title: Patient-31.post

status: Public on Oct 31 2015

type: RNA

city: Durham

first: Wei

last: Chen

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

country: USA

institute: Duke University

description: Patients with biologically favorable early stage breast cancer participating in an IRB approved phase I dose-escalation preoperative radiotherapy protocol.

hyb_protocol: Hybridization of samples to Affymetrix GeneChip arrays was performed according to Affymetrix manual instructions .

scan_protocol: Scanning of Affymetrix GeneChip arrays was performed according to the Affmetrix manual instructions.

data_processing: Gene level expression estimates were obtained with Affymetrix Expression Console software (v.1.3) using RMA-Sketch workflow.  Differential expression for paired samples was evaluated using the Bioconductor limma package with correction for multiple comparisons.  Genes with FDR adjusted p-values (q-values) less than 0.05 were selected as differentially expressed in response to radiation. This set of genes was then tested for radiation dose effect using linear regression of the log2 fold change over dosage received. Those genes with regression p-values less than 0.0005 and q-values less than 0.25 were selected as having dose effect.  Gene set analysis (GSA) was performed with the R package GSA using “two class paired” problem type and 100,000 permutations to estimate false discovery rates. The gene set collection used is “all GO (gene ontology) gene sets” which contains 1454 gene sets in total.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer

extract_protocol: FFPE RNA extraction and labeling was performed using the RNeasy FFPE kit from Qiagen, and the SensationPlus™ FFPE Amplification and Labeling Kit (Affymetrix, Inc. catalog # 902312). All total RNA samples were assessed for quality using a NanoDrop ND8000 Spectrophotometer for absorbance ratios, and the Agilent Bioanalyzer 2100 for RIN scores.  Whole transcriptome expression analysis was evaluated with HTA 2.0 arrays (Affymetrix, Inc. catalog # 902162).

treatment_protocol: Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.

tag: tissue

value: breast cancer

tag: dose

tag: pre or post treatment

value: post


title: Patient-21.post

label_protocol: SensationPlus™ FFPE Amplification and Labeling Kit (Affymetrix, Inc. catalog # 902312).


title: Patient-29.post


title: Patient-06.pre

value: pre


title: Patient-20.post


title: Patient-13.pre


title: Patient-26.post


title: Patient-31.post-BR


title: Patient-27.post


title: Patient-28.post


title: Patient-20.post-BR


title: Patient-23.post


title: Patient-11.post

value: 18 Gy


title: Patient-16.post


title: Patient-29.post-BR


title: Patient-10.post


title: Patient-09.post


title: Patient-09.post-BR


title: Patient-08.post

value: 15 Gy


title: Patient-07.post


title: Patient-18.post


title: Patient-05.post


title: Patient-17.post


title: Patient-04.post


title: Patient-21.pre


title: Patient-31.pre-BR


title: Patient-18.pre


title: Patient-16.pre


title: Patient-29.pre


title: Patient-27.pre


title: Patient-01.post


title: Patient-31.pre


title: Patient-07.pre


title: Patient-08.pre


title: Patient-05.pre


title: Patient-04.pre


title: Patient-32.post-BR


title: Patient-28.pre


title: Patient-23.pre


title: Patient-10.pre


title: Patient-32.post


title: Patient-11.pre


title: Patient-17.pre


title: Patient-20.pre


title: Patient-09.pre


title: Patient-01.pre


title: Patient-26.pre


title: Patient-22.post


title: Patient-30.post


title: Patient-15.post


title: Patient-15.post-BR


title: Patient-13.post


title: Patient-14.pre


title: Patient-32.pre-BR


title: Patient-30.pre


title: Patient-15.pre-BR


title: Patient-19.pre


title: Patient-22.pre


title: Patient-06.post


title: Patient-14.post


title: CCSS_26158238

type: genomic

city: Bethesda

first: Rose

last: Yang

address: 9100 Rockville pike

institute: NIH

description: CGH

hyb_protocol: Test and reference DNA were co-hybridized to Agilent CGH arrays containing 244,000 probes tiled across the genome.

scan_protocol: Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction software and R package snapCGH et al

molecule: genomic DNA

source_name: Breast cancer

label_protocol: Sufficient DNA (1 μg) was obtained from 30 cases. Test and reference DNA (from Promega) were labeled with Cy5 and Cy3 respectively

extract_protocol: Ten 5-μm unstained tumor sections were used for DNA extraction with the enrichment for tumor cells by micro-dissection

tag: age

value: FFPE

tag: histology

value: Leukemia

source_name: Promega Male

tag: sample type

value: reference


title: Patient-32.pre


title: CCSS_26020735

description: CGH

value: Kidney(Wilms)


title: CCSS_18080328

description: CGH

value: Bone cancer


title: CCSS_18080285

description: CGH

value: NHL


title: CCSS_26064443

description: CGH

value: HD


title: CCSS_26016891

description: CGH


title: CCSS_04068923

description: CGH


title: CCSS_18208137

description: CGH


title: Patient-15.pre


title: CCSS_05097073

description: CGH


title: CCSS_23144861

description: CGH


title: CCSS_18080293

description: CGH


title: CCSS_15179993

description: CGH


title: CCSS_04195643

description: CGH


title: CCSS_08224721

description: CGH


title: CCSS_04068393

description: CGH


title: CCSS_04068293

description: CGH


title: CCSS_12160053

description: CGH


title: CCSS_09203583

description: CGH


title: CCSS_08226102

description: CGH

value: Soft tissue sarcoma


title: CCSS_08217873

description: CGH


title: CCSS_06235633

description: CGH


title: CCSS_04068271

description: CGH


title: p53+/-Fbxw7+/- rapamycin [US84903607_252800514825_S01_GE1_1100_Jul11_1_3]

city: Berkeley

first: Antoine

middle: M

last: Snijders

state: CA

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

hyb_protocol: Hybridizations performed commercially by Ambry Genetics

organism: Mus musculus

source_name: mouse thymic lymphoma after 4Gy X-ray treated with rapamycin

extract_protocol: Total RNA was isolated by homogenizing the frozen tissue in Trizol reagent (Invitrogen) followed by phase separation using chloroform. RNA was further purified utilizing the RNeasy mini kit (Qiagen; 74104) and DNA was removed using RNase-free DNase (Qiagen; 79254).

treatment_protocol: At 5 weeks of age, mice were exposed whole-body to a single dose of 4 Gy X-ray irradiation.  Mice were divided randomly into two groups and treated with rapamycin or placebo.

tag: genotype/variation

tag: strain

tag: age x-ray exposure

tag: x-ray exposure

value: 4Gy X-ray

tag: age rapamycin exposure

tag: protocol

value: rapamycin exposure:4mg/kg/day 10 weeks by subcutaneous slow-release pellet

tag: time after exposure

value: thymic lymphoma


title: p53+/-Fbxw7+/- placebo [US84903607_252800514825_S01_GE1_1100_Jul11_2_2]

scan_protocol: Hybridizations performed commercially by Ambry Genetics

source_name: mouse thymic lymphoma after 4Gy X-ray treated with placebo

value: placebo pellet 0mg/kg/day 10 weeks by subcutaneous slow-release pellet


title: CCSS_04067183

description: CGH


title: p53+/-Fbxw7+/- rapamycin [US84903607_252800514825_S01_GE1_1100_Jul11_1_4]

data_processing: Hybridizations performed commercially by Ambry Genetics


title: CCSS_03014663

description: CGH


title: p53+/-Fbxw7+/- placebo [US84903607_252800514825_S01_GE1_1100_Jul11_2_3]

label_protocol: Hybridizations performed commercially by Ambry Genetics


title: p53+/-Fbxw7+/- placebo [US84903607_252800514825_S01_GE1_1100_Jul11_2_4]


title: p53+/-Fbxw7+/+ rapamycin [US84903607_252800514821_S01_GE1_1100_Jul11_2_1]


title: CCSS_04067693

description: CGH


title: p53+/-Fbxw7+/+ rapamycin [US84903607_252800514821_S01_GE1_1100_Jul11_2_3]


title: CCSS_04067723

description: CGH


title: p53+/-Fbxw7+/+ placebo [US84903607_252800514825_S01_GE1_1100_Jul11_1_1]


title: CCSS_06234214

description: CGH


title: CCSS_1003243

description: CGH


title: p53+/-Fbxw7+/- rapamycin [US84903607_252800514825_S01_GE1_1100_Jul11_2_1]


title: p53+/-Fbxw7+/+ placebo [US84903607_252800514821_S01_GE1_1100_Jul11_2_4]


title: p53+/-Fbxw7+/+ placebo [US84903607_252800514821_S01_GE1_1100_Jul11_2_2]


title: p53+/-Fbxw7+/- placebo [US84903607_252800514825_S01_GE1_1100_Jul11_1_2]


title: CCSS_03014738

description: CGH


title: CCSS_04066233

description: CGH


title: p53+/-Fbxw7+/- rapamycin [US84903607_252800514821_S01_GE1_1100_Jul11_1_4]


title: p53+/-Fbxw7+/+ placebo [US84903607_252800514821_S01_GE1_1100_Jul11_1_3]


title: CCSS_1001723

description: CGH


title: p53+/-Fbxw7+/+ rapamycin [US84903607_252800514821_S01_GE1_1100_Jul11_1_2]


title: p53+/-Fbxw7+/+ rapamycin [US84903607_252800514820_S01_GE1_1100_Jul11_2_4]


title: p53+/-Fbxw7+/+ rapamycin [US84903607_252800514821_S01_GE1_1100_Jul11_1_1]


title: p53+/-Fbxw7+/+ placebo [US84903607_252800514820_S01_GE1_1100_Jul11_2_3]


title: p53+/-Fbxw7+/- placebo [US84903607_252800514820_S01_GE1_1100_Jul11_2_1]


title: p53+/-Fbxw7+/- placebo [US84903607_252800514820_S01_GE1_1100_Jul11_1_2]


title: p53+/-Fbxw7+/+ placebo [US84903607_252800514820_S01_GE1_1100_Jul11_1_3]


title: p53+/-Fbxw7+/- placebo [US84903607_252800514820_S01_GE1_1100_Jul11_1_1]


title: p53+/-Fbxw7+/- rapamycin [US84903607_252800514820_S01_GE1_1100_Jul11_1_4]


title: p53+/-Fbxw7+/- placebo [US84903607_252800514820_S01_GE1_1100_Jul11_2_2]


title: p53+/-Fbxw7+/+ rapamycin [US84903607_252800514819_S01_GE1_1100_Jul11_1_3]


title: p53+/-Fbxw7+/- rapamycin [US84903607_252800514819_S01_GE1_1100_Jul11_2_1]


title: p53+/-Fbxw7+/+ rapamycin [US84903607_252800514819_S01_GE1_1100_Jul11_2_4]


title: p53+/-Fbxw7+/- rapamycin [US84903607_252800514819_S01_GE1_1100_Jul11_2_2]


title: p53+/-Fbxw7+/- rapamycin [US84903607_252800514819_S01_GE1_1100_Jul11_1_4]


title: p53+/-Fbxw7+/- placebo [US84903607_252800514819_S01_GE1_1100_Jul11_2_3]


title: p53+/-Fbxw7+/+ placebo [US84903607_252800514819_S01_GE1_1100_Jul11_1_1]


title: p53+/-Fbxw7+/+ placebo [US84903607_252800514810_S01_GE1_1100_Jul11_2_3]


title: p53+/-Fbxw7+/- rapamycin [US84903607_252800514810_S01_GE1_1100_Jul11_1_3]


title: p53+/-Fbxw7+/- placebo [US84903607_252800514819_S01_GE1_1100_Jul11_1_2]


title: p53+/-Fbxw7+/- placebo [US84903607_252800514810_S01_GE1_1100_Jul11_2_1]


title: p53+/-Fbxw7+/- placebo [US84903607_252800514810_S01_GE1_1100_Jul11_2_4]


title: p53+/-Fbxw7+/- rapamycin [US84903607_252800514810_S01_GE1_1100_Jul11_1_2]


title: p53+/-Fbxw7+/- placebo [US84903607_252800514810_S01_GE1_1100_Jul11_2_2]


title: p53+/-Fbxw7+/+ rapamycin [US84903607_252800514810_S01_GE1_1100_Jul11_1_1]


title: p53+/-Fbxw7+/- rapamycin [US84903607_252800514810_S01_GE1_1100_Jul11_1_4]


title: number 159 pig heart

city: beijing

first: Jihan

last: Xia

state: beijing

address: No. 2 Yuanmingyuan West Road, Beijing,

country: China

institute: Chinese academy of agrigultural sciences

description:
Gene expression data from control group
Bama minipig_159

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Slides were scanned by GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA, US) and   Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Sus scrofa

source_name: pig heart in control group

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

growth_protocol: The control group consisted of 6 Bama pigs fed a control diet, and the HFHSD group comprised 6 pigs that were induced with a HFHS diet, which included 37% sucrose, 53% control diet and 10% pork lard for 23 months.

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

treatment_protocol: The pigs were fasted for 12 hours and euthanized with ketamine and xylazine. Pig hearts were sampled and preserved in liquid nitrogen.

value: heart

tag: phenotype

value: normal

tag: diet

value: normal diet


title: number 157 pig heart

description:
Gene expression data from control group
Bama minipig_157


title: number 161 pig heart

description:
Gene expression data from control group
Bama minipig_161


title: number 146 pig heart

description:
Gene expression data from HFHSD group
Bama minipig_146

source_name: pig heart in HFHSD group

value: cardiac hypertrophy and fatty heart

value: HFHS diet for 23 months


title: number 144 pig heart

description:
Gene expression data from HFHSD group
Bama minipig_144


title: number 140 pig heart

description:
Gene expression data from HFHSD group
Bama minipig_140


title: MDA-MB-231_mimic-5'isomiR-140-3p_rep2

city: Heidelberg

first: Cindy

last: Körner

address: INF 580

department: Molecular Genome Analysis

country: Germany

institute: DKFZ

hyb_protocol: Standard Illumina Hybridisation Protocol  Part # 11322355 (Whole-Genome Gene Expression  Direct Hybridization Assay Guide) 750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina Human HT-12-Microarray.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol

data_processing: The data were normalised using quantile normalisation with using the Bioconductor preprocessCore package in R

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologie) is used to generate single-stranded cRNA from input amounts of 500ng total RNA

growth_protocol: MCF10A cells were cultured in DMEM-F12 medium and MDA-MB-231 cells were cultured in RPMI medium as described in the paper associated with this microarray.

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

treatment_protocol: Cells were seeded in 6 well plates and transfected using Lipofectamin2000 and a final mimic concentration of 30nM. RNA was harvested 48h after transfection and microarray analysis was performed.

tag: cell line


title: number 138 pig heart

description:
Gene expression data from HFHSD group
Bama minipig_138


title: MDA-MB-231_mimic-hsa-140-3p_rep1


title: number 126 pig heart

description:
Gene expression data from HFHSD group
Bama minipig_126


title: number 120 pig heart

description:
Gene expression data from HFHSD group
Bama minipig_120


title: MDA-MB-231_mimic-hsa-140-3p_rep2


title: MDA-MB-231_mimic-5'isomiR-140-3p_rep1


title: MDA-MB-231_mimic-ctrl2_rep1


title: MDA-MB-231_mimic-ctrl1_rep1


title: treatment ITS+ #1

city: ithaca

first: Ming

last: yang

address: 316 tower road

institute: Cornell

description: gene expression data from bovine ovarian cortical pieces

hyb_protocol: Complementary RNA was hybridized on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Bovine GeneChips were scanned using Genearray 3000 scanner (Affymetrix)

data_processing: Affymetrix Genechip Operating Software (GCOS) was used to analyze array data of pairs of control vs. insulin-treated samples

organism: Bos taurus

source_name: cortical pieces cultured with ITS+

label_protocol: Biotin-labled complementary RNA was produced uisng Genechip IVT labeling kit according to the manufacturer's instructions.

extract_protocol:
materials: Bovine fetal ovaries were collected from a slaughterhouse
First, trizol extraction of total RNA was performed. Then, purification was performed using Rneasy kit

treatment_protocol: Bovine ovarian cortical pieces were cultured with control medium or insulin for 2 days

value: fetal ovarian cortical pieces

tag: cultured medium

value: with insulin (ITS+)


title: MCF10A_mimic-5'isomiR-140-3p_rep1


title: control TS+ #2

source_name: cortical pieces cultured with TS+

tag: tissue

value: TS+ (transferrin, selenous acid, BSA, and linoleic acid)


title: MCF10A_mimic-ctrl2_rep1


title: control TS+ #3


title: treatment ITS+ #3


title: MCF10A_mimic-5'isomiR-140-3p_rep2


title: MCF10A_mimic-hsa-140-3p_rep1


title: treatment ITS+ #2


title: MCF10A_mimic-hsa-140-3p_rep2


title: control TS+ #1


title: BMDM_Nrf2+/+_Keap1-2_Replicate4

city: Frankfurt am Main

first: Daniel

last: Margerie

address: Industrial Park Hoechst, Building H831

department: R&D, Digital Data Sciences

institute: Sanofi-Aventis Deutschland GmbH

description: Gene expression data from mouse bone marrow derived macrophages

hyb_protocol: 15 µg cRNA samples were fragmented at 94 degree Celsius for 35 min in 40 mM Tris/acetate pH 8.1, 100 mM KOAc and 30 mM MgOAc, added to hybridisation buffer and hybridised to Affymetrix GeneChip for 16-18 hours at 45 degree Celsius and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix).

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

data_processing: The data were analyzed with Array Studio (Omicsoft Corp., Cary, NC, USA) using default settings and RMA as normalization method.

label: Biotin

source_name: Bone Marrow Derived Murine Macrophages (BMDM), Nrf2 +/+, Keap1-2 treated

label_protocol: Biotin-UPT and -CTP labelled cRNA was transcribed in vitro using Enzo BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, NY, NY) and purified by RNeasy cleanup and ethanol precipitation.

growth_protocol: Bone Marrow Derived Murine Macrophages (BMDM) were generated from total bone marrow of 12 week old Nrf2+/+ and Nrf2-/- mice .

extract_protocol: Total RNA was prepared using the Rneasy Mini Kit

treatment_protocol: Compounds were prepared as DMSO stock solutions and further diluted in growth medium (RPMI medium (GIBCO) containing 10% heat-inactivated FBS (PAA). BMDM were incubated with the indicated concentrations of the compounds at a fixed DMSO concentration of 0.2 (v/v) %. For the gene-array studies the incubation time was 4 h, before RNA was isolated. In the case of the nitric oxide (NO) release assay BMDM were preincubated for 1 h in the presence of the compounds before lipopolysaccharides (LPS) from E. coli (055:B5, Sigma) were added to a final concentration of 1 µg/ml. After 48 h, NO release and RNA was isolated for gene expression studies. Cell viability was determined by the determination of lactate dehydrogenase release using the Cytotox-ONE assay (Promega).

tag: genotype

value: bone marrow

tag: cell type

value: macrophages

value: C57BL/6 J

tag: treatment


title: CCSS_04066883

description: CGH

tag: age

value: FFPE

tag: histology

value: HD

value: reference


title: BMDM_Nrf2+/+_Keap1-1_Replicate4

source_name: Bone Marrow Derived Murine Macrophages (BMDM), Nrf2 +/+, Keap1-1 treated


title: BMDM_Nrf2+/+_Keap1-2_Replicate2


title: Normal lung fibroblast 3

city: Seoul

first: Hyun Sub

last: Cheong

address: #1007, Teihard Hall, Sogang Univ. Baekbum-ro 35, Mapo-gu

department: Genetic Epidemiology

country: South Korea

institute: SNP Genetics, Inc.

description: fibroblast 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Normal lung fibroblast 3

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

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

value: Lung fibroblst


title: Normal lung fibroblast 4

description: fibroblast 4

source_name: Normal lung fibroblast 4


title: Normal lung fibroblast 2

description: fibroblast 2

source_name: Normal lung fibroblast 2


title: BMDM_Nrf2+/+_Keap1-2_Replicate3


title: BMDM_Nrf2+/+_Keap1-1_Replicate1


title: BMDM_Nrf2+/+_Keap1-2_Replicate1


title: Normal lung fibroblast 1

description: fibroblast 1

source_name: Normal lung fibroblast 1


title: IPF Rapidly lung fibroblst 1-3

description: fibroblst 1-3

source_name: IPF Rapidly lung fibroblst 1-3


title: IPF Slowly lung fibroblast 2-4

description: fibroblast 2-4

source_name: IPF Slowly lung fibroblast 2-4


title: BMDM_Nrf2+/+_siControl_Replicate3

source_name: Bone Marrow Derived Murine Macrophages (BMDM), Nrf2 +/+, siControl

value: siControl


title: BMDM_Nrf2+/+_siControl_Replicate2


title: IPF Slowly lung fibroblast 2-3

description: fibroblast 2-3

source_name: IPF Slowly lung fibroblast 2-3


title: IPF Rapidly lung fibroblst 1-2

description: fibroblst 1-2

source_name: IPF Rapidly lung fibroblst 1-2


title: BMDM_Nrf2-/-_RA839_Replicate4

source_name: Bone Marrow Derived Murine Macrophages (BMDM), Nrf2 -/-, RA839 treated


title: BMDM_Nrf2+/+_siControl_Replicate4


title: BMDM_Nrf2+/+_siControl_Replicate1


title: IPF Slowly lung fibroblast 2-2

description: fibroblast 2-2

source_name: IPF Slowly lung fibroblast 2-2


title: IPF Slowly lung fibroblast 2-1

description: fibroblast 2-1

source_name: IPF Slowly lung fibroblast 2-1


title: IPF Rapidly lung fibroblst 1-1

description: fibroblst 1-1

source_name: IPF Rapidly lung fibroblst 1-1


title: BMDM_Nrf2-/-_RA839_Replicate3


title: MCF10A_mimic-ctrl1_rep1


title: IPF Rapidly lung fibroblst 1-4

description: fibroblst 1-4

source_name: IPF Rapidly lung fibroblst 1-4


title: BMDM_Nrf2+/+_Keap1-1_Replicate2


title: BMDM_Nrf2-/-_RA839_Replicate2


title: HUT78_JAKi_30min_rep3

city: Santander

first: Nerea

last: Martinez

address: Avda Cardenal Herrera Oria

country: Spain

institute: IDIVAL

description: Sample 8

hyb_protocol: Microarray: Human Gene Expression G3 60K (Agilent microarray design ID 028004, P/N G4851A). Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (ºC): 65. Duration: 17 hours

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed

data_processing: Background correction: normexp; Within arrays normalization: loess;  Between arrays normalization: quantiles

source_name: HUT78 treated with JAKi 30min

label_protocol: Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010. Amplification: by RNA polymerases.Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores.

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin (Invitrogen Corporation, USA) in a humidified atmosphere at 37°C with 5% CO2

extract_protocol: Total RNA was isolated by Trizol reagent (Invitrogen). RNA quality was checked using total RNA (small fraction chip) with the Agilent 2100 Bioanalyzer (Agilent Technologies) and by 1% agarose electrophoresis, following standard procedures

treatment_protocol: Cells were incubated with INCB018424 (using an IC50 concentration) at two times (30 minutes and 3 hours)

value: JAKi

tag: time

source_name: Universal Human Reference RNA Stratagene

value: untreated


title: BMDM_Nrf2-/-_DMSO_Replicate2

source_name: Bone Marrow Derived Murine Macrophages (BMDM), Nrf2 -/-, untreated DMSO control

tag: strain

value: DMSO


title: HUT78_JAKi_3h_rep2

description: Sample 6

source_name: HUT78 treated with JAKi 3h


title: HUT78_JAKi_3h_rep3

description: Sample 9


title: BMDM_Nrf2-/-_DMSO_Replicate3


title: ES cell-derived granule cells at Day 18 (3)

city: New York

first: Michelle E.

last: Ehrlich

state: NY

address: 1 Gustave L. Levy Pl, New York, NY 10029

department: Department of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

description: Microarray gene expression data

hyb_protocol: Samples were hybridized with Mouse Gene 1.0 ST Arrays (Affymetrix) and scanned at the The Rockefeller University Genomics Resource Center.

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

data_processing: The Affymetrix microarray profiles were processed using the ExpressionFileCreator tool in GenePattern to map gene probes into gene symbols (www.genepattern.org). The resulting expression dataset A, was decomposed using Non-Negative Matrix Factorization into two matrices: A ~ W x H, using the methodology from Brunet et al. 2004 and Tamayo et al. 2007, including a procedure to determine the number of metagenes. The columns of the first matrix represent the degree to which each metagene depends on the profile of each gene. The second matrix shows how the profile can be described in terms of the metagenes defined by the first matrix. The metagenes were visualized using heat maps and multidimensional scaling biplot projections.

molecule: polyA RNA

source_name: differentiated mouse ES cells

label_protocol: Purified RNA was converted to double-stranded cDNA using the SuperScript GeneChip Expression 3’-Amplification Reagents Two-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) and the GeneChip T7-Oligo Primer (Affymetrix, Santa Clara, CA). The cDNA was used for the in vitro synthesis of cRNA using the MEGAscriptT7 Kit (Ambion, Austin, TX). cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA). 600 ng or less of clean cRNA was used in the second-cycle cDNA synthesis reaction using the SuperScript GeneChip Expression 3’-Amplification Reagents Two-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) and random primers (Affymetrix, Santa Clara, CA). The cDNA was purified using the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA). Purified cDNA was used for the in vitro synthesis of biotin-labeled cRNA using the GeneChip IVT Labeling Kit (Affymetrix, Santa Clara, CA). cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) and fragmented into 35-200 base pair fragments using a magnesium acetate buffer (Affymetrix, Santa Clara, CA).

growth_protocol: Whole cerebella and differentiated ES cells were collected and mRNA was purified using translating ribosome affinity purification (TRAP) method.

value: differentiated ES cells


title: HUT78_control_rep3

description: Sample 7

source_name: HUT78 untreated

value: control


title: BMDM_Nrf2+/+_RA839_Replicate3

source_name: Bone Marrow Derived Murine Macrophages (BMDM), Nrf2 +/+, RA839 treated


title: BMDM_Nrf2-/-_RA839_Replicate1


title: BMDM_Nrf2+/+_RA839_Replicate1


title: ES cell-derived granule cells at Day 18 (1)

description: Microarray gene expression data

extract_protocol: Whole cerebella and differentiated ES cells were collected and mRNA was purified using translating ribosome affinity purification (TRAP) method.


title: HUT78_JAKi_30min_rep2

description: Sample 5


title: SKOV3shRNARELB1

city: México

first: Vilma

middle: Araceli

last: Maldonado

state: Distrito Federal

address: Periferico  4809

department: Investigacion

country: Mexico

institute: INMEGEN

description: Gene expresión data of SKOV3shRNARELB1

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Raw CEL data were normalized using the Robust Multi-array Average (RMA) method, as implemented in the oligo package . The Limma R package was used for differential expression analysis . We identified genes with a >2-fold change and a crude p<0.05.

label: non

label_protocol: Affymetrix protocol

growth_protocol: The SKOV3 cells were transiently transfected with Lipofectamine LTX (LT Invitrogen) with siRNA-RELB: . An siRNA directed against luciferase (siRNA-Luc) was employed as a control. The cells were analyzed for RelB expression 24 hours after transfection

extract_protocol: Extraction RNA with Trizol

treatment_protocol: Only the transfection

tag: transfection

value: RELB inhibited


title: SKOV3shRNALuc2

description: Gene expresión data of SKOV3shLuc2

value: Vector


title: SKOV3shRNALuc3

description: Gene expresión data of SKOV3shLuc3


title: BMDM_Nrf2-/-_DMSO_Replicate1


title: BMDM_Nrf2+/+_RA839_Replicate4


title: BMDM_Nrf2+/+_RA839_Replicate2


title: SKOV3shRNARELB3

description: Gene expresión data of SKOV3shRNARELB3


title: SKOV3shRNALuc1

description: Gene expresión data of SKOV3shLuc1


title: SKOV3shRNARELB2

description: Gene expresión data of SKOV3shRNARELB2


title: BMDM_Nrf2+/+_DMSO_Replicate2

source_name: Bone Marrow Derived Murine Macrophages (BMDM), Nrf2 +/+, untreated DMSO control


title: BMDM_Nrf2-/-_DMSO_Replicate4


title: HUT78_control_rep2

description: Sample 4


title: BMDM_Nrf2+/+_DMSO_Replicate3


title: ES cell-derived granule cells at Day 15 treated with vitamin C (2)

description: Microarray gene expression data


title: ES cell-derived granule cells at Day 15 treated with vitamin C (3)

description: Microarray gene expression data


title: ES cell-derived granule cells at Day 15 (3)

description: Microarray gene expression data


title: BMDM_Nrf2+/+_DMSO_Replicate4


title: ES cell-derived granule cells at Day 11 (2)

description: Microarray gene expression data


title: ES cell-derived granule cells at Day 11 (1)

description: Microarray gene expression data


title: non-differentiated mouse ES cells (2)

description: Microarray gene expression data

source_name: non-differentiated mouse ES cells

value: non-differentiated ES cells


title: P56 cerebellar granule cells (3)

description: Microarray gene expression data

source_name: mouse cerebella

value: cerebellum


title: P56 cerebellar granule cells (1)

description: Microarray gene expression data


title: P21 cerebellar granule cells (1)

description: Microarray gene expression data


title: P21 cerebellar granule cells (2)

description: Microarray gene expression data


title: BMDM_Nrf2+/+_DMSO_Replicate1

value: bone marrow


title: P56 cerebellar granule cells (2)

description: Microarray gene expression data


title: P18 cerebellar granule cells (3)

description: Microarray gene expression data


title: P18 cerebellar granule cells (2)

description: Microarray gene expression data


title: ES cell-derived granule cells at Day 15 treated with vitamin C (1)

description: Microarray gene expression data


title: ES cell-derived granule cells at Day 15 (2)

description: Microarray gene expression data


title: P12 cerebellar granule cells (1)

description: Microarray gene expression data


title: P7 cerebellar granule cells (1)

description: Microarray gene expression data


title: P12 cerebellar granule cells (2)

description: Microarray gene expression data


title: ES cell-derived granule cells at Day 11 (3)

description: Microarray gene expression data


title: ES cell-derived granule cells at Day 15 (1)

description: Microarray gene expression data


title: non-differentiated mouse ES cells (3)

description: Microarray gene expression data


title: non-differentiated mouse ES cells (1)

description: Microarray gene expression data


title: ES cell-derived granule cells at Day 18 (2)

description: Microarray gene expression data


title: P0 cerebellar granule cells (2)

description: Microarray gene expression data


title: P21 cerebellar granule cells (3)

description: Microarray gene expression data


title: P7 cerebellar granule cells (3)

description: Microarray gene expression data


title: P12 cerebellar granule cells (3)

description: Microarray gene expression data


title: P7 cerebellar granule cells (2)

description: Microarray gene expression data


title: P0 cerebellar granule cells (3)

description: Microarray gene expression data


title: P0 cerebellar granule cells (1)

description: Microarray gene expression data


title: SKBR3_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line SKBR3 - 42966

hyb_protocol: Hybridization of samples to Affymetrix GeneChip arrays was performed according to Affymetrix manual instructions . RNA from the cell lines was hybridized to Affymetrix U133A2.0 arrays and processed in the Duke Microarray Core facility. Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.

scan_protocol: Scanning of Affymetrix GeneChip arrays was performed according to the Affmetrix manual instructions

data_processing: The Affymetrix HG U133 A2.0 Gene Chip array interrogates mRNA expression based on 22,000 probe sets corresponding to 14,500 annotated human genes. All statistical analyses were conducted using the R statistical environment and extension packages from CRAN and the Bioconductor project. Gene expression estimates were obtained from Affymetrix arrays using the RMA algorithm. The quality of the resultant microarrays was assessed using R/Bioconductor. To check for sample outliers and batch effects, principal component analysis of the global gene expression was conducted. Batch effects were corrected by scale-shift normalization prior to analysis.

label_protocol: Affymetrix ENZO labeling kit for the cell lines (for the Affymetrix U133A2 arrays).

growth_protocol: In order to identify differences in the radiation response gene expression profiles of specific breast cancer subtypes, we exposed 16 biologically-diverse breast tumor cell lines to 0 or 5GY radiation. Microarray analysis was performed on RNA harvested from those cell lines. Microarray analysis was performed on RNA harvested from those cell lines.  Samples were run in triplicate.  Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (25, 26) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms. Cell lines growth conditions: MCF7, ZR751, MDAMB231, and SUM159 were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Hyclone, SH30071.03) and 1X Antibiotic-Antimycotic (Gibco, 15240-062).   SUM149 cells were grown in Ham's F-12 medium supplemented with 5% fetal bovine serum (Hyclone, SH30071.03), 5ug/ml Insulin (Sigma-Aldrich®, I- 5500), 1ug/ml Hydrocortisone (Sigma-Aldrich®, H-4001) and 1X Antibiotics / Antimycotic (Gibco, 15240-062). T47D cells were grown in MEM-alpha medium (Gibco, 12561) supplemented with 6% of fetal bovine serum (Hyclone, SH30071.03), 12mM Hepes (Gibco15630), 1XMEM NEAA(Gibco 11140), 1mM Sodium Pyruvate (Gibco, 11360), 1ug/ml insulin (Sigma-Aldrich®, I-5500), 1ug/ml Hydrocortisone (Sigma-Aldrich®, H-4001), 12.5ng/ml EGF (Sigma-Aldrich®, E4127) and 1X Antibiotic-Antimycotic (Gibco, 15240-062).   AU565 and HCC1965 cells were grown in RPMI1640 medium supplemented with 10% of fetal bovine serum (Hyclone, SH30071.03), 1XSodium Pyruvate (Gibco 11360-070), 10mM Hepes(Gibco, 15630) and 1X Antibiotic-Antimycotic (Gibco, 15240-062). BT474 and SKBR3 cells were grown in RPMI1640 medium supplemented with 10% of fetal bovine serum (Hyclone, SH30071.03) and 1X Antibiotic-Antimycotic(Gibco, 15240-062).   BT549 were grown in RPMI1640 medium supplemented with 10% of fetal bovine serum (Hyclone, SH30071.03), 1XSodium Pyruvate (Gibco 11360-070), 10mM Hepes(Gibco, 15630), 8ug/ml Insulin(life technology 12585014) and 1X Antibiotic-Antimycotic(Gibco, 15240-062).   CAMA1 cells were grown in MEM (Gibco 11095-080) medium supplemented with 10% of fetal bovine serum (Hyclone, SH30071.03), 1XSodium Pyruvate (Gibco 11360-070), 1XNEAA (Gibco 11140) and 1X Antibiotic-Antimycotic (Gibco, 15240-062).  HBL100 cells were grown in McCoy’s 5a medium (Gibco 16600-082) supplemented with 10% of fetal bovine serum (Hyclone, SH30071.03) and1X Antibiotic-Antimycotic (Gibco, 15240-062).  MCF10A cells were grown in DMEM/F12 (GIBCO 11330-032) medium supplemented with 5% of Horse Serum (Invitrogen #16050-122), 0.5ug/ml of hydrocortisone(Sigma-Aldrich®,H4001), 10ug/ml of  Insulin (life technology 12585014), 20ng/ml of EGF(Sigma-Aldrich® ,  e9644) and 1X Antibiotic-Antimycotic (Gibco, 15240-062).  MCF12A cells were grown in DMEM/F12 (GIBCO11330-032) medium supplemented with 10% of fetal bovine serum (Hyclone, SH30071.03), 1ug/ml of hydrocortisone (Sigma-Aldrich, H-4001), 5ug/ml of Insulin (life technology 12585014) and 1X Antibiotic-Antimycotic (Gibco, 15240-062).  DKAT cells were grown in MEGM (Lonza, CC-3150) medium and 1X Antibiotic-Antimycotic (Gibco, 15240-062).  All cell lines were maintained in a humidified incubator with 5% CO2 atmosphere at 37o C.

extract_protocol: Microarray analysis was performed on RNA harvested from those cell lines.  Samples were run in triplicate. Isolation of RNA. Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.

treatment_protocol: 16 cell lines representing luminal HER2- (MCF7, T47D, ZR751, CAMA-1), luminal-HER2+ (BT474, SKBR3, AU565), HER2+ (HCC1954) and basal (SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, and DKAT) breast cancer cell lines were evaluated for response to a single dose of 5Gy.

value: breast cancer

tag: clinical subtype

value: luminal (Her2+)


title: SKBR3_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line SKBR3 - 42968


title: SKBR3_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line SKBR3 - 42965


title: P43-T1-Tum

city: Muscat

first: Manal

middle: Humaid

last: Al Khanbashi

address: Al Khod

department: Medicine

country: Oman

institute: Sultan Qaboos University

description: Tissue Gene expression from locally advanced breast cancer tissue biopsies

hyb_protocol: Hybridization, washing, and staining were performed according to the standard protocols from Affymetrix.

scan_protocol: Arrays were scanned using the Affymetrix® GeneChip® Scanner 3000.

data_processing: Raw data analyzed in Affymetrix ExpressionConsole using method: RMA-DABG, transformation: log2. ANOVA was run initially contrasting the normal versus the tumor tissue. Then a probe list was generated from these significant results (p<0.05), filtering by differences that have a <-2 or >2 fold change.

source_name: Cancer breast tissue, after first chemo dose

label_protocol: A total of 500 ng of RNA was labeled using the FlashTagTM Biotin HSR RNA labeling kit from Affymatrix

growth_protocol: These are clinical samples from locally advanced breast cancer cases undergoing neo-adjuvant chemotherapy treatment

extract_protocol: Total RNA was extracted following the manufacturer protcol of  mirVana miRNA isolation kit

treatment_protocol: The first time point are tissue at diagnosis where no treatment was adminstered but the timepoint 2, 3 and 4 are after the conventional neo-adjuvant chemotherapy treatment

tag: diagnosis

tag: biopsy

value: Cancer biopsy tissue


title: MCF12A_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF12A - 42959

value: basal


title: MCF12A_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF12A - 42961


title: P43-T4-Tum

source_name: Cancer breast tissue, after forth chemo dose


title: MCF12A_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF12A - 42962


title: P47-T2-Tum

source_name: Cancer breast tissue, after second chemo dose


title: P47-T1-Tum


title: MCF12A_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF12A - 42960


title: P43-T2-Tum


title: P43-T3-Tum

source_name: Cancer breast tissue, after third chemo dose


title: P47-T3-Tum


title: P47-T4-Tum


title: SKBR3_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line SKBR3 - 42967


title: SKBR3_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line SKBR3 - 42963


title: SKBR3_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line SKBR3 - 42964


title: P58-T4-Tum


title: MCF12A_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF12A - 42958


title: MCF12A_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF12A - 42957


title: BMDM_Nrf2+/+_Keap1-1_Replicate3

source_name: Bone Marrow Derived Murine Macrophages (BMDM), Nrf2 +/+, Keap1-1 treated

value: macrophages

value: C57BL/6 J


title: MCF10A_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF10A - 42956


title: MCF10A_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF10A - 42955


title: P58-T2-Tum


title: MCF10A_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF10A - 42954


title: P58-T3-Tum


title: P58-T1-Tum


title: MCF10A_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF10A - 42953


title: MCF10A_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF10A - 42952


title: P54-T3-Tum


title: HBL100_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line HBL100 - 42941


title: P48-T1-Tum


title: HCC1954_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line HCC1954 - 42950

value: basal (Her2+)


title: HBL100_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line HBL100 - 42939


title: HCC1954_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line HCC1954 - 42945


title: HBL100_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line HBL100 - 42942


title: P48-T4-Tum

description: Tissue Gene expression from locally advanced breast cancer tissue biopsies


title: P54-T2-Tum


title: P50-T1-Tum


title: HCC1954_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line HCC1954 - 42948


title: HCC1954_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line HCC1954 - 42949


title: HBL100_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line HBL100 - 42943


title: P44-T1-Tum


title: HCC1954_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line HCC1954 - 42946


title: P54-T4-Tum


title: P50-T4-Tum


title: P39-T4-Tum


title: P44-T4-Tum


title: HCC1954_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line HCC1954 - 42947


title: HBL100_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line HBL100 - 42944


title: MCF10A_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF10A - 42951


title: P54-T1-Tum


title: DKAT_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line DKAT - 42938

value: DKAT


title: DKAT_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line DKAT - 42937


title: HBL100_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line HBL100 - 42940


title: DKAT_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line DKAT - 42935


title: P18 cerebellar granule cells (1)

description: Microarray gene expression data


title: DKAT_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line DKAT - 42936


title: DKAT_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line DKAT - 42933


title: CAMA1_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line CAMA1 - 42927

value: luminal (Her2-)


title: P05-T4-Tum


title: CAMA1_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line CAMA1 - 42931


title: CAMA1_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line CAMA1 - 42929


title: CAMA1_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line CAMA1 - 42928


title: P08-T4-Nor

description: Tissue Gene expression from locally advanced breast cancer tissue biopsies

source_name: Normal breast tissue, after forth chemo dose

value: Normal tissue biopsy adjacent to cancer tissue


title: BT549_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line BT549 - 42926


title: P08-T3-Tum


title: CAMA1_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line CAMA1 - 42932


title: DKAT_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line DKAT - 42934


title: BT474_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line BT474 - 42918


title: BT549_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line BT549 - 42922


title: P02-T4-Tum


title: P08-T4-Tum


title: P05-T1-Tum


title: BT549_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line BT549 - 42921


title: CAMA1_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line CAMA1 - 42930


title: BT549_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line BT549 - 42924


title: BT474_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line BT474 - 42920


title: BT549_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line BT549 - 42923


title: BT474_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line BT474 - 42919


title: P08-T2-Nor

source_name: Normal breast tissue, after second chemo dose


title: BT474_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line BT474 - 42917


title: BT549_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line BT549 - 42925


title: P02-T1-Tum


title: P39-T1-Tum


title: P08-T3-Nor

source_name: Normal breast tissue, after third chemo dose


title: BT474_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line BT474 - 42915


title: BT474_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line BT474 - 42916


title: P08-T2-Tum


title: P08-T1-Tum


title: AU565_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line AU565 - 42913


title: AU565_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line AU565 - 42912


title: AU565_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line AU565 - 42914


title: SUM149_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line s149 - 35056


title: AU565_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line AU565 - 42910