title: Tumor from ApcD14/+:Arrb2+/+ mouse 12

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 12


title: Tumor from ApcD14/+:Arrb2+/+ mouse 15

status: Public on Jan 20 2012

type: RNA

city: Montpellier

first: Caroline

last: Bonnans

address: 141 rue de la Cardonille

department: Oncology

country: France

institute: Functional Genomic Institute

hyb_protocol: The two labelled aRNA were mixed, fragmented and hybridized on one array of a Nimblegen 12-plex microarray according the manufacturer's instructions.

scan_protocol: Scanned on an Innopsys Innoscan900 scanner.

data_processing: Images were quantified using Nimblescan V2.5. The rawdata were normalized by Lowess and a quantile normalization was applied (Limma Package).

molecule: total RNA

organism: Mus musculus

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 15

label_protocol: For the preparation of the labelled Cy3- and Cy5- aRNA target, one microgram of total RNA samples were amplified and labelled using Amino Allyl Message Amp II aRNA amplification kit (Ambion, Austin, TX, USA), according the manufacturer’s instructions.

growth_protocol: Tumors kept in RNA later at -80°C before RNA extraction

extract_protocol: Total RNA extracted by RNable according to manufacturer's instructions

tag: strain

tag: mouse

tag: genotype/variation

tag: tissue

value: tumor

tag: sample type

value: Test

source_name: Pool of equimolar RNA of each sample

value: Reference


title: Tumor from ApcD14/+:Arrb2+/+ mouse 11

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 11


title: Tumor from ApcD14/+:Arrb2+/+ mouse 16

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 16


title: Tumor from ApcD14/+:Arrb2+/+ mouse 13

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 13


title: Tumor from ApcD14/+:Arrb2+/+ mouse 14

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 14


title: Tumor from ApcD14/+:Arrb2+/+ mouse 9

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 9


title: Tumor 5 from ApcD14/+ mouse 1

source_name: Tumor 5 from ApcD14/+ mouse 1

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


title: Tumor from ApcD14/+:Arrb2+/+ mouse 4

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 4


title: Tumor from ApcD14/+:Arrb2+/+ mouse 6

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 6


title: Tumor from ApcD14/+:Arrb2+/+ mouse 10

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 10


title: Tumor from ApcD14/+:Arrb2+/+ mouse 2

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 2


title: Tumor from ApcD14/+:Arrb2+/+ mouse 3

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 3


title: Tumor from ApcD14/+:Arrb2+/+ mouse 7

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 7


title: Tumor from ApcD14/+:Arrb2+/+ mouse 8

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 8


title: Tumor from ApcD14/+:Arrb2+/+ mouse 1

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 1


title: Tumor from ApcD14/+:Arrb2+/+ mouse 5

source_name: Tumor from ApcD14/+:Arrb2+/+ mouse 5


title: T47D, copy number variation SNP6.0 WYETH_BREAST replicate

type: genomic

city: San Diego

first: Keith

middle: A

last: Ching

state: CA

address: 10777 Science Center Dr.

department: Computational Sciences

country: USA

institute: Pfizer, Inc.

hyb_protocol: Protocol per manufacturer's protocol (Affymetrix, Santa Clara, CA).

data_processing: Affymetrix SNP6.0 data were processed using the aroma.affymetrix R package according to the methods of H. Bengtsson et al., (Bengtsson, Irizarry et al. 2008 [PMID 18204055]).

label: biotin

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: DNA were isolated using an DNeasy kit (Qiagen, Germantown, MD).

tag: cell line


title: MDAMB436, copy number variation SNP6.0 WYETH_BREAST replicate

scan_protocol: Protocol per manufacturer's protocol (Affymetrix, Santa Clara, CA).


title: SUM52PE, copy number variation SNP6.0 WYETH_BREAST replicate

label_protocol: Protocol per manufacturer's protocol (Affymetrix, Santa Clara, CA).


title: HCC2157, copy number variation SNP6.0 WYETH_BREAST replicate


title: SUM159PT, copy number variation SNP6.0 WYETH_BREAST replicate


title: MDAMB415, copy number variation SNP6.0 WYETH_BREAST replicate


title: MDAMB134VI, copy number variation SNP6.0 WYETH_BREAST replicate


title: HCC38, copy number variation SNP6.0 WYETH_BREAST replicate


title: SUM44PE, copy number variation SNP6.0 WYETH_BREAST replicate


title: n-3 PUFA endometrium, biological rep6, animal 7667

city: Athenry

first: Dermot

middle: G

last: Morris

state: Co. Galway

address: Animal & Grassland Research and Innovation Centre, Mellows Campus

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

description: Gene expression data from day 17 endometrium of n-3 PUFA fed heifers

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GCOS

data_processing: All microarray analyses including preprocessing, normalization and statistical analysis were carried out using R (R, 2007) version 2.6 and Bioconductor version 2.1. Data were quality assessed before and after normalization using a number of in-built quality control methods implemented in the Bioconductor affycoretools and associated packages. Microarray data were preprocessed using the mmgMOS normalization method using the default settings and differential expression (DE) was calculated using the puma DE method both implemented in the Bioconductor package “puma”. As many of the original annotations for the Affymetrix bovine chip are erroneous, remapped annotations were determined using the “bovinedaiplusv6cdf” chip definition file (CDF) which returned ‘Entrez Gene’ gene name identifiers. This annotation is based on the CDF-Merger procedure as described by De Leeuw et al. 2008, which generates a hybrid CDF based on the standard Affymetrix CDF (version 26) and the custom Brainarray (version 11.0.1) CDF.

organism: Bos taurus

source_name: Bovine endometrium on day 17; n-3 PUFA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 ug total RNA (Genechip® Expression Analysis Technical Manual, 2005-2008, Affymetrix). cRNA was subjected to two rounds of linear amplification using the GeneChip® Expression 3’-Amplification Two-Cycle cDNA Synthesis kit (Affymetrix Inc., Santa Clara, CA) according to the manufacturer’s instructions. cDNA was synthesized during the first cycle and biotin-labeled nucleotides were incorporated during the second in vitro transcription reaction.

extract_protocol: Total RNA was prepared from 100 mg of fragmented frozen endometrial tissue using the TRIzol extraction method. Samples were subsequently purified and treated for contaminating genomic DNA using RNeasy clean-up kits in accordance with manufacturer’s guidelines supplied (QIAGEN, Crawley, West Sussex, UK).

treatment_protocol: Intercaruncular endometrial tissue was collected by peeling from the underlying uterine myometrium and samples of approximately 4 cm2 and weighing 2.5 g were dissected. Samples

tag: treatment

value: n-3 PUFA

value: uterine endometrium

tag: genotype

value: Charolais X

tag: age

value: 2 yrs


title: n-3 PUFA endometrium, biological rep7, animal 7559


title: ZR7530, copy number variation SNP6.0 WYETH_BREAST replicate


title: SUM225CWN, copy number variation SNP6.0 WYETH_BREAST replicate


title: SKBR3, copy number variation SNP6.0 WYETH_BREAST replicate


title: MT3, copy number variation SNP6.0 WYETH_BREAST replicate


title: MDAMB468, copy number variation SNP6.0 WYETH_BREAST replicate


title: HCC202, copy number variation SNP6.0 WYETH_BREAST replicate


title: MDAMB157, copy number variation SNP6.0 WYETH_BREAST replicate


title: SUM149PT, copy number variation SNP6.0 WYETH_BREAST replicate


title: JIMT1, copy number variation SNP6.0 WYETH_BREAST replicate


title: UACC812, copy number variation SNP6.0 WYETH_BREAST replicate


title: HS578T, copy number variation SNP6.0 WYETH_BREAST replicate


title: SUM185PE, copy number variation SNP6.0 WYETH_BREAST replicate


title: MCF7, copy number variation SNP6.0 WYETH_BREAST replicate


title: HCC1954, copy number variation SNP6.0 WYETH_BREAST replicate


title: HCC1806, copy number variation SNP6.0 WYETH_BREAST replicate


title: n-3 PUFA endometrium, biological rep3, animal 7627


title: n-3 PUFA endometrium, biological rep2, animal 7641


title: MDAMB361, copy number variation SNP6.0 WYETH_BREAST replicate


title: Control endometrium, biological rep6, animal 7549

description: Gene expression data from day 17 endometrium of control fed heifers

source_name: Bovine endometrium on day 17; control

value: palmitic acid


title: n-3 PUFA endometrium, biological rep4, animal 7596


title: n-3 PUFA endometrium, biological rep1, animal 7564


title: Control endometrium, biological rep7, animal 7533


title: HCC1599, copy number variation SNP6.0 WYETH_BREAST replicate


title: HCC2218, copy number variation SNP6.0 WYETH_BREAST replicate


title: Control endometrium, biological rep3, animal 7608


title: n-3 PUFA endometrium, biological rep5, animal 7603


title: Control endometrium, biological rep4, animal 7604


title: Control endometrium, biological rep1, animal 7631


title: Control endometrium, biological rep2, animal 7668


title: SigF induced genes reverse strand 4

city: Lausanne

first: Ruben

middle: C

last: Hartkoorn

state: Vaud

address: SV 3533 (Bâtiment SV) Station 19

department: GHI/SV

country: Switzerland

institute: EPFL

description: Reverse strand comparison of Cy5 (test) to Cy3 (reference)

hyb_protocol: Labelled cDNA was hybridized to microarrays in an Agilent Technologies Microarray chamber at 55°C for 72 h in the following buffer: 1 M NaCl, 50 mM MES, 20% formamide, 20 mM EDTA, 1% Triton X-100.

scan_protocol: Arrays were scanned using an Agilent Technologies microarray scanner, following which results were extracted using the Genepix Pro 5.0 software

data_processing: Values were median normalised followed by log2 loess transformion

organism: Mycobacterium tuberculosis H37Rv

source_name: H37Rv::pMYsigF with P-IA (test)

growth_protocol: Cultured 3 days in the presence of pristinamycin-IA

extract_protocol: Log phase H37Rv::pMY769 and H37Rv::pMYsigF cultures were diluted to OD600 of 0.05 and split into two 50 mL cultures. After overnight incubation, P-IA (final concentration 2 ug/mL) was added to one culture and an equivalent volume of DMSO to the other. After 72 hr incubation (rotary mixer, 4°C) RNA was extracted using 6M GTC (6M guanidine thiocyanate, 0.75 % sodium N-lauryl sarcosine, 37.5 mM sodium citrate, 0.75% tween 80 and 0.15 M β-mercaptoethanol) and TRIzol (Invitrogen) as described previously (28). Extracted RNA was treated twice by RQ1 DNase (Promega) as per the manufacturer’s instructions, and cleaned up using an RNAeasy minikit (Qiagen). RNA quantity and quality was assessed by Nanodrop, agarose gel electrophoresis and PCR to confirm the absence of DNA. mRNA was reverse transcribed and cDNA labeled using RevertAID-H-minus reverse transcriptase (Fermentas) according to the manufacturer’s instructions, using 1-4 μg purified mRNA, random hexamers and either Cy3-dCTP or Cy5-dCTP (GE healthcare). Reverse transcription was performed using the following conditions: 10 min 25°C, 90 min 45 °C, 5 min 70 °C. Labelled cDNA was treated with RNase H and RNase A (30 min, 37°C), followed by cDNA clean-up using GFX purification kit (GE Healthcare).

value: :pMYsigF

value: with Pristinamycin

source_name: H37Rv::pMYsigF without P-IA (reference)

growth_protocol: Cultured 3 days in the absence of pristinamycin-IA


title: Control endometrium, biological rep5, animal 7554


title: SigF induced genes reverse strand 3

label_protocol: mRNA was reverse transcribed and cDNA labeled using RevertAID-H-minus reverse transcriptase (Fermentas) according to the manufacturer’s instructions, using 1-4 μg purified mRNA, random hexamers and either Cy3-dCTP or Cy5-dCTP (GE healthcare). Reverse transcription was performed using the following conditions: 10 min 25°C, 90 min 45 °C, 5 min 70 °C. Labelled cDNA was treated with RNase H and RNase A (30 min, 37°C), followed by cDNA clean-up using GFX purification kit (GE Healthcare).


title: SigF induced genes forward strand 3

description: Forward strand comparison of Cy5 (test) to Cy3 (reference)


title: SigF induced genes reverse strand 2

description: Reverse strand comparison of Cy3 (reference) to Cy5 (test)


title: SigF induced genes forward strand 4


title: MDAMB175, copy number variation SNP6.0 WYETH_BREAST replicate


title: SUM190PT, copy number variation SNP6.0 WYETH_BREAST replicate


title: SigF induced genes forward strand 2

description: Forward strand comparison of Cy3 (reference) to Cy5 (test)


title: SigF induced genes reverse strand 1


title: SigF induced genes forward strand 1


title: Pristinamycin induced genes reverse strand 3

source_name: H37Rv::pMY769 with P-IA (test)

source_name: H37Rv::pMY769 without P-IA (reference)


title: HCC1187, copy number variation SNP6.0 WYETH_BREAST replicate


title: HCC1569, copy number variation SNP6.0 WYETH_BREAST replicate


title: Pristinamycin induced genes reverse strand 2


title: Pristinamycin induced genes forward strand 3


title: EVSAT, copy number variation SNP6.0 WYETH_BREAST replicate

source_name: EVSAT

value: EVSAT


title: ZR751, copy number variation SNP6.0 WYETH_BREAST replicate


title: EFM192A, copy number variation SNP6.0 WYETH_BREAST replicate


title: COLO824, copy number variation SNP6.0 WYETH_BREAST replicate


title: EFM19, copy number variation SNP6.0 WYETH_BREAST replicate


title: Pristinamycin induced genes forward strand 2


title: CAMA1, copy number variation SNP6.0 WYETH_BREAST replicate


title: Pristinamycin induced genes forward strand 1


title: Pristinamycin induced genes reverse strand 1


title: BT474, copy number variation SNP6.0 WYETH_BREAST replicate


title: BT20, copy number variation SNP6.0 WYETH_BREAST replicate


title: ZR751, copy number variation SNP6.0 WYETH_BREAST


title: CAL51, copy number variation SNP6.0 WYETH_BREAST replicate


title: CAL851, copy number variation SNP6.0 WYETH_BREAST replicate


title: CAL120, copy number variation SNP6.0 WYETH_BREAST replicate


title: L1236 B_4 D_4 (exon)

city: Bethesda

first: Brian

middle: Andrew

last: Lewis

state: MD

address: 9000 Rockville Pike

department: metabolism Branch

institute: National Cancer Institute-NIH

hyb_protocol: Samples wre hybridize to Affymetrix human Gene ST 1.0 GeneChIP in Affymetrix hybridization oven at 45C, 60 rpm for 16 hours.

scan_protocol: Slides were scanned on Affymetrix geneChip scanner 3000.

data_processing: Data were collected using Affymetrix AGCC software. Statistical and clustering analysis was performed with Partek genomics Suite software using RMA normalization algorithm.

source_name: Human Hodgkin Lymphoma Cell Line

label_protocol: Sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.

growth_protocol: Hodgkin Lymphoma cells are culture in RPMI medium supplemented with 20% FBS

extract_protocol: TRIZOL

treatment_protocol: HL cell lines were spin-infected using a retrovirus that delivers a specific shRNA to knock down REL-B expression twice in consecutive days. Cell are split into two populations. One is infected and uninduced and the second one is treated with doxyciline to induce the expression of REL-B shRNA.

value: infected induced shREL-B


title: HCC1008, copy number variation SNP6.0 WYETH_BREAST replicate


title: L1236 B_4 Un_4 (exon)

value: infected uninduced shREL-B


title: SUM52PE, copy number variation SNP6.0 WYETH_BREAST


title: T47D, copy number variation SNP6.0 WYETH_BREAST


title: AU565, copy number variation SNP6.0 WYETH_BREAST replicate


title: UACC812, copy number variation SNP6.0 WYETH_BREAST


title: BT549, copy number variation SNP6.0 WYETH_BREAST replicate


title: SUM225CWN, copy number variation SNP6.0 WYETH_BREAST


title: L1236 B_1 D_4 (exon)


title: L1236 B_1 Un_4 (exon)


title: ZR7530, copy number variation SNP6.0 WYETH_BREAST


title: SUM185PE, copy number variation SNP6.0 WYETH_BREAST


title: L1236 B_4 D_1 (exon)


title: SUM44PE, copy number variation SNP6.0 WYETH_BREAST


title: SUM190PT, copy number variation SNP6.0 WYETH_BREAST


title: ZR7530, gene expression array U133Plus2 Good_BREAST_WYETH

data_processing: Data were normalized using Bioconductor and the R package gcrma.

extract_protocol: RNA were isolated using an RNeasy kit (Qiagen, Germantown, MD).


title: ZR751, gene expression array U133Plus2


title: L1236 B_4 Un_1 (exon)


title: UACC812, gene expression array U133Plus2


title: ZR7530, gene expression array U133Plus2 PFIZER


title: L1236 B_1 Un_1 (exon)


title: SUM159PT, copy number variation SNP6.0 WYETH_BREAST


title: UACC62, gene expression array U133Plus2


title: SUM149PT, copy number variation SNP6.0 WYETH_BREAST


title: UACC257, gene expression array U133Plus2 replicate 2


title: UO31, gene expression array U133Plus2


title: UACC257, gene expression array U133Plus2 replicate 1


title: SKBR3, copy number variation SNP6.0 WYETH_BREAST


title: U251, gene expression array U133Plus2 replicate 1


title: U251, gene expression array U133Plus2 replicate 2


title: MT3, copy number variation SNP6.0 WYETH_BREAST


title: TK10, gene expression array U133Plus2


title: L1236 B_1 D_1 (exon)


title: MDAMB468, copy number variation SNP6.0 WYETH_BREAST


title: T47D, gene expression array U133Plus2 replicate 2


title: MDAMB415, copy number variation SNP6.0 WYETH_BREAST


title: T47D, gene expression array U133Plus2 Good_BREAST_WYETH


title: SW48, gene expression array U133Plus2


title: T47D, gene expression array U133Plus2 replicate 1


title: SUM52PE, gene expression array U133Plus2 replicate 2


title: MDAMB436, copy number variation SNP6.0 WYETH_BREAST


title: MDAMB453, copy number variation SNP6.0 WYETH_BREAST


title: SUM52PE, gene expression array U133Plus2 replicate 1


title: MDAMB231, copy number variation SNP6.0 WYETH_BREAST


title: MDAMB175, copy number variation SNP6.0 WYETH_BREAST


title: MDAMB361, copy number variation SNP6.0 WYETH_BREAST


title: SUM225CWN, gene expression array U133Plus2 replicate 2


title: SUM225CWN, gene expression array U133Plus2 replicate 1


title: SUM185PE, gene expression array U133Plus2


title: MDAMB157, copy number variation SNP6.0 WYETH_BREAST


title: SUM159PT, gene expression array U133Plus2 Good_BREAST_WYETH


title: SUM149PT, gene expression array U133Plus2


title: SUM159PT, gene expression array U133Plus2 Medium_BREAST_WYETH


title: MDAMB134VI, copy number variation SNP6.0 WYETH_BREAST


title: HS578T, copy number variation SNP6.0 WYETH_BREAST


title: SNU5, gene expression array U133Plus2


title: SNUC1, gene expression array U133Plus2


title: HCC70, copy number variation SNP6.0 WYETH_BREAST


title: SNU16, gene expression array U133Plus2


title: HCC38, copy number variation SNP6.0 WYETH_BREAST


title: MCF7, copy number variation SNP6.0 WYETH_BREAST


title: HCC202, copy number variation SNP6.0 WYETH_BREAST


title: SNB75, gene expression array U133Plus2 replicate 3


title: JIMT1, copy number variation SNP6.0 WYETH_BREAST


title: SNU1, gene expression array U133Plus2


title: HCC2157, copy number variation SNP6.0 WYETH_BREAST


title: HCC1599, copy number variation SNP6.0 WYETH_BREAST


title: SNB75, gene expression array U133Plus2 replicate 1


title: SNB75, gene expression array U133Plus2 replicate 2


title: HCC1806, copy number variation SNP6.0 WYETH_BREAST


title: SKUT1B, gene expression array U133Plus2 replicate 2


title: HCC1187, copy number variation SNP6.0 WYETH_BREAST


title: HCC1143, copy number variation SNP6.0 WYETH_BREAST


title: HCC1954, copy number variation SNP6.0 WYETH_BREAST


title: HCC1419, copy number variation SNP6.0 WYETH_BREAST


title: SN12C, gene expression array U133Plus2 replicate 2


title: HCC1395, copy number variation SNP6.0 WYETH_BREAST


title: SN12C, gene expression array U133Plus2 replicate 1


title: EVSAT, copy number variation SNP6.0 WYETH_BREAST


title: SKUT1B, gene expression array U133Plus2 replicate 1


title: SNB19, gene expression array U133Plus2


title: SKNEP, gene expression array U133Plus2

source_name: SKNEP

value: SKNEP


title: HCC1569, copy number variation SNP6.0 WYETH_BREAST


title: EFM19, copy number variation SNP6.0 WYETH_BREAST


title: HCC1937, copy number variation SNP6.0 WYETH_BREAST


title: EFM192A, copy number variation SNP6.0 WYETH_BREAST


title: SKMEL28, gene expression array U133Plus2


title: COLO824, copy number variation SNP6.0 WYETH_BREAST


title: HCC1008, copy number variation SNP6.0 WYETH_BREAST


title: SKBR3, gene expression array U133Plus2 replicate 2


title: SKMEL2, gene expression array U133Plus2 replicate 1


title: CAL851, copy number variation SNP6.0 WYETH_BREAST


title: SKMEL5, gene expression array U133Plus2


title: SKMEL2, gene expression array U133Plus2 replicate 2


title: SKBR3, gene expression array U133Plus2 replicate 1


title: SGC7901, gene expression array U133Plus2


title: CAMA1, copy number variation SNP6.0 WYETH_BREAST


title: SF539, gene expression array U133Plus2 replicate 1


title: CAL120, copy number variation SNP6.0 WYETH_BREAST


title: SF295, gene expression array U133Plus2


title: SF539, gene expression array U133Plus2 replicate 2


title: SF268, gene expression array U133Plus2 replicate 2


title: SF268, gene expression array U133Plus2 replicate 1


title: CAL51, copy number variation SNP6.0 WYETH_BREAST


title: RXF393, gene expression array U133Plus2 replicate 2


title: BT474, copy number variation SNP6.0 WYETH_BREAST


title: AU565, copy number variation SNP6.0 WYETH_BREAST


title: RXF393, gene expression array U133Plus2 replicate 1


title: BT549, copy number variation SNP6.0 WYETH_BREAST


title: RKO, gene expression array U133Plus2

source_name: RKO

value: RKO


title: BT20, copy number variation SNP6.0 WYETH_BREAST


title: UO31, copy number variation SNP6.0 WYETH_NCI50


title: RL952, gene expression array U133Plus2


title: PC3, gene expression array U133Plus2 Good_NCI50_WYETH


title: UACC257, copy number variation SNP6.0 WYETH_NCI50


title: PC3, gene expression array U133Plus2 PFIZER


title: HCC2218, copy number variation SNP6.0 WYETH_BREAST


title: U251, copy number variation SNP6.0 WYETH_NCI50


title: T47D, copy number variation SNP6.0 WYETH_NCI50


title: OVCAR4, gene expression array U133Plus2 replicate 2


title: OVCAR5, gene expression array U133Plus2


title: OVCAR3, gene expression array U133Plus2


title: SNB75, copy number variation SNP6.0 WYETH_NCI50


title: OVCAR4, gene expression array U133Plus2 replicate 1


title: OVCAR8, gene expression array U133Plus2 replicate 1


title: SNB19, copy number variation SNP6.0 WYETH_NCI50


title: NCIN87, gene expression array U133Plus2


title: NUGC4, gene expression array U133Plus2


title: OVCAR8, gene expression array U133Plus2 replicate 2


title: NUGC3, gene expression array U133Plus2


title: SKMEL5, copy number variation SNP6.0 WYETH_NCI50


title: NCIN592, gene expression array U133Plus2


title: SF539, copy number variation SNP6.0 WYETH_NCI50


title: SN12C, copy number variation SNP6.0 WYETH_NCI50


title: UACC62, copy number variation SNP6.0 WYETH_NCI50


title: SKMEL2, copy number variation SNP6.0 WYETH_NCI50


title: NCIN417, gene expression array U133Plus2


title: SKOV3, copy number variation SNP6.0 WYETH_NCI50


title: NCIH82, gene expression array U133Plus2


title: NCIH889, gene expression array U133Plus2


title: RXF393, copy number variation SNP6.0 WYETH_NCI50


title: NCIH841, gene expression array U133Plus2


title: NCIH647, gene expression array U133Plus2 replicate 2


title: SW620, copy number variation SNP6.0 WYETH_NCI50


title: NCIH526, gene expression array U133Plus2


title: NCIH69, gene expression array U133Plus2


title: NCIH520, gene expression array U133Plus2 replicate 1


title: NCIH520, gene expression array U133Plus2 replicate 2


title: Epstein-Barr virus–transformed human lymphoblastoid cell lines_female pooled

city: Kanazawa

first: Yo

last: Niida

state: Ishikawa

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa Univ.

description: This sample is pooled LCLs from five normal human female, separate to Xp active and Xm active clones respectively and remixed.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: human lymphoblastoid cell lines

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
LCLs were established from normal adults, including ten males (18 to 48 years old) and five females (17 to 45 years old), with B95-8 supernatant. LCLs were maintained in culture with RPMI1640 medium with 10% FCS.
For female LCLs, to separate Xp active and Xm active clones, serial dilution and re-expansion was performed. DNA was extracted from each clone and X chromosome activation state was examined by HUMARA analysis.

extract_protocol: Same amounts of Xp active and Xm active female LCL clones from five females and the same amounts of LCL clones from ten males were pooled respectively. Total RNA was isolated by Trizol Reagents (invitrogen).

tag: gender

value: female

tag: phenotype

value: normal


title: NCIH460, gene expression array U133Plus2 Good_NCI50_WYETH


title: OVCAR8, copy number variation SNP6.0 WYETH_NCI50


title: OVCAR5, copy number variation SNP6.0 WYETH_NCI50


title: TK10, copy number variation SNP6.0 WYETH_NCI50


title: NCIH460, gene expression array U133Plus2 PFIZER


title: SF295, copy number variation SNP6.0 WYETH_NCI50


title: NCIH378, gene expression array U133Plus2


title: NCIH441, gene expression array U133Plus2


title: Epstein-Barr virus–transformed human lymphoblastoid cell lines_male pooled

description: This sample is pooled LCLs from normal 10 human male.

value: male


title: gastric cancer case21-LN

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

institute: Oita university, Faculty of Medicine

description: Non-neoplastic tissue in the same patient was used as the source of control DNA

hyb_protocol: dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65? for 24 h

scan_protocol: A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5?m

data_processing: Microarray images were analyzed by using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were subsequently imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies).Microarray images were analyzed using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies). The log2ratio of Cy5 (tumor) to Cy3 (Control) was normalized by the Centralization Algorithm in DNA Analytics. Aberrant regions were determined by the ADM-2 algorithm at a threshold of 12.0 in DNA Analytics. To detect gains and losses, we set the values of parameters for aberration filters as: minimum number of probes in region 2, minimum absolute average log2ratio for region 0.263034, maximum number of aberrant regions 10000, and percentage penetrance per feature 0. We set the value of the minimum absolute average log2ratio at 0.263034 to detect regions showing a change in the averaged copy number equal to or more than 1.2-fold (log2(1.2)=0.263034).

source_name: gastric cancer : FFPE sample

label_protocol: Agilent Genomic DNA Labeling Kit Plus(Agilent)

extract_protocol: standard proteinase K-digestion method

tag: case

tag: the depth of invasion

value: submucosal

tag: the portion of lcm

value: metastatic lymph node

tag: lymph node metastasis

source_name: non-neoplestic gastric mucosa : FFPE sample


title: NCIH358, gene expression array U133Plus2


title: NCIH647, gene expression array U133Plus2 replicate 1


title: PC3, copy number variation SNP6.0 WYETH_NCI50


title: NCIH345, gene expression array U133Plus2


title: NCIH596, gene expression array U133Plus2


title: NCIH249, gene expression array U133Plus2


title: NCIH2405, gene expression array U133Plus2


title: OVCAR3, copy number variation SNP6.0 WYETH_NCI50


title: NCIH2347, gene expression array U133Plus2


title: gastric cancer case8-LN


title: NCIH522, copy number variation SNP6.0 WYETH_NCI50


title: NCIH23, gene expression array U133Plus2


title: SKMEL28, copy number variation SNP6.0 WYETH_NCI50


title: NCIH226, gene expression array U133Plus2 replicate 2


title: NCIH226, gene expression array U133Plus2 PFIZER


title: gastric cancer case7-LN


title: NCIH226, gene expression array U133Plus2 replicate 1


title: gastric cancer case4-LN


title: gastric cancer case6-LN


title: NCIH209, gene expression array U133Plus2


title: NCIH2141, gene expression array U133Plus2


title: NCIH1993, gene expression array U133Plus2


title: NCIH23, copy number variation SNP6.0 WYETH_NCI50


title: MDAMB435, copy number variation SNP6.0 WYETH_NCI50


title: SF268, copy number variation SNP6.0 WYETH_NCI50


title: gastric cancer case3-LN


title: NCIH460, copy number variation SNP6.0 WYETH_NCI50


title: NCIH2107, gene expression array U133Plus2


title: NCIH2170, gene expression array U133Plus2


title: NCIADRRES, copy number variation SNP6.0 WYETH_NCI50

source_name: NCIADRRES

value: NCIADRRES


title: gastric cancer case9-LN


title: OVCAR4, copy number variation SNP6.0 WYETH_NCI50


title: gastric cancer case2-LN


title: NCIH196, gene expression array U133Plus2


title: MALME3M, copy number variation SNP6.0 WYETH_NCI50


title: NCIH1869, gene expression array U133Plus2 replicate 2


title: NCIH1869, gene expression array U133Plus2 replicate 1


title: NCIH226, copy number variation SNP6.0 WYETH_NCI50


title: NCIH1770, gene expression array U133Plus2


title: NCIH187, gene expression array U133Plus2


title: gastric cancer case27-3


title: gastric cancer case27-1

value: mucosal


title: gastric cancer case1-LN


title: NCIH1666, gene expression array U133Plus2 replicate 3


title: LOXIMVI, copy number variation SNP6.0 WYETH_NCI50

source_name: LOXIMVI

value: LOXIMVI


title: M14, copy number variation SNP6.0 WYETH_NCI50


title: IGROVI, copy number variation SNP6.0 WYETH_NCI50

source_name: IGROVI

value: IGROVI


title: NCIH1666, gene expression array U133Plus2 replicate 2


title: MB231, copy number variation SNP6.0 WYETH_NCI50


title: NCIH1666, gene expression array U133Plus2 replicate 1


title: gastric cancer case26-3


title: NCIH1703, gene expression array U133Plus2


title: NCIH1651, gene expression array U133Plus2


title: gastric cancer case26-1


title: NCIH1650, gene expression array U133Plus2


title: NCIH1581, gene expression array U133Plus2


title: NCIH1963, gene expression array U133Plus2


title: NCIH1395, gene expression array U133Plus2 replicate 1


title: NCIH146, gene expression array U133Plus2


title: HOP92, copy number variation SNP6.0 WYETH_NCI50


title: gastric cancer case23-3


title: NCIH1184, gene expression array U133Plus2


title: gastric cancer case24-1


title: NCIH1355, gene expression array U133Plus2


title: NCIH1299, gene expression array U133Plus2


title: KIM12, copy number variation SNP6.0 WYETH_NCI50


title: MX1, gene expression array U133Plus2 replicate 2


title: NCIH1395, gene expression array U133Plus2 replicate 2


title: HS578T, copy number variation SNP6.0 WYETH_NCI50


title: NCIADRRES, gene expression array U133Plus2 replicate 1


title: gastric cancer case23-1


title: EKVX, copy number variation SNP6.0 WYETH_NCI50

source_name: EKVX

value: EKVX


title: gastric cancer case25-3


title: HOP62, copy number variation SNP6.0 WYETH_NCI50


title: gastric cancer case22-3


title: HCT15, copy number variation SNP6.0 WYETH_NCI50


title: MX1, gene expression array U133Plus2 replicate 1


title: HCC2998, copy number variation SNP6.0 WYETH_NCI50


title: gastric cancer case22-1


title: MX1, gene expression array U133Plus2 PFIZER


title: NCIADRRES, gene expression array U133Plus2 replicate 2


title: HCT116, copy number variation SNP6.0 WYETH_NCI50


title: MKN74, gene expression array U133Plus2


title: gastric cancer case21-3


title: MKN45, gene expression array U133Plus2


title: gastric cancer case24-3


title: MKN1, gene expression array U133Plus2


title: MFE296, gene expression array U133Plus2 replicate 2


title: MT3, gene expression array U133Plus2


title: gastric cancer case20-4


title: MFE280, gene expression array U133Plus2


title: gastric cancer case21-1


title: CAKI1, copy number variation SNP6.0 WYETH_NCI50


title: MFE296, gene expression array U133Plus2 replicate 1


title: MDAMB436, gene expression array U133Plus2 replicate 2


title: gastric cancer case20-2


title: MDAMB453, gene expression array U133Plus2


title: MKN7, gene expression array U133Plus2


title: gastric cancer case19-3


title: gastric cancer case19-1


title: MDAMB436, gene expression array U133Plus2 replicate 1


title: MDAMB415, gene expression array U133Plus2 replicate 3


title: MDAMB415, gene expression array U133Plus2 replicate 2


title: COLO205, copy number variation SNP6.0 WYETH_NCI50


title: MDAMB415, gene expression array U133Plus2 replicate 4


title: 786O, copy number variation SNP6.0 WYETH_NCI50


title: MDAMB415, gene expression array U133Plus2 replicate 1


title: gastric cancer case18-3


title: ACHN, copy number variation SNP6.0 WYETH_NCI50

source_name: ACHN

value: ACHN


title: BT549, copy number variation SNP6.0 WYETH_NCI50


title: gastric cancer case18-1


title: MDAMB175, gene expression array U133Plus2 replicate 1


title: MDAMB175, gene expression array U133Plus2 replicate 2


title: gastric cancer case17-3


title: A498, copy number variation SNP6.0 WYETH_NCI50


title: MDAMB157, gene expression array U133Plus2


title: gastric cancer case17-1


title: MDAMB231, gene expression array U133Plus2 Good_BREAST_WYETH


title: MDAMB231, gene expression array U133Plus2 Good_NCI50_WYETH


title: NCIN417, copy number variation SNP6.0


title: MDA435, gene expression array U133Plus2 replicate 2


title: SKNEP, copy number variation SNP6.0


title: gastric cancer case16-3


title: MDA435, gene expression array U133Plus2 replicate 1


title: MCG803, gene expression array U133Plus2


title: MCF7, gene expression array U133Plus2 replicate 2


title: Female_dKO_Treated_4

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

description: total RNA

hyb_protocol: Labeled samples were hybridized overnight to the Agilent 4X44 Whole Mouse Genome Array.

scan_protocol: Arrays were washed and then scanned with the model G2565B Agilent DNA microarray Scanner (Agilent Technologies).

data_processing: Median intensities of each element on the array were captured with Agilent Feature Extraction version 9.53 (Agilent Technologies). Quality control diagnostic plots were prepared for each array, and those failing to exhibit high-quality hybridizations were excluded from further analysis, resulting in the final dataset containing four biological replicates for each condition. The subsequent analysis was performed as previously (Rieck et al. 2009).

label_protocol: Amplified cDNA was prepared using the WT-Ovation Pico Amplification System (NuGEN Technologies). Amplified cDNA was directly labeled using the BioPrime Array CGH Genomic Labeling System with Cy3-labeled nucleotides (GE Amersham Biosciences).

extract_protocol: Total RNA was extracted from liver samples and sorted cells using Trizol and RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: A two-step strategy was used for hepatocarcinogenesis. Briefly, 14-15 day old mice were injected with DEN (20 mg/kg body weight) to initiate tumor growth and at two weeks after initial injection mice were injected with TCPOBOP (3 mg/kg body weight) to promote tumor growth once every two weeks for a total of eight times.

value: Female

value: dKO

value: DEN-Treated

tag: tissue type

value: liver tumor


title: NCIH841, copy number variation SNP6.0


title: gastric cancer case14-4


title: gastric cancer case15-4


title: Female_dKO_Treated_2

description: total RNA


title: A549, copy number variation SNP6.0 WYETH_NCI50


title: gastric cancer case16-1


title: MCF12A, gene expression array U133Plus2


title: NCIN187, copy number variation SNP6.0


title: gastric cancer case13-3


title: gastric cancer case14-2


title: Male_dKO_Treated_4

description: total RNA

value: Male


title: NCIH526, copy number variation SNP6.0


title: Male_dKO_Treated_3

description: total RNA


title: NCIH69, copy number variation SNP6.0


title: gastric cancer case13-1


title: LS153, gene expression array U133Plus2


title: Male_dKO_Treated_2

description: total RNA


title: Female_dKO_Treated_3

description: total RNA


title: M14, gene expression array U133Plus2


title: MCF7, gene expression array U133Plus2 replicate 1


title: gastric cancer case12-3


title: NCIH378, copy number variation SNP6.0


title: gastric cancer case12-1


title: NCIH82, copy number variation SNP6.0


title: NCIH524, copy number variation SNP6.0


title: LS123, gene expression array U133Plus2


title: Male_dKO_Treated_1

description: total RNA


title: NCIH889, copy number variation SNP6.0


title: Female_dKO_Treated_1

description: total RNA


title: Female_dKO_Untreated_4

description: total RNA

value: Untreated


title: Female_dKO_Untreated_2

description: total RNA


title: LNCAP, gene expression array U133Plus2

source_name: LNCAP

value: LNCAP


title: gastric cancer case10-3

value: female


title: KM12, gene expression array U133Plus2 replicate 1


title: Female_dKO_Untreated_3

description: total RNA


title: pBAD-SgrS 2

type: mixed

city: Würzburg

first: Kai

last: Papenfort

state: Würzburg

address: Josef-Schneider Str.2/BAU D15

department: RNA Biology

country: Germany

institute: IMIB Würzburg

hyb_protocol: Microarray slide were hybridized in a water bath over night at 63C. For detailed protocol see: http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: Axon GenePix4000A, 10nm resolution scan

data_processing: Data centering was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centered ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Salmonella enterica SL1344

label_protocol: total RNA was labelled with Cy3 using random hexamers and reverse transcriptase (Stratagene AffinityScript) while genomic DNA was labelled with Cy5 using the Invitrogen BioPrime DNA Labeling System

growth_protocol: Salmonella carrying pBAD-ctr or pBAD-SgrS were grown in LB-media to OD=1.5.

extract_protocol: SV40 RNA isolation Kit (promega). GenomicDNA was extracted using the Qiagen 'Genomic DNA' Kit

treatment_protocol: At OD=1.5, 0.2% (final conc.) L-arabinose was added. Total RNA was isolated 10 min post treatment.

value: pBAD-SgrS


title: gastric cancer case11-1

value: male

value: submucosal


title: KM12, gene expression array U133Plus2 replicate 2


title: NCIH446, copy number variation SNP6.0


title: KLE, gene expression array U133Plus2 replicate 2

source_name: KLE

value: KLE


title: Female_dKO_Untreated_1

description: total RNA


title: NCIH249, copy number variation SNP6.0


title: gastric cancer case10-1

value: mucosal


title: MCF10A, gene expression array U133Plus2


title: NCIH209, copy number variation SNP6.0


title: pBAD-ctr.2

value: pBAD-ctr


title: Female_WT_Untreated_4

description: total RNA

value: WT


title: pBAD-ctr.3


title: NCIH2107, copy number variation SNP6.0


title: gastric cancer case8-4


title: IM95M, gene expression array U133Plus2


title: NCIH1184, copy number variation SNP6.0


title: gastric cancer case9-3


title: KLE, gene expression array U133Plus2 replicate 1


title: KATOIII, gene expression array U133Plus2

source_name: KATOIII

value: KATOIII


title: pBAD-ctr.1


title: ZR751, copy number variation SNP6.0


title: Female_WT_Untreated_2

description: total RNA


title: gastric cancer case11-4


title: pBAD-SgrS 1


title: pBAD-SgrS 3


title: Female_WT_Untreated_1

description: total RNA


title: gastric cancer case7-3


title: Female_WT_Treated_4

description: total RNA


title: Female_WT_Untreated_3

description: total RNA


title: NCIH196, copy number variation SNP6.0


title: gastric cancer case7-1


title: IGROV1, gene expression array U133Plus2 replicate 4


title: Female_WT_Treated_3

description: total RNA


title: IM95, gene expression array U133Plus2


title: gastric cancer case6-1


title: MDAMB436, copy number variation SNP6.0


title: IGROV1, gene expression array U133Plus2 replicate 3


title: MX1, copy number variation SNP6.0


title: Female_WT_Treated_1

description: total RNA


title: IGROV1, gene expression array U133Plus2 replicate 2


title: LCS-426A

first: Xin

middle: Wei

last: Wang

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description: No additional information.

hyb_protocol: Sample Hybridization Protocol Other: 25 µg Cot-1 DNA (Invitrogen, Carlsbad, CA), 1/10 volume of 10x Blocking Agent (Agilent, Santa Clara, CA) and an equal amount of 2× Hybridization Buffer (Agilent, Santa Clara, CA) were added to the labeled genomic DNA, denatured at 95°C for 5 min and preincubated at 37°C for 30 min in a water bath. Hybridizations were carried out on Human Genome CGH 105A Oligo Microarray glass slides (G4412A, Agilent, Santa Clara, CA). DNA samples were hybridized onto the array for 36~V40 hours at 65°C utilizing the DNA Microarray Hybridization Chamber SureHyb and Hybridization Oven (Agilent, Santa Clara, CA). After hybridization arrays were disassembled at room temperature, they were subsequently washed in wash solution 1 (0.5×SSPE and 0.005% N-Lauroylsarcosine) at room temperature for 5 min and wash solution 2 (0.1×SSPE and 0.005% N-Lauroylsarcosine) at 37°C for 1 min.

scan_protocol: Agilent Scanning Protocol Other: Dried array slides were scanned using the DNA Microarray Scanner (Agilent, Santa Clara, CA).

data_processing:
Agilent Data Processing Protocol
Calculation Method: Raw image files of the arrays were processed using Feature Extraction software 8.1 using default CGH parameters (Agilent, Santa Clara, CA). Spot values were normalized using the default linear-lowess normalization.

source_name: Promega human genomic DNA - Male

label_protocol:
Cy3 Labeling Protocol
Other: Five micrograms of reference DNA of the opposite gender (human genomic DNA, Promega, San Luis Obispo, CA) were digested with the restriction enzymes AluI and RsaI (10U/uL; Invitrogen, Carlsbad, CA). Digested DNA was purified using QIAprep Spin Miniprep Kit (QIAGEN, Valencia, CA) and labeled using the BioPrime Array CGH Genomic Labeling kit (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions in a volume of 50 µl with a modified dNTP mix containing 120 µM each of dATP, dGTP, and dCTP; 60 µM dTTP; and 60 µM Cy3-dUTP (GE Amersham, Piscataway, NJ). Reference DNA was pooled, purified and concentrated to 79 µl using Vivaspin 500 concentrator (VS0122, 30k MWCO, Vivascience, Littleton, MA).

extract_protocol:
Promega Genomic DNA Purification
Other: Genomic DNA obtained from multiple anonymous donors was purified by the method described in Sambrook et al. Greater than 90% of the DNA is longer than 50kb in size as measured by pulsed-field gel electrophoresis. (See: http://www.promega.com/)

tag: Gender

label_protocol:
Cy5 Labeling Protocol
Other: Five micrograms of genomic DNA were digested with the restriction enzymes AluI and RsaI (10U/uL; Invitrogen, Carlsbad, CA). Digested DNA was purified using QIAprep Spin Miniprep Kit (QIAGEN, Valencia, CA) and labeled using the BioPrime Array CGH Genomic Labeling kit (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions in a volume of 50 µl with a modified dNTP mix containing 120 µM each of dATP, dGTP, and dCTP; 60 µM dTTP; and 60 µM Cy5-dUTP (GE Amersham, Piscataway, NJ). Tumor DNA was pooled, purified and concentrated to 79 µl using Vivaspin 500 concentrator (VS0122, 30k MWCO, Vivascience, Littleton, MA).

extract_protocol:
Phenol/Chloroform Extraction Protocol
Other: Genomic tumor cell DNA was isolated from microdissected fresh frozen clinical tumor samples using proteinaseK digestion (P2308, Sigma-Aldrich, St. Louis, MO) and subsequent Phenol/Chlororform extraction.

tag: Tissue

value: liver tumor tissue

tag: Disease state

value: Hepatocellular carcinoma (HCC)

tag: Individual


title: Female_WT_Treated_2

description: total RNA

value: Female


title: gastric cancer case6-3


title: MCF12A, copy number variation SNP6.0


title: gastric cancer case8-2


title: IGROV1, gene expression array U133Plus2 replicate 1


title: LCS-415A

description: No additional information.

source_name: Promega human genomic DNA - Female


title: LCS-424A

description: No additional information.


title: LCS-406A

description: No additional information.


title: gastric cancer case5-4


title: MCF10A, copy number variation SNP6.0


title: NCIH1963, copy number variation SNP6.0


title: 184A1, copy number variation SNP6.0


title: Male_WT_Treated_4

description: total RNA

value: DEN-Treated


title: Male_WT_Treated_3

description: total RNA

value: liver tumor


title: HS746T, gene expression array U133Plus2


title: Male_WT_Treated_2

description: total RNA

value: Male


title: gastric cancer case5-2


title: HS578T, gene expression array U133Plus2 PFIZER


title: Male_WT_Treated_1

description: total RNA


title: LCS-401A

description: No additional information.


title: HS578T, gene expression array U133Plus2 Good_NCI50_WYETH


title: LCS-403A

description: No additional information.


title: HS578T, gene expression array U133Plus2 Good_BREAST_WYETH


title: LCS-400A

description: No additional information.


title: gastric cancer case3-4


title: CACO2, copy number variation SNP6.0


title: gastric cancer case4-4


title: LCS-393A

description: No additional information.


title: LCS-366A

description: No additional information.


title: gastric cancer case4-1


title: gastric cancer case2-4


title: LCS-358A

description: No additional information.


title: HPET13, gene expression array U133Plus2 replicate 2


title: SKBR3, copy number variation SNP6.0


title: HEC1B, gene expression array U133Plus2


title: L1236 B_4 Un_4 (gene)

source_name: Human Hodgkin Lymphoma Cell Line

value: infected uninduced shREL-B


title: L1236 B_4 D_1 (gene)

value: infected induced shREL-B


title: NCIH146, copy number variation SNP6.0


title: L1236 B_4 D_4 (gene)


title: L1236 B_4 Un_1 (gene)


title: L1236 B_1 D_4 (gene)


title: HEC1A, gene expression array U133Plus2 replicate 1


title: HEC1A, gene expression array U133Plus2 replicate 2


title: LCS-344A

description: No additional information.

value: female


title: gastric cancer case1-3


title: gastric cancer case3-2


title: LCS-343A

description: No additional information.


title: LCS-357A

description: No additional information.


title: HPET13, gene expression array U133Plus2 replicate 1


title: HPET5, gene expression array U133Plus2


title: HPET11, gene expression array U133Plus2


title: gastric cancer case1-1


title: HGC27, gene expression array U133Plus2


title: HCC827, gene expression array U133Plus2


title: LCS-346A

description: No additional information.


title: LCS-347A

description: No additional information.


title: HCT15, gene expression array U133Plus2


title: LCS-341A

description: No additional information.


title: LCS-339A

description: No additional information.


title: LCS-333A

description: No additional information.


title: HCC4006, gene expression array U133Plus2


title: L1236 B_1 Un_4 (gene)


title: L1236 B_1 Un_1 (gene)


title: L1236 B_1 D_1 (gene)


title: HCC2998, gene expression array U133Plus2 replicate 1


title: HCC2998, gene expression array U133Plus2 replicate 2


title: 2056-NB_DEAD

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

description: Gene expression

hyb_protocol: Labelled cRNAs were hybridized to whole-genome oligonucleotide microarrays containing 41,000 human transcripts (Agilent Technologies) following the manufacture's instructions (One-color microarray-based gene expression analysis protocol, v5.5). Briefly, 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome 4x44K Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%). Microarray performance was assessed by QC metric tool.

data_processing:
The scanned TIFF images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (Agilent protocol GE1-v5_95_Feb07) to obtain background subtracted and spatially detrended Processed Signal intensities. The output of Feature Extraction was analyzed with the Agi4x44PreProcess package. After within-array median-summarization of probe intensities within replicates, probe intensities were log base 2 transformed and normalized across arrays with the quantile normalization method implemented in Bioconductor.
Bioconductor normalized data are provided as supplementary files on the Series record.

source_name: human neuroblastoma tumor

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA as detailed in the One-color microarray-based gene expression analysis protocol, v5.5 (www.agilent.com). Dye incorporation and cRNA yield were checked with Nanodrop (Thermo Scientific).

extract_protocol: Total RNA was isolated by using the RNAeasy Mini Kit (Qiagen) according to manufacturer’s protocol. Total RNA was quantified and quality control assessed by Nano LabChip® assay on the 2100 Bioanalyzer (Agilent Technologies). Only samples with a RNA Integrity Number >7 were included in the study.

treatment_protocol: primary tumor samples collected at diagnosis, immediately freezed and stored at -80°C.

tag: disease status

value: neuroblastoma

tag: patient stage

value: stage 4

tag: cell type

value: stored NB primary tumor, from patient dead with disease


title: 2368-NB_DEAD

description: Gene expression


title: LCS-076A

description: No additional information.

value: male


title: HCC2218, gene expression array U133Plus2

tag: cell line


title: LCS-196A

description: No additional information.


title: 2003-NB_DEAD

description: Gene expression


title: 2144-NB_DEAD

description: Gene expression


title: 2100-NB_DEAD

description: Gene expression


title: 30do mouse spermatids replicate 2

city: Canberra

first: Rohan

last: Williams

state: ACT

address: Garran Rd ACTON

country: Australia

institute: ANU

description: Gene expression data from 30 do mouse spermatids

hyb_protocol: We employed standard Affymetrix hybridisation protocol (45C for 17 hours at 60 rpm)

scan_protocol: Arrays were scanned using a GCS 3000 7G scanner

data_processing: CEL files were generated Affymetrix GeneChip Command Console (AGCC) software. Further analysis performed in R (see manuscript)

source_name: 30do mouse spermatids

label_protocol: 200ng of total RNA using the Ambion WT kit

growth_protocol: Balb/c male mice were kept in cages till they reach the age of 30 days old

extract_protocol: Testis tubules from wild type Balb/c mice were placed in 1-2 ml of ice-cold PBS-GL buffer (PBS supplemented with 5.6mM D-glucose, 5.4mM DL-lactate, 0.5mM DTT, 0.2mM PMSF, and protease inhibitor cocktail (Roche)) and dissected with scissors followed by homogenisation with 3-4 strokes in a Dounce homogeniser (pestle type A, cell integrity monitored by microscopy). The cellular mixture was filtered through a 70µm cell strainer to obtain a single cell suspension

treatment_protocol: Balb/c 30do male mice were killed by CO2, testes were exised dy the scissors

tag: background strain

value: BALB/c

value: 30 days old

tag: organ

value: testes


title: LCS-254A

description: No additional information.


title: 30do mouse spermatids replicate 1

tag: gender

tag: age


title: KOSTIM4

city: Barcelona

first: Cristina

last: Lopez-Rodriguez

address: Carrer Dr. Aiguader, 88

department: Medicine and Life Sciences

country: Spain

institute: Universitat Pompeu Fabra

description: Gene expression data from murine bone-marrow derived macrophages

hyb_protocol: Sample was hybridized to Mouse Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 640

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed using the RMA algorithm and then SAM was applied to calculate significant differential expression between samples

label: Biotin

source_name: Total RNA from murine bone-marrow derived macrophages

label_protocol: 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix)

extract_protocol: RNeasy Kit QIAGEN

tag: treatment

value: LPS

value: murine bone-marrow derived macrophages

tag: genotype

value: NFAT5 KO

tag: genetic background


title: HCC2935, gene expression array U133Plus2


title: KO4

value: unstimulated


title: LCS-073A

description: No additional information.

value: liver tumor tissue

value: Hepatocellular carcinoma (HCC)


title: LCS-075A

description: No additional information.


title: 30do mouse spermatids replicate 3


title: HCC1806, gene expression array U133Plus2 Good_BREAST_WYETH


title: LCS-072A

description: No additional information.


title: 1995-NB_DEAD

description: Gene expression


title: WTSTIM4

value: wild type


title: 1439-NB_DEAD

description: Gene expression


title: WT4


title: 1243-NB_DEAD

description: Gene expression


title: 2362-NB_RC

description: Gene expression

value: stored NB primary tumor, from patient in complete remission


title: KOSTIM3


title: LCS-071A

description: No additional information.


title: LCS-068A

description: No additional information.


title: LCS-069A

description: No additional information.


title: HCC1806, gene expression array U133Plus2 PFIZER


title: HCC1569, gene expression array U133Plus2


title: 806-NB_DEAD

description: Gene expression


title: WTSTIM3


title: HCC1143, gene expression array U133Plus2


title: LCS-066A

description: No additional information.


title: LCS-065A

description: No additional information.


title: LCS-067A

description: No additional information.


title: WT3


title: HCC1395, gene expression array U133Plus2


title: HCC1187, gene expression array U133Plus2


title: 2035-NB_RC

description: Gene expression


title: KO3


title: HCC202, gene expression array U133Plus2

tag: origin

value: breast


title: 1905-NB_RC

description: Gene expression


title: 1893-NB_RC

description: Gene expression


title: LCS-063A

description: No additional information.

value: female


title: LCS-064A

description: No additional information.


title: HCC70, gene expression array U133Plus2 replicate 2


title: KOSTIM2


title: HCC38, gene expression array U133Plus2


title: WTSTIM2


title: KO2


title: LCS-062A

description: No additional information.


title: WT2


title: 1889-NB_RC

description: Gene expression

value: neuroblastoma


title: GTL16, gene expression array U133Plus2 Pfizer

value: stomach


title: GAM022, gene expression array U133Plus2


title: 1864-NB_RC

description: Gene expression

value: stage 4


title: KO1


title: WTSTIM1


title: LCS-061A

description: No additional information.

value: male


title: LCS-058A

description: No additional information.


title: 1684-NB_RC

description: Gene expression


title: LCS-059A

description: No additional information.


title: 1445-NB_RC

description: Gene expression


title: 1401-NB_RC

description: Gene expression


title: FU97, gene expression array U133Plus2


title: LCS-057A

description: No additional information.


title: LCS-060A

description: No additional information.


title: KOSTIM1


title: HCC70, gene expression array U133Plus2 replicate 1


title: 789-NB_RC

description: Gene expression


title: EVSA, gene expression array U133Plus2 replicate 2

source_name: EVSA

value: EVSA


title: LCS-056A

description: No additional information.


title: EKVX, gene expression array U133Plus2

value: EKVX

value: lung


title: 1965-NB_DEAD

description: Gene expression

value: stored NB primary tumor, from patient dead with disease


title: 1045-NB_RC

description: Gene expression


title: 19-GD2+

description: Gene expression

source_name: human neuroblastoma cells

treatment_protocol: fresh BM samples from patients with stage 4 NB older than 18 months at diagnosis were subjected to immunomagnetic separation, after lysis of erythrocytes, cells were incubated for 30 minutes at 4°C with the anti-GD2 mAb in the presence of human Fc blocking reagent. After washing, the cell pellet was incubated for 15 minutes at 4°C with goat anti-mouse IgG2a microbeads (Miltenyi). Cells were then washed twice, suspended in 500 uL of sterile ice-cold PBS and loaded onto a MS column (Miltenyi).The GD2 positive fractions were then subjected to RNA extraction.

value: Neuroblast freshly isolated GD2 positive cells, from bone marrow


title: 20-GD2+

description: Gene expression


title: LCS-054A

description: No additional information.


title: 3917-GD2+

description: Gene expression


title: WT1

value: murine bone-marrow derived macrophages


title: GAM016, gene expression array U133Plus2


title: LCS-053A

description: No additional information.


title: LCS-051A

description: No additional information.


title: LCS-055A

description: No additional information.


title: EVSA, gene expression array U133Plus2 replicate 1


title: 15_GD2+

description: Gene expression


title: 17-GD2+

description: Gene expression


title: COLO824, gene expression array U133Plus2 replicate 2


title: ECC1, gene expression array U133Plus2 replicate 1

value: endometrium


title: 7-GD2+

description: Gene expression


title: EFM19, gene expression array U133Plus2


title: 14-GD2+

description: Gene expression


title: 13-GD2+

description: Gene expression


title: COLO824, gene expression array U133Plus2 replicate 1


title: LCS-042A

description: No additional information.

value: liver tumor tissue


title: DU145T, gene expression array U133Plus2

value: prostate


title: ECC1, gene expression array U133Plus2 replicate 2


title: LCS-048A

description: No additional information.

value: Hepatocellular carcinoma (HCC)


title: LCS-049A

description: No additional information.


title: LCS-047A

description: No additional information.


title: LCS-045A

description: No additional information.


title: 6-GD2+

description: Gene expression


title: COLO320HSR, gene expression array U133Plus2


title: EFM192A, gene expression array U133Plus2


title: 3-GD2+

description: Gene expression


title: 2-GD2+

description: Gene expression


title: CAMA1, gene expression array U133Plus2 replicate 1


title: HCC1419, gene expression array U133Plus2


title: LCS-044A

description: No additional information.


title: COLO205, gene expression array U133Plus2


title: LCS-041A

description: No additional information.


title: LCS-038A

description: No additional information.


title: LCS-039A

description: No additional information.


title: lsPERK_Control_DMSO-rep3

city: Indianapolis

first: Ron

last: Wek

state: IN

address: 635 Barnhill Dr. MS4065

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

description:
Gene expression data from mouse liver
lsPERK-nostress-3
RW02M014.CHP
RW02M014.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with GCOS generating MAS 5.0 data using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: Mouse liver

label_protocol: Biotinylated cRNA were prepared according to the standard 3'IVT Affymetrix protocol from 100ng of total RNA

extract_protocol: Total RNA was isolated from liver tissue using TRIzol reagent (Invitrogen) following the manufacturers instructions, a RNeasy mini kit (Qiagen) was used to further purify samples.

tag: tissue

value: liver

tag: genotype/variation

value: lsPERK

value: 0.3% DMSO

tag: response to treatment

value: control


title: CAMA1, gene expression array U133Plus2 replicate 2

value: breast


title: CALU6, gene expression array U133Plus2


title: lsPERK_Control_DMSO-rep2

description:
Gene expression data from mouse liver
lsPERK-nostress-2
RW02M013.CHP
RW02M013.CEL


title: CAL851, gene expression array U133Plus2 replicate 2


title: CALU1, gene expression array U133Plus2


title: lsPERK_6hTUN-rep4

description:
Gene expression data from mouse liver
lsPERK-stress-4
RW02M008.CHP
RW02M008.CEL

value: 1mg/kg Tunicamycin

value: ER stress


title: LCS-036A

description: No additional information.

tag: Gender

value: female

value: male

tag: Tissue

tag: Disease state


title: CAL120, gene expression array U133Plus2


title: CAL851, gene expression array U133Plus2 replicate 1


title: lsPERK_Control_DMSO-rep1

description:
Gene expression data from mouse liver
lsPERK-nostress-1
RW02M012.CHP
RW02M012.CEL


title: LCS-034A

description: No additional information.

tag: Individual


title: LCS-033A

description: No additional information.


title: LCS-029A

description: No additional information.


title: lsPERK_6hTUN-rep2

description:
Gene expression data from mouse liver
lsPERK-stress-2
RW02M006.CHP
RW02M006.CEL


title: LCS-027A

description: No additional information.


title: LCS-037A

description: No additional information.


title: lsPERK_6hTUN-rep1

description:
Gene expression data from mouse liver
lsPERK-stress-1
RW02M005.CHP
RW02M005.CEL


title: CACO2, gene expression array U133Plus2 replicate 1


title: WT_Control_DMSO-rep1

description:
Gene expression data from mouse liver
WT-nostress-1
RW02M009.CHP
RW02M009.CEL

value: WT


title: BT549, gene expression array U133Plus2 Pfizer


title: LCS-025A

description: No additional information.


title: CACO2, gene expression array U133Plus2 replicate 2


title: WT_Control_DMSO-rep3

description:
Gene expression data from mouse liver
WT-nostress-3
RW02M011.CHP
RW02M011.CEL


title: BT549, gene expression array U133Plus2


title: WT_Control_DMSO-rep2

description:
Gene expression data from mouse liver
WT-nostress-2
RW02M010.CHP
RW02M010.CEL


title: LCS-028A

description: No additional information.


title: LCS-023A

description: No additional information.


title: WT_6hTUN-rep4

description:
Gene expression data from mouse liver
WT_stress-4
RW02M004.CHP
RW02M004.CEL


title: LCS-024A

description: No additional information.


title: BT549, gene expression array U133Plus2 replicate 2


title: WT_6hTUN-rep3

description:
Gene expression data from mouse liver
WT_stress-3
RW02M003.CHP
RW02M003.CEL


title: LCS-022A

description: No additional information.


title: BT549, gene expression array U133Plus2 replicate 1


title: LCS-020A

description: No additional information.


title: BT20, gene expression array U133Plus2 replicate 2


title: WT_6hTUN-rep1

description:
Gene expression data from mouse liver
WT_stress-1
RW02M001.CHP
RW02M001.CEL


title: BT474, gene expression array U133Plus2


title: LCS-019A

description: No additional information.


title: AGS, gene expression array U133Plus2

source_name: AGS

value: AGS

value: stomach


title: BGC823, gene expression array U133Plus2


title: AU565, gene expression array U133Plus2 replicate 2


title: AU565, gene expression array U133Plus2 replicate 1


title: A549, gene expression array U133Plus2

value: lung


title: LCS-007A

description: No additional information.


title: AZ521, gene expression array U133Plus2


title: WT_6hTUN-rep2

description:
Gene expression data from mouse liver
WT_stress-2
RW02M002.CHP
RW02M002.CEL


title: BT20, gene expression array U133Plus2 replicate 1


title: LCS-012A

description: No additional information.


title: A498, gene expression array U133Plus2

value: renal


title: 7860, gene expression array U133Plus2


title: LCS-004A

description: No additional information.

value: liver tumor tissue


title: LCS-015A

description: No additional information.


title: LCS-009A

description: No additional information.


title: lsPERK_6hTUN-rep3

description:
Gene expression data from mouse liver
lsPERK-stress-3
RW02M007.CHP
RW02M007.CEL


title: 184A1, gene expression array U133Plus2


title: LCS-002A

description: No additional information.


title: LCS-016A

description: No additional information.


title: LCS-006A

description: No additional information.


title: LCS-001A

description: No additional information.


title: LCS-005A

description: No additional information.


title: Sample114_phenotype1_race3

status: Public on Jan 19 2012

city: Chicago

first: Chiang-Ching

last: Huang

state: IL

address: 680 N. Lake Shore Dr., Suite 1400

institute: Northwestern University

description: Female peripheral blood samples for atherosclerosis study

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was log transformed and then quantile normalized based on the output of Illumina BeadStudio software.

source_name: peripheral blood cells

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: disease state

value: atherosclerosis

tag: ethnicity

value: African-American

value: blood


title: Sample115_phenotype1_race1

value: non-Hispanic white


title: Sample118_phenotype0_race1

value: no atherosclerosis


title: Sample117_phenotype0_race3


title: Sample116_phenotype0_race1


title: Sample119_phenotype0_race1


title: Sample112_phenotype0_race1


title: Sample111_phenotype1_race4

value: Hispanic


title: LCS-003A

description: No additional information.

value: Hepatocellular carcinoma (HCC)


title: Sample110_phenotype0_race1


title: Sample102_phenotype1_race4


title: Sample106_phenotype0_race2

value: Chinese


title: Sample108_phenotype0_race4


title: Sample105_phenotype1_race1


title: Sample104_phenotype1_race1


title: Sample109_phenotype0_race4


title: Sample103_phenotype0_race1


title: Sample101_phenotype0_race1


title: Sample100_phenotype0_race1


title: Sample113_phenotype1_race1


title: Sample107_phenotype1_race1


title: Sample99_phenotype0_race1


title: Sample98_phenotype1_race1


title: Sample97_phenotype0_race3


title: Sample95_phenotype0_race3


title: Sample96_phenotype0_race3


title: Sample94_phenotype1_race3


title: Sample93_phenotype0_race1


title: Sample86_phenotype1_race4


title: Sample91_phenotype1_race1


title: Sample89_phenotype0_race1


title: Sample88_phenotype0_race1


title: Sample84_phenotype0_race3


title: Sample83_phenotype0_race3


title: Sample82_phenotype0_race3


title: Sample85_phenotype1_race1


title: Sample87_phenotype1_race3


title: Sample81_phenotype0_race3


title: Sample80_phenotype0_race1


title: Sample79_phenotype1_race1


title: Sample75_phenotype0_race1


title: Sample90_phenotype0_race1


title: 15645_HepatocellularTumors_HF-17229_SPR424_Map100kXba

city: South San Francisco

first: Peter

last: Haverty

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

hyb_protocol: Affymetrix 100K protocol

scan_protocol: Affymetrix 100K protocol

data_processing: Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005). The dChip-normalized signal intensities were converted to log2 ratios. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment.

label_protocol: Affymetrix 100K protocol

growth_protocol: Tumor samples were acquired from commercial vendors.

extract_protocol: Qiagen AllPrep extraction kit was used according to the manufacturer's instructions

treatment_protocol: Untreated

tag: disease

value: Hepatocellular Carcinoma


title: 15649_HepatocellularTumors_HF-17493_SPR424_Map100kXba


title: 15651_HepatocellularTumors_HF-17499_SPR424_Map100kXba


title: Sample76_phenotype1_race4


title: Sample73_phenotype0_race4


title: Sample78_phenotype1_race1


title: 15653_HepatocellularTumors_HF-17592_SPR424_Map100kXba


title: 15655_HepatocellularTumors_HF-17693_SPR424_Map100kXba


title: 15641_HepatocellularTumors_HF-17224_SPR424_Map100kXba


title: Sample71_phenotype0_race1


title: Sample74_phenotype0_race3


title: Sample77_phenotype0_race1


title: Sample72_phenotype1_race2


title: Sample66_phenotype0_race3


title: Sample68_phenotype1_race1


title: Sample69_phenotype1_race1


title: 15643_HepatocellularTumors_HF-17225_SPR424_Map100kXba


title: Sample92_phenotype0_race4


title: Sample67_phenotype0_race3


title: Sample65_phenotype1_race1


title: CH01051_control_phenotype0_race1

description:
tissue: blood,gender:male,race:white
White male peripheral blood samples for atherosclerosis study

data_processing: The data was log transformed and then quantile normalized based on the output of Illumina BeadStudio software. The supplementary data includes both raw and normalized data, which can be loaded using Bioconductor lumi package.


title: 15639_HepatocellularTumors_HF-17079_SPR424_Map100kXba


title: CH00122_control_phenotype0_race1


title: Sample70_phenotype1_race4


title: 15647_HepatocellularTumors_HF-17268_SPR424_Map100kXba


title: CH33742_control_phenotype0_race1


title: Sample62_phenotype0_race4


title: Sample64_phenotype1_race1


title: 15633_HepatocellularTumors_HF-16443_SPR424_Map100kXba


title: CH12173_control_phenotype0_race1


title: 15637_HepatocellularTumors_HF-17078_SPR424_Map100kXba


title: CH12206_control_phenotype0_race1


title: Sample63_phenotype0_race2


title: Sample61_phenotype1_race3


title: Sample56_phenotype0_race1


title: Sample58_phenotype0_race4


title: Sample50_phenotype1_race1


title: CH22726_control_phenotype0_race1


title: Sample60_phenotype0_race1


title: Sample53_phenotype0_race1


title: Sample59_phenotype0_race3


title: 15627_HepatocellularTumors_HF-16437_SPR424_Map100kXba


title: CH01615_control_phenotype0_race1


title: Sample54_phenotype1_race3


title: 15631_HepatocellularTumors_HF-16441_SPR424_Map100kXba


title: 15635_HepatocellularTumors_HF-16920_SPR424_Map100kXba


title: Sample51_phenotype0_race1


title: Sample52_phenotype0_race3


title: CH14099_case_phenotype1_race1


title: 15629_HepatocellularTumors_HF-16439_SPR424_Map100kXba


title: Sample55_phenotype0_race1


title: 15625_HepatocellularTumors_HF-16291_SPR424_Map100kXba


title: CH20147_case_phenotype1_race1


title: 15623_HepatocellularTumors_HF-16292_SPR424_Map100kXba


title: CH22717_case_phenotype1_race1


title: Sample48_phenotype1_race3


title: Sample47_phenotype1_race3


title: 15621_HepatocellularTumors_HF-16293_SPR424_Map100kXba


title: 15619_HepatocellularTumors_HF-5203_SPR424_Map100kXba


title: Sample49_phenotype0_race4


title: Sample41_phenotype0_race1


title: 15654_HepatocellularTumors_HF-17693_SPR424_Map100kHind


title: Sample43_phenotype1_race3


title: CH05234_case_phenotype1_race1


title: Sample42_phenotype0_race1


title: Sample46_phenotype1_race3


title: CH35786_case_phenotype1_race1


title: CH06874_case_phenotype1_race1


title: Sample38_phenotype0_race3


title: Sample44_phenotype0_race4


title: Sample39_phenotype1_race1


title: Sample40_phenotype1_race1


title: 15617_HepatocellularTumors_HF-1662-(2)_SPR424_Map100kXba


title: CH26238_control_phenotype0_race1


title: Sample45_phenotype0_race1


title: CH21596_case_phenotype1_race1


title: CH00709_case_phenotype1_race1


title: heart male pbs 90 dpi rep3

city: Baltimore

first: DeLisa

last: Fairweather

address: 615 N Wolfe St

department: Environmental Health Sciences

institute: Johns Hopkins University

description: Gene expression data of male hearts after a 90 day treatment of CVB3

hyb_protocol: Hybridization cocktails were prepared as recommended for arrays of Mini/169 format using reagents in the Affymetrix Hybridization Wash Stain kit. Hybridization mix and fragmented, labeled ST-sscDNA were incubated at 99oC for 2 min and 45oC for 5 min, and then centrifuged at maximum speed for 5 min prior to pipetting into the GeneChips (Affymetrix Mouse Gene ST 1.0). Hybridization was performed at 45oC for 18 hours at 60RPM in the Affymetrix rotisserie hybridization oven. The signal amplification protocol for washing and staining of eukaryotic targets was performed in an automated fluidies station (Affymetrix FS450) using Affymetrix protocol FS450_0001.

scan_protocol: Arrays were transferred to a GCS3000 laser scanner with autoloader and 3G upgrade (Affymetrix) and scanned at an emission wavelength of 570nm at 2.5 um resolution

data_processing:
CEL files were imported and analyzed with the default algorithm workflow RMA-Sketch, which includes RMA background correction, and Sketch-Quantile normalization.
The values recommended by Affymetrix as QC metrics include Positive vs. negative AUC (assessment of sensitivity and specificity), as well as all probeset mean and all probeset relative log expression.

label: Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (biotin)

source_name: male heart 90 days post pbs injection

label_protocol: RNAs were processed for hybridization to Affymetrix Mouse Gene ST 1.0 microarrays using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay, according to manufacturer's recommended protocol. One hundred nanograms of total RNA was amplified.

extract_protocol: Hearts were homogenized in 2mL TRIzol according to the manufacturer's protocol. PureLink Micro-to-midi Total RNA purification System was used for extraction and purification of RNA

treatment_protocol: Mice were treated with either PBS or heart-passaged CVB3 intraperitoneally. Mice were harvested at 90 days post infection and hearts were flash frozen in liquid nitrogen for RNA extraction.

tag: strain

value: BALB/C

value: 8-10 weeks

value: PBS

value: Male

tag: time

value: 90 dpi

value: heart


title: 15652_HepatocellularTumors_HF-17592_SPR424_Map100kHind


title: 15650_HepatocellularTumors_HF-17499_SPR424_Map100kHind


title: Sample36_phenotype0_race1


title: Sample32_phenotype0_race1


title: Sample34_phenotype1_race2


title: heart male CVD3 90 dpi rep2

description: Gene expression data of female hearts after a 90 day treatment of CVB3

source_name: male heart 90 days post cvb3 injection

tag: age

tag: gender


title: heart male CVD3 90 dpi rep3

tag: treatment


title: Sample35_phenotype1_race2


title: 15648_HepatocellularTumors_HF-17493_SPR424_Map100kHind


title: heart male pbs 90 dpi rep2


title: 15646_HepatocellularTumors_HF-17268_SPR424_Map100kHind


title: Sample29_phenotype1_race4


title: Sample31_phenotype1_race1


title: Sample33_phenotype0_race1


title: heart male pbs 90 dpi rep1


title: Sample28_phenotype0_race1


title: Sample30_phenotype0_race1


title: 15644_HepatocellularTumors_HF-17229_SPR424_Map100kHind


title: Sample27_phenotype0_race3


title: heart male CVD3 90 dpi rep1


title: Sample26_phenotype0_race1


title: Sample24_phenotype0_race1


title: 15640_HepatocellularTumors_HF-17224_SPR424_Map100kHind


title: 15642_HepatocellularTumors_HF-17225_SPR424_Map100kHind


title: Sample25_phenotype1_race1


title: heart female pbs 90 dpi rep3

description: Gene expression data of female hearts after a 90 day treatment of PBS

source_name: female heart 90 days post pbs injection

value: Female


title: 15638_HepatocellularTumors_HF-17079_SPR424_Map100kHind


title: Sample23_phenotype1_race1


title: Sample57_phenotype0_race1


title: heart female pbs 90 dpi rep2


title: heart female CVD3 90 dpi rep3

description: Gene expression data of male hearts after a 90 day treatment of PBS

source_name: female heart 90 days post cvb3 injection

treatment_protocol: Mice were treated with either PBS or heart-passaged CVB3 intraperitoneally. Mice were harvested at 10 days post infection and hearts were flash frozen in liquid nitrogen for RNA extraction.


title: Sample20_phenotype0_race1


title: 15634_HepatocellularTumors_HF-16920_SPR424_Map100kHind


title: heart female pbs 90 dpi rep1


title: Sample21_phenotype0_race1


title: Sample22_phenotype0_race4


title: heart female CVD3 90 dpi rep2


title: Sample15_phenotype1_race1


title: Sample17_phenotype1_race1


title: 15636_HepatocellularTumors_HF-17078_SPR424_Map100kHind


title: 15630_HepatocellularTumors_HF-16441_SPR424_Map100kHind


title: Sample18_phenotype0_race1


title: Sample19_phenotype0_race1


title: heart male CVD3 10 dpi rep3

description: Gene expression data of male hearts after a 10 day treatment of CVB3

source_name: male heart 10 days post cvb3 injection

value: 10 dpi


title: heart female CVD3 90 dpi rep1


title: Sample12_phenotype0_race4


title: 15628_HepatocellularTumors_HF-16439_SPR424_Map100kHind


title: 15632_HepatocellularTumors_HF-16443_SPR424_Map100kHind


title: Sample13_phenotype1_race1

value: atherosclerosis


title: 15626_HepatocellularTumors_HF-16437_SPR424_Map100kHind


title: 15624_HepatocellularTumors_HF-16291_SPR424_Map100kHind


title: Sample14_phenotype0_race1


title: Sample11_phenotype0_race3

value: African-American


title: Sample16_phenotype0_race1

value: blood


title: heart female CVD3 10 dpi rep3

description: Gene expression data of female hearts after a 10 day treatment of CVB3

source_name: female heart 10 days post cvb3 injection


title: heart female CVD3 10 dpi rep2


title: 15620_HepatocellularTumors_HF-16293_SPR424_Map100kHind


title: 15622_HepatocellularTumors_HF-16292_SPR424_Map100kHind


title: heart male CVD3 10 dpi rep1


title: heart female CVD3 10 dpi rep1


title: heart male pbs 10 dpi rep3

description: Gene expression data of male hearts after a 10 day treatment of PBS

source_name: male heart 10 days post pbs injection


title: Sample6_phenotype0_race3


title: Sample8_phenotype0_race2


title: 15618_HepatocellularTumors_HF-5203_SPR424_Map100kHind


title: Sample7_phenotype0_race1

value: non-Hispanic white


title: heart male pbs 10 dpi rep1


title: Sample9_phenotype1_race3


title: heart male CVD3 10 dpi rep2


title: Sample10_phenotype1_race3


title: Sample4_phenotype0_race1

value: no atherosclerosis


title: Sample5_phenotype1_race3


title: heart male pbs 10 dpi rep2


title: 15616_HepatocellularTumors_HF-1662-(2)_SPR424_Map100kHind


title: heart female pbs 10 dpi rep2

description: Gene expression data of female hearts after a 10 day treatment of PBS

source_name: female heart 10 days post pbs injection


title: heart female pbs 10 dpi rep3


title: Sample37_phenotype1_race1


title: Sample2_phenotype1_race1


title: Adipose TZD rep3

status: Public on Jan 18 2012

city: Dallas

first: Wei

last: Tang

state: TX

address: 6000 Harry Hines Blvd.

department: Developmental Biology

institute: UT Southwestern Medical Center at Dallas

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI

source_name: Adipose progenitors, TZD, 2month

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

growth_protocol: Adult (2-6 months old) PPARgamma-tTA;tetO-H2B-GFP mice were housed in a 12:12 light:dark cycle and chow and water were provided ad libitum.

extract_protocol: White adipose tissues (inguinal, interscapular and gonadal white adipose tissues) were digested with collagenase for 2 hours at 37 degree with gentle shaking, and stromal-vascular fraction was collected and GFP+ cells from this fraction were FACS-sorted. RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice were fed with normal chow or rosiglitazone-containing normal chow (0.0075%) for 2 months.

tag: source tissue

value: white adipose tissue

tag: developmental stage

value: adult (2-6 month old)

tag: cell type

value: GFP+ stromal-vascular cells

value: rosiglitazone


title: dex

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression data were obtained from macrophage THP-1 cells.

hyb_protocol: Agilent hybridization protocol 65C 10rpm 17 h.

scan_protocol: Agilent arrays were scanned using the Agilent Scanner G2565BA.

data_processing: The data was first processed by background correction and then quantile normalization using Agilent Feature Extraction Software was version 9.5.3.1.

label: Agilent  part #5190-0442 Quick-Amp Labeling kit 1-color.

source_name: macrophage THP-1 cells

label_protocol: 300 ng of Qiagen-purified total RNA

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

value: macrophage cells

tag: cell line

value: THP-1 cells

tag: treatment group

value: dex


title: Sample3_phenotype1_race3

tag: tissue


title: heart female pbs 10 dpi rep1

value: BALB/C

value: 8-10 weeks

value: PBS


title: Adipose No TZD rep2

description: replicate 2

source_name: Adipose progenitors, no TZD, 2month

value: untreated


title: Adipose No TZD rep1

description: replicate 1


title: Adipose TZD rep1

description: replicate 1


title: B6 wildtype control 7

first: Camron

middle: D

last: Bryant

address: 920 E. 58th Street, CLSC 501

department: Human Genetics

institute: The University of Chicago

description:
11-1844_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype

hyb_protocol: The details for the hyb/wash/stain are in the Affy protocol: http://media.affymetrix.com/support/downloads/manuals/wt_term_label_ambion_user_manual.pdf.  Briefly, the hybridization cocktail was made with the Affy Hyb buffer, DMSO, Oligo B2 and 20X eukaryotic controls and hybridized to the gene arrays for 17hrs at 45C. The arrays were then washed and stained with SAPE (Streptavidin Phycoerythrin binds to the biotin) and scanned.

scan_protocol: Affymetrix GeneChip  Scanner 3000 7G.  Affymetrix GeneChip Command Console (AGCC) software generated the raw data files including the CEL files.

data_processing: Data were processed using both Affymetrix Gene Expression Console Software and Affymetrix Powertools robust multichip average (RMA) analysis.  Both gave the same results.  However, prior to generating RMA values, we eliminated 145 probes from analysis using the Affymetrix powertools kill list option.  We provide the text file named kill list that we used for probe masking.  After generating RMA values, we then corrected for batch effects (2 batches) using the ComBat.R script which is also provided.  Thus, the RMA values provided on the matrix template are those obtained following probe masking and following correction for batch effects.

source_name: left and right striatum

label_protocol: Precision Biomarker Resources processed the RNA and scanned the arrays.  Here is the protocol manual with all of the details for the amplification: http://tools.invitrogen.com/content/sfs/manuals/cms_064619.pdf.  Briefly, we started with 100ng of total RNA, subjected it to first strand and second strand cDNA generation followed by 16hr IVT amplification making cRNA. The cRNA was bead purified and then 10µg was put into the second cycle sscDNA reaction. 5.5µg of sscDNA was then fragmented and end labeled with biotin.

extract_protocol: RNA was extracted using Trizol® (Invitrogen, Carlsbad, CA) and chloroform and then precipitated with ethanol and resuspended.  The solution was then passed through RNeasy® columns (Qiagen), quality checked using the Agilent 2100 Bioanalyzer (Santa Clara, CA),

treatment_protocol: Mice were housed as same-sex littermates, 2-5 per cage.  Mice were naïve at the time of rapid decapitation for brain tissue harvesting.

tag: batch

value: batch 2

tag: genotype

value: homozygous for B6 in congenic region

tag: Sex

value: male

tag: age (days old)


title: control

value: control


title: Adipose No TZD rep3

description: replicate 3


title: B6 wildtype control 5

description:
11-1842_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype

value: female


title: B6 wildtype control 6

description:
11-1843_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype


title: Sample1_phenotype1_race1

tag: disease state

value: atherosclerosis

tag: ethnicity

value: non-Hispanic white

value: blood


title: B6 wildtype control 8

description:
11-1845_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype


title: B6 wildtype control 3

description:
11-1840_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype


title: B6 wildtype control 4

description:
11-1841_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype


title: B6 wildtype control 1

description:
11-1838_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype


title: homozygous congenic 7

description:
11-1836_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype

value: homozyygous for A/J in congenic region


title: homozygous congenic 8

description:
11-1837_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype


title: B6 wildtype control 2

description:
11-1839_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype


title: homozygous congenic 6

description:
11-1835_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype


title: c106


title: LNCAP_3

city: Zuerich

first: Mark

last: Robinson

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

institute: University of Zuerich

description: Sample name: 6264509024_R03C02

hyb_protocol: According to manufacturer's protocol.

scan_protocol: According to manufacturer's protocol.

data_processing: R/Bioconductor 'minfi' package, with default parameters {RG.raw <- read.450k.exp(base = slide.folder, targets = files.table); methyl.norm <- preprocessIllumina(RG.raw, bg.correct = TRUE, normalize = controls); beta.table <- getBeta(methyl.norm)}, to generate beta values

label: Cy5 and Cy3

source_name: LNCaP cells

label_protocol: According to manufacturer's protocol.

growth_protocol: 37 deg C with 5% CO2

extract_protocol: DNA was extracted using the QIAamp Mini Kit (Qiagen) following manufacturers instructions.

treatment_protocol: Native DNA was used

value: prostate

value: LNCaP


title: LNCAP_2

description: Sample name: 6264509024_R02C02


title: PREC_3

description: Sample name: 6264509024_R06C02

source_name: PrEC cells

value: PrEC


title: PREC_1

description: Sample name: 6264509024_R04C02


title: Haematopoietic Stem/Progenitor cells expressing AML1/ETO-HA_ChIP with anti-H4Ac antibody_Array B

city: Madrid

first: Sara

last: Alvarez

address: C/Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

description: Three biological replicates per sample were prepared and hybridized on the same array set.

hyb_protocol: 1ug of each ChIP and Input labeled DNA were hybridized in Agilent hybridization chambers for up to 40 hours at 65ºC at 20rpm. The arrays were washed 5 minutes in wash buffer 1, and then 1 minute in wash buffer 2 at 37ºC.

scan_protocol: Arrays were scanned on an Agilent scanner per manufacturer´s protocol. The images obtained were processed using the Agilent Feature Extractor software application (v.9.5.3.1).

data_processing: The Agilent ChIP Analytics 1.3 software package was used to perform a linear scan across the regions represented on the promoter array. The software performs  both dye-bias and interarray normalization. A whole ChIP error model was used to calculate the confidence values from the enrichment ratio and the signal intensity of each probe.  It calculates the log of the ratio of intensity in the IP-enriched channel to intensity in the genomic DNA channel for each probe and use the neighborhood error model to calculate confidence vaues for each spot on each array (single-probe p value). This error model converts the intensity information in both channels to an X score which is dependent on both the absolute value of intensities and background noise in each channel. The X scores are assumed to be normally distributed, thus enabling a p value to be calculated for the enrichment ratio observed at each feature.

source_name: H4Ac ChIP DNA from HSPC expressing the AML1/ETO fusion protein

label_protocol: ChIP or Input DNA were labeled using the Bioprime® DNA-Labeling system protocol (Life Technologies, Carlsbad, CA) with random priming and Cy5/Cy3 fluorescent dyes, respectively.

extract_protocol: ChIP assays were performed as described elsewhere (Ballestar et al., EMBO J., 2003 [PMID 14633992]). Three biological replicates were prepared and hybridized on the same array set. ChIP products were amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma, Saint Louis, MO) and purified using the UltraCleanTM GelSpinTM DNA purification kit (MO BIO laboratories, Inc., Carlsbad, CA).

treatment_protocol: HSPCs were 1% formaldehyde crosslinked after 12-17 weeks in culture.

value: cord blood

value: CD34+ hematopoietic stem/progenitor cells (HSPCs)

tag: source

value: normal donors

tag: transduction

value: AML1/ETO fusion protein

tag: chip antibody

tag: antibody vendor

value: Millipore

tag: antibody catalog number

tag: antibody lot number

source_name: Input DNA from HSPCs expressing the AML1/ETO fusion protein


title: homozygous congenic 2

description:
11-1831_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype

value: batch 2


title: homozygous congenic 5

description:
11-1834_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype


title: homozygous congenic 3

description:
11-1832_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype


title: homozygous congenic 4

description:
11-1833_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype


title: Adipose TZD rep2

description: replicate 2

tag: source tissue

value: white adipose tissue

tag: developmental stage

value: adult (2-6 month old)

value: GFP+ stromal-vascular cells

tag: strain

tag: treatment

value: rosiglitazone


title: KO_Inf_replicate 4

city: Braunschweig

first: Sabin

last: Bhuju

address: Salzdhalumerstr

institute: Lionex

description: Gene expression after infecting BMM from SOCS1 mutant with M. tuberculosis

hyb_protocol: Following fragmentation, 1.8 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. Agilent micorarray were washed according to manufacture instruction.

scan_protocol: Agilent microchips  were scanned using the Feature extraction software FE 10.5 (Agilent)

data_processing: Scaling (Genespring GX 11, Agilent)

source_name: SOCS1 mutant infected

label_protocol: Cy3 cRNA were prepared according to the standard Agilent protocol from 200 ng total RNA (Quick Amp Labeling Kit, Agilent).

growth_protocol: The bone marrow cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) containing glucose and supplemented with 2 mM L-glutamine, 10% FCS, 10 mM Hepes, 100 mg/ml streptomycin, 100 U/ml penicillin (all from Sigma, St Louis, MO), and 20 to 30% L929 cell-conditioned medium (as a source of macrophage-colony stimulating factor).

extract_protocol: Total RNA isolation

treatment_protocol: M. tuberculosis Harlingen strain were inoculated by the aerosol route by using a nose-only exposure unit

tag: genotype/variation

value: SOCS Knockout Mutant

tag: tissue

value: bone marrow derived macrophage (BMM)

tag: infection

value: Infected


title: dex_c106

description: Gene expression data were obtained from macrophage THP-1 cells.

tag: cell type

value: macrophage cells

tag: cell line

value: THP-1 cells

tag: treatment group


title: KO_Inf_replicate 3


title: Haematopoietic Stem/Progenitor cells transfected with empty vector_ChIP with anti-H3K9me3 antibody_Array B

source_name: H3K9me3 ChIP DNA from HSPC transduced with the empty vector

value: vector

value: Abcam

source_name: Input DNA from HSPCs transduced with the empty vector


title: LNCAP_1

description: Sample name: 6264509024_R01C02

value: prostate

value: LNCaP


title: Haematopoietic Stem/Progenitor cells transfected with empty vector_ChIP with anti-H4Ac antibody_Array B

source_name: H4Ac ChIP DNA from HSPC transduced with the empty vector

value: cord blood

value: CD34+ hematopoietic stem/progenitor cells (HSPCs)

value: normal donors


title: homozygous congenic 1

description:
11-1830_CB_(MoGene-1_0-st-v1).CEL
not littermates of the other genotype

tag: batch

value: batch 2

tag: genotype

value: homozyygous for A/J in congenic region

tag: Sex

value: female

tag: age (days old)


title: PREC_2

description: Sample name: 6264509024_R05C02

value: PrEC


title: heterozygous congenic 5

description:
11-0505_CB
both genotypes were littermates with each other

value: batch 1

value: heterozygous for B6, A/J in congenic region

value: male


title: Haematopoietic Stem/Progenitor cells expressing AML1/ETO-HA_ChIP with anti-H3K9me3 antibody_Array B

source_name: H3K9me3 ChIP DNA from HSPC expressing the AML1/ETO fusion protein

tag: source

tag: transduction

value: AML1/ETO fusion protein

tag: chip antibody

tag: antibody vendor


title: KO_Inf_replicate 2

value: SOCS Knockout Mutant

value: bone marrow derived macrophage (BMM)

value: Infected


title: KO_Inf_replicate 1


title: Haematopoietic Stem/Progenitor cells transfected with empty vector_ChIP with anti-HDAC1 antibody_Array B

source_name: HDAC1 ChIP DNA from HSPC transduced with the empty vector

value: vector

value: Affinity BioReagents

tag: antibody catalog number

tag: antibody lot number


title: heterozygous congenic 4

description:
11-0504_CB
both genotypes were littermates with each other


title: Haematopoietic Stem/Progenitor cells expressing AML1/ETO-HA_ChIP with anti-HA antibody_Array B

description:
Immunopurified anti-HA made in-house: clone H9658 Monoclonal Antibodies Unit, CNIO, Madrid, Spain.

Three biological replicates per sample were prepared and hybridized on the same array set.

source_name: HA-AML1/ETO ChIP DNA from HSPC expressing the AML1/ETO fusion protein

value: anti-HA


title: KO_NonInf_replicate 4

description: Gene expression in noninfected BMM from SOCS1 mutant

source_name: SOCS1 mutant noninfected

value: Not Infected


title: heterozygous congenic 3

description:
11-0502_CB
both genotypes were littermates with each other


title: LFS-adrenocortical carcinoma tumor 4

city: Toronto

first: Diana

middle: M

last: Merino

state: Ontario

address: 686 Bay St.

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

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

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

data_processing: Genotyping (CN5) and copy number analysis (Birdseed_v2) with the Affymetrix Genotyping Console. Standard export of copy number results (.CN5.CNCHP file)

source_name: LFS-adrenocortical carcinoma tumor 4

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from tissues on dry ice by standard Proteinase K-SDS protocol, followed by phenol-chloroform extraction and ethanol precipitation.

tag: tumor type

value: adrenocortical carcinomas


title: LFS-rhabdomyosarcoma tumor 1

source_name: LFS-rhabdomyosarcoma tumor 1

value: rhabdomyosarcoma


title: LFS-adrenocortical carcinoma tumor 3

source_name: LFS-adrenocortical carcinoma tumor 3


title: LFS-extra-renal rhabdoid tumor 1

source_name: LFS-extra-renal rhabdoid tumor 1

value: extra-renal rhabdoid tumor


title: LFS-adrenocortical carcinoma tumor 2

source_name: LFS-adrenocortical carcinoma tumor 2


title: heterozygous congenic 6

description:
11-0506_CB
both genotypes were littermates with each other

source_name: left and right striatum


title: LFS-rhabdomyosarcoma tumor 2

source_name: LFS-rhabdomyosarcoma tumor 2


title: KO_NonInf_replicate 3

tag: genotype/variation


title: heterozygous congenic 2

description:
11-0498_CB
both genotypes were littermates with each other


title: Haematopoietic Stem/Progenitor cells transfected with empty vector_ChIP with anti-HA antibody_Array B

source_name: HA-AML1/ETO ChIP DNA from HSPC transduced with the empty vector

tag: tissue

value: cord blood

value: CD34+ hematopoietic stem/progenitor cells (HSPCs)

value: normal donors