title: d/d-10w-sa, biological rep2


title: RNA-UPPP-24

status: Public on Jan 01 2013

type: RNA

city: Baltimore

first: Michael

middle: F

last: Ochs

state: MD

address: 550 North Broadway, Ste 1103

department: Oncology Biostatistics

country: USA

institute: Johns Hopkins University

description:
Sample name: 27933
PHen-HNC-27933-1a-hsExon1_(HuEx-1_0-st-v2).CEL

hyb_protocol: The labeled sense strand DNA was hybridized to the Affymetrix GeneChip human Exon 1.0 ST arrays for 17hr at 45 C with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cDNA.  The staining was further amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 3.4 (AGCC v3.4) software from Affymetrix.

data_processing:
Analysis was performed in R with the oligo package, RMA was used for normalization at both exon and gene levels
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na30.hg19.transcript.csv

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Ctrl 124

label_protocol: RNA from control and experimental samples were labeled using the Whole Transcript Sense Target Labeling protocol described by Affymetrix and reagent from Ambion and Affymetrix. Briefly, 100ng of total RNA was used to synthesize first strand cDNA using random oligonucleotides with T7 promoter as primer and the SuperScript Choice System (Invitrogen, Carlsbad, California).  Following the double stranded cDNA synthesis, the double strand cDNA was purified using magnetic beads, and cRNA was generated through in vitro transcription.  10 ug of cRNA was then used to generate sense strand cDNA using random primer, dNTP-dUTP mix, and Superscript II reverse transcriptase (Invitrogen, Carlsbad, California).  The resulting sense strand cDNA was then purified, fragmented using UDG and APE at 37C for 60 minutes, and terminal labeled with biotinylated nucleotide and terminal DNA transferase at 37C for 60 minutes.

growth_protocol: human HNSCC and UPPP surgical samples

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

treatment_protocol: human surgical specimens, flash frozen

tag: sample identifier

value: Ctrl 124

tag: sample type

value: normal

tag: disease state

value: control (UPPP)


title: testis_Sgms1_rep3

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description:
SAMPLE 7
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

organism: Mus musculus

source_name: testis

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: strain

tag: tissue

value: testis

tag: genotype/variation

value: Sgms1 mutant

tag: age

value: 27 weeks

tag: mouse id


title: RNA-UPPP-21

description:
Sample name: 27910
PHen-HNC-27910-1a-hsExon1_(HuEx-1_0-st-v2)_2.CEL

source_name: Ctrl 121

value: Ctrl 121


title: AML [2542_19jun08]

city: Rotterdam

middle: van

last: Vliet

address: Lichtenauerlaan 40

department: Bioinformatics

country: Netherlands

institute: SkylineDx

description: Not Applicable

hyb_protocol: As described in the AMLprofiler IFU (instructions for use), Hybridized for 17 hours, 45C at 60 rpm in Affymetrix Hybridization oven

scan_protocol: As described in the AMLprofiler IFU (instructions for use) on an Affymetrix GeneChip System 3000Dx v.2

data_processing: DM algorithm implemented in the Affymetrix Power Tools (APT 1.10.2).

label: Biotin

source_name: AML

label_protocol: We used 10 µg of total RNA to prepare antisense biotinylated RNA. Single-stranded complementary DNA (cDNA) and double-stranded cDNA were synthesized according to the manufacturer’s protocol (Invitrogen Life Technologies) with the use of the T7-(deoxythymidine)24-primer (Genset). In vitro transcription was performed with biotin-11-cytidine triphosphate and biotin-16-uridine triphosphate (Perkin–Elmer) and the MEGAScript T7 labeling kit (Ambion). Double-stranded cDNA and complementary RNA (cRNA) were purified and fragmented with the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: Not Applicable

extract_protocol: After thawing, cells were washed once with Hanks’balanced-salt solution. High-quality total RNA was extracted by lysis with guanidinium thiocyanate followed by cesium chloride–gradient purification. RNA levels, quality, and purity were assessed with the use of the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent). None of the samples showed RNA degradation (ratio of 28S ribosomal RNA to 18S ribosomal RNA of at least 2) or contamination by DNA.

treatment_protocol: Not Applicable

tag: cohort

value: Training

tag: npm1 status

value: NPM1 wt


title: AML [2543_18apr08]

description: Not Applicable


title: d/d-10w-sa, biological rep3

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were imported into Affymetrix Expression Console Software, and CHP files were generated.

source_name: Hippocampus of d/d mouse treatment with Kainate acid

label_protocol: The Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) were used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: Each mouse was maintained in SPF condition and sacrificed at 14 months of age.

extract_protocol: Total RNA was isolated using a combination of Isogen (Nippon Gene) and the RNeasy Mini Kit (Qiagen), according to the manufacturers’ instructions.

treatment_protocol: Brains were removed from each mouse under pentobarbital anesthesia (i.p), with perfusion of 40 ml of saline via the left ventricle. Hippocampi were isolated and preserved at –80°C until RNA preparation.

value: Hippocampus

tag: genotype

value: d/d (lacking FosB protein)

value: 10 weeks

tag: Sex

value: female

tag: treatment

value: saline


title: RNA-UPPP-20

description:
Sample name: 27903
PHen-HNC-27903-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 120

value: Ctrl 120


title: testis_Sgms1_rep2

description:
SAMPLE 6
replicate 2


title: G/G-10w-sa, biological rep3

source_name: Hippocampus of G/G mouse treatment with saline

value: G/G (fosB-null)


title: RNA-UPPP-19

description:
Sample name: 27929
PHen-HNC-27929-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 119

value: Ctrl 119


title: G/G-10w-sa, biological rep2


title: AML [2541_04jun08]

description: Not Applicable


title: AML [2525_17jun08]

description: Not Applicable

value: NPM1 A


title: AML [2535_16may08]

description: Not Applicable


title: AML [2534_03jun08]

description: Not Applicable


title: H3R17ME2-array4

type: genomic

city: Chicago

first: Jie

last: Zhou

state: ILLINOIS

address: 900 East 57th Street, KCBD 10100

institute: University of Chicago IGSB

description:
control CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
H3R17ME2 ChIP - Array 4

hyb_protocol: According to standard Affymetrix protocols: Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).

data_processing:
Tiling array data were normalized and analyzed as described (Hua et al, 2009). Briefly, raw data were normalized within ChIP and control groups and for each genomic position a local dataset composed of intensities for all adjacent probes within a window of +/-250 bp was generated. A one-tailed Wilcoxon Rank Sum test was then applied to compare control and ChIP experiments and was performed in a sliding window across all tiled genomic regions. Significantly enriched probes (p < 1e-3) were locally extended by merging adjacent enriched probes within 100 bp and these merged regions were defined as transcription factor bound regions.
results file descriptions: Bed files for enriched ChIP sites of each of 6 chromatins marks.

molecule: genomic DNA

source_name: H3R17ME2 ChIP

label_protocol: ChIPed DNA was amplified using linker-mediated PCR amplification method. 2mM dUTP was added to the 10mM dNTP mix during the amplification.

growth_protocol: MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.

extract_protocol: According to the standard chromatin extraction protocol (see Sujun et al, 2009).

treatment_protocol: MCF7 Cells were grown in growing in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml),  until 80% confluence. ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.

tag: cell type

value: MCF7 cells

tag: chromatin mark

tag: antibody vendor

value: abcam

tag: antibody catalog #

source_name: Input DNA


title: RNA-UPPP-18

description:
Sample name: 26383
PHen-HNC-26383-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 118

tag: sample identifier

value: Ctrl 118

value: normal

value: control (UPPP)


title: RNA-UPPP-17

description:
Sample name: 27927
PHen-HNC-27927-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 117

value: Ctrl 117

tag: sample type


title: wt-10w-sa, biological rep3

source_name: Hippocampus of wt mouse treatment with saline

value: wild type


title: testis_Sgms1_rep1

description:
SAMPLE 5
replicate 1

value: testis

value: Sgms1 mutant

value: 27 weeks


title: G/G-10w-sa, biological rep1

value: Hippocampus

value: 10 weeks


title: testis_wt_rep2

description:
SAMPLE 2
replicate 2

value: wt


title: testis_wt_rep4

description:
SAMPLE 4
replicate 4


title: testis_wt_rep1

description:
SAMPLE 1
replicate 1


title: d/d-aged-non, biological rep2

source_name: Hippocampus of d/d aged mouse

value: d/d (lacking FosB protein)

value: 64.7 weeks

value: female

tag: epilepsy status

value: non


title: RNA-UPPP-16

description:
Sample name: 27953
PHen-HNC-27953-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 116

value: Ctrl 116

tag: disease state


title: wt-10w-sa, biological rep1

tag: tissue

tag: strain

value: saline


title: wt-10w-sa, biological rep2

tag: age


title: testis_wt_rep3

description:
SAMPLE 3
replicate 3

tag: genotype/variation

tag: mouse id


title: H3K4triM_E-array4

description:
control CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
H3K4triM_E ChIP - Array 4

scan_protocol: According to standard Affymetrix protocols: Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).

source_name: H3K4triM_E ChIP

value: MCF7 cells

value: abcam


title: RNA-UPPP-15

description:
Sample name: 27916
PHen-HNC-27916-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 115

value: Ctrl 115

value: normal

value: control (UPPP)


title: RNA-UPPP-13

description:
Sample name: 25343
PHen-HNC-25343-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 113

value: Ctrl 113


title: AML [2516_13jun08]

description: Not Applicable

tag: cohort

value: Training

tag: npm1 status

value: NPM1 wt


title: RNA-UPPP-14

description:
Sample name: 27909
PHen-HNC-27909-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 114

value: Ctrl 114


title: AML [2514_27may08]

description: Not Applicable


title: d/d-aged-non, biological rep1

value: Hippocampus

tag: genotype

value: 70 weeks

tag: Sex


title: G/G-aged-non, biological rep1

source_name: Hippocampus of G/G aged mouse without epilepsy

value: G/G (fosB-null)

value: 71 weeks


title: AML [2511_16may08]

description: Not Applicable

source_name: AML


title: G/G-aged-non, biological rep2

value: female


title: RNA-UPPP-12

description:
Sample name: 25335
PHen-HNC-25335-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 112

value: Ctrl 112


title: AML [2510_5jun08]

description: Not Applicable


title: AML [2524_10jun08]

description: Not Applicable

value: NPM1 A


title: RNA-UPPP-10

description:
Sample name: 25341
PHen-HNC-25341-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 110

value: Ctrl 110


title: H3K4mM-array4

description:
control CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
H3K4mM ChIP - Array 4

source_name: H3K4mM ChIP

tag: cell type

value: MCF7 cells


title: RNA-UPPP-11

description:
Sample name: 25305
PHen-HNC-25305-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 111

value: Ctrl 111


title: H3K27triM-array4

description:
control CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
H3K27triM ChIP - Array 4

source_name: H3K27triM ChIP

tag: chromatin mark

value: Upstate


title: FAIRE-array4

description:
control CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
FAIRE ChIP - Array 4

source_name: FAIRE ChIP

value: FAIRE

tag: antibody vendor

source_name: Input DNA


title: H2AZ_Ace-array4

description:
control CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
H2AZ_Ace ChIP - Array 4

source_name: H2AZ_Ace ChIP

value: Abcam

tag: antibody catalog #


title: XBP1-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
XBP1 ChIP - Array 4

data_processing: Tiling array data were normalized and analyzed as described (Hua et al, 2009). Briefly, raw data were normalized within ChIP and control groups and for each genomic position a local dataset composed of intensities for all adjacent probes within a window of +/-250 bp was generated. A one-tailed Wilcoxon Rank Sum test was then applied to compare control and ChIP experiments and was performed in a sliding window across all tiled genomic regions. Significantly enriched probes (p < 1e-3) were locally extended by merging adjacent enriched probes within 100 bp and these merged regions were defined as transcription factor bound regions. Peaks located in the BAC regions, overlaps with GFP peaks, and overlaps with repetitive regions in the genome are filtered.

source_name: XBP1 ChIP

growth_protocol:
MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.
For each NR with known ligand, MCF7 Cells were hormone-deprived for 3 days and then were treated with 100 nM NR ligand at 80% confluence. ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine. For orphan NRs and NR-cofactors, no ligand was used and ChIP was performed with cells growing in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml).

extract_protocol: ChIPed DNA was amplified using linker-mediated PCR amplification method. 2mM dUTP was added to the 10mM dNTP mix during the amplification.

treatment_protocol: According to the standard chromatin extraction protocol (Shang et al., 2000).

value: transgenic MCF7

tag: transcription factor

tag: tag

value: modified LAP (localization and affinity purification) tag containing GFP

tag: chip antibody

value: Goat anti-GFP


title: G/G-aged-epi, biological rep3

source_name: Hippocampus of G/G aged mouse with epilepsy

value: 69 weeks

tag: epilepsy status

value: epilepsy


title: VDR-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
VDR ChIP - Array 4

source_name: VDR ChIP

value: VDR


title: NR2C2-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
NR2C2 ChIP - Array 4

source_name: NR2C2 ChIP


title: AML [2498_22apr08]

description: Not Applicable

value: Training

value: NPM1 wt


title: RNA-UPPP-08

description:
Sample name: 26855
PHen-HNC-26855-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 108

tag: sample identifier

value: Ctrl 108

tag: sample type

value: normal

tag: disease state

value: control (UPPP)


title: G/G-aged-epi, biological rep2

tag: tissue

value: Hippocampus

tag: strain

value: G/G (fosB-null)

tag: age

value: 69.6 weeks

value: female


title: AML [2497_22may08]

description: Not Applicable

tag: cohort

tag: npm1 status


title: NR2C1-S-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
NR2C1-S ChIP - Array 4

source_name: NR2C1-S ChIP


title: AML [2490_11jun08]

description: Not Applicable

value: NPM1 B


title: RNA-UPPP-09

description:
Sample name: 25319
PHen-HNC-25319-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 109

value: Ctrl 109


title: AML [2509_5jun08]

description: Not Applicable


title: RNA-UPPP-07

description:
Sample name: 26315
PHen-HNC-26315-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 107

value: Ctrl 107


title: AML [2480_18jun08]

description: Not Applicable

source_name: AML


title: G/G-aged-epi, biological rep1

tag: genotype

value: 71 weeks

tag: Sex


title: wt-aged-non, biological rep3

source_name: Hippocampus of wt aged mouse

value: wild type

value: 70.3 weeks

value: non


title: NR2C1-L-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
NR2C1-L ChIP - Array 4

source_name: NR2C1-L ChIP

tag: cell type

value: transgenic MCF7

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP


title: RNA-UPPP-06

description:
Sample name: 26845
PHen-HNC-26845-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 106

value: Ctrl 106


title: AML [2507_27may08]

description: Not Applicable

value: Training

value: NPM1 A


title: THRA-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
THRA ChIP - Array 4

source_name: THRA ChIP

value: THRA


title: AML [2468_9may08]

description: Not Applicable

value: NPM1 wt


title: RNA-UPPP-05

description:
Sample name: 26860
PHen-HNC-26860-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 105

value: Ctrl 105

value: normal

value: control (UPPP)


title: AML [2467_18jun08]

description: Not Applicable


title: RNA-UPPP-04

description:
Sample name: 25475
PHen-HNC-25475-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 104

value: Ctrl 104


title: wt-aged-non, biological rep1

value: Hippocampus

value: female


title: SPDEF-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
SPDEF ChIP - Array 4

source_name: SPDEF ChIP

value: SPDEF

source_name: Input DNA


title: wt-aged-non, biological rep2

value: wild type

value: 68.7 weeks


title: RNA-UPPP-03

description:
Sample name: 25496
PHen-HNC-25496-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 103

value: Ctrl 103


title: RXRB-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
RXRB ChIP - Array 4

source_name: RXRB ChIP

value: transgenic MCF7

value: RXRB

value: modified LAP (localization and affinity purification) tag containing GFP


title: AML [2466_13jun08]

description: Not Applicable

value: Training


title: RNA-UPPP-02

description:
Sample name: 26342
PHen-HNC-26342-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 102

value: Ctrl 102


title: T-Cre conditional Tbx1 heterozygous control periotic tissue at E12.5, biological replicate 5

city: Bronx

first: Tingwei

last: Guo

state: NY

address: 1301 Morris Park Avenue, Room 408

department: Genetics

institute: Albert Einstein College of Medicine

description:
Control5
Gene expression data from early stage of auditory and vestibular system specification (E12.5).

hyb_protocol: 10ug of cRNA was hybridized for 16hrs at 45C on Affymetrix Mouse Gene ST 1.0 arrays.

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

data_processing: Data was analyzed by RMA using Affymetrix Expression Console software version 1.1 using Affymetrix default protocols.

source_name: E12.5 periotic tissue, T-Cre conditional Tbx1 heterozygous control

label_protocol: Biotinylated cRNA was prepared according to Affymetrix protocols from 300ng of total RNA.

growth_protocol: Timed matings were dissected at embryonic day 12.5, and periotic tissue was isolated and immediately processed for RNA isolation. Embryos were dissected and microdissected in cold PBS.

extract_protocol: Qiagen RNeasy Micro kit according to the manufacturer's protocol.

value: T-Cre conditional Tbx1 heterozygote

value: microdissected periotic tissue


title: RXRA-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
RXRA ChIP - Array 4

source_name: RXRA ChIP

value: RXRA

value: Goat anti-GFP


title: RORC-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
RORC ChIP - Array 4

source_name: RORC ChIP

value: RORC


title: AML [2326_29may08]

description: Not Applicable

value: NPM1 A


title: AML [2327_29apr08]

description: Not Applicable

value: NPM1 wt


title: RNA-HNSCC-50

description:
Sample name: 27867
PHen-HNC-27867-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 50

value: Pt 50

value: tumor

value: HNSCC


title: T-Cre conditional Tbx1 heterozygous control periotic tissue at E12.5, biological replicate 3

description:
Control3
Gene expression data from early stage of auditory and vestibular system specification (E12.5).


title: AML [2306_16may08]

description: Not Applicable


title: T-Cre conditional Tbx1 heterozygous control periotic tissue at E12.5, biological replicate 4

description:
Control4
Gene expression data from early stage of auditory and vestibular system specification (E12.5).


title: RNA-UPPP-01

description:
Sample name: 25498
PHen-HNC-25498-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 101

value: Ctrl 101

value: normal

value: control (UPPP)


title: PPARG-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
PPARG ChIP - Array 4

source_name: PPARG ChIP

value: transgenic MCF7

value: PPARG


title: AML [2305_5jun08]

description: Not Applicable

source_name: AML

value: Training


title: RNA-HNSCC-46

description:
Sample name: 27893
PHen-HNC-27893-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 46

value: Pt 46


title: T-Cre conditional Tbx1 heterozygous control periotic tissue at E12.5, biological replicate 2

description:
Control2
Gene expression data from early stage of auditory and vestibular system specification (E12.5).

value: T-Cre conditional Tbx1 heterozygote


title: T-Cre conditional Tbx1 heterozygous control periotic tissue at E12.5, biological replicate 1

description:
Control1
Gene expression data from early stage of auditory and vestibular system specification (E12.5).

value: microdissected periotic tissue


title: T-Cre conditional Tbx1 knockout periotic tissue at E12.5, biological replicate 4

description:
MestKO4
Gene expression data from early stage of auditory and vestibular system specification (E12.5).

source_name: E12.5 periotic tissue, T-Cre conditional Tbx1 knockout

value: T-Cre conditional Tbx1 knockout


title: T-Cre conditional Tbx1 knockout periotic tissue at E12.5, biological replicate 5

description:
MestKO5
Gene expression data from early stage of auditory and vestibular system specification (E12.5).


title: RNA-HNSCC-49

description:
Sample name: 25024
PHen-HNC-25024-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 49

value: Pt 49


title: RNA-HNSCC-48

description:
Sample name: 25240
PHen-HNC-25240-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 48

value: Pt 48


title: T-Cre conditional Tbx1 knockout periotic tissue at E12.5, biological replicate 3

description:
MestKO3
Gene expression data from early stage of auditory and vestibular system specification (E12.5).


title: RNA-HNSCC-45

description:
Sample name: 27939
PHen-HNC-27939-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 45

value: Pt 45


title: RORA-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
RORA ChIP - Array 4

source_name: RORA ChIP

value: RORA

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP


title: AML [2304_10jun08]

description: Not Applicable

value: NPM1 wt


title: PPARD-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
PPARD ChIP - Array 4

source_name: PPARD ChIP

value: PPARD

source_name: Input DNA


title: PPARA-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
PPARA ChIP - Array 4

source_name: PPARA ChIP

value: PPARA


title: AML [2302_18apr08]

description: Not Applicable


title: AML [2300_04jun08]

description: Not Applicable

value: NPM1 A


title: RNA-HNSCC-44

description:
Sample name: 27955
PHen-HNC-27955-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 44

value: Pt 44

value: tumor

value: HNSCC


title: NR4A2-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
NURR1 ChIP - Array 4

source_name: NR4A2 ChIP

value: transgenic MCF7


title: AML [2299_25apr08]

description: Not Applicable

value: Training

value: NPM1 D


title: AML [2297_16may08]

description: Not Applicable


title: AML [2301_18jun08]

description: Not Applicable


title: PGR-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
NR3C1 ChIP - Array 4

source_name: PGR ChIP

value: PGR


title: RNA-HNSCC-42

description:
Sample name: 25016
PHen-HNC-25016-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 42

value: Pt 42


title: RNA-HNSCC-40

description:
Sample name: 25218
PHen-HNC-25218-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 40

value: Pt 40


title: NR2F2-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
NR2F2 ChIP - Array 4

source_name: NR2F2 ChIP


title: T-Cre conditional Tbx1 knockout periotic tissue at E12.5, biological replicate 2

description:
MestKO2
Gene expression data from early stage of auditory and vestibular system specification (E12.5).

value: T-Cre conditional Tbx1 knockout

value: microdissected periotic tissue


title: NR4A1-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
NR4A1 ChIP - Array 4

source_name: NR4A1 ChIP

value: modified LAP (localization and affinity purification) tag containing GFP


title: NR2F1-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
NR2F1 ChIP - Array 4

source_name: NR2F1 ChIP

value: Goat anti-GFP


title: AML [2293_04jun08]

description: Not Applicable

source_name: AML

value: NPM1 wt


title: NR1D2-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
NR1D2 ChIP - Array 4

source_name: NR1D2 ChIP


title: RNA-HNSCC-39

description:
Sample name: 27937
PHen-HNC-27937-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 39

value: Pt 39


title: AML [2292_5jun08]

description: Not Applicable


title: AML [2296_14may08]

description: Not Applicable


title: T-Cre conditional Tbx1 knockout periotic tissue at E12.5, biological replicate 1

description:
MestKO1
Gene expression data from early stage of auditory and vestibular system specification (E12.5).

source_name: E12.5 periotic tissue, T-Cre conditional Tbx1 knockout


title: NR1D1-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
NR1D1 ChIP - Array 4

source_name: NR1D1 ChIP


title: RNA-HNSCC-37

description:
Sample name: 25698
PHen-HNC-25698-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 37

value: Pt 37


title: RNA-HNSCC-43

description:
Sample name: 27498
PHen-HNC-27498-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 43

value: Pt 43


title: RNA-HNSCC-36

description:
Sample name: 26111
PHen-HNC-26111-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 36

value: Pt 36


title: AML [2291_12jun08]

description: Not Applicable


title: NIH 3T3_Control_biological rep3

city: Philadelphia

first: Michele

last: Wozniak

state: PA

address: 210 S. 33rd St., 510 Skirkanich

department: Bioengineering

institute: University of Pennsylvania

description: Gene expression data from serum-stimulated NIH 3T3 cells expressing control shRNA plasmid.

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized   for 16 hr at 45 C on Mouse Gene 1.0ST Arrays. GeneChips were   washed and stained in the Affymetrix Fluidics Station 450 .

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

data_processing: The data were analyzed with the RMA algorithm in Expression Console.

source_name: NIH 3T3 cells stably expressing pLKO.1 (control vector) stimulated with serum

label_protocol: Biotinylated cRNA were prepared according to the  standard Affymetrix protocol from 0.1 ug total RNA using the Ambion WT Expression Kit (GeneChip Expression Analysis Technical Manual, www.affymetrix.com).

growth_protocol: Cells were cultured in high-glucose DMEM containing 10% bovine serum.

extract_protocol: Total RNA was extracted using Qiagen RNeasy mini kits according to the manufacturer's instructions.

treatment_protocol: Cells were serum starved overnight (serum-free DMEM), then stimulated with 10% bovine serum for one hour, then lysed.

tag: cell line

value: NIH 3T3 cells

tag: genotype/variation

value: control


title: NIH 3T3_NetKD_biological rep2

description: Gene expression data from serum-stimulated NIH 3T3 cells expressing Net shRNA.

source_name: NIH 3T3 cells stably expressing Net shRNA stimulated with serum

value: Net knockdown


title: NIH 3T3_SapKD_biological rep3

description: Gene expression data from serum-stimulated NIH 3T3 cells expressing Sap-1 shRNA.

source_name: NIH 3T3 cells stably expressing Sap-1 shRNA stimulated with serum

value: Sap-1 knockdown


title: NR1H2-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
NR1H3 ChIP - Array 4

source_name: NR1H3 ChIP

value: transgenic MCF7

tag: transcription factor

source_name: Input DNA


title: RNA-HNSCC-34

description:
Sample name: 25282
PHen-HNC-25282-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 34

value: Pt 34

value: tumor

value: HNSCC


title: NIH 3T3_NetKD_biological rep3


title: AML [2290_25apr08]

description: Not Applicable

value: Training


title: NIH 3T3_SapKD_biological rep2


title: JUND-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
JUND ChIP - Array 4

source_name: JUND ChIP

value: JUND

tag: tag


title: NIH 3T3_SapKD_biological rep1


title: AML [2289_25apr08]

description: Not Applicable


title: NIH 3T3_Control_biological rep2


title: JUNB-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
JUNB ChIP - Array 4

source_name: JUNB ChIP

value: JUNB

value: modified LAP (localization and affinity purification) tag containing GFP

tag: chip antibody


title: AML [2288_22apr08]

description: Not Applicable

value: NPM1 wt


title: AML [2287_9may08]

description: Not Applicable


title: NR3C1-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
NR3C1 ChIP - Array 4

source_name: NR3C1 ChIP

value: Goat anti-GFP


title: RNA-HNSCC-30

description:
Sample name: 27432
PHen-HNC-27432-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 30

value: Pt 30


title: NIH 3T3_Control_biological rep1


title: RNA-HNSCC-29

description:
Sample name: 27484
PHen-HNC-27484-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 29

value: Pt 29


title: AML [2286_22may08]

description: Not Applicable

source_name: AML

value: NPM1 A


title: AML [2284_18jun08]

description: Not Applicable


title: AML [2285_03jun08]

description: Not Applicable


title: RNA-HNSCC-31

description:
Sample name: 26161
PHen-HNC-26161-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 31

value: Pt 31


title: RNA-HNSCC-32

description:
Sample name: 26156
PHen-HNC-26156-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 32

value: Pt 32


title: FOSB-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
FOSB ChIP - Array 4

source_name: FOSB ChIP

value: FOSB


title: NIH 3T3_NetKD_biological rep1

value: NIH 3T3 cells

value: Net knockdown


title: JUN-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
JUN ChIP - Array 4

source_name: JUN ChIP

value: transgenic MCF7

value: JUN


title: RNA-HNSCC-26

description:
Sample name: 27887
PHen-HNC-27887-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 26

value: Pt 26

value: tumor

value: HNSCC


title: AML [2283_27may08]

description: Not Applicable

value: Training


title: RNA-HNSCC-25

description:
Sample name: 28000
PHen-HNC-28000-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 25

value: Pt 25


title: Lamellar_day1_rat12483

city: St. Louis

first: Jennifer

last: McKenzie

state: MO

address: 660 S. Euclid, Box 8233

department: Orthopedic Surgery

institute: Washington University in St. Louis

description: replicate 1

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina BeadStudio software (Illumina Beadscan, v3)

organism: Rattus norvegicus

source_name: Lamellar, day 1

label_protocol: RNA transcripts were amplified by T7 linear amplification (MessageAmp TotalPrep amplification kit; ABI-Ambion

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

value: Fischer 344

value: 5 months

tag: gender

value: male

value: bone - right ulna (central 5 mm)

tag: microarray chip

tag: sentrix position

value: L


title: ELK-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
ELK ChIP - Array 4

source_name: ELK ChIP

value: ELK

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP


title: FOSL1-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
FOSL1 ChIP - Array 4

source_name: FOSL1 ChIP


title: Lamellar_day3_rat12435

description: replicate 1

source_name: Lamellar, day 3

value: J


title: FOSL2-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
FOSL2 ChIP - Array 4

source_name: FOSL2 ChIP

source_name: Input DNA


title: RNA-HNSCC-24

description:
Sample name: 27879
PHen-HNC-27879-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 24

tag: sample identifier

value: Pt 24

tag: sample type

tag: disease state


title: Lamellar_1hr_rat12498

description: replicate 1

source_name: Lamellar, 1 hr

tag: strain

tag: age

tag: tissue

value: H


title: Woven_1hr_rat12505

description: replicate 1

source_name: Woven, 1 hr

value: I


title: Lamellar_day1_rat12467

description: replicate 1

value: K


title: Lamellar_day1_rat12478

description: replicate 1

value: F


title: Woven_day3_rat12480

description: replicate 1

source_name: Woven, day 3

value: E


title: AML [2281_18apr08]

description: Not Applicable

source_name: AML

tag: cohort

value: Training

tag: npm1 status

value: NPM1 wt


title: Lamellar_1hr_rat12485

description: replicate 1

value: Fischer 344

value: G


title: RNA-HNSCC-21

description:
Sample name: 27896
PHen-HNC-27896-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 21

value: Pt 21

value: tumor

value: HNSCC


title: FOS-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
FOS ChIP - Array 4

source_name: FOS ChIP

tag: cell type

value: transgenic MCF7

value: FOS


title: Lamellar_day3_rat12473

description: replicate 1

value: 5 months

value: male

value: bone - right ulna (central 5 mm)

value: D


title: RNA-HNSCC-28

description:
Sample name: 26147
PHen-HNC-26147-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 28

value: Pt 28


title: AML [2280_19jun08]

description: Not Applicable


title: AML [2282_9may08]

description: Not Applicable

value: NPM1 A


title: RNA-HNSCC-22

description:
Sample name: 25531
PHen-HNC-25531-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 22

value: Pt 22


title: ATF1-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
ATF1 ChIP - Array 4

source_name: ATF1 ChIP

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP


title: AML [2279_18jun08]

description: Not Applicable

value: Training

value: NPM1 wt


title: RNA-HNSCC-23

description:
Sample name: 25277
PHen-HNC-25277-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 23

value: Pt 23


title: RNA-HNSCC-20

description:
Sample name: 27315
PHen-HNC-27315-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 20

value: Pt 20


title: Woven_day3_rat12472

description: replicate 1

value: Fischer 344

value: C


title: RNA-HNSCC-19

description:
Sample name: 25167
PHen-HNC-25167-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 19

value: Pt 19

value: tumor

value: HNSCC


title: H3R17ME2-array3

description:
control CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
H3R17ME2 ChIP - Array 3

source_name: H3R17ME2 ChIP

value: MCF7 cells

tag: chromatin mark

tag: antibody vendor

value: abcam

tag: antibody catalog #


title: H3K4triM_E-array3

description:
control CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
H3K4triM_E ChIP - Array 3

source_name: H3K4triM_E ChIP


title: AR-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
AR ChIP - Array 4

source_name: AR ChIP

value: transgenic MCF7

tag: transcription factor

value: AR

tag: tag


title: AML [2278_28may08]

description: Not Applicable

value: NPM1 A


title: Lamellar_1hr_rat12469

description: replicate 1

value: 5 months

tag: gender

value: male

value: bone - right ulna (central 5 mm)

value: B


title: AML [2276_25apr08]

description: Not Applicable

value: Training

value: NPM1 wt


title: RNA-HNSCC-18

description:
Sample name: 27894
PHen-HNC-27894-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 18

value: Pt 18


title: Lamellar_1hr_rat12446

description: replicate 1

value: Fischer 344

tag: microarray chip

value: A


title: H3K4mM-array3

description:
control CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
H3K4mM ChIP - Array 3

source_name: H3K4mM ChIP

source_name: Input DNA


title: H3K27triM-array3

description:
control CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
H3K27triM ChIP - Array 3

source_name: H3K27triM ChIP

value: Upstate


title: AML [2275_19jun08]

description: Not Applicable


title: AML [2274_11jun08]

description: Not Applicable


title: H2AZ_Ace-array3

description:
control CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
H2AZ_Ace ChIP - Array 3

source_name: H2AZ_Ace ChIP

value: Abcam


title: Lamellar_day3_rat12511

description: replicate 1

source_name: Lamellar, day 3

tag: sentrix position

value: L


title: RNA-HNSCC-16

description:
Sample name: 25213
PHen-HNC-25213-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 16

tag: sample identifier

value: Pt 16

value: tumor

value: HNSCC


title: FAIRE-array3

description:
control CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
FAIRE ChIP - Array 3

source_name: FAIRE ChIP

value: MCF7 cells

value: FAIRE


title: RNA-HNSCC-14

description:
Sample name: 26645
PHen-HNC-26645-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 14

value: Pt 14

tag: sample type


title: XBP1-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
XBP1 ChIP - Array 3

source_name: XBP1 ChIP

value: transgenic MCF7

value: modified LAP (localization and affinity purification) tag containing GFP

tag: chip antibody

value: Goat anti-GFP


title: Normal_rat12474

description: replicate 1

source_name: Normal

tag: strain

value: 5 months

value: male

value: bone - right ulna (central 5 mm)

value: I


title: RNA-HNSCC-13

description:
Sample name: 25579
PHen-HNC-25579-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 13

value: Pt 13

tag: disease state


title: RNA-HNSCC-15

description:
Sample name: 26144
PHen-HNC-26144-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 15

value: Pt 15


title: VDR-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
VDR ChIP - Array 3

source_name: VDR ChIP

value: VDR


title: AML [2272_03jun08]

description: Not Applicable

source_name: AML

value: Training

value: NPM1 B


title: Woven_1hr_rat12479

description: replicate 1

source_name: Woven, 1 hr

value: Fischer 344

tag: age

tag: tissue

value: H


title: RNA-HNSCC-12

description:
Sample name: 27898
PHen-HNC-27898-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 12

value: Pt 12

value: tumor

value: HNSCC


title: NR2C2-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
NR2C2 ChIP - Array 3

source_name: NR2C2 ChIP

value: transgenic MCF7


title: AML [2268_19jun08]

description: Not Applicable

tag: cohort

tag: npm1 status

value: NPM1 A


title: NR2C1-S-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
NR2C1-S ChIP - Array 3

source_name: NR2C1-S ChIP

tag: cell type

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP


title: RNA-HNSCC-11

description:
Sample name: 26162
PHen-HNC-26162-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 11

value: Pt 11


title: AML [2273_11jun08]

description: Not Applicable

value: NPM1 wt


title: Woven_day1_rat12482

description: replicate 1

source_name: Woven, day 1

value: 5 months

value: male

value: bone - right ulna (central 5 mm)

value: K


title: NR2C1-L-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
NR2C1-L ChIP - Array 3

source_name: NR2C1-L ChIP

source_name: Input DNA


title: Lamellar_day1_rat12462

description: replicate 1

source_name: Lamellar, day 1

value: F


title: AML [2271_9may08]

description: Not Applicable

value: Training


title: AML [2267_11jun08]

description: Not Applicable


title: AML [2266_04jun08]

description: Not Applicable


title: RNA-HNSCC-17

description:
Sample name: 25014
PHen-HNC-25014-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 17

value: Pt 17


title: AML [2270_20may08]

description: Not Applicable


title: Lamellar_day3_rat12488

description: replicate 1

source_name: Lamellar, day 3

value: Fischer 344

value: J


title: THRA-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
THRA ChIP - Array 3

source_name: THRA ChIP

value: THRA


title: Woven_day1_rat12443

description: replicate 1

value: E


title: RNA-HNSCC-10

description:
Sample name: 26193
PHen-HNC-26193-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 10

value: Pt 10

value: tumor

value: HNSCC


title: RNA-HNSCC-09

description:
Sample name: 25699
PHen-HNC-25699-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 9

value: Pt 9


title: AML [2265_20may08]

description: Not Applicable


title: CREB1-array4

description:
Ch2 input ctrl CEL files: input1-4.CEL, input2-4.CEL, input3-4.CEL
CREB1 ChIP - Array 4

source_name: CREB1 ChIP

value: transgenic MCF7

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP


title: SPDEF-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
SPDEF ChIP - Array 3

source_name: SPDEF ChIP

value: SPDEF


title: RNA-HNSCC-07

description:
Sample name: 26137
PHen-HNC-26137-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 7

value: Pt 7


title: RNA-HNSCC-08

description:
Sample name: 25191
PHen-HNC-25191-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 8

value: Pt 8


title: AML [2263_29apr08]

description: Not Applicable

source_name: AML

value: NPM1 wt


title: Lamellar_day1_rat12444

description: replicate 1

value: 5 months

value: male

value: bone - right ulna (central 5 mm)

value: C


title: RXRB-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
RXRB ChIP - Array 3

source_name: RXRB ChIP

value: RXRB


title: Woven_day1_rat12477

description: replicate 1

value: Fischer 344

value: B


title: RNA-HNSCC-06

description:
Sample name: 26198
PHen-HNC-26198-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 6

value: Pt 6

value: tumor


title: AML [2262_11jun08]

description: Not Applicable

value: Training


title: RORC-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
RORC ChIP - Array 3

source_name: RORC ChIP

value: transgenic MCF7

value: RORC


title: RORA-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
RORA ChIP - Array 3

source_name: RORA ChIP

value: RORA

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP


title: AML [2261_20jun08]

description: Not Applicable

value: NPM1 A


title: AML [2260_29apr08]

description: Not Applicable

value: NPM1 wt


title: PPARG-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
PPARG ChIP - Array 3

source_name: PPARG ChIP

value: PPARG


title: Lamellar_day3_rat12481

description: replicate 1

value: 5 months

value: male

value: A


title: Normal_rat12447

description: replicate 1

source_name: Normal

value: bone - right ulna (central 5 mm)

value: L


title: AML [2259_20may08]

description: Not Applicable


title: Woven_1hr_rat12484

description: replicate 1

source_name: Woven, 1 hr

value: Fischer 344

value: K


title: RNA-HNSCC-04

description:
Sample name: 25031
PHen-HNC-25031-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 4

value: Pt 4

value: tumor

value: HNSCC


title: AML [2257_18jun08]

description: Not Applicable

value: Training


title: AML [2256_04jun08]

description: Not Applicable


title: RNA-HNSCC-03

description:
Sample name: 25059
PHen-HNC-25059-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 3

value: Pt 3


title: Normal_rat12486

description: replicate 1

value: I


title: RNA-HNSCC-05

description:
Sample name: 25287
PHen-HNC-25287-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 5

value: Pt 5


title: RXRA-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
RXRA ChIP - Array 3

source_name: RXRA ChIP

value: transgenic MCF7

value: RXRA

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP

source_name: Input DNA


title: RNA-HNSCC-02

description:
Sample name: 27925
PHen-HNC-27925-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 2

value: Pt 2


title: Woven_day3_rat12489

description: replicate 1

source_name: Woven, day 3

value: 5 months

value: male

value: H


title: PPARA-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
PPARA ChIP - Array 3

source_name: PPARA ChIP

value: PPARA


title: RORC-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
RORC ChIP - Array 7

value: RORC


title: AML [2255_12jun08]

description: Not Applicable

value: NPM1 wt


title: PGR-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
NR3C1 ChIP - Array 3

source_name: PGR ChIP

value: PGR


title: Normal_rat12470

description: replicate 1

value: Fischer 344

value: bone - right ulna (central 5 mm)

value: G


title: RXRB-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
RXRB ChIP - Array 7

value: RXRB


title: AML [2253_5jun08]

description: Not Applicable

source_name: AML

value: Training


title: PPARD-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
PPARD ChIP - Array 3

source_name: PPARD ChIP

value: transgenic MCF7

value: PPARD


title: RORA-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
RORA ChIP - Array 7

value: RORA

value: modified LAP (localization and affinity purification) tag containing GFP


title: RXRA-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
RXRA ChIP - Array 7

value: RXRA

value: Goat anti-GFP


title: NR4A2-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
NURR1 ChIP - Array 3

source_name: NR4A2 ChIP


title: NR4A1-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
NR4A1 ChIP - Array 3

source_name: NR4A1 ChIP


title: Lamellar_day1_rat12493

description: replicate 1

source_name: Lamellar, day 1

value: 5 months

value: male

value: J


title: PPARD-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
PPARD ChIP - Array 7


title: PPARA-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
PPARA ChIP - Array 7

value: PPARA


title: NR2F2-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
NR2F2 ChIP - Array 3

source_name: NR2F2 ChIP


title: AML [2252_16may08]

description: Not Applicable

value: NPM1 wt


title: AML [2251_12jun08]

description: Not Applicable


title: NR2F1-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
NR2F1 ChIP - Array 3

source_name: NR2F1 ChIP


title: PGR-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
NR3C1 ChIP - Array 7

value: PGR


title: NR1D2-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
NR1D2 ChIP - Array 3

source_name: NR1D2 ChIP


title: NR1D1-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
NR1D1 ChIP - Array 3

source_name: NR1D1 ChIP


title: PPARG-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
PPARG ChIP - Array 7

source_name: PPARG ChIP

value: PPARG


title: NR4A1-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
NR4A1 ChIP - Array 7


title: NR4A2-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
NURR1 ChIP - Array 7


title: RNA-HNSCC-01

description:
Sample name: 25182
PHen-HNC-25182-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Pt 1

value: Pt 1

value: tumor

value: HNSCC


title: Normal_rat12499

description: replicate 1

source_name: Normal

value: Fischer 344

value: bone - right ulna (central 5 mm)

value: F


title: AML [2248_12jun08]

description: Not Applicable

value: Training

value: NPM1 A


title: AML [2249_28may08]

description: Not Applicable


title: AML [2250_20may08]

description: Not Applicable


title: NR1H2-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
NR1H3 ChIP - Array 3

source_name: NR1H3 ChIP

value: transgenic MCF7

value: modified LAP (localization and affinity purification) tag containing GFP

source_name: Input DNA


title: NR2F2-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
NR2F2 ChIP - Array 7

value: Goat anti-GFP


title: AML [2247_03jun08]

description: Not Applicable


title: JUND-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
JUND ChIP - Array 3

source_name: JUND ChIP

value: JUND


title: NR2F1-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
NR2F1 ChIP - Array 7


title: AML [2245_18jun08]

description: Not Applicable


title: AML [2246_27may08]

description: Not Applicable

value: NPM1 B


title: JUNB-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
JUNB ChIP - Array 3

source_name: JUNB ChIP

value: JUNB


title: AML [2244_12jun08]

description: Not Applicable


title: NR1D2-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
NR1D2 ChIP - Array 7


title: Woven_day1_rat12450

description: replicate 1

source_name: Woven, day 1

value: 5 months

value: male

value: G


title: JUN-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
JUN ChIP - Array 3

source_name: JUN ChIP

value: JUN


title: AML [2243_22may08]

description: Not Applicable

source_name: AML

value: NPM1 wt


title: NR1D1-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
NR1D1 ChIP - Array 7


title: NR3C1-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
NR3C1 ChIP - Array 3

source_name: NR3C1 ChIP


title: Woven_day1_rat12459

description: replicate 1

value: D


title: FOSL2-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
FOSL2 ChIP - Array 3

source_name: FOSL2 ChIP


title: Normal_rat12454

description: replicate 1

value: Fischer 344

value: E


title: AML [2242_12jun08]

description: Not Applicable


title: JUND-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
JUND ChIP - Array 7


title: AML [2241_19jun08]

description: Not Applicable


title: JUNB-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
JUNB ChIP - Array 7


title: AML [2240_04jun08]

description: Not Applicable


title: Woven_1hr_rat12452

description: replicate 1

source_name: Woven, 1 hr

value: bone - right ulna (central 5 mm)

value: C


title: NR1H2-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
NR1H3 ChIP - Array 7


title: Woven_day1_rat12461

description: replicate 1

value: L


title: JUN-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
JUN ChIP - Array 7

value: transgenic MCF7


title: AML [2239_14may08]

description: Not Applicable

value: Training

value: NPM1 A


title: FOSB-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
FOSB ChIP - Array 3

source_name: FOSB ChIP

value: FOSB

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP


title: Lamellar_day3_rat12491

description: replicate 1

source_name: Lamellar, day 3

value: 5 months

value: B


title: AML [2238_20may08]

description: Not Applicable


title: Woven_day3_rat12502

description: replicate 1

source_name: Woven, day 3

value: male

value: H


title: FOS-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
FOS ChIP - Array 3

source_name: FOS ChIP

value: FOS


title: Lamellar_day3_rat12460

description: replicate 1

value: K


title: NR3C1-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
NR3C1 ChIP - Array 7


title: FOSL1-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
FOSL1 ChIP - Array 3

source_name: FOSL1 ChIP


title: ELK-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
ELK ChIP - Array 3

source_name: ELK ChIP

value: ELK


title: FOSL2-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
FOSL2 ChIP - Array 7


title: Woven_day1_rat12466

description: replicate 1

value: Fischer 344

value: A


title: Lamellar_1hr_rat12471

description: replicate 1

source_name: Lamellar, 1 hr

value: bone - right ulna (central 5 mm)

value: D


title: AML [2237_04jun08]

description: Not Applicable

value: NPM1 wt


title: Woven_day3_rat12490

description: replicate 1

value: G


title: Woven_day1_rat12504

description: replicate 1

value: I


title: CREB1-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
CREB1 ChIP - Array 3

source_name: CREB1 ChIP

value: transgenic MCF7


title: Woven_1hr_rat12463

description: replicate 1

value: J


title: Woven_1hr_rat12468

description: replicate 1

value: C


title: Lamellar_1hr_rat12506

description: replicate 1

value: 5 months

value: E


title: Woven_1hr_rat12500

description: replicate 1

value: male

value: F


title: AML [2236_5jun08]

description: Not Applicable

value: Training

value: NPM1 A


title: FOSL1-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
FOSL1 ChIP - Array 7

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP

source_name: Input DNA


title: Woven_day3_rat12448

description: replicate 1

value: Fischer 344

value: A


title: Lamellar_1hr_rat12453

description: replicate 1

value: bone - right ulna (central 5 mm)

value: B


title: ATF1-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
ATF1 ChIP - Array 3

source_name: ATF1 ChIP


title: AR-array3

description:
Ch2 input ctrl CEL files: input1-3.CEL, input2-3.CEL, input3-3.CEL
AR ChIP - Array 3

source_name: AR ChIP

value: AR


title: FOS-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
FOS ChIP - Array 7

value: FOS


title: ELK-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
ELK ChIP - Array 7

value: transgenic MCF7

value: ELK


title: CREB1-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
CREB1 ChIP - Array 7


title: AML [2235_10jun08]

description: Not Applicable

value: NPM1 wt


title: Lamellar_day1_rat12451

description: replicate 1

source_name: Lamellar, day 1

value: 5 months

value: D


title: AML [2233_10jun08]

description: Not Applicable


title: AML [2234_10jun08]

description: Not Applicable


title: AML [2231_20may08]

description: Not Applicable


title: FOSB-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
FOSB ChIP - Array 7

value: FOSB


title: ATF1-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
ATF1 ChIP - Array 7


title: AR-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
AR ChIP - Array 7


title: AML [2229_18jun08]

description: Not Applicable


title: AML [2230_20jun08]

description: Not Applicable


title: H3R17ME2-array5

description:
control CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
H3R17ME2 ChIP - Array 5

source_name: H3R17ME2 ChIP

value: MCF7 cells

tag: chromatin mark

tag: antibody vendor

value: abcam


title: AML [2228_29apr08]

description: Not Applicable

source_name: AML

value: Training


title: Mouse Adult LVCP 2

city: Parkville

first: Shane

middle: A

last: Liddelow

state: Victoria

address: Level 8 Medical Building, Grattan Street

department: Pharmacology

country: Australia

institute: The University of Melbourne

description: Transcript-level data

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the University at Albany Centre for Functional Genomics (Rensselaer, NY, USA).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Three separate arrays on separate pooled plexus samples were completed. For gene level analysis, the Affymetrix Power Tools software (Affymetrix) was used to normalise scanned images and to summarise the probe set. Briefly, raw array data was RMA normalised (robust multichip analysis, Irizarry et al., 2003) per chip median and filtered to include the top 80th percentile of genes expressed. Following an un-paired t-test (p < 0.05), a Benjamini-Hochberg false discovery rate correction (Benjamini & Hochberg, 1995; Zaykin et al., 2000) was applied.

source_name: Healthy adult females, pooled (n=10)

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Whole lateral ventricular choroid plexus was excised under RNAse-free PBS, spun at 3000rpm for 30 seconds and snap frozen in liquid nitrogen.

extract_protocol: RNA was isolated from ~50 µg of plexus supernatant with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions including gDNA elimination and QiaShredder columns (Qiagen). A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

tag: developmental stage

value: adult

value: female

value: lateral ventricular choroid plexus


title: H3K4triM_E-array5

description:
control CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
H3K4triM_E ChIP - Array 5

source_name: H3K4triM_E ChIP

tag: antibody catalog #


title: Mouse Adult LVCP 3

description: Transcript-level data

tag: gender


title: AML [2227_29may08]

description: Not Applicable

value: NPM1 A


title: AML [2226_04jun08]

description: Not Applicable


title: PDAC CAFs DAC replicate C

city: New York

first: Benjamin

last: Tycko

address: 1130 St. Nicholas Ave.

department: ICG

institute: Columbia University

description:
SAMPLE 6
replicate 3

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

source_name: PDAC CAFs

growth_protocol: Short-term explant culture of cancer-associated fibroblasts (CAFs) from a pancreatic tumor in a KPC-Brca1 mouse.

extract_protocol: Total RNA extracted with Trizol reagent.

treatment_protocol: Treatment with 2 micromolar 5-aza-dC (decitabine; DAC) for 48 hours; control is untreated.

value: PDAC CAFs

tag: agent

value: DAC [2 micromolar]


title: H3K27triM-array5

description:
control CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
H3K27triM ChIP - Array 5

source_name: H3K27triM ChIP

value: Upstate


title: H3K4mM-array5

description:
control CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
H3K4mM ChIP - Array 5

source_name: H3K4mM ChIP


title: Mouse Adult LVCP 1

description: Transcript-level data


title: Mouse E15 LVCP 3

description: Transcript-level data

source_name: Healthy E15 pups, pooled (n=30) mixed sex

value: E15 pup

value: mixed


title: PDAC epithelial cells replicate C

description:
SAMPLE 3
replicate 3

source_name: PDAC epithelial cells

growth_protocol: Short-term explant culture of malignant epithelial cells from a pancreatic tumor in a KPC-Brca1 mouse.

treatment_protocol: Treatment with 0.5 micromolar 5-aza-dC (decitabine; DAC) for 48 hours; control is untreated.

value: PDAC epithelial cells

value: no DAC


title: PDAC CAFs DAC replicate B

description:
SAMPLE 5
replicate 2


title: PDAC epithelial cells DAC replicate C

description:
SAMPLE 6
replicate 3

value: DAC [0.5 micromolar]


title: PDAC epithelial cells DAC replicate A

description:
SAMPLE 4
replicate 1


title: Mouse E15 LVCP 2

description: Transcript-level data


title: AML [2225_25apr08]

description: Not Applicable


title: PDAC CAFs replicate C

description:
SAMPLE 3
replicate 3


title: PDAC epithelial cells replicate A

description:
SAMPLE 1
replicate 1


title: PDAC epithelial cells replicate B

description:
SAMPLE 2
replicate 2


title: H2AZ_Ace-array5

description:
control CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
H2AZ_Ace ChIP - Array 5

source_name: H2AZ_Ace ChIP

value: Abcam


title: PDAC epithelial cells DAC replicate B

description:
SAMPLE 5
replicate 2


title: PDAC CAFs DAC replicate A

description:
SAMPLE 4
replicate 1


title: PDAC CAFs replicate B

description:
SAMPLE 2
replicate 2


title: AML [2224_14may08]

description: Not Applicable

value: NPM1 B


title: FAIRE-array5

description:
control CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
FAIRE ChIP - Array 5

source_name: FAIRE ChIP

value: MCF7 cells

value: FAIRE


title: XBP1-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
XBP1 ChIP - Array 5

source_name: XBP1 ChIP

value: transgenic MCF7

tag: transcription factor

tag: tag

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP


title: VDR-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
VDR ChIP - Array 5

source_name: VDR ChIP

value: VDR


title: NR2C2-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
NR2C2 ChIP - Array 5

source_name: NR2C2 ChIP

source_name: Input DNA


title: AML [2220_03jun08]

description: Not Applicable

value: Training

value: NPM1 wt


title: AML [2222_03jun08]

description: Not Applicable


title: AML [2223_9may08]

description: Not Applicable


title: H3R17ME2-array2

description:
control CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
H3R17ME2 ChIP - Array 2

value: abcam


title: AML [2219_20jun08]

description: Not Applicable


title: AML [2218_27may08]

description: Not Applicable


title: NR2C1-S-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
NR2C1-S ChIP - Array 5

source_name: NR2C1-S ChIP


title: NR2C1-L-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
NR2C1-L ChIP - Array 5

source_name: NR2C1-L ChIP


title: H3K4triM_E-array2

description:
control CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
H3K4triM_E ChIP - Array 2


title: Bacteroides thetaiotaomicron_phase2_MM-HMO_rep1

city: Stanford

first: Angela

middle: M

last: Marcobal

state: California

address: 299 Campus Drive

department: Microbiology and Immunology

institute: Stanford University

description: 2 ml minimal medium-human milk oligosaccharides (1.5%) culture of  B.thetaiotaomicron VPI-5482; grown to middle of second logarithmic growth phase; replicate 1 of 2

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The raw data were RMA-MS normalized using R-2.9.1. and log2 transformed, excluding other species present on chip.

organism: Bacteroides thetaiotaomicron

source_name: bacterial

label_protocol: Enzo Biochemicals Bioarray terminal labeling kit

extract_protocol: Qiagen Rneasy mini column extraction, Ambion DNA free treatment


title: Bacteroides thetaiotaomicron_mid log phase_MM-Lactose_rep1

description: 2 ml minimal medium lactose (0.5%) culture of  B.thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 1 of 2


title: THRA-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
THRA ChIP - Array 5

source_name: THRA ChIP

value: THRA


title: Bacteroides thetaiotaomicron_phase2_MM-HMO_rep2

description: 2 ml minimal medium-human milk oligosaccharides (1.5%) culture of  B.thetaiotaomicron VPI-5482; grown to middle of second logarithmic growth phase; replicate 2 of 2


title: Bacteroides thetaiotaomicron_phase1_MM-HMO_rep2

description: 2 ml minimal medium-human milk oligosaccharides (1.5%) culture of  B.thetaiotaomicron VPI-5482; grown to middle of first logarithmic growth phase; replicate 2 of 2


title: Bacteroides thetaiotaomicron_mid log phase_MM-Galactose_rep2

description: 2 ml minimal medium galactose (0.5%) culture of  B.thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 2 of 2


title: AML [2215_07may08]

description: Not Applicable

source_name: AML


title: AML [2216_9may08]

description: Not Applicable


title: Mouse E15 LVCP 1

description: Transcript-level data

value: E15 pup

value: lateral ventricular choroid plexus


title: Bacteroides thetaiotaomicron_mid log phase_MM-Lactose_rep2

description: 2 ml minimal medium lactose (0.5%) culture of  B.thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 2 of 2


title: Bacteroides thetaiotaomicron_phase1_MM-HMO_rep1

description: 2 ml minimal medium-human milk oligosaccharides (1.5%) culture of  B.thetaiotaomicron VPI-5482; grown to middle of first logarithmic growth phase; replicate 1 of 2


title: PA01 infected 3

city: Detroit

first: Fu-Shin

middle: X

last: Yu

state: Michigan

address: 4717 St. Antoine, Room K417

department: Ophthalmology

institute: Wayne State University School of Medicine

description: replicate 3

source_name: Corneal epithelial cells

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

value: 6-8 weeks

value: Cornea

tag: infection

value: Pseudomonas aeruginosa infected (6 h post infection)


title: Flag + PA01 infected 3

description: replicate 3

value: flagellin pretreated (24 h), followed by Pseudomonas aeruginosa infection (6 h)


title: H3K4mM-array2

description:
control CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
H3K4mM ChIP - Array 2


title: SPDEF-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
SPDEF ChIP - Array 5

source_name: SPDEF ChIP

value: SPDEF

tag: chip antibody


title: Flag + PA01 infected 1

description: replicate 1

tag: strain


title: AML [2214_20may08]

description: Not Applicable

value: NPM1 A


title: H3K27triM-array2

description:
control CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
H3K27triM ChIP - Array 2

source_name: H3K27triM ChIP

value: MCF7 cells

value: Upstate


title: RXRB-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
RXRB ChIP - Array 5

source_name: RXRB ChIP

value: transgenic MCF7

value: RXRB

value: modified LAP (localization and affinity purification) tag containing GFP


title: PDAC CAFs replicate A

description:
SAMPLE 1
replicate 1

source_name: PDAC CAFs

value: PDAC CAFs

value: no DAC


title: AML [2212_19jun08]

description: Not Applicable

value: Training

value: NPM1 wt


title: RXRA-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
RXRA ChIP - Array 5

source_name: RXRA ChIP

value: RXRA

value: Goat anti-GFP


title: Control 3

description: replicate 3

value: 6-8 weeks


title: PA01 infected 1

description: replicate 1

value: Cornea


title: AML [2211_18apr08]

description: Not Applicable


title: FAIRE-array2

description:
control CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
FAIRE ChIP - Array 2

value: FAIRE


title: AML [2209_29apr08]

description: Not Applicable


title: RORA-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
RORA ChIP - Array 5

source_name: RORA ChIP

value: RORA


title: RORC-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
RORC ChIP - Array 5

source_name: RORC ChIP

value: RORC


title: XBP1-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
XBP1 ChIP - Array 2

source_name: XBP1 ChIP


title: VDR-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
VDR ChIP - Array 2

source_name: VDR ChIP

value: VDR


title: Bacteroides thetaiotaomicron_mid log phase_MM-Galactose_rep1

description: 2 ml minimal medium galactose (0.5%) culture of  B.thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 1 of 2


title: Flag + PA01 infected 2

description: replicate 2

value: flagellin pretreated (24 h), followed by Pseudomonas aeruginosa infection (6 h)


title: H2AZ_Ace-array2

description:
control CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
H2AZ_Ace ChIP - Array 2

source_name: H2AZ_Ace ChIP

value: MCF7 cells

value: Abcam


title: PPARG-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
PPARG ChIP - Array 5

source_name: PPARG ChIP

value: transgenic MCF7

value: PPARG

source_name: Input DNA


title: PA01 infected 2

description: replicate 2

value: Pseudomonas aeruginosa infected (6 h post infection)


title: NR2C2-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
NR2C2 ChIP - Array 2

source_name: NR2C2 ChIP

value: modified LAP (localization and affinity purification) tag containing GFP


title: Control 1

description: replicate 1


title: NR2C1-S-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
NR2C1-S ChIP - Array 2

source_name: NR2C1-S ChIP


title: AML [2208_11jun08]

description: Not Applicable

value: Training


title: Control 2

description: replicate 2


title: YAL6 (6042498052_A)

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

description:
YAL6
6042498052_A

data_processing: The data were normalised using quantile normalisation with Genomestudio

source_name: gastrocnemius muscles

extract_protocol: RNA was extracted using the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: male

value: 8 months

value: gastrocnemius muscles

tag: sample type

value: young ad libitum


title: AML [2206_18jun08]

description: Not Applicable

source_name: AML

value: NPM1 A


title: YAL6 (6042498027_F)

description:
YAL6
6042498027_F

tag: age


title: YAL6 (6042498063_C)

description:
YAL6
6042498063_C

tag: tissue


title: YAL5 (6042498063_F)

description:
YAL5
6042498063_F


title: NR2C1-L-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
NR2C1-L ChIP - Array 2

source_name: NR2C1-L ChIP

value: Goat anti-GFP


title: PGR-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
NR3C1 ChIP - Array 5

source_name: PGR ChIP

value: PGR


title: YAL6 (6042498026_D)

description:
YAL6
6042498026_D


title: AML [2205_04jun08]

description: Not Applicable

tag: cohort

value: NPM1 wt


title: AML [2207_12jun08]

description: Not Applicable

tag: npm1 status


title: AML [2203_20jun08]

description: Not Applicable


title: NR4A2-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
NURR1 ChIP - Array 5

source_name: NR4A2 ChIP

tag: cell type


title: THRA-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
THRA ChIP - Array 2

source_name: THRA ChIP

value: THRA


title: YAL4 (6042498052_E)

description:
YAL4
6042498052_E


title: PPARD-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
PPARD ChIP - Array 5

source_name: PPARD ChIP

value: PPARD


title: NR4A1-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
NR4A1 ChIP - Array 5

source_name: NR4A1 ChIP


title: NR2F2-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
NR2F2 ChIP - Array 5

source_name: NR2F2 ChIP


title: AML [2202_20jun08]

description: Not Applicable


title: RXRB-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
RXRB ChIP - Array 2

source_name: RXRB ChIP

value: RXRB


title: PPARA-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
PPARA ChIP - Array 5

source_name: PPARA ChIP

value: PPARA


title: SPDEF-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
SPDEF ChIP - Array 2

source_name: SPDEF ChIP

value: transgenic MCF7

value: SPDEF


title: AML [2200_20jun08]

description: Not Applicable


title: AML [2201_29may08]

description: Not Applicable


title: RXRA-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
RXRA ChIP - Array 2

source_name: RXRA ChIP

value: RXRA


title: AML [2199_29may08]

description: Not Applicable


title: YAL3 (6042498063_B)

description:
YAL3
6042498063_B


title: YAL2 (6042498052_D)

description:
YAL2
6042498052_D


title: RORC-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
RORC ChIP - Array 2

source_name: RORC ChIP

value: RORC

value: modified LAP (localization and affinity purification) tag containing GFP


title: NR1D2-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
NR1D2 ChIP - Array 5

source_name: NR1D2 ChIP

source_name: Input DNA


title: YAL2 (6042498027_A)

description:
YAL2
6042498027_A

value: male


title: NR1D1-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
NR1D1 ChIP - Array 5

source_name: NR1D1 ChIP


title: AML [2197_20jun08]

description: Not Applicable

value: Training


title: AML [2198_27may08]

description: Not Applicable


title: RORA-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
RORA ChIP - Array 2

source_name: RORA ChIP

value: RORA


title: JUND-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
JUND ChIP - Array 5

source_name: JUND ChIP

value: JUND


title: NR1H2-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
NR1H3 ChIP - Array 5

source_name: NR1H3 ChIP


title: PPARD-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
PPARD ChIP - Array 2


title: JUNB-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
JUNB ChIP - Array 5

source_name: JUNB ChIP

value: JUNB


title: PPARA-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
PPARA ChIP - Array 2

value: Goat anti-GFP


title: NR2F1-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
NR2F1 ChIP - Array 5

source_name: NR2F1 ChIP


title: AML [2196_16may08]

description: Not Applicable

source_name: AML


title: AML [2194_27may08]

description: Not Applicable


title: AML [2195_19jun08]

description: Not Applicable

value: NPM1 A


title: PGR-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
NR3C1 ChIP - Array 2

source_name: PGR ChIP

value: PGR


title: JUN-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
JUN ChIP - Array 5

source_name: JUN ChIP

value: JUN


title: PPARG-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
PPARG ChIP - Array 2

source_name: PPARG ChIP

value: PPARG


title: NR4A2-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
NURR1 ChIP - Array 2

source_name: NR4A2 ChIP


title: NR3C1-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
NR3C1 ChIP - Array 5

source_name: NR3C1 ChIP


title: FOSL2-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
FOSL2 ChIP - Array 5

source_name: FOSL2 ChIP


title: NR4A1-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
NR4A1 ChIP - Array 2

source_name: NR4A1 ChIP


title: AML [2192_11jun08]

description: Not Applicable

value: NPM1 wt


title: OCR5 (6042498026_F)

description:
OCR5
6042498026_F

source_name: gastrocnemius muscles

value: 24 months

value: gastrocnemius muscles

value: old caloric restricted


title: OCR4 (6042498052_B)

description:
OCR4
6042498052_B


title: YAL1 (6042498026_A)

description:
YAL1
6042498026_A

value: 8 months

value: young ad libitum


title: FOSB-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
FOSB ChIP - Array 5

source_name: FOSB ChIP

value: transgenic MCF7

value: FOSB

value: modified LAP (localization and affinity purification) tag containing GFP


title: OCR2 (6042498063_E)

description:
OCR2
6042498063_E

value: male


title: OCR2 (6042498027_D)

description:
OCR2
6042498027_D


title: FOSL1-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
FOSL1 ChIP - Array 5

source_name: FOSL1 ChIP

source_name: Input DNA


title: OAL6 (6042498052_F)

description:
OAL6
6042498052_F

value: old ad libitum


title: AML [2190_22apr08]

description: Not Applicable

value: Training


title: NR2F1-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
NR2F1 ChIP - Array 2

value: Goat anti-GFP


title: FOS-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
FOS ChIP - Array 5

source_name: FOS ChIP

value: FOS


title: OCR1 (6042498026_C)

description:
OCR1
6042498026_C


title: NR1D2-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
NR1D2 ChIP - Array 2

source_name: NR1D2 ChIP


title: AML [2188_28may08]

description: Not Applicable


title: AML [2187_03jun08]

description: Not Applicable


title: AML [2186_17jun08]

description: Not Applicable


title: AML [2191_04jun08]

description: Not Applicable

value: NPM1 A


title: ELK-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
ELK ChIP - Array 5

source_name: ELK ChIP

value: ELK


title: ATF1-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
ATF1 ChIP - Array 5

source_name: ATF1 ChIP


title: JUND-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
JUND ChIP - Array 2

source_name: JUND ChIP

value: JUND


title: NR1H2-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
NR1H3 ChIP - Array 2

source_name: NR1H3 ChIP


title: OAL4 (6042498063_A)

description:
OAL4
6042498063_A


title: AML [2193_29apr08]

description: Not Applicable

source_name: AML


title: OAL3 (6042498063_D)

description:
OAL3
6042498063_D


title: AML [2184_10jun08]

description: Not Applicable

value: NPM1 wt


title: AR-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
AR ChIP - Array 5

source_name: AR ChIP

value: AR


title: OAL3 (6042498027_B)

description:
OAL3
6042498027_B

value: 24 months

value: gastrocnemius muscles


title: OAL1 (6042498026_B)

description:
OAL1
6042498026_B


title: AML [2185_11jun08]

description: Not Applicable


title: OCR5 (6042498052_C)

description:
OCR5
6042498052_C

value: old caloric restricted


title: H3R17ME2-array7

description:
control CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
H3R17ME2 ChIP - Array 7

source_name: H3R17ME2 ChIP

value: MCF7 cells

tag: chromatin mark

value: abcam


title: JUN-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
JUN ChIP - Array 2

source_name: JUN ChIP

value: transgenic MCF7

value: JUN


title: NR3C1-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
NR3C1 ChIP - Array 2

source_name: NR3C1 ChIP

value: modified LAP (localization and affinity purification) tag containing GFP


title: AML [2182_9may08]

description: Not Applicable


title: NR1D1-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
NR1D1 ChIP - Array 2

source_name: NR1D1 ChIP


title: H3K4mM-array7

description:
control CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
H3K4mM ChIP - Array 7

source_name: H3K4mM ChIP

tag: antibody vendor


title: AML [2179_14may08]

description: Not Applicable


title: AML [2181_28may08]

description: Not Applicable


title: Staphylococcus aureus_PTAP_60min_replicate3

city: Ft. Meade

first: Prashanthi

last: Mulinti

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

description: PTAP treatment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 500)

data_processing: Affymetrix GeneChip Command Console (AGCC) version 3.0, MAS5.0 algorithm

organism: Staphylococcus aureus

source_name: Staphylococcus aureus_PTAP_60min

label_protocol: Approximately 500 ng of total RNA was processed to produce biotinylated aRNA targets.500 ng of total RNA sample was first polyadenylated at the 3′ end with Poly(A) Polymerase. The A-tailed RNA was then reverse transcribed using oligo(dT) primers containing a T7 RNA polymerase promoter. The resulting cDNA with a T7 promoter was purified and further used to produce biotin labeled aRNA by incorporating Biotin 11-UTP (Ambion) in the vitro transcription (IVT) reaction. The quality of the aRNA synthesized was assessed on a RNA LabChip using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.). The biotin labeled aRNA was fragmented using 5X fragmentation buffer (200mM Tris-acetate (pH 8.1), 500mM KOAc, 150mM MgOAc) and 20 μg of the fragmented aRNA was hybridized to the S.aureus Affymetrix® GeneChip array for 16 hours at 45°C according to manufacturer’s instructions (Affymetrix, Inc.).

growth_protocol: S.aureus cultures were grown until an optical density at 600nm (OD600) reached the early logarithmic phase (~ 0.8). OD600  was measured using a Lambda 25 spectrophotometer (Perkin-Elmer). For microarray study. a concentration of 0.07 mM PTAP dissolved in DMSO was added to 5 ml of the log phase culture and equivalent amount of DMSO only was added to the control culture. The cultures were incubated for 10 and 60 min at 37ºC.

extract_protocol: S. aureus cultures (five control, five 10 min and five 60 min treatments) were collected at the indicated times (10 and 60 min) and immediately mixed with 2 volumes of RNA protect (Qiagen) for 5 min at room temperature. Cells were harvested by centrifugation at 5000 rpm for 10 min at 25ºC. Cells were frozen at −80°C. Frozen cells were thawed and lysed using 100 μl of a 5 mg/ml lysostaphin (AMBI products, LLC) solution in 20 mM sodium acetate buffer (pH 4.6) for 30 min at 37ºC with gently shaking. Total RNA was extracted from the lysed cells using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. RNA was eluted in 25 μl of RNase free distilled H2O (Fisher Scientific) and quantified by NanoDrop spectrophotometer (NanoDrop Technologies), and the quality of the sample was assessed by capillary electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.). Approximately 5 μl (~ 500 ng) of total RNA from each sample was linearly amplified (two rounds) using MessageAmp™ II Bacteria Kit (Ambion) following manufacturer’s instruction.

treatment_protocol: No treatment

value: NCTC 8325


title: AML [2183_22may08_2]

description: Not Applicable

value: Training

value: NPM1 non-ABD


title: Staphylococcus aureus_PTAP_60min_replicate4

description: PTAP treatment


title: Staphylococcus aureus_PTAP_60min_replicate1

description: PTAP treatment


title: CREB1-array5

description:
Ch2 input ctrl CEL files: input1-5.CEL, input2-5.CEL, input3-5.CEL
CREB1 ChIP - Array 5

source_name: CREB1 ChIP

value: Goat anti-GFP


title: OCR3 (6042498027_C)

description:
OCR3
6042498027_C

source_name: gastrocnemius muscles

value: male


title: H3K27triM-array7

description:
control CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
H3K27triM ChIP - Array 7

source_name: H3K27triM ChIP

value: Upstate

source_name: Input DNA


title: JUNB-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
JUNB ChIP - Array 2

source_name: JUNB ChIP

value: JUNB


title: AML [2177_29may08]

description: Not Applicable

value: NPM1 A


title: H2AZ_Ace-array7

description:
control CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
H2AZ_Ace ChIP - Array 7

source_name: H2AZ_Ace ChIP

value: Abcam


title: FOS-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
FOS ChIP - Array 2

source_name: FOS ChIP

value: FOS


title: FAIRE-array7

description:
control CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
FAIRE ChIP - Array 7

source_name: FAIRE ChIP

value: FAIRE


title: Staphylococcus aureus_PTAP_10min_replicate4

description: PTAP treatment

source_name: Staphylococcus aureus_PTAP_10min


title: ELK-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
ELK ChIP - Array 2

source_name: ELK ChIP

value: ELK


title: FOSL1-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
FOSL1 ChIP - Array 2

source_name: FOSL1 ChIP


title: CREB1-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
CREB1 ChIP - Array 2


title: VDR-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
VDR ChIP - Array 7

source_name: VDR ChIP

value: VDR


title: NR2F2-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
NR2F2 ChIP - Array 2

source_name: NR2F2 ChIP


title: ATF1-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
ATF1 ChIP - Array 2

source_name: ATF1 ChIP


title: NR2C2-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
NR2C2 ChIP - Array 7

source_name: NR2C2 ChIP


title: Staphylococcus aureus_PTAP_10min_replicate3

description: PTAP treatment


title: AML [2172_9may08]

description: Not Applicable

source_name: AML

value: NPM1 wt


title: Staphylococcus aureus_PTAP_10min_replicate2

description: PTAP treatment


title: Staphylococcus aureus_PTAP_10min_replicate1

description: PTAP treatment


title: AML [2173_11jun08]

description: Not Applicable


title: AML [2175_27may08]

description: Not Applicable


title: Staphylococcus aureus_no treatment control_0min_replicate4

description: No treatment

source_name: Staphylococcus aureus_no treatment_0min


title: AML [2174_13jun08]

description: Not Applicable


title: NR2C1-S-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
NR2C1-S ChIP - Array 7

source_name: NR2C1-S ChIP

value: transgenic MCF7


title: Staphylococcus aureus_no treatment control_0min_replicate3

description: No treatment


title: AR-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
AR ChIP - Array 2

source_name: AR ChIP

value: AR


title: XBP1-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
XBP1 ChIP - Array 7

source_name: XBP1 ChIP

value: modified LAP (localization and affinity purification) tag containing GFP


title: Staphylococcus aureus_no treatment control_0min_replicate2

description: No treatment

value: NCTC 8325


title: AML [2171_20may08]

description: Not Applicable

value: Training


title: Staphylococcus aureus_no treatment control_0min_replicate1

description: No treatment


title: AML [2170_18jun08]

description: Not Applicable


title: NR2C1-L-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
NR2C1-L ChIP - Array 7

source_name: NR2C1-L ChIP

source_name: Input DNA


title: THRA-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
THRA ChIP - Array 7

source_name: THRA ChIP

value: THRA


title: H3K4triM_E-array1

description:
control CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
H3K4triM_E ChIP - Array 1

source_name: H3K4triM_E ChIP

value: MCF7 cells

value: abcam


title: SPDEF-array7

description:
Ch2 input ctrl CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
SPDEF ChIP - Array 7

source_name: SPDEF ChIP

value: SPDEF

value: Goat anti-GFP


title: Staphylococcus aureus_OBPCP_60min_replicate4

description:
SAMPLE 14
OBPCP treatment

data_processing: Affymetrix GeneChip Command Console (AGCC) version 3.0, MAS5 algorithm

source_name: Staphylococcus aureus_OBPCP_60min

growth_protocol: S.aureus cultures were grown until an optical density at 600nm (OD600) reached the early logarithmic phase (~ 0.8). OD600  was measured using a Lambda 25 spectrophotometer (Perkin-Elmer). For microarray study. a concentration of 0.07 mM OBPCP dissolved in DMSO was added to 5 ml of the log phase culture and equivalent amount of DMSO only was added to the control culture. The cultures were incubated for 10 and 60 min at 37ºC.


title: AML [1551_17jun08]

description: Not Applicable

value: NPM1 non-ABD


title: H3R17ME2-array1

description:
control CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
H3R17ME2 ChIP - Array 1

source_name: H3R17ME2 ChIP


title: AML [1747_17jun08]

description: Not Applicable

value: NPM1 A


title: Staphylococcus aureus_OBPCP_60min_replicate5

description:
SAMPLE 15
OBPCP treatment


title: AML [2169_28may08]

description: Not Applicable


title: AML [1432_11jun08]

description: Not Applicable

value: NPM1 B


title: H3K27triM-array1

description:
control CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
H3K27triM ChIP - Array 1

source_name: H3K27triM ChIP

value: Upstate


title: Staphylococcus aureus_OBPCP_60min_replicate3

description:
SAMPLE 13
OBPCP treatment


title: Staphylococcus aureus_OBPCP_60min_replicate2

description:
SAMPLE 12
OBPCP treatment


title: Staphylococcus aureus_OBPCP_60min_replicate1

description:
SAMPLE 11
OBPCP treatment


title: XBP1-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
XBP1 ChIP - Array 1


title: H3K4mM-array1

description:
control CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
H3K4mM ChIP - Array 1

source_name: H3K4mM ChIP


title: AML [1316_20jun08]

description: Not Applicable


title: H3K4triM_E-array7

description:
control CEL files: input1-7.CEL, input2-7.CEL, input3-7.CEL
H3K4triM_E ChIP - Array 7


title: Staphylococcus aureus_OBPCP_10min_replicate5

description:
SAMPLE 10
OBPCP treatment

source_name: Staphylococcus aureus_OBPCP_10min


title: Staphylococcus aureus_OBPCP_10min_replicate4

description:
SAMPLE 9
OBPCP treatment


title: AML [2178_28may08]

description: Not Applicable


title: OAL5 (6042498027_E)

description:
OAL5
6042498027_E

source_name: gastrocnemius muscles

value: male

value: 24 months

value: gastrocnemius muscles

value: old ad libitum


title: VDR-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
VDR ChIP - Array 1

source_name: VDR ChIP

value: transgenic MCF7

value: VDR


title: OAL2 (6042498026_E)

description:
OAL2
6042498026_E


title: Staphylococcus aureus_OBPCP_10min_replicate3

description:
SAMPLE 8
OBPCP treatment

value: NCTC 8325