title: DMT-treated MEFs, biological rep1

description:
Gene expression data from iCMs generated from MEFs
DMT1

value: MYOCD, MEF2C, TBX5


title: DMT-treated MEFs, biological rep2

status: Public on Apr 22 2013

type: RNA

city: Philadelphia

first: Russell

middle: C

last: Addis

state: PA

address: 3400 Civic Center Blvd, Bldg 421, SCTR 9-196

department: Cell and Developmental Biology

country: USA

institute: University of Pennsylvania

description:
Gene expression data from iCMs generated from MEFs
DMT2

hyb_protocol: The labeling, hybridization, and scanning procedures were performed by the University of Pennsylvania Molecular Profiling facility

data_processing: Initial data analysis was performed using Affymetrix Microarray Suite 5.0 and further analyzed using PartekGS software.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: zeocin-selected iCMs

growth_protocol: MEFs were grown in DMEM with 10% fetal bovine serum and 1X Glutamax.

extract_protocol: Putative iCMs were enriched by selecting for zeocin resistance driven by the TroponinT-GCaMP5-Zeo reporter and collected in Trizol at Day 21 post-transduction (7 days after initiation of zeocin selection, 300 μg/mL).  Non-transduced MEFs were cultured and collected at Day 21.  Samples were collected in triplicate from independent biological replicates and total RNA was prepared by the University of Pennsylvania Molecular Profiling Facility.

treatment_protocol: MEFs were plated into poly-L-lysine-coated 6 well dishes at 75,000 cells/well on Day -2, with 500 μL (≥ 2.5x105 IFU) each of rtTA lentivirus (FUdeltaGW-rtTA, Addgene plasmid 19780) and TroponinT-GCaMP-Zeo reporter lentivirus per well with 2 mL MEF medium. The following day (Day -1), culture medium was replaced with 2 mL fresh MEF medium and cells were transduced with 500 μL (≥ 2.5x105 IFU) of each tetO-transcription factor lentivirus. The next day (Day 0), medium was switched to 3 mL/well Reprogramming Medium consisting of AGM (Lonza CC-3186) without EGF, supplemented with 2 μg/mL doxycycline (Sigma).

tag: transcription factor treatment


title: NGMT-treated MEFs, biological rep2

description:
Gene expression data from iCMs generated from MEFs
MEF8

scan_protocol: The labeling, hybridization, and scanning procedures were performed by the University of Pennsylvania Molecular Profiling facility

value: NKX2.5, GATA4, MEF2C, TBX5


title: BJ LTSTERas, treated with vorinostat, 12 hour, rep3

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

description: BJ LTSTERas 25uM SAHA 12hr replicate 3 scan 2

hyb_protocol: Full-length cRNA (20μg) was fragmented to 35-200bp lengths by incubation with cRNA fragmentation reagent for 35 minutes at 94°C. Fragmented cRNA (15μg) was added to a hybridisation mix according to Affymetrix instructions and hybridized to Affymetrix HG U133 plus 2.0 probe arrays at 45°C in an Affymetrix Hybridisation oven 640 with 60rpm rotation for 16 hours. Array washes and three-stage streptavidin phycoerythrin (SAPE) staining was performed according the manufacturer’s instructions on a GeneChip fluidics station 450 (Affymetrix, Santa Clara, CA, USA).

scan_protocol: HG U133 plus 2.0 arrays were individually scanned using an Affymetrix GeneChip 3000 scanner with GeneChip Operating Software (GCOS, Affymetrix, Santa Clara, CA, USA).

data_processing: Intensities from the Affymetrix arrays were background corrected, normalised and summarised using the GC-Robust Multi-Array Analysis (GC-RMA) algorithm. Probe sets were defined by the default Affymetrix HG U133 plus 2.0 chip definition file. Box-plots of expression intensities and RNA degradation plots confirmed good consistent quality of the samples and the hybridisations. Differential expression analysis of the normalized log2-expression values was performed using the Bioconductor software package limma. All the arrays were analysed together using a linear model. Empirical Bayes moderated t-tests were used to assess differential expression between the BJ and BJLTSTERas fibroblasts and between untreated and treated cells. Specifically, baseline differences between the cell lines were identified by comparing untreated BJ and to BJ LTSTERas fibroblasts at Time 0hr. Probe sets responding to DMSO or vorinostat were identified by comparing each of the 4, 12, or 24 hour time points back to untreated cells, and this was done separately for BJ and BJ LTSTERas fibroblasts. For all comparisons, probe sets were considered to be significantly differentially expressed if the fold-change exceeded 1.5 (i.e. 50% difference in expression) and the false discovery rate (FDR) was less than 0.05. Probe sets responding differently to vorinostat treatment in BJ LTSTERas fibroblasts as compared to BJ cells (i.e. contrast genes), were identified using empirical Bayes moderated F-tests. F-tests allowed us to combine information across the three treatment time points, looking for probe-sets with differing responses at any of the times. First we used an F-test to find probe sets whose gene expression changes (from 0 hour to any of 4, 12 or 24 hours vorinostat treatment) was different in BJ fibroblasts compared to BJ LTSTERas fibroblasts. This test is analogous to testing for interaction in a two-way ANOVA. Second, we subtracted from this list any probe set whose expression response to vorinostat could not be distinguished from that to DMSO (the vehicle control). To do this, we used an F-test to find probe sets whose response to vorinostat relative to DMSO was different between BJ fibroblasts and BJ LTSTERas fibroblasts at any of the paired time points. Only probe sets detected by both the above F-tests were retained in the contrast list. The final contrast list contained therefore only bona fide vorinostat-responding genes. For all F-tests, probe sets were considered statistically significant if the FDR was less than 0.05 and at least one comparison involved in the test achieved a 1.5 fold change.

organism: Homo sapiens

source_name: BJ LTSTERas_treated with vorinostat_12 hr

label_protocol: Biotin labelled cRNA was synthesised from cDNA using a GeneChip IVT labelling kit (Affymetrix, Santa Clara, CA, USA) in a total reaction volume of 40μL. cRNA was purified and concentrated using the GeneChip sample cleanup module.

growth_protocol: BJ and BJ LTSTERas cells (kindly provided by Prof. William Hahn, Dan Farber Cancer Institute, Boston, MA) were grown in media containing 4 parts HEPES buffered DMEM, pH 7.4 (SAFC Biosciences, Brooklyn, Australia) to 1 part Medium 199 (Sigma, St Louis, MO, USA), supplemented with 15% (v/v) Fetal Bovine Serum (FBS, Commonwealth Serum Laboratories, Parkville, Australia), 1x GlutaMAX (Invitrogen, Carlsbad, CA, USA), 100U/mL penicillin and 100μg/mL streptomycin (Life Technologies, Inc. Grand Island, NY, USA).  All cells were maintained at 37°C in a humidified incubator containing 5% CO2.

extract_protocol: Total RNA (2μg) was prepared for hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays according to manufacturer recommendations. Poly-A RNA controls from Bacillus subtilis (lys, phe, thr and dap) were diluted in Poly-A control dilution buffer (serial dilutions of 1:20, 1:50 and 1:25) and 2μL of the third serial dilution was spiked into each RNA sample prior to cDNA synthesis. RNA was reverse transcribed using a one-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and all annealing, amplification and incubation steps were performed in accordance with manufacturer instructions. Double stranded cDNA was purified using a GeneChip sample cleanup module according to manufacturers instructions (Affymetrix, Santa Clara, CA, USA) and cDNA was eluted from columns with 14μL cDNA elution buffer.

treatment_protocol: Vorinostat (100mM) stock solution was made in dimethyl sulphoxide (DMSO, Sigma, St Louis, MO, USA) and stored at -20°C.  Cells were incubated with vorinostat and DMSO for 0-24 hours.

tag: cell type

value: tumorigenic BJ (human foreskin) fibroblasts

tag: treated with

value: Vorinostat (25uM)

tag: time

value: 12 hour


title: genomic DNA from CD14 B-cells_C111 (BeadChip)

type: genomic

city: Cambridge

first: Thomas

middle: A

last: Down

address: Tennis Court Road

department: WT/CRUK Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description:
Sample name: C111
normal CD14 cells

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio softwarre

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the Qiagen DNeasy kit.

tag: individual identifier

tag: monozygotic twin relationship

value: MZ twin of C12

value: CD14 cells


title: LP_0_2w_62_CC1_10008_Liver

city: RTP

first: Longlong

last: Yang

state: NC

address: 6 Davis Dr.

institute: CIIT Centers for Health Research

description: LP_0_2w_62_CC1_10008_Liver_(HT_Rat230_PM)_C08: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA normalization with Partek software program

organism: Rattus norvegicus

label_protocol: standard Affymetrix protocol

extract_protocol: Extraction Method: Qiagen

treatment_protocol: in vivo Treatment: Corn Oil Control 1, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 2, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: rna integrity number

tag: bioanalyzer results

value: Excellent

tag: sample preservation

value: Frozen

tag: strain or line

value: Spague Dawley Crl:CD(SD)

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: Adult

tag: sacrifice method

value: Pentobarbital, Exsanguinated

tag: Sex

value: Male

tag: units of age

value: weeks

tag: tissue

value: Liver

tag: tissue harvest methods

value: Slices from each of the lobes were pooled together for microarray analysis


title: genomic DNA from CD14 B-cells_C112 (BeadChip)

description:
Sample name: C112
normal CD14 cells

tag: individual identifier

tag: monozygotic twin relationship

tag: cell type


title: GMT-treated MEFs, biological rep2

description:
Gene expression data from iCMs generated from MEFs
MEF6

label_protocol: The labeling, hybridization, and scanning procedures were performed by the University of Pennsylvania Molecular Profiling facility

tag: transcription factor treatment

value: GATA4, MEF2C, TBX5


title: BJ LTSTERas, untreated, rep2

description: BJ LTSTERas 0hr replicate 2

source_name: BJ LTSTERas_untreated

tag: treated with

value: none (untreated)

tag: time

value: 0 hour


title: BJ LTSTERas, treated with vorinostat, 24 hour, rep2

description: BJ LTSTERas 25uM SAHA 24hr replicate 2

source_name: BJ LTSTERas_treated with vorinostat_24 hr

value: tumorigenic BJ (human foreskin) fibroblasts

value: Vorinostat (25uM)

value: 24 hour


title: BJ LTSTERas, untreated, rep1

description: BJ LTSTERas 0hr


title: LP_0_2w_61_CC1_10008_Liver

description: LP_0_2w_61_CC1_10008_Liver_(HT_Rat230_PM)_C07: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: rna integrity number

tag: bioanalyzer results

value: Good


title: BJ LTSTERas, untreated, rep3

description: BJ LTSTERas 0hr replicate 3


title: BJ LTSTERas, treated with vorinostat, 12 hour, rep2

description: BJ LTSTERas 25uM SAHA 12hr replicate 2

value: 12 hour


title: BJ, treated with DMSO, 4 hour, rep3

description: BJ DMSO 4hr replicate 3

source_name: BJ_treated with DMSO_4 hr

value: Normal BJ (human foreskin) fibroblasts

value: DMSO

value: 4 hour


title: genomic DNA from CD14 B-cells_C122 (BeadChip)

description:
Sample name: C122
normal CD14 cells

value: MZ twin of C11

value: CD14 cells


title: 0F MEFs, biological rep3

description:
Gene expression data from MEFs that did not receive any transcription factor treatment
MEF3

value: No TF


title: 0F MEFs, biological rep1

description:
Gene expression data from MEFs that did not receive any transcription factor treatment
MEF1


title: GMT-treated MEFs, biological rep1

description:
Gene expression data from iCMs generated from MEFs
MEF5


title: genomic DNA from CD14 B-cells, 3rd pair, 1st individual_T31 (BeadChip)

description:
Sample name: T31
normal CD14 cells

value: MZ twin of T32


title: genomic DNA from CD14 B-cells, 2nd pair, 2nd individual_T22 (BeadChip)

description:
Sample name: T22
normal CD14 cells

value: MZ twin of T21


title: 0F MEFs, biological rep2

description:
Gene expression data from MEFs that did not receive any transcription factor treatment
MEF2


title: BJ, treated with vorinostat, 4 hour, rep2

description: BJ 25uM SAHA 4hr replicate 2

source_name: BJ_treated with vorinostat_4 hr


title: BJ, treated with vorinostat, 24 hour, rep3

description: BJ 25uM SAHA 24hr replicate 3

source_name: BJ_treated with vorinostat_24 hr


title: genomic DNA from CD14 B-cells, 2nd pair, 1st individual_T21 (BeadChip)

description:
Sample name: T21
normal CD14 cells

value: MZ twin of T22


title: BJ, treated with DMSO, 24 hour, rep2

description: BJ DMSO 24hr replicate 2

source_name: BJ_treated with DMSO_24 hr


title: BJ, treated with DMSO, 12 hour, rep2

description: BJ DMSO 12hr replicate 2

source_name: BJ_treated with DMSO_12 hr


title: BJ, treated with DMSO, 24 hour, rep1

description: BJ DMSO 24 hour Replicate 1


title: BJ, treated with DMSO, 4 hour, rep1

description: BJ DMSO 4 hour Replicate 1


title: BJ, treated with vorinostat, 4 hour, rep1

description: BJ 25uM SAHA 4 hour Replicate 1


title: BJ, treated with DMSO, 24 hour, rep3

description: BJ DMSO 24hr replicate 3


title: genomic DNA from CD14 B-cells, 1st pair 1st individual_T11 (BeadChip)

description:
Sample name: T11
normal CD14 cells


title: BJ, treated with DMSO, 12 hour, rep1

description: BJ DMSO 12 hour Replicate 1


title: BJ, treated with DMSO, 12 hour, rep3

description: BJ DMSO 12hr replicate 3


title: BJ, treated with vorinostat, 24 hour, rep2

description: BJ 25uM SAHA 24hr replicate 2


title: BJ, treated with vorinostat, 12 hour, rep2

description: BJ 25uM SAHA 12hr replicate 2

source_name: BJ_treated with vorinostat_12 hr


title: BJ, treated with DMSO, 4 hour, rep2

description: BJ DMSO 4hr replicate 2


title: BJ, treated with vorinostat, 4 hour, rep3

description: BJ 25uM SAHA 4hr replicate 3


title: siTARDBP 3

city: Houston

first: Yun-Yong

last: Park

state: TX

address: 7435 Fannin St.

department: Systems Biology

institute: UT, MD Anderson Cancer Center

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 47231 probes on the Human-Ht12 beadChip ver.  were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to a ver. 3 of the Illumina Human-Ht-12 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

label: Biotin

source_name: SK-Hep1  hepatocellular carcinoma cell line

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer's protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: cell line

tag: knockdown

value: siTARDBP


title: BJ, treated with vorinostat, 12 hour, rep3

description: BJ 25uM SAHA 12hr replicate 3


title: siTARDBP 1


title: BJ, treated with vorinostat, 24 hour, rep1

description: BJ 25uM SAHA 24 hour Replicate 1


title: BJ, treated with vorinostat, 12 hour, rep1

description: BJ 25uM SAHA 12 hour Replicate 1


title: siLuc 2

value: control


title: BJ, untreated, biological rep3

description: BJ 0hr replicate 3

value: none (untreated)

value: 0 hour


title: siLuc 1


title: genomic DNA from CD14 B-cells, 3rd pair, 2nd individual_T32 (BeadChip)

description:
Sample name: T32
normal CD14 cells

value: MZ twin of T31


title: PDGFRb+ murine vascular smooth muscle cells, 48 hrs imatinib, 404732

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description:
404732_2CGE_635.pair
404732_2CGE_635_48h
Gene expression changes after 48 hours of imatinib in PDGFRb+ murine vascular smooth muscle cells.

hyb_protocol: cRNA was fragmented to uniform size and verified on the Bioanalyzer. NimbleGen MM8_60mer mouse gene expression microarrays (Roche NimbleGen, Inc. WI, USA) were hybridized with the cRNA target.

scan_protocol: NimbleGen MS 200 scanner, following their standard operating protocol. See http://www.nimblegen.com/.

data_processing: The raw data (.pair file) was processed using RMA analysis (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 2003, 4(2):249) as implemented in the NimbleScan software package, version 2.5.26 (Roche NimbleGen, Inc.), with normalization and background correction.

label_protocol: Biotinylated cRNA were prepared according to the standard NimbleGen labeling protocol. See http://www.nimblegen.com/.

extract_protocol: Total RNA was extracted using the All Prep RNA/DNA kit (Qiagen, Valencia, CA) according to the manufacturer's protocols.

tag: strain

tag: treatment

value: imatinib

tag: treatment dosage

value: 10 uM

tag: treatment duration

value: 48 hours


title: siLuc 3


title: PDGFRb+ murine vascular smooth muscle cells, 0 hrs, 404684

description:
404684_2CGE_532.pair
404684_2CGE_532_0h
Gene expression changes in 0 hr baseline PDGFRb+ murine vascular smooth muscle cells.

source_name: PDGFRb+ murine vascular smooth muscle cells, baseline

value: 0 hours


title: PDGFRb+ murine vascular smooth muscle cells, 24 hrs imatinib, 404684

description:
404684_2CGE_635.pair
404684_2CGE_635_24h
Gene expression changes after 24 hours of imatinib in PDGFRb+ murine vascular smooth muscle cells.

value: 24 hours


title: BJ, untreated, biological rep2

description: BJ 0hr replicate 2

value: Normal BJ (human foreskin) fibroblasts


title: H3 turnover in ago1epe1 deletion mutant

status: Public on Apr 21 2013

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

hyb_protocol: 500 ng of Cy3 labeled WCE DNA was mixed with 500 ng of Cy5 labeled ChIP DNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer

scan_protocol: Slides were scanned using Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software version 8.5

data_processing: Log ratios of ChIP over WCE were obtained by dividing normalized median Cy5 value over its corrresponding Cy3 value

organism: Schizosaccharomyces pombe

source_name: whole cell extract (WCE) genomic DNA

label_protocol: WCE DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy3 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Exponentially growing cultures of fission yeast cells expressing an ectopic copy of FLAG tagged histone H3 under the control of inv1 promoter were synchronized by Hydroxyurea and expression of H3-FLAG was induced by changing the carbon source of the medium to Sucrose.

extract_protocol: Chromatin was extracted from cross-linked cells following lysis with bead beater and using micrococcal nuclease (MNase). Chromatin immunoprecipitated DNA recovered with anti-FLAG antibody. After reverse cross-linked and digested with Rnase A and proteinase K, DNA was recovered by Qiagen QIAquick PCR column.

treatment_protocol: Cells were crosslinked with 1% Formaldehyde

tag: genotype/variation

value: ago1epe1 deletion mutant

tag: antibody

value: None (whole cell extract)

source_name: ago1epe1 deletion mutant - H3-FLAG IP

label_protocol: ChIP DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy5 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

value: anti-FLAG


title: H3 turnover in epe1 overexpressing cells

value: epe1 over-expressing

source_name: epe1 over-expressing - H3-FLAG IP


title: Anergic Cre rep2

city: Chicago

first: Yan

last: Zheng

state: IL

institute: University of Chicago

description:
Gene expression data from anergic Egr2-deleted Th1 T cells
An Cre 02

hyb_protocol: The fragmented cRNA (12 µg) was then hybridized to Affymetrix mouse genome 430 2.0 expression arrays for 16 h at 45°C with 60 rpm in Affymetrix hybridization oven 640.

scan_protocol: The arrays were scanned by Affymetrix Gene Chip Scanner 3000 7G and CEL.

data_processing: Intensity files were generated by Gene Chip Operating Software v. 1.4 (MicroArray Suite 5.0)

source_name: Anergic Egr2-deleted Th1 T cells

label_protocol: The RNAs were labeled with biotin and fragmented using GeneChip 3’ IVT Express Kit according to Affymetrix protocol.

growth_protocol: OVA-specific Th1 cell clones were generated from CAR Tg x Egr2flox/flox mice.

extract_protocol: Total cellular RNA was purified using RNeasy Mini Kit (Qiagen).

treatment_protocol: CAR Tg x Egr2flox/flox Th1 T cells were infected with an empty (EV) or a Cre-expressing adenovirus, Egr2 deletion was confirmed by immunoblot.  The T cells were then left untreated (Control) or anergized (Anergic) by immobilized anti-CD3 for 16 hours, and microarray was conducted after 1 day of rest in culture medium.

tag: cell type

value: Th1 T cells

value: immobilized anti-CD3


title: Anergic EV rep3

description:
Gene expression data from anergic wild-type Th1 T cells
An EV 03

source_name: Anergic wild-type Th1 T cells

value: wild-type


title: H3 turnover in ago1 deletion mutant

value: ago1 deletion mutant

source_name: ago1 deletion mutant - H3-FLAG IP


title: H3 turnover in swi6chp2 deletion mutant

value: swi6chp2 deletion mutant

source_name: swi6chp2 deletion mutant - H3-FLAG IP


title: Control Cre rep2

description:
Gene expressoin data from control Egr2-deleted Th1 T cells
Ctrl Cre 02

source_name: Control Egr2-deleted Th1 T cells

value: untreated (Control)


title: Control EV rep3

description:
Gene expression data from control wild-type Th1 T cells
Ctrl EV 03

source_name: Control wild-type Th1 T cells


title: Control Cre rep3

description:
Gene expressoin data from control Egr2-deleted Th1 T cells
Ctrl Cre 03


title: Anergic EV rep2

description:
Gene expression data from anergic wild-type Th1 T cells
An EV 02


title: H3 turnover in epe1 deletion mutant

value: epe1 deletion mutant

source_name: epe1 deletion mutant - H3-FLAG IP


title: Control EV rep1

description:
Gene expression data from control wild-type Th1 T cells
Ctrl EV 01


title: PDGFRb+ murine vascular smooth muscle cells, 0 hrs, 404732

description:
404732_2CGE_532.pair
404732_2CGE_532_0h
Gene expression changes in 0 hr baseline PDGFRb+ murine vascular smooth muscle cells.


title: H3 turnover in clr3 deletion mutant

value: clr3 deletion mutant

source_name: clr3 deletion mutant - H3-FLAG IP


title: H3 turnover in swi6 deletion mutant

value: swi6 deletion mutant

source_name: swi6 deletion mutant - H3-FLAG IP


title: H3 turnover in chp2 deletion mutant

value: chp2 deletion mutant

source_name: chp2 deletion mutant - H3-FLAG IP


title: Control Cre rep1

description:
Gene expressoin data from control Egr2-deleted Th1 T cells
Ctrl Cre 01


title: Anergic Cre rep1

description:
Gene expression data from anergic Egr2-deleted Th1 T cells
An Cre 01


title: Control EV rep2

description:
Gene expression data from control wild-type Th1 T cells
Ctrl EV 02


title: Anergic Cre rep3

description:
Gene expression data from anergic Egr2-deleted Th1 T cells
An Cre 03


title: BJ, untreated, biological rep1

description: BJ 0 hour Replicate 1

tag: treated with

value: none (untreated)

value: 0 hour


title: Anergic EV rep1

description:
Gene expression data from anergic wild-type Th1 T cells
An EV 01


title: H3 turnover in dcr1 deletion mutant

value: dcr1 deletion mutant

source_name: dcr1 deletion mutant - H3-FLAG IP


title: H3 turnover in K_delta_ura4_ON cells

source_name: K_delta_ura4_ON - H3-FLAG IP


title: H3 turnover in clr4 deletion mutant

value: clr4 deletion mutant

source_name: clr4 deletion mutant - H3-FLAG IP


title: H3 turnover in K_delta_ura4_OFF cells

value: None (whole cell extract)

source_name: K_delta_ura4_OFF - H3-FLAG IP


title: H3 turnover in Wild-type cells

source_name: whole cell extract (WCE) genomic DNA

value: Wild-type

source_name: Wild-type - H3-FLAG IP

value: anti-FLAG


title: M_133A_49_nAcc_1_C_r_p

status: Public on Apr 20 2013

city: Ann Arbor

first: Andy

middle: W

last: Lin

state: MI

address: 205 Zina Pitcher Place

department: MBNI

institute: University of Michigan

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: The data were analyzed with the RMA method using custom CDF file hgu133ahsentrezg.cdf.

source_name: Post-mortem human brain tissue: Nucleus Accumbens

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

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

tag: genechip assay site

value: M

tag: original genechip type

tag: subject id

tag: brain region

value: nucleus accumbens


title: M_133A_126_nAcc_0_C


title: M_133A_22_nAcc_1_C_r_p


title: M_133A_39_nAcc_1_C_r_p


title: M_133A_26_nAcc_1_C_r_p


title: M_133A_50_nAcc_1_C_r_p


title: M_133A_49_nAcc_1_C


title: M_133A_50_nAcc_1_C


title: M_133A_125_nAcc_1_C


title: M_133A_23_nAcc_1_C_r_p


title: M_133A_115_nAcc_0_C


title: M_133A_131_nAcc_1_C


title: M_133A_28_nAcc_1_C_r_p


title: M_133A_25_nAcc_1_C_r_p


title: M_133A_19_nAcc_0_C_r_p


title: M_133A_53_nAcc_0_C


title: M_133A_101_nAcc_1_C_r_p


title: M_133A_31_nAcc_0_C_r2_p


title: DNMT1-3

first: Wayne

last: Hancock

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: 10 microgram of labeled aRNA was fragmented, and 6.5 microgram of the fragmented aRNA was hybridized to the Affymetrix Mouse 430A_2 chips.  Hybridization conditions were 16hrs at 45C.

scan_protocol: The chips were washed using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450 and scanned on an Affymetrix Genechip Scanner.

data_processing: Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a, Affymetrix). Array data were analyzed using MAYDAY (Version 2.10). Array data were subjected to robust multi-array average (RMA) normalization. Normalized data were used for calculating fold changes of up- and down-regulated genes using Student's T-test. Data underwent z-score transformation for display.

source_name: Regulatory T-cells CD4+CD25+

label_protocol: 100ng of totalRNA was labeled using Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)

extract_protocol: Total RNA was isolated using Rneasy (Quiagen). RNA integrity and quantity was analyzed using a DU640 (Beckman-Coulter).


title: WT 3

value: Wild type


title: WT 2


title: M_133A_55_nAcc_1_C


title: WT 1


title: M_133A_3_nAcc_1_C_p


title: M_133A_1_nAcc_1_C_p


title: M_133A_2_nAcc_1_C_p


title: M_133A_4_nAcc_1_C_p


title: M_133A_5_nAcc_1_C_p


title: M_133A_8_nAcc_1_C_p


title: M_133A_9_nAcc_1_C_r_p


title: M_133A_18_nAcc_1_C_p


title: M_133A_9_nAcc_1_C_p


title: M_133A_102_nAcc_1_C_p


title: M_133A_17_nAcc_1_C_p


title: M_133A_16_nAcc_1_C_p


title: M_133A_24_nAcc_1_C_p


title: siTARDBP 2

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 47231 probes on the Human-Ht12 beadChip ver.  were used.

source_name: SK-Hep1  hepatocellular carcinoma cell line

value: siTARDBP


title: M_133A_29_nAcc_1_C_p


title: M_133A_7_nAcc_0_C_p


title: M_133A_15_nAcc_0_C_r_p


title: M_133A_30_nAcc_1_C_r_p


title: M_133A_32_nAcc_1_C_p


title: M_133A_21_nAcc_0_C_p


title: M_133A_30_nAcc_1_C_p


title: M_133A_27_nAcc_0_C_p


title: M_133A_105_nAcc_0_C_p


title: M_133A_103_nAcc_0_C_p


title: M_133A_11_nAcc_1_C_p


title: M_133A_33_nAcc_1_C_p


title: M_133A_15_nAcc_0_C_p


title: M_133A_13_nAcc_1_C_p


title: M_133A_14_nAcc_1_C_p


title: M_133A_106_nAcc_1_C_p


title: M_133A_33_nAcc_1_C_r_p


title: M_133A_108_nAcc_0_C_p


title: M_133A_43_nAcc_1_C_p


title: M_133A_121_nAcc_1_C_p


title: M_133A_33_nAcc_1_C


title: M_133A_116_nAcc_0_C_p


title: M_133A_27_nAcc_0_C


title: M_133A_111_nAcc_0_C_p


title: M_133A_102_nAcc_1_C


title: M_133A_30_nAcc_1_C


title: M_133A_111_nAcc_0_C


title: M_133A_112_nAcc_1_C


title: M_133A_108_nAcc_0_C


title: M_133A_103_nAcc_0_C


title: M_133A_105_nAcc_0_C


title: M_133A_29_nAcc_1_C


title: M_133A_36_nAcc_0_C_p


title: M_133A_32_nAcc_1_C


title: M_133A_116_nAcc_0_C


title: M_133A_121_nAcc_1_C


title: M_133A_112_nAcc_1_C_p


title: M_133A_34_nAcc_1_C


title: M_133A_43_nAcc_1_C


title: M_133A_37_nAcc_1_C


title: M_133A_35_nAcc_1_C


title: M_133A_40_nAcc_1_C


title: M_133A_42_nAcc_1_C


title: M_133A_106_nAcc_1_C


title: M_133A_38_nAcc_0_C


title: M_133A_52_nAcc_1_C_r_p


title: M_133A_47_nAcc_1_C


title: M_133A_51_nAcc_1_C_r_p


title: M_133A_41_nAcc_1_C_r_p


title: M_133A_44_nAcc_1_C


title: D_133A_25_nAcc_1_C_p

value: D


title: M_133A_36_nAcc_0_C


title: M_133A_51_nAcc_1_C


title: M_133A_41_nAcc_1_C


title: D_133A_101_nAcc_1_C_p


title: D_133A_19_nAcc_0_C_p


title: D_133A_22_nAcc_1_C_p


title: M_133A_54_nAcc_1_C


title: M_133A_52_nAcc_1_C


title: D_133A_26_nAcc_1_C_p


title: D_133A_23_nAcc_1_C_p


title: M_133A_48_nAcc_1_C_r_p


title: D_133A_125_nAcc_1_C


title: D_133A_115_nAcc_0_C


title: M_133A_46_nAcc_0_C


title: D_133A_31_nAcc_0_C_p


title: D_133A_28_nAcc_1_C_p


title: D_133A_39_nAcc_1_C_p


title: D_133A_53_nAcc_0_C


title: D_133A_49_nAcc_1_C


title: D_133A_50_nAcc_1_C


title: M_133A_45_nAcc_1_C


title: DNMT1-1


title: D_133A_130_nAcc_1_C


title: D_133A_55_nAcc_1_C


title: D_133A_27_nAcc_0_C_p


title: D_133A_131_nAcc_1_C


title: D_133A_108_nAcc_0_C_p


title: D_133A_30_nAcc_1_C_p


title: D_133A_111_nAcc_0_C_p


title: D_133A_102_nAcc_1_C_p


title: D_133A_106_nAcc_1_C_p


title: D_133A_32_nAcc_1_C_p


title: D_133A_33_nAcc_1_C_p


title: D_133A_29_nAcc_1_C_p


title: D_133A_36_nAcc_0_C_p


title: DNMT1-2


title: D_133A_44_nAcc_1_C


title: D_133A_41_nAcc_1_C


title: D_133A_43_nAcc_1_C_p


title: D_133A_105_nAcc_0_C_p


title: D_133A_42_nAcc_1_C


title: D_133A_34_nAcc_1_C


title: D_133A_116_nAcc_0_C_p


title: D_133A_37_nAcc_1_C


title: D_133A_103_nAcc_0_C_p


title: D_133A_35_nAcc_1_C


title: D_133A_48_nAcc_1_C


title: D_133A_45_nAcc_1_C


title: D_133A_38_nAcc_0_C


title: D_133A_46_nAcc_0_C


title: D_133A_40_nAcc_1_C


title: D_133A_121_nAcc_1_C_p


title: D_133A_47_nAcc_1_C


title: D_133A_52_nAcc_1_C


title: D_133A_51_nAcc_1_C


title: M_133A_23_HC_1_C_p

source_name: Post-mortem human brain tissue: Hippocampus

value: hippocampus


title: M_133A_22_HC_1_C_p


title: M_133A_28_HC_1_C_p


title: M_133A_25_HC_1_C_p


title: M_133A_101_HC_1_C_p


title: M_133A_39_HC_1_C_p


title: M_133A_115_HC_0_C


title: M_133A_1_HC_1_C_p


title: M_133A_55_HC_1_C


title: M_133A_50_HC_1_C


title: M_133A_3_HC_1_C_p


title: M_133A_4_HC_1_C_p


title: M_133A_53_HC_0_C


title: M_133A_125_HC_1_C


title: M_133A_131_HC_1_C


title: M_133A_126_HC_0_C


title: M_133A_2_HC_1_C_p


title: M_133A_5_HC_1_C_p


title: M_133A_11_HC_1_C_p


title: M_133A_26_HC_1_C_p


title: M_133A_7_HC_0_C_p


title: M_133A_13_HC_1_C_p


title: M_133A_19_HC_0_C_p


title: M_133A_49_HC_1_C


title: M_133A_9_HC_1_C_p


title: M_133A_8_HC_1_C_p


title: M_133A_15_HC_0_C_p


title: M_133A_17_HC_1_C_p


title: M_133A_16_HC_1_C_p


title: M_133A_21_HC_0_C_p


title: M_133A_112_HC_1_C_p


title: M_133A_43_HC_1_C_p


title: M_133A_111_HC_0_C_p


title: M_133A_32_HC_1_C_p


title: M_133A_108_HC_0_C_p


title: M_133A_36_HC_0_C_p


title: M_133A_33_HC_1_C_p


title: M_133A_105_HC_0_C_p


title: M_133A_103_HC_0_C_p


title: M_133A_116_HC_0_C_p


title: M_133A_14_HC_1_C_p


title: M_133A_102_HC_1_C_p


title: M_133A_24_HC_1_C_p


title: M_133A_29_HC_1_C_p


title: M_133A_34_HC_1_C


title: M_133A_35_HC_1_C


title: M_133A_106_HC_1_C_p


title: M_133A_27_HC_0_C_p


title: M_133A_44_HC_1_C


title: M_133A_41_HC_1_C


title: M_133A_37_HC_1_C


title: M_133A_42_HC_1_C


title: M_133A_38_HC_0_C


title: M_133A_48_HC_1_C


title: M_133A_40_HC_1_C


title: M_133A_45_HC_1_C


title: M_133A_121_HC_1_C_p


title: M_133A_51_HC_1_C


title: M_133A_46_HC_0_C


title: M_133A_52_HC_1_C


title: D_133A_22_HC_1_C_p


title: D_133A_19_HC_0_C_p


title: D_133A_23_HC_1_C_p


title: D_133A_101_HC_1_C_p


title: D_133A_31_HC_0_C_p


title: D_133A_39_HC_1_C_p


title: D_133A_49_HC_1_C


title: D_133A_26_HC_1_C_p


title: D_133A_130_HC_1_C


title: D_133A_115_HC_0_C


title: D_133A_126_HC_0_C


title: D_133A_53_HC_0_C


title: D_133A_50_HC_1_C


title: D_133A_25_HC_1_C_p


title: D_133A_131_HC_1_C


title: D_133A_55_HC_1_C


title: D_133A_29_HC_1_C_p


title: D_133A_27_HC_0_C_p


title: D_133A_102_HC_1_C_p


title: D_133A_32_HC_1_C_p


title: D_133A_103_HC_0_C_p


title: D_133A_28_HC_1_C_p


title: D_133A_106_HC_1_C_p


title: D_133A_108_HC_0_C_p


title: D_133A_125_HC_1_C


title: D_133A_41_HC_1_C


title: D_133A_33_HC_1_C_p


title: D_133A_116_HC_0_C_p


title: D_133A_112_HC_1_C_p


title: D_133A_36_HC_0_C_p


title: D_133A_111_HC_0_C_p


title: D_133A_43_HC_1_C_p


title: D_133A_46_HC_0_C


title: D_133A_45_HC_1_C


title: D_133A_105_HC_0_C_p


title: D_133A_34_HC_1_C


title: D_133A_42_HC_1_C


title: D_133A_40_HC_1_C


title: D_133A_35_HC_1_C


title: D_133A_44_HC_1_C


title: D_133A_121_HC_1_C_p


title: D_133A_52_HC_1_C


title: D_133A_47_HC_1_C


title: M_133A_115_DLPFC_0_C

source_name: Post-mortem human brain tissue: Dorsolateral Prefrontal Cortex

value: dorsolateral prefrontal cortex


title: D_133A_37_HC_1_C


title: D_133A_48_HC_1_C


title: M_133A_126_DLPFC_0_C


title: D_133A_38_HC_0_C


title: M_133A_125_DLPFC_1_C


title: D_133A_51_HC_1_C


title: M_133A_131_DLPFC_1_C


title: M_133A_49_DLPFC_1_C


title: M_133A_50_DLPFC_1_C


title: M_133A_31_HC_0_C_p


title: M_133A_55_DLPFC_1_C


title: M_133A_53_DLPFC_0_C


title: M_133A_3_DLPFC_1_C_p


title: M_133A_1_DLPFC_1_C_p


title: M_133A_5_DLPFC_1_C_p


title: M_133A_2_DLPFC_1_C_p


title: M_133A_4_DLPFC_1_C_p


title: M_133A_6_DLPFC_1_C_p


title: M_133A_7_DLPFC_0_C_p


title: M_133A_8_DLPFC_1_C_p


title: M_133A_13_DLPFC_1_C_p


title: M_133A_9_DLPFC_1_C_p


title: M_133A_14_DLPFC_1_C_p


title: M_133A_15_DLPFC_0_C_p


title: M_133A_12_DLPFC_1_C_p


title: M_133A_10_DLPFC_1_C_p


title: M_133A_16_DLPFC_1_C_p


title: M_133A_17_DLPFC_1_C_p


title: M_133A_18_DLPFC_1_C_p


title: M_133A_102_DLPFC_1_C


title: M_133A_20_DLPFC_1_C_p


title: M_133A_24_DLPFC_1_C_p


title: M_133A_32_DLPFC_1_C


title: M_133A_29_DLPFC_1_C


title: M_133A_32_DLPFC_1_C_r


title: M_133A_30_DLPFC_1_C


title: M_133A_11_DLPFC_1_C_p


title: M_133A_106_DLPFC_1_C


title: M_133A_33_DLPFC_1_C


title: M_133A_103_DLPFC_0_C


title: M_133A_27_DLPFC_0_C


title: M_133A_108_DLPFC_0_C


title: M_133A_116_DLPFC_0_C


title: M_133A_105_DLPFC_0_C


title: M_133A_43_DLPFC_1_C


title: M_133A_111_DLPFC_0_C


title: M_133A_104_DLPFC_0_C


title: M_133A_36_DLPFC_0_C


title: M_133A_109_DLPFC_1_C


title: M_133A_34_DLPFC_1_C


title: M_133A_35_DLPFC_1_C


title: M_133A_37_DLPFC_1_C


title: M_133A_121_DLPFC_1_C


title: M_133A_113_DLPFC_1_C


title: M_133A_41_DLPFC_1_C


title: M_133A_44_DLPFC_1_C


title: M_133A_46_DLPFC_0_C


title: M_133A_38_DLPFC_0_C


title: M_133A_42_DLPFC_1_C


title: M_133A_47_DLPFC_1_C


title: M_133A_47_DLPFC_1_C_r


title: M_133A_45_DLPFC_1_C_r


title: M_133A_48_DLPFC_1_C


title: M_133A_46_DLPFC_0_C_r


title: M_133A_52_DLPFC_1_C_r


title: D_133A_19_DLPFC_0_C_p


title: I_133A_125_DLPFC_1_C

value: I


title: D_133A_28_DLPFC_1_C_p


title: I_133A_131_DLPFC_1_C


title: D_133A_25_DLPFC_1_C_p


title: D_133A_49_DLPFC_1_C_p


title: D_133A_125_DLPFC_1_C_p


title: M_133A_51_DLPFC_1_C


title: M_133A_51_DLPFC_1_C_r


title: M_133A_52_DLPFC_1_C


title: M_133A_128_DLPFC_1_C


title: M_133A_54_DLPFC_1_C_r


title: M_133A_54_DLPFC_1_C


title: I_133A_115_DLPFC_0_C


title: I_133A_50_DLPFC_1_C


title: I_133A_126_DLPFC_0_C


title: M_133A_129_DLPFC_0_C


title: I_133A_49_DLPFC_1_C


title: I_133A_53_DLPFC_0_C


title: D_133A_101_DLPFC_1_C_p


title: I_133A_55_DLPFC_1_C


title: I_133A_130_DLPFC_1_C


title: D_133A_22_DLPFC_1_C_p


title: D_133A_55_DLPFC_1_C_r_p


title: D_133A_23_DLPFC_1_C_p


title: D_133A_26_DLPFC_1_C_p


title: D_133A_126_DLPFC_0_C


title: D_133A_115_DLPFC_0_C


title: D_133A_53_DLPFC_0_C


title: D_133A_39_DLPFC_1_C_p


title: D_133A_50_DLPFC_1_C_p


title: D_133A_49_DLPFC_1_C_r_p


title: D_133A_125_DLPFC_1_C_r_p


title: D_133A_50_DLPFC_1_C_r_p


title: D_133A_49_DLPFC_1_C


title: D_133A_55_DLPFC_1_C_p


title: D_133A_125_DLPFC_1_C


title: D_133A_130_DLPFC_1_C


title: D_133A_50_DLPFC_1_C


title: D_133A_131_DLPFC_1_C


title: D_133A_9_DLPFC_1_C_p


title: D_133A_55_DLPFC_1_C


title: D_133A_14_DLPFC_1_C_p


title: D_133A_8_DLPFC_1_C_p


title: D_133A_12_DLPFC_1_C_p


title: D_133A_7_DLPFC_0_C_p


title: D_133A_15_DLPFC_0_C_p


title: D_133A_11_DLPFC_1_C_p


title: D_133A_17_DLPFC_1_C_p


title: D_133A_20_DLPFC_1_C_p


title: D_133A_24_DLPFC_1_C_p


title: D_133A_16_DLPFC_1_C_p


title: D_133A_27_DLPFC_0_C


title: D_133A_29_DLPFC_1_C


title: D_133A_102_DLPFC_1_C


title: D_133A_10_DLPFC_1_C_p


title: D_133A_103_DLPFC_0_C


title: D_133A_112_DLPFC_1_C


title: D_133A_30_DLPFC_1_C


title: D_133A_18_DLPFC_1_C_p


title: D_133A_33_DLPFC_1_C


title: D_133A_105_DLPFC_0_C


title: D_133A_108_DLPFC_0_C


title: D_133A_36_DLPFC_0_C


title: D_133A_106_DLPFC_1_C


title: D_133A_116_DLPFC_0_C


title: D_133A_34_DLPFC_1_C


title: D_133A_109_DLPFC_1_C


title: D_133A_121_DLPFC_1_C


title: D_133A_35_DLPFC_1_C


title: D_133A_43_DLPFC_1_C


title: D_133A_107_DLPFC_0_C


title: D_133A_104_DLPFC_0_C


title: D_133A_32_DLPFC_1_C


title: D_133A_117_DLPFC_0_C


title: D_133A_119_DLPFC_0_C


title: D_133A_42_DLPFC_1_C


title: D_133A_110_DLPFC_0_C


title: D_133A_113_DLPFC_1_C


title: D_133A_41_DLPFC_1_C


title: D_133A_37_DLPFC_1_C


title: D_133A_111_DLPFC_0_C


title: D_133A_38_DLPFC_0_C


title: D_133A_120_DLPFC_1_C


title: D_133A_44_DLPFC_1_C


title: D_133A_45_DLPFC_1_C


title: D_133A_123_DLPFC_1_C


title: D_133A_114_DLPFC_0_C


title: D_133A_118_DLPFC_0_C


title: D_133A_48_DLPFC_1_C


title: D_133A_52_DLPFC_1_C


title: D_133A_46_DLPFC_0_C


title: D_133A_124_DLPFC_1_C


title: D_133A_122_DLPFC_1_C


title: D_133A_127_DLPFC_1_C


title: M_133A_19_CB_0_C_p

source_name: Post-mortem human brain tissue: Cerebellum

value: cerebellum


title: D_133A_51_DLPFC_1_C


title: M_133A_22_CB_1_C_p


title: D_133A_129_DLPFC_0_C


title: D_133A_54_DLPFC_1_C


title: M_133A_23_CB_1_C_p


title: M_133A_101_CB_1_C_p


title: M_133A_26_CB_1_C_p


title: M_133A_28_CB_1_C_p


title: M_133A_25_CB_1_C_p


title: D_133A_47_DLPFC_1_C


title: M_133A_31_CB_0_C_p


title: D_133A_128_DLPFC_1_C


title: M_133A_126_CB_0_C


title: M_133A_49_CB_1_C


title: M_133A_50_CB_1_C


title: M_133A_53_CB_0_C


title: M_133A_131_CB_1_C


title: M_133A_55_CB_1_C


title: I_133A_23_CB_1_C_p


title: I_133A_22_CB_1_C_p


title: I_133A_19_CB_0_C_p


title: M_133A_125_CB_1_C


title: I_133A_126_CB_0_C


title: I_133A_26_CB_1_C_p


title: I_133A_28_CB_1_C_p


title: I_133A_101_CB_1_C_p


title: I_133A_39_CB_1_C_p


title: I_133A_49_CB_1_C


title: I_133A_27_CB_0_C


title: I_133A_50_CB_1_C


title: I_133A_125_CB_1_C


title: I_133A_31_CB_0_C_p


title: I_133A_130_CB_1_C


title: I_133A_53_CB_0_C


title: I_133A_29_CB_1_C


title: I_133A_30_CB_1_C


title: I_133A_25_CB_1_C_p


title: I_133A_32_CB_1_C


title: I_133A_131_CB_1_C


title: I_133A_55_CB_1_C


title: I_133A_34_CB_1_C


title: I_133A_33_CB_1_C


title: I_133A_43_CB_1_C


title: I_133A_36_CB_0_C


title: I_133A_37_CB_1_C


title: I_133A_38_CB_0_C


title: I_133A_40_CB_1_C


title: I_133A_41_CB_1_C


title: I_133A_120_CB_1_C


title: I_133A_44_CB_1_C


title: I_133A_45_CB_1_C


title: I_133A_48_CB_1_C


title: M_133A_39_CB_1_C_p


title: I_133A_42_CB_1_C


title: I_133A_46_CB_0_C


title: I_133A_119_CB_0_C


title: D_133A_32_CB_1_C_p


title: I_133A_52_CB_1_C


title: D_133A_106_CB_1_C_p


title: D_133A_112_CB_1_C_p


title: D_133A_30_CB_1_C_p


title: D_133A_33_CB_1_C_p


title: D_133A_104_CB_0_C


title: D_133A_102_CB_1_C_p


title: I_133A_118_CB_0_C


title: D_133A_29_CB_1_C_p


title: I_133A_54_CB_1_C


title: D_133A_107_CB_0_C


title: I_133A_51_CB_1_C


title: D_133A_43_CB_1_C_p


title: I_133A_47_CB_1_C


title: D_133A_113_CB_1_C


title: M_133A_101_AnCg_1_C_p

source_name: Post-mortem human brain tissue: Anterior Cingulate

value: anterior cingulate


title: D_133A_110_CB_0_C


title: M_133A_31_AnCg_0_C_p


title: D_133A_109_CB_1_C


title: M_133A_19_AnCg_0_C_p


title: M_133A_25_AnCg_1_C_p


title: M_133A_28_AnCg_1_C_p


title: D_133A_34_CB_1_C


title: D_133A_35_CB_1_C


title: M_133A_39_AnCg_1_C_p


title: M_133A_1_AnCg_1_C_p


title: M_133A_22_AnCg_1_C_p


title: M_133A_23_AnCg_1_C_p


title: I_133A_35_CB_1_C


title: D_133A_116_CB_0_C_p


title: M_133A_26_AnCg_1_C_p


title: D_133A_37_CB_1_C


title: D_133A_36_CB_0_C_p


title: M_133A_6_AnCg_1_C_p


title: D_133A_38_CB_0_C


title: M_133A_3_AnCg_1_C_p


title: M_133A_13_AnCg_1_C_p


title: M_133A_4_AnCg_1_C_p


title: M_133A_2_AnCg_1_C_p


title: D_133A_42_CB_1_C


title: D_133A_40_CB_1_C


title: M_133A_5_AnCg_1_C_p


title: M_133A_7_AnCg_0_C_p


title: M_133A_14_AnCg_1_C_p


title: M_133A_8_AnCg_1_C_p


title: M_133A_105_AnCg_0_C


title: M_133A_106_AnCg_1_C


title: M_133A_15_AnCg_0_C_p


title: M_133A_18_AnCg_1_C_p


title: M_133A_11_AnCg_1_C_p


title: M_133A_27_AnCg_0_C


title: M_133A_111_AnCg_0_C


title: M_133A_108_AnCg_0_C


title: M_133A_29_AnCg_1_C


title: M_133A_21_AnCg_0_C_p


title: M_133A_24_AnCg_1_C_p


title: M_133A_43_AnCg_1_C


title: M_133A_10_AnCg_1_C_p


title: M_133A_32_AnCg_1_C


title: M_133A_17_AnCg_1_C_p


title: M_133A_36_AnCg_0_C


title: M_133A_9_AnCg_1_C_p


title: M_133A_102_AnCg_1_C


title: M_133A_116_AnCg_0_C


title: M_133A_40_AnCg_1_C


title: M_133A_20_AnCg_1_C_p


title: M_133A_121_AnCg_1_C


title: M_133A_34_AnCg_1_C


title: M_133A_12_AnCg_1_C_p


title: M_133A_37_AnCg_1_C


title: M_133A_16_AnCg_1_C_p


title: M_133A_38_AnCg_0_C


title: M_133A_35_AnCg_1_C


title: M_133A_33_AnCg_1_C


title: M_133A_103_AnCg_0_C


title: M_133A_42_AnCg_1_C


title: M_133A_41_AnCg_1_C


title: M_133A_30_AnCg_1_C


title: M_133A_44_AnCg_1_C


title: M_133A_51_AnCg_1_C


title: M_133A_52_AnCg_1_C


title: M_133A_47_AnCg_1_C


title: M_133A_46_AnCg_0_C


title: M_133A_48_AnCg_1_C


title: I_133A_101_AnCg_1_C_p


title: M_133A_54_AnCg_1_C


title: I_133A_50_AnCg_1_C


title: I_133A_23_AnCg_1_C_p


title: I_133A_53_AnCg_0_C


title: M_133A_45_AnCg_1_C


title: I_133A_8_AnCg_1_C_p


title: I_133A_3_AnCg_1_C_p


title: I_133A_19_AnCg_0_C_p


title: I_133A_22_AnCg_1_C_p


title: I_133A_39_AnCg_1_C_p


title: I_133A_28_AnCg_1_C_p


title: I_133A_49_AnCg_1_C


title: I_133A_31_AnCg_0_C_p


title: I_133A_6_AnCg_1_C_p


title: I_133A_13_AnCg_1_C_p


title: I_133A_1_AnCg_1_C_p


title: I_133A_26_AnCg_1_C_p


title: I_133A_25_AnCg_1_C_p


title: I_133A_2_AnCg_1_C_p


title: I_133A_9_AnCg_1_C_p


title: I_133A_115_AnCg_0_C


title: I_133A_55_AnCg_1_C


title: I_133A_131_AnCg_1_C


title: I_133A_126_AnCg_0_C


title: I_133A_10_AnCg_1_C_p


title: I_133A_7_AnCg_0_C_p


title: I_133A_5_AnCg_1_C_p


title: I_133A_11_AnCg_1_C_p


title: I_133A_14_AnCg_1_C_p


title: I_133A_4_AnCg_1_C_p


title: I_133A_17_AnCg_1_C_p


title: I_133A_18_AnCg_1_C_p


title: I_133A_15_AnCg_0_C_p


title: I_133A_16_AnCg_1_C_p


title: I_133A_12_AnCg_1_C_p


title: I_133A_21_AnCg_0_C_p


title: I_133A_36_AnCg_0_C


title: I_133A_37_AnCg_1_C


title: I_133A_30_AnCg_1_C


title: I_133A_43_AnCg_1_C


title: I_133A_35_AnCg_1_C


title: I_133A_33_AnCg_1_C


title: I_133A_20_AnCg_1_C_p


title: I_133A_24_AnCg_1_C_p


title: I_133A_106_AnCg_1_C


title: I_133A_41_AnCg_1_C


title: I_133A_38_AnCg_0_C


title: I_133A_29_AnCg_1_C


title: I_133A_34_AnCg_1_C


title: I_133A_27_AnCg_0_C


title: I_133A_102_AnCg_1_C


title: I_133A_42_AnCg_1_C


title: I_133A_40_AnCg_1_C


title: I_133A_46_AnCg_0_C


title: I_133A_45_AnCg_1_C


title: I_133A_47_AnCg_1_C


title: I_133A_32_AnCg_1_C


title: I_133A_118_AnCg_0_C


title: I_133A_120_AnCg_1_C


title: I_133A_48_AnCg_1_C


title: I_133A_51_AnCg_1_C


title: I_133A_119_AnCg_0_C


title: I_133A_44_AnCg_1_C


title: I_133A_54_AnCg_1_C


title: I_133A_52_AnCg_1_C


title: I_133A_23_Amy_1_C_p

source_name: Post-mortem human brain tissue: Amygdala

value: amygdala


title: I_133A_22_Amy_1_C_p


title: I_133A_28_Amy_1_C_p


title: I_133A_19_Amy_0_C_p


title: I_133A_25_Amy_1_C_p


title: I_133A_26_Amy_1_C_p


title: I_133A_31_Amy_0_C_p


title: I_133A_101_Amy_1_C_p


title: I_133A_30_Amy_1_C


title: Sample 12

city: Umeå

first: Nathaniel

middle: Robert

last: Street

address: Umeå Plant Science Centre

department: Plant Physiology

country: Sweden

institute: Umeå University

hyb_protocol: We used the cDNA synthesis, amplification, microarray hybridisation and washing protocols supplied by Agilent (Agilent Technologies, Waldbronn, Germany) with no modifications. All hybridisations were performed using only one sample and using Cy3.

scan_protocol: Arrays were scanned at 5 μm resolution, using a Scanarray 4000 microarray analysis system scanner (Perkin-Elmer, Boston, MA, USA).

data_processing: Spot data were extracted using GenePix (v5, Axon Instruments Inc, Union City, CA, USA). Microarray normalisation and analyses were performed using Bioconductor packages in R. A between microarray quantile normalisation was performed using the normalizeBetweenArrays command from the limma package. B statistics, as implemented in the limma package, were used to fit a linear model to identify genes with a high probability of differential expression between sexes.

organism: Populus tremula

source_name: Mature leaves

growth_protocol: Mature leaves were sampled from wild-growing trees in the area around Umeå. All leaves were from over-wintered buds.

extract_protocol: Total RNA was extracted from 0.5 g tissue using a slightly modified version of the CTAB method. Precipitated RNA was further purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol. RNA concentration and purity were measured using a NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and integrity was analysed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: All trees samples were wild-growing, sexually mature Populus tremula

tag: tissue

value: Mature leaves

tag: Sex

value: Female


title: Sample 15

label_protocol: We used the cDNA synthesis, amplification, microarray hybridisation and washing protocols supplied by Agilent (Agilent Technologies, Waldbronn, Germany) with no modifications. All hybridisations were performed using only one sample and using Cy3.

value: Male


title: Sample 19


title: I_133A_39_Amy_1_C_p


title: I_133A_102_Amy_1_C


title: Sample 13


title: Sample 16


title: Sample 20


title: Sample 9


title: Sample 17


title: Sample 14


title: Sample 7


title: Sample 10


title: I_133A_32_Amy_1_C


title: I_133A_29_Amy_1_C


title: Sample 11


title: I_133A_43_Amy_1_C


title: I_133A_36_Amy_0_C


title: I_133A_106_Amy_1_C


title: Sample 6


title: I_133A_27_Amy_0_C


title: I_133A_34_Amy_1_C


title: Sample 5


title: Sample 8


title: Sample 18


title: I_133A_33_Amy_1_C


title: Sample 1


title: I_133A_38_Amy_0_C


title: Sample 4


title: DM Donor [DM_582B]

city: Gaithersburg

first: Christopher

middle: Allen

last: Morehouse

address: One Medimmune Way

institute: Medimmune LLC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using frma in R.

source_name: skin biopsy specimen_DM Donor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Ambion mirVana miRNA/RNA Kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Gene expression profiling of healthy donor and dermatomyositis patient skin biopsy specimens.

tag: dx

value: DM

tag: age

tag: gender

value: F


title: DM Donor [DM_573]


title: Sample 3


title: I_133A_41_Amy_1_C


title: I_133A_42_Amy_1_C


title: Sample 2


title: DM Donor [DM_563]


title: I_133A_44_Amy_1_C


title: I_133A_48_Amy_1_C


title: DM Donor [DM_555]


title: DM Donor [DM_568B]


title: DM Donor [DM_561]


title: DM Donor [DM_568A]


title: DM Donor [DM_582A]


title: I_133A_47_Amy_1_C


title: I_133A_45_Amy_1_C


title: I_133A_51_Amy_1_C


title: I_133A_52_Amy_1_C


title: I_133A_46_Amy_0_C


title: I_133A_37_Amy_1_C


title: DM Donor [DM_476]


title: DM Donor [DM_531]


title: I_133A_40_Amy_1_C


title: I_133A_54_Amy_1_C


title: DM Donor [DM_503]


title: DM Donor [DM_493]


title: D_133A_101_Amy_1_C_p


title: DM Donor [DM_475B]


title: D_133A_25_Amy_1_C_p


title: DM Donor [DM_462B]


title: D_133A_28_Amy_1_C_p


title: DM Donor [DM_464B]


title: D_133A_23_Amy_1_C_p


title: DM Donor [DM_460B]


title: DM Donor [DM_475A]


title: D_133A_39_Amy_1_C_p


title: D_133A_29_Amy_1_C_p


title: DM Donor [DM_467]


title: D_133A_30_Amy_1_C_p


title: D_133A_102_Amy_1_C_p


title: DM Donor [DM_462A]


title: DM Donor [DM_460A]


title: D_133A_32_Amy_1_C_p


title: DM Donor [DM_432]


title: D_133A_106_Amy_1_C_p


title: D_133A_33_Amy_1_C_p


title: DM Donor [DM_464A]


title: DM Donor [DM_404]


title: DM Donor [DM_369]


title: DM Donor [DM_392b]


title: DM Donor [DM_429]


title: DM Donor [DM_366]


title: DM Donor [DM_392]


title: D_133A_43_Amy_1_C_p


title: D_133A_34_Amy_1_C


title: D_133A_19_Amy_0_C_p


title: DM Donor [DM_354]


title: D_133A_38_Amy_0_C


title: D_133A_42_Amy_1_C


title: D_133A_48_Amy_1_C


title: DM Donor [DM_327]


title: DM Donor [DM_315]


title: DM Donor [DM_281]


title: D_133A_40_Amy_1_C


title: DM Donor [DM_258]


title: D_133A_44_Amy_1_C


title: D_133A_41_Amy_1_C


title: D_133A_36_Amy_0_C_p


title: D_133A_45_Amy_1_C


title: DM Donor [DM_328]


title: DM Donor [DM_314]


title: DM Donor [DM_212B]


title: DM Donor [DM_208]


title: D_133A_46_Amy_0_C


title: DM Donor [DM_212A]


title: DM Donor [DM_247]


title: DM Donor [DM_201]


title: DM Donor [DM_334]


title: DM Donor [DM_216]


title: DM Donor [DM_182B]


title: DM Donor [DM_249]


title: D_133A_37_Amy_1_C


title: DM Donor [DM_217]


title: D_133A_47_Amy_1_C


title: DM Donor [DM_167]


title: D_133A_52_Amy_1_C


title: D_133A_51_Amy_1_C


title: D_133A_54_Amy_1_C


title: DM Donor [DM_160]


title: Healthy Donor [HD_186]

source_name: skin biopsy specimen_Healthy Donor

value: healthy


title: Healthy Donor [HD_173B]

value: M


title: rsa3_Na_24 h_rep2

city: College Park

first: Jianhua

last: Zhu

address: 2102 Plant Sciences Building

department: Plant Science and Landscape Architecture

institute: University of Maryland

description: Gene expression data from Arabidopsis rsa3-1 mutant plants under salt stress

hyb_protocol: Following fragmentation, 10 µg of cRNA was hybridized for 16 h at 45°C on Affymetrix ATH1 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The datasets were subjected to the Robust Multiarray Averaging (RMA) normalization method. The normalized data were further analyzed and p-values were generated by the affymGUI component of Bioconductor in statistics environment R with the default parameters.Genes were selected by the RankProd (non-paramteric method based on the estimated percentage of false discoveries (p value < 0.05)) method. Normalized expression values presented in Matrix table are log2 values.

organism: Arabidopsis thaliana

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

growth_protocol: Arabidopsis seedlings on Murashige and Skoog (MS) medium agar plates (1x MS salts, 2% sucrose, 1.2% agar, pH 5.7) were  grown under cool, white light (~120 μmol m-2 s-1) at 21 ± 1℃ with a 16-h-light/8-h-dark photoperiod.

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen) following the manufacturer's instructions.

treatment_protocol: Six-day-old wild type and rsa3-1 mutant plants were subjuected to salt stress at 120 mM NaCl for 24 h.

tag: ecotype

value: Columbia gl1 expressing RD29A::LUC transgene

value: rsa3-1 mutant

value: whole seedlings

value: 120 mM NaCl for 24 h

value: Six-day-old


title: castration-93

city: tianjin

first: ning

last: jiang

address: hexi district pingjiang road 23

department: urology institute

country: China

institute: tianjin medical university

description: Gene expression data from uncastrasion tumor-93

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Wheat Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.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 AGCC.

data_processing: The data were normalized using Robust Multi-array Average(RMA) .

source_name: castration-93  LNCAP cell Orhotopic xenograft tumor of prostate cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: Ten male athymic Balb/c nude mice (Beijing HFK Bio-Technology Co. Ltd.) were injected subcutaneouslly with 2×106 LNCaP cells suspended in 0.1 mL of Matrigel (BD Biosciences), half of the mice were castrated when tumors reached 10mm and the tumors were allowed to growth back and later transplanted orthotopically into the prostate ventral lobe of intact or castrated Balb/c mice. The later procedure was repeated at least twice before tumors were dissected and snap frozen for further analysis.

value: LNCAP

tag: host strain

value: Balb/c nude

value: mouse prostate

tag: intervention

value: castration


title: castration-91

description: Gene expression data from castrasion tumor-91

source_name: castration-91 LNCAP cell Orhotopic xenograft tumor of prostate cancer

treatment_protocol: half of the mice were castrated when tumors reached 10mm and the tumors were allowed to growth back and later transplanted orthotopically into the prostate ventral lobe of intact


title: Healthy Donor [HD_171]


title: rsa3_Na_24 h_rep1

tag: treatment


title: castration-90

description: Gene expression data from castrasion tumor-90

source_name: castration-90    LNCAP cell Orhotopic xenograft tumor of prostate cancer


title: uncastrasion-66P

description: Gene expression data from uncastrasion tumor-66P

source_name: uncastrasion-66P LNCAP cell Orhotopic xenograft tumor of prostate cancer

value: uncastrasion


title: DM Donor [DM_498]


title: Healthy Donor [HD_173A]


title: uncastrasion-65P

description: Gene expression data from uncastrasion tumor-65P

source_name: uncastrasion-65P    LNCAP cell Orhotopic xenograft tumor of prostate cancer


title: uncastrasion-51P

description: Gene expression data from uncastrasion tumor-51P

source_name: uncastrasion-51P  LNCAP cell Orhotopic xenograft tumor of prostate cancer


title: WT_Na_24 h_rep1

description: Gene expression data from Arabidopsis wild type plants under salt stress

source_name: Arabidopsis wild type, 120 mM NaCl, 24 h.

tag: genotype/variation

value: wild type


title: castration-57P

description: Gene expression data from castrasion tumor-57P

source_name: castration-57P LNCAP cell Orhotopic xenograft tumor of prostate cancer


title: MLL_00360

city: Munich

first: Andreas

last: Roller

address: Max-Lebsche-Platz 31

country: Germany

institute: Munich Leukemia Laboratory

description: control

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

growth_protocol: not applicable

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.

treatment_protocol: untreated samples

tag: case

tag: disease state

value: Acute myeloid leukemia (AML)

tag: mutation

value: GATA2 mut


title: uncastrasion-75

description: Gene expression data from uncastrasion tumor-75

source_name: uncastrasion-75 LNCAP cell Orhotopic xenograft tumor of prostate cancer

tag: cell type


title: WT_Na_24 h_rep2


title: D_133A_22_Amy_1_C_p

tag: genechip assay site

value: D

tag: original genechip type

value: amygdala


title: MLL_00359

description: control


title: Ppara KO TFEB-injected, biological replicate 3

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Gene expression data from liver of injected mouse

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse 430A_2 Array

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

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: liver of TFEB-injected Ppara KO mouse

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT labelling kit (Affymetrix).

extract_protocol: Total RNAs from either injected and not-injected Ppara KO mouse livers were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

treatment_protocol: The liver from three Ppara KO mice (one month old) was injected with an adenoviral vector, while the liver from other three mice (one month old) was not-injected

tag: background strain

tag: tissue type

value: liver

value: Ppara KO


title: D_133A_31_Amy_0_C_p

tag: subject id

tag: brain region


title: Delta_off_rep2

first: Timothy

last: Newton

address: Addenbrooke's Hospital

hyb_protocol: Hybridization was carried out following the beadchip manufacturer's instructions (Illumina)

scan_protocol: Illumina iScan  with iScan Control Software 1.3.10+

data_processing: Raw data were pre-processed using R software (http://www.r-project.org) and the bioconductor (http://www.bioconductor.org) package lumi (Du et al., 2008).  Probes were removed from the data set where the Illimuna detection p-value was greater than 0.01.  The data were then transformed using the variance stabilisation transformation algorithm (VST) and normalised using the quantile normalisation method.  Differentially expressed genes for each condition (wild-type neuroserpin ‘on’ versus wild-type neuroserpin ‘off’, G392E neuroserpin ‘on’ versus G392E neuroserpin ‘off and Δ neuroserpin ‘on’ versus Δ neuroserpin ‘off’’) were identified by fitting linear models with the bioconductor R package limma (Smyth, 2004).  To account for multiple hypotheses testing, p-values were adjusted using the Benjamini & Hochberg False Discovery Rate (FDR) correction (Benjamini and Hochberg, 1995).  In order to assess the gene expression profiles at a pathway level, Gene Set Enrichment analysis (Subramanian et al., 2005) was performed on the normalised gene expression values for each group. Gene Set Enrichment analysis uses a priori defined gene sets to determine pathway differences between two phenotypic states.  Gene expression data is therefore evaluated at the pathway level rather than the single gene. Gene Set Enrichment analysis first ranks the genes according to their relative difference in gene expression.  The ranked list is then compared to gene sets (pathways) and an enrichment score (ES) is calculated for each gene.  When a gene is present in the gene set of interest, the running enrichment score is increased.  If the gene is absent the running enrichment score is decreased.  The enrichment statistic is the maximum deviation of the running enrichment score from zero.  Statistical significance is assessed by performing a permutation test procedure.  To account for the differences in gene set size, a normalised enrichment score (NES) is calculated.  Estimated significance levels are also adjusted for multiple hypothesis testing.  False Discovery Rate (FDR) is the estimated probability that a gene set with a given enrichment statistic represents a false-positive finding.  A total of 639 pathways (gene sets) were analysed from Kyoto Encyclopedia of Genes and Genomes, Reactome, and BioCarta databases (http://www.genome.jp/kegg/pathway.html, http://www.reactome.org/ and http://www.biocarta.com/genes/index.asp respectively). Gene sets containing less than 15 and greater than 500 genes were filtered out, along with gene sets containing no genes from the input data set.

source_name: Delta, no doxycycline

label_protocol: Sample was labelled with biotin as part of the Ambion Total Prep kit (Ambion, UK) protocol.

growth_protocol: 250,000 Cells per well were grown in six well plates for 72 hours.  The cells were cultured in DMEM supplemented with 10% v/v Tet-free approved FBS (Clontech), 200 µg/ml Geneticin and 100 µg/ml Hygromycin B (both selective antibiotics from Invitrogen, Paisley, UK), at 37°C and 5% v/v CO2 in a humidified incubator.

extract_protocol: Cells were collected by trypsinisation and pelleted at 700 g for 10 min at 4⁰C.  RNA was isolated with Tri Reagent (Sigma).  RNA amplification was performed using Ambion Total Prep kit (Ambion, UK)

treatment_protocol: Neuroserpin expression was induced in 'on' samples with 2 ug/ml doxycycline 48 hours before collection.  'off' samples remained untreated.

value: HeLa

value: Transfected with Delta Neuroserpin


title: Delta_on_rep3

source_name: Delta, 2 ug/ml doxycycline


title: MLL_00361

description: control


title: Delta_off_rep3


title: Ppara KO TFEB-injected, biological replicate 1


title: MLL_00354

description: control

value: ASXL1/GATA2/TET2/DNMT3A wt


title: Delta_on_rep1


title: Ppara KO TFEB-injected, biological replicate 2


title: MLL_00352

description: control


title: Ppara KO not-injected, biological replicate 3

description: Gene expression data from liver of not-injected mouse

source_name: liver of not-injected Ppara KO mouse


title: MLL_00348

description: control

value: TET2 mut


title: MLL_00358

description: control


title: MLL_00349

description: control


title: Delta_off_rep1


title: Delta_on_rep2


title: MLL_00353

description: control


title: parental_off_rep3

source_name: parental, no doxycycline

value: Untransfected parental clontech cell line


title: MLL_00355

description: control


title: MLL_00350

description: control


title: MLL_00347

description: control


title: Ppara KO not-injected, biological replicate 1


title: parental_off_rep2


title: parental_on_rep3

source_name: parental, 2 ug/ml doxycycline


title: MLL_00344

description: control


title: parental_on_rep2


title: Ppara KO not-injected, biological replicate 2


title: MLL_00343

description: control


title: MLL_00346

description: control


title: MLL_00345

description: control


title: MLL_00342

description: control


title: C57WT, TFEB-injected, biological replicate 3

source_name: liver of TFEB-injected mouse

extract_protocol: Total RNAs from either injected and not-injected livers were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

treatment_protocol: The liver from three mice (one month old) was injected with an adenoviral vector, while the liver from other three mice (one month old) was not-injected


title: MLL_00341

description: control


title: C57WT, TFEB-injected, biological replicate 2


title: parental_off_rep1


title: parental_on_rep1


title: C57WT, biological replicate 3

source_name: liver of not-injected mouse


title: C57WT, biological replicate 2


title: C57WT, TFEB-injected, biological replicate 1


title: MLL_00339

description: control


title: MLL_00334

description: control


title: MLL_00336

description: control


title: MLL_00337

description: control


title: Subject 1030 visit 4

city: Madison

first: Sameer

last: Mathur

state: WI

address: 600 Highland Ave.

institute: University of Wisconsin-Madison

description: RNA extracted from sputum cells 48 hours after whole lung allergen challenge

hyb_protocol: used Agilent 60-mer oligo microarray processing protocol with Agilent gene expression hybridization kit

scan_protocol: Agilent microarray scanner system

data_processing: software used: Agilent feature extraction software and Rosetta Resolver gene expression data analysis system

source_name: sputum sample

label_protocol: Cy3 labeling performed using Agilent low input quick amp kit

extract_protocol: 500,000 sputum cells resuspended in RLT buffer and sent to Miltenyi Biotec for total RNA isolation using standard techniques. RNA amplified with Agilent low input quick amp kit

treatment_protocol: whole lung allergen challenge

tag: age

value: female

value: sputum cells

tag: collection time


title: MLL_00333

description: control


title: MLL_00338

description: control


title: Subject 1030 visit 2

description: RNA extracted from sputum cells at baseline

tag: gender

value: at baseline


title: starved, biological replicate2

source_name: wt mouse starved

extract_protocol: Total RNAs from either starved and control livers were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

treatment_protocol: The liver from two mice (one month old) was starved for 24 hours, while the liver from other two wt mice (one month old) was use as control

tag: tissue

value: starved for 24 h

tag: genetic background


title: starved, biological replicate1

tag: treatment


title: MLL_00332

description: control


title: Subject 1011 visit 2


title: MLL_00340

description: control


title: Subject 1009 visit 4

value: male

value: 48 hours after whole lung allergen challenge


title: MLL_00327

description: control

value: Acute myeloid leukemia (AML)

value: ASXL1 mut/ TET2 mut


title: MLL_00331

description: control


title: MLL_00330

description: control


title: MLL_00335

description: control

value: GATA2 mut


title: Subject 1009 visit 2


title: control, biological replicate 2

source_name: wt mouse

value: control


title: Subject 1011 visit 4


title: MLL_00326

description: control


title: MLL_00329

description: control


title: MLL_00328

description: control


title: control, biological replicate 1

value: liver


title: MLL_00325

description: control

value: ASXL1 mut


title: Injected, biological replicate 3

description: Gene expression data from liver of injected mouse.

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on the GeneChip Mouse 430A_2 Array.

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

data_processing: The data were analyzed with the Bioconductor package Affy using the RMA method for normalizing and summarizing probe level intensity measurements.

source_name: liver of injected mouse, overexpressing TFEB

extract_protocol: Total RNAs from injected and not-injected livers were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with the RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

treatment_protocol: The livers from three mice (one month old) were injected with an adenoviral vector (helper-dependent adenovirus serotype 5) expressing hTFEB under the control of the liver-specific PEPCK promoter (PMID 20461064), while the livers from three other mice (one month old) were not injected.

value: 1 month

value: injected


title: C57WT, biological replicate 1

tag: genotype/variation

value: wild type


title: Subject 1007 visit 4


title: Subject 1007 visit 2


title: MLL_00324

description: control

tag: case


title: Subject 1004 visit 4


title: Injected, biological replicate 2


title: MLL_00323

description: control

tag: disease state


title: CTL, biological replicate 3

description: Gene expression data from liver of not-injected mouse.

source_name: liver of not-injected mouse, control

value: not injected


title: Injected, biological replicate 1


title: Subject 1004 visit 2


title: LGLL MSC, biological rep2

city: Tampa

first: Adam

last: Mailloux

state: FL

address: 12902 Magnolia Drive

department: Immunology

institute: Moffitt Cancer Center & Research Institute

description: Gene expression data from LGLL MSCs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to the Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scaner.

data_processing: The data were analyzed with the Affymetrix GCOS 1.4 software using the MAS 5.0 alorighthm with default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Cultured adherent fraction from LGLL bone marrow aspirate; passage 7-9

label_protocol: Biotinylated cRNA were prepared according to the Ambion Message Amp Premier protocl using 100 ng of total RNA (Ambion).

growth_protocol: MSCs were grown in alpha-modified eagles medium supplemented with 10% FBS, penicillin (100 units/ml), and streptomycin (100 units/ml).  Cultures were passaged prior to 80% confluence

extract_protocol: Isolation of total RNA was performed using the Qiagen RNEasy column according to the manufacturer's instructions.

value: LGLL

value: MSC

tag: passage state

value: later (senescence)


title: LGLL MSC, biological rep1

description: Gene expression data from LGLL MSCs

tag: cell type


title: Subject 1002 visit 2

value: female

value: sputum cells

value: at baseline


title: Subject 1002 visit 4

value: 48 hours after whole lung allergen challenge


title: MLL_00322

description: control

value: Acute myeloid leukemia (AML)

tag: mutation


title: Normal MSC later passage, biological rep1

description: Gene expression data from normal MSCs later passage

source_name: Cultured adherent fraction from normal bone marrow aspirate; passage 7-9

value: normal

value: later


title: EGDe at time 60 (Replicate3)

status: Public on Apr 19 2013

city: Zurich

first: Carolina

last: Arguedas-Villa

state: Zurich

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

hyb_protocol: Labeled samples were dried in a speed-vac and fragmented with Febit's Fragmentation Buffer and afterwards, the Febit's propietary standard Hybridization Buffer (20 ul per array) was added. Hydridization was done automatically for 16h at 45°C using the Geniom RT Analyzer

scan_protocol: Scanned on the Febit Geniom® RT Analyzer

data_processing: Images were quantified using Geniom Wizard Software

organism: Listeria monocytogenes EGD-e

source_name: 4°C at time 60

label_protocol: 1µg of mRNA was amplified and biotin labeled using the MessageAmpTMII-Bacteria Kit and the MessageAmpTMII-Biotin Enhanced Kit according to manufacturer's instructions (Febit protocols 010 and 019).

extract_protocol: Total RNA extracted using mini RNA extraction kit  following manufacturer's instructions; 5ug were depleted of 16S and 23S using MicrobExpress Kit according with manufacturer's intructions prior to transcriptome profiling

tag: strain

value: EGD-e

tag: culture condition

value: 4°C at time 60


title: EGDe at time 120 (Replicate2)

source_name: 4°C at time 120

value: 4°C at time 120


title: EGDe at time 30 (Replicate3)

source_name: 4°C at time 30

value: 4°C at time 30


title: CTL, biological replicate 2

tag: background strain

value: 1 month

value: liver


title: EGDe at time 120 (Replicate1)


title: EGDe at time 60 (Replicate2)


title: EGDe at time 30 (Replicate2)


title: EGDe at time 120 (Replicate3)


title: EGDe at time 0 (Replicate3)

source_name: 4°C at time 0

value: 4°C at time 0


title: EGDe at time 0 (Replicate2)


title: EGDe at time 0 (Replicate1)


title: Normal MSC later passage, biological rep2


title: EGDe at time 60 (Replicate1)


title: EGDe at time 30 (Replicate1)


title: MLL_00351

description: control

value: ASXL1/GATA2/TET2/DNMT3A wt


title: Normal MSC early passage, biological rep1

description: Gene expression data from normal MSCs early passage

source_name: Cultured adherent fraction from normal bone marrow aspirate; passage 2-3

value: MSC

value: early


title: Th2 (control siRNA) a-TCR stim

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

country: Japan

institute: Chiba University

description: Gene expression data from mock-transfected Th2 cells stimulated with anti-TCR mAb for 4hrs

hyb_protocol: cRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Expression values were determined using Affymetrix GeneChip Command Console Software (AGCC) and Console Software (Expression Console).

source_name: primary CD4 T cells from spleen cultured for 5 days in Th2 condition

label_protocol: Total RNA was labeled using the GeneChip 3' IVT Express Kit

growth_protocol: Splenic CD4 T cells were prepared using a magnetic cell sorter (AutoMACS; Miltenyi Biotec) yielding a purity of >98%. Where indicated, cells from C57BL/6 mice were stimulated with immobilized anti-TCR mAb (H57−597; 3 mg/ml) and anti-CD28 mAb under Th2-culture conditions for 2days in vitro.  Th2 conditions; 25 U/ml IL-2, 100 U/ml IL-4.  After culturing for 3 more days, the cells were harvested.

treatment_protocol: Th2 culture cells were collected and treated with control siRNA (AM4635; Applied Biosystems) or Gata3 siRNA (s66482; Applied Biosystems) using the Mouse T cell Nucleofector Kit (Amaxa) according to the manufacturer's protocol. Mock- or Gata3 siRNA-transfected Th2 cells were harvested after 24hrs, and stimulated with or without immobilized anti-TCR mAb (H57－597; 3 mg/ml) for 4hrs. Then cells were collected and resuspendet in the Trizol solution (GibcoBRL).

value: CD4 T


title: Th2 (Gata3 siRNA) a-TCR stim

description: Gene expression data from Gata3 siRNA-transfected Th2 cells stimulated with anti-TCR mAb for 4hrs


title: Th2 (control siRNA)

description: Gene expression data from mock-transfected Th2 cells

value: mock-transfected


title: brain tissue sample, mutant mice, biological replica 2

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

institute: Children's National Medical Center

description: Gene Expression data from brain tissue, mutant mice with PWS-IC del

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

data_processing: The data were analyzed with Probe Logarithmic Intensity Error  (PLIER) using Affymetrix Expression Console program.

source_name: Prader-Willi syndrome imprinting center deletion (PWS-IC del) mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: F1 hybrid of the FVB and B6

value: PWS-IC del

value: whole brain


title: X30_SEOC_R76

city: Frederick

first: Ludmila

last: Szabova

address: 1050 Boyles Street

department: CAPR

institute: Frederick National Laboratory for Cancer Research

hyb_protocol: Labeled cDNA (4.4 ug) of each sample was hybridized to Affymetrix mouse 430 2.0 GeneChip array.at 45°C for 16 hrs. GeneChip arrays were washed on Affymetrix Fluidics Station 450 using manufacturer’s recommended scripts and scanned on Affymetrix GeneChip scanner 3000. Data were collected using Affymetrix AGCC software.

data_processing: The obtained .cel files were processed and normalized by RMA (robust multi-chip average). Principle component analysis (PCA) was plotted (Figure S7A) by using the first two principle components based on 45,048 probes with excluding affymetrix control probes on mouse 430 2.0 array. 9,070 probes out of the total 45,048 probes on the chip were obtained by filtering with coefficient of variation greater than 8%. After standardization (mean as 0 and standard deviation as 1), the data was subjected to two-dimensional unsupervised hierarchical clustering with agglomerative approach using Pearson correlation coefficient as similarity metric by avearge linkage (Figure S7B). Both clustering and PCA analysis were done within partek genomic suite (www.partek.com).

source_name: ovarian tumor

label_protocol: RNA (10 ng) was amplified and labeled with Ovation Whole Blood Solution kit (Nugen) following manufacturer’s protocol.

extract_protocol: Total RNA was isolated from flash frozen tumor pieces using TRIZOL reagent (Invitrogen) according the manufacturer’s protocol with the modification of binding the precipitated RNA on RNAeasy column (Qiagen) for consequent washing and elution. For control RNA, frozen 10 μm ovary sections were stained with Methylgreen (Vector Laboratories) containing RNAProtect (Sigma) for 20 seconds, followed by dehydration in 100% ethanol and xylene. Ovarian surface epithelial cells were microdissected from frozen sections using PixCell IIe laser capture microdissection instrument (Arcturus). Targets of ovarian epithelium collected from 20 sections were combined for a single RNA extraction as lysates. RNA was isolated by AllPrep RNA/DNA extraction kit (Qiagen) with the protocol for simultaneous recovery of small and large RNAs. RNA quality was assayed with an Agilent Bioanalyzer. All samples used for microarray analysis had high quality score (RIN >9).

tag: strain background

value: FVB/NJ

value: ovarian tumor


title: brain tissue sample, mutant mice, biological replica 3


title: Th2-4th (control siRNA)

description: Gene expression data from mock-transfected Th2-4th cells

source_name: Four-week cultured Th2 cells generated from primary splenic CD4 T cells

growth_protocol: Splenic CD4 T cells were stimulated under Th2 culture conditions for 5 days in vitro. The Th2 cells were further cultured in vitro for another 2 days in the absence of any exogenous cytokines. The cultured CD4 T cells were then restimulated with immobilized anti-TCR mAbs with IL-2 and anti-IL-4 mAbs for 5 days. This cycle was repeated three times. (Th2-4th cells)

treatment_protocol: Th2-4th cells were collected and treated with control siRNA (AM4635; Applied Biosystems) or Gata3 siRNA (s66482; Applied Biosystems) using the Mouse T cell Nucleofector Kit (Amaxa) according to the manufacturer's protocol. Mock- or Gata3 siRNA-transfected Th2-4th cells were harvested after 24hrs, and stimulated with or without immobilized anti-TCR mAb (H57－597; 3 mg/ml) for 4hrs. Then cells were collected and resuspendet in the Trizol solution (GibcoBRL).


title: muscle Vastus Lateralis, mutant mice, biological replica 3

description: Gene Expression data from m.VastusLateralis, mutant mice with PWS-IC del

value: skeletal muscle (Vastus Lateralis)


title: Th2-4th (control siRNA) a-TCR stim

description: Gene expression data from mock-transfected Th2-4th cells stimulated with anti-TCR mAb for 4hrs


title: muscle Vastus Lateralis, mutant mice, biological replica 2


title: ptc6 + Rapamycin vs ptc6 – Rapamycin_Exp_2

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

description: Spots with either a diameter smaller than 120 microm, or fluorescence intensity for Cy3 and Cy5 lower than 150 units, were not considered for further analysis.

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42 ºC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 microl of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five microg of salmon sperm DNA was added to the mix before denaturation for 3 min at 95 ºC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42 ºC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 microm. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

data_processing:
The GEPAS v4.0 package (http://www.gepas.org/, now a part of the Babelomics 4 project) was used to process the data: the "Preprocessing" tool was used to merge replicates and give the average value.
The normalization method we used to generate the data reported in the VALUE columns was the ratio of means for the non-flagged genes. Spots with saturated values were excluded from the normalization process.

organism: Saccharomyces cerevisiae

source_name: ptc6 mutant cells treated with Rapamycin

label_protocol: Fluorescent labeled cDNA was prepared from 8 microg of purified total RNA by the indirect dUTP-labeling method, using the CyScribe post-labeling kit (GE Healthcare)

growth_protocol: Thirty ml of yeast culture were grown at 28 ºC in YPD rich medium, harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 ºC until RNA purification

extract_protocol: Total RNA was purified using the Ambion RiboPure™-Yeast Total RNA Isolation Kit.

treatment_protocol: A 60 ml cell culture at OD660=0.5 was split in two halves. To obtain the "Channel 1" sample, one of the 30 ml aliquots was treated with 200 ng/ml of Rapamycin for one hour.

value: ptc6 mutant

tag: treated with

value: 200 ng/ml of Rapamycin for 1hr

source_name: Mock-treated ptc6 mutant cells

treatment_protocol: A 60 ml cell culture at OD660=0.5 was split in two halves. To obtain the "Channel 2" sample, one of the 30 ml aliquots was mock-treated for one hour.

tag: sample type

value: mock-treated control


title: muscle Vastus Lateralis, mutant mice, biological replica 1


title: brain tissue sample, wild type mice, biological replica 4

description: Gene Expression data from brain tissue, wild type mice

source_name: wild-type control

value: wild-type


title: ptc1 ptc6 + Rapamycin vs ptc1 ptc6 – Rapamycin_Exp_2

source_name: ptc1 ptc6 double mutant cells treated with Rapamycin

value: ptc1 ptc6 double mutant

source_name: Mock-treated ptc1 ptc6 double mutant cells

extract_protocol: Total RNA was purified using the Ambion RiboPure™-Yeast Total RNA Isolation Kit


title: Th2-4th (Gata3 siRNA) a-TCR stim

description: Gene expression data from Gata3 siRNA-transfected Th2-4th cells stimulated with anti-TCR mAb for 4hrs

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


title: brain tissue sample, wild type mice, biological replica 2


title: brain tissue sample, mutant mice, biological replica 1


title: Normal MSC early passage, biological rep2

value: normal


title: brain tissue sample, wild type mice, biological replica 1


title: ptc6 + Rapamycin vs ptc6 – Rapamycin_Exp_1


title: muscle Vastus Lateralis, wild type mice, biological replica 4

description: Gene Expression data from m.VastusLateralis, wild type mice


title: brain tissue sample, wild type mice, biological replica 3


title: muscle Vastus Lateralis, wild type mice, biological replica 1


title: wt + Rapamycin vs wt – Rapamycin_Exp_1

source_name: wt cells treated with Rapamycin

treatment_protocol: A 60 ml cell culture at OD660=0.5 was split in two halves. To obtain the Channel 1 sample, one of the 30 ml aliquots was treated with 200 ng/ml of Rapamycin for one hour.

value: wild type

source_name: Mock-treated cells.

treatment_protocol: A 60 ml cell culture at OD660=0.5 was split in two halves. To obtain the Channel 2 sample, one of the 30 ml aliquots was mock-treated for one hour.


title: wt + Rapamycin vs wt – Rapamycin_Exp_2


title: muscle Vastus Lateralis, wild type mice, biological replica 2


title: muscle Vastus Lateralis, wild type mice, biological replica 3


title: ptc1 ptc6 + Rapamycin vs ptc1 ptc6 – Rapamycin_Exp_1


title: ptc1 ptc6 vs wt_ Exp_1

source_name: ptc1 ptc6 mutant strain in log phase culture

growth_protocol: Cells were grown at 28 ºC in YPD rich medium until OD660=0.6-0.7. Thirty ml of yeast culture was harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 ºC until RNA purification.

treatment_protocol: Untreated cells

value: ptc1::NAT ptc6::kanMX4 (ptc1ptc6 double mutant)

source_name: wt strain in log phase culture


title: ptc1 ptc6 vs wt_ Exp_2

growth_protocol: Cells were grown at 28 ºC in YPD rich medium until OD660=0.6-0.7. Thirty ml of yeast culture was harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 ºC until RNA purification


title: ptc1 ptc6 vs wt_ Exp_4


title: ptc1 ptc6 vs wt_ Exp_3


title: ptc6 vs wt_ Exp_6

source_name: ptc6 mutant strain in log phase culture

value: ptc6::kanMX4 (ptc6 mutant)


title: ptc6 vs wt_ Exp_2


title: ptc6 vs wt_ Exp_1


title: ptc6 vs wt_ Exp_5


title: 99T_mRNA

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

institute: IOR

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files and provided as an Excel spreadsheet. The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using quantile normalization.
Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system.

source_name: Breast tissue

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol by the Ohio State Microarray Core Facility

extract_protocol: RNA was isolated from FFPE tissue using Recover ALL kit (Ambion)

value: Breast

tag: status

value: primary triple negative cancer

value: Female

tag: age at diagnosis

tag: best stage

tag: grade


title: 98T_mRNA

tag: tissue

tag: gender


title: p53KO_saline_0h_rep4

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression in p53-deficient lung at baseline.

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

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

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: p53-null lung

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

extract_protocol: Whole lung was collected and flash frozen in liquid nitrogen. Total lung RNA was isolated using the Qiagen RNeasy kit following the manufacturer's recommendations.

treatment_protocol: 8-week-old male mice received aerosolized saline for 30 min prior to collection of lung for RNA processing.

tag: strain/background

tag: genotype

value: p53 null

value: lung

tag: age

value: 8 weeks

value: male

tag: treatment

value: saline


title: p53KO_saline_0h_rep2


title: p53KO_saline_0h_rep1


title: p53KO_saline_0h_rep3


title: p53KO_saline_0h_rep5


title: C57_saline_0h_rep3

description: Gene expression in WT lung at baseline.

source_name: wild type lung


title: 97T_mRNA


title: C57_saline_0h_rep5

description: Gene expression in WT lung at baseline.


title: C57_saline_0h_rep4

description: Gene expression in WT lung at baseline.


title: 96T_mRNA


title: C57_saline_0h_rep2

description: Gene expression in WT lung at baseline.


title: 94T_mRNA


title: 93T_mRNA


title: 91T A4_mRNA


title: 91T B3_mRNA


title: 9T_mRNA


title: C57_saline_0h_rep1

description: Gene expression in WT lung at baseline.


title: 95T_mRNA


title: 87T_mRNA


title: 88T_mRNA


title: 86T_mRNA


title: 8T_mRNA


title: 82T_mRNA


title: 79T_mRNA


title: 75T_mRNA


title: 73T_mRNA


title: 7T_mRNA


title: 89T_mRNA


title: 72T_mRNA


title: 69T_mRNA


title: 68T_mRNA


title: 66T_mRNA


title: 67T_mRNA


title: 65T_mRNA


title: WT_SCC_expression_no_Doxo_1_(422108)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Expression profiling of wild-type SCC cells without doxorubicin treatment.

hyb_protocol: Standard NimbleGen protocol

scan_protocol: Standard NimbleGen protocol

data_processing: RMA normalization by NimbleGen. Gene RMA calls calculated from 8 samples per gene by NimbleGen are included as a supplementary file.

label_protocol: Standard NimbleGen protocol

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit.

tag: cell type

value: squamous cell carcinoma

tag: genotype/variation


title: 64T_mRNA


title: 76T_mRNA


title: 71T_mRNA


title: CTL, biological replicate 1

source_name: liver of not-injected mouse, control

value: 1 month

value: liver

value: not injected


title: 62T_mRNA


title: WT_SCC_expression_Doxo_2_(422156)

description: Expression profiling of wild-type SCC cells after 18 hours of doxorubicin treatment.

value: wild-type


title: 60T_mRNA


title: WT_SCC_expression_Doxo_1_(422155)


title: p53_SCC_expression_Doxo_2_(422230)

description: Expression profiling of p53 -/- SCC cells after 18 hours of doxorubicin treatment.


title: p53_SCC_expression_Doxo_1_(422229)


title: WT_SCC_expression_no_Doxo_2_(422153)


title: 63T_mRNA


title: p53_SCC_expression_no_Doxo_1_(422157)

description: Expression profiling of p53 -/- SCC cells without doxorubicin treatment.


title: 61T_mRNA


title: p53_SCC_expression_no_Doxo_2_(422225)


title: 51T_mRNA


title: 59T_mRNA


title: 55T_mRNA


title: 58T_mRNA


title: 52T_mRNA


title: 5T_mRNA


title: 50T_mRNA


title: 49T_mRNA


title: 57T_mRNA


title: 54T_mRNA


title: 46T_mRNA


title: 45T_mRNA


title: 48T_mRNA


title: 47T_mRNA


title: 80T_mRNA


title: 53T_mRNA


title: 43T_mRNA


title: 42T_mRNA


title: 39T_mRNA


title: 35T_mRNA


title: 38T_mRNA


title: 44T_mRNA


title: 32T_mRNA


title: 28T_mRNA


title: 33T_mRNA


title: 36T_mRNA


title: 30T_mRNA


title: 22T_mRNA


title: 3T_mRNA


title: 37T_mRNA


title: 197T_mRNA


title: 196T_mRNA


title: 31T_mRNA


title: 26T_mRNA


title: 23T_mRNA


title: 24T_mRNA


title: 198T_mRNA


title: 195T_mRNA


title: 192T_mRNA


title: 193T_mRNA


title: 34T_mRNA


title: 191T_mRNA


title: 190T_mRNA


title: 20T_mRNA


title: WT_SCC_CATCH-IT_Met_(438028_2)

description: Negative control of CATCH-IT profiling of wild-type SCC cells in methionine.

data_processing: The dye-bias correction of Peng, et al (PMID PMC1913544) was applied to bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 computedby NimbleGen. The supplementary gff and wig files contain the bi-weight mean adjusted log base 2 ratios in MM9 coordinates.

extract_protocol: CATCH-IT was performed as previously described (PMID: 20508129) with some modifications. Briefly, tissue culture medium was replaced with DMEM media without methionine (Invitrogen Cat# 21013-024) supplemented with 1X glutamine, 0.2 mM L-cystine, 10% FBS, and 1% penicillin-streptomycin, and cells were grown at 37C for starvation fro 30 minutes, followed by 30 minutes incubation at 37C with 4 mM azidohomoalanine (Anaspec Cat# 63669) added to the media. Cells were then harvested, washed with 1X PBS, and resuspended in ice-cold TM2 buffer (10 mM Tris, pH=7.5, 2mM MgCl2). Cells were lysed using 0.2% of NP-40 and nuclei were isolated, followed by digestion of micrococcal nuclease for 10 minutes to produce mostly mononucleosomes. Biotin coupling, chrmatin extraction, streptavidin pulldown, urea wash, and DNA isolation were then performed as previously described.

source_name: Input


title: 187T_mRNA


title: 19T_mRNA


title: 189T_mRNA


title: 183T_mRNA


title: WT_SCC_CATCH-IT_Aha_(446572_2)

description: CATCH-IT profiling of wild-type SCC cells in azidohomoalanine.


title: 182T_mRNA


title: 179T_mRNA


title: 18T_mRNA


title: 178T_mRNA


title: 180T_mRNA


title: 181T_mRNA


title: 172T_mRNA


title: 177T_mRNA


title: 175T_mRNA


title: 171T_mRNA


title: 174T_mRNA


title: 176T_mRNA


title: 168T_mRNA


title: 167T_mRNA


title: 166T_mRNA


title: 170T_mRNA


title: 163T_mRNA


title: 17T_mRNA


title: 165T_mRNA


title: 154T_mRNA


title: 56T_mRNA


title: 157T_mRNA


title: 160T_mRNA


title: 158T_mRNA


title: 151T_mRNA


title: 155T_mRNA


title: 152T_mRNA


title: 162T_mRNA


title: 16T_mRNA


title: 15T_mRNA


title: 149T_mRNA


title: 147T_mRNA


title: 150T_mRNA


title: 144T_mRNA


title: 161T_mRNA


title: 145T_mRNA


title: 143T_mRNA


title: 141T_mRNA


title: 142T_mRNA


title: 140T_mRNA


title: 138T_mRNA


title: 136T_mRNA


title: 135T_mRNA


title: 14T_mRNA


title: 137T_mRNA