title: HaCaT_Smad2/3_ChIP-chip

description:
Smad2/3 binding sites at promoter regions of the human epidermal keratinocyte cell line HaCaT (mapped to NCBIv36/hg18).
Both Smad2/3 ChIP and input samples were prepared as biological duplicates.

This Sample represents a re-analysis of GSM298710.

hyb_protocol: Each sample was hybridized to the array in 200 ul containing 1XHybridization buffer (Affymetrix), 50pM Control oligonucleotide (oligo B2, Affymetrix), Herring Sperm DNA (0.1mg/ml), Acetylated BSA (0.5mg/ml), and 7% DMSO. Samples were denatured at 100C for 10 minutes, and then put on ice before being hybridized for 16 hours at 45C in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix).

scan_protocol: Arrays were scanned using the Genechip Scanner3000 7G following the library array description.

data_processing: Array intensity data from ChIP and input were compared by the MAT (Model-based Analysis of Tiling-array) algorithm, using the software provided by the laboratory of X. Shirley Liu (http://chip.dfci.harvard.edu/~wli/MAT/). We calculated the MAT score and mapped the results to genomic positions in the human genome assembly hg 18 (NCBI Build 36).

source_name: HaCaT, Smad2/3 ChIP DNA

label_protocol: DNA was amplified by the IVT (In vitro transcription) method. For the labeling, DNA was fragmented by DNaseI. DNA was end-labeled by Terminal Transferase with biotin-11-ddATP.

growth_protocol: HaCaT cells were cultured as described (Koinuma et al., Mol Cell Biol 2009 [PMID 18955504]). Cells were grown in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: ChIP was performed as described (Koinuma et al., Mol Cell Biol 2009 [PMID 18955504]).

treatment_protocol: Cells were stimulated with 3 ng/ml of TGF-beta for 1.5 h.

tag: cell line

value: HaCaT

value: epidermal keratinocytes

value: TGF-beta

tag: treatment duration

value: 1.5 hrs

tag: chip antibody

tag: antibody vendor

value: BD Biosciences

tag: antibody catalog number

source_name: HaCaT, Smad2/3 input DNA


title: HepG2_Smad2/3_ChIP-chip

status: Public on Jun 08 2011

type: genomic

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: Smad2/3 binding sites at promoter regions of the human hepatoblastoma cell line HepG2 (mapped to NCBIv36/hg18).

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: HepG2, Smad2/3 ChIP DNA

growth_protocol: HepG2 and Hep3B cells were maintained in MEM medium (GIBCO) supplemented with 10% FBS (Thermo Scientific, Rockford, IL), 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 100 U/ml of penicillin G, and 100 µg/ml of streptomycin. Cells were grown in a humidified incubator with 5% CO2 at 37°C.

tag: cell type

value: hepatoblastoma cells

tag: treatment

source_name: HepG2, Smad2/3 input DNA


title: Hep3B_Smad2/3_ChIP-chip

description: Smad2/3 binding sites at promoter regions of the human hepatocellular carcinoma cell line Hep3B (mapped to NCBIv36/hg18).

source_name: Hep3B, Smad2/3 ChIP DNA

value: hepatocellular carcinoma cells

source_name: Hep3B, Smad2/3 input DNA


title: Patient 7, Average Clinical Course

type: RNA

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: Gene Expression Data from lymphocytes

hyb_protocol: 15 µg of fragmented cRNA were incubated with the chip in 200 µl of hybridization solution in Hybridization Oven 640 (Affymetrix) at 45°C for 16 hours. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual.

scan_protocol: Microarrays were scanned with the Affymetrix GeneChip Scanner 7G

data_processing:
the signals were processed using the GeneChip expression analysis algorithm (version 2, Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 200.
Absolute and comparison analyses were performed with Affymetrix MAS (version 5.0, Affymetrix) software using default parameters.

label: biotin

molecule: total RNA

source_name: human lymphocytes from CLN3 patients

label_protocol: 100 ng total RNA were used for first strand cDNA-synthesis (Two-Cycle Target Labeling Kit; Affymetrix) according to the GeneChip Expression Analysis Technical Manual. Synthesis of biotin-labeled cRNA was carried out using the IVT Labeling Kit (Affymetrix) and cleaned up (Sample Cleanup Module, Affymetrix)

growth_protocol: Lymphocytes were prepared from fresh patient blood samples by Ficoll-gradient centrifugation

extract_protocol: extraction of total RNA was performed according to the manufacturer's instructions (RNeasy® Micro Kit, Qiagen, Hilden, Germany)

tag: sample type

value: CLN3 1kb Deletion (c.462-677del), Female, 9 Years

tag: disease state

tag: genoytpe

value: CLN3 1kb Deletion (c.462-677del)

tag: gender

value: Female

tag: age

value: 9 Years

tag: disease progression

value: Average Clinical Course

value: lymphocyte


title: ShuS4 strain 8 hours after infection

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

country: USA

institute: J Craig Venter Institute

hyb_protocol: RNA samples were reverse transcribed to produce cDNA using SuperScript III (Invitrogen) and then subjected to qRT-PCR using Roche Sybr Green 2x matermix on the Roche 480 Light Cycler in 384-well format. Genes for each sample were represented in duplicates. Reactions were carried out at 10ul final volume. Each reaction contained 10ng of total RNA. PCR activation at 95°C for 10 min was followed by 70 cycles of 15 s at 95°C, 10 s at 55°C and 10 s at 70°C. Sybr green fluorescence was captured in each cycle following 70°C extension.

data_processing:
For each sample/data point the data was produced in quadruplicates (or duplicates for 0 time data point).
Replicates were averaged and then the quantile normalization was performed for each strain.

label: Sybr Green

organism: Francisella tularensis

source_name: Francisella tularensis ShuS4 strain during macrophage infection

extract_protocol: Ambion mirVana RNA extraction

tag: sample source

value: macrophages

tag: strain


title: 243 MPA

city: Cambridge

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

country: United Kingdom

institute: University of Cambridge

description: myo

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 1.12.4). It was vst transformed and quantile normalized.

source_name: myometrium

label_protocol: standard as recommended by illumina

growth_protocol: Strips of myometrium maintained in culture medium (Phenol red-free DMEM, 10% charcoal-stripped serum; 2mM L-glutamine, antibiotics) under 0.6g tension for approx. 65hrs

extract_protocol: Trizol method, according to manufacturer's (Invitrogen) instructions

treatment_protocol: Medroxyprogesterone Acetate (10-7M) or vehicle (0.01% EtOH)

tag: patient id

tag: tissue

value: myometrium

tag: developmental stage

value: pregnant, term, non-laboring


title: 242 vehicle

description: myo

value: vehicle


title: 11135

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

hyb_protocol: Manufacturer's protocol.

scan_protocol: ScanArray5000 (Packard BioChip Technologies).

data_processing: Agilent Genomic Workbench scanning software according to the manufacturer's protocol.

source_name: Control

label_protocol: Manufacturer's protocol.

extract_protocol: Purified whole blood DNAs (0.5μg) from probands (Simons Foundation Autism Simplex Collection).

value: normal control

value: male

source_name: Autism proband

value: idiopathic autism spectrum disorder (ASD)

value: whole blood


title: 11526


title: 11370


title: 242 MPA

description: myo


title: 240 MPA

description: myo


title: 240 vehicle

description: myo


title: 11215


title: Grit-Blasted-HFtreated_24h_rep1

city: Palma de Mallorca

first: Marta

last: Monjo

state: Illes Balears

address: Edifici del IUNICS, 1er pis, Laboratori de Biologia Molecular.Universitat de les Illes Balears. Cra. Valldemossa km 7.5

department: IUNICS (Health Sciences Research Institute)

country: Spain

institute: UIB (University of the Balearic Islands)

hyb_protocol: Hybridization, washing and staining was performed on the GeneChips Fluidics Station 450 (Affymetrix), according to recommendations from Affymetrix

scan_protocol: The chips were scanned on the Affymetrix GeneArray 2500 scanner.

data_processing: The data sets were processed by the Affymetrix mas5.0 software, and signal values representing the expression level of each transcript were generated. Data were analyzed through the use of Ingenuity Pathways Analysis (Ingenuity® Systems, www.ingenuity.com)

source_name: Human osteoblasts cultured for 24 hours on titanium grit-blasted HF treated surfaces

label_protocol: Double-stranded cDNA and biotin-labeled cRNA probes were created from 5 µg of total RNA using the Superscript Choice system (Invitrogen Life Technologies, Carlsbad, CA, USA) and the Bioarray (Enzo Biochem, New York, NY, USA), respectively.

growth_protocol: Normal human osteoblasts (NHOst cell system, Cambrex BioScience, Walkersville, MD, USA) from tibia of one donor (male, forty-one years old) were grown in Osteoblast Growth Media (OGM) containing 10% fetal bovine serum, ascorbic acid and antibiotics (gentamicin sulfate and amphotetericin-B) (Cambrex BioScience, Walkersville, MD, USA). Cells were subcultured 1:4 before reaching confluence using PBS (PAA Laboratories GmbH, Austria) and trypsin/EDTA (Sigma, St. Louis, MO, USA).

extract_protocol: RNA was isolated using Trizol reagent (Life Technologies, Gaithersburg, MD, USA), according to manufacturer's instructions, and further purified using the RNeasy kit (Qiagen, Valencia, CA, USA) in order to remove organic components.

treatment_protocol: Cells were cultured onto different titanium disks to test the effect of the surface modification. Titanium disks (n=6) were placed in a 6-well plate and 2x105 cells were seeded on each disk.

value: osteoblast

value: grit-blasted-HF treated


title: Patient 5, Average Clinical Course

description: Gene Expression Data from lymphocytes

value: CLN3 1kb Deletion (c.462-677del), Female, 18 Years

value: 18 Years


title: ShuS4 strain 4 hours after infection


title: fed sample, subject 7

city: Iowa City

first: Christopher

last: Adams

state: IA

address: 540G EMRB, 200 Hawkins Drive

institute: University of Iowa

description: skeletal muscle RNA from fed human

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Mouse Exon 1.0 ST arrays, and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven.

scan_protocol: Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.  Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing:
RMA normalization
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: vastus lateralis

label_protocol: 50 ng total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN MinElute Reaction Cleanup column (QIAGEN Cat #28204) according to modifications from NuGEN.  Four μg of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.  Five μg of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

extract_protocol: Total RNA was extracted using TRIzol solution (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Biopsies were obtained from the vastus lateralis muscle of healthy adult human subjects under fed and fasted conditions.

tag: individual

value: subject 7

value: fed

value: vastus lateralis

tag: Sex


title: Polished_24h_rep1

source_name: Human osteoblasts cultured for 24 hours on titanium polished surfaces

value: polished


title: Grit-Blasted_24h_rep1

source_name: Human osteoblasts cultured for 24 hours on titanium grit-blasted surfaces

value: grit-blasted


title: 238 MPA

description: myo


title: fed sample, subject 5

description: skeletal muscle RNA from fed human

value: subject 5

value: female


title: fasting sample, subject 7

description: skeletal muscle RNA from fasted human

value: fasting


title: Patient 6, Average Clinical Course

description: Gene Expression Data from lymphocytes

value: CLN3 1kb Deletion (c.462-677del), Male, 10 Years

value: CLN3 1kb Deletion (c.462-677del)

value: Male

value: 10 Years

value: Average Clinical Course

value: lymphocyte


title: fasting sample, subject 6

description: skeletal muscle RNA from fasted human

value: subject 6


title: ShuS4 strain 0 hours after infection

value: macrophages


title: fed sample, subject 6

description: skeletal muscle RNA from fed human


title: ShuS4 strain 2 hours after infection


title: LVS strain 0 hours after infection

source_name: Francisella tularensis LVS strain during macrophage infection

value: LVS


title: LVS strain 8 hours after infection


title: REMAGUS02_R02_7

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: Gene expression data from Breast Cancer

hyb_protocol: Following fragmentation, 10 ug of labelled cRNA were hybridized for 16 hr on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip GCS3000 scanner.

data_processing: Raw data were controlled using Genechip Operating Software and Affymetrix MAS5 algorithm to control the quality of hybridization and synthesis steps. Raw data were analysed using R/Bioconductor and normalized by GC-RMA method.

source_name: Breast tumors biopsies

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix two round amplification  protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. A cleanup with RNAII Nucleospin was conducted according Macherey Nagel recommendations

value: Breast tumors biopsies

tag: oestrogen receptor

value: negative

tag: progesterone receptor

tag: her2 status

tag: histological grade

value: III

tag: centre

value: centre 1


title: fasting sample, subject 5

description: skeletal muscle RNA from fasted human

tag: treatment

value: vastus lateralis


title: fed sample, subject 4

description: skeletal muscle RNA from fed human

value: subject 4

value: fed


title: fasting sample, subject 4

description: skeletal muscle RNA from fasted human

value: fasting

value: female


title: 238 vehicle

description: myo

value: vehicle

value: myometrium

value: pregnant, term, non-laboring


title: 237 vehicle

description: myo


title: fed sample, subject 1

description: skeletal muscle RNA from fed human

value: subject 1


title: fasting sample, subject 1

description: skeletal muscle RNA from fasted human


title: LVS strain 4 hours after infection


title: 237 MPA

description: myo


title: fed sample, subject 3

description: skeletal muscle RNA from fed human

value: subject 3

value: male


title: fasting sample, subject 2

description: skeletal muscle RNA from fasted human

value: subject 2


title: LVS strain 2 hours after infection

value: macrophages

value: LVS


title: 236 vehicle

description: myo


title: fed sample, subject 2

description: skeletal muscle RNA from fed human


title: fasting sample, subject 3

description: skeletal muscle RNA from fasted human


title: 234 MPA

description: myo


title: Breast_IDC_177

status: Public on Jun 07 2011

city: New York

first: Thalia

last: Farazi

state: NY

address: 1230 York Ave, BOX 186

department: Lab of RNA Molecular Biology

institute: Rockefeller University

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8770.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8773.txt
experiment vs. control raw data files: 8770.str.r.txt, 8770.str.n.txt
control vs. experiment raw data files: 8773.swp.r.txt, 8773.swp.n.txt
raw data matrix file: 14735.c.txt

hyb_protocol: Preheated hybridization buffer (25% formamide, 5X SSC, 0.1% SDS) was added and arrays were hybridised overnight 42C to human 35K oligo microarrays

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing:
Images were quantified using Genepix 5.1 Software. The Limma (linear models for microarray data) package of Bioconductor (http://www.bioconductor.org) was used for importing the data, normalizing the arrays and identifying differentially expressed genes. Control spots and spots with more than 10% saturation, a diameter smaller than 60 um or signal intensity less than 20 counts above background were excluded from the analysis. Data were corrected for local background (method normexp) and normalized within arrays by print-tip loess normalization and between arrays by quantile normalization
Supplementary data files are labeled as follows: str.r.txt represent raw and str.n.txt normalized data for comparison of experiment (Cy3) vs. reference (Cy5); swp.r.txt represent raw and swp.n.txt normalized data for comparison of reference (Cy3) vs. experiment (Cy5); c.txt contain processed data for the dye-swap merged comparison of experimental vs. reference.

source_name: Breast tissue

label_protocol: Two ug of total RNA was amplified and labeled using Ambion's Amino Allyl MessageAmp‚® aRNA kit and protocol (Ambion Inc., Austin, TX). For each microarray experiment, 2.0 ug aliquots of aRNA were labeled with Cy5 (Amersham Biosciences, Buckinghamshire, UK). The labeled aRNAs were mixed with equal amounts of Cy3-labeled reference aRNA. To the mixture of labeled reference and sample RNA, 20 ug human COT-1 DNA (Invitrogen, Carlsbad, CA), 8 ug yeast tRNA (Invitrogen) and 20 ug polyadenylic acid (Sigma-Aldrich, St. Louis, MO) were added.

growth_protocol: Tissues Collected from patients.

extract_protocol: Fresh-frozen (frozen immediately after surgery and stored at -80°C) normal and tumor tissue was collected. RNA was isolated from approximately thirty 30-µm cryosections corresponding to approximately 20 mg of tissue, using the first and last section to assess tumor content; only samples containing more than 50% tumor were further characterized. The tissues were homogenized in Trizol using a Polytron instrument (polytron®, PT, MR2100, Kinematica AG, Luzern) for 1 min and total RNA was isolated according to manufacturer's instructions.

treatment_protocol: No treatment.

tag: esr/er ihc (1=positive, 0=negative)

tag: pgr/pr ihc (1=positive, 0=negative)

tag: erbb2 ihc (1=positive, 0=negative)

tag: tag

value: Reference pool of 100 breast carcinomas


title: Breast_IDC_179

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8812.str.r.txt, 8812.str.n.txt
control vs. experiment raw data files: 8816.swp.r.txt, 8816.swp.n.txt
raw data matrix file: 14801.c.txt


title: Breast_IDC_182

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8797.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8796.txt
experiment vs. control raw data files: 8797.str.r.txt, 8797.str.n.txt
control vs. experiment raw data files: 8796.swp.r.txt, 8796.swp.n.txt
raw data matrix file: 14772.c.txt


title: Breast_IDC_178

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8814.str.r.txt, 8814.str.n.txt
control vs. experiment raw data files: 8811.swp.r.txt, 8811.swp.n.txt
raw data matrix file: 14800.c.txt


title: Breast_IDC_176

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8778.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8779.txt
experiment vs. control raw data files: 8778.str.r.txt, 8778.str.n.txt
control vs. experiment raw data files: 8779.swp.r.txt, 8779.swp.n.txt
raw data matrix file: 14751.c.txt


title: Breast_IDC_180

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8772.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8771.txt
experiment vs. control raw data files: 8771.str.r.txt, 8771.str.n.txt
control vs. experiment raw data files: 8772.swp.r.txt, 8772.swp.n.txt
raw data matrix file: 14736.c.txt


title: Breast_IDC_181A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8768.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8769.txt
experiment vs. control raw data files: 8768.str.r.txt, 8768.str.n.txt
control vs. experiment raw data files: 8769.swp.r.txt, 8769.swp.n.txt
raw data matrix file: 14734.c.txt


title: 234 vehicle

description: myo


title: Breast_Adenoid_171

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7124.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7123.txt
experiment vs. control raw data files: 7123.str.r.txt, 7123.str.n.txt
control vs. experiment raw data files: 7124.swp.r.txt, 7124.swp.n.txt
raw data matrix file: 12106.c.txt


title: Breast_IDC_173

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8832.str.r.txt, 8832.str.n.txt
control vs. experiment raw data files: 8831.swp.r.txt, 8831.swp.n.txt
raw data matrix file: 14838.c.txt


title: Breast_IDC_172

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8780.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8781.txt
experiment vs. control raw data files: 8780.str.r.txt, 8780.str.n.txt
control vs. experiment raw data files: 8781.swp.r.txt, 8781.swp.n.txt
raw data matrix file: 14752.c.txt


title: Breast_Metaplastic_174

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7252.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7251.txt
experiment vs. control raw data files: 7251.str.r.txt, 7251.str.n.txt
control vs. experiment raw data files: 7252.swp.r.txt, 7252.swp.n.txt
raw data matrix file: 12273.c.txt


title: Breast_IDC_168

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_9106.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_9105.txt
experiment vs. control raw data files: 9106.str.r.txt, 9106.str.n.txt
control vs. experiment raw data files: 9105.swp.r.txt, 9105.swp.n.txt
raw data matrix file: 15255.c.txt


title: Breast_IDC_164

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8710.str.r.txt, 8710.str.n.txt
control vs. experiment raw data files: 8713.swp.r.txt, 8713.swp.n.txt
raw data matrix file: 14675.c.txt


title: Breast_Metaplastic_166A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7253.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7254.txt
experiment vs. control raw data files: 7254.str.r.txt, 7254.str.n.txt
control vs. experiment raw data files: 7253.swp.r.txt, 7253.swp.n.txt
raw data matrix file: 12274.c.txt


title: NSBAg2

first: Takafusa

last: Hikichi

address: 1-21-1 Toyama, Shinjuku-ku

institute: National Center for Global Health and Medicine

hyb_protocol: Agilent one-color gene expression hyb/wash protocol. 1.65 ug of Cy3 labeled RNA was hybridized to Agilent Whole Mouse Genome microarrays (4 x 44K: GPL4134) at 60C for 17 hours and subsequently washed according to the Agilent standard hybridization protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2539A Microarray Scanner at 5 micron resolution. Images were quantified using Agilent Feature Extraction software version 9.5.3.1

data_processing: Agilent Feature Extraction software; gProcessedSignal; processed Cy3 Signal

organism: Mus musculus

label_protocol: Agilent one-color Low RNA Fluorecent Liner Amplification kit labeling protocol. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.25 ug RNA according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: RNA was prepared using the ISOGEN kit (Nippon gene co, Tokyo Japan) following the manufacturer's recommendations.   All RNA wwere quantified using a NanoDrop-1000 spectrophotometer.

tag: cell type

value: Neural progenitor cells

tag: cell line


title: Breast_Apocrine_170

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8728.str.r.txt, 8728.str.n.txt
control vs. experiment raw data files: 8729.swp.r.txt, 8729.swp.n.txt
raw data matrix file: 14670.c.txt


title: iHep-9F

value: induced Hepatic progenitor cells

tag: inducer

value: NSBAg2 using retroviral vectors of 9 transcription factors


title: Breast_IDC_169

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8730.str.r.txt, 8730.str.n.txt
control vs. experiment raw data files: 8732.swp.r.txt, 8732.swp.n.txt
raw data matrix file: 14672.c.txt


title: Breast_IDC_167A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8813.str.r.txt, 8813.str.n.txt
control vs. experiment raw data files: 8815.swp.r.txt, 8815.swp.n.txt
raw data matrix file: 14802.c.txt


title: Breast_IDC_175A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8834.str.r.txt, 8834.str.n.txt
control vs. experiment raw data files: 8833.swp.r.txt, 8833.swp.n.txt
raw data matrix file: 14839.c.txt


title: HNG2

value: Hepatic progenitor cells

tag: strain

value: STOCK Tg(Nanog-GFP, Puro)1 Yam

tag: development stage


title: iHep-10F

value: NSBAg2 using retroviral vectors of 10 transcription factors


title: HB1


title: Breast_IDC_163

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_9124.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_9123.txt
experiment vs. control raw data files: 9124.str.r.txt, 9124.str.n.txt
control vs. experiment raw data files: 9123.swp.r.txt, 9123.swp.n.txt
raw data matrix file: 15280.c.txt


title: NSEB5-2C

value: Mouse Neural progenitor cells


title: Breast_IDC_165

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8715.str.r.txt, 8715.str.n.txt
control vs. experiment raw data files: 8711.swp.r.txt, 8711.swp.n.txt
raw data matrix file: 14671.c.txt


title: Mixture

value: Mixture

value: Swiss Webster


title: NS21


title: NS195R


title: NPC-Zfp451

source_name: NPC in which Zfp451 was overexpressed

tag: overexpressed tf


title: Breast_IDC_161

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_7617.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7616.txt
experiment vs. control raw data files: 7617.str.r.txt, 7617.str.n.txt
control vs. experiment raw data files: 7616.swp.r.txt, 7616.swp.n.txt
raw data matrix file: 12878.c.txt


title: Breast_IDC_162

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8708.str.r.txt, 8708.str.n.txt
control vs. experiment raw data files: 8709.swp.r.txt, 8709.swp.n.txt
raw data matrix file: 14677.c.txt


title: NPC-Etv6

source_name: NPC in which Etv6 was overexpressed


title: NPC-Pdx1

source_name: NPC in which Pdx1 was overexpressed


title: NPC-Nfxl1

source_name: NPC in which Nfxl1 was overexpressed


title: Breast_IDC_156

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_7651.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7650.txt
experiment vs. control raw data files: 7651.str.r.txt, 7651.str.n.txt
control vs. experiment raw data files: 7650.swp.r.txt, 7650.swp.n.txt
raw data matrix file: 12972.c.txt


title: Breast_Apocrine_160

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8809.str.r.txt, 8809.str.n.txt
control vs. experiment raw data files: 8810.swp.r.txt, 8810.swp.n.txt
raw data matrix file: 14799.c.txt


title: NPC-Gatad2b

source_name: NPC in which Gatad2b was overexpressed


title: NPC-Crebzf

source_name: NPC in which Crebzf was overexpressed

value: Crebzf


title: Breast_IDC_157

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8707.str.r.txt, 8707.str.n.txt
control vs. experiment raw data files: 8703.swp.r.txt, 8703.swp.n.txt
raw data matrix file: 14678.c.txt


title: NPC-EGFP

source_name: NPC in which EGFP was overexpressed

value: EGFP


title: Breast_IDC_158

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8712.str.r.txt, 8712.str.n.txt
control vs. experiment raw data files: 8716.swp.r.txt, 8716.swp.n.txt
raw data matrix file: 14676.c.txt


title: N31Pax6(Dox+24hr)


title: NPC-Hmga2

source_name: NPC in which Hmga2 was overexpressed


title: NPC-Pax6

source_name: NPC in which Pax6 was overexpressed


title: Breast_IDC_159

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8704.str.r.txt, 8704.str.n.txt
control vs. experiment raw data files: 8705.swp.r.txt, 8705.swp.n.txt
raw data matrix file: 14681.c.txt


title: Breast_IDC_155A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8706.str.r.txt, 8706.str.n.txt
control vs. experiment raw data files: 8702.swp.r.txt, 8702.swp.n.txt
raw data matrix file: 14680.c.txt


title: NPC-Sox11

source_name: NPC in which Sox11 was overexpressed


title: Breast_IDC_154

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8652.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8651.txt
experiment vs. control raw data files: 8652.str.r.txt, 8652.str.n.txt
control vs. experiment raw data files: 8651.swp.r.txt, 8651.swp.n.txt
raw data matrix file: 14559.c.txt


title: NPC-Esx1

source_name: NPC in which Esx1 was overexpressed


title: iNPC-5TFs

value: induced Neural progenitor cells

tag: transcription factors used to induce mefs


title: NPC-mock

source_name: NPC

value: mock


title: iNPC-6TFs


title: N31EGFP(Dox+24hr)


title: Breast_IDC_153A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8727.str.r.txt, 8727.str.n.txt
control vs. experiment raw data files: 8726.swp.r.txt, 8726.swp.n.txt
raw data matrix file: 14673.c.txt


title: mad672

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite 6.5 using the RMA algorithmn

source_name: mouse model primary retinoblastoma tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

extract_protocol: details and references in manuscript

treatment_protocol: all samples are untreated tissues

tag: genotype/variation


title: mad671


title: Breast_IDC_150

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8653.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8654.txt
experiment vs. control raw data files: 8653.str.r.txt, 8653.str.n.txt
control vs. experiment raw data files: 8654.swp.r.txt, 8654.swp.n.txt
raw data matrix file: 14562.c.txt


title: mad673


title: mad667


title: mad670


title: mad668


title: Breast_IDC_152A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_7620.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7621.txt
experiment vs. control raw data files: 7620.str.r.txt, 7620.str.n.txt
control vs. experiment raw data files: 7621.swp.r.txt, 7621.swp.n.txt
raw data matrix file: 12883.c.txt


title: mad665


title: Breast_IDC_147

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8669.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8671.txt
experiment vs. control raw data files: 8669.str.r.txt, 8669.str.n.txt
control vs. experiment raw data files: 8671.swp.r.txt, 8671.swp.n.txt
raw data matrix file: 14585.c.txt


title: mad663


title: Breast_IDC_148A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8821.str.r.txt, 8821.str.n.txt
control vs. experiment raw data files: 8819.swp.r.txt, 8819.swp.n.txt
raw data matrix file: 14812.c.txt


title: mad666


title: mad660


title: mad661


title: Breast_Apocrine_149

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8724.str.r.txt, 8724.str.n.txt
control vs. experiment raw data files: 8725.swp.r.txt, 8725.swp.n.txt
raw data matrix file: 14674.c.txt


title: Breast_Atypical Medullary_141

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7034.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7033.txt
experiment vs. control raw data files: 7033.str.r.txt, 7033.str.n.txt
control vs. experiment raw data files: 7034.swp.r.txt, 7034.swp.n.txt
raw data matrix file: 11976.c.txt


title: Breast_IDC_146

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_9121.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_9122.txt
experiment vs. control raw data files: 9121.str.r.txt, 9121.str.n.txt
control vs. experiment raw data files: 9122.swp.r.txt, 9122.swp.n.txt
raw data matrix file: 15279.c.txt


title: mad664


title: mad669


title: mad662


title: Breast_IDC_139A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8681.str.r.txt, 8681.str.n.txt
control vs. experiment raw data files: 8684.swp.r.txt, 8684.swp.n.txt
raw data matrix file: 14616.c.txt


title: 236 MPA

description: myo

source_name: myometrium

tag: patient id

tag: tissue

value: myometrium

tag: developmental stage

value: pregnant, term, non-laboring


title: Breast_Adenoid_138

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7120.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7119.txt
experiment vs. control raw data files: 7119.str.r.txt, 7119.str.n.txt
control vs. experiment raw data files: 7120.swp.r.txt, 7120.swp.n.txt
raw data matrix file: 12104.c.txt


title: mad656


title: mad659


title: mad654


title: mad650

description: MDMX

value: MDMX


title: mad653

description: MDMX


title: mad655


title: mad658


title: mad652

description: MDMX


title: mad651

description: MDMX


title: mad647


title: Breast_Metaplastic_136

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7052.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7051.txt
experiment vs. control raw data files: 7051.str.r.txt, 7051.str.n.txt
control vs. experiment raw data files: 7052.swp.r.txt, 7052.swp.n.txt
raw data matrix file: 12004.c.txt

value: Reference pool of 100 breast carcinomas


title: Breast_Atypical Medullary_137

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7032.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7031.txt
experiment vs. control raw data files: 7031.str.r.txt, 7031.str.n.txt
control vs. experiment raw data files: 7032.swp.r.txt, 7032.swp.n.txt
raw data matrix file: 11975.c.txt


title: mad648

description: MDMX


title: mad649

description: MDMX


title: mad644


title: mad657


title: mad646


title: mad645


title: mad643


title: Breast_Atypical Medullary_135

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7049.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7050.txt
experiment vs. control raw data files: 7050.str.r.txt, 7050.str.n.txt
control vs. experiment raw data files: 7049.swp.r.txt, 7049.swp.n.txt
raw data matrix file: 12001.c.txt


title: Breast_Atypical Medullary_131

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7038.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7037.txt
experiment vs. control raw data files: 7037.str.r.txt, 7037.str.n.txt
control vs. experiment raw data files: 7038.swp.r.txt, 7038.swp.n.txt
raw data matrix file: 11982.c.txt


title: mad641


title: Breast_Metaplastic_130

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7062.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7061.txt
experiment vs. control raw data files: 7061.str.r.txt, 7061.str.n.txt
control vs. experiment raw data files: 7062.swp.r.txt, 7062.swp.n.txt
raw data matrix file: 12021.c.txt


title: Breast_Metaplastic_132

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7039.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7040.txt
experiment vs. control raw data files: 7040.str.r.txt, 7040.str.n.txt
control vs. experiment raw data files: 7039.swp.r.txt, 7039.swp.n.txt
raw data matrix file: 11985.c.txt


title: mad640

description: TKO

value: TKO


title: mad639

description: TKO


title: Breast_Atypical Medullary_134

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7030.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7029.txt
experiment vs. control raw data files: 7029.str.r.txt, 7029.str.n.txt
control vs. experiment raw data files: 7030.swp.r.txt, 7030.swp.n.txt
raw data matrix file: 11970.c.txt


title: Breast_Metaplastic_129

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7244.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7243.txt
experiment vs. control raw data files: 7243.str.r.txt, 7243.str.n.txt
control vs. experiment raw data files: 7244.swp.r.txt, 7244.swp.n.txt
raw data matrix file: 12269.c.txt


title: mad637

description: TKO


title: Breast_Atypical Medullary_128

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7060.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7059.txt
experiment vs. control raw data files: 7059.str.r.txt, 7059.str.n.txt
control vs. experiment raw data files: 7060.swp.r.txt, 7060.swp.n.txt
raw data matrix file: 12016.c.txt


title: mad638

description: TKO


title: mad636

description: TKO


title: mad642


title: mad541


title: mad634

description: TKO


title: mad633

description: TKO


title: mad635

description: TKO


title: Breast_Metaplastic_127

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7036.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7035.txt
experiment vs. control raw data files: 7035.str.r.txt, 7035.str.n.txt
control vs. experiment raw data files: 7036.swp.r.txt, 7036.swp.n.txt
raw data matrix file: 11979.c.txt


title: Breast_Atypical Medullary_126A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7058.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7057.txt
experiment vs. control raw data files: 7057.str.r.txt, 7057.str.n.txt
control vs. experiment raw data files: 7058.swp.r.txt, 7058.swp.n.txt
raw data matrix file: 12013.c.txt


title: mad534


title: mad538


title: mad530


title: mad540


title: mad537


title: mad528


title: mad532


title: Breast_IDC_125

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8657.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8658.txt
experiment vs. control raw data files: 8657.str.r.txt, 8657.str.n.txt
control vs. experiment raw data files: 8658.swp.r.txt, 8658.swp.n.txt
raw data matrix file: 14571.c.txt


title: Breast_IDC_123

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8672.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8670.txt
experiment vs. control raw data files: 8672.str.r.txt, 8672.str.n.txt
control vs. experiment raw data files: 8670.swp.r.txt, 8670.swp.n.txt
raw data matrix file: 14586.c.txt


title: mad527


title: Breast_IDC_124A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_9125.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_9126.txt
experiment vs. control raw data files: 9125.str.r.txt, 9125.str.n.txt
control vs. experiment raw data files: 9126.swp.r.txt, 9126.swp.n.txt
raw data matrix file: 15281.c.txt


title: Breast_Metaplastic_122A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7248.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7247.txt
experiment vs. control raw data files: 7247.str.r.txt, 7247.str.n.txt
control vs. experiment raw data files: 7248.swp.r.txt, 7248.swp.n.txt
raw data matrix file: 12271.c.txt


title: mad531


title: Breast_IDC_120

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8677.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8676.txt
experiment vs. control raw data files: 8677.str.r.txt, 8677.str.n.txt
control vs. experiment raw data files: 8676.swp.r.txt, 8676.swp.n.txt
raw data matrix file: 14596.c.txt


title: Breast_IDC_119A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8663.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8661.txt
experiment vs. control raw data files: 8663.str.r.txt, 8663.str.n.txt
control vs. experiment raw data files: 8661.swp.r.txt, 8661.swp.n.txt
raw data matrix file: 14574.c.txt


title: mad535


title: mad526


title: mad536


title: Breast_IDC_118

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 8808.str.r.txt, 8808.str.n.txt
control vs. experiment raw data files: 8805.swp.r.txt, 8805.swp.n.txt
raw data matrix file: 14789.c.txt


title: Breast_IDC_121A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8673.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8674.txt
experiment vs. control raw data files: 8673.str.r.txt, 8673.str.n.txt
control vs. experiment raw data files: 8674.swp.r.txt, 8674.swp.n.txt
raw data matrix file: 14594.c.txt


title: mad539


title: Breast_Apocrine_117

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8665.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8666.txt
experiment vs. control raw data files: 8665.str.r.txt, 8665.str.n.txt
control vs. experiment raw data files: 8666.swp.r.txt, 8666.swp.n.txt
raw data matrix file: 14583.c.txt


title: mad523


title: Breast_IDC_115

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_9150.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_9151.txt
experiment vs. control raw data files: 9150.str.r.txt, 9150.str.n.txt
control vs. experiment raw data files: 9151.swp.r.txt, 9151.swp.n.txt
raw data matrix file: 15322.c.txt


title: Breast_IDC_116

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_9166.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_9167.txt
experiment vs. control raw data files: 9166.str.r.txt, 9166.str.n.txt
control vs. experiment raw data files: 9167.swp.r.txt, 9167.swp.n.txt
raw data matrix file: 15335.c.txt


title: Breast_IDC_114

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8664.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8660.txt
experiment vs. control raw data files: 8664.str.r.txt, 8664.str.n.txt
control vs. experiment raw data files: 8660.swp.r.txt, 8660.swp.n.txt
raw data matrix file: 14572.c.txt


title: mad520


title: mad521


title: Breast_IDC_113

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8678.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8675.txt
experiment vs. control raw data files: 8678.str.r.txt, 8678.str.n.txt
control vs. experiment raw data files: 8675.swp.r.txt, 8675.swp.n.txt
raw data matrix file: 14595.c.txt


title: mad518


title: mad512


title: mad782

description: single tumor cell

source_name: retinoblastoma

label_protocol: Affymterix standard methods were applied after Cepko  isolation anmd RNA amplification

extract_protocol: details and references in manuscript, singel cell methodolgy and RNA amplification method developed by Cepko lab referenced in text

value: single retinoblastoma tumor cell


title: Breast_IDC_111

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8762.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8761.txt
experiment vs. control raw data files: 8762.str.r.txt, 8762.str.n.txt
control vs. experiment raw data files: 8761.swp.r.txt, 8761.swp.n.txt
raw data matrix file: 14722.c.txt


title: mad511


title: mad785

description: single tumor cell


title: mad783

description: single tumor cell


title: mad786

description: single tumor cell


title: Breast_IDC_112

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8758.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8759.txt
experiment vs. control raw data files: 8758.str.r.txt, 8758.str.n.txt
control vs. experiment raw data files: 8759.swp.r.txt, 8759.swp.n.txt
raw data matrix file: 14721.c.txt


title: mad513


title: mad519


title: mad784

description: single tumor cell


title: mad509


title: Breast_IDC_110

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8764.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8765.txt
experiment vs. control raw data files: 8764.str.r.txt, 8764.str.n.txt
control vs. experiment raw data files: 8765.swp.r.txt, 8765.swp.n.txt
raw data matrix file: 14724.c.txt


title: Breast_IDC_109

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8790.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8793.txt
experiment vs. control raw data files: 8790.str.r.txt, 8790.str.n.txt
control vs. experiment raw data files: 8793.swp.r.txt, 8793.swp.n.txt
raw data matrix file: 14770.c.txt


title: mad779

description: single tumor cell


title: mad780

description: single tumor cell


title: mad515


title: Breast_IDC_108

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8791.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8792.txt
experiment vs. control raw data files: 8791.str.r.txt, 8791.str.n.txt
control vs. experiment raw data files: 8792.swp.r.txt, 8792.swp.n.txt
raw data matrix file: 14769.c.txt


title: mad508


title: mad781

description: single tumor cell


title: mad778

description: single tumor cell


title: Breast_IDC_107A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8788.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8789.txt
experiment vs. control raw data files: 8788.str.r.txt, 8788.str.n.txt
control vs. experiment raw data files: 8789.swp.r.txt, 8789.swp.n.txt
raw data matrix file: 14768.c.txt


title: Breast_IDC_106

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-2
ArrayExpress data file: BioDataCube_For_MeasuredData_8785.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_8784.txt
experiment vs. control raw data files: 8785.str.r.txt, 8785.str.n.txt
control vs. experiment raw data files: 8784.swp.r.txt, 8784.swp.n.txt
raw data matrix file: 14754.c.txt


title: mad776

description: single tumor cell


title: mad503


title: mad777

description: single tumor cell


title: mad506


title: mad502


title: Breast_Normal_104A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12871.str.r.txt, 12871.str.n.txt
control vs. experiment raw data files: 12872.swp.r.txt, 12872.swp.n.txt
raw data matrix file: 21408.c.txt


title: Breast_Normal_105A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12873.str.r.txt, 12873.str.n.txt
control vs. experiment raw data files: 12874.swp.r.txt, 12874.swp.n.txt
raw data matrix file: 21409.c.txt


title: Breast_Normal_103A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12837.str.r.txt, 12837.str.n.txt
control vs. experiment raw data files: 12846.swp.r.txt, 12846.swp.n.txt
raw data matrix file: 21415.c.txt


title: mad775

description: single tumor cell


title: mad505


title: Human MCF7 cells, L3MBTL2 Replicate 1

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

description: Human MCF7 cells

hyb_protocol: Cy-labedled ChIP Samples

scan_protocol: NimbleScan

data_processing: Fluorescence intensity raw data was obtained from scanned images of the oligonucleotide tiling arrays using NimbleScan 2.2 extraction software (NimbleGen Systems). For each spot on the array, log2-ratios of the Cy5-labeled test sample versus the Cy3-labeled reference sample were calculated. Then, the biweight mean of this log2 ratio was subtracted from each point; this procedure similar to mean-normalization of each channel

source_name: MCF7 cells

label_protocol: standard NimbleGen protocol

extract_protocol: ChIP-chip

tag: antibody

tag: antibody manufacturer

value: produced in Danny Reinber's lab

tag: sample type

value: control total input


title: mad501


title: mad500


title: Breast_Normal_101

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12869.str.r.txt, 12869.str.n.txt
control vs. experiment raw data files: 12870.swp.r.txt, 12870.swp.n.txt
raw data matrix file: 21407.c.txt

source_name: Breast tissue

tag: esr/er ihc (1=positive, 0=negative)

tag: pgr/pr ihc (1=positive, 0=negative)


title: Human MCF7 cells, E2F6 Replicate 1

description: Human MCF7 cells

value: Santa Cruz

tag: antibody catalog #

tag: antibody lot #


title: Breast_Normal_100A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12875.str.r.txt, 12875.str.n.txt
control vs. experiment raw data files: 12876.swp.r.txt, 12876.swp.n.txt
raw data matrix file: 21410.c.txt

tag: erbb2 ihc (1=positive, 0=negative)

tag: tag


title: mad772

description: single tumor cell

tag: cell type


title: mad496


title: Breast_Normal_102A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12847.str.r.txt, 12847.str.n.txt
control vs. experiment raw data files: 12848.swp.r.txt, 12848.swp.n.txt
raw data matrix file: 21416.c.txt


title: mad771

description: single tumor cell


title: Human MCF7 cells, L3MBTL1 Replicate 1

description: Human MCF7 cells

tag: cell line


title: mad773

description: single tumor cell


title: mad495


title: mad498


title: mad770

description: single tumor cell


title: mad774

description: single tumor cell


title: Breast_Normal_99A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12867.str.r.txt, 12867.str.n.txt
control vs. experiment raw data files: 12868.swp.r.txt, 12868.swp.n.txt
raw data matrix file: 21406.c.txt


title: mad493


title: mad492


title: mad768

description: single tumor cell


title: mad769

description: single tumor cell


title: mad491


title: mad490


title: Breast_Normal_96

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12861.str.r.txt, 12861.str.n.txt
control vs. experiment raw data files: 12862.swp.r.txt, 12862.swp.n.txt
raw data matrix file: 21403.c.txt


title: Breast_Normal_95A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12843.str.r.txt, 12843.str.n.txt
control vs. experiment raw data files: 12844.swp.r.txt, 12844.swp.n.txt
raw data matrix file: 21414.c.txt


title: mad489


title: Breast_Normal_98A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12863.str.r.txt, 12863.str.n.txt
control vs. experiment raw data files: 12864.swp.r.txt, 12864.swp.n.txt
raw data matrix file: 21404.c.txt


title: mad486


title: Breast_IDC_92A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11981.str.r.txt, 11981.str.n.txt
control vs. experiment raw data files: 11982.swp.r.txt, 11982.swp.n.txt
raw data matrix file: 20456.c.txt


title: mad707

description: primary tumor

value: primary tumor


title: Breast_Normal_97

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12865.str.r.txt, 12865.str.n.txt
control vs. experiment raw data files: 12866.swp.r.txt, 12866.swp.n.txt
raw data matrix file: 21405.c.txt


title: mad485


title: mad710

description: xenograft-passaged

value: xenograft-passaged


title: Breast_IDC_90

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11954.str.r.txt, 11954.str.n.txt
control vs. experiment raw data files: 11955.swp.r.txt, 11955.swp.n.txt
raw data matrix file: 20468.c.txt


title: mad708

description: primary tumor


title: mad714

description: xenograft-passaged


title: mad767

description: single tumor cell


title: mad487


title: mad709

description: xenograft-passaged


title: mad687

description: primary tumor


title: Breast_IDC_94A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13036.str.r.txt, 13036.str.n.txt
control vs. experiment raw data files: 13037.swp.r.txt, 13037.swp.n.txt
raw data matrix file: 21721.c.txt


title: Breast_IDC_93A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11952.str.r.txt, 11952.str.n.txt
control vs. experiment raw data files: 11953.swp.r.txt, 11953.swp.n.txt
raw data matrix file: 20467.c.txt


title: mad481

description: MDMX


title: mad483


title: mad686

description: primary tumor


title: Breast_IDC_87

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11992.str.r.txt, 11992.str.n.txt
control vs. experiment raw data files: 11993.swp.r.txt, 11993.swp.n.txt
raw data matrix file: 20464.c.txt


title: Breast_IDC_88A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12203.str.r.txt, 12203.str.n.txt
control vs. experiment raw data files: 12204.swp.r.txt, 12204.swp.n.txt
raw data matrix file: 20499.c.txt


title: Breast_IDC_89A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13054.str.r.txt, 13054.str.n.txt
control vs. experiment raw data files: 13055.swp.r.txt, 13055.swp.n.txt
raw data matrix file: 21731.c.txt


title: mad681

description: primary tumor


title: mad688

description: primary tumor


title: mad621

description: primary tumor


title: mad478

description: MDMX


title: Breast_IDC_86A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12005.str.r.txt, 12005.str.n.txt
control vs. experiment raw data files: 12006.swp.r.txt, 12006.swp.n.txt
raw data matrix file: 20485.c.txt


title: mad620

description: primary tumor


title: mad476

description: MDMX


title: mad479

description: MDMX


title: mad477

description: MDMX


title: mad619

description: primary tumor


title: Breast_IDC_84

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12539.str.r.txt, 12539.str.n.txt
control vs. experiment raw data files: 12540.swp.r.txt, 12540.swp.n.txt
raw data matrix file: 20983.c.txt


title: Breast_IDC_83A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12329.str.r.txt, 12329.str.n.txt
control vs. experiment raw data files: 12330.swp.r.txt, 12330.swp.n.txt
raw data matrix file: 20450.c.txt


title: Breast_IDC_85A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11965.str.r.txt, 11965.str.n.txt
control vs. experiment raw data files: 11966.swp.r.txt, 11966.swp.n.txt
raw data matrix file: 20474.c.txt


title: Breast_IDC_81A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12228.str.r.txt, 12228.str.n.txt
control vs. experiment raw data files: 12229.swp.r.txt, 12229.swp.n.txt
raw data matrix file: 20512.c.txt


title: Breast_IDC_82

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12009.str.r.txt, 12009.str.n.txt
control vs. experiment raw data files: 12010.swp.r.txt, 12010.swp.n.txt
raw data matrix file: 20488.c.txt


title: mad618

description: primary tumor


title: mad480

description: MDMX


title: mad617

description: primary tumor


title: mad544

description: primary tumor


title: mad474

description: MDMX


title: mad473

description: MDMX


title: Breast_IDC_80

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12207.str.r.txt, 12207.str.n.txt
control vs. experiment raw data files: 12208.swp.r.txt, 12208.swp.n.txt
raw data matrix file: 20501.c.txt


title: Breast_IDC_79

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12557.str.r.txt, 12557.str.n.txt
control vs. experiment raw data files: 12558.swp.r.txt, 12558.swp.n.txt
raw data matrix file: 20993.c.txt


title: mad472

description: MDMX


title: mad471

description: MDMX


title: mad543

description: primary tumor


title: mad475

description: MDMX


title: Breast_IDC_78A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12527.str.r.txt, 12527.str.n.txt
control vs. experiment raw data files: 12528.swp.r.txt, 12528.swp.n.txt
raw data matrix file: 20848.c.txt


title: mad468

description: MDMX


title: mad542

description: primary tumor


title: mad409

description: primary tumor


title: Breast_IDC_77

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13052.str.r.txt, 13052.str.n.txt
control vs. experiment raw data files: 13053.swp.r.txt, 13053.swp.n.txt
raw data matrix file: 21730.c.txt


title: mad470

description: MDMX


title: mad466

description: MDMX


title: mad411

description: primary tumor


title: Breast_IDC_76

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12513.str.r.txt, 12513.str.n.txt
control vs. experiment raw data files: 12514.swp.r.txt, 12514.swp.n.txt
raw data matrix file: 20841.c.txt


title: Breast_IDC_75A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11714.str.r.txt, 11714.str.n.txt
control vs. experiment raw data files: 11715.swp.r.txt, 11715.swp.n.txt
raw data matrix file: 19395.c.txt


title: mad465

description: MDMX


title: Breast_IDC_74

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11983.str.r.txt, 11983.str.n.txt
control vs. experiment raw data files: 11984.swp.r.txt, 11984.swp.n.txt
raw data matrix file: 20457.c.txt


title: mad464

description: MDMX


title: Breast_IDC_73

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13044.str.r.txt, 13044.str.n.txt
control vs. experiment raw data files: 13045.swp.r.txt, 13045.swp.n.txt
raw data matrix file: 21725.c.txt


title: mad410

description: primary tumor


title: mad463

description: MDMX


title: mad407

description: primary tumor


title: mad406

description: primary tumor


title: mad462

description: MDMX


title: mad405

description: primary tumor


title: mad408

description: primary tumor


title: Breast_IDC_72

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13042.str.r.txt, 13042.str.n.txt
control vs. experiment raw data files: 13043.swp.r.txt, 13043.swp.n.txt
raw data matrix file: 21724.c.txt


title: mad452


title: mad449


title: mad402

description: primary tumor


title: Breast_IDC_66A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12511.str.r.txt, 12511.str.n.txt
control vs. experiment raw data files: 12512.swp.r.txt, 12512.swp.n.txt
raw data matrix file: 20840.c.txt


title: mad488


title: Breast_IDC_67

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11438.str.r.txt, 11438.str.n.txt
control vs. experiment raw data files: 11439.swp.r.txt, 11439.swp.n.txt
raw data matrix file: 18920.c.txt


title: Breast_IDC_68

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12521.str.r.txt, 12521.str.n.txt
control vs. experiment raw data files: 12522.swp.r.txt, 12522.swp.n.txt
raw data matrix file: 20845.c.txt


title: mad448


title: mad447


title: Breast_IDC_71

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11977.str.r.txt, 11977.str.n.txt
control vs. experiment raw data files: 11978.swp.r.txt, 11978.swp.n.txt
raw data matrix file: 20454.c.txt


title: mad403

description: primary tumor


title: mad451


title: mad394

description: primary tumor


title: Breast_IDC_69A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12483.str.r.txt, 12483.str.n.txt
control vs. experiment raw data files: 12484.swp.r.txt, 12484.swp.n.txt
raw data matrix file: 20826.c.txt


title: mad393

description: primary tumor


title: mad404

description: primary tumor


title: Breast_IDC_70A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11718.str.r.txt, 11718.str.n.txt
control vs. experiment raw data files: 11719.swp.r.txt, 11719.swp.n.txt
raw data matrix file: 19397.c.txt


title: mad446


title: mad391

description: primary tumor


title: mad445


title: mad395

description: primary tumor


title: mad392

description: primary tumor


title: mad443


title: Breast_IDC_65A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11581.str.r.txt, 11581.str.n.txt
control vs. experiment raw data files: 11582.swp.r.txt, 11582.swp.n.txt
raw data matrix file: 19089.c.txt


title: mad390

description: primary tumor