

organism: Mus musculus

source_name: Testes

extract_protocol:
Testes were decapsulated in HBSS (Mediatech  Inc.) and digested with collagenase IV (1 mg/ml in HBSS) at 37 °C for 3 min with gentle agitation.  After washing with HBSS, samples were digested with 0.25 ml of DNase I (7 mg/ml, Sigma Inc.) and 1 ml of Trypsin/EDTA (0.25%, Invitrogen Inc.) at 37 °C for 10 min.  Digestion was stopped by adding 1 ml of media (MEMa + 10% FBS) and GFP+ cells were sorted using a FACSAria II machine (BD Biosciences).
Reverse transcription and cDNA amplification was performed with C1 Single-Cell Microfluidic Auto Prep System (Fluidigm) using the SMARTer Ultra Low RNA Kit (Clontech Inc.) with modifications: 1) addition of ERCC RNA Spike-In Mix (4456740, Ambion) at 1:40,000 dilution to the lysis reaction buffer; 2) inclusion of supplemental primer (5’-AAGCAGTGGTATCAACGCAGAGTACNNNNNN, diluted to 12µM in the supplied Clontech Dilution buffer) to Lysis Mix A for a final concentration of 4.2µM.  Final libraries were prepared for sequencing using the NexteraXT dual barcoding system (Illumina, Inc.).

tag: genotype

value: Rhox10 Knockout

tag: age

value: Postnatal Day 3

value: Id4-eGFP Positive


title: MDS-N12

description:
MDS
LOW RISK MYELODYSPLASTIC SYNDROME


title: HD-sci

description:
HD
HEALTHY DONOR - CONTROL

source_name: MSCs Microvesicles (MSC-MVs)_HD

value: control


title: YCC-3 [SNP]

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

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

data_processing:
Data in .CEL format was processed in the following order (Deng et. al., 2012): (1) Normalization: Raw .CEL files were processed using Affymetrix Genotyping Console 4.2. Reference models were created from SNP6.0 profiles of normal gastric tissues according to the hybridization batch. Copy number changes in cell lines and primary tumor samples were determined by using the reference model from primary normal samples. (2) Segmentation:  Copy number segmentation data was produced using the circular binary segmentation (CBS) algorithm implemented in the DNAcopy R package.
copy number altered regions followed by the copy number alteration status

source_name: Gastric cancer cell line

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from flash-frozen gastric tumors and matched non-maligant gastric tissues using a Qiagen genomic DNA extraction kit.

tag: tissuetype

value: Gastric cancer cell line

tag: histology

value: Poorly differentiated


title: HD-10306

description:
HD
HEALTHY DONOR - CONTROL


title: HD-10360

description:
HD
HEALTHY DONOR - CONTROL


title: HD-10408

description:
HD
HEALTHY DONOR - CONTROL


title: Outer medulla, 2-amino-4-nitrophenol treated, Day 28, replicate 2

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

country: Japan

institute: Chemicals Evaluation and Research Institute, Japan

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60 deg C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Rat GE 8x60K Microarray Toxplus for 17 hours at 65 deg C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 deg C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 035170_D_F_20110629) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Four-week-old specific-pathogen-free (SPF) male Crl:CD Sprague-Dawley (SD) rats were obtained from Charles River Laboratories Japan, Inc. (Kanagawa, Japan). The rats were maintained in an air-conditioned animal room (temperature: 23 ± 2°C, relative humidity: 55% ± 15%) under a 12-h light/dark cycle. After a 1-week acclimatization period, healthy 5-week-old male animals were randomly divided into groups of four or five rats each and were given the test compounds in a suitable vehicle by gavage for up to 28 days.

extract_protocol: RNA was prepared using the miRNA Neasy kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 2-Amino-4-nitrophenol (ANP) was purchased from Wako Pure Chemicals (Osaka, Japan). The ANP was dissolved in corn oil, and the animals were dosed orally once daily for 28 days. A microarray analysis was performed for three of the four or five animals from each group obtained after 14 and 28 days of treatment. After one and seven days of treatment, three of the four animals obtained from each group were mixed and subjected to one microarray analysis.

value: 2-Amino-4-nitrophenol (750 mg/kg/day)

tag: strain

value: Sprague-Dawley

tag: treatment time

value: Day 28

value: male


title: Outer medulla, 2-amino-4-nitrophenol treated, Day 28, replicate 1


title: Outer medulla, 2-amino-4-nitrophenol treated, Day 28, replicate 3


title: Outer medulla, VC, Day 28, replicate 1

source_name: Outer medulla, VC, Day 28, replicate 1

value: Corn Oil


title: Outer medulla, VC, Day 28, replicate 3

source_name: Outer medulla, VC, Day 28, replicate 3


title: Outer medulla, 2-amino-4-nitrophenol treated, Day 14, replicate 2

value: Day 14


title: Outer medulla, 2-amino-4-nitrophenol treated, Day 14, replicate 1


title: IFN pos signature 3

value: female

value: purified CD123+BDCA4+ plasmacytoid dendritic sorted cell-population


title: Outer medulla, VC, Day 14, replicate 1

source_name: Outer medulla, VC, Day 14, replicate 1


title: Outer medulla, VC, Day 14, replicate 3

source_name: Outer medulla, VC, Day 14, replicate 3


title: Outer medulla, 2-amino-4-nitrophenol treated, Day 1, mixed

value: Day 1


title: Outer medulla, VC, Day 1, mixed

source_name: Outer medulla, VC, Day 1, mixed


title: Outer medulla, 2-amino-4-nitrophenol treated, Day 14, replicate 3


title: Outer medulla, VC, Day 28, replicate 2

source_name: Outer medulla, VC, Day 28, replicate 2


title: Renal cortex, tert-butyl alchol treated, isoflurane anesthesia, replicate 2 (B96)

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60 deg C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Rat GE 8x60K Microarray Toxplus for 17 hours at 65 deg C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 deg C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 035170_D_F_20110629) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Five week-old male Sprague-Dawley (Crl:CD(SD)) Rat were purchased from Charles River Japan. They were housed in an air-conditioned room at 21 to 25 deg C and 40 to 70% humidity, with a 12 h light, 12 h dark cycle. Rats were maintained on a basal diet (Oriental Yeast Co.), with tap water ad libitum.

treatment_protocol: Three animals were administrated water for four weeks, the other three animals were administrated tert-butyl alchol (1000 mg/kg/day) for four weeks.

value: tert-butyl alchol

tag: dose

value: 1000 mg/kg/day

tag: anesthesia

value: Isoflurane

value: renal cortex


title: Renal cortex, tert-butyl alchol treated, CO2-O2 anesthesia, replicate 3 (B96)


title: Renal cortex, tert-butyl alchol treated, isoflurane anesthesia, replicate 3 (B96)


title: Renal cortex, VC, isoflurane anesthesia, replicate 3 (B96)

source_name: Renal cortex, VC, isoflurane anesthesia

value: water


title: Renal cortex, VC, isoflurane anesthesia, replicate 2 (B96)


title: Outer medulla, VC, Day 14, replicate 2

source_name: Outer medulla, VC, Day 14, replicate 2


title: Renal cortex, tert-butyl alchol treated, isoflurane anesthesia, replicate 1 (B96)


title: Renal cortex, VC, isoflurane anesthesia, replicate 1 (B96)


title: Renal cortex, o-nitroanisole treated, replicate 2 (B94)

source_name: Renal cortex, o-nitroanisole

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated o-nitroanisole (400 mg/kg/day) for four weeks.

value: o-Nitroanisole

value: 400 mg/kg/day


title: Renal cortex, VC, CO2-O2 anesthesia, replicate 3 (B96)

source_name: Renal cortex, VC, CO2-O2 anesthesia


title: Renal cortex, o-nitroanisole treated, replicate 1 (B94)


title: Renal cortex, VC, CO2-O2 anesthesia, replicate 2 (B96)


title: Renal cortex, VC, replicate 3 (B94)

source_name: Renal cortex, VC


title: Outer medulla, VC, Day 7, mixed

source_name: Outer medulla, VC, Day 7, mixed

value: Day 7


title: soil_clipping-warming_rep6

city: Norman

first: Jizhong

last: Zhou

state: OK

address: 101 David L Boren Blvd

department: Department of Microbiology and Plant Biology

institute: University of Oklahoma

hyb_protocol: The labeled target was re-suspended in 120 µl hybridization solution containing 50% formamide, 3 x SSC, 10 µg of unlabeled herring sperm DNA (Promega, Madison, WI), and 0.1% SDS, and the mix was denatured at 95°C for 5 min and kept at 50°C until it was deposited directly onto a microarray.  Hybridizations were performed with a TECAN Hybridization Station HS4800 Pro (TECAN, US) according to the manufacturer’s recommended method. This equipment allows up to 48 hybridizations at one time, and well reproducible results were obtained.

scan_protocol: After washing and drying, the microarray was scanned by ScanArray Express Microarray Scanner (Perkin Elmer, Boston, MA) at 633 nm using a laser power of 90% and a photomultiplier tube (PMT) gain of 75%. The ImaGene version 6.0 (Biodiscovery, El Segundo, CA) was then used to determine the intensity of each spot, and identify poor-quality spots.

data_processing: Raw signal intensities from ImaGene were submitted to the online Microarray Data Manager (http://ieg.ou.edu/entrance.html) and analyzed by the following steps: (i) Removing spots flagged as 1 or 3 by ImaGene and with a signal to noise ratio (SNR) less than 2.0; (ii) Normalizing signal intensities at three levels: individual sub-grids within a slide, technical replicates, and across different slides; (iii) Removing genes with less than 1/3 detected positive probes, or two; (iv) Removing probes appearing in only one replicate. After these steps, a total of 3022 functional genes were obtained. The sum of signal intensities in each sample was calculated and the average of sums was used to multiply the relative abundance of each probe. A natural logarithm transformation was performed for the amplified relative abundance plus 1.

organism:
Bacteria
Archaea
Fungi
Viruses

label_protocol: Whole community genome was amplified with 50 ng template DNA. 2.5 µg amplified DNAs was labeled using Cy5. First, the whole amplified products were mixed with 20 μL random primers, denatured at 99.9 °C for 5 min, and then immediately chilled on ice. Following denaturation, the labeling master mix containing 2.5 μL dNTP (5 mM dAGC-TP, 2.5 mM dTTP), 1 μL Cy-5 dUTP (Amersham, Piscataway, NJ), 80 U of the large Klenow fragment (Invitrogen, Carlsbad, CA), and 2.5 μL water were added and then incubated at 37°C for 3 hours, followed by heating at 95 °C for 3 min. Labeled DNA was purified using the QIA quick purification kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions, measured on a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE), and then dried down in a SpeedVac (ThermoSavant, Milford, MA) at 45 °C for 45 min.

growth_protocol: Microbial analyses were performed for soil samples collected from the top 15 cm in April 2007 and October 2008. Each sample was composited from four soil cores (2.5 cm diameter) and sieved through 2 mm sieves. All samples were transported to the laboratory immediately after sieving and stored at -80 °C.

extract_protocol: Soil DNA was extracted by freeze-grinding mechanical lysis as described previously in Zhou et al 1996 and purified using a low melting agarose gel followed by a phenol extraction.

treatment_protocol: The field experiment was established in November 1999. A paired factorial design was applied, of which warming (targeting ambient +2 °C) was set as a main factor and clipping as a nested factor. The warming treatment was achieved by suspending infrared radiators (Kalglo Electronics, Bethlehem, Pennsylvania, USA) at 1.5 m above the ground. Dummy infrared radiators were used in control plots to mimic the shading effect from the device. There were six pairs of unwarmed and warmed plots. Each unwarmed or warmed plot (2 m × 2 m) was divided into four 1 m ×1 m subplots. Plants in two diagonal subplots were harvested at 10 cm above the ground annually, usually in August, as the clipping treatment.

tag: sample

value: tall grassland subsuface (0-15cm) soil

tag: sample group

value: warmed and plant clipped yearly


title: Outer medulla, 2-amino-4-nitrophenol treated, Day 7, mixed

tag: treatment

value: 2-Amino-4-nitrophenol (750 mg/kg/day)

value: Sprague-Dawley


title: Renal cortex, tert-butyl alchol treated, CO2-O2 anesthesia, replicate 2 (B96)

value: male

tag: tissue


title: Renal cortex, tert-butyl alchol treated, CO2-O2 anesthesia, replicate 1 (B96)


title: Renal cortex, o-nitroanisole treated, replicate 3 (B94)


title: Renal cortex, VC, CO2-O2 anesthesia, replicate 1 (B96)


title: soil_clipping-warming_rep5


title: soil_clipping-warming_rep3


title: soil_clipping-warming_rep2


title: soil_clipping-warming_rep1


title: WT, rep B, 0min vs. TUP1(K270R),CYC8(K735R,K736R,K738R,K748R), rep B, 60min

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

hyb_protocol: reference URL : http://dunham.gs.washington.edu/UWAgilentRNA.pdf

scan_protocol: Pixel Size : 10 Scan Date : 2013-06-16 Scan Time : 12:55:13 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file

organism: Saccharomyces cerevisiae

growth_protocol: media : yeast complete

extract_protocol:
Extracted molecule : Total RNA
Extraction method : acid phenol prep http://dunham.gs.washington.edu/MDyeastRNA.pdf

treatment_protocol: Time : 0 minutes

tag: strain name

value: Wild type

tag: replicate

value: B

tag: time

value: 0 minutes

growth_protocol: media : yeast complete+1.2M sorbitol

treatment_protocol: Time : 60 minutes

value: 60 minutes


title: soil_clipping-no warming_rep3

source_name: soil_clipping-no warming

value: plant clipped yearly


title: soil_clipping-no warming_rep4


title: Renal cortex, VC, replicate 1 (B94)

value: Corn Oil

tag: gender


title: soil_clipping-no warming_rep6


title: WT, rep B, 0min vs. TUP1(K270R),CYC8(K735R,K736R,K738R,K748R), rep B, 30min

label_protocol: reference URL : http://dunham.gs.washington.edu/UWAgilentRNA.pdf

treatment_protocol: Time : 30 minutes

value: 30 minutes


title: Renal cortex, VC, replicate 2 (B94)

value: renal cortex


title: IFN neg signature 2

source_name: IFN neg signature

tag: disease state

value: IFNneg pSS

value: female

tag: age at inclusion

tag: cell type

value: purified CD123+BDCA4+ plasmacytoid dendritic sorted cell-population


title: Renal cortex, o-anthranilic acid treated, replicate 3 (B97)

source_name: Renal cortex, o-anthranilic acid

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated o-anthranilic acid (1000 mg/kg/day) for four weeks.

value: o-Anthranilic acid

value: 1000 mg/kg/day


title: WT, rep B, 0min vs. TUP1(K270R),CYC8(K735R,K736R,K738R,K748R), rep B, 0min

scan_protocol: Pixel Size : 10 Scan Date : 2013-06-16 Scan Time : 12:39:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: soil_clipping-no warming_rep2

value: tall grassland subsuface (0-15cm) soil


title: soil_clipping-no warming_rep1


title: WT, rep B, 0min vs. CYC8(K735R,K736R,K738R,K748R), rep B, 60min


title: soil_no clipping-warming_rep5

source_name: soil_no clipping-warming

value: warmed


title: soil_no clipping-warming_rep4


title: soil_no clipping-warming_rep3


title: soil_no clipping-warming_rep6


title: soil_clipping-no warming_rep5


title: Renal cortex, o-anthranilic acid treated, replicate 2 (B97)

value: Sprague-Dawley


title: Renal cortex, o-anthranilic acid treated, replicate 1 (B97)

value: male


title: soil_clipping-warming_rep4

value: warmed and plant clipped yearly


title: soil_no clipping-warming_rep2


title: soil_no clipping-warming_rep1


title: WT, rep B, 0min vs. CYC8(K735R,K736R,K738R,K748R), rep B, 0min

value: Wild type

value: B


title: soil_no clipping-no warming_rep6

source_name: soil_no clipping-no warming

value: control


title: WT, rep B, 0min vs. TUP1(K270R), rep B, 30min

value: 0 minutes


title: WT, rep B, 0min vs. TUP1(K270R), rep B, 60min

value: 60 minutes


title: soil_no clipping-no warming_rep5


title: soil_no clipping-no warming_rep4


title: soil_no clipping-no warming_rep3


title: Renal cortex, VC, replicate 1 (B97)

value: Corn Oil


title: Renal cortex, VC, replicate 2 (B97)

value: renal cortex


title: soil_no clipping-no warming_rep1


title: soil_no clipping-no warming_rep2


title: WT, rep B, 0min vs. TUP1(K270R), rep B, 0min


title: Renal cortex, o-anisidine hydrochloride treated, replicate 3 (B98)

source_name: Renal cortex, o-anisidine hydrochloride

treatment_protocol: Three animals were administrated water for four weeks, the other three animals were administrated o-anisidine hydrochloride (700 mg/kg/day) for four weeks.

value: o-Anisidine hydrochloride

value: 700 mg/kg/day


title: WT, rep B, 0min vs. WT, rep B, 60min

description: WT, rep B, 0min vs. WT, rep B, 60min


title: WT, rep B, 0min vs. WT, rep B, 30min

description: WT, rep B, 0min vs. WT, rep B, 30min

value: 30 minutes


title: WT, rep B, 0min vs. CYC8(K735R,K736R,K738R,K748R), rep B, 30min


title: Renal cortex, o-anisidine hydrochloride treated, replicate 2 (B98)


title: Renal cortex, p-nitroanisole treated, replicate 2 (B123)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 045522_D_F_20130222) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Renal cortex, p-nitroanisole

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated p-nitroanisole (500 mg/kg/day) for four weeks.

value: p-Nitroanisole

value: 500 mg/kg/day


title: WT, rep B, 0min vs. WT, rep A, 0min

description: WT, rep B, 0min vs. WT, rep A, 0min

value: A


title: Renal cortex, p-nitroanisole treated, replicate 3 (B123)


title: TUP1(K270R),CYC8(K735R,K736R,K738R,K748R), rep A, 60min vs. WT, rep A, 0min


title: Renal cortex, VC, replicate 2 (B98)

value: water


title: Renal cortex, p-nitroanisole treated, replicate 1 (B123)

value: Sprague-Dawley


title: Renal cortex, o-anisidine hydrochloride treated, replicate 1 (B98)

value: male


title: Renal cortex, VC, replicate 3 (B123)


title: Renal cortex, VC, replicate 2 (B123)


title: Renal cortex, VC, replicate 3 (B98)


title: TUP1(K270R),CYC8(K735R,K736R,K738R,K748R), rep A, 30min vs. WT, rep A, 0min

scan_protocol: Pixel Size : 10 Scan Date : 2013-06-16 Scan Time : 12:47:13 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: Renal cortex, VC, replicate 1 (B98)


title: Renal cortex, VC, replicate 1 (B123)


title: TUP1(K270R),CYC8(K735R,K736R,K738R,K748R), rep A, 0min vs. WT, rep A, 0min


title: CYC8(K735R,K736R,K738R,K748R), rep A, 60min vs. WT, rep A, 0min


title: Renal cortex, cisplatin treated, Intravenous injection, replicate 3 (B15-6)

treatment_protocol: Three animals were administrated water for four weeks, the other three animals were administrated cisplatin (3.75 mg/kg/day) for four weeks.

value: Cisplatin

value: 0.75 mg/kg/day

tag: administration

value: Intravenous injection


title: CYC8(K735R,K736R,K738R,K748R), rep A, 30min vs. WT, rep A, 0min

value: Wild type


title: Renal cortex, cisplatin treated, Intravenous injection, replicate 2 (B15-6)


title: Renal cortex, cisplatin treated ,Intravenous injection, replicate 1 (B15-6)

source_name: Renal cortex, cisplatin treated, Intravenous injection


title: Renal cortex, tris(2-chloroethyl)phosphate treated, replicate 3 (B99)

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated tris(2-chloroethyl)phosphate (400 mg/kg/day) for four weeks.

value: 400 mg/kg/day


title: Renal cortex, tris(2-chloroethyl)phosphate treated, replicate 2 (B99)


title: Renal cortex, VC, Intravenous injection, replicate 2 (B15-6)

source_name: Renal cortex, VC, Intravenous injection


title: CYC8(K735R,K736R,K738R,K748R), rep A, 0min vs. WT, rep A, 0min

value: 0 minutes


title: Renal cortex, tris(2-chloroethyl)phosphate treated, replicate 1 (B99)


title: Renal cortex, VC, Intravenous injection, replicate 1 (B15-6)


title: Renal cortex, VC, replicate 3 (B99)

value: Corn Oil


title: Renal cortex, cisplatin treated, Gavage, replicate 3 (B114)

source_name: Renal cortex, cisplatin treated, Gavage

value: 3.75 mg/kg/day

value: Gavage

value: renal cortex


title: Renal cortex, cisplatin treated, Gavage, replicate 1 (B114)


title: Renal cortex, VC, Intravenous injection, replicate 3 (B15-6)


title: Renal cortex, cisplatin treated, Gavage, replicate 2 (B114)


title: TUP1(K270R), rep A, 60min vs. WT, rep A, 0min

value: TUP1(K270R), replicate A

value: 60 minutes


title: Renal cortex, VC, Gavage, replicate 3 (B114)

source_name: Renal cortex, VC, Gavage


title: Renal cortex, VC, Gavage, replicate 2 (B114)


title: Renal cortex, 4,4'-thiobis(6-tert-butyl-m-cresol) treated, replicate 3 (B109)

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated 4,4'-thiobis(6-tert-butyl-m-cresol) (300 mg/kg/day) for four weeks.

value: 300 mg/kg/day


title: Renal cortex, VC, replicate 2 (B99)


title: Renal cortex, phenolphthalein treated, replicate 3 (B93)

source_name: Renal cortex, phenolphthalein

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated phenolphthalein (1000 mg/kg/day) for four weeks.

value: Phenolphthalein

value: 1000 mg/kg/day


title: Renal cortex, VC, Gavage, replicate 1 (B114)

value: water

value: Sprague-Dawley


title: Renal cortex, 4,4'-thiobis(6-tert-butyl-m-cresol) treated, replicate 1 (B109)

value: male


title: Renal cortex, 4,4'-thiobis(6-tert-butyl-m-cresol) treated, replicate 2 (B109)


title: WT, rep A, 60min vs. WT, rep A, 0min

description: WT, rep A, 60min vs. WT, rep A, 0min

value: A


title: Renal cortex, VC, replicate 2 (B109)


title: Renal cortex, VC, replicate 1 (B109)


title: Renal cortex, phenolphthalein treated, replicate 2 (B93)


title: Renal cortex, VC, replicate 1 (B99)


title: TUP1(K270R), rep A, 0min vs. WT, rep A, 0min


title: TUP1(K270R), rep A, 30min vs. WT, rep A, 0min

value: 30 minutes


title: WT, rep A, 30min vs. WT, rep A, 0min

description: WT, rep A, 30min vs. WT, rep A, 0min

value: Wild type


title: Renal cortex, tricresyl phosphate treated, replicate 3 (B115)

source_name: Renal cortex, tricresyl phosphate

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated tricresyl phosphate (200 mg/kg/day) for four weeks.

value: Tricresyl phosphate

value: 200 mg/kg/day


title: Renal cortex, phenolphthalein treated, replicate 1 (B93)


title: Renal cortex, tricresyl phosphate treated, replicate 2 (B115)


title: Renal cortex, VC, replicate 3 (B97)

value: Corn Oil


title: Renal cortex, VC, replicate 3 (B115)


title: Renal cortex, VC, replicate 2 (B93)


title: Renal cortex, VC, replicate 3 (B93)


title: Renal cortex, sulfone bis(p-chlorophenyl) treated, replicate 3 (B124)

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated sulfone bis(p-chlorophenyl) (250 mg/kg/day) for four weeks.

value: Sulfone bis(p-chlorophenyl

value: 250 mg/kg/day


title: Renal cortex, tricresyl phosphate treated, replicate 1 (B115)

value: renal cortex


title: Renal cortex, VC, replicate 2 (B115)


title: Renal cortex, VC, replicate 3 (B109)


title: Renal cortex, VC, replicate 1 (B115)


title: Renal cortex, sulfone bis(p-chlorophenyl) treated, replicate 1 (B124)


title: Renal cortex, VC, replicate 1 (B124)


title: Renal cortex, sulfone bis(p-chlorophenyl) treated, replicate 2 (B124)


title: Renal cortex, potassium bromate treated, replicate 3 (B117)

source_name: Renal cortex, potassium bromate

treatment_protocol: Three animals were administrated water for four weeks, the other three animals were administrated potassium bromate (100 mg/kg/day) for four weeks.

value: Potassium bromate

value: 100 mg/kg/day


title: Renal cortex, nitrilotriacetic acid trisodium monohydrate treated, replicate 3 (B101)

treatment_protocol: Three animals were administrated water for four weeks, the other three animals were administrated nitrilotriacetic acid trisodium monohydrate (1000 mg/kg/day) for four weeks.

value: Nitrilotriacetic acid trisodium monohydrate


title: Renal cortex, VC, replicate 3 (B124)


title: Renal cortex, VC, replicate 2 (B124)


title: Renal cortex, potassium bromate treated, replicate 2 (B117)


title: Renal cortex, VC, replicate 3 (B117)


title: Renal cortex, nitrilotriacetic acid trisodium monohydrate treated, replicate 2 (B101)


title: Renal cortex, nitrilotriacetic acid trisodium monohydrate treated, replicate 1 (B101)


title: Renal cortex, VC, replicate 3 (B101)


title: Renal cortex, potassium bromate treated, replicate 1 (B117)


title: Renal cortex, VC, replicate 2 (B101)


title: Renal cortex, VC, replicate 1 (B117)


title: Renal cortex, VC, replicate 1 (B93)


title: Renal cortex, VC, replicate 1 (B101)


title: Renal cortex, phenylbutazone treated, replicate 3 (B121)

source_name: Renal cortex, phenylbutazone

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated phenylbutazone (200 mg/kg/day) for four weeks.

value: Phenylbutazone


title: Renal cortex, VC, replicate 2 (B117)

source_name: Renal cortex, VC


title: Renal cortex, phenylbutazone treated, replicate 1 (B121)


title: Renal cortex, phenylbutazone treated, replicate 2 (B121)


title: Renal cortex, VC, replicate 3 (B121)


title: Renal cortex, VC, replicate 2 (B121)


title: RAW264.7_LPS+DHA5HT_rep4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1).

source_name: RAW264.7 cell line

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: RAW264.7 mouse macrophages were grown and maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 1% streptomycin and penicillin at 37°C in a 5% CO2 humidified air atmosphere.

extract_protocol: RNA of RAW264.7 cells was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: RAW264.7 cells were seeded in 6-wells plates (2.5 105 cells/mL, 2 ml per well) and left overnight to adhere. RAW264.7 macrophages were stimulated for 24 hr with 1)  LPS (1 µg/ml) and vehicle control or 2) LPS (1 µg/ml) and 1 µM of DHA-5-HT or 3) vehicle control or 4) 1 µM of DHA-5-HT

value: Lipopolysaccharode (LPS, 1 µg/ml) plus docosahexaenoyl serotonin (DHA-5-HT, 1 µM)

tag: exposure time (hrs)


title: RAW264.7_DHA5HT_rep4

value: Docosahexaenoyl serotonin (DHA-5-HT), 1 µM


title: RAW264.7_LPS_rep4

value: Lipopolysaccharode (LPS), 1 µg/ml


title: Renal cortex, n-nitrosodimethylamine treated, replicate 3 (B106)

source_name: Renal cortex, n-nitrosodimethylamine

treatment_protocol: Three animals were administrated water for four weeks, the other three animals were administrated n-nitrosodimethylamine (4 mg/kg/day) for four weeks.

value: n-Nitrosodimethylamine

value: 4 mg/kg/day

tag: strain

value: Sprague-Dawley

value: male


title: RAW264.7_control_rep4

value: Control (solvent, ethanol 0.1% v/v)


title: Renal cortex, n-nitrosodimethylamine treated, replicate 2 (B106)


title: Renal cortex, VC, replicate 1 (B121)


title: Renal cortex, n-nitrosodimethylamine treated, replicate 1 (B106)


title: RAW264.7_LPS+DHA5HT_rep3


title: Renal cortex, ochratoxin A treated, replicate 2 (B122)

source_name: Renal cortex, ochratoxin A

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated ochratoxin A (1 mg/kg/day) for four weeks.

value: Ochratoxin A

value: 1 mg/kg/day


title: Renal cortex, ochratoxin A treated, replicate 3 (B122)


title: Renal cortex, ochratoxin A treated, replicate 1 (B122)


title: Renal cortex, VC, replicate 3 (B106)

value: water


title: Renal cortex, VC, replicate 2 (B106)


title: RAW264.7_LPS_rep3


title: Renal cortex, VC, replicate 3 (B122)

value: Corn Oil


title: Renal cortex, VC, replicate 2 (B122)

value: renal cortex


title: Renal cortex, VC, replicate 1 (B106)


title: RAW264.7_DHA5HT_rep3


title: Renal cortex, VC, replicate 1 (B122)


title: Renal cortex, N,N'-dinitrosopentamethylenetetramine treated, replicate 2 (B113)

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated N,N'-dinitrosopentamethylenetetramine (200 mg/kg/day) for four weeks.

value: N,N'-Dinitrosopentamethylenetetramine

value: 200 mg/kg/day


title: Renal cortex, bromodichloromethane treated, isoflurane anesthesia, replicate 3 (B103)

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated bromodichloromethane (200 mg/kg/day) for four weeks.

value: Bromodichloromethane

value: Isoflurane


title: Renal cortex, VC, replicate 2 (B113)


title: RAW264.7_control_rep3


title: RAW264.7_LPS_rep2


title: Renal cortex, VC, replicate 1 (B113)


title: Renal cortex, bromodichloromethane treated, isoflurane anesthesia, replicate 1 (B103)


title: Renal cortex, N,N'-dinitrosopentamethylenetetramine treated, replicate 1 (B113)


title: Renal cortex, N,N'-dinitrosopentamethylenetetramine treated, replicate 3 (B113)


title: Renal cortex, bromodichloromethane treated, isoflurane anesthesia, replicate 2 (B103)


title: RAW264.7_DHA5HT_rep2


title: Renal cortex, VC, replicate 3 (B111)

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated monuron (200 mg/kg/day) for four weeks.


title: RAW264.7_LPS+DHA5HT_rep2

value: Lipopolysaccharode (LPS, 1 µg/ml) plus docosahexaenoyl serotonin (DHA-5-HT, 1 µM)


title: Renal cortex, VC, replicate 3 (B113)


title: RAW264.7_control_rep2


title: Renal cortex, monuron treated, replicate 2 (B111)

source_name: Renal cortex, monuron

value: Monuron


title: Renal cortex, VC, replicate 2 (B111)


title: RAW264.7_LPS+DHA5HT_rep1

value: Docosahexaenoyl serotonin (DHA-5-HT), 1 µM


title: Renal cortex, monuron treated, replicate 1 (B111)


title: Renal cortex, VC, replicate 1 (B111)


title: RAW264.7_LPS_rep1

value: Lipopolysaccharode (LPS), 1 µg/ml


title: Renal cortex, VC, isoflurane anesthesia, replicate 2 (B103)

source_name: Renal cortex, VC, isoflurane anesthesia


title: Renal cortex, monuron treated, replicate 3 (B111)


title: Renal cortex, VC, isoflurane anesthesia, replicate 1 (B103)


title: Renal cortex, VC, isoflurane anesthesia, replicate 3 (B103)


title: Renal cortex, bromodichloromethane treated, CO2-O2 anesthesia, replicate 3 (B92)


title: Renal cortex, ethylenediamine dihydrochloride treated, replicate 2 (B119)

treatment_protocol: Three animals were administrated water for four weeks, the other three animals were administrated ethylenediamine dihydrochloride (500 mg/kg/day) for four weeks.

value: Ethylenediamine dihydrochloride

value: 500 mg/kg/day


title: Renal cortex, ethylenediamine dihydrochloride treated, replicate 1 (B119)

value: Sprague-Dawley

value: male


title: Renal cortex, VC, replicate 3 (B119)


title: Renal cortex, bromodichloromethane treated, CO2-O2 anesthesia, replicate 2 (B92)


title: RAW264.7_control_rep1

value: Control (solvent, ethanol 0.1% v/v)


title: Renal cortex, VC, CO2-O2 anesthesia, replicate 3 (B92)

source_name: Renal cortex, VC, CO2-O2 anesthesia


title: Renal cortex, VC, replicate 1 (B119)


title: Renal cortex, VC, replicate 2 (B110)

treatment_protocol: Three animals were administrated water for four weeks, the other three animals were administrated dipropylene glycol (1000 mg/kg/day) for four weeks.


title: Renal cortex, VC, replicate 2 (B119)


title: Renal cortex, dipropylene glycol treated, replicate 1 (B110)

source_name: Renal cortex, dipropylene glycol

value: Dipropylene glycol

value: 1000 mg/kg/day


title: Renal cortex, VC, replicate 3 (B110)

value: water


title: Renal cortex, bromodichloromethane treated, CO2-O2 anesthesia, replicate 1 (B92)

value: renal cortex


title: Renal cortex, anthraquinone treated, replicate 3 (B104)

source_name: Renal cortex, anthraquinone

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated anthraquinone (1000 mg/kg/day) for four weeks.

value: Anthraquinone


title: Renal cortex, VC, CO2-O2 anesthesia, replicate 2 (B92)

value: Corn Oil


title: Renal cortex, dipropylene glycol treated, replicate 2 (B110)


title: Renal cortex, dipropylene glycol treated, replicate 3 (B110)


title: Renal cortex, VC, replicate 1 (B120)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 045522_D_F_20130222) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated chlorothalonil (500 mg/kg/day) for four weeks.


title: Renal cortex, VC, replicate 3 (B120)


title: Wild_pig_thymus_2

city: Seoul

first: Yun-Jung

last: Choi

address: 120 Neungdon-ro,Gwangjib-gu

department: Animal biotechnology

country: South Korea

institute: KONKUK University

description: Replicate 2

hyb_protocol: 1650ng of each labeled cRNA was fragmented by adding 11 μl 10 x blocking agent and 2.2 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 55 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint HD Porcine GE 4X44K Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: Raw data were extracted using the software provided by Agilent Feature Extraction Software(v11.0.1.1). The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate raw data text file, providing expression data for each gene probed on the array. Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.

organism: Sus scrofa

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 200ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

extract_protocol: Total RNA was extracted and purified from the thymus of WT and IL2RG KO pigs using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturer’s  protocol. The RNA quality was verified using an Agilent Bioanalyzer 2100 (Agilent Technologies; Palo Alto, CA, USA). Generation of double-stranded cDNA, preparation and labeling of cRNA, hybridization to Agilent SurePrint HD Porcine GE Microarrays 4x44K (v2) Microarry (Agilent®) , washing, and scanning with Agilent Microarray Scanner D (Agilent Technologies, Inc.).

tag: genotype

value: wildtype

value: thymus

tag: breed

value: Minnesota miniature swine


title: Renal cortex, chlorothalonil treated, replicate 1 (B120)

source_name: Renal cortex, chlorothalonil

value: Chlorothalonil

tag: dose


title: Renal cortex, VC, replicate 1 (B110)


title: Renal cortex, VC, replicate 2 (B120)


title: Renal cortex, VC, replicate 2 (B104)


title: Renal cortex, VC, CO2-O2 anesthesia, replicate 1 (B92)

tag: anesthesia


title: Renal cortex, anthraquinone treated, replicate 1 (B104)


title: Renal cortex, ethylenediamine dihydrochloride treated, replicate 3 (B119)


title: Renal cortex, VC, replicate 3 (B104)


title: Renal cortex, anthraquinone treated, replicate 2 (B104)


title: RAW264.7_DHA5HT_rep1

value: Docosahexaenoyl serotonin (DHA-5-HT), 1 µM


title: Wild_pig_thymus_1

description: Replicate 1


title: IL2RG+/-_pig_thymus_2

description: Replicate 2


title: Renal cortex, chlorothalonil treated, replicate 3 (B120)

source_name: Renal cortex, ethylenediamine dihydrochloride


title: Renal cortex, chlorothalonil treated, replicate 2 (B120)


title: Renal cortex, VC, replicate 3 (B108)

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated carbon tetrachloride (100 mg/kg/day) for four weeks.


title: Renal cortex, carbon tetrachloride treated, replicate 3 (B108)

source_name: Renal cortex, carbon tetrachloride

value: Carbon tetrachloride

value: 100 mg/kg/day


title: Renal cortex, carbon tetrachloride treated, replicate 2 (B108)


title: Renal cortex, carbon tetrachloride treated, replicate 1 (B108)


title: Renal cortex, VC, replicate 3 (B107)

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated benzyl acetate (1000 mg/kg/day) for four weeks.


title: Renal cortex, VC, replicate 2 (B108)


title: IL2RG+/-_pig_thymus_1

description: Replicate 1


title: Renal cortex, benzyl acetate treated, replicate 2 (B107)

source_name: Renal cortex, benzyl acetate

value: Benzyl acetate


title: Renal cortex, benzyl acetate treated, replicate 3 (B107)

value: Sprague-Dawley


title: Renal cortex, 2-amino-4-nitrophenol treated, replicate 3 (B95)

source_name: Renal cortex, 2-amino-4-nitrophenol

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated 2-amino-4-nitrophenol (750 mg/kg/day) for four weeks.

value: 750 mg/kg/day

value: male


title: Renal cortex, 2,2-bis(bromomethyl)-1,3-propanediol treated, replicate 2 (B100)

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated 2,2-bis(bromomethyl)-1,3-propanediol (1000 mg/kg/day) for four weeks.


title: Renal cortex, VC, replicate 1 (B104)


title: Wild_pig_spleen_1

description: Replicate 1

data_processing: Raw data were extracted using the software provided by Agilent Feature Extraction Software (v11.0.1.1). The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate raw data text file, providing expression data for each gene probed on the array. Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.

extract_protocol: Total RNA was extracted and purified from the spleen of WT and IL2RG KO pigs using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturer’s  protocol. The RNA quality was verified using an Agilent Bioanalyzer 2100 (Agilent Technologies; Palo Alto, CA, USA). Generation of double-stranded cDNA, preparation and labeling of cRNA, hybridization to Agilent SurePrint HD Porcine GE Microarrays 4x44K (v2) Microarry (Agilent®) , washing, and scanning with Agilent Microarray Scanner D (Agilent Technologies, Inc.).

value: spleen


title: Renal cortex, 2-amino-4-nitrophenol treated, replicate 1 (B95)


title: Wild_pig_spleen_2

description: Replicate 2


title: Renal cortex, benzyl acetate treated, replicate 1 (B107)

value: 1000 mg/kg/day


title: Renal cortex, 2,2-bis(bromomethyl)-1,3-propanediol treated, replicate 1 (B100)


title: Wild_pig_spleen_3

description: Replicate 3


title: Renal cortex, VC, replicate 1 (B108)


title: IL2RG +/-_pig_spleen

source_name: IL2RG +/-_pig_spleen

value: IL2RG +/-


title: Renal cortex, VC, replicate 1 (B95)

value: renal cortex


title: Renal cortex, VC, replicate 3 (B100)


title: Renal cortex, VC, replicate 2 (B95)


title: Renal cortex, 2-amino-4-nitrophenol treated, replicate 2 (B95)


title: Renal cortex, 2,2-bis(bromomethyl)-1,3-propanediol treated, replicate 3 (B100)


title: wt_embryos-st8-rep2

city: College Park

first: William

middle: R

last: Anderson

state: MD

address: 4112 Plant Sciences Building

department: Entomology

institute: University of Maryland

description: w[118] germ-line clone stage 8 embryos

hyb_protocol: Samples were fragmented and hybridized on GeneChip Drosophila Genome Array per standard protocols at IBBR core facility on the UMD Shady Grove campus.

scan_protocol: Arrays were scanned per standard protocols at IBBR core facility on the UMD Shady Grove campus.

data_processing:
Affymetrix drosophila2 genechip CEL files were imported into BioConductor/R using the ReadAffy function of the affy package and assigned to developmental stage (5,6,8), wildtype or ftz-f1 mutant condition (0,1) and batch number (processing and hybridization batch). Using 3 replicates of 3 stages and 2 states of ftz-f1 gave a total of 18 genechip arrays. All arrays were normalized by the expresso function using quantiles normalization, only perfect match, and median polish summary method. This produced log2 expression results.
Differentially expressed genes showing a response to the presence or absence of functional Ftz-F1, were identified in R using the microarray analysis of variance package, maanova, was run in oneColor mode fitting a mixed effect ANOVA model using the formula ŷ=Stage+Ftz.F1+Batch. Batch represents the groups of RNA that were processed and hybridized on the same day and was treated as a random or non-repeatable term in the model. The function matest was run with a permutation count of 100 to compute the p-value for the Ftz.F1 model term. p-values were further controlled for the N discovery rate using the Q-value method of the adjPval function. Probesets having an FDR adjusted p-value < 0.05 were considered potential target genes.

organism: Drosophila melanogaster

source_name: w- glc stage 8 embryos

label_protocol: Samples were processed using the standard Affymetrix one-cycle cDNA synthesis protocol.

growth_protocol: ftz-f1[19] heterozygous or control females were mated to w[1118] males in collection cages at 25°C and allowed to lay eggs for up to 2 hours.specific stages, each pool was monitored closely and selected by visual inspection at late cellularization, stage 5 (when the invaginating cell membrane had reached approximately 80-90% of its maximal depth and before any sign of the cephalic furrow invagination was visible), at the onset of gastrulation, stage 6 (when the cephalic furrow had invaginated approximately one full cell depth), or at mid germband extension, stage 8 (when the posterior end of the germband had extended approximately half way towards the cephalic furrow. Embryos were manipulated using a small needle.

extract_protocol: Embryos at the desired stage of development, were transferred to 100ul of TRIZOL on ice. Approximately 100 embryos were collected per sample. Individual collections were stored at -80oC. Each experiment was done in triplicate. Total RNA was extracted using the Qiagen RNEasy kit according to standard protocols.

treatment_protocol: Eggs were dechorionated in 3% sodium hypochlorite for 3 minutes and then covered with halocarbon oil and aged. Embryos were visualized under phase contrast optics at 100-200x magnification. Individual embryos were pooled into groups of roughly equivalent developmental stages and kept out of the light path of the microscope as much as possible. To generate pools of embryos at

value: dechorionated embryo

value: w[118] germ-line clones

tag: Stage

value: germband extension

tag: batch


title: Renal cortex, VC, replicate 1 (B107)

tag: treatment

value: Corn Oil

tag: tissue


title: Renal cortex, VC, replicate 3 (B95)


title: wt_embryos-st8-rep1

description: w[118] germ-line clone stage 8 embryos

tag: replicate


title: wt_embryos-st8-rep3

description: w[118] germ-line clone stage 8 embryos


title: Renal cortex, 4-hydroxy-m-phenylenediammonium dichloride treated, replicate 3 (B125)

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated 4-hydroxy-m-phenylenediammonium dichloride (100 mg/kg/day) for four weeks.


title: Renal cortex, VC, replicate 1 (B100)


title: Renal cortex, VC, replicate 2 (B107)


title: wt_embryos-st6-rep3

description: w[118] germ-line clone stage 6 embryos

source_name: w- glc stage 6 embryos

value: gastrulation


title: Renal cortex, 4-hydroxy-m-phenylenediammonium dichloride treated, replicate 1 (B125)


title: wt_embryos-st5-rep3

description: w[118] germ-line clone stage 5 embryos

source_name: w- glc stage 5 embryos

value: cellularization


title: Renal cortex, VC, replicate 3 (B125)

source_name: Renal cortex, VC


title: Renal cortex, VC, replicate 2 (B100)


title: wt_embryos-st6-rep1

description: w[118] germ-line clone stage 6 embryos


title: wt_embryos-st6-rep2

description: w[118] germ-line clone stage 6 embryos


title: Renal cortex, 1-amino-2,4-dibromoanthraquinone treated, replicate 3 (B102)

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated 1-amino-2,4-dibromoanthraquinone (1000 mg/kg/day) for four weeks.


title: Renal cortex, 4-hydroxy-m-phenylenediammonium dichloride treated, replicate 2 (B125)


title: wt_embryos-st5-rep2

description: w[118] germ-line clone stage 5 embryos


title: ftz-f1_embryos-st8-rep3

description: ftz-f1[19] germ-line clone stage 8 embryos

source_name: ftz-f1 glc stage 8 embryos

value: Ftz-F1[19] germ-line clones


title: Renal cortex, VC, replicate 2 (B125)


title: wt_embryos-st5-rep1

description: w[118] germ-line clone stage 5 embryos


title: Renal cortex, 1-amino-2,4-dibromoanthraquinone treated, replicate 2 (B102)


title: Renal cortex, VC, replicate 1 (B102)


title: Renal cortex, 1-amino-2,4-dibromoanthraquinone treated, replicate 1 (B102)


title: Renal cortex, VC, replicate 1 (B125)


title: Renal cortex, VC, replicate 3 (B102)


title: Renal cortex, 1,2,3-trichloropropane treated, replicate 3 (B105)

source_name: Renal cortex, 1,2,3-trichloropropane

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated 1,2,3-trichloropropane (75 mg/kg/day) for four weeks.

value: 75 mg/kg/day


title: Renal cortex, VC, replicate 2 (B102)


title: Renal cortex, 1,2-dibromoethane treated, replicate 2 (B118)

source_name: Renal cortex, 1,2-dibromoethane

treatment_protocol: Three animals were administrated corn oil for four weeks, the other three animals were administrated 1,2-dibromoethane (75 mg/kg/day) for four weeks.


title: ftz-f1_embryos-st6-rep2

description: ftz-f1[19] germ-line clone stage 6 embryos

source_name: ftz-f1 glc stage 6 embryos


title: ftz-f1_embryos-st8-rep2


title: ftz-f1_embryos-st6-rep1


title: Renal cortex, 1,2-dibromoethane treated, replicate 3 (B118)


title: Renal cortex, 1,2,3-trichloropropane treated, replicate 1 (B105)


title: Renal cortex, VC, replicate 3 (B118)


title: Renal cortex, VC, replicate 2 (B118)


title: ftz-f1_embryos-st8-rep1


title: Renal cortex, VC, replicate 1 (B105)


title: Renal cortex, 1,2,3-trichloropropane treated, replicate 2 (B105)


title: Renal cortex, 1,2-dibromoethane treated, replicate 1 (B118)


title: ftz-f1_embryos-st6-rep3


title: ftz-f1_embryos-st5-rep2

description: ftz-f1[19] germ-line clone stage 5 embryos

source_name: ftz-f1 glc stage 5 embryos


title: Renal cortex, VC, replicate 1 (B118)


title: Renal cortex, VC, replicate 2 (B105)


title: Renal cortex, VC, replicate 3 (B105)


title: ftz-f1_embryos-st5-rep3


title: ftz-f1_embryos-st5-rep1


title: Macrophage Population C, Vac only, replicate 1

status: Public on Sep 26 2016

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Five micrograms of cDNA was hybridized for 16h at 45C on a Mouse Gene 2.0 ST GeneChip array

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.6

source_name: CD11blo, CD11chi, MHCIIlo cells following vaccination only

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).

growth_protocol: Cells were harvested from collagenase-digested lungs of mice and FACS sorted using the following gating strategy: Ly-6Ghi (neutrophils) and CD4,8,or19+ (lymphocytes) were outgated from Propidium iodide negative CD45+ cells. CD11b was used to identify CD11blo and CD11bhi fractions that were sub-fractionated with CD11c and MHCII. The CD11bhi, CD11chi, MHCIIlo population was defined as population A, the CD11bhi, CD11clo, MHCIIhi as population B, and the CD11blo, CD11chi, MHC IIlo as population C.

extract_protocol: Total RNA was extreacted using the Qiagen RNeasy Plus Mini Kit

treatment_protocol: Immediately after FACS, cells were suspended in RLT buffer (QIAGEN) with 40 mM dithiothreitol.

value: macrophage

value: lung

tag: cell markers

value: CD11blo, CD11chi, MHCIIlo


title: Macrophage Population C, Vac only, replicate 3


title: Macrophage Population B, Vac only, replicate 3

source_name: CD11bhi, CD11clo, MHCIIhi cells following vaccination only

value: CD11bhi, CD11clo, MHCIIhi


title: Macrophage Population B, Vac only, replicate 2


title: Macrophage Population C, Untreated, replicate 1

source_name: CD11blo, CD11chi, MHCIIlo cells, untreated


title: Macrophage Population B, Untreated, replicate 3

source_name: CD11bhi, CD11clo, MHCIIhi cells, untreated


title: Macrophage Population A, Vac only, replicate 2

source_name: CD11bhi, CD11chi, MHCIIlo cells following vaccination only

value: CD11bhi, CD11chi, MHCIIlo


title: Macrophage Population B, Vac only, replicate 1


title: Macrophage Population B, Untreated, replicate 2


title: Macrophage Population C, Vac+CY, replicate 1

source_name: CD11blo, CD11chi, MHCIIlo cells following vaccination and cyclophosphamide treatment


title: Macrophage Population C, Vac+CY, replicate 2


title: Macrophage Population C, Vac+CY, replicate 3


title: Macrophage Population C, Untreated, replicate 3


title: Macrophage Population C, Vac only, replicate 2


title: Macrophage Population B, Untreated, replicate 1


title: Macrophage Population B, Vac+CY, replicate 1

source_name: CD11bhi, CD11clo, MHCIIhi cells following vaccination and cyclophosphamide treatment


title: Macrophage Population A, Vac only, replicate 3


title: Macrophage Population C, Untreated, replicate 2


title: Macrophage Population B, Vac+CY, replicate 3


title: Macrophage Population A, Vac+CY, replicate 2

source_name: CD11bhi, CD11chi, MHCIIlo cells following vaccination and cyclophosphamide treatment


title: Macrophage Population B, Vac+CY, replicate 2


title: Macrophage Population A, Vac only, replicate 1


title: Macrophage Population A, Vac+CY, replicate 3


title: Macrophage Population A, Vac+CY, replicate 1


title: 928_Ku70-/- BPA 4_1

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression after 4 h in BPA treated MEFs

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNA was fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12.0), using the 1-color defaults for all parameters.

source_name: Ku70-/- MEFs, 150 uM BPA 4 h, replicate 1

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Ku70-/- MEFs were grown at 37°C in a 10% CO2 incubator in DMEM supplemented with glutamine, 10% FBS, 1% non-essential amino acids, and 1% sodium pyruvate. Cells were routinely tested and found to be free of mycoplasma contamination.

extract_protocol: 4 and 24 h after treatment cells were washed twice in PBS, and total cellular RNA was isolated using the RNeasy Midi Kit according to the manufacturer’s instructions. Residual genomic DNA was removed by on-column digestion with RNase-free DNase I.

treatment_protocol: Ku70-/- cells were seeded in 145 mm dishes at 1×10^6 cells/dish and cultured to 80% confluency. Cells were then treated with BPA, KBrO3 or co-exposed to BPA and KBrO3. KBrO3 only cells were treated for 1 h with 20 mM KBrO3, washed with HBSS, then fresh medium was added to cells. Cells were allowed to repair for an additional 3 or 23 h following treatment. For BPA only treatment, cells were incubated for 4 or 24 h in medium containing 150 μM BPA. For co-exposure, cell were incubated with 150 μM BPA for 1 h, then 20 mM KBrO3 and 150 μM BPA for 1 h, washed with HBSS, then fresh medium with 150 μM BPA was added, and cells were allowed to repair for an additional 3 or 23 h.

value: immortalized mouse embryonic fibroblasts

tag: gene deletion

value: Ku70 (Xrcc6)


title: 928_Ku70-/- BPA 4_2

source_name: Ku70-/- MEFs, 150 uM BPA 4 h, replicate 2


title: 928_Ku70-/- Control_3

description: Gene expression in control samples

source_name: Ku70-/- MEFs, untreated control, replicate 3


title: 928_Ku70-/- Control_1

description: Gene expression in control samples

source_name: Ku70-/- MEFs, untreated control, replicate 1


title: 928_Ku70-/- BPA 24_2

description: Gene expression after 24 h in BPA treated MEFs

source_name: Ku70-/- MEFs, 150 uM BPA 24 h, replicate 2


title: 895_Ku70-/- KBrO3 + BPA 24_3

description: Gene expression after 24 h in KBrO3 and BPA treated MEFs

source_name: Ku70-/- MEFs, 20 mM KBrO3 + 150 uM BPA 24 h, replicate 3


title: 928_Ku70-/- BPA 24_1

source_name: Ku70-/- MEFs, 150 uM BPA 24 h, replicate 1


title: 928_Ku70-/- BPA 4_3

source_name: Ku70-/- MEFs, 150 uM BPA 4 h, replicate 3


title: 928_Ku70-/- Control_2

description: Gene expression in control samples

source_name: Ku70-/- MEFs, untreated control, replicate 2


title: 928_Ku70-/- BPA 24_3

source_name: Ku70-/- MEFs, 150 uM BPA 24 h, replicate 3


title: 895_Ku70-/- KBrO3 + BPA 24_2

source_name: Ku70-/- MEFs, 20 mM KBrO3 + 150 uM BPA 24 h, replicate 2


title: 895_Ku70-/- KBrO3 + BPA 4_3

description: Gene expression after 4 h in KBrO3 and BPA treated MEFs

source_name: Ku70-/- MEFs, 20 mM KBrO3 + 150 uM BPA 4 h, replicate 3


title: 895_Ku70-/- KBrO3 + BPA 4_2

source_name: Ku70-/- MEFs, 20 mM KBrO3 + 150 uM BPA 4 h, replicate 2


title: 895_Ku70-/- KBrO3 4_3

description: Gene expression after 4 h in KBrO3 treated MEFs

source_name: Ku70-/- MEFs, 20 mM KBrO3 4 h, replicate 3


title: 895_Ku70-/- KBrO3 + BPA 24_1

source_name: Ku70-/- MEFs, 20 mM KBrO3 + 150 uM BPA 24 h, replicate 1


title: Normal karyo-15

city: Ghent

first: Farzaneh

last: Ghazavi

address: De Pintelaan 185

department: Center of medical genetics

country: Belgium

institute: Gent university hospital

description: Gene expression of T-ALL patient bone marrow sample

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating  hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with SureScan High-Resolution Technology using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: bone marrow

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labling kit (Agilent) according to the manufacturer's instructions, followed by miRNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was harvested with the miRNeasy mini kit (Qiagen) with Dnase treatment on-column.

tag: diagnosis

value: b-cell precursor acute lymphoblastic leukemia (BCP-ALL)


title: 895_Ku70-/- Control 4_1

description: Gene expression in control samples


title: 895_Ku70-/- Control 4_2

description: Gene expression in control samples


title: 895_Ku70-/- KBrO3 24_2

description: Gene expression after 24 h in KBrO3 treated MEFs

source_name: Ku70-/- MEFs, 20 mM KBrO3 24 h, replicate 2


title: 895_Ku70-/- KBrO3 4_1

source_name: Ku70-/- MEFs, 20 mM KBrO3 4 h, replicate 1


title: 895_Ku70-/- KBrO3 + BPA 4_1

source_name: Ku70-/- MEFs, 20 mM KBrO3 + 150 uM BPA 4 h, replicate 1


title: Normal karyo-17

description: Gene expression of T-ALL patient blood sample


title: 895_Ku70-/- KBrO3 24_3

source_name: Ku70-/- MEFs, 20 mM KBrO3 24 h, replicate 3


title: 895_Ku70-/- KBrO3 4_2

source_name: Ku70-/- MEFs, 20 mM KBrO3 4 h, replicate 2


title: Normal karyo-12


title: 895_Ku70-/- KBrO3 24_1

source_name: Ku70-/- MEFs, 20 mM KBrO3 24 h, replicate 1


title: Normal karyo-16


title: Normal karyo-13


title: Normal karyo-14


title: Normal karyo-7


title: Normal karyo-10


title: Normal karyo-3


title: 895_Ku70-/- Control 4_3

description: Gene expression in control samples

source_name: Ku70-/- MEFs, untreated control, replicate 3


title: Normal karyo-11


title: Normal karyo-4


title: Normal karyo-9


title: Normal karyo-8


title: Normal karyo-5


title: Normal karyo-6

description: Gene expression of T-ALL patient EM sample


title: E2A-PBX1-7


title: Hyperdiploid-10


title: E2A-PBX1-4


title: E2A-PBX1-5


title: Hyperdiploid-14


title: Hyperdiploid-9


title: Hyperdiploid-12


title: E2A-PBX1-3


title: E2A-PBX1-2


title: E2A-PBX1-6


title: E2A-PBX1-1


title: Hyperdiploid-11


title: Normal karyo-1


title: Hyperdiploid-15


title: Hyperdiploid-2


title: ETV6-RUNX1-20


title: Hyperdiploid-3


title: Hyperdiploid-8


title: Hyperdiploid-5


title: ETV6-RUNX1-24


title: Hyperdiploid-4


title: Hyperdiploid-7


title: Normal karyo-2


title: ETV6-RUNX1-22


title: ETV6-RUNX1-25


title: Hyperdiploid-13


title: Hyperdiploid-1


title: ETV6-RUNX1-21


title: Hyperdiploid-6


title: ETV6-RUNX1-23


title: ETV6-RUNX1-12


title: ETV6-RUNX1-18


title: ETV6-RUNX1-14


title: REH-fusionKD-2

source_name: Cell line

growth_protocol: Cells were grown in RPMI supplemented with 10% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

treatment_protocol: Cells were seeded at 1*10^6 cells/ml and treated with either shRNA against the ETV6/RUNX1 fusion or non-targeting shRNA.

tag: cell line

value: REH

tag: shRNA target

value: ETV6/RUNX1 fusion


title: ETV6-RUNX1-4


title: ETV6-RUNX1-11


title: ETV6-RUNX1-19


title: ETV6-RUNX1-15


title: ETV6-RUNX1-9


title: ETV6-RUNX1-16


title: ETV6-RUNX1-7


title: ETV6-RUNX1-1


title: REH-fusionKD-1


title: ETV6-RUNX1-5


title: ETV6-RUNX1-8


title: ETV6-RUNX1-10


title: REH-fusionKD-3


title: ETV6-RUNX1-6


title: REH-NTC-1

value: non-targeting


title: ETV6-RUNX1-3


title: ETV6-RUNX1-2


title: REH-NTC-3


title: Double knock-down of ETV6 and NFKB1 replicate 3

first: Christopher

middle: L

last: Plaisier

state: Washington

address: 401 Terry Avenue North

institute: Institute for Systems Biology

description:
Transcriptome of U251 cells transfected with ETV6 and NFKB1 siRNA.
ETV6_NFKB1_siRNA_3

hyb_protocol: The cRNA probes were then hybridized using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).

scan_protocol: The chips were scanned using the GeneArray scanner (Affymetrix) to produce CEL files.

data_processing: A rigorous quality control pipeline was developed to prepare the gene expression microarray data for analysis. First, the CEL files were imported into R using the justRMA function of the Affymetrix library from Bioconductor, which applies background subtraction and quantile normalization. An alternate CDF file (U133Plus2msk.cdf.gz) was used to exclude mis-targeted and nonspecific probes from the microarrays (Zhang et al. 2005), and probesets with less than 7 remaining probes were also excluded. Probesets with more than 50% absent calls were excluded, as calculated using the panp package from Bioconductor.

source_name: Double knock-down of ETV6 and NFKB1

label_protocol: Samples were then converted to cRNA probes using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).

growth_protocol: U251 were acquired from the ATCC and cultured in DMEM with 10% FBS and 1% penicillin/streptomycin. All cell lines were cultured at 37°C in a humidified 5% CO2 incubator. Cell count and viability were determined using a Countess cell counter (Life Technologies).

extract_protocol: Total RNA including miRNAs was extracted from cell pellets using the mirVANA miRNA kit (Life Technologies) according to the manufacturer's instructions.

treatment_protocol: The ON-TARGETplus SMARTpool siRNA (Dharmacon) were used to knock-down ETV6  and NFKB1. Each siRNA was added at 50 nM. Using a fluorescently labeled small RNA molecule and a requirement of 90% transfection efficiency, it was determined the U251 cell line was optimally transfected with Dharmafect 2 at 0.1µl. A siRNA that does not target any known human transcript was tested at the same concentration as a negative control to correct for off-target effects.

value: glioblastoma cell line U251

tag: sirna

value: ETV6 and NFKB1 siRNA


title: Single knock-down of NFKB1 siRNA replicate 3

description:
Transcriptome of U251 cells transfected with NFKB1 siRNA.
NFKB1_siRNA_3

source_name: Single knock-down of NFKB1 siRNA

value: NFKB1 siRNA


title: REH-NTC-2


title: Double knock-down of ETV6 and NFKB1 replicate 1

description:
Transcriptome of U251 cells transfected with ETV6 and NFKB1 siRNA.
ETV6_NFKB1_siRNA_1


title: ETV6-RUNX1-13


title: ETV6-RUNX1-17


title: CD34-positive HSCs

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

country: Germany

institute: Leibniz Institute DSMZ

description: Gene expression data from HSCs.

hyb_protocol: Samples were prepared for and measured on Affymetrix HG-U133-Plus2 Chip (Santa Clara/CA).

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

data_processing: After RMA-background correction, quantile normalisation of spot intensities, data were subtracted by the mean and logarithmically transformed. Data processing was done via R/Bioconductor using limma and affy packages.

source_name: Primary CD34+ HSCs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.

extract_protocol: Primary samples of CD34+ HSCs were harvested by leukapheresis from healthy volunteers by magnetic cell sorting (Miltenyi Biotech). Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: cell type

value: hematopoietic stem cells (HSCs)

tag: cell subtype

tag: disease status

value: healthy


title: Double knock-down of ETV6 and NFKB1 replicate 2

description:
Transcriptome of U251 cells transfected with ETV6 and NFKB1 siRNA.
ETV6_NFKB1_siRNA_2


title: Single knock-down of NFKB1 siRNA replicate 2

description:
Transcriptome of U251 cells transfected with NFKB1 siRNA.
NFKB1_siRNA_2


title: Single knock-down of ETV6 siRNA replicate 1

description:
Transcriptome of U251 cells transfected with ETV6 siRNA.
ETV6_siRNA_1

source_name: Single knock-down of ETV6 siRNA

value: ETV6 siRNA


title: Single knock-down of ETV6 siRNA replicate 3

description:
Transcriptome of U251 cells transfected with ETV6 siRNA.
ETV6_siRNA_3


title: Control siRNA replicate 2

description:
Transcriptome of U251 cells transfected with control siRNA.
Control_siRNA_2

source_name: Control siRNA

value: Control siRNA


title: Control siRNA replicate 3

description:
Transcriptome of U251 cells transfected with control siRNA.
Control_siRNA_3


title: Single knock-down of NFKB1 siRNA replicate 1

description:
Transcriptome of U251 cells transfected with NFKB1 siRNA.
NFKB1_siRNA_1


title: Single knock-down of ETV6 siRNA replicate 2

description:
Transcriptome of U251 cells transfected with ETV6 siRNA.
ETV6_siRNA_2


title: H097-P12-1mois-d

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

country: France

institute: IRHS

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Pair-data files were extracted from the scanned images using DEVA 1.2.1 software (Roche).

data_processing: Statistical analyses were performed using R version 2.14.1 (R Development Core Team, 2011) and the package LIMMA 3.10.1 (Smyth G.K., 2005) from the Bioconductor project. Data were normalized by the lowess method from LIMMA.

organism: Malus domestica

source_name: Apple 'H097' fruit flesh,plot P12, 1 month of cold storage

label_protocol: 200ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized.

growth_protocol: Fruits were grown at INRA, Angers (Experimental unit of Bois L'Abbé-La Rétuziére).

extract_protocol: Derived from the apple tissues RNA extraction method (Gasic et al., 2004) and pine tree RNA isolation method (Chang et al., 1993)

treatment_protocol: Cold storage at 1°C after harvest at optimum maturity

tag: organ

value: Fruit

tag: tissus

value: Parenchyma

tag: genetic background

value: Hybrid H097

tag: genotype

value: Wild-type

tag: plot

tag: tissue developmental stage

value: Harvested at optimum maturity

value: Cold storage for 30 days after harvest


title: H097-P12-1mois-c

tag: treatment


title: Control siRNA replicate 1

description:
Transcriptome of U251 cells transfected with control siRNA.
Control_siRNA_1


title: W029-P12-110DAF-a

source_name: Apple 'W029' fruit flesh,plot P12, 110 days after flowering

value: Hybrid W029

value: Fruit development, 110 days after flowering


title: V083-PH-1mois-b

source_name: Apple 'V083' fruit flesh,plot PH, 1 month of cold storage

value: Hybrid V083

value: PH


title: I016-PH-1mois-a

source_name: Apple 'I016' fruit flesh,plot PH, 1 month of cold storage

extract_protocol: Rienth et al. 2014

value: Hybrid I016


title: H074-P12-rec-b

source_name: Apple 'H074' fruit flesh,plot P12, at harvest

value: Hybrid H074


title: H074-PH-1mois-a

source_name: Apple 'H074' fruit flesh,plot PH, 1 month of cold storage


title: I095-PH-1mois-b

source_name: Apple 'I095' fruit flesh,plot PH, 1 month of cold storage

value: Hybrid I095


title: V034-P12-rec-b

source_name: Apple 'V034' fruit flesh,plot P12, at harvest

value: Hybrid V034


title: W029-P12-110DAF-b


title: H074-PH-2mois-b

source_name: Apple 'H074' fruit flesh,plot PH, 2 month of cold storage

value: Cold storage for 60 days after harvest


title: V034-P12-110DAF-b

source_name: Apple 'V034' fruit flesh,plot P12, 110 days after flowering


title: H097-PH-1mois-a

source_name: Apple 'H097' fruit flesh,plot PH, 1 month of cold storage


title: H097-PH-1mois-b


title: H097-P12-2mois-b

source_name: Apple 'H097' fruit flesh,plot P12, 2 month of cold storage


title: V034-P12-110DAF-a


title: H074-P12-rec-a


title: I062-PH-1mois-a

source_name: Apple 'I062' fruit flesh,plot PH, 1 month of cold storage

value: Hybrid I062


title: H097-P12-2mois-a


title: V034-P12-rec-a


title: I062-PH-1mois-b


title: I095-PH-1mois-a


title: I016-PH-2mois-b

source_name: Apple 'I016' fruit flesh,plot PH, 2 month of cold storage


title: V083-PH-1mois-a


title: I016-PH-2mois-a


title: H074-PH-110DAF-b

source_name: Apple 'H074' fruit flesh,plot PH, 110 days after flowering


title: H074-P12-60DAF-b

source_name: Apple 'H074' fruit flesh,plot P12, 60 days after flowering

value: Fruit development, 60 days after flowering


title: I016-PH-110DAF-b

source_name: Apple 'I016' fruit flesh,plot PH, 110 days after flowering

value: Fruit


title: I016-P12-60DAF-b

source_name: Apple 'I016' fruit flesh,plot P12, 60 days after flowering

value: Parenchyma


title: H074-PH-110DAF-a


title: H074-PH-2mois-a


title: I016-PH-110DAF-a


title: I016-P12-60DAF-a


title: H097-P12-110DAF-b

source_name: Apple 'H097' fruit flesh,plot P12, 110 days after flowering

value: Hybrid H097


title: H074-P12-60DAF-a

value: Wild-type


title: H097-P12-110DAF-a


title: H097-P12-60DAF-b

source_name: Apple 'H097' fruit flesh,plot P12, 60 days after flowering


title: I095-P12-60DAF-b

source_name: Apple 'I095' fruit flesh,plot P12, 60 days after flowering


title: V083-P12-1mois-b

source_name: Apple 'V083' fruit flesh,plot P12, 1 month of cold storage

value: Harvested at optimum maturity


title: I062-P12-1mois-a

source_name: Apple 'I062' fruit flesh,plot P12, 1 month of cold storage

value: Cold storage for 30 days after harvest


title: V083-P12-1mois-a


title: I062-P12-60DAF-b

source_name: Apple 'I062' fruit flesh,plot P12, 60 days after flowering


title: I062-P12-1mois-b


title: I062-P12-60DAF-a


title: I095-P12-60DAF-a


title: H097-P12-60DAF-a


title: H074-P12-110DAF-a

source_name: Apple 'H074' fruit flesh,plot P12, 110 days after flowering


title: I095-P12-110DAF-a

source_name: Apple 'I095' fruit flesh,plot P12, 110 days after flowering


title: W029-PH-110DAF-a

source_name: Apple 'W029' fruit flesh,plot PH, 110 days after flowering

value: Hybrid W029


title: W029-PH-110DAF-b

value: Fruit development, 110 days after flowering


title: V083-P12-60DAF-a

source_name: Apple 'V083' fruit flesh,plot P12, 60 days after flowering

value: Hybrid V083


title: V034-PH-110DAF-b

source_name: Apple 'V034' fruit flesh,plot PH, 110 days after flowering

value: PH


title: V034-PH-110DAF-a


title: V083-P12-60DAF-b


title: I016-P12-110DAF-b

source_name: Apple 'I016' fruit flesh,plot P12, 110 days after flowering

value: Hybrid I016


title: H074-P12-110DAF-b

value: Hybrid H074


title: I016-P12-110DAF-a


title: I016-P12-1mois-a

source_name: Apple 'I016' fruit flesh,plot P12, 1 month of cold storage


title: H074-P12-1mois-a

source_name: Apple 'H074' fruit flesh,plot P12, 1 month of cold storage


title: W029-P12-1mois-b

source_name: Apple 'W029' fruit flesh,plot P12, 1 month of cold storage


title: V034-P12-1mois-a

source_name: Apple 'V034' fruit flesh,plot P12, 1 month of cold storage


title: I016-P12-1mois-b


title: I095-P12-110DAF-b

value: Hybrid I095


title: H074-P12-1mois-b


title: H097-PH-60DAF-b

source_name: Apple 'H097' fruit flesh,plot PH, 60 days after flowering


title: V034-P12-60DAF-b

source_name: Apple 'V034' fruit flesh,plot P12, 60 days after flowering

value: Hybrid V034


title: V034-P12-60DAF-a


title: I095-PH-60DAF-b

source_name: Apple 'I095' fruit flesh,plot PH, 60 days after flowering


title: V034-P12-1mois-b


title: W029-P12-60DAF-b

source_name: Apple 'W029' fruit flesh,plot P12, 60 days after flowering


title: W029-P12-1mois-a


title: I062-PH-2mois-b

source_name: Apple 'I062' fruit flesh,plot PH, 2 month of cold storage

value: Cold storage for 60 days after harvest


title: V083-PH-110DAF-b

source_name: Apple 'V083' fruit flesh,plot PH, 110 days after flowering


title: I062-PH-2mois-a

value: Hybrid I062


title: V083-PH-110DAF-a


title: I062-PH-110DAF-b

source_name: Apple 'I062' fruit flesh,plot PH, 110 days after flowering


title: H097-PH-60DAF-a

value: Fruit development, 60 days after flowering


title: I095-PH-rec-b

source_name: Apple 'I095' fruit flesh,plot PH, at harvest

value: Fruit


title: H097-PH-rec-b

source_name: Apple 'H097' fruit flesh,plot PH, at harvest

value: Parenchyma


title: H097-PH-110DAF-a

source_name: Apple 'H097' fruit flesh,plot PH, 110 days after flowering

value: Hybrid H097


title: H097-PH-110DAF-b

value: Wild-type


title: V083-PH-2mois-b

source_name: Apple 'V083' fruit flesh,plot PH, 2 month of cold storage

value: Harvested at optimum maturity


title: I062-P12-110DAF-b

source_name: Apple 'I062' fruit flesh,plot P12, 110 days after flowering


title: I095-PH-rec-a


title: I062-P12-110DAF-a


title: I062-PH-110DAF-a


title: H097-PH-rec-a


title: I095-PH-110DAF-b

source_name: Apple 'I095' fruit flesh,plot PH, 110 days after flowering


title: V083-P12-110DAF-b

source_name: Apple 'V083' fruit flesh,plot P12, 110 days after flowering


title: I062-PH-60DAF-a

source_name: Apple 'I062' fruit flesh,plot PH, 60 days after flowering


title: V083-PH-60DAF-b

source_name: Apple 'V083' fruit flesh,plot PH, 60 days after flowering


title: V083-PH-60DAF-a


title: V083-PH-2mois-a


title: I062-PH-60DAF-b


title: H097-P12-1mois-b

source_name: Apple 'H097' fruit flesh,plot P12, 1 month of cold storage

value: Cold storage for 30 days after harvest


title: H097-P12-1mois-a


title: I016-PH-60DAF-b

source_name: Apple 'I016' fruit flesh,plot PH, 60 days after flowering


title: I095-P12-1mois-b

source_name: Apple 'I095' fruit flesh,plot P12, 1 month of cold storage


title: I095-PH-60DAF-a

source_name: Apple 'I095' fruit flesh,plot PH, 60 days after flowering


title: I016-PH-60DAF-a


title: H074-PH-60DAF-b

source_name: Apple 'H074' fruit flesh,plot PH, 60 days after flowering


title: I095-P12-1mois-a


title: I016-P12-2mois-a

source_name: Apple 'I016' fruit flesh,plot P12, 2 month of cold storage


title: H074-PH-60DAF-a


title: H074-P12-2mois-a

source_name: Apple 'H074' fruit flesh,plot P12, 2 month of cold storage


title: I016-P12-2mois-b


title: W029-P12-60DAF-a

source_name: Apple 'W029' fruit flesh,plot P12, 60 days after flowering

value: Hybrid W029


title: H074-P12-2mois-b


title: V083-P12-2mois-a

source_name: Apple 'V083' fruit flesh,plot P12, 2 month of cold storage


title: I062-P12-2mois-b

source_name: Apple 'I062' fruit flesh,plot P12, 2 month of cold storage


title: V083-P12-2mois-b


title: W029-P12-2mois-a

source_name: Apple 'W029' fruit flesh,plot P12, 2 month of cold storage


title: V034-P12-2mois-b

source_name: Apple 'V034' fruit flesh,plot P12, 2 month of cold storage


title: Late_Relapse_GC_19251

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

institute: INSERM

description: GC subtype

hyb_protocol: Affymetrix SNP6 protocol

scan_protocol: Affymetrix SNP6 protocol

data_processing: Row data were extracted with the CRLMM algorithm, under R software

source_name: Lymph node

label_protocol: Affymetrix SNP6 protocol

extract_protocol: Genomic DNA extracted from frozen lymph node biopsies

treatment_protocol: Fresh-frozen lymph node biopsies from the CORAL trial

tag: tissue

value: Diffuse large B-cell lymphoma

tag: type

value: Late Relapse


title: Late_Relapse_GEP_UN_19253

description: Gene expression profile unavailable


title: I062-P12-2mois-a


title: V034-P12-2mois-a


title: I095-PH-2mois-a

source_name: Apple 'I095' fruit flesh,plot PH, 2 month of cold storage

value: PH


title: Early_Relapse_GC_19249

description: GC subtype

value: Early Relapse


title: H097-PH-2mois-a

source_name: Apple 'H097' fruit flesh,plot PH, 2 month of cold storage


title: H097-PH-2mois-b


title: V034-PH-2mois-b

source_name: Apple 'V034' fruit flesh,plot PH, 2 month of cold storage


title: W029-P12-2mois-b


title: Early_Relapse_GC_19247

description: GC subtype


title: Early_Relapse_GEP_UN_19210

description: Gene expression profile unavailable


title: W029-PH-2mois-b

source_name: Apple 'W029' fruit flesh,plot PH, 2 month of cold storage


title: I095-PH-2mois-b


title: W029-PH-1mois-b

source_name: Apple 'W029' fruit flesh,plot PH, 1 month of cold storage


title: V034-PH-1mois-a

source_name: Apple 'V034' fruit flesh,plot PH, 1 month of cold storage


title: Late_Relapse_GEP_UN_19206

description: Gene expression profile unavailable


title: Early_Relapse_ABC_19208

description: ABC subtype


title: V034-PH-2mois-a


title: W029-PH-2mois-a


title: V083-P12-110DAF-a

source_name: Apple 'V083' fruit flesh,plot P12, 110 days after flowering

value: Hybrid V083

value: Fruit development, 110 days after flowering


title: Late_Relapse_ABC_19184

description: ABC subtype


title: W029-PH-1mois-a


title: H074-PH-1mois-b

source_name: Apple 'H074' fruit flesh,plot PH, 1 month of cold storage

value: Hybrid H074


title: Late_Relapse_ABC_19182

description: ABC subtype


title: Early_Relapse_ABC_18845

description: ABC subtype


title: Late_Relapse_GC_19180

description: GC subtype


title: I016-PH-1mois-b

source_name: Apple 'I016' fruit flesh,plot PH, 1 month of cold storage

value: Hybrid I016


title: I095-PH-110DAF-a

source_name: Apple 'I095' fruit flesh,plot PH, 110 days after flowering

value: Hybrid I095


title: V034-PH-1mois-b

value: Hybrid V034


title: Late_Relapse_GEP_UN_18843

description: Gene expression profile unavailable


title: Early_Relapse_GC_18841

description: GC subtype


title: Late_Relapse_GC_18839

description: GC subtype


title: H074-PH-rec-b

source_name: Apple 'H074' fruit flesh,plot PH, at harvest

value: Fruit


title: Late_Relapse_GC_19186

description: GC subtype


title: I016-PH-rec-b

source_name: Apple 'I016' fruit flesh,plot PH, at harvest

value: Parenchyma


title: H074-PH-rec-a


title: Late_Relapse_GC_18837

description: GC subtype


title: H097-P12-rec-b

source_name: Apple 'H097' fruit flesh,plot P12, at harvest

value: Hybrid H097


title: Early_Relapse_ABC_18833

description: ABC subtype


title: I095-P12-rec-b

source_name: Apple 'I095' fruit flesh,plot P12, at harvest

value: Wild-type


title: Late_Relapse_ABC_18831

description: ABC subtype


title: I095-P12-rec-a

value: Harvested at optimum maturity


title: Early_Relapse_GEP_UP_18776

description: Gene expression profile unpredictable


title: Early_Relapse_GC_18780

description: GC subtype


title: Early_Relapse_ABC_18835

description: ABC subtype


title: H097-P12-rec-a


title: I016-PH-rec-a


title: V034-PH-rec-b

source_name: Apple 'V034' fruit flesh,plot PH, at harvest


title: Early_Relapse_GC_18774

description: GC subtype


title: V034-PH-rec-a


title: W029-PH-rec-a

source_name: Apple 'W029' fruit flesh,plot PH, at harvest


title: Late_Relapse_ABC_18764

description: ABC subtype

source_name: Lymph node


title: Late_Relapse_GEP_UN_18766

description: Gene expression profile unavailable


title: W029-PH-rec-b


title: V083-P12-rec-b

source_name: Apple 'V083' fruit flesh,plot P12, at harvest


title: Late_Relapse_GC_18727

description: GC subtype


title: Early_Relapse_GC_18778

description: GC subtype


title: Late_Relapse_GC_18725

description: GC subtype


title: Early_Relapse_GEP_UN_18723

description: Gene expression profile unavailable


title: Late_Relapse_ABC_18721

description: ABC subtype


title: I062-P12-rec-b

source_name: Apple 'I062' fruit flesh,plot P12, at harvest

value: Hybrid I062


title: Late_Relapse_GC_18717

description: GC subtype


title: Early_Relapse_GEP_UP_18768

description: Gene expression profile unpredictable


title: Late_Relapse_GEP_UN_18762

description: Gene expression profile unavailable


title: Early_relapse_GC_18711

description: GC subtype


title: Early_relapse_GC_18713

description: GC subtype


title: I062-P12-rec-a


title: V083-PH-rec-a

source_name: Apple 'V083' fruit flesh,plot PH, at harvest


title: V083-P12-rec-a


title: Early_relapse_ABC_18709

description: ABC subtype


title: Late_relapse_GEP_UN_18430

description: Gene expression profile unavailable


title: I062-PH-rec-a

source_name: Apple 'I062' fruit flesh,plot PH, at harvest


title: Late_relapse_GEP_UN_18396

description: Gene expression profile unavailable


title: I062-PH-rec-b


title: V083-PH-rec-b


title: Late_Relapse_ABC_18719

description: ABC subtype


title: Early_relapse_GC_18715

description: GC subtype


title: wt pro-B cells, biological rep2

city: Barcelona

first: Maribel

last: Parra

address: Avda. Gran Via 199-203, L'Hospitalet de Llobregat

department: Cancer Epigenetics and Biology Programme (PEBC)

institute: Bellvitge Biomedical Research Institute (IDIBELL)

description: Gene expression data from wild type pro-B cells

hyb_protocol: PCR amplified biotinylated cDNA were hybridized against Affymetrix HT MG-430 PM Array Plate (Mouse Genome 430 PM strip)

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Affymatrix CEL files were background corrected and normalized using Bioconductor package “affy” using method rma.

source_name: Purified pro-B cells from wild type mice

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled using GeneChip Mapping 10K Xba Assay Kit (Affymetrix; catalog # 900441), according to manufacturer's instructions.

growth_protocol: B220+CD43+IgM- pro-B cells were isolated on a MoFlo sorter (Beckman-Coulter, Inc.) and resuspended in Trizol (Quiagen) reagent for further RNA extraction.

extract_protocol: RNA was extracted with a combination of Trizol and RNeasy minikit (Qiagen)

treatment_protocol: Biological triplicates of wold type and HDAC7 deficient pro-B cells.

value: pro-B cells

value: wild type


title: wt pro-B cells, biological rep3


title: HDAC7 deficient pro-B cells, biological rep2

description: Gene expression data from HDAC7 deficient pro-B cells

source_name: Purified pro-B cells from HDAC7 deficient mice

value: HDAC7 deficient


title: HDAC7 deficient pro-B cells, biological rep3