title: UM-UC-3_control siRNA_48h

city: Guangzhou

first: Xu

last: Chen

state: Guangdong

address: 107. W. Yanjiang Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

description: No

hyb_protocol: Hybridization was performed at 45℃ with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640). The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4. An invariant set normalization procedure was performed to normalize the different arrays using DNA-chip analyzer [dChip]

source_name: bladder cancer cell line UM-UC-3

label_protocol: An aliquot of 0.1 µg of total RNA was used to synthesize double-stranded cDNA, then produce biotin-tagged cRNA using the MessageAmpTM Premier RNA Amplification Kit. The resulting bio-tagged cRNA were fragmented to strands of 35–200 bases in length according to the protocols from Affymetrix.

growth_protocol: UM-UC-3 was cultured in DMEM (Gibco) supplemented with 10% FBS (Shanghai ExCell Biology, China) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.

treatment_protocol: siRNA transfections were done with 75 nM siRNA and Lipofectamine RNAimax (Life technologies) following manufacturer's instructions.

tag: cell type

value: bladder cancer

tag: sirna

value: Negetive control

tag: sirna target point on wdr5 cds

tag: sirna sequence

value: UUCUCCGAACGUGUCACGUTT

tag: inhibition rate (relative to control sirna)


title: UM-UC-3_si-WDR5-3_48h

status: Public on Feb 09 2015

type: RNA

country: China

description: No

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: cell line

value: CCCAGUCCAACCUUAUUGUTT


title: CLL-1_US-24h miRNA

status: Public on Feb 10 2015

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

country: Italy

institute: Consiglio Nazionale delle Ricerche (CNR)

description: miRNA expression data from CLL cells-unstimulated-24h

hyb_protocol: The detailed protocol for sample preparations and array processing is available from Genishere (http://www.genisphere.com).

data_processing: RMA normalization and probe summarization carried out on the human specific and control probe sets.

source_name: Peripheral blood from CLL patient-unstimulated-24h

label_protocol: Biotin-labeling using the FlashTagTM Biotin HSR RNA Labeling Kit.

growth_protocol: Peripheral blood mononuclear cells isolated from untreated CLL samples and pools derived from healthy donors were enriched in CD19+ B cells. (≥98%) and subsequently cultured and stimulated with a F(ab')2 anti-human IgM

extract_protocol: RNA extraction with TRIzol reagent followed by isopropanol precipitation.

treatment_protocol: Stimulation with a F(ab')2 anti-human IgM.

tag: tissue

value: Peripheral blood

tag: tp53 status

value: WT

tag: FISH analysis

tag: binet stage

value: A

tag: disease status

value: Progressive

tag: ighv status

value: M

tag: ighv gene

tag: gender

tag: age


title: P0374

type: genomic

city: Wilmington

first: Grace

last: Hobson

state: Delaware

address: 1600 Rockland Road

department: Nemours Biomedical Research

country: USA

institute: Nemours/AI duPont Hospital for Children

description: Blood from a patient with Pelizaeus_Merzbacher disease

hyb_protocol: The arrays were hybridized to the Affymetrix Cytogenetics Whole-Genome 2.7M Array, washed and stained using an Affymetrix fluidic station 640 and the Affymetrix Cytogenetics Reagent Kit as per the Affymetric Cytogenetics Assay Protocol.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Command Console and Affymetrix Scanner 3000 7G as per the Affymetric Cytogenetics Assay Protocol.

data_processing: Affymetrix Chromosome Analysis Suite v1.0.1 with Cytogenetics Array na30.1 annotation was used to create cy2wg.chchp files which contain log2 ratios and copy number states.  The HMM diagonal weight was set to 0.88, HMM minimum segment size was set to 1 and Smooth Signal Graphing sigma span was set to 3.

molecule: genomic DNA

source_name: Genomic DNA from P374

label_protocol: Genomic DNA samples (100 ng) were labelled using the Affymetrix Cytogenetics Reagent Kit as per the Affymetrix Cytogenetics Assay Protocol.

extract_protocol: DNA was isolated according to the manufacturer's instructions using Gentra Puregene Blood kit (now obtained through Qiagen)

tag: diagnosis

value: Pelizaeus-Merzbacher disease

value: male

value: blood


title: Control3

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description: RNA data from MDA-MB-453 cells

hyb_protocol: Samples were hybridized to Affymetrix Gene Human Gene 2.0 ST Arrays for 17 h at 45C before washing, staining, and scanning.  Gene 1.0 ST Arrays (Affymetrix) for 17 h at 45 8C  before washing, staining, and scanning.

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

data_processing: Data were analyzed using Partek Genomics Suite. Briefly, CEL files were imported using RMA background correction, Partek’s own GC content correction, and mean probe summarization. Differential gene expression was assessed by ANOVA, with the p-value adjusted using a step-up multiple test correction to control the false discovery rate.    Partek Genomics Suite

source_name: Empty, veh 3

label_protocol: Total RNA (300 ng) was linearly amplified and converted to cDNA using an Ambion WT Expression Kit, then fragmented, and labeled using an Affymetrix GeneChip WT Terminal Labeling and Controls Kit  linearly amplified and converted to cDNA using the  Ambion WT Expression Kit, then fragmented, and  labeled using the GeneChip WT Terminal Labeling  and Controls Kit

growth_protocol: MDA-MB-453 cells were grown in RPMI-1640 medium containing 10% charcoal stripped serum

extract_protocol: 24 h after DHT/vehicle treatment, RNA was extracted using TRIzol and purified using a Qiagen RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: MDA-MB-453 cells (6.6x10 5 cells/well in a 6-well plate) were transfected with 1 μg of plasmid DNA designed to express AR or AR-V7 or empty vector using Lipofectamine-2000. After 4 h, cells were treated with 1 nM DHT or ethanol (vehicle control).


title: WT_ESC_WT

city: Rehovot

first: Asaf

last: Zviran

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
Gene expression data of WT MBD3 mouse Embryonic Stem Cells (ESC).
NOTE - this is the same sample published in GSM874650.

hyb_protocol: Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.

data_processing: The data were analyzed with Matlab affyRMA command, with MoGene_1_0-st-v1.r3.cdf annotation file.

label: Biotin

organism: Mus musculus

source_name: WT V6.5 ES

label_protocol: 250 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: N2B2715% KSR 2i/LIF mouse ESC media on mouse irradiated DR4 MEF cells.

extract_protocol: mRNA was extracted by TRIZOL reagent (Invitrogen) according to manufacturer's instructions.

treatment_protocol: Cells were washed with PBS and then harvested by trypsinization for RNA extraction.

tag: genotype/variation

value: Embryonic Stem Cell (ESC)

tag: stage in reprogramming

value: established ES


title: P0298

source_name: Genomic DNA from P298


title: UM-UC-3_si-WDR5-2_48h

description: No

tag: cell type

tag: sirna

value: GCUCAGAGGAUAACCUUGUTT


title: KSE_4_23_WT1_04242007_5-3_JC

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Affymetrix System Manual

scan_protocol: Refer to the Affymetrix System Manual

data_processing: Scanned raw data were normalized by using robust multiarray analysis (RMA) algorithm implemented in GenePattern genomic analysis toolkit (www.broadinstitute.org/genepattern).

organism: Danio rerio

source_name: zebrafish larvae (120 hours post fertilization)

label_protocol: Refer to the Affymetrix System Manual

growth_protocol: The progeny of uhrf1hi272+/- fish (Sadler et al., 2007) was used in most experiments.  Tg(fabp10:hUHRF1-GFP)  were outcrossed to uhrf1hi272+/- fish and F2-F5 fish were used.

extract_protocol: RNA was extracted by using TRIzol reagent (Life Technologies) according to manufacturer's instruction.

treatment_protocol: uhrf1 mutant versus wildtype zebrafish larvae at 120 days post fertilization

tag: phenotype

value: Wildtype


title: KSE_4_23_MT2_04242007_5-2_JC

value: UHRF1 mutant


title: KSE_4_23_WT3_04242007_5-5_JC


title: WT_8day_DOX

description:
Gene expression data of WT MBD3 mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming.
NOTE - this is the same sample published in GSM874654.

source_name: WT 4 days after dox induction

value: MBD3+/+ transgenic for DOX inducible OSKM reprogramming

value: Embryonic Fibroblast Cells (MEF)

value: 8 days after DOX induction


title: P820

description: Blood from a patient with Pelizaeus-Merzbacher disease

hyb_protocol: Proprietary

scan_protocol: Proprietary

data_processing: Nimblegen processed the raw data using proprietary algorithms and provided log2 transformed (test/control) ratios which had been calculated from normalized values.  Data for probes between chrX:103050175 and chrX:103254801 (a low copy repeat region of the genome) that were annotated by Nimblegen to hybridize to two locations were then removed.

source_name: Genomic DNA from P820

label_protocol: Proprietary

source_name: Genomic DNA from NM002

value: Normal (healthy)


title: P642

source_name: Genomic DNA from P642


title: P674

source_name: Genomic DNA from P674


title: KSE_4_23_MT1_04242007_5-1_JC


title: P558

source_name: Genomic DNA from P558


title: P113

source_name: Genomic DNA from P113


title: P1150

source_name: Genomic DNA from P1150


title: DNA methylation level in control group

city: beijing

first: Huixia

last: Yang

address: No.8 xishiku street,Xicheng District

institute: Peking Unversity First Hospital

description: DNA methylation in normal rat

hyb_protocol: The labeled genomic DNA (31μg) was dried at 45℃ and diluted in 5.6 μl Sample Tracking Control. Then hybridized in 14.4 μl Hybridization solution (containing 2X Hybridization Buffer, Hybridization Component A, Alignment Oligo). Arrays were hybridized in Maui hybridization stations for 40-72 hr at 42 °C, and then washed in 42 °C with buffer (containing VWR Water, 10X Wash Buffer (I, II or III), 1M DTT) by using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on a NimbleGen MS 200 Microarray Scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using NimbleScan 2.6 software,which transformed image signal to digital signal, following using segMNT algorithm to analyse the normalized signal ratio.

organism: Rattus norvegicus

source_name: IP DNA from adipose tissue sample in control group

label_protocol: 1. Add 4μL β-mercaptoethanol to 2200μL Random Primer Buffer, Mix by pulse-vortexing. Use 1050 μL Random Primer Buffer (containing β-mercaptoethanol) to dilute cy3-Random Nonamers and cy5-Random Nonamers respectively. 2. Add 500ng genomic DNA to LHC(Labeling and Hybridization Control). Then add 2μLLCH-1 to test Sample, and 2μLLCH-2 to Reference Sample, amount to 40μL respectively. Add test Sample (containing LLCH-1) to cy3-Random Nonamers, and Reference Sample (containing LLCH-2) to cy5-Random Nonamers, amount to 80μL respectively. 98 °C for 10 min，4°C for 2min. 3. Prepare dNTP/Klenow Master Mix (20μL): 8μL Nuclease-free Water, 10μL 10mM dNTP Mix, 2μL Klenow Fragment (3’->5’ exo-)50U/μl. 4. Add dNTP/Klenow Master Mix (20μL) to Sample mixtures (80μL) respectively. 37 °C  for 2 hr. 5. Add 21.5μL Stop Solution to stop reaction. 6. Then purify the label reaction liquid

extract_protocol: Total genomic DNA was isolated from 50mg visceral fat tissue using commercial kit (Tiangen, China),

treatment_protocol: visceral fat tissue dissected from the 28 week old rat.

value: female

tag: strain

value: wistar

value: visceral fat

source_name: Input DNA from adipose tissue sample in control group


title: BM-MSC_donor167696_H3K4_rep2

city: Silver Spring

first: Patrick

middle: J

last: Lynch

state: MD

address: 10903 New Hampshire Ave.

institute: US Food and Drug Administration

hyb_protocol: Cy3 and Cy5 labeled ChIP and input DNA was precipitated with isopropanol, and hybridized to arrays in 18 µl of Hybrization buffer (NimbleGen) in Maui hybridization stations for 16-18 h at 42C, and then washed vigorously for 2 minutes in Wash Buffer 1, 1 minute in Wash Buffer 2, and 15 seconds in Wash Buffer 3. Hybridization buffers and wash buffers were supplied by the array manufacturer (NimbleGen) and all hybridization and wash steps were completed using manufacturer's protocols (http://www.nimblegen.com/support/dna-microarray-support.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/support/dna-microarray-support.html).

data_processing: Data were extracted using NimbleScan v2.6 software according to manufacturer's instructions (http://www.nimblegen.com/support/dna-microarray-support.html) and normalized with pMA2C v. 1.3.3 with robust C=2 method

source_name: H3K4me3 ChIP DNA from MSC cells

label_protocol: 10 ng of ChIP and input DNA were amplified using the GenomePlex Whole Genome Amplification kit (Sigma) and isolated using PCR clean-up DNA columns (Qiagen). 15 µg of amplified ChIP and input DNA were labeled with Cy3 and Cy5 dyes, respectively, using the manufacturer's protocol (NimbleGen, Roche; http://www.nimblegen.com/support/dna-microarray-support.html).

extract_protocol: Approximately 4x10E6 cells were fixed with 1% formaldehyde in PBS for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 0.4 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0, 20 mM Na-Butyrate, 1 mM PMSF, 2 µg/mL pepstatin A, 1 µg/mL aprotinin, and 1x complete protease inhibitors; Roche) for at least 10 min on ice. The crosslinked chromatin was sheared to an average size of 700 bp by twelve 10-second pulses using a Misonix sonicator (Qsonica) and spun at 16,000 x g for 10 minutes at 4°C. Supernatants were collected and diluted 10-fold in IP buffer (10 mM Tris, pH 7.5, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-Deoxycholate, 140 mM NaCl, 20 mM Na-Butyrate, 1 mM PMSF, 2 µg/mL pepstatin A, 1 µg/mL aprotinin, and 1x complete protease inhibitors; Roche). Chromatin aliquots from ~2.5 x 10E5 cells were incubated overnight at 4°C with 25 µL magnetic Dynabeads Protein-A (Invitrogen) and 5 µL of antibodies. Beads were washed 3 times in IP buffer and once in Tris-EDTA, pH 8.0, and resuspended in 500 µL of elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS, and 20 µg/mL RNase A; Invitrogen) and incubated at 37°C for 30 minutes. Protease K (Invitrogen) was added to 50 µg/mL and cross-links were reversed and proteins digested for 2.5 hours at 68°C. DNA was isolated from the ChIP samples and the input material (at 1% of the material used for ChIP) by phenol chroloform extraction and ethanol precipitation and resuspended in 10 µl of 10 mM Tris, pH 7.5. Isolated DNA was quantified by picogreen (Life Technologies).

tag: donor

value: bone marrow MSC

source_name: Input DNA from MSC cells


title: P518

source_name: Genomic DNA from P518

tag: tissue


title: BM-MSC_donor8F3560_H3K27_rep1

source_name: H3K27me3 ChIP DNA from MSC cells


title: Mouse_ATF6aKO_colon_UT_rep1

status: Public on Feb 08 2015

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

country: Japan

institute: Institute for Genome Research

description: Gene expression of mouse (ATF6aKO) untreated colon

hyb_protocol: 1.65ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent Fragmentation buffer and 2x Agilent Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17.5 hours at 65°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°C GE Wash buffer 2 (Agilent), then air-dried immediately.

scan_protocol: Slides were scanned immediately after washing and drying on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%, NoXDR setting).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Mouse, ATF6aKO, colon, UT, rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the Low Input Quick Amp Labeling Kit (One-Color) (Agilent) according to the manufacturer's instructions, followed by RNeasy mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: All the mouse protocols were approved by the Animal Experimentation Committee of the University of Tokushima. The mice were housed in a room maintained at 22℃ (71.6 F), with a 12:12 h light-dark cycle starting from 8:00 AM under SPF conditions.

extract_protocol: The colons of the untreated or DSS-treated mice were snap frozen in Liquid nitrogen, and total RNA was extracted using the conventional acid guanidinium thiocyanate phenol-chloroform (AGPC) procedure and cleaned up using the RNeasy MinElute Cleanup Kit according to manufactuer's instructions (QIAGEN Valencia, CA).

treatment_protocol: Colitis was induced with 3% DSS, 36,000-50,000 M.W. (MP Biomedicals, Lot No. 3865K) in the drinking water for 3 days.

value: colon

tag: genotype

tag: treatment

value: untreated


title: BM-MSC_donor8F3560_H3K4_rep2


title: P250

source_name: Genomic DNA from P250

value: Pelizaeus-Merzbacher disease

value: male


title: Mouse_ATF6aKO_colon_DSS_rep2

description: Gene expression of mouse (ATF6aKO) colon after 3days treatment of 3% DSS

source_name: Mouse, ATF6aKO, colon, DSS, rep2

value: DSS for 3 days


title: Mouse_ATF6bKO_colon_DSS_rep2

description: Gene expression of mouse (ATF6bKO) colon after 3days treatment of 3% DSS

source_name: Mouse, ATF6bKO, colon, DSS, rep2


title: Mouse_ATF6bKO_colon_UT_rep1

description: Gene expression of mouse (ATF6bKO) untreated colon

source_name: Mouse, ATF6bKO, colon, UT, rep1


title: BM-MSC_donor8F3560_H3K4_rep1


title: DNA methylation level in GDM group

description: DNA methylation in GDM rat

source_name: IP DNA from adipose tissue sample in GDM group

source_name: Input DNA from adipose tissue sample in GDM group


title: Mouse_ATF6aKO_colon_UT_rep2

source_name: Mouse, ATF6aKO, colon, UT, rep2


title: BM-MSC_donor1632_H3K4_rep2


title: BM-MSC_donor167696_H3K27_rep1


title: Mouse_WT_colon_UT_rep2

description: Gene expression of mouse (WT) colon after 3days treatment of 3% DSS

source_name: Mouse, WT, colon, UT, rep2

value: WT


title: BM-MSC_donor8F3560_H3K27_rep2


title: P842

source_name: Genomic DNA from P842

value: blood

source_name: Genomic DNA from NM002


title: Mouse_ATF6bKO_colon_DSS_rep1

source_name: Mouse, ATF6bKO, colon, DSS, rep1


title: BM-MSC_donor167696_H3K27_rep2


title: Mouse_ATF6aKO_colon_DSS_rep1

source_name: Mouse, ATF6aKO, colon, DSS, rep1


title: BM-MSC_donor1632_H3K4_rep1

source_name: H3K4me3 ChIP DNA from MSC cells


title: P500

source_name: Genomic DNA from P500


title: Mouse_ATF6bKO_colon_UT_rep2

source_name: Mouse, ATF6bKO, colon, UT, rep2


title: Mouse_WT_colon_DSS_rep2

description: Gene expression of mouse (WT) untreated colon

source_name: Mouse, WT, colon, DSS, rep2


title: Mouse_WT_colon_UT_rep1

source_name: Mouse, WT, colon, UT, rep1


title: BM-MSC_donor1632_H3K27_rep2

source_name: H3K27me3 ChIP DNA from MSC cells

source_name: Input DNA from MSC cells


title: Mek1gof (replicate 2)

city: Berlin

first: Ozlem

last: Akilli Ozturk

address: Robert-Rosslestr. 10

department: Cancer Research

country: Germany

institute: Max Delbruck Center for Molecular Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplif Kit

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: C57/BL6;129Ola mixed

value: 15 days

value: dorsal skin


title: BM-MSC_donor1632_H3K27_rep1


title: Double (replicate 2)

source_name: Double


title: Double (replicate 3)


title: BM-MSC_donor167696_H3K4_rep1


title: Mek1gof (replicate 1)


title: Mouse_WT_colon_DSS_rep1

source_name: Mouse, WT, colon, DSS, rep1


title: Shp2lof (replicate 3)


title: Mek1gof (replicate 4)


title: Double (replicate 4)


title: Shp2lof (replicate 4)


title: Shp2lof (replicate 1)


title: control (replicate 2)

source_name: control


title: control (replicate 4)


title: P10 control (replicate 9)

source_name: P10 control

value: 10 days


title: Mek1gof (replicate 3)


title: Shp2lof (replicate 2)


title: control (replicate 3)


title: control (replicate 1)


title: P10 mutant (replicate 6)

source_name: P10 mutant


title: P10 control (replicate 5)


title: P15 control (replicate 5)

source_name: P15 control


title: P10 control (replicate 8)


title: P10 control (replicate 4)


title: P10 control (replicate 6)


title: P10 control (replicate 7)


title: P10 mutant (replicate 4)


title: P10 control (replicate 10)


title: P10 mutant (replicate 2)


title: P10 control (replicate 1)


title: P10 mutant (replicate 1)


title: P15 control (replicate 6)


title: P15 control (replicate 4)


title: P10 control (replicate 3)


title: P15 mutant (replicate 6)

source_name: P15 mutant


title: P15 control (replicate 3)


title: P10 control (replicate 2)


title: P10 mutant (replicate 3)


title: P15 control (replicate 2)


title: P15 control (replicate 1)


title: P15 mutant (replicate 2)


title: P10 mutant (replicate 5)


title: TCF3-PBX1 transduced BCL6fl/fl mouse bone marrow pre-B cells transduced with Cre for BCL6 deletion, repeat 2

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

hyb_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

data_processing: The CEL files were processed with Affymetrix GeneExpression Console software (Version 1.1) using MAS5 normalization

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual)

extract_protocol: Extraction Method: Qiagen RNeasy Kit

tag: sample type

value: TCF3-PBX1 transduced BCL6fl/fl mouse bone marrow pre-B cells with Cre-mediated BCL6 deletion

tag: genetic background

value: bone marrow pre-B cells

value: Cre-mediated BCL6 deletion


title: P15 mutant (replicate 4)


title: TCF3-PBX1 transduced BCL6fl/fl mouse bone marrow pre-B cells transduced with an empty vector (EV), repeat 3

scan_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

value: wild type


title: P15 mutant (replicate 3)


title: P15 mutant (replicate 5)


title: P15 mutant (replicate 1)


title: TCF3-PBX1 transduced BCL6fl/fl mouse bone marrow pre-B cells transduced with an empty vector (EV), repeat 2


title: TCF3-PBX1 transduced BCL6fl/fl mouse bone marrow pre-B cells transduced with Cre for BCL6 deletion, repeat 1


title: TCF3-PBX1 transduced BCL6fl/fl mouse bone marrow pre-B cells transduced with Cre for BCL6 deletion, repeat 3


title: RPE, mock_rep1

status: Public on Feb 07 2015

city: Helsinki

first: Maria

last: Anastasina

address: Tukholmankatu 8

department: Institute for Molecular Medicine, Finland

country: Finland

institute: University of Helsinki

data_processing: quantile normalized using Limma package for R from Bioconductor

source_name: RPE cell line

label_protocol: Standard Illumina label protocol

growth_protocol: Peripheral blood mononuclear cells were isolated form Buffy coats obtained from healthy donors. Macrophages were differentiated from PBMCs in serum-free medium containing granulocyte-macrophage colony stimulating factor for 7 days.

extract_protocol: Total RNA was isolated from infected and non-infected macrophages after 8 hours of infection using Qiagen Rneasy Plus mini kit.

treatment_protocol: Macrohages were infected with Influenza A viruses at multiplicity of infection = 1 in serum-free medium.

tag: time post infection, h


title: Double (replicate 1)


title: RKAA_infected_rep_2

source_name: Macrophages


title: RPE, mock_rep2


title: Macrophages, mock_rep1


title: infection_RKAA_rep3


title: Macrophages, mock_rep2


title: WSN_infected_rep_2


title: infection_RKAA_rep2


title: RPE, mock_rep3


title: infection_WT_rep3


title: shRNA NFAT1 4T1 cells_3

city: Orsay

first: Jacques

last: GHYSDAEL

address: Centre Universitaire, Bat 110

country: France

institute: Institut Curie

hyb_protocol: Following fragmentation, 10 μg of cRNAs were hybridized for 16 hours at 45oC, 60 rpm on Mouse GeneChip® 430 2.0 arrays. The chips were then washed and stained in the GeneChip® Fluidics Station 450 using the FS450_0004 script.

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G. Raw data were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.2

data_processing: CEL files were processed with R to calculate probeset signal intensities using Robust Multi-array Average (RMA) algorithms

source_name: 4T1_NFAT1 shRNA

label_protocol: Biotinylated cRNA targets were prepared from 200 ng of total RNA using the “MessageAmp™ Premier RNA Amplification Kit from Ambion, according to the Instruction Manual # 4386269 Revision B, 18 september 2007

growth_protocol: 4T1 adherent cell were transduced with a control vector or an shRNA NFAT1 expressing vector. After 10 days of selection cells were trypsinized and collected from culture dishes. Cells were next lysed following the Rneasy kit from QUIAGEN

extract_protocol: Total RNA was isolated using the RNeasy kit from QIAGEN

tag: cell line

value: highly tumorigenic and metastatic mammary tumor cells

tag: transduced with

value: NFAT1 shRNA


title: RKAA_infected_rep_1


title: WSN_infected_rep_1


title: infection_WT_rep1


title: Uninfected-Rep2

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

country: India

institute: IISER Bhopal

description: SAMPLE 2.rma-dabg-Signal

hyb_protocol: 500 ng RNA were hybridised for 16h at 60 rpm at 48°C on Affymetrix GeneChip miRNA 4.0 Array and scanned by Affymetrix 3000 7G.

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

data_processing: Scanned images of microarray chips were analyzed using Affymetrix Expression Console with the default RMA settings. Raw data were processed and Nromalized on basis of organism human using RMA algorithm. The normalized data (CHP files) processed  for the differential miRNA analysis in Affymetrix TAC software.

label_protocol: omplex probes were produced from total RNA using the FlashTag™ Biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA, USA)

extract_protocol: Small RNA extraction using miRVana miRNA isolation Kit.

tag: infected with

value: none (uninfected)


title: Uninfected-Rep1

description: SAMPLE 1.rma-dabg-Signal


title: NDV-6h-Rep1

description: SAMPLE 3.rma-dabg-Signal

value: NDV-LasoTa for 6hrs


title: TCF3-PBX1 transduced BCL6fl/fl mouse bone marrow pre-B cells transduced with an empty vector (EV), repeat 1


title: shRNA NFAT1 4T1 cells_1


title: infection_RKAA_rep1


title: infection_WT_rep2


title: control 4T1 cells_3

value: control shRNA


title: shRNA NFAT1 4T1 cells_2


title: Patient 3 CYB-26768

status: Public on Feb 06 2015

city: wuhan

first: yaobin

last: chen

address: Tongji Hospital, Wuhan,jiefang road 1095

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology,

description:
paraffin tissue
CYB-26768

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

source_name: angiosarcoma

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

extract_protocol: Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacture's instructions

tag: patient id

value: Patient 3

tag: age

value: 48 years

tag: gender

value: male

tag: survival status

value: deceased

tag: tissue type

value: angiosarcoma


title: Patient 4 CYB-1

description:
paraffin tissue
CYB-1

source_name: capillary hemangiomas

value: Patient 4

value: 40 years

value: alive

value: capillary hemangiomas


title: Patient 5 CYB-2

description:
paraffin tissue
CYB-2

value: Patient 5

value: 49 years

value: female


title: Patient 6 CYB-3

description:
paraffin tissue
CYB-3

value: Patient 6

value: 38 years


title: Patient 2 CYB-18043

description:
paraffin tissue
CYB-18043

value: Patient 2

value: 47 years


title: Patient 1 CYB-5954

description:
paraffin tissue
CYB-5954

value: Patient 1

value: 65 years


title: control 4T1 cells_2

tag: cell type

value: highly tumorigenic and metastatic mammary tumor cells

value: control shRNA


title: 24hr_HDMYZ_DMSO_6

status: Public on Feb 05 2015

city: New Haven

first: Yanwen

last: Guo

state: CT

address: 214K 10 Amistad St

department: Genetics

institute: Yale University

hyb_protocol: Labeled biotinylated miRNAs were hybridized to colored beads with covalently bound detection probes in 1.5X TMAC buffer (1.5X TMAC Buffer: for each 50ml, add 45ml 5M TMAC (Sigma T3411-1L), 0.375ml 20% sarkosyl, 3.75ml 1M Tris-Cl pH8.0, 0.6ml 5M EDTA and 0.275ml water) on a PCR machine, with 95ºC for 5minutes and 50ºC on hold for more than 4 hours. The detection beads are created by covalently coupling 5’-animo-modified oligonucleotide-capture probes (complementary to miRNAs) to carboxylated 5-micron polystyrene beads, with one miRNA coupled to beads with a specific color combination. Bead color is made possible by variably mixing two fluorescent dyes at variable ratios (up to 500 combinations), and can be easily differentiated with flow cytometry. After the hybridization, the beads were washed once with 1X TMAC buffer (dilute 1.5X TMAC with water), followed by binding of the fluorescent streptavidin-phycoerythrin to biotin at 50ºC for 10 minutes.  The beads were washed twice with 1X TMAC buffer before detection by flow cytometry.

scan_protocol: Beads detection were performed with flow cytometry (Luminex FlexMap 3D machine) to identify the specific bead color (reflecting miRNA identity) and quantify phycoerythrin intensity on the bead (reflecting the level of hybridized miRNAs).

data_processing: Profiling data were first scaled according to the post-labelling-controls and then the pre-labelling-controls, in order to normalize readings from different probe/bead sets for the same sample, and to normalize for the labelling efficiency, respectively. Data were thresholded at 16 and log2-transformed.

source_name: HDMYZ cells, 0.4% DMSO, 24 hours

label_protocol: miRNAs were enriched from total RNA through hybridization-based miRNA capturing in a 96-well format. Subsequent biochemical reactions are performed in the same capture plate, involving ligating mature miRNAs with 3’ adaptor and 5’ adaptor consecutively and reverse transcribing from a primer complementary to the 3’adatpor. Lastly, PCR-based labeling is then performed with a common pair of primers matching 5’ and 3’ adaptors, with the 5’ adaptor-matching primer containing a biotin label.

growth_protocol: HeLa, PC-3, IMR-90, MEF and MCF-7 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin. HDMYZ, K562 and Raji cells were cultured in RPMI with 10% FBS and 1% Penicillin-Streptomycin. mESCs were cultured on MEF feeders in DMEM media supplemented with 15%FBS (Hyclone), 1% MEM Non-Essential Amino Acids, 1% Penicillin-Streptomycin, 0.8% 2-Mercaptoethanol and 1000U/ml ESGRO (Millipore). For harvesting mESCs samples, cells were de-MEFed by trypsinizing and plating on Gelatin-coated (Millipore) plates for 40 minutes to deplete MEF. Human embryonic stem cell research was performed on a protocol approved by the hESC Oversight Committee at Yale University. H1 hESCs (WA01, WiCell) were maintained in a undifferentiated state by culturing on Matrigel-coated plates (BD Biosciences), with DMEM/F12 medium supplemented with 1% MEM-nonessential amino acids, 1mM l-glutamine, 1% penicillin-streptomycin, 50 ng/mL bFGF (Millipore), 1X N2 supplements, and 1X B27 supplements (Invitrogen), and with a daily medium change. Differentiation of hESCs into neuronal progenitor cells were performed following a published method (Cohen et al. 2007) with modifications. Embryoid bodies were generated by detaching undifferentiated H1 colonies from plates with diapase (Stem Cell Technology), and put on extra-low attachment plates (Corning) with DMEM/F12, supplemented with 2 mM L-glutamine, 1% P/S, 1X B27 supplements, 250ng/ml Noggin (PeproTech), and 20ng/ml bFGF. The medium was changed every 2 days for a total of four weeks with the last week medium eliminating Noggin. All cell culture reagents were from Invitrogen unless noted otherwise.

extract_protocol: Cells were collected with Trizol reagent (Invitrogen). Total RNA extraction was performed following manufacturer's protocol.

treatment_protocol: Cells were plated in six-well plates at around 200,000 cells/well. A media change was performed one day after plating. ActD and DRB treatment were started after confluency (around two days after plating) for 0, 2, 4, 6, 12, and 24 hours post treatment with biological duplicate (ActD treatment) or biological triplicate (DRB treatment). The concentration of ActD and DRB for different cell lines were titrated to achieve rapid c-myc down-regulation after 2 hours of ActD and DRB treatment. After treatment at indicated time points, cells were washed with PBS once and lysed in TriZol reagent immediately (Invitrogen)

tag: cell type origin

value: hodgkin's lymphoma

tag: transcription inhibitor treatment

value: 0.4% DMSO

tag: time post treatment

value: 24 hours


title: control 4T1 cells_1


title: 24hr_HDMYZ_ActD_4

source_name: HDMYZ cells, 2ug/ml ActD, 24 hours

value: 2ug/ml ActD


title: NDV-6h-Rep2

description: SAMPLE 4.rma-dabg-Signal

value: NDV-LasoTa for 6hrs


title: Cholesterol.2 (II)

city: Corvallis

first: Stephen

last: Ramsey

state: OR

address: Dryden Hall 208A

department: Biomedical Sciences

institute: Oregon State University

description: Analysis (II)

hyb_protocol: Labeled aRNA was hybridized onto the GeneChip® Mouse Genome 430 2.0 using the GeneChip Hybridization Oven 640, and the GeneChip was stained in a GeneChip Fluidics Station 450 with streptavidin-phycoerythrin conjugate.

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

data_processing:
Probe-level intensities for all six samples (baseline, cholesterol-treated, and HDL-recovered) were background-adjusted and normalized using the Robust Multichip Average procedure.
Probe-level log2 intensities were combined into probesets using probe-to-probeset mappings from the University of Michigan CustomCDF project version 13, based on Ensembl Gene identifiers (release 58).

source_name: Aortic vascular smooth muscle cells_cholesterol

label_protocol: RNA samples were reverse transcribed to cDNA, transcribed to obtain labeled aRNA, purified, and fragmented using the GeneChip 3’ IVT Express kit.

growth_protocol: Mouse aortic VSMCs were isolated from thoracic aortas of 8 week-old C57BL/6 mice (as described in Rong et al., Proc Nat Acad Sci USA, v100, pp13531–13536, 2003) and subconfluent cell preparations (≤ five passages) were grown in DMEM containing 10% FBS, 100 units/mL penicillin, and 100 μg/mL streptomycin, and incubated at 37 °C with 5% CO2 / 95% air.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). RNA quality was analyzed with an Agilent Bioanalyzer.

treatment_protocol: Cells were either harvested at baseline or treated with 10 μg/mL Cholesterol:methyl-β-cyclodextrin complex (1:6 molar ratio) for 72 h and then harvested, or treated with cholesterol for 72 h and then treated with 100 μg/mL HDL for an additional 72 h and then harvested.

tag: strain

value: 8 weeks-old

tag: stimulus

value: cholesterol

value: primary aortic smooth muscle cells (SMCs)


title: Hep3B_UV_40J_replicate2_Dyeswap

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

hyb_protocol: Slides were hybridized following manufacturer protocol, with the exception that we hybridized 6 micrograms of each amplified cRNA sample and the Agilent hybridization oven was set to 60ºC.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing: Raw data were processed using SAPO (http://bioinfo.ciberehd.org/SAP.ang.htm) and CGEM (http://bioinfo.ciberehd.org/CGEM.ang.html) alternative splicing analysis tools, obtaining lowess normalized log2ratios. Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

source_name: human hepatoma Hep3B cells untreated

label_protocol: Sample was labeled using the Quick-Amp labeling kit, no dye (Agilent 5190-0447) and cyanine 5-CTP and cyanine 3-CTP (Perkin-Elmer NEL580, NEL581). Purified using Quiagen RNeasy mini kit. Quality control assessed by Agilent Bioanalyzer 2100.

growth_protocol: Hep3B cells were grown in IMDM medium supplemented with 10% fetal bovine serum, penicillin and streptomycin (Gibco), and maintained at 37°C in humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated using the RNAspin Mini Kit (GE Healthcare). An additional treatment with DNAse was performed using the TURBO DNA-free Kit  (Ambion inc).    Quality assessment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

treatment_protocol: Human hepatoma Hep3B cells were Hep3B cells were washed two times with PBS and then irradiated with 40J/m2 UV light; fresh medium was immediately added after the irradiation and the cells were incubated at 37 C and collected 6 hours after the treatment for the RNA preparation.

value: hepatoma

source_name: Hep3B cells treated with 10 J/m2 UV light


title: 24hr_HDMYZ_ActD_3


title: Hep3B_UV_40J_replicate3_Dyeswap


title: Cholesterol.1 (I)

description: Analysis (I)


title: Cholesterol.2 (I)

description: Analysis (I)


title: Cholesterol.1 (II)

description: Analysis (II)


title: HDL.1 (II)

description: Analysis (II)

source_name: Aortic vascular smooth muscle cells_HDL

value: HDL


title: 12hr_HDMYZ_ActD_4

source_name: HDMYZ cells, 2ug/ml ActD, 12 hours

value: 12 hours


title: 12hr_HDMYZ_ActD_5


title: 12hr_HDMYZ_DMSO_6

source_name: HDMYZ cells, 0.4% DMSO, 12 hours


title: Baseline.2 (II)

description: Analysis (II)

source_name: Aortic vascular smooth muscle cells_baseline


title: Baseline.2 (I)

description: Analysis (I)


title: 24hr_HDMYZ_ActD_5


title: 12hr_HDMYZ_ActD_3


title: 6hr_HDMYZ_ActD_4

source_name: HDMYZ cells, 2ug/ml ActD, 6 hours

value: 6 hours


title: 6hr_HDMYZ_DMSO_6

source_name: HDMYZ cells, 0.4% DMSO, 6 hours


title: Hep3B_UV_40J_replicate3

source_name: human hepatoma Hep3B cells treated with 10 J/m2 UV light

source_name: Hep3B cells untreated


title: 6hr_HDMYZ_ActD_5


title: 6hr_HDMYZ_ActD_3


title: Hep3B_UV_40J_replicate2


title: 4hr_HDMYZ_DMSO_6

source_name: HDMYZ cells, 0.4% DMSO, 4 hours

value: 4 hours


title: Hep3B_UV_40J_replicate1_Dyeswap


title: HDL.2 (II)

description: Analysis (II)


title: 2hr_HDMYZ_DMSO_6

source_name: HDMYZ cells, 0.4% DMSO, 2 hours

value: 2 hours


title: 4hr_HDMYZ_ActD_5

source_name: HDMYZ cells, 2ug/ml ActD, 4 hours


title: 2hr_HDMYZ_ActD_4

source_name: HDMYZ cells, 2ug/ml ActD, 2 hours


title: 4hr_HDMYZ_ActD_4


title: 2hr_HDMYZ_ActD_5


title: 4hr_HDMYZ_ActD_3


title: 0hr_HDMYZ_9

source_name: HDMYZ cells, 0ug/ml , 0 hour

value: 0 hour


title: 0hr_HDMYZ_8


title: 24hr_neuralprogenitor_DMSO_3

source_name: neural progenitors, 0.3% DMSO, 24 hours

value: human embryonic stem cell (H1) derived neural progenitors

value: 0.3% DMSO


title: 0hr_HDMYZ_7

value: hodgkin's lymphoma


title: 24hr_neuralprogenitor_ActD_1

source_name: neural progenitors, 30ug/ml ActD, 24 hours

value: 30ug/ml ActD


title: Baseline.1 (I)

description: Analysis (I)


title: 12hr_neuralprogenitor_DMSO_3

source_name: neural progenitors, 0.3% DMSO, 12 hours


title: 24hr_neuralprogenitor_ActD_2

value: 24 hours


title: 0hr_HDMYZ_6


title: 2hr_HDMYZ_ActD_3

value: 2ug/ml ActD


title: 12hr_neuralprogenitor_ActD_2

source_name: neural progenitors, 30ug/ml ActD, 12 hours


title: 6hr_neuralprogenitor_ActD_1

source_name: neural progenitors, 30ug/ml ActD, 6 hours


title: Hep3B_UV_40J_replicate1


title: 4hr_neuralprogenitor_DMSO_3

source_name: neural progenitors, 0.3% DMSO, 4 hours


title: 6hr_neuralprogenitor_ActD_2


title: 6hr_neuralprogenitor_DMSO_3

source_name: neural progenitors, 0.3% DMSO, 6 hours


title: Baseline.1 (II)

description: Analysis (II)

source_name: Aortic vascular smooth muscle cells_baseline


title: 12hr_neuralprogenitor_ActD_1


title: 2hr_neuralprogenitor_DMSO_3

source_name: neural progenitors, 0.3% DMSO, 2 hours


title: 4hr_neuralprogenitor_ActD_2

source_name: neural progenitors, 30ug/ml ActD, 4 hours


title: 4hr_neuralprogenitor_ActD_1


title: 2hr_neuralprogenitor_ActD_1

source_name: neural progenitors, 30ug/ml ActD, 2 hours


title: 0hr_neuralprogenitor_3

source_name: neural progenitors, 0ug/ml , 0 hour


title: 0hr_neuralprogenitor_2


title: 2hr_neuralprogenitor_ActD_2


title: 12hr_MEF_ActD_2

source_name: mouse embryonic fibroblasts, 1.5ug/ml ActD, 12 hours

value: mouse embryonic fibroblast

value: 1.5ug/ml ActD


title: 24hr_MEF_ActD_1

source_name: mouse embryonic fibroblasts, 1.5ug/ml ActD, 24 hours


title: 24hr_MEF_DMSO_3

source_name: mouse embryonic fibroblasts, 0.3% DMSO, 24 hours


title: 6hr_MEF_ActD_2

source_name: mouse embryonic fibroblasts, 1.5ug/ml ActD, 6 hours


title: 12hr_MEF_DMSO_3

source_name: mouse embryonic fibroblasts, 0.3% DMSO, 12 hours


title: 12hr_MEF_ActD_1


title: 6hr_MEF_ActD_1


title: 4hr_MEF_ActD_2

source_name: mouse embryonic fibroblasts, 1.5ug/ml ActD, 4 hours


title: 2hr_MEF_DMSO_3

source_name: mouse embryonic fibroblasts, 0.3% DMSO, 2 hours


title: 2hr_MEF_ActD_1

source_name: mouse embryonic fibroblasts, 1.5ug/ml ActD, 2 hours


title: 24hr_mESC_DMSO_3

source_name: mouse embryonic stem cells, 0.3% DMSO, 24 hours

value: mouse embryonic stem cell


title: 6hr_MEF_DMSO_3

source_name: mouse embryonic fibroblasts, 0.3% DMSO, 6 hours


title: 24hr_MEF_ActD_2


title: 24hr_mESC_ActD_2

source_name: mouse embryonic stem cells, 1.5ug/ml ActD, 24 hours


title: 0hr_neuralprogenitor_1


title: 24hr_mESC_ActD_1


title: 0hr_MEF_1

source_name: mouse embryonic fibroblasts, 0ug/ml , 0 hour


title: 2hr_MEF_ActD_2


title: 4hr_MEF_DMSO_3

source_name: mouse embryonic fibroblasts, 0.3% DMSO, 4 hours


title: 0hr_MEF_3


title: 4hr_MEF_ActD_1


title: 12hr_mESC_DMSO_3

source_name: mouse embryonic stem cells, 0.3% DMSO, 12 hours


title: 6hr_mESC_DMSO_3

source_name: mouse embryonic stem cells, 0.3% DMSO, 6 hours


title: 6hr_mESC_ActD_2

source_name: mouse embryonic stem cells, 1.5ug/ml ActD, 6 hours


title: 12hr_mESC_ActD_1

source_name: mouse embryonic stem cells, 1.5ug/ml ActD, 12 hours


title: 12hr_mESC_ActD_2


title: 0hr_MEF_2


title: 0hr_mESC_3

source_name: mouse embryonic stem cells, 0ug/ml , 0 hour


title: 2hr_mESC_ActD_1

source_name: mouse embryonic stem cells, 1.5ug/ml ActD, 2 hours


title: 4hr_mESC_DMSO_3

source_name: mouse embryonic stem cells, 0.3% DMSO, 4 hours


title: 4hr_mESC_ActD_2

source_name: mouse embryonic stem cells, 1.5ug/ml ActD, 4 hours


title: 2hr_mESC_ActD_2


title: 6hr_mESC_ActD_1


title: 4hr_mESC_ActD_1


title: 2hr_mESC_DMSO_3

source_name: mouse embryonic stem cells, 0.3% DMSO, 2 hours


title: 2hr_K562_DRB_1

source_name: K562 cells, 50uM DRB, 2 hours

value: myelogenous leukemia

value: 50uM DRB


title: 6hr_K562_DRB_3

source_name: K562 cells, 50uM DRB, 6 hours


title: 6hr_K562_DRB_1


title: 4hr_K562_DRB_2

source_name: K562 cells, 50uM DRB, 4 hours


title: 12hr_K562_DRB_2

source_name: K562 cells, 50uM DRB, 12 hours


title: 0hr_mESC_2


title: 24hr_K562_DRB_1

source_name: K562 cells, 50uM DRB, 24 hours


title: 2hr_K562_DRB_3


title: 0hr_K562_3

source_name: K562 cells, 0uM, 0 hour


title: 0hr_K562_4


title: 4hr_K562_DRB_3


title: 0hr_K562_5


title: 12hr_K562_DRB_1


title: 6hr_K562_DRB_2


title: 24hr_K562_DRB_2


title: 4hr_K562_DRB_1


title: 0hr_mESC_1


title: 2hr_K562_DRB_2


title: 12hr_K562_DRB_3


title: 24hr_IMR90_DRB_3

source_name: IMR90 cells, 26uM DRB, 24 hours

value: fibroblast

value: 26uM DRB


title: 24hr_K562_DRB_3


title: 24hr_IMR90_DRB_2


title: 24hr_IMR90_DRB_1


title: 12hr_IMR90_DRB_2

source_name: IMR90 cells, 26uM DRB, 12 hours

value: 12 hours


title: 6hr_IMR90_DRB_2

source_name: IMR90 cells, 26uM DRB, 6 hours

value: 6 hours


title: 12hr_IMR90_DRB_3


title: 6hr_IMR90_DRB_3


title: 12hr_IMR90_DRB_1


title: 2hr_IMR90_DRB_2

source_name: IMR90 cells, 26uM DRB, 2 hours

value: 2 hours


title: 2hr_IMR90_DRB_1


title: 2hr_IMR90_DRB_3


title: 6hr_IMR90_DRB_1


title: 4hr_IMR90_DRB_3

source_name: IMR90 cells, 26uM DRB, 4 hours

value: 4 hours


title: 0hr_IMR90_5

source_name: IMR90 cells, 0uM, 0 hour

value: 0 hour


title: 4hr_IMR90_DRB_1


title: 0hr_IMR90_4


title: 24hr_IMR90_ActD_1

source_name: IMR90 cells, 20ug/ml ActD, 24 hours

value: 20ug/ml ActD


title: 24hr_IMR90_ActD_2


title: 4hr_IMR90_DRB_2


title: 12hr_IMR90_ActD_2

source_name: IMR90 cells, 20ug/ml ActD, 12 hours


title: 0hr_IMR90_2

source_name: IMR90 cells, 0ug/ml , 0 hour


title: 6hr_IMR90_ActD_1

source_name: IMR90 cells, 20ug/ml ActD, 6 hours


title: 4hr_IMR90_ActD_1

source_name: IMR90 cells, 20ug/ml ActD, 4 hours


title: 0hr_IMR90_1


title: 24hr_HeLa_DRB_3

source_name: HeLa cells, 50uM DRB, 24 hours

value: cervical cancer


title: 2hr_IMR90_ActD_2

source_name: IMR90 cells, 20ug/ml ActD, 2 hours


title: 24hr_HeLa_DRB_1


title: 2hr_IMR90_ActD_1


title: 4hr_IMR90_ActD_2


title: 6hr_IMR90_ActD_2


title: 0hr_IMR90_3


title: 12hr_IMR90_ActD_1


title: 12hr_HeLa_DRB_3

source_name: HeLa cells, 50uM DRB, 12 hours


title: 2hr_HeLa_DRB_2

source_name: HeLa cells, 50uM DRB, 2 hours


title: 0hr_HeLa_5

source_name: HeLa cells, 0uM, 0 hour


title: 2hr_HeLa_DRB_3


title: 2hr_HeLa_DRB_1


title: 4hr_HeLa_DRB_2

source_name: HeLa cells, 50uM DRB, 4 hours


title: 4hr_HeLa_DRB_1


title: 12hr_HeLa_DRB_1


title: 6hr_HeLa_DRB_1

source_name: HeLa cells, 50uM DRB, 6 hours


title: 6hr_HeLa_DRB_2


title: 6hr_HeLa_DRB_3


title: 4hr_HeLa_DRB_3


title: 0hr_HeLa_3


title: 48hr_HDMYZ_DRB_3

source_name: HDMYZ cells, 45uM DRB, 48 hours

value: hodgkin's lymphoma

value: 45uM DRB

value: 48 hours


title: 12hr_HeLa_DRB_2


title: 12hr_HDMYZ_DRB_2

source_name: HDMYZ cells, 45uM DRB, 12 hours


title: 48hr_HDMYZ_DRB_1


title: 24hr_HDMYZ_DRB_3

source_name: HDMYZ cells, 45uM DRB, 24 hours

value: 24 hours


title: 24hr_HDMYZ_DRB_1


title: 12hr_HDMYZ_DRB_1


title: 24hr_HDMYZ_DRB_2


title: 12hr_HDMYZ_DRB_3


title: 6hr_HDMYZ_DRB_1

source_name: HDMYZ cells, 45uM DRB, 6 hours


title: 0hr_HeLa_4


title: 48hr_HDMYZ_DRB_2


title: 2hr_HDMYZ_DRB_3

source_name: HDMYZ cells, 45uM DRB, 2 hours


title: 6hr_PC3_ActD_1

source_name: PC-3 cells, 0.1ug/ml ActD, 6 hours

value: prostate cancer

value: 0.1ug/ml ActD


title: 0hr_HDMYZ_3

source_name: HDMYZ cells, 0uM, 0 hour


title: 6hr_HDMYZ_DRB_3


title: 4hr_PC3_ActD_1

source_name: PC-3 cells, 0.1ug/ml ActD, 4 hours


title: 4hr_HDMYZ_DRB_1

source_name: HDMYZ cells, 45uM DRB, 4 hours


title: 0hr_HDMYZ_5


title: 4hr_PC3_ActD_2


title: 4hr_HDMYZ_DRB_3


title: 2hr_HDMYZ_DRB_2


title: 6hr_HDMYZ_DRB_2


title: 24hr_PC3_ActD_2

source_name: PC-3 cells, 0.1ug/ml ActD, 24 hours


title: 12hr_PC3_ActD_2

source_name: PC-3 cells, 0.1ug/ml ActD, 12 hours


title: 0hr_HDMYZ_4


title: 2hr_HDMYZ_DRB_1


title: 2hr_PC3_ActD_2

source_name: PC-3 cells, 0.1ug/ml ActD, 2 hours


title: 24hr_K562_ActD_2

source_name: K562 cells, 1.4ug/ml ActD, 24 hours

value: myelogenous leukemia

value: 1.4ug/ml ActD


title: 0hr_PC3_1

source_name: PC-3 cells, 0ug/ml , 0 hour


title: 2hr_PC3_ActD_1


title: 0hr_PC3_2


title: 12hr_K562_ActD_1

source_name: K562 cells, 1.4ug/ml ActD, 12 hours


title: 24hr_K562_ActD_1


title: 6hr_K562_ActD_2

source_name: K562 cells, 1.4ug/ml ActD, 6 hours


title: 6hr_PC3_ActD_2


title: 24hr_PC3_ActD_1


title: 12hr_PC3_ActD_1


title: 24hr_HeLa_ActD_2

source_name: HeLa cells, 0.2ug/ml ActD, 24 hours

value: 0.2ug/ml ActD


title: 2hr_K562_ActD_2

source_name: K562 cells, 1.4ug/ml ActD, 2 hours


title: 12hr_HeLa_ActD_2

source_name: HeLa cells, 0.2ug/ml ActD, 12 hours


title: 0hr_K562_2

source_name: K562 cells, 0ug/ml , 0 hour


title: 4hr_K562_ActD_1

source_name: K562 cells, 1.4ug/ml ActD, 4 hours


title: 2hr_K562_ActD_1


title: 6hr_K562_ActD_1


title: 12hr_HeLa_ActD_1


title: 4hr_HeLa_ActD_1

source_name: HeLa cells, 0.2ug/ml ActD, 4 hours


title: 12hr_HDMYZ_ActD_1

source_name: HDMYZ cells, 2ug/ml ActD, 12 hours

value: 2ug/ml ActD


title: 0hr_HeLa_1

source_name: HeLa cells, 0ug/ml , 0 hour


title: 6hr_HDMYZ_ActD_1

source_name: HDMYZ cells, 2ug/ml ActD, 6 hours


title: 12hr_HDMYZ_ActD_2

value: 12 hours


title: 24hr_HDMYZ_ActD_1

source_name: HDMYZ cells, 2ug/ml ActD, 24 hours


title: 0hr_HeLa_2


title: 6hr_HDMYZ_ActD_2

value: 6 hours


title: 6hr_HeLa_ActD_2

source_name: HeLa cells, 0.2ug/ml ActD, 6 hours


title: 2hr_HeLa_ActD_1

source_name: HeLa cells, 0.2ug/ml ActD, 2 hours

value: 2 hours


title: 0hr_K562_1


title: 24hr_HeLa_ActD_1


title: 6hr_HeLa_ActD_1


title: 4hr_HDMYZ_ActD_2

source_name: HDMYZ cells, 2ug/ml ActD, 4 hours

value: 4 hours


title: 4hr_HeLa_ActD_2


title: 24hr_HDMYZ_ActD_2


title: 2hr_HDMYZ_ActD_2

source_name: HDMYZ cells, 2ug/ml ActD, 2 hours


title: 0hr_HDMYZ_2

source_name: HDMYZ cells, 0ug/ml, 0 hour

value: 0 hour


title: 2hr_HDMYZ_ActD_1


title: 4hr_HDMYZ_ActD_1


title: 0hr_HDMYZ_1


title: EU4

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

hyb_protocol: Following quality control confirmation, total-RNA was amplified using the Affymetrix IVT Express kit, hybridized to Affymetrix Rat GeneChip 230 2.0 microarrays according to manufacturer’s instructions (Affymetrix).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: All data was analysed in Genespring GX12 (Agilent); .CEL files from the SL and the EU arrays (n=5) were uploaded subject to quartile RMA normalization where the median was used for baseline before statistical differences between the two conditions were determined using an unpaired t-test for unequal variance (Welch) with a Benjamini Hotchberg multiple test correction applied to maintain a corrected p-value of <0.05.

source_name: SON - EUHYDRATED CONTROL

extract_protocol: Rats were stunned (which involves a blow to the head) then decapitated with a small animal guillotine (Harvard Apparatus, Holliston, MA, USA). The brain was rapidly removed from the cranium and placed in an ice-cold brain matrix (ASI Instruments, Warren, MI, USA). One section of approximately 1mm thickness was taken and the SON carefully dissected on a bed of ice under a dissecting microscope (Leica, Germany). After isolation, the samples were immediately placed in Eppendorf tubes containing RNAlater® (Ambion, Huntingdon, UK). Tissue was mechanically homogenised in QIAzol Lysis Reagent (QIAgen, Crawley, UK) and the aqueous phase removed after centrifugation through a Phase Lock Gel column (Eppendorf, Cambridge, UK). Total RNA was purified with RNeasy Micro Kit MinElute Spin Columns (Qiagen, Crawley, UK) and eluted into 14μl of RNase free water.

treatment_protocol: SL ANIMALS WERE SUBJECT TO 7-DAYS SALT-LOADING WITH 2% SALINE (w/v)

value: Sprague Dawley

tag: stress

value: euhydrated

tag: tissue

value: supraoptic nucleus (SON) of the hypothalamus


title: SL5

source_name: SON - 7-DAY SALT LOAD (2%W.V)

label_protocol: Following quality control confirmation, total-RNA was amplified using the Affymetrix IVT Express kit, hybridized to Affymetrix Rat GeneChip 230 2.0 microarrays according to manufacturer’s instructions (Affymetrix).

value: salt loaded


title: EU5


title: EU3


title: SL1


title: SL3


title: MKN74_transfected_lipofectamin_only

city: Koto-ku

first: kyotaro

last: HIRASHIMA

state: Tokyo

address: 3-8-31 Ariake

department: Cancer Chemotherapy Center

institute: The JFCR-Cancer Inst.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Gene-level expression signals were obtained by processing of raw data with the RMA procedure using GeneSpring GX (Agilent Technologies).

source_name: Human gastric cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: The transfected cells were cultured in 24-well EZ-BindShut II plate (IWAKI) with low-adhesion surface in 1 mL DMEM and harvested 72 hours after transfection.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: Lipofectamine RNAiMAX (Invitrogen) was used in reverse transfection experiments to transfect 1.0 ug (approximately 100 pmol per well) of above described oligonucleotides into 3.0 x 10^5 cells as described in the manufacturer's protocol (Invitrogen).

tag: treatment

value: lipofectamin only


title: MLL-11

city: LOS ANGELES

first: Dinesh

middle: S

last: Rao

address: 750 CHARLES E YOUNG DRIVE, 12-272 FACTOR

department: PATHOLOGY AND LABORATORY MEDICINE

institute: UCLA

hyb_protocol: Labeled cRNA was hybridized to the Agilent SurePrint G3 Human gene expression 8x60K microarray according to the manufacturer's protocol.

scan_protocol: The arrays were scanned on an Agilent G2565CA microarray scanner at 100% PMT and 3 um resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_10_Apr08) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The Agilent feature extraction raw data files were loaded into the R environment and analyzed using the R library of the Linear Models for Microarray Data (LIMMA). The raw data were preprocessed for background correction and normalized between arrays using the quantile method, summarized by taking the average of replicates for each gene, and subsequently log2-transformed.

source_name: patient B20

label_protocol: 100 ng of total RNA was labeled using LowInputQuick Amp Labeling kit (Agilent 5190-2305) following manufacturer instructions.

growth_protocol: Not applicable, these are primary human B-ALL samples

extract_protocol: RNA Extraction was performed using Trizol reagent.

value: bone marrow

tag: translocation

value: MLL


title: EU1


title: SL2


title: MLL-14

source_name: patient B23

treatment_protocol: Not applicable, these are primary human B-ALL samples


title: EU2


title: RS4;11/BALR2si#2/DMSO

description: Gene expression from RS4;11 cells with knockdown of BALR-2

hyb_protocol: 15 µg of fragmented cRNA was used for hybridization. The arrays were stained with phycoerythrin-streptavidin and the signal intensity was amplified by treatment with a biotin-conjugated anti-streptavidin antibody, followed by a second staining using phycoerythrin-streptavidin.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: The data were analyzed with MATLAB using Affymetrix analysis functions: RMA background adjustment followed by quantile normalization

source_name: RS4;11 cells with knockdown of BALR2, vehicle treated

label_protocol: 3μg of total RNA per sample was prepared according to the manufacturer's protocols (Affymetrix)

growth_protocol: Cells were grown in RPMI media supplemented with RPMI with 10% FBS, 100 units/ml penicillin, 100 units/ml streptomycin, and 50 uM 2-Mercaptoethanol.

extract_protocol: Total RNA was isolated from all cell lines using the Rneasy kit by Qiagen, and isolated according to the protocol provided by Qiagen.

treatment_protocol: Cells were treated with prednisolone solubilized in DMSO at a concentration of 250 ug/mL for 12 hopurs

tag: transduction

value: DMSO


title: Lung Tumors_KRAS mutated Mice_STAT3 Deficient_13 Weeks

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

hyb_protocol: Affymetrix GeneChip® Mouse Gene 1.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

label_protocol: 100ng of total RNA were amplified and labeled using the Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

growth_protocol: Mice (wild-type, Kras LSL G12D and Kras LSL G12D:Stat3 loxp/loxp) were kept under standard  animal husbandry

extract_protocol: RNAeasy Kit (Quiagen#74104)

treatment_protocol: 8 weeks old mice (wild-type, Kras LSL G12D and Kras LSL G12D:Stat3 loxp/loxp) were intranasally inhaled with adenovirus expressing Cre recombinase and lung tumors (and control lungs) were collected at 13 weeks post-adenoviral infection.

value: male


title: RS4;11/Vector/DMSO

description: Gene expression from vector transduced RS4;11 cells

source_name: RS4;11 control vector cells, vehicle treated

value: Vector


title: MLL-15

source_name: patient B24


title: Lung Tumors_KRAS mutated Mice_13 Weeks

source_name: Lung Tumors_KRAS mutated Mice_13 Weeks


title: MKN74_transfected_AS1411_ODN

value: AS1411 ODN

tag: cell line


title: MLL-10

source_name: patient B19


title: MKN74_transfected_(uuaccc)^4_ORN

value: (uuaccc)^4 ORN


title: SL4


title: MKN74_transfected_(uuaggg)^4_ORN

value: (uuaggg)^4 ORN


title: RS4;11/BALR2si#2/PRED

description: Gene expression from RS4;11 cells with knockdown of BALR-2 and prednisolone treatment

source_name: RS4;11 cells with knockdown of BALR2, prednisolone treated

value: Prednisolone, 250 ug/mL


title: MLL-13

source_name: patient B22


title: MLL-12

source_name: patient B21


title: Lung_Wildtype_Control Mice_13 weeks

source_name: Lung_Wildtype_Control Mice_13 weeks


title: HBC4_transfected_AS1411_ODN

source_name: Human breast cancer cell line


title: HBC4_transfected_lipofectamin_only


title: RS4;11/Vector/PRED

description: Gene expression from vector transduced RS4;11 cells after prednisolone treatment.

source_name: RS4;11 control vector cells, prednisolone treated


title: HBC4_transfected_(uuaggg)^4_ORN


title: E2A-PBX1-13

source_name: patient B14


title: PC-3_transfected_lipofectamin_only

source_name: Human prostate cancer cell line


title: E2A-PBX1-14

source_name: patient B15


title: E2A-PBX1-15

source_name: patient B16


title: PC-3_transfected_AS1411_ODN


title: MLL-8

source_name: patient B17


title: HBC4_transfected_(uuaccc)^4_ORN


title: PC-3_transfected_(uuaccc)^4_ORN


title: Ctx_WT_11m_GN34_5

city: Los Angeles

first: X.

middle: William

address: 695 Charles E. Young Dr. South, Gonda 3524

department: Semel Institute

institute: University of California, Los Angeles

description: GN34-5 (Ctx)

hyb_protocol: After a second Ribogreen quant and normalization step, amplified and labeled cRNA was hybridized overnight at 58°C to Illumina MouseRef-8 v2.0 expression arrays.

scan_protocol: Array chips were scanned using an iScan reader, and expression data were extracted and compiled using BeadStudio software (Illumina).

data_processing: Raw data were analyzed by using Bioconductor packages as previously described (Coppola 2011). Quality assessment was performed by examining the interarray Pearson correlation and clustering based on the top variant genes was assessed.

source_name: Mouse Brain

label_protocol: 100 ng of total RNA isolated from cortical and striatal tissue processed as described above. Samples were quantitated using Ribogreen fluorescent assay and normalized to 10 ng/ul prior to amplification. Amplified and labeled cRNA was produced using the Illumina specific Ambion TotalPrep kit. 1st and 2nd strand cDNA was produced using the Ambion kit and purified using a robotic assisted magnetic capture step. Biotinylated cRNA was produced from the cDNA template in a reverse transcription reaction.

extract_protocol: Tissue samples were thawed and disrupted in Trizol using a 1mL syringe (26ga needle) and passed through a Qiagen QiaShredder column before proceeding with RNA extraction using the Qiagen Rneasy Mini kit per the manufacturer's direction.  This included an on-column DNase (Qiagen) digestion.

value: FvB/NJ

tag: brain region

value: Cortex

tag: genotype

value: Wildtype

tag: replicate

tag: Sex

value: M

tag: internal sample number


title: PC-3_transfected_(uuaggg)^4_ORN


title: MKN74_overexpresshTERT_LongTelomeres

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

source_name: Human gastric cancer cell line

growth_protocol: 1 x 10^6 cells were subcutaneously injected into 5-week-old female nude mice with a BALB/c genetic background. When the tumor reached at least 5 mm in diameter, mice were euthanized and the tumor tissue was collected.

extract_protocol: TissueLyser and RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: no treatment.

tag: sample type

value: hTERT


title: MLL-9

source_name: patient B18


title: E2A-PBX1-11

source_name: patient B12


title: E2A-PBX1-10

source_name: patient B11


title: Ctx_WT_7m_HD12_1

description: HD12-1 (Ctx)

tag: age

value: F


title: E2A-PBX1-8

source_name: patient B9


title: HBC4_basalhTERT_ShortTelomeres

value: control


title: E2A-PBX1-12

source_name: patient B13


title: E2A-PBX1-9

source_name: patient B10


title: HBC4_overexpresshTERT_LongTelomeres


title: Ctx_TG_2m_GN51_3

description: GN51-3 (Ctx)


title: PC-3_basalhTERT/cre_ShortTelomeres


title: Ctx_WT_2m_GN50_4

description: GN50-4 (Ctx)


title: Str_WT_11m_GN34_5

description: GN34-5 (Str)

value: Striatum


title: PC-3_basalhTERT/cre_LongTelomeres

value: LhTERTL/cre


title: Str_WT_2m_GN51_5

description: GN51-5 (Str)


title: 31

city: Moscow

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

data_processing: The data were normalised using quantile normalisation in R.

source_name: Kidney cancer

label_protocol: Total RNA was amplified by Illumina® Whole-Genome DASL HT Assay Kit

extract_protocol: Total  RNA was extracted with The RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Ambion) according to manufacturer instruction. RNA was quantified using Nanodrop.

tag: gender


title: 48

value: female


title: Ctx_WT_7m_GN1_1

last: Yang

description: GN1-1 (Ctx)


title: TEL-AML1-14

source_name: patient B8

value: bone marrow


title: Ctx_TG_11m_NTN2_1

description: NTN2-1 (Ctx)


title: 36


title: 28

value: male


title: PC-3_overexpresshTERT_LongTelomeres

value: LhTERTL


title: Str_WT_7m_GN2_3

description: GN2-3 (Str)


title: TEL-AML1-13

source_name: patient B7


title: PC-3_basalhTERT_ShortTelomeres


title: 22


title: Ctx_WT_11m_GN47_1

description: GN47-1 (Ctx)


title: 5


title: Ctx_WT_2m_GN51_5

description: GN51-5 (Ctx)


title: TEL-AML1-11

source_name: patient B5


title: 33


title: TEL-AML1-8

source_name: patient B2


title: Str_WT_7m_GN1_1

description: GN1-1 (Str)


title: TEL-AML1-12

source_name: patient B6


title: 66

source_name: Bladder cancer

extract_protocol: Total  RNA was extracted with Trizol reagent according to manufacture instruction. RNA was quantified using Nanodrop.

tag: tumor tnm classification and grade, g

value: T3bN1M0, G2

tag: primary or recurrent tumor growth

value: Recurrent


title: LPS-ERRα-/- BMDM #3

city: Daejeon

first: Jae-Min

last: Yuk

address: Jung-Gu Munhwa dong

department: Department of Microbiology

country: South Korea

institute: College of Medicine, Chungnam National University

hyb_protocol: Each 1,650ng of Cy3-labeled cRNA was fragmented at 60°C for 30 min (Agilent Gene Expression Hybridization Kit) and then hybridized to mouse whole genome 8 × 60K oligo microarray v2 slide (Agilent Technologies Inc.) at 65°C for 17 h. After hybridization, the arrays were washed consecutively by using Gene Expression Wash Pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.3.2.1 (Agilent) using default parameters (protocol GE1-1105_Oct12 and Grid: 028005_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Cell line

label_protocol: High-quality RNA samples were processed for genome-wide transcript expression using Agilent Mouse GE 8 × 60K V2 microarrays (Agilent Technologies Inc.). The Low Input Quick Amp Labeling Kit (Agilent Technologies Inc.) was used for labeling and hybridization. The sample was labeled with the aid of T7 RNA polymerase in the presence of Cy3-CTP. The Cy3-labeled cRNAs were purified using RNeasy MiniElute Cleanup kit (Qiagen). The yield and label incorporation efficiencies were measured with the aid of a spectrophotometer (NanoDrop Lite, Thermo Fisher Scientific, Inc).

growth_protocol: BMDMs were differentiated for 5–7 days in medium containing macrophage colony-stimulating factor. The culture medium consisted of Dulbecco's modiﬁed Eagle's medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1 mM sodium pyruvate, 50 U/mL penicillin, 50 μg/mL streptomycin, and 5×10 5 M 2-mercaptoethanol.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions

treatment_protocol: BMDMs from ERRα +/+ and ERRα -/- mice were incubated with LPS (100 ng/mL)

tag: strain background

tag: genotype/variation

value: ERRα-/-

value: 6-8 wks

tag: cell type

value: Bone marrow-dereived macrophages (BMDM)

tag: treated with

value: 100 ng/ml LPS


title: 72

value: Primary


title: 69


title: Ctx_TG_7m_GN2_2

description: GN2-2 (Ctx)

tag: strain

value: FvB/NJ

value: Cortex


title: PBS-ERRα+/+ BMDM #3

value: ERRα+/+

value: PBS (solvent control)


title: Str_TG_2m_GN51_1

description: GN51-1 (Str)

value: Striatum

value: M


title: 68


title: Str_WT_2m_GN50_4

description: GN50-4 (Str)

value: Wildtype

value: F


title: 60

value: male

value: T1NxM0, G1


title: Ctx_TG_2m_GN51_1

description: GN51-1 (Ctx)


title: TEL-AML1-10

source_name: patient B4

value: bone marrow

tag: translocation


title: PBS-ERRα-/- BMDM #3


title: MLL-7

source_name: patient A20

value: MLL


title: Ctx_WT_7m_GN1_3

description: GN1-3 (Ctx)

source_name: Mouse Brain


title: 64

value: Recurrent


title: LPS-ERRα+/+ BMDM #3

value: 6-8 wks


title: TEL-AML1-7

source_name: patient B1


title: 43

source_name: Normal bladder mucosa

value: no information


title: 56

value: female

value: T3bN0M0, G3


title: TEL-AML1-9

source_name: patient B3


title: Str_TG_7m_GN2_1

description: GN2-1 (Str)

value: FvB/NJ


title: Str_TG_7m_GN1_4

description: GN1-4 (Str)


title: PBS-ERRα-/- BMDM #2

value: ERRα-/-

value: Bone marrow-dereived macrophages (BMDM)


title: Pool A

source_name: Pooled normal bladder mucosa samples


title: LPS-ERRα-/- BMDM #2

value: 100 ng/ml LPS


title: Pool B


title: 55

value: Primary


title: 13


title: Ctx_TG_7m_GN1_2

description: GN1-2 (Ctx)

value: Cortex

value: M


title: MLL-5

source_name: patient A18


title: MLL-5-2

source_name: patient A19


title: Str_TG_11m_GN37_3

description: GN37-3 (Str)

value: Striatum


title: MKN74_basalhTERT_ShortTelomeres

source_name: Human gastric cancer cell line

tag: cell line

value: control


title: Ctx_TG_2m_GN50_3

description: GN50-3 (Ctx)

tag: brain region

value: F


title: Ctx_WT_2m_GN80_2

description: GN80-2 (Ctx)

tag: genotype

value: Wildtype


title: MLL-1

source_name: patient A14

value: bone marrow

value: MLL


title: Str_WT_7m_HD12_1

description: HD12-1 (Str)

tag: replicate


title: LPS-ERRα+/+ BMDM #2

value: ERRα+/+

value: 6-8 wks

value: male


title: E2A-PBX1-7

source_name: patient A13


title: MLL-3

source_name: patient A16


title: MLL-4

source_name: patient A17


title: E2A-PBX1-4

source_name: patient A10


title: AdAH v-miRNA(-) 1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: AdAH(-) 1

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: AdAH v-miRNA(-)

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Cells were plated to 10 cm collagen-coated dishes in culture medium containing 150 microgram of hygromycin per ml.

extract_protocol: Total RNAs were isolated from growing cells using TRIzol (Invitrogen) according to manufacturer's instructions.

treatment_protocol: No treatment

tag: cell line background

value: AdAH

value: adenoid epithelium-derived cell

tag: infected with

value: BART-deleted EBV

tag: bart mirna expression

value: negative


title: AdAH v-miRNA(+) 2

description: AdAH(+) 2

source_name: AdAH v-miRNA(+)

value: BART-restored EBV

value: positive


title: Ctx_TG_7m_GN1_4

description: GN1-4 (Ctx)

value: FvB/NJ

tag: age

value: Cortex

tag: Sex

tag: internal sample number


title: MLL-2

source_name: patient A15


title: Ctx_TG_2m_GN50_1

description: GN50-1 (Ctx)


title: AdAH v-miRNA(+) 1

description: AdAH(+) 1


title: E2A-PBX1-2

source_name: patient A8


title: E2A-PBX1-5

source_name: patient A11


title: HEK293 v-miRNA(+) 2

description: 293 (+) 2

source_name: HEK293 v-miRNA(+)

value: embryonic kidney cell


title: HEK293 v-miRNA(-) 1

description: 293 (-) 1

source_name: HEK293 v-miRNA(-)


title: E2A-PBX1-3

source_name: patient A9


title: Str_WT_2m_GN80_2

description: GN80-2 (Str)

source_name: Mouse Brain

value: Striatum

value: M


title: E2A-PBX1-6

source_name: patient A12


title: PBS-ERRα+/+ BMDM #2

source_name: Cell line

value: Bone marrow-dereived macrophages (BMDM)

tag: gender

value: PBS (solvent control)


title: Str_TG_7m_GN1_2

description: GN1-2 (Str)


title: Ctx_WT_2m_GN50_2

description: GN50-2 (Ctx)

value: Wildtype

value: F


title: Str_TG_11m_NTN28_2

description: NTN28-2 (Str)


title: TEL-AML1-6

source_name: patient A6

value: bone marrow


title: E2A-PBX1-1

source_name: patient A7


title: HEK293 v-miRNA(-) 2

description: 293 (-) 2


title: TEL-AML1-5

source_name: patient A5


title: Ctx_WT_7m_GN2_3

description: GN2-3 (Ctx)


title: Str_TG_11m_NTN2_1

description: NTN2-1 (Str)


title: 36

hyb_protocol: Hybridization was performed according to CustomArray ElectraSense™ Hybridization and Detection protocol. Hybridization mix contained 2.5 ug of labeleled DNA library, 6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt solution, 100 ng/ul sonicated calf thymus gDNA, 0,05% SDS. Hybridization mix was incubated with chip overnight at 50ºC.

scan_protocol: Hybridization efficiency was detected electrochemically using CustomArray ElectraSense™ Detection Kit and ElectraSense™ 4X2K/12K Reader.

source_name: Kidney cancer

label_protocol: Complete Whole Transcriptome Amplification WTA2 Kit  (Sigma) was used for reverse transcription and library amplification. Manufacturers protocol was modified by adding to amplification reaction dNTP mix containing biotinylated dUTP, resulting to final proportion dTTP/biotin-dUTP as 5/1.

value: female

tag: tumor classification (tnm) and grade (g)


title: 48


title: Ctx_TG_11m_GN37_3

description: GN37-3 (Ctx)


title: HEK293 v-miRNA(+) 1

description: 293 (+) 1


title: 33


title: 28

value: male


title: TEL-AML1-2

source_name: patient A2


title: TEL-AML1-3

source_name: patient A3


title: 5


title: Str_TG_2m_GN50_3

description: GN50-3 (Str)


title: Str_TG_2m_GN51_3

description: GN51-3 (Str)


title: Str_TG_7m_GN2_2

description: GN2-2 (Str)


title: 22


title: T-PLL_9

city: Munich

first: Anna

last: Stengel

address: Max-Lebsche-Platz 31

institute: MLL Münchner Leukämielabor GmbH

description: Human Genomic DNA male

hyb_protocol: The labeled and combines test and reference DNA was hybridized to the array fo 16-20h and washed using manufacturer's protocols (http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf)

scan_protocol: Arrays were scanned on an NimbleGen MS 200 Microarray Scanner per manufacturer's protocol (http://www.nimblegen.com/downloads/support/scanner_ms200_manual_v1p0.pdf).

data_processing: Arrays were processed using DEVA 1.2.1 software with Nimblegen's standard protocol (http://www.nimblegen.com/downloads/support/06271090001_DEVA_UserGuide_v1p2.pdf). Processed data files contain the scaled, log2 ratio of T-PLL/reference

source_name: T-cell prolymphocytic leukemia

label_protocol: 0,5 µg genomic DNA was directly labeled by Klenow random priming with Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf).

extract_protocol: DNA was extracted according to standard methods

value: Male

source_name: human reference DNA


title: Ctx_TG_7m_GN2_1

description: GN2-1 (Ctx)


title: T-PLL_8

description: Human Genomic DNA male


title: T-PLL_7

description: Human Genomic DNA female

value: Female


title: Str_WT_11m_WT1

description: WT1 (Str)


title: 31


title: T-PLL_6

description: Human Genomic DNA male


title: TEL-AML1-4

source_name: patient A4


title: Str_WT_11m_GN34_1

description: GN34-1 (Str)


title: Ctx_TG_11m_GN36_1

description: GN36-1 (Ctx)


title: T-PLL_5

description: Human Genomic DNA male


title: Str_TG_11m_GN36_1

description: GN36-1 (Str)


title: Ctx_TG_11m_NTN28_2

description: NTN28-2 (Ctx)


title: T-PLL_39

description: Human Genomic DNA female


title: Ctx_WT_11m_GN34_1

description: GN34-1 (Ctx)


title: Str_WT_11m_GN47_1

description: GN47-1 (Str)


title: TEL-AML1-1

source_name: patient A1


title: Str_WT_2m_GN50_2

description: GN50-2 (Str)


title: T-PLL_34

description: Human Genomic DNA female


title: Str_WT_7m_GN1_3

description: GN1-3 (Str)


title: MRT560Gy-irradiated tumour 48hr_07D39 IT

city: Parkville

first: Yuqing

state: Victoria

address: Royal Women's Hospital Level 7, 20 Flemington Rd

institute: University of Melbourne

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina data was formatted into a Partek project data file. Partek Genomics Suite version 6.6 was used for normalization and analysis. Robust multichip average algorithm (RMA) background correction and qunatile normalization were applied to probe intensities.

source_name: MRT560Gy-irradiated tumour 48hr

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

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

tag: strain background

value: BALB/c

value: 6-8 months

value: mouse breast tumor cell line

tag: treatment group

value: MRT560Gy-irradiated 48hr


title: MRT560Gy-irradiated tumour 48hr_07D40 IT

description: replicate 4

tag: cell type


title: Ctx_WT_11m_WT1

description: WT1 (Ctx)

tag: strain

value: FvB/NJ

value: Cortex


title: BB11Gy-irradiated tumour 48hr_07D26 IT

description: replicate 2

source_name: BB11Gy-irradiated tumour 48hr

value: BB11Gy-irradiated 48hr


title: T-PLL_33

description: Human Genomic DNA male


title: BB22Gy-irradiated tumour 48hr_07D28 IT

description: replicate 4

source_name: BB22Gy-irradiated tumour 48hr

value: BB22Gy-irradiated 48hr


title: T-PLL_51

description: Human Genomic DNA female


title: MRT560Gy-irradiated tumour 48hr_07D38 IT

description: replicate 2


title: MRT560Gy-irradiated tumour 48hr_07D37 IT

description: replicate 1


title: BB22Gy-irradiated tumour 48hr_07D27 IT

description: replicate 3


title: BB11Gy-irradiated tumour 48hr_07D25 IT

description: replicate 1


title: T-PLL_28

description: Human Genomic DNA male


title: T-PLL_3

description: Human Genomic DNA female


title: Str_TG_2m_GN50_1

description: GN50-1 (Str)

value: Striatum


title: T-PLL_27

description: Human Genomic DNA male


title: T-PLL_50

description: Human Genomic DNA male


title: T-PLL_49

description: Human Genomic DNA male


title: MRT560Gy-irradiated tumour 24hr_07D47 IT

description: replicate 3

source_name: MRT560Gy-irradiated tumour 24hr

value: MRT560Gy-irradiated 24hr


title: T-PLL_26

description: Human Genomic DNA male


title: T-PLL_48

description: Human Genomic DNA male


title: MRT560Gy-irradiated tumour 24hr_07D46 IT

description: replicate 2


title: BB22Gy-irradiated tumour 24hr_07D22 IT

description: replicate 4

source_name: BB22Gy-irradiated tumour 24hr

value: BB22Gy-irradiated 24hr


title: T-PLL_23

description: Human Genomic DNA female


title: T-PLL_47

description: Human Genomic DNA female


title: SORT#1_DN3b_+IL7

city: Toronto

first: Paul

last: Kowalski

state: Ontario

address: PGCRL - 686 Bay St

department: Developmental and Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

description: SAMPLE 30

hyb_protocol: Illumina Direct Hyb Assay workflow, used Cy3-streptavidin to detect hybridized cDNA

scan_protocol: using Illumina BeadArray System

data_processing: Genome Studio V2011.1 followed by R Bio-conductor 2.13.0. Raw signals from 25697 probes were pre-processed to perform background subtraction, quantile normalization and log2  transformation before using moderated T-tests within Bioconductor package Limma (Linear Models for Microarray Data). Empirical Bayes smoothing was applied to the standard errors.

label: biotin+ Cy3-streptavidin

label_protocol: Illumina Direct Hyb Assay workflow was used: 250 ng total RNA converted into dscDNA, amplified and biotinylated with Illumina TotalPrep™-96 RNA Amplification Kit

growth_protocol: DN3a (Lin-cKit-CD25+CD71loFSClo), DN3b (Lin-cKit-CD25+CD71hiFSChi) and DN4 (Lin-cKit-CD25-CD71hiFSChi) thymocytes were sorted from Il7r+/+ mice (4 independent sorts).

extract_protocol: Rneasy RNA isolation kit was used as per manufacturer's protocol (Qiagen)

treatment_protocol: Sorted DN3a, DN3b and DN4 thymocytes were rested for 1h at 370 C in a humidified atmosphere with 5% CO2, and then left untreated or stimulated with IL7 (10 ng/ml, Stem Cell Technologies) for 3h before isolating total cellular RNA.

tag: tissue

value: thymus


title: AdAH v-miRNA(-) 2

description: AdAH(-) 2

source_name: AdAH v-miRNA(-)

value: AdAH

value: adenoid epithelium-derived cell

value: BART-deleted EBV

value: negative


title: MRT560Gy-irradiated tumour 24hr_07D48 IT

description: replicate 4

tag: cell line


title: MRT560Gy-irradiated tumour 24hr_07D43 IT

description: replicate 1


title: T-PLL_22

description: Human Genomic DNA male

value: Male


title: T-PLL_46

description: Human Genomic DNA female

value: Female


title: T-PLL_32

description: Human Genomic DNA female


title: SORT#1_DN4_+IL7

description: SAMPLE 24


title: SORT#1_DN4_-IL7

description: SAMPLE 23


title: T-PLL_45

description: Human Genomic DNA male


title: T-PLL_20

description: Human Genomic DNA female


title: T-PLL_44

description: Human Genomic DNA male


title: SORT#1_DN3b_-IL7

description: SAMPLE 25


title: SORT#1_DN3a_-IL7

description: SAMPLE 26


title: BB22Gy-irradiated tumour 24hr_07D21 IT

description: replicate 3

value: BALB/c

value: 6-8 months


title: SORT#2_DN3a_-IL7

description: SAMPLE 22


title: T-PLL_2

description: Human Genomic DNA male


title: T-PLL_43

description: Human Genomic DNA female


title: T-PLL_19

description: Human Genomic DNA male


title: SORT#2_DN3b_-IL7

description: SAMPLE 19


title: T-PLL_21

description: Human Genomic DNA female


title: T-PLL_42

description: Human Genomic DNA male


title: T-PLL_41

description: Human Genomic DNA female


title: T-PLL_18

description: Human Genomic DNA female


title: T-PLL_4

description: Human Genomic DNA male


title: MRT560Gy-irradiated tumour 4hr_32-07d69

description: replicate 2

source_name: MRT560Gy-irradiated tumour 4hr

value: mouse breast tumor cell line

value: MRT560Gy-irradiated 4hr


title: BB11Gy-irradiated tumour 24hr_07D20 IT

description: replicate 2

source_name: BB11Gy-irradiated tumour 24hr

value: BB11Gy-irradiated 24hr


title: T-PLL_16

description: Human Genomic DNA male


title: MRT560Gy-irradiated tumour 4hr_31-07d68

description: replicate 1


title: MRT560Gy-irradiated tumour 4hr_34-07d71

description: replicate 4


title: MRT560Gy-irradiated tumour 4hr_33-07d70

description: replicate 3


title: T-PLL_38

description: Human Genomic DNA male


title: SORT#1_DN3a_+IL7

description: SAMPLE 27


title: SORT#2_DN4_-IL7

description: SAMPLE 17


title: SORT#2_DN3b_+IL7

description: SAMPLE 18


title: SORT#4_DN3b_-IL7

description: SAMPLE 14


title: BB22Gy-irradiated tumour 4hr_38-07d82

description: replicate 4

source_name: BB22Gy-irradiated tumour 4hr

value: BB22Gy-irradiated 4hr


title: T-PLL_15

description: Human Genomic DNA female


title: T-PLL_37

description: Human Genomic DNA female


title: T-PLL_17

description: Human Genomic DNA male


title: BB22Gy-irradiated tumour 4hr_37-07d81

description: replicate 3


title: T-PLL_14

description: Human Genomic DNA male


title: SORT#4_DN3a_-IL7

description: SAMPLE 12


title: BB11Gy-irradiated tumour 24hr_07D19 IT

description: replicate 1


title: SORT#4_DN3a_+IL7

description: SAMPLE 11


title: T-PLL_31

description: Human Genomic DNA male


title: T-PLL_40

description: Human Genomic DNA female


title: Unirradiated control tumour_41-07d91

description: replicate 3

source_name: Unirradiated control tumour

value: Unirradiated control


title: BB11Gy-irradiated tumour 4hr_36-07d80

description: replicate 2

source_name: BB11Gy-irradiated tumour 4hr

value: BB11Gy-irradiated 4hr


title: T-PLL_13

description: Human Genomic DNA male


title: SORT#2_DN3a_+IL7

description: SAMPLE 20


title: T-PLL_30

description: Human Genomic DNA male


title: SORT#2_DN4_+IL7

description: SAMPLE 21


title: SORT#4_DN4_-IL7

description: SAMPLE 10


title: T-PLL_25

description: Human Genomic DNA female


title: Unirradiated control tumour_42-07d92

description: replicate 4


title: T-PLL_36

description: Human Genomic DNA male


title: T-PLL_24

description: Human Genomic DNA male


title: T-PLL_29

description: Human Genomic DNA male


title: Unirradiated control tumour_40-07d90

description: replicate 2


title: T-PLL_35

description: Human Genomic DNA female


title: SORT#4_DN4_+IL7

description: SAMPLE 13


title: T-PLL_1

description: Human Genomic DNA male


title: T-PLL_10

description: Human Genomic DNA male


title: T-PLL_12

description: Human Genomic DNA male


title: T-PLL_11

description: Human Genomic DNA male


title: SORT#4_DN3b_+IL7

description: SAMPLE 9


title: SORT#3_DN3b_-IL7

description: SAMPLE 4


title: BB11Gy-irradiated tumour 4hr_35-07d79

description: replicate 1


title: SORT#3_DN4_-IL7

description: SAMPLE 5


title: SORT#3_DN3b_+IL7

description: SAMPLE 6


title: SORT#3_DN3a_-IL7

description: SAMPLE 1


title: Infant Odor Shock Paired. Adult FST No Odor rep7

status: Public on Feb 04 2015

city: Philadelphia

first: Gordon

middle: A.

last: Barr

state: PA

address: 3615 Civic Center Blvd

department: Anesthesiology and Critical Care Medicine

institute: Children's Hospital of Philadelphia

hyb_protocol: According to protocols provided by the manufacturer.

scan_protocol: Arrays were scanned with the Affymetrix GeneArray Scanner 3000 7G.

data_processing: Preprocessing, background correction and normalization (RMA) for perfect match probes only. All infant treated groups were normalized together with other experimental conditions not reported here. Differential expression between controls and the depressive phenotype groups and the depressive and rescue phenotype groups conditions was determined on logged (base 2) data by Ranked Products. Correction for multiple testing was with pfp as described.

source_name: Brain:Bilateral Amygdala

label_protocol: Nugen Linear RNA Amplification(Part #: 3100-12) and Fragmentation & Labeling(Part #: 4200-12) methods.

growth_protocol: After infant treatment, animals were weaned and allowed to grow up without intervention until adult testing.

extract_protocol: Approximately 60 milligrams fresh frozen tissue from each sample was used in this experiment. Total RNA was isolated using Trizol Reagent (Invitrogen, Cat. No: 15596), which contains phenol and guanidine isothiocyanate, to maintain the integrity of the RNA during sample homogenization. Addition of chloroform followed by centrifugation separated the solution into a RNA-containing aqueous phase and an organic phase. Total RNA was then recovered from the aqueous phase using isopropanol. The precipited RNA pellet, after washed with 75% Ethanol and Air-Dried, was redissolved in DEPC H2O. The quality of the RNA was tested by Gel Analysis and 260/280 ratio of OD (Optical Density) which should be between 1.8 and 2.0.The quantity of the RNA was measured by the OD reading at 260 nm (1 OD equals 40 _g / ml of RNA).

treatment_protocol: Infant Olfactory Conditioning: Pups were placed in individual 600mL beakers and given a 10 min acclimation period prior to conditioning to allow for recovery from experimental handling. During a conditioning session, pups received 9-11 pairings of a 30 second peppermint odor with 0.5mA hindlimb shock during the last 1 second of odor, with an intertrial interval (ITI) of 4 minutes. The odor (peppermint, McCormick & Co Inc.,) was delivered by a flow dilution olfactometer (2 liters/min flow rate) at a concentration of 1:10 peppermint vapor. The control group did not receive shock. Pups were returned to the home cage immediately after conditioning. Adult FST testing with and without odor: Depressive-like behavior was tested in a cylinder that was filled with water (25±1°C and changed for each test) to achieve a depth that prevented both escape and the tail from touching the bottom. Animals were habituated for 15 minutes one day prior to testing (day 1), and tested for a duration of 5 minutes on the next day (day 2). The time the animal spent immobile (passive floating without struggling, in a slightly hunched but upright position with the head slightly immersed and minor movements necessary to maintain the head above water) was recorded. For odor presentation during the FST, a Plexiglas lid containing an odor tube covered the FST apparatus to ensure the odor did not dissipate. This, in part, was intended to replicate previous work showing that both natural maternal odor and learned artificial maternal odor can rescue depressive-like behavior in the social behavior test and the FST.

tag: tx

value: Depressive Phenotype

value: Bilateral Amygdala


title: Infant Odor Shock Paired. Adult FST No Odor rep2


title: Infant Odor Shock Paired. Adult FST No Odor rep8


title: Infant Odor Shock Paired. Adult FST With Odor rep5

value: Rescue Phenotype


title: Infant No Shock. Adult  FST with no Odor rep5

value: Control


title: Infant Odor Shock Paired. Adult FST With Odor rep6


title: Infant Odor Shock Paired. Adult FST With Odor rep7


title: Infant Odor Shock Paired. Adult FST With Odor rep8


title: Infant Odor Shock Paired. Adult FST With Odor rep4


title: Infant Odor Shock Paired. Adult FST No Odor rep3


title: Infant Odor Shock Paired. Adult FST No Odor rep4


title: Infant Odor Shock Paired. Adult FST With Odor rep1


title: Infant Odor Shock Paired. Adult FST No Odor rep1


title: Infant No Shock. Adult  FST with no Odor rep8


title: Infant No Shock. Adult  FST with no Odor rep6


title: Infant Odor Shock Paired. Adult FST No Odor rep5


title: Infant Odor Shock Paired. Adult FST With Odor rep3


title: Infant Odor Shock Paired. Adult FST With Odor rep2


title: Infant No Shock. Adult  FST with no Odor rep2


title: SORT#3_DN4_+IL7

description: SAMPLE 3

value: thymus


title: Infant No Shock. Adult  FST with no Odor rep7


title: pre-meiotic [S2_16_72_2]

city: Leicester

first: Adeolu

last: Adewoye

address: University Road

institute: University of Leicester

description: NimbleGen high resolution mouse aCGH data

hyb_protocol: carried out by  Roche NimbleGen Service Laboratory (Reykjavík, Iceland)

data_processing:
Data was QC and processed in R using  DNAcopy package
normalised log2 (test/control) ratio provided in *segMNT.txt file.

extract_protocol: DNA was extracted from spleen by phenol-chloroform following standard protocols with 1% SDS and 300 μg/ml proteinase K (Roche Diagnostics limited)

value: offspring of cross between C57BL6/J (male) and CBA/Ca (female)

tag: sample group

value: offspring of 3 Gy whole-body acute irradiated paternal and non-exposed maternal

tag: exposed status of the sperm (that gave rise to the offspring)

value: pre meiotic

value: spleen

source_name: spleen_DNA from maternal and paternal

treatment_protocol: mixture of equal spleen_DNA concentration from maternal and paternal hybridised against DNA from each offspring

value: C57BL6/J (male) and CBA/Ca (female)

tag: sample type

value: reference; equal mixture of paternal and maternal DNA


title: pre-meiotic [S2_24_88_2]

scan_protocol: carried out by  Roche NimbleGen Service Laboratory (Reykjavík, Iceland)


title: pre-meiotic [S2_24_87_4]

label_protocol: carried out by  Roche NimbleGen Service Laboratory (Reykjavík, Iceland)


title: pre-meiotic [S2_21_82_6]


title: pre-meiotic [S2_30_100_7]


title: pre-meiotic [S2_27_93_2]


title: pre-meiotic [S2_16_72_6]


title: pre-meiotic [S2_30_100_2]


title: pre-meiotic [S2_30_100_1]


title: pre-meiotic [S2_16_71_2]


title: pre-meiotic [S2_30_96_3]


title: Infant No Shock. Adult  FST with no Odor rep4


title: SORT#3_DN3a_+IL7

description: SAMPLE 2


title: Infant Odor Shock Paired. Adult FST No Odor rep6


title: pre-meiotic [S2_24_87_5]


title: Unirradiated control tumour_39-07d89

description: replicate 1

value: BALB/c

value: 6-8 months

value: mouse breast tumor cell line


title: Infant No Shock. Adult  FST with no Odor rep3


title: pre-meiotic [S2_13_65_1]


title: pre-meiotic [S2_30_96_5]


title: pre-meiotic [S2_16_72_1]


title: pre-meiotic [S2_16_72_4]


title: pre-meiotic [S2_16_71_6]


title: pre-meiotic [S2_24_88_1]


title: Zeb1-siRNA-48h biol replicate 1

city: Oxford

first: Alexander

last: Feuerborn

address: South Parks Road

institute: Sir William Dunn School of Pathology

description: Gene expression data from NM18 cells transfected with Zeb1 siRNA for 48h

hyb_protocol: After fragmentation, 10µg of cRNA were hybridized for 16hrs at 45°C on MOE430A mouse GeneChips

scan_protocol: Arrays were scanned using GeneChip™ 3000 7G-scanner

data_processing: The data was analyzed using R(v.3.0.2)/Bioconductor (v.2.13)

source_name: NM18 transfected with Zeb1 siRNA replicate 1

label_protocol: Biotinylated cRNA was generated according to standard Affymetrix protocols from 100ng total RNA (GeneAtlas™ 3'-IVT Express Kit, P/N 702833 Rev. 4)

growth_protocol: Cells were grown under standard cell culture conditions (37°C, 5% CO2) in ATCC DMEM-media, 10%FCS, 10µg/ml insulin

extract_protocol: Total RNA was extracted using Rneasy Mini kit according to manufacturer's instructions (Qiagen), including on-column digest

treatment_protocol: Cells were reverse transfected for 48hrs

value: mammary gland

tag: transfected with

value: Zeb1 siRNA


title: pre-meiotic [S2_16_72_7]


title: Zeb1-siRNA-48h biol replicate 3

source_name: NM18 transfected with Zeb1 siRNA replicate 3


title: Zeb1-siRNA-48h biol replicate 2

source_name: NM18 transfected with Zeb1 siRNA replicate 2


title: pre-meiotic [S2_16_71_5]