title: control tumor 3

city: Los Angeles

first: Erik

middle: S

last: Anderson

state: CA

address: 6-567 MRL, 675 Charles E. Young Drive South

department: MBIDP

institute: UCLA

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HJAY_r1.pgf
meta-probeset file: HJAY_r1.full.mps

source_name: U87 cell line

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: U87 cell line xenografted onto mice and allowed to grow into tumors

extract_protocol: All samples were separated for RNA and protein level analysis.  Total RNA was isolated using Trizol reagent (Invitrogen).  RNA samples were treated with Dnase and subsequently phenol-chloroform extracted prior to labeling.

treatment_protocol: Xenografted mice were treated identically during this study.

tag: xenograft recipient mice strain

value: NOD/SCID/gamma


title: RXF 393_Passage 4 xenograft_R5

status: Public on Jul 01 2013

type: RNA

city: Frederick

first: Luke

middle: Hunter

last: Stockwin

state: MD

address: Ft. Detrick

department: DTP

country: USA

institute: NCI Frederick

description:
RXF 393 P04 T5
Gene expression data from RXF 393 Passage 4 xenograft.

hyb_protocol: Samples were hybridized according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

scan_protocol: Microarray images were captured using a GeneChip® 3000 Scanner.

data_processing: Affymetrix Expression Console v1.3.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: RXF 393, passage 4 xenograft

label_protocol: The RNA samples were submitted to Expression Analysis, Inc. (Durham, NC) for microarray analysis using the GeneChip® Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Samples were labeled according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

growth_protocol: All cell lines were obtained from the Division of Cancer Treatment and Diagnosis Tumor Repository (DTP, FNLCR, Frederick, MD) or American Type Culture Collection (ATCC) (Manassas, Va). In addition, the identities of all cell lines used in this study were confirmed using Identifiler® STR genotyping (Applied Biosystems). All mice used in the study were obtained from the Animal Production Program (FNLCR, Frederick, MD). Tumor cells for inoculation were derived from the 4th in vitro passage from cryopreserved cell stocks. Cells (1 x 10^7 cells/0.1 ml/inoculation) were inoculated subcutaneously into mice (n=10 or more mice depending on the tumor cell line). For comparative purposes, 2-3 samples of in vitro cultivated cells at passage 4 post-cryopreservation were also prepared for microarray analysis (P0). When tumors at P1, P4 and P10 reached approximately 500 mg (10x10 mm), 5 tumors were harvested, cut into small pieces and flash frozen in liquid nitrogen using pre-chilled tubes. Samples were transferred to a -70°C freezer for holding prior to processing. Serial tumor passage was achieved by harvesting donor tumor material (n=2 to 5 donors) at each passage, mincing the tumors (2x2 mm fragments), pooling the samples and inoculating the next recipients subcutaneously using tumor implant trocars. Athymic nude mice (nu/nu NCr) served as the primary host for most xenograft studies. In several instances (particularly with human leukemias and lymphomas) it was difficult to establish and passage tumors in nu/nu NCr mice. In these instances, SCID.NCr or NOD.SCID/NCr mice were assessed for suitability. In general, female mice were used as they are less aggressive, easily group-housed and routinely used in xenograft experiments. Male mice were used for prostate tumors (PC-3, PC-3/M). Finally, in those instances where hormone effects on tumor growth are important (e.g., estradiol-dependent breast), mice were supplemented with estradiol.

extract_protocol: Total RNA was isolated using RNeasy (Qiagen).

tag: originating cell line

value: RXF 393

tag: tumor type

value: poorly differentiated hypernephroma

tag: in vivo passage


title: lung cancer sample Case 3

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
raw ch1: US22502676_252252210471_S01_CGH_107_Sep09_1_2.txt
raw ch2: US22502676_252252210471_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from normal lung mucosa of 10 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent G2505B microarray scanner, protocol according to Agilent.

data_processing: Median Signal intensity minus median Background intensity; excluding negative values. To overcome potential wave bias due to differences in GC-content of the different chromosomal regions, a smoothing algorithm was applied on our dataset as described by van de Wiel et al, Bioinformatics 2009; 25(9):1099-1104.

molecule: genomic DNA

source_name: lung cancer

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA isolation protocol available via http://www.vumc.com/branch/microarrays/. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

treatment_protocol: Sequential series of 10 μm FFPE-sections of each tissue specimen were used for DNA extraction.

tag: tissue

value: lung

tag: gender

value: male

source_name: normal lung mucosa, pooled DNA from 10 individuals

value: female


title: Q607_Tumour_Roche

city: Brisbane

first: Peter

last: Simpson

address: Royal Brisbane & Women's Hospital

department: UQ Centre for Clinical Research

country: Australia

institute: The University of Queensland

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays and incubated overnight at 48C. After hybridisation, BeadChips were washed and subjected to single-base extension and allele-specific staining.

scan_protocol: BeadChips were coated with XC4/ethanol , dried for 1 hour and scanned on an iScan System (Illumina) using 'Infinium HD' scan settings.

data_processing: Overall SNP call rates and B allele frequency (BAF) and log R ratio (LRR) values for each SNP were extracted, calculated and exported using GenomeStudio version2010.3 (Illumina). The BAF, LRR and copy number calls were visualized/calculated using the genoCN method (Sun et al. Nucleic Acids Research 2009; 37(16): 5365-5377), implemented in R version 2.15.0.

label: C-Bio and A-DNP

source_name: Breast Tumour

label_protocol: 100ng of DNA was subjected to FFPE DNA Restore. DNA was labelled according to the Infiniium HD FFPE Assay protocol. The genomic DNA samples were denatured using 0.1N NaOH, neutralised using RPM buffer before being whole-genome amplified in an overnight reaction at 37C using the MSM amplification master mix. After incubation the amplified DNA was fragmented with a fragmentation mix (FMS), precipitated with isopropanol and a precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Tumour cores were punched from the FFPE blocks to enrich for tumour epithelial cells. Extraction of genomic DNA from these FFPE cores was performed using two different methods: the DNeasy Blood and Tissue Kit (QIAGEN) and the High Pure DNA Template Preparation Kit (Roche). Both methods were performed according to the manufacturer’s instructions with the following exceptions for both techniques: (i) some tissue samples were pre-treated in 1M sodium thiocyanate overnight at 37oC to remove cross-links and (ii) for all cases an extended tissue digestion step was performed over three nights with supplementary Proteinase K added every 24 hours. Eluted DNA was assessed for purity using the Nanodrop-2000 and double stranded DNA was quantified using the Qubit® fluorometer (Invitrogen) as per manufacturer’s instructions.

tag: year of diagnosis

tag: sample type

value: Surgical

tag: tissue type

value: FFPE

tag: tissue histology

value: IDC-NST, grade 3

tag: tumor immunophenotype

value: ER +ve; PgR -ve; HER2 -ve

tag: dna extraction method

value: Roche

tag: sodium thiocyanate treatment performed

value: YES

tag: ffpe restore performed


title: Control- P7R2

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

country: Sweden

institute: Umeå University

description:
Stimulated T cells
Sample name: P7R2

hyb_protocol: Standard Illumina hybridization protocol. Illumina HT-12 v.4 arrays.

scan_protocol: Standard Illumina scanning protocol. Scanned in a BeadArray reader.

data_processing: The data were normalised using quantile normalisation in the GenomeStudio Gene expression module.

label: biotin

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit. Quality control was performed with the Agilent Bioanalyzer.

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with the Agilent Bioanalyzer.

tag: disease state

value: Stimulated T cells (control)

tag: tumor/control

value: Control

tag: cpg island methylator phenotype (cimp) subgroup


title: head and neck cancer sample Case 3

source_name: head and neck cancer

value: tonsil


title: RXF 393_originating cell line_R1

description:
RXF 393 P0 T1
Gene expression data from RXF 393 originating cell line.

source_name: RXF 393, originating cell line


title: RXF 393_originating cell line_R2

description:
RXF 393 P0 T2
Gene expression data from RXF 393 originating cell line.


title: control tumor 1

tag: xenograft recipient mice strain


title: control tumor 2


title: Q607_Tumour_Roche_no sodium thiocyanate

value: NO


title: EGFRvIII tumor 2


title: cervical cancer sample Case 1

description:
raw ch1: US22502676_252252210471_S01_CGH_107_Sep09_1_1.txt
raw ch2: US22502676_252252210471_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from normal lung mucosa of 10 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

source_name: cervical cancer

value: cervix uteri


title: Control- S1PHA

description:
Stimulated T cells
Sample name: S1PHA


title: EGFRvIII tumor 1

value: NOD/SCID/gamma


title: lung cancer sample Case 1


title: T-ALL sample 38

description:
BM TALL sample
Sample name: 38

value: BM TALL sample

value: Tumor


title: EGFRvIII tumor 3


title: PC-3/M_Passage 10 xenograft_R5

description:
PC-3/M P10 T5
Gene expression data from PC-3/M Passage 10 xenograft.

source_name: PC-3/M, passage 10 xenograft

tag: originating cell line

value: adenocarcinoma prostate PC-3 subline isolated from liver metastasis in mice


title: Q590_Tumour_Roche_replicate 1

value: ER +ve; PgR +ve; HER2 3+


title: T-ALL sample 36

description:
BM TALL sample
Sample name: 36


title: V.2 with array type Cotton from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description: In this study we characterized the fiber transcriptomes of the two species, Gossypium hirsutum and Gossypium barbadense that were parental genotypes of a RIL mapping population used previously for phenotypic QTL and expression QTL mapping., We used 454 deep pyrosequencing to characterize cDNAs from developing fibers at two key developmental time-points; 10 and 22 days post anthesis. A unigene set was assembled and annotated, and differential digital gene expression was assessed from the different time-point and genotype representations of the reads within assembled contigs. As a complementary approach, we conducted microarray-based hybridization profiling using the cotton Affymetrix gene chip and labeled cDNAs from fibers at 11 dpa and for the same two genotypes and compared differentially expressed genes identified by the two platforms. The 454 unigenes were also mined for the presence of microsatellite repeats and SNPs that will be useful markers for mapping and marker-assisted selection in cotton improvement.

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Gossypium barbadense

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: seed - Grown in soil in temperature controlled glasshouse with natural lighting. 30oC day, 22oC night cycle

treatment_protocol: no treatment

tag: genotype

tag: age

value: 11 days post-anthesis (DPA)

value: fiber

tag: harvest date


title: Ezh2_PL2F8_2 of 2

city: ROCHESTER

first: Haojie

last: Huang

state: MINNESOTA

address: 200 1st ST SW

institute: Mayo Clinic

description: Ezh2 ChIP vs. input in PL2F8 ES cells

hyb_protocol: http://www.nimblegen.com/products/lit/06584098001_NG_Epigenetics_UGuide_v1p0.pdf Chapter 4. Hybridizing & Washing

scan_protocol: http://www.nimblegen.com/products/lit/06584098001_NG_Epigenetics_UGuide_v1p0.pdf Chapter 5. Scanning Two-Color Arrays

data_processing:
http://www.nimblegen.com/products/lit/06584098001_NG_Epigenetics_UGuide_v1p0.pdf Chapter 6. Extracting Data with DEVA Software
Signal intensity data is extracted from the scanned images of each array using Roche NimbleGen NimbleScan software. Signal intensities for each probe are saved in pair files (.pair), the raw data format for ChIP-chip experiments. The log2 normalized ratio for each sample in the matrix table is the ratio of the input signals for the ChIP samples and their corresponding Input samples that were co-hybridized to the array. The log2 ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

organism: Mus musculus

source_name: Input DNA of PL2F8 murine ES cells

label_protocol: http://www.nimblegen.com/products/lit/06584098001_NG_Epigenetics_UGuide_v1p0.pdf  Chapter 3. Labeling Samples

growth_protocol: PL2F8 cells were cultured in KNOCKOUTTM DMEM medium (Invitrogen) supplemented with 15% embryonic stem screened FBS (Hyclone), 0.1 mM, 2-mercaptoethanol, 1 mM L-glutamine (Invitrogen) and 103 unit/ml LIF (Millipore) on 0.1% gelatin-coated dishes. Cells were cultured at 37°C supplied with 5% CO2.

extract_protocol: Brca1 wild-type (AB2.2) and Brca1 deficient (PL2F8) ES cells were harvested and subjected to ChIP assay with Ezh2 antibody. Fragmented DNA obtained from ChIP assay was repaired by DNA Terminator End Repair Kit (Lucigen Corporation, Middleton, WI) and purified by QIAquick PCR purification kit. Then two unidirectional linkers JW102 and JW103 were annealed and ligated to the blunt ends DNA at 16°C overnight. The purified products were amplified to 2 μg by LM-PCR. NimbleGen Mouse ChIP 3x720K RefSeq Promoter Array (Roche) were used for the hybridization.

tag: cell line

value: PL2F8 ES cell line [Shyam K. Sharan lab (National Cancer Institute at Frederick, Frederick, MD, USA]

tag: strain

tag: antibody

source_name: ChIP enriched DNA with Ezh2 antibody (Cell Signaling, Catalog No. #5246, Lot No. 4)

value: Ezh2 (Catalog No. #5246, Lot No. 4)


title: PC-3/M_Passage 10 xenograft_R3

description:
PC-3/M P10 T3
Gene expression data from PC-3/M Passage 10 xenograft.

tag: tumor type

tag: in vivo passage


title: Ezh2_AB2.2_1 of 2

description: Ezh2 ChIP vs. input in AB2.2 ES cells

source_name: Input DNA of AB2.2 murine ES cells

growth_protocol: AB2.2 cells were cultured in KNOCKOUTTM DMEM medium (Invitrogen) supplemented with 15% embryonic stem screened FBS (Hyclone), 0.1 mM, 2-mercaptoethanol, 1 mM L-glutamine (Invitrogen) and 103 unit/ml LIF (Millipore) on 0.1% gelatin-coated dishes. Cells were cultured at 37°C supplied with 5% CO2.

value: AB2.2 ES cell line [Shyam K. Sharan lab (National Cancer Institute at Frederick, Frederick, MD, USA]


title: Q590_Tumour_Roche_replicate 2

tag: year of diagnosis

tag: sample type

value: Surgical

tag: tissue type

value: FFPE

tag: tissue histology

value: IDC-NST, grade 3

tag: tumor immunophenotype

value: Roche


title: G.30 with array type Cotton from Affymetrix

organism: Gossypium hirsutum

value: Guazuncho 2

tag: tissue


title: T-ALL sample 34

description:
BM TALL sample
Sample name: 34

tag: disease state

tag: tumor/control

tag: cpg island methylator phenotype (cimp) subgroup


title: Q607_Normal

source_name: Normal Blood

value: Blood

value: whole blood

tag: dna extraction method

value: Qiagen blood maxi kit

tag: sodium thiocyanate treatment performed

value: NO

tag: ffpe restore performed


title: Q590_Tumour_Roche_non-restored

value: YES


title: Q590_Tumour_Roche_replicate 3


title: Ezh2_PL2F8_1 of 2

description: Ezh2 ChIP vs. input in PL2F8 ES cells

tag: cell line


title: PC-3/M_Passage 10 xenograft_R1

description:
PC-3/M P10 T1
Gene expression data from PC-3/M Passage 10 xenograft.

tag: originating cell line

value: adenocarcinoma prostate PC-3 subline isolated from liver metastasis in mice


title: Q590_Tumour_Roche_no sodium thiocyante_replicate 2

value: ER +ve; PgR +ve; HER2 3+


title: V.1 with array type Cotton from Affymetrix

tag: genotype

tag: age

value: 11 days post-anthesis (DPA)

tag: harvest date


title: PC-3/M_Passage 10 xenograft_R2

description:
PC-3/M P10 T2
Gene expression data from PC-3/M Passage 10 xenograft.

tag: tumor type

tag: in vivo passage


title: Q590_Tumour_Roche_no sodium thiocyante_replicate 1

tag: year of diagnosis

tag: sample type

tag: tissue type


title: T-ALL sample 26

description:
BM TALL sample
Sample name: 26

value: BM TALL sample

value: Tumor


title: PC-3/M_Passage 10 xenograft_R4

description:
PC-3/M P10 T4
Gene expression data from PC-3/M Passage 10 xenograft.


title: Ezh2_AB2.2_2 of 2

description: Ezh2 ChIP vs. input in AB2.2 ES cells

tag: strain

tag: antibody

value: Ezh2 (Catalog No. #5246, Lot No. 4)


title: T-ALL sample 27

description:
BM TALL sample
Sample name: 27

tag: disease state

tag: tumor/control


title: G.29 with array type Cotton from Affymetrix

tag: tissue

value: fiber


title: T-ALL sample 32

description:
BM TALL sample
Sample name: 32

tag: cpg island methylator phenotype (cimp) subgroup


title: PC-3/M_Passage 4 xenograft_R5

description:
PC-3/M P04 T5
Gene expression data from PC-3/M Passage 4 xenograft.

source_name: PC-3/M, passage 4 xenograft


title: PC-3/M_Passage 4 xenograft_R4

description:
PC-3/M P04 T4
Gene expression data from PC-3/M Passage 4 xenograft.


title: T-ALL sample 23

description:
BM TALL sample
Sample name: 23


title: Q590_Tumour_FreshFrozen_replicate 3

value: Surgical

value: fresh frozen

tag: tissue histology

tag: tumor immunophenotype

tag: dna extraction method

value: Qiagen

tag: sodium thiocyanate treatment performed

tag: ffpe restore performed


title: T-ALL sample 23 repeat

description:
Replicate of Sample 23
Sample name: 23-II


title: T-ALL sample 20

description:
BM TALL sample
Sample name: 20


title: Ezh2_NS_R1

description: Ezh2 ChIP vs. input in R1 ES cells transfected with control siRNA

source_name: Input DNA of R1 ES cells

growth_protocol: R1 ES cells were cultured in KNOCKOUTTM DMEM medium (Invitrogen) supplemented with 15% embryonic stem screened FBS (Hyclone), 0.1 mM, 2-mercaptoethanol, 1 mM L-glutamine (Invitrogen) and 103 unit/ml LIF (Millipore) on 0.1% gelatin-coated dishes. Cells were cultured at 37°C supplied with 5% CO2.

extract_protocol: R1 ES cells were transfected with control siRNA and Brca1 specific siRNA. At 48h after transfection, cells were harvested and subjected to ChIP assay with Ezh2 antibody. Fragmented DNA obtained from ChIP assay was repaired by DNA Terminator End Repair Kit (Lucigen Corporation, Middleton, WI) and purified by QIAquick PCR purification kit. Then two unidirectional linkers JW102 and JW103 were annealed and ligated to the blunt ends DNA at 16°C overnight. The purified products were amplified to 2 μg by LM-PCR.

treatment_protocol: R1 ES cells were transfected with control siRNA.

tag: cell line

value: R1 murine ES cell line [ATCC SCRC-1011]

tag: transfection

value: control siRNA

source_name: ChIP enriched DNA with Ezh2 antibody (Cell signaling technology, Catalog #5246, Lot 4)

value: anti-Ezh2  (Cell signaling technology, Catalog #5246, Lot 4)


title: Q590_Tumour_FreshFrozen_replicate 1

value: IDC-NST, grade 3


title: Q590_Tumour_FreshFrozen_replicate 2


title: PC-3/M_Passage 4 xenograft_R1

description:
PC-3/M P04 T1
Gene expression data from PC-3/M Passage 4 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: PC-3/M_Passage 4 xenograft_R2

description:
PC-3/M P04 T2
Gene expression data from PC-3/M Passage 4 xenograft.


title: T-ALL sample 19

description:
BM TALL sample
Sample name: 19


title: T-ALL sample 13

description:
BM TALL sample
Sample name: 13


title: PC-3/M_Passage 4 xenograft_R3

description:
PC-3/M P04 T3
Gene expression data from PC-3/M Passage 4 xenograft.


title: T-ALL sample 25

description:
BM TALL sample
Sample name: 25


title: T-ALL sample 18

description:
BM TALL sample
Sample name: 18


title: PC-3/M_Passage 1 xenograft_R4

description:
PC-3/M P01 T4
Gene expression data from PC-3/M Passage 1 xenograft.

source_name: PC-3/M, passage 1 xenograft


title: PC-3/M_Passage 1 xenograft_R3

description:
PC-3/M P01 T3
Gene expression data from PC-3/M Passage 1 xenograft.


title: PC-3/M_Passage 1 xenograft_R5

description:
PC-3/M P01 T5
Gene expression data from PC-3/M Passage 1 xenograft.


title: T-ALL sample 10

description:
BM TALL sample
Sample name: 10


title: Ezh2_siBr_R1

description: Ezh2 ChIP vs. input in R1 ES cells transfected with Brca1 specific siRNA

treatment_protocol: R1 ES cells were transfected with Brca1 specific siRNA.

value: Brca1 specific siRNA


title: PC-3/M_Passage 1 xenograft_R2

description:
PC-3/M P01 T2
Gene expression data from PC-3/M Passage 1 xenograft.


title: PC-3/M_Passage 1 xenograft_R1

description:
PC-3/M P01 T1
Gene expression data from PC-3/M Passage 1 xenograft.


title: T-ALL sample 16

description:
BM TALL sample
Sample name: 16


title: Q590_Normal_replicate 2

tag: year of diagnosis

tag: sample type

value: Blood

tag: tissue type

value: whole blood

value: Qiagen blood maxi kit

value: NO


title: 540_Norm_Qia

source_name: Normal Lymph node

value: FFPE

value: YES


title: HBEC3_p53_KRAS_cMYC_R10_c8

first: Jill

middle: Everland

last: Larsen

state: Queensland

address: Rode Road, Chermside

department: Thoracic Medicine

institute: The Prince Charles Hospital

description: Sample name: HBEC3-KTRL53Mc8(R10)

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing:
Bead-level data were obtained using GenomeStudio (Gene expression Version 1.7.0).
Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

source_name: Human bronchial epithelial cell (HBEC) immortalized with cdk4 and hTERT

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

growth_protocol: Cells were grown in adherent conditions and cell pellets were harvested when cells were ~70% confluent.

extract_protocol: RNA was isolated using RNeasy mini kit (QIAGEN, Valencia, CA) and quality was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).

value: yes

tag: cmyc

tag: soft agar clone

tag: growth media


title: T-ALL sample 5

description:
BM TALL sample
Sample name: 5

tag: disease state

value: BM TALL sample

tag: tumor/control

value: Tumor

tag: cpg island methylator phenotype (cimp) subgroup


title: 318_Tumour_Roche

value: Surgical

tag: tissue histology

tag: tumor immunophenotype

value: ER +ve; PgR +ve; HER2 -ve

tag: dna extraction method

value: Roche


title: Q590_Normal_replicate 1

tag: sodium thiocyanate treatment performed

tag: ffpe restore performed


title: PC-3/M_originating cell line_R3

description:
PC-3/M P0 T3
Gene expression data from PC-3/M originating cell line.

source_name: PC-3/M, originating cell line

tag: originating cell line

value: adenocarcinoma prostate PC-3 subline isolated from liver metastasis in mice


title: T-ALL sample 1

description:
BM TALL sample
Sample name: 1


title: HBEC3_p53_KRAS_cMYC_R10_c2

description: Sample name: HBEC3-KTRL53Mc2(R10)


title: PC-3_Passage 10 xenograft_R5

description:
PC-3 P10 T5
Gene expression data from PC-3 Passage 10 xenograft.

source_name: PC-3, passage 10 xenograft

tag: tumor type

value: adenocarcinoma prostate


title: PC-3/M_originating cell line_R2

description:
PC-3/M P0 T2
Gene expression data from PC-3/M originating cell line.

tag: in vivo passage


title: PC-3_Passage 10 xenograft_R4

description:
PC-3 P10 T4
Gene expression data from PC-3 Passage 10 xenograft.


title: T-ALL sample 7

description:
BM TALL sample
Sample name: 7


title: 540_Tumour_Qia

source_name: Breast Tumour

tag: year of diagnosis

value: ER +ve; PgR +ve; HER2 3+

value: Qiagen


title: 540_Norm_Roche

tag: sample type


title: 318_Norm_Qia

tag: tissue type


title: HBEC3_p53_KRAS_cMYC_R10_c1

description: Sample name: HBEC3-KTRL53Mc1(R10)

tag: cmyc


title: PC-3_Passage 10 xenograft_R3

description:
PC-3 P10 T3
Gene expression data from PC-3 Passage 10 xenograft.


title: 540_Tumour_Roche

value: IDC-NST, grade 3


title: PC-3/M_originating cell line_R1

description:
PC-3/M P0 T1
Gene expression data from PC-3/M originating cell line.


title: 276_Tumour_Qia

value: ER -ve; PgR -ve; HER2 3+


title: PC-3_Passage 10 xenograft_R1

description:
PC-3 P10 T1
Gene expression data from PC-3 Passage 10 xenograft.


title: PC-3_Passage 10 xenograft_R2

description:
PC-3 P10 T2
Gene expression data from PC-3 Passage 10 xenograft.


title: 318_Norm_Roche


title: HBEC3_p53_KRAS_cMYC_R10

description: Sample name: HBEC3-KTRL53M22(R10)

tag: soft agar clone

value: no


title: HBEC3_p53_KRAS_R10_c9

description: Sample name: HBEC3-KTRL53c9(R10)

tag: growth media


title: 318_Tumour_Qia


title: 276_Norm_Roche


title: HBEC3_p53_KRAS_R10_c8

description: Sample name: HBEC3-KTRL53c8(R10)


title: HBEC3_p53_KRAS_cMYC_KSFM

description: Sample name: HBEC3-KTRL53M22

value: KSFM


title: PC-3_Passage 4 xenograft_R5

description:
PC-3 P04 T5
Gene expression data from PC-3 Passage 4 xenograft.

source_name: PC-3, passage 4 xenograft


title: PC-3_Passage 4 xenograft_R3

description:
PC-3 P04 T3
Gene expression data from PC-3 Passage 4 xenograft.


title: 007_Tumour_Roche_non-restored

value: ER -ve; PgR -ve; HER2 -ve

value: NO


title: HBEC3_p53_KRAS_R10_c7

description: Sample name: HBEC3-KTRL53c7(R10)


title: 276_Tumour_Roche

value: FFPE

value: YES


title: 007_Tumour_Qia_non-restored


title: HBEC3_p53_KRAS_cMYC_R10_c7

description: Sample name: HBEC3-KTRL53Mc7(R10)

value: yes


title: PC-3_Passage 4 xenograft_R4

description:
PC-3 P04 T4
Gene expression data from PC-3 Passage 4 xenograft.


title: PC-3_Passage 4 xenograft_R2

description:
PC-3 P04 T2
Gene expression data from PC-3 Passage 4 xenograft.


title: HBEC3_p53_KRAS_R10_c6

description: Sample name: HBEC3-KTRL53c6(R10)


title: HBEC3_p53_KRAS_R10_c11

description: Sample name: HBEC3-KTRL53c11(R10)


title: HBEC3_p53_KRAS_R10_c5

description: Sample name: HBEC3-KTRL53c5(R10)


title: PC-3_Passage 4 xenograft_R1

description:
PC-3 P04 T1
Gene expression data from PC-3 Passage 4 xenograft.


title: HBEC3_p53_KRAS_R10_c1

description: Sample name: HBEC3-KTRL53c1(R10)


title: Scramble shRNA, undifferentiated

city: Birmingham

first: Hao

last: Jiang

state: AL

address: 1825 University Blvd

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

description:
Scramble shRNA, undifferentiated
SAMPLE E; 5110583017_E

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Results were analyzed by GeneSpring GX 10.0.2. Genes were filtered on Flags Present or Marginal. Signals were normalized against the median in each sample.

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit for Illumina arrays

growth_protocol: E14 cells were cultured on 0.1% gelatinized tissue-culture plates in complete ESC growth medium supplemented with LIF

extract_protocol: Total RNAs were extracted using the RNeasy kit (Qiagen).

treatment_protocol: Cells stably infected with viruses expressing indicated shRNAs were either untreated or treated with retinoic acid (RA) for differentiation (four days depletion of LIF followed by four days of 1 µM all-trans RA on monolayer culture.

tag: cell type

value: E14 cells

tag: infected with

value: Scramble shRNA (control)

tag: genotype/variation

value: control

tag: treated with

tag: differentiation status

value: undifferentiated


title: AKAP95 shRNA, undifferentiated

description:
AKAP95 shRNA, undifferentiated
SAMPLE F; 5110583017_F

source_name: E14_AKAP95 KD_undifferentiated

value: AKAP95 shRNA

value: AKAP95 knockdown


title: PC-3_Passage 1 xenograft_R5

description:
PC-3 P01 T5
Gene expression data from PC-3 Passage 1 xenograft.

source_name: PC-3, passage 1 xenograft

value: adenocarcinoma prostate


title: 007_Tumour_Qia_replicate 2

value: Surgical

tag: tissue histology

tag: tumor immunophenotype

tag: dna extraction method

value: Qiagen


title: 007_Tumour_Roche

value: IDC-NST, grade 3

value: Roche

tag: sodium thiocyanate treatment performed

tag: ffpe restore performed


title: PC-3_Passage 1 xenograft_R2

description:
PC-3 P01 T2
Gene expression data from PC-3 Passage 1 xenograft.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: 276_Norm_Qia

tag: year of diagnosis

tag: sample type

tag: tissue type


title: 007_Tumour_Qia_replicate 1


title: AKAP95 shRNA, RA-differentiated

description:
AKAP95 shRNA, RA-differentiated
SAMPLE B; 5110583017_B

source_name: E14_AKAP95 KD_differentiated

value: retinoic acid (RA)

value: RA-differentiated


title: HBEC3_p53_KRAS_R10

description: Sample name: HBEC3-KTRL53(R10)

tag: cmyc

value: no

tag: soft agar clone

tag: growth media


title: HBEC3_p53_KRAS_KSFM

description: Sample name: HBEC3-KTRL53(new)

value: KSFM


title: 80_Tumour_Qia

source_name: Tumour Bone metastasis

value: Autopsy

value: FFPE

value: YES


title: PC-3_Passage 1 xenograft_R1

description:
PC-3 P01 T1
Gene expression data from PC-3 Passage 1 xenograft.


title: Scramble shRNA, RA-differentiated

description:
Scramble shRNA, RA-differentiated
SAMPLE A; 5110583017_A

tag: cell type

value: E14 cells

tag: infected with

value: Scramble shRNA (control)

tag: genotype/variation


title: 74_Tumour_Roche_replicate 2

source_name: Tumour lung metastasis

tag: tissue histology


title: 007_Norm_Qia

tag: tumor immunophenotype


title: 80_Norm_Qia

source_name: Normal Kidney

tag: dna extraction method


title: PC-3_Passage 1 xenograft_R3

description:
PC-3 P01 T3
Gene expression data from PC-3 Passage 1 xenograft.


title: PC-3_Passage 1 xenograft_R4

description:
PC-3 P01 T4
Gene expression data from PC-3 Passage 1 xenograft.


title: wt DP with Dex+ culture, biological rep1

status: Public on Jun 24 2013

city: Kobe

first: Masaki

last: Okano

state: Hyogo

address: 2-2-3 Minatojima-Minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description:
Dex+_wildtype_1
Flk1+/PDGFRa+ mesoderm cells derived from wildtype ES cells, with further 4-days culture in the presence of dexamethasone to activate Gata4GR transgene.

hyb_protocol: The 10 micro-g cRNA was hybridized at 45 C for 16 hours on the GeneChip Mouse Genome 430 2.0 array (Affymetrix) according to the Affymetrix Standard Protocol. GeneChips were washed and stained using the EukGE-Ws2v5_450 protocol in the Affymetrix Fluidics Station 450.

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

data_processing: Data values were calculated using the Bioconductor implementation (affy module) of the RMA algorithm in conjunction with quantiles normalisation of perfect match values (mismatches ignored). The specific function call used was: expresso(data, bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=median.polish).

label_protocol: Biotinylated cRNA were prepared using a two-cycle target-labeling assay according to the Affymetrix protocol from 50 ng total RNA (Small Sample Labeling Protocol Version II).

growth_protocol: ES cells were plated onto a type IV collagen-coated 10-cm dish in the differentiation medium (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 4 days.

extract_protocol: Total RNA was isolated by TRIZOL Reagent (Invitrogen) and cleaned up by the RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocols.

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using anti-Flk1 and anti-PDGFRa antibodies.  Flk1/PDGFRa double-positive cells were sorted by FACS-Aria (BD Biosciences). The cells were further cultured on type IV collagen-coated dishes in the differentiation medium  (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 4 days in the presence of dexamethasone.

tag: background strain

value: 129sv/Jae ES cell line (J1)

tag: genotype

value: wildtype, stably expressing Gata4-glucocorticoid receptor ligand-binding domain fusion gene

tag: clone name

value: Flk1+/PDGFRa+ mesoderm cells

tag: gata4gr induction

value: yes


title: 74_Tumour_Roche_replicate 1

tag: sodium thiocyanate treatment performed

tag: ffpe restore performed


title: mt DP with Dex- culture, biological rep2

description:
Dex-_mutant_2
Flk1+/PDGFRa+ mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- ES cells, with further 4-days culture in the absence of dexamethasone (without Gata4GR induction).

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using anti-Flk1 and anti-PDGFRa antibodies.  Flk1/PDGFRa double-positive cells were sorted by FACS-Aria (BD Biosciences). The cells were further cultured on type IV collagen-coated dishes in the differentiation medium  (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 4 days in the absence of dexamethasone.

value: Dnmt3a-/-Dnmt3b-/-, stably expressing Gata4-glucocorticoid receptor ligand-binding domain fusion gene


title: wt DP with Dex+ culture, biological rep2

description:
Dex+_wildtype_2
Flk1+/PDGFRa+ mesoderm cells derived from wildtype ES cells, with further 4-days culture in the presence of dexamethasone to activate Gata4GR transgene.


title: mt DP with Dex+ culture, biological rep2

description:
Dex+_mutant_2
Flk1+/PDGFRa+ mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- ES cells, with further 4-days culture in the presence of dexamethasone to activate Gata4GR transgene.


title: 74_Norm_Roche_replicate 2

tag: year of diagnosis

tag: sample type


title: mt DP with Dex- culture, biological rep1

description:
Dex-_mutant_1
Flk1+/PDGFRa+ mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- ES cells, with further 4-days culture in the absence of dexamethasone (without Gata4GR induction).


title: wt DP with Dex- culture, biological rep1

description:
Dex-_wildtype_1
Flk1+/PDGFRa+ mesoderm cells derived from wildtype ES cells, with further 4-days culture in the absence of dexamethasone (without Gata4GR induction).


title: mt DP with Dex+ culture, biological rep1

description:
Dex+_mutant_1
Flk1+/PDGFRa+ mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- ES cells, with further 4-days culture in the presence of dexamethasone to activate Gata4GR transgene.


title: DP from wt ES, biological rep1

description:
DP_wildtype_p_1
Flk1+/PDGFRa+ mesoderm cells derived from wildtype ES cells.

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using anti-Flk1 and anti-PDGFRa antibodies. Flk1/PDGFRa double-positive cells were sorted by FACS-Aria (BD Biosciences).

value: wildtype


title: DP from mt ES, biological rep2

description:
DP_mutant_2
Flk1+/PDGFRa+ mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- ES cells.


title: DP from wt ES, biological rep2

description:
DP_wildtype_2
Flk1+/PDGFRa+ mesoderm cells derived from wildtype ES cells.


title: wt DP with Dex- culture, biological rep2

description:
Dex-_wildtype_2
Flk1+/PDGFRa+ mesoderm cells derived from wildtype ES cells, with further 4-days culture in the absence of dexamethasone (without Gata4GR induction).


title: PE from mt ES, biological rep2

description:
PE_mutant_2
Primitive endoderm cells directly differentiated from Dnmt3a-/-Dnmt3b-/- ES cells.

source_name: Primitive endoderm cells directly differentiated from Dnmt3a-/-Dnmt3b-/- mouse ES cells by activation of Gata4GR transgene

growth_protocol: ES cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 10% fetal calf serum (FCS), 0.1 mM nonessential amino acids (Invitrogen), 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, and 2000 U/ml leukemia inhibitory factor (LIF) on gelatinized culture dishes without feeder cells.

treatment_protocol: 100 nM dexamethasone (Dex) was added to ES cells stably expressing Gata4GR. Total RNA was prepared 4 days after addition of Dex.

value: primitive endoderm cells


title: 007_Norm_Roche

value: Surgical

tag: tissue type

value: Roche


title: 74_Norm_Roche_replicate 1


title: 74_Tumour_Qia_replicate 1

value: Qiagen


title: mt ES, biological rep2

description:
ES_mutant_2
Undifferentiated Dnmt3a-/-Dnmt3b-/- mouse ES cells.

source_name: Undifferentiated Dnmt3a-/-Dnmt3b-/- mouse ES cells, without Gata4GR induction

treatment_protocol: The cells were lysed in TRIZOL reagent and used for RNA preparation.

value: undifferentiated mouse ES cells

value: no


title: mt ES, biological rep1

description:
ES_mutant_1
Undifferentiated Dnmt3a-/-Dnmt3b-/- mouse ES cells.


title: 74_Norm_Qia_replicate 2

value: Autopsy


title: PE from wt ES, biological rep1

description:
PE_wildtype_1
Primitive endoderm cells directly differentiated from wildtype ES cells.

source_name: Primitive endoderm cells directly differentiated from wildtype mouse ES cells by activation of Gata4GR transgene


title: wt ES, biological rep2

description:
ES_wildtype_2
Undifferentiated wildtype mouse ES cells.

source_name: Undifferentiated wildtype mouse ES cells, without Gata4GR induction


title: PE from wt ES, biological rep2

description:
PE_wildtype_2
Primitive endoderm cells directly differentiated from wildtype ES cells.


title: Control_siRNA_TGFbeta_2

status: Public on Jun 20 2013

city: Basel

first: Neha

last: Tiwari

address: Mattenstrasse 28

country: Switzerland

institute: University of Basel

hyb_protocol: Hybridization was performed according to the standard Affymetrix procedure.

scan_protocol: Scanning was performed with Affymetrix GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Probesets were summarized and probeset-level values normalized with the rma(target=core) function from R/Bioconductor package oligo (version 1.14.0).

source_name: NMuMG, control siRNA, TGFβ treated

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen).

treatment_protocol: NMuMG cells were transfected with control siRNA (siControl) or siRNA against Sox4 (siSox4) in the presence (2 days) or absence of 2ng/ml TGFβ.

tag: cell line

value: NMuMG

tag: sirna

value: control

tag: treatment

value: TGFβ


title: PE from mt ES, biological rep1

description:
PE_mutant_1
Primitive endoderm cells directly differentiated from Dnmt3a-/-Dnmt3b-/- ES cells.

tag: cell type


title: Control_siRNA_2

source_name: NMuMG, control siRNA, no treatment


title: E13.5 brain_Nf2 cKO_rep 3

status: Public on Jun 19 2013

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description:
cao020
Gene expression data from E13.5 mouse dorsal telencephalon lacking Nf2.

hyb_protocol: Following fragmentation, 5 micrograms of biotinylated cRNA was hybridized for 16 hr at 45C on an array (Affymetrix HT MG-430 PM Array Plate). GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Signals from scanned arrays were summarized using the RMA method. Data from E11.5 and E13.5 mice were summarized as two separate groups. For the RMA summarization, the E11.5 data were generated using Affymetrix Expression Console v1.1, while the E13.5 data were generated using Partek Genomics Suite software v6.5.

source_name: E13.5 mouse dorsal telencephalon, Nf2 knockout

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT Express protocol starting with 100 ng of total RNA (GeneChip 3' IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix).

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

treatment_protocol: Tissues were dissected in cold PBS, frozen in ethanol/dry ice slurry, and stored at -80 degree.

tag: genetic background

value: mixed

tag: tissue

value: dorsal telencephalon

tag: age


title: 74_Tumour_Qia_replicate 2

value: FFPE

tag: tissue histology

tag: tumor immunophenotype

tag: dna extraction method

value: YES


title: Control_siRNA_1


title: wt ES, biological rep1

description:
ES_wildtype_1
Undifferentiated wildtype mouse ES cells.

tag: background strain

value: 129sv/Jae ES cell line (J1)

tag: genotype

value: wildtype, stably expressing Gata4-glucocorticoid receptor ligand-binding domain fusion gene

tag: clone name


title: E13.5 brain_Nf2 cKO_rep 1

description:
cao018
Gene expression data from E13.5 mouse dorsal telencephalon lacking Nf2.


title: E11.5 brain_control_rep 3

description:
cao014
Gene expression data from E11.5 mouse forebrain and midbrain with basal levels of YAP activity.

source_name: E11.5 mouse forebrain and midbrain, YAP control

value: forebrain and midbrain

value: Nes-rtTA


title: DP from mt ES, biological rep1

description:
DP_mutant_p_1
Flk1+/PDGFRa+ mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- ES cells.

value: Flk1+/PDGFRa+ mesoderm cells

tag: gata4gr induction


title: 74_Norm_Qia_replicate 1

tag: year of diagnosis

tag: sodium thiocyanate treatment performed

tag: ffpe restore performed


title: E13.5 brain_Nf2 control_rep 2

description:
cao016
Gene expression data from E13.5 mouse dorsal telencephalon lacking one allele of Nf2.

source_name: E13.5 mouse dorsal telencephalon, Nf2 control


title: E11.5 brain_control_rep 2

description:
cao012
Gene expression data from E11.5 mouse forebrain and midbrain with basal levels of YAP activity.


title: E11.5 brain_dTG_rep 1

description:
cao009
Gene expression data from E11.5 mouse forebrain and midbrain with high levels of YAP activity.

source_name: E11.5 mouse forebrain and midbrain, YAP overexpression


title: EWI-2 KD cells 1

status: Public on Jun 15 2013

city: Clayton

first: Konstantin

last: Knoblich

state: VIC

address: 15 Innovation Walk

department: Biochemistry and Molecular Biology

institute: Monash University

description: EWI-2 KD1

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed. The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: Data are processed using GenePattern. The ExpressionFileCreator module is used to normalize (RMA normalization algorithm) and create processed file (gct).

source_name: SK-mel-28, EWI-2 knockdown

label_protocol: RNA is converted to cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: Stably transfected cells with either shRNA for EWI-2 or control vector were collected and pelleted.

extract_protocol: Total RNA was extracted and purified using RNeasy kit (Qiagen) from each pellet.

tag: shRNA


title: EWI-2 KD cells 2

description: EWI-2 KD2


title: Control cells 2

description: Control 2

source_name: SK-mel-28, control


title: Control cells 1

description: Control 1


title: E13.5 brain_Nf2 cKO_rep 2

description:
cao019
Gene expression data from E13.5 mouse dorsal telencephalon lacking Nf2.


title: E11.5 brain_dTG_rep 2

description:
cao011
Gene expression data from E11.5 mouse forebrain and midbrain with high levels of YAP activity.


title: Brg1-/- replicate 1

status: Public on Jun 04 2013

city: Boston

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

hyb_protocol: According to the manufacturer’s instructions

scan_protocol: GeneChip arrays were scanned according Affymetrix standard protocol using Scanner type M10

data_processing: MAS 5.0 algorithm

source_name: Brg1-deficient MEFs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Primary mouse embryonic fibroblasts were harvested from E13.5 embryos and maintained in DMEM containing 10% FBS, 1% NEAA, 2mm glutamine

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

treatment_protocol: Cre was introduced into the cells via retroviral infection and selected in media containing 2.5ug/ml puromycin.

tag: strain background

value: C57BL/6 and 129 mixed

tag: genotype/variation

value: Primary mouse embryonic fibroblasts (MEFs)


title: 446134A01 - mtr4_2 vs. WT_2

status: Public on Jun 30 2013

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

description: Identification and comparison of the RNA substrates that accumulate in hen2 and mtr4 mutants.

hyb_protocol: WT_2 Cy5 / mtr4_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: InnoScan900_MAPIX, Cy3:pmt voltage 532nm,650V,laser power 5%, Cy5:635nm,pmt voltage 700V,laser power 5%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green). For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - Media   MS agar + 0.5% glucose  hygrometry   n.d.  Temperature   20°C  Light   16 h light/8h darkness

treatment_protocol: No treatment

tag: ecotype

value: Columbia

value: wild-type

tag: harvest date

tag: genotype/variation = mtr4 mutant


title: 436357A03 - WT_2 vs. mtr4_2

hyb_protocol: mtr4_2 Cy5 / WT_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: mtr4 mutant


title: Brg1-/- replicate 3

tag: cell type


title: 449095A01 - WT_2 vs. hen2_2

hyb_protocol: hen2_2 Cy5 / WT_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: hen2 mutant


title: 446134A03 - hen2_1 vs. WT_1

hyb_protocol: WT_1 Cy5 / hen2_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype/variation = hen2 mutant


title: 446134A02 - WT_1 vs. hen2_1

hyb_protocol: hen2_1 Cy5 / WT_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 436357A01 - WT_1 vs. mtr4_1

hyb_protocol: mtr4_1 Cy5 / WT_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Snf5-/- replicate 3

source_name: Snf5-deficient MEFs


title: Snf5-/- replicate 2


title: 449095A02 - hen2_2 vs. WT_2

hyb_protocol: WT_2 Cy5 / hen2_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 436357A02 - mtr4_1 vs. WT_1

hyb_protocol: WT_1 Cy5 / mtr4_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: E11.5 brain_dTG_rep 3

description:
cao013
Gene expression data from E11.5 mouse forebrain and midbrain with high levels of YAP activity.

tag: genetic background

tag: tissue

tag: age


title: E13.5 brain_Nf2 control_rep 1

description:
cao015
Gene expression data from E13.5 mouse dorsal telencephalon lacking one allele of Nf2.

tag: genotype


title: WT replicate 3

source_name: WT MEFs

value: wild type


title: Snf5-/- replicate 1


title: WT replicate 2


title: WT replicate 1


title: Control_siRNA_TGFbeta_1

tag: cell line

value: NMuMG

tag: sirna

value: control

tag: treatment

value: TGFβ


title: Mutant testes at P21, biological rep1

status: Public on Jun 01 2013

city: Taipei

first: Hsiang-Ying

last: Chen

address: 128 Sec. 2, Academia Rd.

country: Taiwan

institute: IBMS

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneChIP Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: testes, Dazap1 mutant

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

growth_protocol: Testes were dissected from P21 mice.

treatment_protocol: Not applicable.

tag: strain

value: mixed C57BL/6 and 129

value: Dazap1 mutant

value: testes


title: Mutant testes at P21, biological rep3


title: Wild-type testes at P21, biological rep3

source_name: testes, wild-type


title: Mutant testes at P21, biological rep2


title: Wild-type testes at P21, biological rep1


title: Wild-type testes at P21, biological rep2


title: Adult mutant testis, biological rep3

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes, and centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450.

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core). Exon-level expression were summarized from the corrected intensities and then quantile normalized.
Probe group file: MoEx-1_0-st-v1.r2.pgf
Meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: testes, Dazap1 mutant, adult

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Testes were dissected from P21 and adult mice.

extract_protocol: All RNA samples were prepared using Trizol. The cDNA synthesis and amplification were performed using the WT cDNA synthesis and amplification kit (Affymetrix).

value: adult


title: Adult mutant testis, biological rep2


title: Adult mutant testis, biological rep1


title: Wild-type testis at P21, biological rep1

source_name: testes, wild-type, P21


title: Wild-type testis at P21, biological rep3


title: Wild-type testis at P21, biological rep2


title: Brg1-/- replicate 4


title: Breast cancer, T94_9_12_04

status: Public on May 26 2013

city: Dublin

first: Colin

last: Clarke

address: Collin's Av.

department: NICB

country: Ireland

institute: Dublin City University

description: Breast cancer data.

hyb_protocol: Hybridisation solution (1 mol/l NaCl, 20 mmol/1 EDTA, 100 mmol/1 2-(N-morpholino) ethanesulfonic acid, and 0.01% Tween 20) was used to pre-hybridise Affymetrix U133 Plus 2.0 oligonucleotide microarrays for 10 minutes at 45°C and 60 rpm. The pre-hybridisation solution was removed and replaced with 200 μl hybridisation solution containing 0.05 μg/μl fragmented cRNA. The arrays were hybridised for 16 hours at 45°C and 60 rpm. Arrays were subsequently washed (Affymetrix Fluidics Station 400) and stained with streptavidin-phycoerythrin (Stain Buffer, 2 mg/ml acetylated BSA and 10 μg/ml streptavidin R-phycoerythrin; Molecular Probes, Inc., Eugene, OR).

scan_protocol: Arrays were scanned on an Affymetrix GCS GeneChip GeneArray scanner. Resulting data was analysed using GCOS, dCHIP, and GeneSpring (Agilent Technologies).

data_processing: All microarray data were called using the GC robust multichip average method (GC-RMA). R and Bioconductor - GCRMA package.

source_name: Breast tissue, cancer

label_protocol: 100 ng of each specimen was amplified and labelled using the Affymetrix GeneChip Eukaryotic 2 Cycle Labelling Assays for Expression Analysis, (Affymetrix; 900494) according to the manufacturer's instructions (www.affymetrix.com/products/reagents/specific/cdna2.affx).

extract_protocol: Samples were homogenised, on ice, in 1 ml TriReagent (Sigma; Poole, UK) and total RNA was subsequently isolated according to the manufacturer's instructions. RNA quantity and purity were assessed at 260 nm and 280 nm using a Nanodrop (ND-1000; Labtech. International); an Agilent Bioanalyser (Agilent 2100; Agilent Technologies) was used to assess RNA qualitatively after isolation and, subsequently, following biotin-labelling and after fragmentation.

treatment_protocol: Tissues were stored at -70°C/-80°C prior to RNA isolation.

value: breast cancer

tag: size

tag: grade

tag: lymph node status

tag: relapse free survival time_days

tag: relapse free survival event

tag: overall survival time_days

tag: overall survival event


title: Breast cancer, T99_20_12_04

description: Breast cancer data.


title: Breast cancer, T98_22_12_04

description: Breast cancer data.


title: Breast cancer, T71_14_12_04

description: Breast cancer data.


title: Breast cancer, T9A_9_12_04

description: Breast cancer data.


title: Breast cancer, T97_3_12_04

description: Breast cancer data.


title: Breast cancer, T70_21_12_04

description: Breast cancer data.


title: Breast cancer, T83_8_12_04

description: Breast cancer data.


title: Breast cancer, T82_15_12_04

description: Breast cancer data.


title: Breast cancer, T80_14_12_04

description: Breast cancer data.


title: Breast cancer, T65_20_12_04

description: Breast cancer data.


title: Breast cancer, T75

description: Breast cancer data.


title: Breast cancer, T72_14_12_04

description: Breast cancer data.


title: E11.5 brain_control_rep 1

description:
cao010
Gene expression data from E11.5 mouse forebrain and midbrain with basal levels of YAP activity.

value: mixed

value: forebrain and midbrain

value: Nes-rtTA


title: Breast cancer, T73_15_12_04

description: Breast cancer data.


title: Breast cancer, T62_26_1_05

description: Breast cancer data.


title: Breast cancer, T69_15_12_04

description: Breast cancer data.


title: Breast cancer, T81_10_12_04

description: Breast cancer data.


title: Breast cancer, T52_15_12_04

description: Breast cancer data.


title: Breast cancer, T66_25_1_05

description: Breast cancer data.


title: Brg1-/- replicate 2

tag: strain background

value: C57BL/6 and 129 mixed

tag: genotype/variation

tag: cell type

value: Primary mouse embryonic fibroblasts (MEFs)


title: Breast cancer, T63_22_12_04

description: Breast cancer data.

tag: tissue


title: Breast cancer, T5_10_12_04

description: Breast cancer data.

tag: age


title: Breast cancer, T49_10_12_04

description: Breast cancer data.


title: Breast cancer, T56_15_12_04

description: Breast cancer data.


title: Breast cancer, T47_20_12_04

description: Breast cancer data.


title: Breast cancer, T51_7_12_04

description: Breast cancer data.


title: Breast cancer, T45_7_12_04

description: Breast cancer data.


title: E13.5 brain_Nf2 control_rep 3

description:
cao017
Gene expression data from E13.5 mouse dorsal telencephalon lacking one allele of Nf2.

tag: genetic background

value: dorsal telencephalon

tag: genotype


title: Breast cancer, T41_20_12_04

description: Breast cancer data.


title: Breast cancer, T43_9_12_04

description: Breast cancer data.


title: Breast cancer, T39_14_12_04

description: Breast cancer data.


title: Breast cancer, T35_3_12_04

description: Breast cancer data.


title: Breast cancer, T36_15_12_04

description: Breast cancer data.


title: Breast cancer, T20_20_12_04

description: Breast cancer data.


title: Breast cancer, T22_10_12_04

description: Breast cancer data.


title: Breast cancer, T38_25_1_05

description: Breast cancer data.


title: Breast cancer, T32_3_12_04

description: Breast cancer data.


title: Breast cancer, T21_21_12_04

description: Breast cancer data.


title: Breast cancer, T34_20_12_04

description: Breast cancer data.


title: Breast cancer, T24_10_12_04

description: Breast cancer data.


title: Breast cancer, T30_8_12_04

description: Breast cancer data.


title: Breast cancer, T33_3_12_04

description: Breast cancer data.


title: Breast cancer, T2_7_12_04

description: Breast cancer data.


title: Breast cancer, T40_9_12_04

description: Breast cancer data.


title: Breast cancer, T23_9_12_04

description: Breast cancer data.


title: Breast cancer, T134_7_12_04

description: Breast cancer data.


title: Breast cancer, T29_14_12_04

description: Breast cancer data.


title: Breast cancer, T131_22_12_04

description: Breast cancer data.


title: Breast cancer, T128_22_12_04

description: Breast cancer data.


title: Breast cancer, T13_9_12_04

description: Breast cancer data.


title: Breast cancer, T129_20_12_04

description: Breast cancer data.


title: Breast cancer, T132

description: Breast cancer data.


title: Breast cancer, T18_22_12_04

description: Breast cancer data.


title: Breast cancer, T127_8_12_04

description: Breast cancer data.


title: Breast cancer, T14_21_12_04

description: Breast cancer data.


title: Breast cancer, T119_8_12_04

description: Breast cancer data.


title: Breast cancer, T114_7_12_04

description: Breast cancer data.


title: Breast cancer, T125_21_12_04

description: Breast cancer data.


title: Breast cancer, T130_8_12_04

description: Breast cancer data.


title: Breast cancer, T124_25_1_05

description: Breast cancer data.


title: Breast cancer, T12_22_12_04

description: Breast cancer data.


title: Breast cancer, T122_9_12_04

description: Breast cancer data.


title: Breast cancer, T115_15_12_04

description: Breast cancer data.


title: Breast cancer, T123_14_12_04

description: Breast cancer data.


title: Breast cancer, T120_10_12_04

description: Breast cancer data.


title: Breast cancer, T109_21_12_04

description: Breast cancer data.


title: Breast cancer, T113_22_12_04

description: Breast cancer data.


title: Breast cancer, T111_14_12_04

description: Breast cancer data.


title: Breast cancer, T108_21_12_04

description: Breast cancer data.


title: Breast cancer, T106_21_12_04

description: Breast cancer data.


title: Breast cancer, T112_3_12_04

description: Breast cancer data.


title: Breast cancer, T107_7_12_04

description: Breast cancer data.


title: Breast cancer, T11_21_12_04

description: Breast cancer data.


title: Breast cancer, T103_9_12_04

description: Breast cancer data.


title: Breast cancer, T104_9_12_04

description: Breast cancer data.


title: Breast cancer, T105B

description: Breast cancer data.


title: Breast cancer, T67_7_12_04

description: Breast cancer data.


title: Breast cancer, T10_8_12_04

description: Breast cancer data.


title: Breast cancer, S7_14_12_04

description: Breast cancer data.


title: Breast cancer, T101A_9_12_04

description: Breast cancer data.


title: Breast cancer, S38_10_12_04

description: Breast cancer data.


title: Breast cancer, S31_3_12_04

description: Breast cancer data.


title: Breast cancer, S35_8_12_04

description: Breast cancer data.


title: Breast cancer, S33_3_12_04

description: Breast cancer data.


title: Breast cancer, S30_14_12_04

description: Breast cancer data.


title: Breast cancer, S37_8_12_04

description: Breast cancer data.


title: Breast cancer, T1_14_12_04

description: Breast cancer data.


title: Breast cancer, S29_10_12_04

description: Breast cancer data.


title: Breast cancer, S22_9_12_04

description: Breast cancer data.


title: Breast cancer, S5_15_12_04

description: Breast cancer data.


title: Breast cancer, S3_20_12_04

description: Breast cancer data.


title: Breast cancer, S26_10_12_04

description: Breast cancer data.


title: Breast cancer, S36_20_12_04

description: Breast cancer data.


title: Breast cancer, S32_3_12_04

description: Breast cancer data.


title: Breast cancer, S6_20_12_04

description: Breast cancer data.


title: Breast cancer, S20_14_12_04

description: Breast cancer data.


title: Breast cancer, S2_15_12_04

description: Breast cancer data.


title: Breast cancer, S15_15_12_04

description: Breast cancer data.


title: Breast cancer, S28_7_12_04

description: Breast cancer data.


title: Breast cancer, S14_21_12_04

description: Breast cancer data.


title: Breast cancer, S1_21_12_04

description: Breast cancer data.


title: Breast cancer, S18_22_12_04

description: Breast cancer data.


title: Normal breast, P5_21_12_04

description: Normal breast tissue data.

source_name: Breast tissue, normal

value: normal breast


title: Breast cancer, S11_14_12_04

description: Breast cancer data.


title: Breast cancer, S10_22_12_04

description: Breast cancer data.


title: Breast cancer, S16_20_12_04

description: Breast cancer data.


title: Normal breast, P4_14_12_04

description: Normal breast tissue data.


title: Normal breast, P3_22_12_04

description: Normal breast tissue data.


title: Normal breast, P9_25_1_05

description: Normal breast tissue data.


title: Normal breast, P8_25_1_05

description: Normal breast tissue data.


title: Normal breast, P18_25_1_05

description: Normal breast tissue data.


title: Normal breast, P12_25_1_05

description: Normal breast tissue data.


title: Normal breast, P14_25_1_05

description: Normal breast tissue data.


title: Normal breast, P13_25_1_05

description: Normal breast tissue data.


title: Normal breast, P10_26_1_05

description: Normal breast tissue data.


title: Normal breast, N5_15_12_04

description: Normal breast tissue data.


title: Normal breast, N6_14_12_04

description: Normal breast tissue data.


title: Normal breast, P21_25_1_05

description: Normal breast tissue data.


title: Normal breast, N4_14_12_04

description: Normal breast tissue data.


title: Rorc KO Th17 cells

status: Public on Apr 17 2013

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from Rorc KO Th17 cells.

hyb_protocol: For each sample, 1.12 ug of Cy3-labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

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

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

source_name: Sorted naïve TH cells (CD4+CD25–CD62Lhigh) from RORc-/- mice, differentiated under TH17 polarizing conditions

label_protocol: Starting with 100ng of total RNA, Cy3-labeled cRNA was produced according to the manufacturer's protocol.

growth_protocol: Naïve Th cells (CD4+CD25-CD62Lhigh) were isolated from RORc+/+ and RORc-/- mice by negative selection using MACS. Cells were cultured in T cell growth media (DMEM, 10%FBS).

extract_protocol: Cells were washed with PBS and then frozen at -80 C until used. Total RNAs were purified with the RNeasy mini kit from Qiagen (Valencia, CA) as by the manufacturer's instructions.

treatment_protocol: Naïve T cells were differentiated under TH17 polarizing conditions (TGFb plus IL-6 in the presence of plate-bound anti-CD3/CD28 mAbs) for 4 days.

value: RORc-/-

value: Th17 cells


title: Breast cancer, S25_10_12_04

description: Breast cancer data.


title: Normal breast, P11_25_1_05

description: Normal breast tissue data.


title: Normal breast, P1_15_12_04

description: Normal breast tissue data.


title: WT naïve T cells

description: Gene expression from WT naïve T cells.

source_name: Sorted naïve TH cells (CD4+CD25–CD62Lhigh) from RORc+/+ mice, undifferentiated

value: WT

value: naïve T cells


title: WT Th17 cells

description: Gene expression from WT Th17 cells.

source_name: Sorted naïve TH cells (CD4+CD25–CD62Lhigh) from RORc+/+ mice, differentiated under TH17 polarizing conditions


title: Rorc KO naïve T cells

description: Gene expression from Rorc KO naïve T cells.

source_name: Sorted naïve TH cells (CD4+CD25–CD62Lhigh) from RORc-/- mice, undifferentiated


title: S06_11735_B8 [mRNA]

status: Public on Apr 12 2013

city: Iowa City

first: Ramakrishna

last: Sompallae

state: IA

address: 285 Newton Road, 5292 CBRB

department: Iowa Institute of Human Genetics

institute: University of Iowa

hyb_protocol: Refer to the Illumina whole-genome DASL Assay System Manual

data_processing: For each probe, replicate mesurements were averaged after removing outliers. Data were were then quantile normalized using R version 2.12

source_name: Metastatic ASPS

extract_protocol: Total RNA was extracted from FFPE samples, cleaned up, and eluted using the RNeasy MiniKit and RNeasy MinElute Cleanup Kit, respectively (Qiagen), according to the manufacturer’s protocol

value: Alveolar soft part sarcoma (ASPS)

tag: tissue type

value: Metastatic ASPS


title: S03M38586_K [mRNA]

scan_protocol: Refer to the Illumina whole-genome DASL Assay System Manual

source_name: Primary ASPS

value: Primary ASPS


title: S06_00168_A1 [mRNA]

label_protocol: Refer to the Illumina whole-genome DASL Assay System Manual


title: Normal breast, N1_15_12_04

description: Normal breast tissue data.


title: S07_15708_C2 [mRNA]


title: S01_35393_5 [mRNA]


title: BS06_22715_A1 [mRNA]


title: N24802_A4 [mRNA]


title: S03F41873_H [mRNA]


title: R23751_A9 [mRNA]


title: K53653_B2 [mRNA]


title: K31695_A3 [mRNA]


title: R23751_A8 [mRNA]


title: S07_8430_A1 [mRNA]


title: ERF6-IOE line, 4h DEX-treated, biological repeat 1

status: Public on Apr 06 2013

city: Ghent

first: Marieke

last: Dubois

address: Technologiepark 927

department: PSB

country: Belgium

institute: VIB-PSB

hyb_protocol: Standard Agronomics protocol.

scan_protocol: Standard Agronomics protocol.

data_processing: Data was processed with Robust Multichip Average (RMA) (background correction, normalization, and summarization) as implemented in BioConductor (Irizarry et al., 2003a; Irizarry et al., 2003b; Gentleman et al., 2004). The Brainarray agronomics1_TAIR9_gene.cdf Chip Definition File (CDF) was used to assign probes to genes (Brainarray). The BioConductor package Limma as well as the Rank Products method was used to identify differentially expressed genes (Breitling et al., 2004; Smyth, 2004).

label_protocol: Standard Affymetrix protocol.

growth_protocol: Plants were grown on MS medium under 16 h light/ 8 h dark cycle at 22°C.

extract_protocol: RNeasy plant mini kit (Qiagen), according to the manufacturer's protocol.

treatment_protocol: Plants were transferred to MS medium containing 5uM dexamethasone for 4 hours.

tag: ecotype

value: leaf 3

tag: treatment

value: 5uM dexamethasone


title: Control line, 4h DEX-treated, biological repeat 1


title: ERF6-IOE line, 4h DEX-treated, biological repeat 2


title: 6993 - YOC

status: Public on Mar 18 2013

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

description: Human knee joint.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with Partek.

source_name: Knee meniscus, young, chondrosis

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

growth_protocol: Injured meniscus tissue was isolated from patients undergoing arthroscopic partial meniscectomy.

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

tag: patient

value: undergoing meniscetomy

value: knee meniscus

value: young (<40 years)

tag: Sex

value: female

tag: body mass index (bmi)

value: obese

tag: chondrosis status

value: chondrosis


title: Control line, 4h DEX-treated, biological repeat 3


title: 6983 - YW1

description: Human knee joint.

source_name: Knee meniscus, young, no chondrosis

value: male

value: overweight

value: no chondrosis


title: ANAS_RNA_13days_rep3

status: Public on Mar 01 2013

city: Berkeley

first: Kimberlee

last: West

address: 207 O'Brien Hall

department: Civil and Environmental Engineering

institute: University of California, Berkeley

description:
RNA9-ANASTimecourse.
Dehalococcoides-containing mixed enrichment culture.

hyb_protocol: RNA was digested to fragments from 50 to 200 bp in length.  Fragmented RNA was hybridized on the custom GeneChip Dehalococcoides Genus-wide Array for 16 hr at 45C and 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data analysis was performed using Affymetrix GeneChip software and the MAS5.0 algorithm. Each microarray was normalized by scaling the signal intensities of the positive control spike-mix to a target signal intensity of 2500 to allow comparison between microarrays.

organism: Dehalococcoides

source_name: ANAS culture RNA taken 13 days after the addition of TCE when all chlorinated ethenes have been depleted for about 9 days

label_protocol: Biotinylated RNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA (Section 3, Chapter 3, GeneChip Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The enrichment culture was maintained in a semi-batch reactor with a 14-day cycle of lactate and trichloroethene amendments.

extract_protocol: Total nucleic acids were extracted with a standard phenol-chloroform-isoamylalcohol protocol. DNA and RNA were separated and purified with the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer's instructions. RNA samples were additionally treated using the AllPrep DNA/RNA Mini Kit (Qiagen) and the DNase-free kit (Ambion) following the manufacturer's instructions to remove any residual DNA.

tag: time point in batch cycle

value: 3:13 days after the addition of TCE

tag: biological replicate


title: 6988 - OW3

description: Human knee joint.

source_name: Knee meniscus, old, chondrosis

value: old (>40 years)


title: 6985 - OL1

description: Human knee joint.

source_name: Knee meniscus, old, no chondrosis

value: lean


title: ANAS_RNA_54hr_rep1

description:
RNA2-ANASTimecourse.
Dehalococcoides-containing mixed enrichment culture.

source_name: ANAS culture RNA taken 54 hrs after the addition of TCE while VC is the only chlorinated ethene present in the sample

value: 2:54 hrs after the addition of TCE


title: ANAS_RNA_27hr_rep2

description:
RNA4-ANASTimecourse.
Dehalococcoides-containing mixed enrichment culture.

source_name: ANAS culture RNA taken 27 hrs after the addition of TCE while TCE, DCE, and VC are present in the sample

value: 1:27 hrs after the addition of TCE


title: ANAS_RNA_13days_rep2

description:
RNA6-ANASTimecourse.
Dehalococcoides-containing mixed enrichment culture.


title: 6989 - OO1

description: Human knee joint.


title: ANAS_RNA_27hr_rep3

description:
RNA7-ANASTimecourse.
Dehalococcoides-containing mixed enrichment culture.


title: ANAS_RNA_54hr_rep2

description:
RNA5-ANASTimecourse.
Dehalococcoides-containing mixed enrichment culture.


title: ANAS_RNA_27hr_rep1

description:
RNA1-ANASTimecourse.
Dehalococcoides-containing mixed enrichment culture.


title: Control line, 4h DEX-treated, biological repeat 2


title: 6986 - OL2

description: Human knee joint.


title: 6991 - YLC

description: Human knee joint.


title: 6990 - OO2

description: Human knee joint.


title: 6982 - YL1

description: Human knee joint.


title: 6992 - YOA

description: Human knee joint.


title: 6984 - YW2

description: Human knee joint.


title: 6987 - OW2

description: Human knee joint.


title: ANAS_RNA_54hr_rep3

description:
RNA8-ANASTimecourse.
Dehalococcoides-containing mixed enrichment culture.


title: ANAS_RNA_13days_rep1

description:
RNA3-ANASTimecourse.
Dehalococcoides-containing mixed enrichment culture.


title: Vibrio vulnificus IscR transcriptome analysis 6

status: Public on Feb 27 2013

city: Seoul

first: Jonggyu

last: Lim

address: Gwanak 599

country: South Korea

institute: Seoul National University

hyb_protocol: 1) Activate slide in pre-Hybridization buffer for 30-60 min at 42°C; 2) Wash the slide with D.W.; 3) Dry the slide with centrifugation (700 rpm) for 5 min.; 4) Add the 35 µl of hybridization buffer into the dried labeled sample tube; 5) Denaturation (95°C, 5min); 6) Centrifuge for 2 min at 11,000 rpm; 7) Mix two labeled samples well; 8) Attach the MAUI lid (heating 65°C); 9) Inject the labeled samples; 10) Sealing; 11) Mix in Lid + slide MAUI Hybridization system (42°C, 16 hrs).

scan_protocol: After hybridization, the arrays were washed, dried and scanned using GenePix 4000B (Axon Instruments, Foster City, CA).

data_processing: Data from three independent experiments were normalized using the Lowess-based intensity/location-dependent normalization method (Yang et al., 2002, Nucleic Acid Research. 30:e15), and then analyzed using the GenePix Pro 3.0 software (Axon Instruments).

organism: Vibrio vulnificus MO6-24/O

source_name: Total cellular RNA from the wild-type V. vulnificus strain

label_protocol: To synthesize aminoallyl-cDNA, reactions were performed with an Amino Allyl cDNA Labeling Kit (Ambion, Austin, TX) according to the manufacturer's procedures with 50 µg of total RNA. The aminoallyl-cDNA from the iscR mutant and wild type were respectively labeled with Cy5 and Cy3 (Ambion).

growth_protocol: The V. vulnificus strains were grown in Luria-Bertani medium supplemented with 2.0% (w/v) NaCl (LBS). All of the media components were purchased from Difco.

extract_protocol: Total cellular RNA from the V. vulnificus strains grown to OD600 0.5 was isolated using an RNeasy® Mini Kit (Qiagen, Valencia, CA), and any residual DNA was removed using DNase I (NEB, Ipswich, MA).

value: wild-type

source_name: Total cellular RNA from the iscR mutant V. vulnificus strain

value: iscR mutant


title: Vibrio vulnificus IscR transcriptome analysis 5


title: Vibrio vulnificus IscR transcriptome analysis 4


title: Vibrio vulnificus IscR transcriptome analysis 3


title: Vibrio vulnificus IscR transcriptome analysis 1


title: Vibrio vulnificus IscR transcriptome analysis 2


title: Senescent post-selection day 7 shtandem Rep1

status: Public on Jan 31 2013

city: Cold Spring Harbor

first: Agustin

last: Chicas

state: NY

address: One Bungtown Road

institute: Memorial Sloan Kettering

description:
S7_shtandemA
Gene expression data from senescent IMR90 cells (PS7) with Jarid1a and Jarid1b hairpin.

hyb_protocol: Hybridization to Human Gene ST 1.0 GeneChips (Affymetrix) was as described in Expression Analysis Technical Manual Affymetrix P/N 702232 Rev 2 (16 hours, 45 degress at 60 rpm). The Wash and Stain Protocol was as described in FS450_0004 using GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Scanning was performed using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with the GC-RMA (Robust Multi-Array Averaging with GC content correction) method of the Bioconductor R package to subtract background, normalize intensities and summarize gene expression levels.

source_name: IMR90, Jarid1a and Jarid1b shRNA, senescent

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human IMR90 cells with different conditions were grown at 37C at 5% CO2. Total RNA was extracted seven (7) days after the end of puromycin selection.

extract_protocol: Total RNA was extracted with the RNeasy Mini Kit (QIAGEN) and utilized for cRNA expression with Message Amp II (Ambion).

treatment_protocol: Human fibroblast (IMR90) cells were infected with retroviral vectors expresssing shRNA targeting Jarid1, Jarid1b or both, and triggered to undergo quiescence by removal of serum or senescence by over-expression of activated ras (Hrasv12).

tag: cell line

value: human fetal lung fibroblast cell line

tag: shRNA

value: Jarid1a and Jarid1b

tag: growth state

value: senescent


title: Senescent post-selection day 7 shJarid1b Rep2

description:
S7_shjarid1bB
Gene expression data from senescent IMR90 cells (PS7) with Jarid1b hairpin.

source_name: IMR90, Jarid1b shRNA, senescent

tag: cell type


title: Senescent post-selection day 3 shtandem

description:
S3_shtandem
Gene expression data from senescent IMR90 cells (PS3) with Jarid1a and Jarid1b hairpin.


title: Quiescent shLuc

description:
LS_shLuc
Gene expression data from quiescent IMR90 cells with control hairpin (shLuciferase).

source_name: IMR90, control shRNA, quiescent

value: shLuciferase control

value: quiescent


title: Quiescent shtandem

description:
LS_shtandem
Gene expression data from quiescent IMR90 cells with Jarid1a and Jarid1b hairpin.

source_name: IMR90, Jarid1a and Jarid1b shRNA, quiescent


title: Senescent post-selection day 7 shJarid1b Rep1

description:
S7_shjarid1bA
Gene expression data from senescent IMR90 cells (PS7) with Jarid1b hairpin.


title: Senescent post-selection day 3 shJarid1a

description:
S3_shJarid1a
Gene expression data from senescent IMR90 cells (PS3) with Jarid1a hairpin.

source_name: IMR90, Jarid1a shRNA, senescent


title: Quiescent shJarid1b

description:
LS_shjarid1b
Gene expression data from quiescent IMR90 cells with Jarid1b hairpin.

source_name: IMR90, Jarid1b shRNA, quiescent


title: ERF6-IOE line, 4h DEX-treated, biological repeat 3

tag: tissue

value: leaf 3

value: 5uM dexamethasone


title: Senescent post-selection day 7 shJarid1a Rep1

description:
S7_shJarid1aA
Gene expression data from senescent IMR90 cells (PS7) with Jarid1a hairpin.


title: Growing shJarid1a

description:
G_shJarid1a
Gene expression data from growing IMR90 cells with Jarid1a hairpin.

source_name: IMR90, Jarid1a shRNA, growing

value: growing


title: Senescent post-selection day 7 shtandem Rep2

description:
S7_shtandemB
Gene expression data from senescent IMR90 cells (PS7) with Jarid1a and Jarid1b hairpin.


title: Senescent post-selection day 3 shLuc

description:
S3_shLuc
Gene expression data from senescent IMR90 cells (PS3) with control hairpin (shLuciferase).

source_name: IMR90, control shRNA, senescent


title: Growing shtandem

description:
G_shtandem
Gene expression data from growing IMR90 cells with Jarid1a and Jarid1b hairpin.

source_name: IMR90, Jarid1a and Jarid1b shRNA, growing


title: Quiescent shJarid1a

description:
LS_shJarid1a
Gene expression data from quiescent IMR90 cells with Jarid1a hairpin.

source_name: IMR90, Jarid1a shRNA, quiescent


title: Senescent post-selection day 3 shJarid1b

description:
S3_shjarid1b
Gene expression data from senescent IMR90 cells (PS3) with Jarid1b hairpin.


title: Senescent post-selection day 7 shJarid1a Rep2

description:
S7_shJarid1aB
Gene expression data from senescent IMR90 cells (PS7) with Jarid1a hairpin.


title: Senescent post-selection day 7 shLuc Rep1

description:
S7_shLucA
Gene expression data from senescent IMR90 cells (PS7) with control hairpin (shLuciferase).


title: pu1-D3-1,2

status: Public on May 04 2013

type: SRA

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: anti-PU.1 ChIP, Day 3, rep1

library_source: genomic

data_processing:
0) genome alignment: Data provided from University of Chicago sequencing center aligned to mm9.
1) peak calling: QuEST 2.4, using threshold of 15 against input (input.extended).
2) post-processing on peaks: threshold was raised from 15 to obtain a FDR (# input peaks/# ChIP peaks) of 1%.
3) peak comparison: final lists of peaks were obtained from replicates: for PU.1, took the coincident peaks between 2 replicates. For IRF-4, took peaks that were found in at least 2 of 3 replicates. Peak coincidence determined by peak positions within 200 bp.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Outputs from steps 2 and 3 are provided as processed data files.
Supplementary_files_format_and_content: GSM1133*.bed (linked to Sample records): Sequence enrichment processed by QuEST at a fixed 1% FDR.
Supplementary_files_format_and_content: GSE46607_*.bed (linked to Series record): QuEST output was merged to create a master peak list by identifying overlapping peaks within 200bp.

source_name: purified primary B cells from Bi-8i mice; stimulated for 3 Days; anti-PU.1 ChIP

growth_protocol: RPMI medium + 10% FCS and supplements (Hepes, 2-Me, glutamine, NEAA, Na-Pyruvate, Pen/Strep); isolated primary cells stimulated as indicated at a density of 0.5million/mL.

extract_protocol:
Lysates were clarified from sonicated nuclei, and transcription factor-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation, DNA was PCR amplified with Illumina primers for 12-14 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer 2 following the manufacturer's protocols.

treatment_protocol: NP-Ficoll (0.01 ng/mL) + CD40L + IL-2 + IL-4 + IL-5.

tag: strain/background

value: resting mature peripheral primary B cells

tag: stimulation duration

value: 3 days

tag: antibody

value: anti-PU.1 (Santa Cruz; sc-352)


title: Growing shJarid1b

description:
G_shjarid1b
Gene expression data from growing IMR90 cells with Jarid1b hairpin.

source_name: IMR90, Jarid1b shRNA, growing


title: Growing shLuc

description:
G_shLuc
Gene expression data from growing IMR90 cells with control hairpin (shLuciferase).

source_name: IMR90, control shRNA, growing


title: Primary tumor 28

status: Public on Jan 01 2013

city: London

first: Wei

last: Dai

address: Du Cane Road

department: Sugery and Cancer

country: United Kingdom

institute: Imperial College London

description: Primary intrahepatic cholangiocarcinoma, Thailand

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software methylation module 1.0.5

label: Cy5 and Cy3

source_name: primary intrahepatic cholangiocarcinoma

label_protocol: Standard Illumina Protocol

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with glutamine (2mM) and 10% fetal bovine serum in humidified 5% CO2 in air incubators at 37 ̊C.

extract_protocol: DNA was extracted and purified from cell lines using the Qiagen DNAeasy Tissue Kit according to standard instructions.

value: primary intrahepatic cholangiocarcinoma

tag: sample type

value: tumor tissue


title: Senescent post-selection day 7 shLuc Rep2

description:
S7_shLucB
Gene expression data from senescent IMR90 cells (PS7) with control hairpin (shLuciferase).


title: Primary tumor 26

description:
U090-T
Primary intrahepatic cholangiocarcinoma, Thailand.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchips using the standard Illumina protocol.

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

data_processing: BeadStudio software methylation module 1.0.5.

label_protocol: Standard Illumina Protocol.

extract_protocol: DNA was extracted and purified from cell lines using the Qiagen DNeasy Tissue Kit according to standard instructions.


title: Primary tumor 27

description:
U030-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 24

description:
P060-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 25

description:
P126-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 21

description:
R103-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 23

description:
T049-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 18

description:
U021-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 14

description:
U059-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 16

description:
T064-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 22

description:
W147-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 15

description:
W025-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 19

description:
T098-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 20

description:
R023-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 17

description:
T005-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 9

description:
R106-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 7

description:
P055-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 12

description:
U095-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 8

description:
P092-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 11

description:
U005-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 13

description:
U044-T
Primary intrahepatic cholangiocarcinoma, Thailand.


title: Primary tumor 6

description:
W022-T
Primary intrahepatic cholangiocarcinoma, Thailand, matched.

value: tumor tissue (W022)


title: Primary tumor 4

description:
W027-T
Primary intrahepatic cholangiocarcinoma, Thailand, matched.

value: tumor tissue (W027)


title: Primary tumor 3

description:
U064-T
Primary intrahepatic cholangiocarcinoma, Thailand, matched.

value: tumor tissue (U064)


title: Primary tumor 5

description:
N082-T
Primary intrahepatic cholangiocarcinoma, Thailand, matched.

value: tumor tissue (N082)