title: GM07044-0hr

description:
Baseline, GM07044

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM11820-6hr

status: Public on Apr 06 2009

type: RNA

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

country: USA

institute: Perelman School of Medicine at the University of Pennsylvania

description:
6hr Post IR, GM11820

Gene expression data from lymphoblastoid cells following 10 Gy irradiation in a 137Cs irradiator.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix GeneChip Human U133A 2.0 Chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Expression Console software using the MAS5 probe summary method and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lymphoblastoid cell line, 6hr

label_protocol: Biotinylated cRNA was prepared using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion/Applied Biosystems) from 1 microg of total RNA following manufacturer's instructions.

growth_protocol: The cells were grown at a density of 500,000 cells/ml in RPMI 1640 with 15% FBS, 1% penicillin-streptomycin, 2mM L-glutamine at 37°C in a humidified 5% CO2 chamber.

extract_protocol: RNA was extracted using the RNeasy Mini-Kit (Qiagen) as per the manufacturer's instructions.

treatment_protocol: 10 Gy of ionizing radiation (IR) in a 137Cs irradiator.

tag: coriell cell line

tag: cell type

value: lymphoblastoid cells

tag: ceph id

tag: relationship

value: daughter

tag: treatment

value: ionizing radiation (IR)

tag: treatment time


title: GM07343-0hr

description:
Baseline, GM07343

Gene expression data from lymphoblastoid cells prior to irradiation.

source_name: Lymphoblastoid cell line, 0hr


title: GM07011-6hr

description:
6hr Post IR, GM07011

Gene expression data from lymphoblastoid cells following 10 Gy irradiation in a 137Cs irradiator.


title: GM11820-0hr

description:
Baseline, GM11820

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM11820-2hr

description:
2hr Post IR, GM11820

Gene expression data from lymphoblastoid cells following 10 Gy irradiation in a 137Cs irradiator.

source_name: Lymphoblastoid cell line, 2hr


title: GM07343-6hr

description:
6hr Post IR, GM07343

Gene expression data from lymphoblastoid cells following 10 Gy irradiation in a 137Cs irradiator.


title: GM07011-2hr

description:
2hr Post IR, GM07011

Gene expression data from lymphoblastoid cells following 10 Gy irradiation in a 137Cs irradiator.


title: GM07343-2hr

description:
2hr Post IR, GM07343

Gene expression data from lymphoblastoid cells following 10 Gy irradiation in a 137Cs irradiator.


title: GM07044-2hr

description:
2hr Post IR, GM07044

Gene expression data from lymphoblastoid cells following 10 Gy irradiation in a 137Cs irradiator.


title: Breast tumor sample 145

status: Public on Jul 23 2008

city: Singapore

first: Kun

last: Yu

department: Cellular & Molecular Research

country: Singapore

institute: National Cancer Centre

description: Gene expression data from breast cancer

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Breast tumor sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Affymetrix).

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

tag: Tissue

value: breast


title: Breast tumor sample 149

description: Gene expression data from breast cancer


title: GM07011-0hr

description:
Baseline, GM07011

Gene expression data from lymphoblastoid cells prior to irradiation.


title: Breast tumor sample 139

description: Gene expression data from breast cancer


title: breast tumor sample 3269

status: Public on Oct 07 2008

city: San Diego

first: Jack

state: CA

address: 3210 Merryfield Row

institute: Veridex, LLC

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: breast tumor tissue

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from cell samples using the Trizol Kit.

tag: breast cancer


title: Breast tumor sample 163

description: Gene expression data from breast cancer


title: Breast tumor sample 179

description: Gene expression data from breast cancer


title: Breast tumor sample 127

description: Gene expression data from breast cancer


title: Breast tumor sample 152

description: Gene expression data from breast cancer


title: Breast tumor sample 151

description: Gene expression data from breast cancer


title: Breast tumor sample 175

description: Gene expression data from breast cancer


title: Breast tumor sample 160

description: Gene expression data from breast cancer


title: Breast tumor sample 108

description: Gene expression data from breast cancer


title: Breast tumor sample 104

description: Gene expression data from breast cancer


title: Breast tumor sample 178

description: Gene expression data from breast cancer


title: Breast tumor sample 96

description: Gene expression data from breast cancer


title: Breast tumor sample 161

description: Gene expression data from breast cancer


title: Breast tumor sample 91

description: Gene expression data from breast cancer


title: Breast tumor sample 134

description: Gene expression data from breast cancer


title: Breast tumor sample 93

description: Gene expression data from breast cancer


title: Breast tumor sample 92

description: Gene expression data from breast cancer


title: Breast tumor sample 86

description: Gene expression data from breast cancer


title: Breast tumor sample 99

description: Gene expression data from breast cancer


title: GM07344-0hr

description:
Baseline, GM07344

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12149-2hr

description:
2hr Post IR, GM12149

Gene expression data from lymphoblastoid cells following 10 Gy irradiation in a 137Cs irradiator.


title: Breast tumor sample 37

description: Gene expression data from breast cancer


title: Breast tumor sample 18

description: Gene expression data from breast cancer


title: Breast tumor sample 31

description: Gene expression data from breast cancer


title: Breast tumor sample 49

description: Gene expression data from breast cancer


title: Breast tumor sample 13

description: Gene expression data from breast cancer


title: Breast tumor sample 36

description: Gene expression data from breast cancer


title: Breast tumor sample 12

description: Gene expression data from breast cancer


title: Breast tumor sample 25

description: Gene expression data from breast cancer


title: Breast tumor sample 20

description: Gene expression data from breast cancer


title: Breast tumor sample 3

description: Gene expression data from breast cancer


title: Breast tumor sample 1

description: Gene expression data from breast cancer


title: Breast tumor sample 21

description: Gene expression data from breast cancer


title: Animal#911 small intestine uninfected naive control

status: Public on Jul 16 2008

city: Beltsville

first: Robert

middle: W

last: Li

state: MD

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

description: see Li & Li, BMC Genomics 2006, 7:234

hyb_protocol: single dye

scan_protocol: Axon GenePix 4000B at 5 uM resolution

data_processing: The data presented here are average fluorescent intensity from either 4 or 8 perfect match oligos that represent a single unique sequence. These data are usually log transformed and subject to quantile normalization method using the R package before analyzed. see Li & Li, BMC Genomics 2006, 7:234

organism: Bos taurus

label_protocol: incorporation

growth_protocol: normal Holstein bull calf (2 to 4 months old fed with hay)

extract_protocol: Trizol following by DNase digestion and Qiagen RNeasy purification

tag: breed

value: Holstein

tag: gender

value: male

tag: tissue

value: small intestine


title: Animal#920 small intestine infected with Cooperia oncophora for 28 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Breast tumor sample 52

description: Gene expression data from breast cancer


title: Breast tumor sample 6

description: Gene expression data from breast cancer


title: Animal#919 small intestine uninfected naive control

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#918 small intestine infected with Cooperia oncophora for 14 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#917 small intestine infected with Cooperia oncophora for 14 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#916 small intestine infected with Cooperia oncophora for 7 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#923 small intestine infected with Cooperia oncophora for 28 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#928 small intestine infected with Cooperia oncophora for 7 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#930 small intestine infected with Cooperia oncophora for 42 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#915 small intestine infected with Cooperia oncophora for 7 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Breast tumor sample 28

description: Gene expression data from breast cancer


title: Animal#927 small intestine infected with Cooperia oncophora for 42 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#871 small intestine infected with Cooperia oncophora for 14 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#872 small intestine infected with Cooperia oncophora for 14 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#881 small intestine infected with Cooperia oncophora for 42 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#913 small intestine infected with Cooperia oncophora for 7 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#878 small intestine uninfected (naive control)

description: see Li & Li, BMC Genomics 2006, 7:234


title: ACK11_7

status: Public on Dec 19 2007

city: Durham

first: Bryan

middle: R.

last: Cullen

state: NC

address: CARL Bldg 427, Research Drive

institute: Duke University Medical Center

description: Arrays were printed at the Duke Microarray Facility using the Genomics Solutions OmniGrid 300 Arrayer. The arrays contain the Human Operon v3.0.2 arrays (Oligo Source) that possess 34,602 unique optimized 70-mers.

hyb_protocol: Sample and reference cDNA were pooled, purified with QIAquick Purification Columns (Qiagen), mixed with hybridization buffer (50% formamide, 5 SSC, and 0.1% SDS), COT-1 DNA, and poly-deoxyadenylic acid to limit nonspecific binding, and heated to 95º C for 2 minutes. This mixture was pipetted onto a microarray slide, and hybridized overnight at 42º C on the MAUI hybridization system (BioMicro Systems). The array was then washed at increasing stringencies before scanning. All protocols are available in greater detail on the Duke Microarray Facility Web site (http://microarray.genome.duke.edu/services/spotted-arrays/protocols).

scan_protocol: Arrays were scanned on a GenePix 4000B microarray scanner (Axon Instruments). All protocols are available in greater detail on the Duke Microarray Facility Web site (http://microarray.genome.duke.edu/services/spotted-arrays/protocols).

data_processing: All arrays were subject to background subtraction followed by loess normalization within each array and scale normalization across all arrays using the arrayMagic package in R (Buness A., Huber W., Steiner K., Sueltmann H., Poustka A. arrayMagic: two-colour cDNA microarray quality control and preprocessing. Bioinformatics 2005 21, 554–556). KNN impute package in GenePattern (Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500) was used to impute missing data if a probe had intensity values for at least half the samples. Otherwise the probes were excluded from analysis. Replicate probes were collapsed to one probe corresponding to the median value of all the replicates.

source_name: Stably Transduced B-Cell Line

label_protocol: Total RNA (10 µg) from each sample and the reference (Universal Human Reference RNA, Stratagene) were hybridized to oligo (dT) primers at 65º C and then incubated at 42º C for 2 hours in the presence of reverse transcriptase, Cy5- or Cy3-dUTP and Cy5- or Cy3-dCTP, and a deoxynucleotide mix. In all cases, BJAB derived RNA samples were labeled with Cy5 and reference samples were labeled with Cy3. NaOH was used to destroy residual RNA. All protocols are available in greater detail on the Duke Microarray Facility Web site (http://microarray.genome.duke.edu/services/spotted-arrays/protocols).

extract_protocol: total RNA was prepared using TRIzol reagent as instructed and 10µg of RNA was used per reaction. RNA quality was ascertained using an Agilent 2100 bioanalyzer (Agilent technologies).

tag: BJAB cells stably transduced with lentiviral vector pNL-SIN-CMV-AcGFP/miR-K12-11


title: ACK11_8

source_name: Universal Human Reference RNA, Stratagene


title: ACK11_3

tag: Universal Human Reference RNA, Stratagene


title: Animal#880 small intestine infected by Cooperia oncophora for 28 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#877 small intestine uninfected (naive control)

description: see Li & Li, BMC Genomics 2006, 7:234


title: Animal#879 small intestine infected by Cooperia oncophora for 28 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: ACGFP_6

tag: BJAB cells stably transduced with lentiviral vector pNL-SIN-CMV-AcGFP


title: Animal#882 small intestine infected with Cooperia oncophora for 42 days

description: see Li & Li, BMC Genomics 2006, 7:234


title: ACK11_2


title: ACK11_9


title: ACGFP_5


title: ACGFP_4


title: ACGFP_3

source_name: B-Cell Line


title: 13B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

status: Public on Dec 10 2007

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: breast tumor biopsy

hyb_protocol: standard Affymetrix procedures except for use of a custom 24-channel fluidics machine and GCS2500 scanner

label_protocol: Approximately 500 ng of total RNA was processed to produce biotinylated cRNA targets using protocol described in Biotechniques. 2003 Mar;34(3):546-50, 552-4, 556

extract_protocol: Biopsies were snap-frozen after collection and stored in liquid nitrogen.  Frozen sections were taken prior to RNA extraction to confirm the presence of cancerous tissue within the specimens.  Only samples in which the malignant component comprised at least 20% of the section area were used in further analyses.  Immediately before RNA extraction the biopsies were pulverised using U2 micro-dismembranator U (Braun Biotech).  Total RNA was extracted from the resultant frozen tissue powder using TRI-reagent (Sigma) according to the manufacturer's recommendations.  Extracted RNA was additionally purified on RNeasy mini columns (Qiagen).  RNA quantity and quality was verified on Bioanalyser 2100 (Agilent).


title: ACGFP_2


title: ACGFP_1


title: BJAB_2

tag: Unmodified BJAB Cell Line


title: ACK11_1


title: BJAB_3


title: BJAB_1


title: ER negative human primary breast tumor EA02014_41301_H133A_JA-2038

status: Public on May 14 2007

city: Chicago

first: Andy

middle: J

last: Minn

state: IL

address: 924 E. 57th Street

institute: University of Chicago

description: Gene expression data from ER negative human primary breast tumor

hyb_protocol: cRNA were hybridized to the Affymetrix U133a GeneChip according to manufacturer's protocols.

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0).

source_name: Primary human breast tumor

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

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

tag: ID

tag: cohort

value: Erasmus

tag: metastasis

tag: lung met first event

tag: lung met all

tag: metastasis free survival (yr)

tag: lung met free survival (yr)

tag: lms status


title: ER negative human primary breast tumor EA02014_41300_H133A_JA-2025


title: ER negative human primary breast tumor EA02014_41294_H133A_JA-1967


title: ER negative human primary breast tumor EA02014_41291_H133A_JA-1939


title: ER negative human primary breast tumor EA02014_41296_H133A_JA-1978


title: ER negative human primary breast tumor EA02014_41293_H133A_JA-1966


title: ER negative human primary breast tumor EA02014_41297_H133A_JA-2001


title: ER negative human primary breast tumor EA02014_41282_H133A_JA-1555


title: ER negative human primary breast tumor EA02014_41298_H133A_JA-2007


title: ER negative human primary breast tumor EA02014_41290_H133A_JA-1938


title: ER negative human primary breast tumor EA02014_41283_H133A_JA-1589


title: ER negative human primary breast tumor EA02014_41286_H133A_JA-1828


title: VDXKIU_16B4

status: Public on Jun 11 2007

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

hyb_protocol: standard Affymetrix procedures.

scan_protocol: standard Affymetrix procedures.

data_processing: MAS5 Bioconductor (target value of 600).

label_protocol: Approximately 1 microgram of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Isolation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)olation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc).

tag: samplename

tag: id

tag: filename

tag: hospital

value: KAR

tag: age

tag: size

tag: Histtype

tag: Angioinv

tag: node

tag: grade

tag: er

tag: risksg

tag: NPI

tag: risknpi

value: Poor


title: ER negative human primary breast tumor EA02014_41285_H133A_JA-1821

tag: ID

tag: cohort

tag: metastasis

tag: lung met first event

tag: lung met all

tag: metastasis free survival (yr)


title: ER negative human primary breast tumor EA02014_41280_H133A_JA-1661

tag: lung met free survival (yr)

tag: lms status


title: VDXOXFU_1415

tag: samplename

tag: id

tag: filename

tag: hospital

value: JRH

tag: age

tag: size


title: ER negative human primary breast tumor EA02014_41287_H133A_JA-1858


title: ER negative human primary breast tumor EA02014_41279_H133A_JA-1650


title: ER negative human primary breast tumor EA02014_41273_H133A_JA-1535


title: ER negative human primary breast tumor EA02014_41278_H133A_JA-1622


title: ER negative human primary breast tumor EA02014_41271_H133A_JA-1524


title: ER negative human primary breast tumor EA02014_41262_H133A_JA-1222


title: ER negative human primary breast tumor EA02014_41276_H133A_JA-1571


title: ER negative human primary breast tumor EA02014_41277_H133A_JA-1593


title: ER negative human primary breast tumor EA02014_41269_H133A_JA-1497


title: ER negative human primary breast tumor EA02014_41265_H133A_JA-1069


title: MM415

status: Public on Sep 12 2007

type: genomic

city: Brisbane

first: Mitchell

last: Stark

address: 300 Herston Rd Herston

country: Australia

institute: QIMR

description: The 76 melanoma cell lines used in this study were derived from primary cutaneous melanomas or melanoma metastases.

hyb_protocol: The dried precipitated pellet was then resuspended in WG-RA1 and hybridized to a beadchip along with WG-RA1 and formamide. The arrays were then incubated overnight at 48°C, after which they underwent single-base extension on a Teflow chamber rack system (Tecan, Männedorf, Switzerland) using WG-XC1, WG-XC2, and WG-TEM.

scan_protocol: After the single-base extension step, the beadchips were stained with WG-LTM and WG-ATM, dried for 1 h, then imaged using a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Beadstudio 2.0 (Illumina). All genomic positions were based upon hg17 from the UCSC Genome Browser.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Melanoma Cell Line

label_protocol: The Infinium II assay was done using Illumina Sentrix HumanHap300 genotyping BeadChip arrays (317K, TagSNP Phase I, v1.1) according to the manufacturer's specifications (Illumina, San Diego, CA). Briefly, 750 ng of genomic DNA were amplified at 37°C overnight, using solutions WG-AMM and WG-MP1. After overnight incubation, the amplified DNA was fragmented using WG-FRG and precipitated with isopropanol after the addition of WG-PA1.

extract_protocol: As per manufacturers protocol using QIAGEN QIamp DNA Blood Maxi Kit

tag: Cell line was derived from a secondary melanoma tumor with the primary being in a non-CSD body site.


title: ER negative human primary breast tumor EA02014_41266_H133A_JA-1412


title: MM603

tag: Cell line was derived from a secondary melanoma tumor with the primary being occult.


title: MM96L

tag: Cell line was derived from a primary melanoma tumor located in a non-CSD body site.


title: ER negative human primary breast tumor EA02014_41268_H133A_JA-1482

tag: ID


title: JA

tag: UNKNOWN


title: ER negative human primary breast tumor EA02014_41251_H133A_JA-632

tag: cohort

tag: metastasis


title: MM253


title: ER negative human primary breast tumor EA02014_41250_H133A_JA-245

tag: lung met first event

tag: lung met all


title: MM466


title: ER negative human primary breast tumor EA02014_41252_H133A_JA-746

tag: metastasis free survival (yr)

tag: lung met free survival (yr)


title: ER negative human primary breast tumor EA02014_41243_H133A_JA-076

tag: lms status


title: D41

tag: Cell line was derived from a secondary melanoma tumor with the primary tumor being in a non-CSD body site.


title: ER negative human primary breast tumor EA02014_41249_H133A_JA-243


title: ER negative human primary breast tumor EA02014_41257_H133A_JA-248


title: ER negative human primary breast tumor EA02014_41245_H133A_JA-123


title: MM386

source_name: Melanoma Cell LIne


title: MM329

tag: Cell line was derived from a primary melanoma tumor found in a non-CSD body site.


title: A06

tag: Cell line derived form secondary melanoma tumor with the primary tumor being in a non-CSD body site


title: ER negative human primary breast tumor EA02014_41260_H133A_JA-941


title: ER negative human primary breast tumor EA02014_41254_H133A_JA-812


title: D24

tag: Cell line was derived from a secondary melanoma with the primary being occult.


title: 210T

status: Public on Mar 10 2007

city: Berlin

first: Andreas

last: Klein

address: Charitéplatz 1

department: Institute of Biochemistry

country: Germany

institute: Charité (CCO)

description: Age at diagnosis: 85, Histology: IDC, Tumor stage: 4, Tumor grade: 3

hyb_protocol: Following fragmentation, the cRNA was hybridized for 16 hr at 45C on GeneChip® Human Genome U133A Array. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.

scan_protocol: Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 2500.

data_processing: The raw experimental microarray data were normalized with the Affymetrix GeneChip analysis software (Microarray Suite Version 5.0). Further analyses were performed with the software “CorrXpression”.

label: Biotin

source_name: Mammary gland from patient with human breast cancer

label_protocol: cRNA was amplified from 1-2 µg of total RNA using the small sample labeling version II protocol (Affymetrix, Santa Clara, CA).

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions (Life Technologies).

tag: Human breast cancer


title: 218T

description: Age at diagnosis: 29, Histology: IDC, Tumor stage: 2, Tumor grade: 2


title: CJM

extract_protocol: As per manufacturers protocol using QIAGEN QIamp Blood DNA Maxi kit.

tag: Cell line derived from secondary melanoma tumor with the primary tumor being occult.


title: 725T

description: Age at diagnosis: 41, Histology: IDC, Tumor stage: 2, Tumor grade: 3


title: 496T

description: Age at diagnosis: 65, Histology: IDC, Tumor stage: 2, Tumor grade: 3


title: 430T

description: Age at diagnosis: 65, Histology: IDC, Tumor stage: 4, Tumor grade: 3


title: 735T

description: Age at diagnosis: 51, Histology: IDC, Tumor stage: 1, Tumor grade: 3


title: X309C49 (HG-U133A)

status: Public on Oct 21 2005

first: Lance

middle: David

last: Miller

address: 60 Bioplois Street, #02-01 Genome

department: Microarray and Expression Genomics

institute: Genome Institute of Singapore

description: Series of 251 tumours

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite Version 5.0

source_name: Breast Tumor

label_protocol: Approximately 10ug of total RNA was processed to produce biotynylated cRNA targets

extract_protocol: Qiagen RNeasy Mini Kit

tag: Breast Tumor tissue


title: 02T

description: Age at diagnosis: 56, Histology: IDC, Tumor stage: 1, Tumor grade: 2


title: X47A87 (HG-U133A)

description: Series of 251 tumours


title: X86A40 (HG-U133A)

description: Series of 251 tumours


title: X54A09 (HG-U133A)

description: Series of 251 tumours


title: X62A02 (HG-U133A)

description: Series of 251 tumours


title: X303C36 (HG-U133A)

description: Series of 251 tumours


title: X279C61 (HG-U133A)

description: Series of 251 tumours


title: X269C68 (HG-U133A)

description: Series of 251 tumours


title: X291C17 (HG-U133A)

description: Series of 251 tumours


title: X252C64 (HG-U133A)

description: Series of 251 tumours


title: X314B55 (HG-U133A)

description: Series of 251 tumours


title: X250C78 (HG-U133A)

description: Series of 251 tumours


title: X287C67 (HG-U133A)

description: Series of 251 tumours


title: X268C87 (HG-U133A)

description: Series of 251 tumours


title: X70A79 (HG-U133A)

description: Series of 251 tumours


title: X249C42 (HG-U133A)

description: Series of 251 tumours


title: X230C47 (HG-U133A)

description: Series of 251 tumours


title: X194B60 (HG-U133A)

description: Series of 251 tumours


title: X193B72 (HG-U133A)

description: Series of 251 tumours


title: X164B81 (HG-U133A)

description: Series of 251 tumours


title: X189B83 (HG-U133A)

description: Series of 251 tumours


title: X144B49 (HG-U133A)

description: Series of 251 tumours


title: X101B88 (HG-U133A)

description: Series of 251 tumours


title: X103B41 (HG-U133A)

description: Series of 251 tumours


title: X224C93 (HG-U133A)

description: Series of 251 tumours


title: X110B34 (HG-U133A)

description: Series of 251 tumours


title: X146B39 (HG-U133A)

description: Series of 251 tumours


title: PF22 EnPnT2N1G2

status: Public on Jun 01 2005

city: Bordeaux

first: Richard

last: Iggo

address: 229 cours de l'Argonne

department: Bergonie Cancer Institute

country: France

institute: University of Bordeaux

description: EORTC 10994

source_name: Biopsy