title: mESC cultured on a 6-well plate

city: Davis

first: Joshua

last: Guild

address: 451 East Health Sciences St. #2619

department: Biomedical Engineering

institute: University of California Davis

hyb_protocol: Genome-wide expression profiling using Mouse Gene 2.0 ST GeneChip arrays (Mouse Gene 2.0 ST; Affymetrix, Santa Clara, CA) was performed according to the manufacturer’s protocols.

data_processing:
Data analysis was performed with the combination of the Expression Console software (version 1.4.1) and the Transcriptome Analysis Console software (version 3.0; Affymetrix, Santa Clara, CA).
Microarray probe intensity values (CEL files) were background-corrected, summarized, log2-transformed, and normalized using the Robust Multi-array Average (RMA16) algorithm and filtered for raw signal intensity values in the range of the 20th-100th percentile (lower/upper cut-off).

source_name: Mouse embryonic stem cell

growth_protocol: D3 (ATCC) mouse ESCs were cultured in 15% serum with 1000U LIF according to standard protocols

extract_protocol: RNA was isolated using the High Pure RNA Isolation Kit (Roche), according to manufacturer’s instructions.

treatment_protocol: Cells were seeding into 6-well plates or microfluidic chambers at a density of 20,000 cells/cm2 and cultured for 3 days prior to harvesting of RNA.

tag: protocol

value: 6-well plate


title: 99-091K_LN CRPC metastasis

status: Public on Dec 18 2015

type: RNA

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Center

description: 99-091K CRPC lymph node metastasis

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505C (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software versions 10.7.3.1 were used to grid and extract the data using the GE2_105_Jan09 protocols with default settings. Data was loess normalized within arrays (normexp background correction with offset 50) and quantile normalized between arrays in R using the Limma Bioconductor package by batch. Control probes were removed, duplicate probes averaged, and spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers were assigned a value of NA. Data was normalized separately for LuCaP xenografts and CRPC metastases. CRPC metastases were subject to an additional normalization step to remove systematic batch effects due to date of RNA-amplification by application of the ComBat function within the sva Bioconductor package to the log2 Cy3 signal intensities. Batches are indicated in the ch2: characteristics: batch field and indicates RNA-amplification batch. Batch normalization was applied to a larger set of CRPC samples than those that appear in this study.

molecule: total RNA

organism: Homo sapiens

label_protocol: amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

tag: gender

value: male

tag: tissue

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

extract_protocol: Eight-micron thick sections from soft tissue CRPC frozen metastases in Optimal Cutting Temperature compound (OCT; Tissue-Tek) were cut using a Leica CM3050S cryostat, collected on PEN Membrane Frame Slides (Life Technologies) and immediately fixed in 95% ethanol. Sections were briefly stained with hematoxylin then dehydrated in 100% ethanol. 5,000-10,000 tumor cells per sample were laser capture microdissected with an Arcturus Veritas instrument and collected on CapSure® Macro LCM Caps (Life Technologies). Digital photographs were taken of tissue sections before, during, and after LCM and assessed by a pathologist to confirm the tumor content. RNA was isolated using the Arcturus PicoPure RNA Isolation Kit and the samples were DNAse treated using the Qiagen RNase-Free DNase Set. Total RNA was amplified two rounds with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

tag: batch

tag: tumor type

value: CRPC metastasis

tag: tumor site

value: LN

tag: patient


title: mESCs cultured in a microchamber

middle: Daniel

state: CA

scan_protocol: Genome-wide expression profiling using Mouse Gene 2.0 ST GeneChip arrays (Mouse Gene 2.0 ST; Affymetrix, Santa Clara, CA) was performed according to the manufacturer’s protocols.

label: biotin

organism: Mus musculus

tag: cell line

value: microchamber


title: 98-372K2_CAP CRPC primary/localized tumor

description: 98-372K2 CRPC bladder_neck primary/localized tumor

extract_protocol: Eight-micron thick sections from CRPC localized tumors in Optimal Cutting Temperature compound (OCT; Tissue-Tek) were cut using a Leica CM3050S cryostat, collected on PEN Membrane Frame Slides (Life Technologies) and immediately fixed in 95% ethanol. Sections were briefly stained with hematoxylin then dehydrated in 100% ethanol. 5,000-10,000 tumor cells per sample were laser capture microdissected with an Arcturus Veritas instrument and collected on CapSure® Macro LCM Caps (Life Technologies). Digital photographs were taken of tissue sections before, during, and after LCM and assessed by a pathologist to confirm the tumor content. RNA was isolated using the Arcturus PicoPure RNA Isolation Kit and the samples were DNAse treated using the Qiagen RNase-Free DNase Set. Total RNA was amplified two rounds with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: CRPC primary/localized


title: 99-064O_LN CRPC metastasis

description: 99-064O CRPC lymph node metastasis


title: 99-069I_CAP CRPC primary/localized tumor

description: 99-069I CRPC bladder_neck primary/localized tumor


title: BE2C_tetoff_KDM4C_D+1

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Regents University

description: RNA expression value

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were normalized, significance determined by ANOVA, and fold change calculated with the Partek Genomics Suite (Partek Inc., St. Louis, MO).

source_name: BE2C_tetoff_KDM4C_D+6 days

label_protocol: TdT-labled cRNA were prepared with an Affymetrix GeneChip WT Terminal labeling kit

growth_protocol: BE(2)-C_tetoff_KDM4C cells were cultured in DME/F-12 1:1 (HyClone SH30023, Thermo Scientific) supplemented with 10% dialyzed FBS (Gibco 26400-036).

extract_protocol: Total RNA was isolated from the cell samples using Trizol (Invitrogen), and RNA quality and quantity was assessed using a Agilent BioAnalyzer and a Nanodrop Spectrophotometer.

treatment_protocol: BE(2)-C_tetoff_KDM4C cells were cultured in the presence or absence of doxycycline for 6 days.

tag: tumor cell line

value: Neuroblastoma

tag: treatment

value: doxycycline


title: S3-H183

city: Houston

first: Suzanne

last: Fuqua

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: log2 gene expression data

hyb_protocol: Standard Affymetix protocol for 3' IVT design

scan_protocol: Scanner GCS3000 7G

data_processing:
The data were analyzed with  Affy package in R, RMA method
Expressions estimated using RMA signal method

source_name: Human breast cancer

label_protocol: 3' IVT express

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

treatment_protocol: breast tumor samples, flash frozen

value: Breast cancer

tag: age (years)

value: Female

tag: race

value: Asian/Pacific Islander

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Discovery TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

tag: tumor grade

value: Poorly Differentiated

tag: positive nodes

tag: metastases

value: No mets

tag: tnbc subtype

value: Basal-Like Immune-Activated (BLIA)


title: 99-091N_LN CRPC metastasis

description: 99-091N CRPC lymph node metastasis

tag: gender

value: male

tag: tissue

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

tag: batch

tag: tumor type

value: CRPC metastasis

tag: tumor site

tag: patient


title: 99-091L_LN CRPC metastasis

description: 99-091L CRPC lymph node metastasis

value: LN


title: 99-069F_LUNG CRPC metastasis

description: 99-069F CRPC lung metastasis

value: LUNG


title: 99-091J_LN CRPC metastasis

description: 99-091J CRPC lymph node metastasis


title: S3-H186

description: log2 gene expression data

value: Breast cancer

tag: age (years)

tag: race

value: Caucasian

tag: body mass index

tag: menopausal status

value: Pre-Menopausal

tag: histology group

tag: tumor size

value: Basal-Like Immune-Suppressed (BLIS)


title: 98-328O_LIVER CRPC metastasis

description: 98-328O CRPC liver metastasis

value: LIVER


title: BE2C_tetoff_KDM4C_D-3

description: RNA expression value

source_name: BE2C_tetoff_KDM4C_D-6 days

tag: tumor cell line

value: Neuroblastoma

tag: cell line

tag: treatment


title: BE2C_tetoff_KDM4C_D+2

description: RNA expression value

value: doxycycline


title: 99-090A2_LIVER CRPC metastasis

description: 99-090A2 CRPC liver metastasis


title: S3-H187

description: log2 gene expression data

value: Female

value: Post-Menopausal

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Discovery TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

tag: tumor grade

value: Luminal-AR (LAR)


title: S3-H184

description: log2 gene expression data

tag: tissue

tag: gender

value: Poorly Differentiated

value: any size with direct extension

tag: positive nodes

tag: metastases

value: No mets

tag: tnbc subtype


title: 98-328J_LN CRPC metastasis

description: 98-328J CRPC lymph node metastasis

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

tag: batch

tag: tumor type

value: CRPC metastasis

tag: tumor site

value: LN

tag: patient


title: S3-H181

description: log2 gene expression data

value: Breast cancer

tag: age (years)

tag: race

value: Caucasian

tag: body mass index

tag: menopausal status

tag: histology group

tag: tumor size

value: Basal-Like Immune-Activated (BLIA)


title: 97-201K_LN CRPC metastasis

description: 97-201K CRPC lymph node metastasis

data_processing: Agilent Feature Extraction software versions 10.1.1.1 were used to grid and extract the data using the GE2-v5_10_Apr08 protocols with default settings. Data was loess normalized within arrays (normexp background correction with offset 50) and quantile normalized between arrays in R using the Limma Bioconductor package by batch. Control probes were removed, duplicate probes averaged, and spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers were assigned a value of NA. Data was normalized separately for LuCaP xenografts and CRPC metastases. CRPC metastases were subject to an additional normalization step to remove systematic batch effects due to date of RNA-amplification by application of the ComBat function within the sva Bioconductor package to the log2 Cy3 signal intensities. Batches are indicated in the ch2: characteristics: batch field and indicates RNA-amplification batch. Batch normalization was applied to a larger set of CRPC samples than those that appear in this study.


title: 97-201J_LN CRPC metastasis

description: 97-201J CRPC lymph node metastasis


title: 12-021H4_LIVER CRPC metastasis

description: 12-021H4 CRPC liver metastasis

value: LIVER


title: S3-H179

description: log2 gene expression data

value: Female

value: Pre-Menopausal

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

tag: pr

tag: triple-negative status


title: 97-201M_LN CRPC metastasis

description: 97-201M CRPC lymph node metastasis

tag: gender

tag: tissue


title: S3-H180

description: log2 gene expression data

value: Discovery TN

value: Negative

value: TN

tag: tumor grade

tag: positive nodes

tag: metastases

tag: tnbc subtype


title: 12-011J1_CAP CRPC primary/localized tumor

description: 12-011J1 CRPC bladder primary/localized tumor

tag: batch

tag: tumor type

value: CRPC primary/localized

tag: tumor site

value: BLADDER

tag: patient


title: S3-H182

description: log2 gene expression data

tag: age (years)

tag: race

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology group

value: Moderately Differentiated

tag: tumor size

value: No mets

value: Basal-Like Immune-Suppressed (BLIS)


title: 97-201I_CAP CRPC primary/localized tumor

description: 97-201I CRPC prostate primary/localized tumor

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

value: PROSTATE


title: 97-201D_LUNG CRPC metastasis

description: 97-201D CRPC lung metastasis

value: CRPC metastasis

value: LUNG


title: 97-201H_CAP CRPC primary/localized tumor

description: 97-201H CRPC bladder primary/localized tumor


title: S3-H175

description: log2 gene expression data

value: Breast cancer

value: Female

value: Caucasian

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

tag: pr

tag: triple-negative status

value: Poorly Differentiated

value: Basal-Like Immune-Activated (BLIA)


title: 12-011D26_CAP CRPC primary/localized tumor

description: 12-011D26 CRPC prostate primary/localized tumor

tag: gender

tag: tissue

value: CRPC primary/localized


title: 11-028L1_LUNG CRPC metastasis

description: 11-028L1 CRPC lung metastasis

tag: batch

tag: tumor type


title: 12-005K1_LUNG CRPC metastasis

description: 12-005K1 CRPC lung metastasis

tag: tumor site

tag: patient


title: 11-028G3_ADRENAL CRPC metastasis

description: 11-028G3 CRPC adrenal metastasis

value: ADRENAL


title: S3-H178

description: log2 gene expression data

tag: age (years)

tag: race

value: Post-Menopausal

value: Infiltrating Ductal Carcinoma

value: Discovery TN

value: Negative

value: TN

tag: tumor grade

tag: positive nodes

tag: metastases

tag: tnbc subtype


title: 10-039E3_LUNG CRPC metastasis

description: 10-039E3 CRPC lung metastasis

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines


title: S3-H173

description: log2 gene expression data

tag: body mass index

tag: menopausal status

value: Pre-Menopausal

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: tumor size

value: No mets

value: Basal-Like Immune-Suppressed (BLIS)


title: S3-H176

description: log2 gene expression data

tag: tissue

value: Breast cancer

tag: gender

tag: set

tag: er

tag: pr

tag: triple-negative status


title: S3-H174

description: log2 gene expression data

tag: age (years)

value: Female

tag: race

value: Mesenchymal (MES)


title: 12-011I7_LN CRPC metastasis

description: 12-011I7 CRPC lymph node metastasis

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

tag: batch

tag: tumor type

value: CRPC metastasis

tag: tumor site

value: LN

tag: patient


title: 10-013J2_LN CRPC metastasis

description: 10-013J2 CRPC lymph node metastasis


title: S3-H177

description: log2 gene expression data

value: Caucasian

tag: body mass index

tag: menopausal status

tag: tumor grade

value: Moderately Differentiated

tag: positive nodes

tag: metastases

tag: tnbc subtype

value: Luminal-AR (LAR)


title: 97-159H2_LIVER CRPC metastasis

description: 97-159H2 CRPC liver metastasis

tag: gender

tag: tissue

value: LIVER


title: S3-H189

description: log2 gene expression data

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Discovery TN

tag: er

value: Negative

value: Poorly Differentiated

tag: tumor size

value: Basal-Like Immune-Activated (BLIA)


title: 10-013G1_RETROPERITONEAL CRPC metastasis

description: 10-013G1 CRPC retroperitoneal metastasis

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

tag: batch

tag: tumor type

value: RETROPERITONEAL


title: S3-H170

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

tag: race

value: Pre-Menopausal

tag: pr

tag: triple-negative status

value: TN

value: No mets


title: S3-H185

description: log2 gene expression data

value: Caucasian

tag: body mass index

tag: menopausal status

tag: tumor grade

tag: positive nodes

value: Mesenchymal (MES)


title: 09-006F1_RENAL CRPC metastasis

description: 09-006F1 CRPC renal metastasis

tag: gender

tag: tissue

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

value: CRPC metastasis

tag: tumor site

value: RENAL

tag: patient


title: S3-H171

description: log2 gene expression data

value: Post-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Discovery TN

tag: metastases

tag: tnbc subtype


title: S3-H172

description: log2 gene expression data

tag: age (years)

tag: race

tag: er

value: Negative

value: Poorly Differentiated

tag: tumor size

value: Basal-Like Immune-Activated (BLIA)


title: 10-013F1_LN CRPC metastasis

description: 10-013F1 CRPC lymph node metastasis

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

tag: batch

tag: tumor type

value: LN


title: 08-093J1_LN CRPC metastasis

description: 08-093J1 CRPC lymph node metastasis


title: 08-020D1_CAP CRPC primary/localized tumor

description: 08-020D1 CRPC prostate primary/localized tumor

value: CRPC primary/localized

value: PROSTATE


title: S3-H168

description: log2 gene expression data

value: Breast cancer

value: Female

tag: body mass index

tag: menopausal status

tag: pr

tag: triple-negative status

value: TN

tag: tumor grade

value: No mets

value: Basal-Like Immune-Suppressed (BLIS)


title: S3-H167

description: log2 gene expression data

tag: tissue

tag: gender

value: Caucasian

tag: histology group

tag: positive nodes


title: 05-165O_ADRENAL CRPC metastasis

description: 05-165O CRPC adrenal metastasis

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

value: CRPC metastasis

tag: tumor site

value: ADRENAL

tag: patient


title: 12-005I2_LIVER CRPC metastasis

description: 12-005I2 CRPC liver metastasis

value: LIVER


title: 05-144Z1_LN CRPC metastasis

description: 05-144Z1 CRPC lymph node metastasis


title: S3-H163

description: log2 gene expression data

tag: age (years)

value: Pre-Menopausal

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Discovery TN

value: Negative

value: Poorly Differentiated

tag: metastases

tag: tnbc subtype


title: S3-H165

description: log2 gene expression data

tag: race

tag: body mass index

tag: er

tag: tumor size


title: S3-H164

description: log2 gene expression data

tag: menopausal status

value: Post-Menopausal

tag: pr

tag: triple-negative status

tag: tumor grade

value: Mesenchymal (MES)


title: 06-081K2_LN CRPC metastasis

description: 06-081K2 CRPC lymph node metastasis

tag: gender

value: male

tag: tissue

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

tag: batch

tag: tumor type

value: LN


title: 08-020N2_LN CRPC metastasis

description: 08-020N2 CRPC lymph node metastasis

tag: tumor site

tag: patient


title: S3-H166

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: TN

tag: positive nodes

value: No mets

value: Basal-Like Immune-Activated (BLIA)


title: 05-217OO3_BONE CRPC metastasis

description: 05-217OO3 CRPC bone metastasis

extract_protocol: The bone metastases which were frozen in OCT blocks were sampled using 1 mm diameter tissue punch in a -20oC cryostat. The sample was obtained from the region of the block where there was tumor based upon a section of an adjacent decalcified FFPE block. RNA was isolated from the tissue cores using RNeasy Plus Micro Kit (Qiagen Inc.). Tissue cores were placed in the kit’s Buffer RLT Plus, to which β-mercaptoethanol had been added, and homogenized with a disposable hard tissue homogenizer tip (Omni International). Total RNA was amplified two rounds with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

value: CRPC metastasis

value: BONE


title: 06-127H3_LN CRPC metastasis

description: 06-127H3 CRPC lymph node metastasis


title: 06-081D3_CAP CRPC primary/localized tumor

description: 06-081D3 CRPC prostate primary/localized tumor

value: CRPC primary/localized

value: PROSTATE


title: 06-081J1_LN CRPC metastasis

description: 06-081J1 CRPC lymph node metastasis


title: 06-081F2_LN CRPC metastasis

description: 06-081F2 CRPC lymph node metastasis


title: 05-187I1_CAP CRPC primary/localized tumor

description: 05-187I1 CRPC prostate primary/localized tumor


title: 05-214G1_LN CRPC metastasis

description: 05-214G1 CRPC lymph node metastasis


title: 06-081I1_LUNG CRPC metastasis

description: 06-081I1 CRPC lung metastasis

value: LUNG


title: 05-144W1_SPLEEN CRPC metastasis

description: 05-144W1 CRPC spleen metastasis

value: SPLEEN


title: 05-217N1_LN CRPC metastasis

description: 05-217N1 CRPC lymph node metastasis


title: S3-H162

description: log2 gene expression data

tag: race

value: Caucasian

tag: body mass index

value: Post-Menopausal

value: Infiltrating Ductal Carcinoma

value: Discovery TN

tag: er

value: Negative

value: Poorly Differentiated

tag: tumor size

tag: metastases

tag: tnbc subtype


title: 05-092H1_LN CRPC metastasis

description: 05-092H1 CRPC lymph node metastasis

tag: gender

value: male

tag: tissue

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: LN


title: 05-144V1_ADRENAL CRPC metastasis

description: 05-144V1 CRPC adrenal metastasis

tag: batch

tag: tumor type

value: ADRENAL


title: S3-H161

description: log2 gene expression data

value: Breast cancer

value: Female

value: Asian/Pacific Islander

tag: menopausal status

value: Pre-Menopausal

tag: pr

tag: triple-negative status

value: TN

tag: tumor grade

value: Basal-Like Immune-Activated (BLIA)


title: 05-144M1_LN CRPC metastasis

description: 05-144M1 CRPC lymph node metastasis

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

value: CRPC metastasis

tag: tumor site

tag: patient


title: S3-H160

description: log2 gene expression data

tag: age (years)

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Moderately Differentiated

tag: positive nodes

value: Basal-Like Immune-Suppressed (BLIS)


title: 05-144R1_CAP CRPC primary/localized tumor

description: 05-144R1 CRPC prostate primary/localized tumor

value: CRPC primary/localized

value: PROSTATE


title: 05-144I1_LN CRPC metastasis

description: 05-144I1 CRPC lymph node metastasis


title: 05-123E2_LN CRPC metastasis

description: 05-123E2 CRPC lymph node metastasis


title: 05-144H1_LN CRPC metastasis

description: 05-144H1 CRPC lymph node metastasis


title: 05-144K1_LUNG CRPC metastasis

description: 05-144K1 CRPC lung metastasis

value: LUNG


title: S3-H159

description: log2 gene expression data

tag: race

value: Caucasian

value: Post-Menopausal

value: Infiltrating Ductal Carcinoma

value: Discovery TN

tag: er

value: Negative

tag: tumor size

value: any size with direct extension

tag: metastases

value: No mets

tag: tnbc subtype

value: Luminal-AR (LAR)


title: 05-144U1_ADRENAL CRPC metastasis

description: 05-144U1 CRPC adrenal metastasis

tag: gender

value: male

tag: tissue

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

tag: batch

tag: tumor type

value: ADRENAL


title: S3-H156

description: log2 gene expression data

value: Breast cancer

value: Female

tag: pr

tag: triple-negative status

value: TN

tag: tumor grade

value: Poorly Differentiated

value: Basal-Like Immune-Activated (BLIA)


title: 05-123D1_CAP CRPC primary/localized tumor

description: 05-123D1 CRPC prostate primary/localized tumor

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

value: CRPC primary/localized

tag: tumor site

value: PROSTATE

tag: patient


title: S3-H157

description: log2 gene expression data

tag: age (years)

value: Caucasian

tag: menopausal status

value: Pre-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

value: Basal-Like Immune-Suppressed (BLIS)


title: 05-092G2_LUNG CRPC metastasis

description: 05-092G2 CRPC lung metastasis

value: CRPC metastasis

value: LUNG


title: 04-101N1_LN CRPC metastasis

description: 04-101N1 CRPC lymph node metastasis

value: male

value: LN


title: 05-092D1_CAP CRPC primary/localized tumor

description: 05-092D1 CRPC bladder primary/localized tumor

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: BLADDER


title: 05-144L1_LUNG CRPC metastasis

description: 05-144L1 CRPC lung metastasis


title: 04-112N1_CAP CRPC primary/localized tumor

description: 04-112N1 CRPC bladder primary/localized tumor


title: 04-112G3_LN CRPC metastasis

description: 04-112G3 CRPC lymph node metastasis


title: 04-149J1_CAP CRPC primary/localized tumor

description: 04-149J1 CRPC prostate primary/localized tumor


title: 04-101H1_PERITONEAL CRPC metastasis

description: 04-101H1 CRPC peritoneal metastasis

value: PERITONEAL


title: 04-112I1_LN CRPC metastasis

description: 04-112I1 CRPC lymph node metastasis


title: S3-H154

description: log2 gene expression data

value: Breast cancer

value: Female

tag: race

tag: body mass index

value: Post-Menopausal

value: Adenocarcinoma/Carcinoma, NOS

value: Invasive carcinoma of the breast

tag: set

value: Discovery TN

tag: er

value: Negative

value: TN

tag: tumor size

tag: positive nodes

value: Mesenchymal (MES)


title: S3-H155

description: log2 gene expression data

tag: tissue

tag: gender

value: Caucasian

value: Infiltrating Ductal Carcinoma

value: Poorly Differentiated

tag: metastases

value: No mets

tag: tnbc subtype

value: Luminal-AR (LAR)


title: S3-H158

description: log2 gene expression data

value: Pre-Menopausal

tag: pr

tag: triple-negative status

tag: tumor grade

value: Moderately Differentiated


title: S3-H152

description: log2 gene expression data

tag: age (years)

value: Basal-Like Immune-Suppressed (BLIS)


title: S3-H153

description: log2 gene expression data

value: Breast cancer

tag: menopausal status

tag: histology group


title: 04-101J1_LN CRPC metastasis

description: 04-101J1 CRPC lymph node metastasis

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

tag: batch

tag: tumor type

value: CRPC metastasis

tag: tumor site

value: LN

tag: patient


title: 04-101F2_CAP CRPC primary/localized tumor

description: 04-101F2 CRPC prostate primary/localized tumor

value: CRPC primary/localized

value: PROSTATE


title: S3-H146

description: log2 gene expression data

value: Female

tag: race

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Discovery TN

tag: er

value: Negative

value: TN

value: Well Differentiated


title: S3-H149

description: log2 gene expression data

tag: tissue

tag: gender

value: Caucasian

value: Infiltrating Ductal Carcinoma

value: Poorly Differentiated

tag: tumor size

tag: positive nodes

value: Basal-Like Immune-Activated (BLIA)


title: S3-H148

description: log2 gene expression data

value: Breast cancer

tag: pr

tag: triple-negative status

tag: tumor grade

tag: tnbc subtype

value: Basal-Like Immune-Suppressed (BLIS)


title: 04-050W1_LN CRPC metastasis

description: 04-050W1 CRPC lymph node metastasis

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

tag: batch


title: S3-H145

description: log2 gene expression data

tag: age (years)

tag: histology group


title: 04-050O2_CAP CRPC primary/localized tumor

description: 04-050O2 CRPC prostate primary/localized tumor

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

tag: tumor type

tag: tumor site

tag: patient


title: 03-192C2_LN CRPC metastasis

description: 03-192C2 CRPC lymph node metastasis

value: CRPC metastasis

value: LN


title: 04-050V1_LN CRPC metastasis

description: 04-050V1 CRPC lymph node metastasis


title: 03-192N2_CAP CRPC primary/localized tumor

description: 03-192N2 CRPC prostate primary/localized tumor

value: CRPC primary/localized

value: PROSTATE


title: patient 194715

city: Fort Collins

first: Daniel

middle: L

last: Gustafson

state: CO

address: 300 West Drake Rd

department: Clinical Sciences

institute: Colorado State University

description: Gene expression data of canine osteosarcoma tumors before treatment

hyb_protocol: Fragmented cRNA was hybridized onto GeneChips.  Hybridized chips were washed, stained and scanned using an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The Affymetrix GeneChip scanner 3000 7G was used to acquire images.

data_processing: Data was analyzed using RMA processing in Bioconductor (www.bioconductor.org)

organism: Canis lupus familiaris

source_name: COS33 tumor sample

label_protocol: The GeneChip® 3'IVT PLUS Reagent Kit (Affymetrix, Santa Clara, CA, USA) was used to synthesize cDNA from total RNA spiked wit hprokaryotic Poly-A RNA as a control.  Biotin-labeled cRNA was then synthesized, followed by cRNA purification and fragmentation according to manufactures protocols.

growth_protocol: Primary tumor collected at time of limb amputation

extract_protocol: Freeze fracture of samples followed by Trizol extraction according to manufacturer's protocols.Resulting RNA was then ran through RNEasy Cleanup protocol from Qiagen.

treatment_protocol: Tumor biopsies at time of presentation were either flash frozen or placed in RNALater before being stored in -80 degree freezers.

value: canine osteosarcoma tumor


title: S3-H143

description: log2 gene expression data

value: Female

tag: race

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology

tag: ajcc stage (7th edition, 2010)

value: Discovery TN

value: Negative

value: Moderately Differentiated

tag: metastases

value: No mets

value: Luminal-AR (LAR)


title: 04-050R1_LN CRPC metastasis

description: 04-050R1 CRPC lymph node metastasis

tag: gender

tag: tissue


title: 04-050N1_CAP CRPC primary/localized tumor

description: 04-050N1 CRPC prostate primary/localized tumor


title: patient 221908


title: S3-H141

description: log2 gene expression data

value: Breast cancer

value: Caucasian

value: Adenocarcinoma/Carcinoma, NOS

value: Adenocarcinoma/Carcinoma, NOS (Probable infiltrating ductal carcinoma)

tag: set

value: Validation TN

tag: er

tag: pr

tag: triple-negative status

value: TN

value: Poorly Differentiated

tag: tumor size

tag: positive nodes

value: Basal-Like Immune-Activated (BLIA)


title: 03-192B2_LUNG CRPC metastasis

description: 03-192B2 CRPC lung metastasis

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

tag: batch

tag: tumor type

value: CRPC metastasis

value: LUNG


title: patient 217020

value: canine osteosarcoma tumor


title: 04-050G2_LN CRPC metastasis

description: 04-050G2 CRPC lymph node metastasis

tag: tumor site

value: LN

tag: patient


title: patient 222189


title: S3-H147

description: log2 gene expression data

tag: age (years)

value: Female

tag: race

tag: histology group

value: Infiltrating Ductal Carcinoma

value: Discovery TN

value: Negative

tag: tumor grade

tag: tnbc subtype


title: S3-H150

description: log2 gene expression data

value: Breast cancer

tag: gender

value: Caucasian

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: metastases

value: Mets found

value: Basal-Like Immune-Suppressed (BLIS)


title: S3-H142

description: log2 gene expression data

tag: tissue

value: Pre-Menopausal

tag: set

value: Validation TN

tag: er

tag: pr

tag: triple-negative status

value: TN

tag: tumor size

value: Mesenchymal (MES)


title: S3-H144

description: log2 gene expression data

tag: age (years)

value: Moderately Differentiated

value: No mets

value: Luminal-AR (LAR)


title: patient 239636

value: canine osteosarcoma tumor


title: patient 245591


title: S3-H140

description: log2 gene expression data

value: Female

tag: race

value: Poorly Differentiated

tag: positive nodes

value: Basal-Like Immune-Activated (BLIA)


title: 03-139M9_RETROPERITONEAL CRPC metastasis

description: 03-139M9 CRPC retroperitoneal metastasis

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

tag: batch

tag: tumor type

value: CRPC metastasis

tag: tumor site

value: RETROPERITONEAL

tag: patient


title: S3-H138

description: log2 gene expression data

value: Breast cancer

tag: gender

value: Caucasian

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

value: Negative

tag: tumor grade

tag: tnbc subtype

value: Basal-Like Immune-Suppressed (BLIS)


title: 03-082OO_BONE CRPC metastasis

description: 03-082OO CRPC bone metastasis

tag: tissue

value: BONE


title: S3-H137

description: log2 gene expression data

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

tag: er

tag: pr

value: TN

tag: metastases

value: No mets


title: patient 214376

value: canine osteosarcoma tumor


title: patient 260710


title: S3-H136

description: log2 gene expression data

tag: age (years)

value: Female

tag: race

tag: triple-negative status

value: Poorly Differentiated

tag: tumor size

tag: positive nodes

value: Mesenchymal (MES)


title: 03-082K2_LN CRPC metastasis

description: 03-082K2 CRPC lymph node metastasis

tag: gender

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

tag: batch

tag: tumor type

tag: tumor site

value: LN

tag: patient


title: 03-081L_LN CRPC metastasis

description: 03-081L CRPC lymph node metastasis

tag: tissue

value: CRPC metastasis


title: S3-H135

description: log2 gene expression data

value: Breast cancer

value: Caucasian

tag: body mass index

tag: histology group

tag: histology

tag: tumor grade

tag: tnbc subtype


title: patient 240749


title: S3-H134

description: log2 gene expression data

tag: menopausal status

value: Pre-Menopausal

value: Infiltrating Ductal Carcinoma

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

value: Negative

tag: pr

tag: metastases

value: Basal-Like Immune-Activated (BLIA)


title: patient 237298


title: 02-065P3_CAP CRPC primary/localized tumor

description: 02-065P3 CRPC prostate primary/localized tumor

tag: gender

value: CRPC primary/localized

value: PROSTATE


title: 02-065W2_SCROTUM CRPC metastasis

description: 02-065W2 CRPC scrotum metastasis

tag: batch

value: SCROTUM


title: 03-027M1_LUNG CRPC metastasis

description: 03-027M1 CRPC lung metastasis

tag: tumor type

value: LUNG


title: 03-130M4_LIVER CRPC metastasis

description: 03-130M4 CRPC liver metastasis

tag: tumor site

value: LIVER


title: S3-H139

description: log2 gene expression data

tag: age (years)

value: Female

tag: race

value: Validation TN

tag: triple-negative status

value: TN

value: Poorly Differentiated

tag: tumor size

tag: positive nodes

value: No mets

value: Basal-Like Immune-Suppressed (BLIS)


title: patient 258525

tag: tissue

value: canine osteosarcoma tumor


title: 02-083D1_LUNG CRPC metastasis

description: 02-083D1 CRPC lung metastasis

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

value: CRPC metastasis

tag: patient


title: S3-H132

description: log2 gene expression data

value: Breast cancer

value: Caucasian

tag: menopausal status

value: Post-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

value: Negative

tag: tumor grade

value: Moderately Differentiated

tag: tnbc subtype


title: patient 195371


title: S3-H133

description: log2 gene expression data

value: Female

value: Pre-Menopausal

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

tag: pr

value: any size with direct extension

tag: metastases

value: Luminal-AR (LAR)


title: patient 252352


title: patient 239929


title: patient 258688


title: patient 236226


title: 02-065N1_SKIN CRPC metastasis

description: 02-065N1 CRPC skin metastasis

tag: gender

tag: batch

tag: tumor type

tag: tumor site

value: SKIN


title: S3-H130

description: log2 gene expression data

tag: age (years)

tag: race

tag: body mass index

value: TXNXMX

value: Validation TN

tag: triple-negative status

value: TN

value: Poorly Differentiated

value: Basal-Like Immune-Activated (BLIA)


title: patient 235194

tag: tissue

value: canine osteosarcoma tumor


title: patient 174094


title: S3-H127

description: log2 gene expression data

value: Breast cancer

tag: menopausal status

tag: histology group

tag: histology

tag: tumor size

tag: positive nodes

value: No mets

value: Basal-Like Immune-Suppressed (BLIS)


title: patient 232031


title: patient 221347


title: S3-H129

description: log2 gene expression data

value: Caucasian

value: Infiltrating Ductal Carcinoma

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

tag: tumor grade

tag: tnbc subtype


title: patient 224989


title: patient 235468


title: patient 221562


title: S3-H125

description: log2 gene expression data

tag: gender

value: Negative

tag: pr

value: Moderately Differentiated


title: S3-H124

description: log2 gene expression data

tag: age (years)

value: Female

value: Asian

tag: metastases

value: Mesenchymal (MES)


title: S3-H126

description: log2 gene expression data

tag: race

tag: body mass index

value: Post-Menopausal


title: patient 220762

tag: tissue


title: S3-H123

description: log2 gene expression data

tag: triple-negative status


title: S3-H122

description: log2 gene expression data

tag: menopausal status

value: Pre-Menopausal

tag: histology group

value: Luminal-AR (LAR)


title: S3-H128

description: log2 gene expression data

tag: histology

value: Validation TN

value: TN

tag: tumor size


title: patient 219598


title: S3-H151

description: log2 gene expression data

tag: ajcc stage (7th edition, 2010)

value: Discovery TN

tag: positive nodes


title: S3-H120

description: log2 gene expression data

tag: set

tag: er

value: Poorly Differentiated


title: S3-H121

description: log2 gene expression data

value: Breast cancer

tag: tumor grade

value: Mets found

tag: tnbc subtype


title: S3-H118

description: log2 gene expression data

tag: gender

tag: pr

value: No mets


title: patient 212456

value: canine osteosarcoma tumor


title: S3-H119

description: log2 gene expression data

tag: age (years)

value: Caucasian

value: Adenocarcinoma/Carcinoma, NOS

value: Invasive carcinoma of the breast with neuroendocrine features

tag: metastases

value: Basal-Like Immune-Suppressed (BLIS)


title: ALZ_AD_F_W_50

type: genomic

city: New York

first: Andrew

last: Sharp

state: NY

address: 1470 Madison Av

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner protocol

data_processing: The methylation value was set to null for probes with a detection p-value >0.01. Probe sequences (50-mer oligonucleotides) were uniquely mapped to the reference human genome hg18 (NCBI36) using BLAT, allowing up to 2 mismatches and 1 gap. Beta values from the autosomal probes were quantile normalized using lumi package in R.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Superior Temporal Gyrus (bulk tissue)

label_protocol: Standard Illumina labelling protocol

extract_protocol: STG tissue samples were subjected to proteinase K digestion and treatment with RNAse A. Genomic DNA was then isolated using standard phenol/chloroform extraction and ethanol precipitation methods.

value: Superior Temporal Gyrus

tag: disease

value: Alzheimers Disease

value: F

tag: age

value: 85 years

tag: race

tag: neuronal proportion


title: patient 219075

tag: tissue


title: ALZ_AD_F_W_392

value: 80 years


title: patient 212126


title: patient 146719


title: S3-H116

description: log2 gene expression data

value: Female

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

value: Validation TN

value: Negative

tag: triple-negative status

value: Basal-Like Immune-Activated (BLIA)


title: ALZ_AD_M_W_566

value: M

value: 83 years


title: patient 218959

value: canine osteosarcoma tumor


title: S3-H117

description: log2 gene expression data

value: Breast cancer

value: Caucasian

value: Adenocarcinoma/Carcinoma, NOS

value: Invasive mammary carcinoma

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

value: TN

value: Poorly Differentiated

tag: tumor size

tag: positive nodes

value: No mets


title: ALZ_NL_F_W_86

value: Superior Temporal Gyrus

value: Control

tag: gender

value: F

value: 67 years


title: ALZ_AD_M_W_755

value: Alzheimers Disease

value: 87 years


title: 03-192F3_LUNG CRPC metastasis

description: 03-192F3 CRPC lung metastasis

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

tag: batch

tag: tumor type

value: CRPC metastasis

tag: tumor site

value: LUNG

tag: patient


title: ALZ_NL_F_B_1040

tag: disease

tag: age

value: 74 years

tag: race

value: AfricanAmerica

tag: neuronal proportion


title: ALZ_NL_F_W_800

tag: tissue

value: 89 years

value: Caucasian


title: S3-H131

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

tag: body mass index

tag: menopausal status

value: Pre-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

value: Validation TN

value: Negative

tag: pr

value: TN

tag: tumor grade

value: Moderately Differentiated

tag: metastases

tag: tnbc subtype

value: Basal-Like Immune-Suppressed (BLIS)


title: ALZ_NL_M_W_1439

value: Superior Temporal Gyrus

value: Control

tag: gender

value: M

value: 66 years


title: patient 205677

value: canine osteosarcoma tumor


title: patient 208768


title: S3-H115

description: log2 gene expression data

value: Menopausal

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

tag: triple-negative status

tag: tumor size

value: No mets

value: Luminal-AR (LAR)


title: S3-H114

description: log2 gene expression data

value: Breast cancer

tag: race

value: Caucasian

value: Post-Menopausal


title: S3-H113

description: log2 gene expression data

tag: tissue

value: Female

value: Infiltrating Ductal Carcinoma


title: Vogel

description:
ACC28
Gene expression data of treatment naïve canine cancer cell lines

source_name: canine cancer cell line

growth_protocol: All cells were maintained in RPMI 1640 culture medium containing 10% fetal bovine serum (FBS), penicillin (100 units/mL), streptomycin (100 ug/mL) and incubated at 37°C in a humidified atmosphere of 5% CO2:95% air.

extract_protocol: RNA was extracted using Qiagen's Rneasy Mini kit (Qiagen, Valencia, CA) according to manufacturer's protocols.

treatment_protocol: RNA from drug naïve cell lines were extracted and subjected to microarray analysis.

tag: cell line

value: Vogel

tag: tumor type

value: osteosarcoma


title: STSA_1

description:
ACC27
Gene expression data of treatment naïve canine cancer cell lines

value: soft tissue sarcoma


title: Yamane

description:
ACC29
Gene expression data of treatment naïve canine cancer cell lines

value: Yamane


title: ALZ_AD_M_W_856

value: Superior Temporal Gyrus

tag: disease

value: Alzheimers Disease

tag: age

value: 83 years

tag: neuronal proportion


title: S3-H110

description: log2 gene expression data

tag: age (years)

tag: body mass index

tag: menopausal status

tag: histology group

tag: histology

value: Validation TN

value: Negative

tag: pr

value: TN

value: Moderately Differentiated

tag: positive nodes


title: S3-H111

description: log2 gene expression data

tag: gender

value: Pre-Menopausal

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

tag: tnbc subtype

value: Basal-Like Immune-Suppressed (BLIS)


title: ALZ_AD_F_W_790

tag: tissue

value: F

value: 73 years

tag: race

value: Caucasian


title: ALZ_NL_M_H_1348

tag: disease

value: Control

value: M

value: 80 years

value: Hispanic


title: Oswald

description:
ACC26
Gene expression data of treatment naïve canine cancer cell lines

tag: cell line

value: Oswald

tag: tumor type

value: lymphoma


title: ALZ_NL_M_A_1088

value: Superior Temporal Gyrus

tag: age

value: Asian

tag: neuronal proportion


title: ALZ_NL_F_W_1049

value: 90 years


title: ALZ_NL_F_W_884

value: 81 years


title: patient 160898

value: canine osteosarcoma tumor


title: S3-H106

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

tag: body mass index

tag: menopausal status

value: Post-Menopausal

value: Infiltrating Ductal Carcinoma

value: Validation TN

value: Negative

tag: triple-negative status

value: TN

tag: tumor grade

value: Moderately Differentiated

tag: tumor size

value: Luminal-AR (LAR)


title: S3-H108

description: log2 gene expression data

tag: gender

value: Caucasian

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: pr

value: any size with direct extension

tag: positive nodes

tag: metastases

value: No mets


title: OS2_4

description:
ACC24
Gene expression data of treatment naïve canine cancer cell lines

tag: cell line

value: osteosarcoma


title: S3-H105

description: log2 gene expression data

tag: tissue

tag: race

value: Asian

tag: set

tag: er

tag: tnbc subtype

value: Basal-Like Immune-Suppressed (BLIS)


title: Nike

description:
ACC23
Gene expression data of treatment naïve canine cancer cell lines

value: Nike

tag: tumor type

value: histiocytosis


title: S3-H103

description: log2 gene expression data

value: Breast cancer

tag: age (years)

tag: menopausal status

value: Pre-Menopausal

value: Adenocarcinoma/Carcinoma, NOS

value: Adenocarcinoma of the breast

tag: triple-negative status


title: S3-H107

description: log2 gene expression data

tag: gender

value: Female

tag: body mass index

value: Post-Menopausal

value: Infiltrating Ductal Carcinoma

value: Validation TN

tag: tumor size


title: S3-H109

description: log2 gene expression data

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

value: Negative

value: TN

tag: tumor grade

value: Poorly Differentiated

value: Basal-Like Immune-Activated (BLIA)


title: S3-H104

description: log2 gene expression data

value: Caucasian

tag: pr

value: Well Differentiated

tag: positive nodes

tag: metastases

value: No mets

value: Mesenchymal (MES)


title: Mackinley

description:
ACC21
Gene expression data of treatment naïve canine cancer cell lines

tag: cell line

value: Mackinley

value: osteosarcoma


title: OSA8

description:
ACC25
Gene expression data of treatment naïve canine cancer cell lines


title: Moresco

description:
ACC22
Gene expression data of treatment naïve canine cancer cell lines

value: Moresco

value: soft tissue sarcoma


title: K9TCC

description:
ACC20
Gene expression data of treatment naïve canine cancer cell lines

value: transitional cell carcinoma


title: Jones

description:
ACC19
Gene expression data of treatment naïve canine cancer cell lines

value: Jones

value: melanoma


title: ALZ_NL_M_B_1349

tag: tissue

value: Superior Temporal Gyrus

tag: disease

value: Control

value: F

tag: age

value: 94 years

tag: race

value: AfricanAmerica

tag: neuronal proportion


title: ALZ_AD_M_W_637

value: Alzheimers Disease

value: M

value: 67 years


title: S3-H100

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

value: Caucasian

tag: menopausal status

value: Pre-Menopausal

value: Infiltrating Ductal Carcinoma

tag: set

value: Validation TN

tag: er

value: Negative

tag: triple-negative status

value: TN

value: Poorly Differentiated

tag: tnbc subtype


title: ALZ_AD_M_W_435

value: Superior Temporal Gyrus

tag: gender

value: 81 years


title: S3-H102

description: log2 gene expression data

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: tumor size

value: Basal-Like Immune-Activated (BLIA)


title: ALZ_AD_F_W_342

value: F

value: 79 years


title: ALZ_NL_F_W_121

value: Control

value: 78 years


title: ALZ_AD_M_W_877

value: Alzheimers Disease

value: M

value: 80 years


title: Gracie

description:
ACC17
Gene expression data of treatment naïve canine cancer cell lines

tag: cell line

value: Gracie

tag: tumor type

value: osteosarcoma


title: DH82

description:
ACC15
Gene expression data of treatment naïve canine cancer cell lines

value: histiocytosis


title: S2-H91B

description: log2 gene expression data

tag: tissue

value: Breast cancer

value: Female

value: Caucasian

tag: body mass index

value: Menopausal

value: Infiltrating Ductal Carcinoma

value: Validation TN

tag: pr

tag: tumor grade

value: Moderately Differentiated

tag: positive nodes

tag: metastases

value: No mets


title: S2-H90

description: log2 gene expression data

tag: age (years)

tag: race

tag: menopausal status

value: Post-Menopausal

tag: set

value: Negative

value: TN

value: Basal-Like Immune-Suppressed (BLIS)


title: HMPOS

description:
ACC18
Gene expression data of treatment naïve canine cancer cell lines

value: HMPOS


title: Fitz

description:
ACC16
Gene expression data of treatment naïve canine cancer cell lines

value: Fitz

value: hemangiosarcoma


title: ALZ_NL_M_W_1250

value: Superior Temporal Gyrus

tag: disease

value: Control

tag: gender

value: M

tag: age

value: 84 years

tag: neuronal proportion


title: S2-H89

description: log2 gene expression data

value: Breast cancer

value: Female

value: Caucasian

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: er

tag: triple-negative status

value: Poorly Differentiated

tag: tumor size

tag: tnbc subtype

value: Mesenchymal (MES)


title: ALZ_NL_F_H_1131

tag: tissue

value: F

value: 81 years

value: Hispanic


title: S2-H88

description: log2 gene expression data

tag: body mass index

value: Pre-Menopausal

value: Infiltrating Ductal Carcinoma

value: Validation TN

value: Negative

tag: pr

value: TN

tag: tumor grade

tag: positive nodes

tag: metastases

value: No mets

value: Basal-Like Immune-Activated (BLIA)


title: D17

description:
ACC13
Gene expression data of treatment naïve canine cancer cell lines

tag: cell line

tag: tumor type

value: osteosarcoma


title: S2-H85B

description: log2 gene expression data

tag: age (years)

tag: gender

tag: race

tag: menopausal status

tag: set


title: DEN-HSA

description:
ACC14
Gene expression data of treatment naïve canine cancer cell lines

value: DEN-HSA

value: hemangiosarcoma


title: ALZ_AD_F_H_475.1

value: Superior Temporal Gyrus

tag: disease

value: Alzheimers Disease

tag: age

value: 67 years

tag: neuronal proportion


title: ALZ_NL_M_W_94

value: Control

value: M

value: 89 years

value: Caucasian


title: S2-H84

description: log2 gene expression data

value: Breast cancer

value: Female

value: Menopausal

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: er

tag: triple-negative status

tag: tumor size

tag: tnbc subtype


title: ALZ_AD_F_W_77

tag: tissue

value: F

value: 76 years


title: ALZ_AD_F_W_76

value: 84 years


title: CML_10C2

description:
ACC9
Gene expression data of treatment naïve canine cancer cell lines

tag: cell line

tag: tumor type

value: melanoma


title: CMT12

description:
ACC11
Gene expression data of treatment naïve canine cancer cell lines

value: mammary tumor


title: ALZ_AD_M_W_6

tag: gender

value: 71 years


title: CLL1390

description:
ACC8
Gene expression data of treatment naïve canine cancer cell lines

value: leukemia


title: CML_6M

description:
ACC10
Gene expression data of treatment naïve canine cancer cell lines


title: CMT27

description:
ACC12
Gene expression data of treatment naïve canine cancer cell lines


title: S2-H81

description: log2 gene expression data

tag: age (years)

tag: race

tag: body mass index

value: Pre-Menopausal

value: Infiltrating Ductal Carcinoma

value: Validation TN

value: Negative

tag: pr

value: TN

tag: tumor grade

value: Poorly Differentiated

tag: positive nodes

tag: metastases

value: No mets

value: Basal-Like Immune-Suppressed (BLIS)


title: CLBL1

description:
ACC7
Gene expression data of treatment naïve canine cancer cell lines

value: lymphoma


title: S2-H83

description: log2 gene expression data

value: Breast cancer

value: Female

value: Caucasian

tag: menopausal status

value: Post-Menopausal

tag: histology group

tag: histology

tag: set

value: Luminal-AR (LAR)


title: S2-H80

description: log2 gene expression data

tag: ajcc stage (7th edition, 2010)

tag: er

tag: triple-negative status

tag: tumor size


title: S2-H79

description: log2 gene expression data

tag: tissue

value: Moderately Differentiated

tag: tnbc subtype


title: C2

description:
ACC6
Gene expression data of treatment naïve canine cancer cell lines

tag: cell line

tag: tumor type

value: mast cell


title: ALZ_NL_F_W_1478

value: Superior Temporal Gyrus

tag: disease

value: Control

tag: gender

value: F

tag: age

value: 86 years

tag: race

tag: neuronal proportion


title: ALZ_NL_M_W_1054

value: M

value: 92 years


title: ALZ_AD_M_W_479

value: Alzheimers Disease

value: 74 years


title: ALZ_AD_M_W_1416

value: 66 years


title: ALZ_AD_F_W_482

value: 79 years


title: S2-H78

description: log2 gene expression data

value: Breast cancer

tag: age (years)

tag: body mass index

value: Infiltrating Ductal Carcinoma

value: Validation TN

value: Negative

tag: pr

value: TN

tag: tumor grade

value: Poorly Differentiated

value: any size with direct extension

tag: positive nodes

tag: metastases

value: No mets

value: Basal-Like Immune-Activated (BLIA)


title: ALZ_NL_M_B_1028

value: Superior Temporal Gyrus

value: Control

value: 88 years

value: AfricanAmerica


title: ALZ_NL_M_W_46

value: M

value: Caucasian


title: Bliley

description:
ACC4
Gene expression data of treatment naïve canine cancer cell lines

value: Bliley

value: transitional cell carcinoma


title: S2-H76

description: log2 gene expression data

value: Breast cancer

value: Female

tag: menopausal status

value: Post-Menopausal

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

tag: triple-negative status

value: Basal-Like Immune-Suppressed (BLIS)


title: S2-H57C

description: log2 gene expression data

tag: tissue

tag: gender

value: Infiltrating Ductal Carcinoma

value: Validation TN

value: Negative

value: TN

value: Moderately Differentiated

tag: tumor size

tag: tnbc subtype


title: 17CM98at

description:
ACC2
Gene expression data of treatment naïve canine cancer cell lines

tag: cell line

tag: tumor type

value: melanoma


title: ALZ_NL_F_W_1263

value: Superior Temporal Gyrus

tag: disease

value: Control

value: F

tag: age

value: 73 years

tag: race

tag: neuronal proportion


title: ALZ_AD_M_W_49

value: Alzheimers Disease

value: M

value: 76 years

value: Caucasian


title: S2-H77

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

tag: body mass index

tag: menopausal status

tag: pr

tag: positive nodes

tag: metastases

value: No mets


title: 1771

description:
ACC1
Gene expression data of treatment naïve canine cancer cell lines

value: lymphoma


title: ALZ_AD_F_W_176

value: 72 years


title: C_TAC

description:
ACC5
Gene expression data of treatment naïve canine cancer cell lines

value: thyroid adenocarcinoma


title: ALZ_NL_M_H_1248

value: 83 years

value: Hispanic


title: S2-H56B

description: log2 gene expression data

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

tag: er

value: Negative

tag: triple-negative status

value: TN

tag: tumor grade

value: Poorly Differentiated

value: Luminal-AR (LAR)


title: S2-H82

description: log2 gene expression data

tag: tissue

tag: gender

value: Post-Menopausal

tag: tumor size

tag: tnbc subtype

value: Basal-Like Immune-Activated (BLIA)


title: Abrams

description:
ACC3
Gene expression data of treatment naïve canine cancer cell lines

tag: cell line

value: Abrams

tag: tumor type

value: osteosarcoma


title: S2-H54B

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

tag: race

value: Caucasian

tag: body mass index

tag: menopausal status


title: S2-H55B

description: log2 gene expression data

value: Pre-Menopausal

tag: histology group

tag: pr

value: any size with direct extension

tag: positive nodes

tag: metastases

value: No mets


title: S1-H73

description: log2 gene expression data

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

value: Basal-Like Immune-Suppressed (BLIS)


title: S1-H72B

description: log2 gene expression data

tag: tissue

tag: gender

value: Infiltrating Ductal Carcinoma

tag: triple-negative status

tag: tumor grade

value: Moderately Differentiated


title: S1-H8

description: log2 gene expression data

value: Validation TN

value: Negative

tag: tumor size

tag: tnbc subtype

value: Mesenchymal (MES)


title: EC50_21 (3_4_G)

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

description:
US22502676_254227910009_S01_GE2_107_Sep09_1_4.txt
total RNA from 5 - 7 animals

hyb_protocol: 825 ng of Cy3-labeled or Cy5-labeled cRNA (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with 4x180k format for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm)  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), washed in acetonitril for 10 seconds, then dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red & Green and PMT is set to 100%.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 042279_D_F_20120723) to obtain mean Red or Green intensities and median Red or Green background intensities. In limma, edwards method for background correction was used (offset = 30), and global loess normalizing was done.

organism: Enchytraeus crypticus

source_name: phenanthrene, EC50, 21 days

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 500 ng total RNA using the Low Input Quick Amp Labeling Kit, two-color (Agilent Technologies) according to the manufacturer's guidelines followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from all animals, using the SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 5 - 7 adult animals which had a visible clitellum were exposed for 4 days in glass jars containing ~30 g of soil at 50% of the soil WHC. Exposure was done at same conditions as incubation. After exposure the animals were extracted from soil with tap water via floatation, put in 1.5 mL tubes and frozen in liquid N2.

tag: soil

value: LUFA2.2 control soil

tag: agent

value: phenanthrene

tag: concentration

tag: time

value: 21 days


title: ALZ_AD_F_W_708

value: Superior Temporal Gyrus

tag: disease

value: Alzheimers Disease

value: F

tag: age

value: 78 years

tag: race

tag: neuronal proportion


title: S1-H71

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

value: Caucasian

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: pr

value: TN

value: Well Differentiated


title: ALZ_NL_F_W_1264

tag: tissue

value: Control

tag: gender

value: 67 years


title: S1-H70

description: log2 gene expression data

value: Pre-Menopausal

value: Infiltrating Ductal Carcinoma

tag: set

value: Validation TN

tag: er

value: Negative

tag: triple-negative status

tag: tumor grade

value: Poorly Differentiated

tag: tumor size

tag: metastases

value: No mets

tag: tnbc subtype


title: ALZ_NL_F_W_532

value: Superior Temporal Gyrus

tag: disease

tag: age

value: 92 years

tag: race

tag: neuronal proportion


title: PMEC_45

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data was analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

organism: Sus scrofa

source_name: PMEC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: Primary cell cultures were established from mammary glands of three lactating sows of commercial herds. 4.4 x 10E5 of the isolated mammary epithelial cells from every individual (three biological replicates) were seeded and cultured in collagen-coated 6-well plates in complete medium without APS (three technical replicates per individual and treatment condition).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Primary mammary epithelial cells (PMEC) were treated with 10E7/ml heat-inactivated S. aureus and E. coli, respectively, for 3 h and for 24 h.

tag: biological replicates

value: ANIMAL_3 III

tag: treatment

value: S. aureus

tag: time


title: EC10_21 (3_4_R)

source_name: phenanthrene, EC10, 21 days

tag: soil

value: LUFA2.2 control soil

tag: agent

value: phenanthrene

tag: concentration

value: 21 days


title: ALZ_AD_F_H_944

tag: tissue

value: Alzheimers Disease

tag: gender

value: F

value: 72 years

value: Hispanic


title: S1-H7

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

value: Caucasian

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

tag: pr

tag: triple-negative status

value: TN

tag: positive nodes

value: Basal-Like Immune-Suppressed (BLIS)


title: ALZ_AD_F_W_183

value: Superior Temporal Gyrus

tag: disease

tag: age

tag: race

tag: neuronal proportion


title: PMEC_44

tag: biological replicates

value: ANIMAL_3 II

tag: treatment

tag: time


title: ALZ_AD_M_W_45

tag: tissue

tag: gender

value: M

value: 82 years


title: EC10_2 (3_3_G)

description:
US22502676_254227910009_S01_GE2_107_Sep09_1_3.txt
total RNA from 5 - 7 animals

source_name: phenanthrene, EC10, 2 days

tag: soil

value: LUFA2.2 control soil

tag: agent

tag: concentration

value: 2 days


title: CTR_2 (3_3_R)

source_name: CTR, 2 days

value: control


title: PMEC_43

value: ANIMAL_3 I

value: S. aureus


title: S1-H9

description: log2 gene expression data

tag: age (years)

tag: body mass index

tag: menopausal status

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

value: Negative

tag: tumor grade

value: Poorly Differentiated

tag: tumor size

tag: metastases

value: No mets

tag: tnbc subtype

value: Basal-Like Immune-Activated (BLIA)


title: S1-H68

description: log2 gene expression data

value: Breast cancer

value: Female

tag: race

value: Caucasian

value: Post-Menopausal

tag: er

tag: pr

tag: triple-negative status

value: TN


title: ALZ_NL_M_W_1343

tag: tissue

value: Superior Temporal Gyrus

tag: disease

value: Control

tag: gender

value: M

tag: age

value: 70 years

tag: neuronal proportion


title: ALZ_NL_F_H_673

value: F

value: 79 years

value: Hispanic


title: ALZ_AD_M_W_462

value: Alzheimers Disease

value: 87 years


title: S1-H69

description: log2 gene expression data

tag: age (years)

tag: body mass index

tag: menopausal status

tag: histology group

value: Infiltrating Ductal Carcinoma

value: Validation TN

value: Negative

value: Poorly Differentiated

value: Mesenchymal (MES)


title: PMEC_42

tag: biological replicates

value: ANIMAL_2 III

tag: treatment

value: S. aureus

tag: time


title: ALZ_NL_F_W_1050

value: 78 years

value: Caucasian


title: CTR_21 (3_2_G)

description:
US22502676_254227910009_S01_GE2_107_Sep09_1_2.txt
total RNA from 5 - 7 animals

source_name: CTR, 21 days

tag: soil

value: LUFA2.2 control soil

tag: agent

value: control

tag: concentration

value: 21 days


title: ALZ_AD_F_W_119

value: Superior Temporal Gyrus

value: F

value: 82 years

tag: race


title: S1-H67

description: log2 gene expression data

value: Breast cancer

value: Female

value: Pre-Menopausal

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

tag: pr

tag: triple-negative status

value: TN

tag: tumor grade

tag: tumor size

tag: tnbc subtype

value: Basal-Like Immune-Activated (BLIA)


title: EC50_21 (3_2_R)

value: phenanthrene


title: ALZ_NL_M_B_1056

tag: tissue

tag: disease

value: Control

tag: gender

value: M

tag: age

value: 68 years

value: AfricanAmerica

tag: neuronal proportion


title: PMEC_41

tag: biological replicates

value: ANIMAL_2 II

tag: treatment

value: S. aureus

tag: time


title: ALZ_AD_F_U_31

value: Alzheimers Disease

value: 88 years

tag: race

value: Unknown


title: PMEC_40

value: ANIMAL_2 I


title: EC50_2 (3_1_G)

description:
US22502676_254227910009_S01_GE2_107_Sep09_1_1.txt
total RNA from 5 - 7 animals

source_name: phenanthrene, EC50, 2 days

tag: soil

value: LUFA2.2 control soil

tag: agent

tag: concentration

value: 2 days


title: PMEC_39

value: ANIMAL_1 III


title: S1-H66

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

value: Caucasian

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

tag: er

value: Negative

tag: pr

value: Poorly Differentiated

tag: positive nodes


title: S1-H65

description: log2 gene expression data

tag: tissue

tag: gender

value: Menopausal

tag: triple-negative status

value: TN

tag: tumor size

tag: metastases

value: No mets

tag: tnbc subtype

value: Basal-Like Immune-Suppressed (BLIS)


title: ALZ_AD_M_W_66

value: Superior Temporal Gyrus

tag: disease

value: Alzheimers Disease

value: M

tag: age

value: 89 years

tag: race

tag: neuronal proportion


title: S1-H64

description: log2 gene expression data

tag: age (years)

tag: body mass index

tag: menopausal status

tag: histology group

tag: tumor grade

value: Luminal-AR (LAR)


title: EC10_21 (2_4_G)

description:
US22502676_254227910008_S01_GE2_107_Sep09_1_4.txt
total RNA from 5 - 7 animals

tag: soil

value: LUFA2.2 control soil

tag: agent

value: phenanthrene

tag: concentration

tag: time

value: 21 days


title: PMEC_38

tag: biological replicates

value: ANIMAL_1 II

tag: treatment

value: S. aureus


title: PMEC_37

value: ANIMAL_1 I


title: ALZ_NL_F_W_659

tag: tissue

value: Control

tag: gender

value: F

value: 73 years

value: Caucasian


title: S1-H63

description: log2 gene expression data

value: Breast cancer

value: Female

value: Post-Menopausal

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

tag: tumor size

tag: tnbc subtype


title: PMEC_36

value: ANIMAL_3 III

value: E. coli


title: ALZ_NL_M_W_1009

value: Superior Temporal Gyrus

tag: disease

value: M

tag: age

value: 76 years

tag: race

tag: neuronal proportion


title: S1-H62

description: log2 gene expression data

tag: age (years)

tag: body mass index

tag: menopausal status

value: Menopausal

tag: histology group

value: Mesenchymal (MES)


title: NC22A_850k

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

description: Infinium MethylationEpic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

extract_protocol: Total DNA was isolated by standard procedures

tag: primary site

value: Colon

tag: primary histology

value: Normal Colon


title: CTR_2 (2_3_G)

description:
US22502676_254227910008_S01_GE2_107_Sep09_1_3.txt
total RNA from 5 - 7 animals

tag: soil

value: LUFA2.2 control soil

tag: agent

value: control

tag: concentration

tag: time

value: 2 days


title: ALZ_NL_F_W_192

tag: tissue

value: Control

tag: gender

value: F

value: 79 years

value: Caucasian


title: NC22A_bis_850k

description: Infinium MethylationEpic


title: EC10_2 (3_1_R)

value: phenanthrene


title: S1-H61

description: log2 gene expression data

value: Breast cancer

value: Female

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

tag: tumor grade

value: Moderately Differentiated

tag: tumor size

tag: positive nodes

tag: metastases

value: No mets

tag: tnbc subtype

value: Basal-Like Immune-Activated (BLIA)


title: H229_oxBS_850k

description: Infinium MethylationEpic

tag: primary site

value: Brain

tag: primary histology

value: Sorted Neurons


title: PMEC_35

tag: biological replicates

value: ANIMAL_3 II

tag: treatment

value: E. coli


title: NCC9_FF_850k

description: Infinium MethylationEpic

value: Kidney

value: Renal Primary Tumor


title: EC50_2 (2_3_R)

tag: soil

value: LUFA2.2 control soil

tag: agent

tag: concentration

tag: time

value: 2 days


title: ALZ_NL_M_W_1039

tag: tissue

value: Superior Temporal Gyrus

tag: disease

value: Control

tag: gender

value: M

tag: age

value: 85 years

tag: race

value: Caucasian

tag: neuronal proportion


title: EC50_21 (2_2_G)

description:
US22502676_254227910008_S01_GE2_107_Sep09_1_2.txt
total RNA from 5 - 7 animals

value: phenanthrene

value: 21 days


title: ALZ_AD_F_W_88

value: Alzheimers Disease

value: F

value: 66 years


title: CTR_21 (2_4_R)

value: control


title: PMEC_34

value: ANIMAL_3 I


title: S1-H60

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

tag: tumor grade

value: Moderately Differentiated

tag: tumor size

tag: positive nodes

value: No mets

value: Luminal-AR (LAR)


title: PMEC_33

tag: biological replicates

value: ANIMAL_2 III

tag: treatment

value: E. coli

tag: time


title: PMEC_32

value: ANIMAL_2 II


title: EC10_2 (2_1_G)

description:
US22502676_254227910008_S01_GE2_107_Sep09_1_1.txt
total RNA from 5 - 7 animals

tag: soil

value: LUFA2.2 control soil

tag: agent

value: phenanthrene

tag: concentration

value: 2 days


title: EC50_21 (2_1_R)

value: 21 days


title: S1-H6

description: log2 gene expression data

tag: tissue

value: Breast cancer

tag: age (years)

tag: gender

tag: race

value: Caucasian

tag: body mass index

tag: menopausal status

value: Pre-Menopausal

value: Poorly Differentiated

tag: metastases

tag: tnbc subtype

value: Mesenchymal (MES)


title: CTR_2 (2_2_R)

value: control


title: ALZ_NL_M_B_1010

value: Superior Temporal Gyrus

tag: disease

value: Control

value: M

tag: age

value: 90 years

value: AfricanAmerica

tag: neuronal proportion


title: S1-H53

description: log2 gene expression data

value: Female

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

tag: tumor size

tag: positive nodes

value: Basal-Like Immune-Activated (BLIA)


title: ALZ_NL_M_W_133

tag: tissue

tag: gender

value: 80 years

tag: race


title: ALZ_AD_M_W_1509

value: Alzheimers Disease

value: 81 years

value: Caucasian


title: PMEC_31

tag: biological replicates

value: ANIMAL_2 I

tag: treatment

value: E. coli

tag: time


title: PMEC_30

value: ANIMAL_1 III


title: ALZ_NL_F_W_1409

value: Superior Temporal Gyrus

tag: disease

value: Control

value: F

tag: age

value: 88 years


title: S1-H59

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

tag: body mass index

tag: menopausal status

value: Menopausal

tag: histology group

value: Other Breast Cancer

value: Medullary Carcinoma

tag: tnbc subtype


title: H229_BS_850k

description: Infinium MethylationEpic

tag: primary site

value: Brain

tag: primary histology

value: Sorted Neurons


title: S1-H58B

description: log2 gene expression data

value: Post-Menopausal

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

tag: tumor grade

value: Poorly Differentiated

tag: tumor size

value: Luminal-AR (LAR)


title: ALZ_AD_M_H_1118

tag: tissue

value: Superior Temporal Gyrus

tag: disease

value: Alzheimers Disease

tag: gender

value: M

value: 73 years

tag: race

value: Hispanic

tag: neuronal proportion


title: CTR_21 (1_4_G)

description:
US22502676_254227910007_S01_GE2_107_Sep09_1_4.txt
total RNA from 5 - 7 animals

tag: soil

value: LUFA2.2 control soil

tag: agent

value: control

tag: concentration

tag: time

value: 21 days


title: S1-H52

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

value: Caucasian

tag: body mass index

tag: menopausal status

tag: histology group

value: Other Breast Cancer

tag: histology

value: Medullary Carcinoma

tag: metastases

value: No mets

tag: tnbc subtype

value: Basal-Like Immune-Activated (BLIA)


title: PMEC_29

tag: biological replicates

value: ANIMAL_1 II

tag: treatment

value: E. coli


title: EC50_2 (1_3_G)

description:
US22502676_254227910007_S01_GE2_107_Sep09_1_3.txt
total RNA from 5 - 7 animals

value: phenanthrene

value: 2 days


title: EC10_2 (1_4_R)


title: ALZ_AD_F_W_676

tag: tissue

value: Superior Temporal Gyrus

tag: disease

value: Alzheimers Disease

value: F

tag: age

value: 69 years


title: Fkh1 OE_G1 replicate 3

city: Los Angeles

first: Jared

middle: M

last: Peace

state: CA - California

address: 1050 Childs Way RRI 203

department: Molecular and Computational Biology

institute: University of Southern California

hyb_protocol: Standard Nimblegen Protocol

scan_protocol: Genepix Personal 4100A Scanner (Axon Instruments)

data_processing: Data was processed using MA2C (Song et. al, 2007)

organism: Saccharomyces cerevisiae

source_name: Fkh1-myc ChIP from S. cerevisiae

label_protocol: Standard Nimblegen Protocol

growth_protocol: For late G1 block, induction, and release, cells (pre-selected on SD-URA for plasmid as appropriate) were inoculated into YEP+2% raffinose at 25°C and grown to mid-log phase

extract_protocol: Genomic DNA was extracted as described in as described in Viggiani CJ, Aparicio JG, Aparicio OM (2009) ChIP-chip to analyze the binding of replication proteins to chromatin using oligonucleotide DNA microarrays. Methods Mol Biol 521: 255-278.

treatment_protocol: Cells were blocked in G1 by resuspension (at O.D. ~0.5) in fresh YEP+2% raffinose +7.5 nM α-factor at 25°C for 3 hrs.  For induction, cells were resuspended in YEP+2% galactose +7.5 nM α-factor at 25°C for 2 hrs.

tag: strain

value: Fkh1 OE (WT pGAL-Fkh1)

tag: time point

value: G1 arrest

source_name: Fkh1-myc ChIP Total from S. cerevisiae


title: CTR_21 (1_3_R)

tag: soil

value: LUFA2.2 control soil

tag: agent

value: control

value: 21 days


title: PMEC_28

value: ANIMAL_1 I

tag: time


title: EC50_2 (1_2_R)

description:
US22502676_254227910007_S01_GE2_107_Sep09_1_2.txt
total RNA from 5 - 7 animals

tag: concentration


title: PMEC_27

value: ANIMAL_3 III

value: unbehandelt


title: EC10_21 (1_2_G)


title: PMEC_26

value: ANIMAL_3 II


title: ALZ_AD_M_W_1487

tag: gender

value: M

value: 84 years

tag: race

value: Caucasian

tag: neuronal proportion


title: Fkh1 OE_G1 replicate 2


title: ALZ_NL_F_H_232

value: Control

value: 74 years

value: Hispanic


title: S1-H4B

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

tag: tumor grade

value: Poorly Differentiated

tag: tumor size

tag: positive nodes

value: No mets

value: Mesenchymal (MES)


title: S1-H49

description: log2 gene expression data

tag: tissue

value: Moderately Differentiated

tag: metastases

tag: tnbc subtype

value: Basal-Like Immune-Suppressed (BLIS)


title: NCC9_FFPE_850k

description: Infinium MethylationEpic

tag: primary site

value: Kidney

tag: primary histology

value: Renal Primary Tumor


title: Fkh1 OE_G1 replicate 1

tag: strain

value: Fkh1 OE (WT pGAL-Fkh1)

tag: time point

value: G1 arrest


title: S1-H51

description: log2 gene expression data

tag: age (years)

tag: gender

tag: race

value: Caucasian

tag: body mass index

tag: menopausal status

value: Pre-Menopausal

tag: histology group

value: Basal-Like Immune-Activated (BLIA)


title: no OE_G1 replicate 3

value: no OE ( WT pGAL)


title: no OE_G1 replicate 2


title: ALZ_AD_M_W_91

value: Superior Temporal Gyrus

tag: disease

value: Alzheimers Disease

value: M

tag: age

value: 92 years

tag: neuronal proportion


title: S1-H50

description: log2 gene expression data

value: Breast cancer

value: Female

value: Post-Menopausal

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

tag: tumor grade

value: Poorly Differentiated

tag: tumor size


title: RCC9_FF_450k

tag: primary site

value: Kidney

tag: primary histology

value: Renal Primary Tumor


title: no OE_G1 replicate 1

tag: strain

tag: time point

value: G1 arrest


title: ALZ_AD_F_B_650

tag: tissue

tag: gender

value: F

value: 86 years

tag: race

value: AfricanAmerica


title: ALZ_NL_M_W_768

value: Superior Temporal Gyrus

tag: disease

value: Control

tag: age

value: 84 years

value: Caucasian


title: CTR_2 (1_1_G)

description:
US22502676_254227910007_S01_GE2_107_Sep09_1_1.txt
total RNA from 5 - 7 animals

tag: soil

value: LUFA2.2 control soil

tag: agent

value: control

tag: concentration

tag: time

value: 2 days


title: PMEC_24

tag: biological replicates

value: ANIMAL_2 III

tag: treatment

value: unbehandelt


title: UCMD patient  repl6

city: Barcelona

first: Susana

last: Kalko

state: BARCELONA

address: c/Rosello 153

department: Bioinformatics Platform

institute: IDIBAPS

hyb_protocol: Following cRNA fragmentation the sample was hybridized on The GeneChip HT HG-U219 Array Plate

scan_protocol: Hybridization, washes and scanning were processed in the Gene Titan instrument, a fully automated array system

data_processing: Raw expression measures were summarized after background correction and normalization steps using the rma methodology in the Expression Console™ Software 1.2.1.20.

source_name: Fibroblast

label_protocol: Sample preparation for microarray hybridization was performed following Affymetrix’s protocols.   The GeneChip3’IVT Express Protocol was used for sample labeling.Briefly from 150 ng total RNA a  biotin labeled cRNA was generated by reverse transcription, followed by an IVT

extract_protocol: Total RNA was extracted from fibroblasts cultures with RNeasy Fibrous Tissue mini kit following the manufacturer's instructions. Quantity and quality of RNA obtained was determined with Nanodrop 8000 Spectrophotometer (Thermo Scientific, Schwerte, Germany) and its integrity with Agilent 2100 Bioanalyzer (Agilent technologies, Waldbronn, Germany). In all samples RNA integrity numbers (RIN) were >8 and 260/280 ratios near 2.0.

tag: cell type

value: dermal fibroblasts

tag: disease state

value: UCMD


title: EC10_21 (1_1_R)

value: phenanthrene

value: 21 days


title: S1-H46

description: log2 gene expression data

value: Breast cancer

tag: age (years)

value: Female

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

tag: tumor size

tag: metastases

value: No mets

tag: tnbc subtype

value: Basal-Like Immune-Suppressed (BLIS)


title: S1-H45

description: log2 gene expression data

tag: tissue

tag: gender

tag: race

value: Caucasian


title: S1-H48

description: log2 gene expression data

value: Pre-Menopausal

tag: tumor grade

value: Moderately Differentiated

tag: positive nodes

value: Mesenchymal (MES)


title: PMEC_23

tag: biological replicates

value: ANIMAL_2 II

tag: treatment

value: unbehandelt

tag: time


title: OC, biological rep3

city: Wageningen

first: Anderson Tadeu

last: Silva

state: Gelderland

address: Droevendaalsesteeg 1

department: Plant Physiology

institute: Wageningen University

description: Gene expression data from germinated Arabidopsis seeds at the stage of opened cotyledon

hyb_protocol: Following fragmentation, 2.5 ug of ss-cDNA were hybridized on the Affymetrix ARAGene 1.1ST Array plates. Plates were washed and stained by the GeneTitan machine using the Affymetrix HWS Kit for the GeneTitan.

scan_protocol: Plates were scanned using the Affymetrix GeneTitan scanner operated by the software program Affymetrix GeneChip Command Console.

data_processing: The Robust Multichip Analysis (RMA-Sketch for gene level analysis) algorithm was used for the summarization. Signal intensities were extracted and analysed using the Bioconductor packages of R. The data was normalized using the RMA algorithm with the TAIRG v17 cdf file.

organism: Arabidopsis thaliana

source_name: Germinated seeds at the stage of opened cotyledon

label_protocol: Biotin-labeled cDNA was prepared using the Affymetrix NuGEN Ovation PicoSL WTA and Biotin Module from 50ng total RNA according to the manufacturer's specifications.

growth_protocol: Seeds were cold stratified for 72 h at 4˚C in 9 cm Petri dishes on two layers of blue filter paper and 10 ml of distilled water. After stratification, seeds were transferred to germination cabinets with constant white light at 22 ˚C.

extract_protocol: Total RNA was extracted following the hot borate protocol modified from Wan and Wilkins (1994) (Maia et al, Plos ONE 2011)

treatment_protocol: Three thousand seeds at each developmental stage were selected using a stereomicoscope.

tag: cultivar

tag: plant organ

value: seedlings

tag: developmental stage


title: PMEC_20

value: ANIMAL_1 II


title: GC, biological rep3

description: Gene expression data from germinated Arabidopsis seeds at the stage of green cotyledon

source_name: Germinated seeds at the stage of green cotyledon


title: PMEC_19

value: ANIMAL_1 I


title: UCMD patient with AA repl6

tag: cell type

value: dermal fibroblasts

tag: disease state

value: UCMD

value: ascorbic acid


title: OC, biological rep2

value: Germinated seeds at the stage of opened cotyledon


title: PMEC_21

value: ANIMAL_1 III


title: OC, biological rep1


title: S1-H44

description: log2 gene expression data

source_name: Human breast cancer

value: Breast cancer

value: Female

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

value: Poorly Differentiated


title: S1-H47

description: log2 gene expression data

tag: tissue

tag: gender

tag: race

value: Caucasian

value: Pre-Menopausal

tag: tumor grade

tag: tumor size

tag: positive nodes

tag: tnbc subtype

value: Basal-Like Immune-Suppressed (BLIS)


title: PMEC_22

tag: biological replicates

value: ANIMAL_2 I

tag: treatment

value: unbehandelt

tag: time


title: S1-H41

description: log2 gene expression data

tag: age (years)

tag: body mass index

tag: menopausal status

tag: histology group

tag: metastases

value: No mets

value: Mesenchymal (MES)


title: UCMD patient  repl4

description: This sample has not been included in this publication, detected as outlier

tag: cell type

value: dermal fibroblasts

tag: disease state

value: UCMD


title: S1-H43

description: log2 gene expression data

tag: tissue

value: Breast cancer

value: Infiltrating Lobular Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

tag: pr

tag: triple-negative status


title: S1-H40

description: log2 gene expression data

tag: gender

value: Female

tag: race

tag: tumor grade

tag: tumor size

tag: positive nodes

tag: tnbc subtype


title: UCMD patient  repl5

tag: treatment


title: UCMD patient with AA repl5

value: ascorbic acid


title: UCMD patient with AA repl4


title: UCMD patient  repl3


title: PMEC_16

tag: biological replicates

value: ANIMAL_3 I

value: S. aureus

tag: time


title: PMEC_18

value: ANIMAL_3 III


title: GC, biological rep2

tag: cultivar

tag: plant organ

value: seedlings

tag: developmental stage

value: Germinated seeds at the stage of green cotyledon


title: S1-H3B

description: log2 gene expression data

tag: tissue

tag: age (years)

value: Caucasian

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

value: Validation TN

value: Negative

value: TN

value: Moderately Differentiated

tag: metastases


title: GC, biological rep1


title: UCMD patient with AA repl3

tag: cell type

value: dermal fibroblasts

tag: disease state

value: UCMD