title: UNC04-0550B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.74

value: I


title: UNC99-0141B-44K

status: Public on Feb 19 2013

type: RNA

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

hyb_protocol: Agilent quick amplification kit protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.78

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken

molecule: total RNA

organism: Homo sapiens

source_name: Human reference

extract_protocol: Total RNA isolated using Qiagen RNeasy mini Kit

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: Breast Tumor

tag: ose (0=alive, 1=dod or doc)

tag: osm (os in months)

tag: rfse (0=no event, 1=first event and can be local, regiol, distant or death event)

tag: rfsm (rfs in months)

tag: sex_(1 = female, 0 = male)

value: Female

tag: race_(0 = non-black, 1 = black)

value: Black

tag: age_(at breast cancer dx)

value: Basal

tag: estrogen receptor  (negative = 0, positive = 1 by ihc)

tag: tumor size_1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin)

tag: nodal status (lymph node negative = 0, positive = 1)

tag: metastatic dx (negative = 0, positive = 1 present at diagnosis)

tag: stage at class level

value: II

tag: her2 status (negative = 0, positive = 1 by ihc)

tag: tissue type

value: Breast Tumor


title: UNC02-0575B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.69

label_protocol: Agilent quick amplification kit protocol

value: LumB


title: UNC04-0297B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.72

value: White

value: III


title: UNC99-0182B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.80


title: 971103B-244Kv5

status: Public on Apr 22 2013

description: Mammary Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software

source_name: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

extract_protocol: Total RNA isolated by stratagene

value: Human Reference B

extract_protocol: Total RNA isolated using Qiagen Rneasy Kit

tag: tumor

value: LumA


title: UNC98-0107B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.75

value: Native American


title: 9830-030118B-C

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.63


title: UNC99-0306B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.83


title: 950165B

description: Mammary Tumor

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125


title: 9830-030619B-New

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.64


title: UNC99-0339B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.84


title: UNC03-0477B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.70


title: BC00094-new

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.1 analysis software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Human Reference B

extract_protocol: Qiagen Rneasy Kit


title: UNC-020464B-core

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

extract_protocol: Total RNA isolated by Stratagene.

source_name: Tissue: Breast Tumor, Subtype: LumA

tag: geo array name


title: 950185B

description: Mammary Tumor

tag: reference


title: UNC-020155B

tag: ose (0=alive, 1=dod or doc)

value: Hispanic


title: UNC-040191B-core

tag: osm (os in months)


title: UNC-010318B

tag: rfse (0=no event, 1=first event and can be local, regiol, distant or death event)


title: 9830-040072B-C

tag: rfsm (rfs in months)


title: UNC-020439B

tag: sex_(1 = female, 0 = male)

value: Male

value: IV


title: UNC-040114B-core

tag: race_(0 = non-black, 1 = black)


title: UNC-010355B

tag: age_(at breast cancer dx)


title: BR97-0137-Custom

tag: estrogen receptor  (negative = 0, positive = 1 by ihc)


title: 9830-010038B

value: Normal-Like

tag: tumor size_1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin)


title: UNC-020306B

tag: nodal status (lymph node negative = 0, positive = 1)


title: UNC-030408B-core

tag: metastatic dx (negative = 0, positive = 1 present at diagnosis)

value: I


title: 010456B-Genomic-Core

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: stage at class level


title: UNC-020297B

value: Female

tag: her2 status (negative = 0, positive = 1 by ihc)


title: BR95-0017-LumB

value: Black

tag: tissue type


title: 010348B-Genomic-Core


title: UNC-020578B

value: Basal


title: UNC-040134B

value: II


title: UNC-040182B

value: Other

value: Breast Tumor


title: UNC04-0547B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.73

value: Asian


title: 9830-030584B-C

value: White


title: 9830-030597B


title: BC00033-T

value: LumB


title: BR00-0284-Custom


title: 010353B-Genomic-Core

value: LumA


title: BC00017-T


title: 960096B

description: Mammary Tumor

value: Human Reference B

tag: tumor


title: 9819-000295B


title: 9830-020018B

tag: geo array name


title: UNC04-0115B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.71

tag: reference

value: III


title: 9830-010118B

tag: ose (0=alive, 1=dod or doc)


title: BC00016-T

tag: osm (os in months)


title: 9830-010130B

tag: rfse (0=no event, 1=first event and can be local, regiol, distant or death event)


title: UNC98-2048B-44K

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.76

tag: rfsm (rfs in months)


title: 9830-000424B

source_name: Breast Tumor, tamoxifen-treated patient

tag: sex_(1 = female, 0 = male)


title: 9830-010255B

tag: race_(0 = non-black, 1 = black)


title: 9830-000248B

tag: age_(at breast cancer dx)


title: BC00063

tag: estrogen receptor  (negative = 0, positive = 1 by ihc)


title: 9830-000517B

tag: tumor size_1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin)


title: 9830-020461B

tag: nodal status (lymph node negative = 0, positive = 1)


title: 9830-030562B

tag: metastatic dx (negative = 0, positive = 1 present at diagnosis)


title: 9830-020416B

tag: stage at class level


title: 9830-000471B

tag: her2 status (negative = 0, positive = 1 by ihc)


title: 9830-010214B

tag: tissue type


title: 9830-000094B


title: 9830-020185B


title: BC00097


title: 9830-000060B


title: 9830-020025B


title: BC00043


title: 9830-020340B


title: BR00-0387


title: 9830-020310B


title: BC00041


title: BR01-0123


title: 9830-010461B


title: 9830-010384B


title: BR00-0344

value: Male


title: BR01-0349


title: Chi-64628

status: Public on Jan 18 2013

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-147

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

tag: tissue


title: BR95-0184

tag: geo array name


title: Chi-6006062

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-140

tag: reference


title: Chi-62389

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-144


title: Chi-7029166-weak

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-141


title: Chi-64574

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-143


title: Chi-7045913

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-142


title: Chi-7016941

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-146


title: Liu-30C Set3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130

source_name: MDA-MB231 scrambled

value: breast cancer

tag: cell line

source_name: 30c MDA-MB231


title: Liu-30C Set3 vs. SCR3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131


title: Chi-8019304

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-138


title: Chi-50382

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-139


title: Chi-8019272

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-148


title: Liu-30C Set2 vs. SCR2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129


title: Liu-30C Set2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128


title: Liu-30C Set1 Repl1


title: Chi-7027919

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131


title: Chi-7045272

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-135


title: Chi-6003933

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-137


title: Chi-62566

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129


title: Chi-6004586

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132


title: Liu-30C Set1 vs. SCR1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126


title: Liu-30C Set1 vs. SCR1 Repl1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127


title: BC00049_R01

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128


title: BC00019T-New

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-145


title: IFNAR-/- CD8a DC, MCMV, replicate 2

status: Public on Oct 17 2012

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

description:
Sample name: MDD_B27
IFNAR-KO spleen CD8a+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.2(pos)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430.2 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400 with the EukGE_WS2v5 protocol.

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

data_processing: The data were RMA normalized in R and Bioconductor, using the limma package.

label: biotin

organism: Mus musculus

label_protocol: Except for sample A7 where only 8 ng was available, 50 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from between 5x10E4 and 3x10E6 cells for each leukocyte subset with the Qiagen micro RNAeasy kit, with on column DNase digestion, according to the manufacturer protocol.

treatment_protocol: Mice were infected intraperitoneally with salivary gland-murine cytomegalovirus (5x10e4 pfu/mouse). Spleens were harvested at 36 hours post-infection and digested with collagenase (Liberase CI), erythrocytes were lysed with NH(4)Cl, and leukocytes were resuspended in PBS EDTA 5mM before sorting by flow cytometry

tag: strain

tag: chimera description

tag: genotype/variation

value: IFNAR-KO

tag: cell type

value: CD8a+ dendritic cells (DC)

tag: infection

value: murine cytomegalovirus


title: WT CD8a DC, steady-state, replicate 2

description:
Sample name: MDD_C36
WT spleen CD8a+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.1(pos)

value: WT


title: WT CD8a DC, MCMV, replicate 2

description:
Sample name: MDD_A13
WT spleen CD8a+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.1(pos)


title: WT CD8a DC, p(I:C), replicate 1

description:
Sample name: MDD_7-CD8a
WT spleen CD8a+ dendritic cells (DC) from poly(I:C)-injected mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos)

hyb_protocol: Following fragmentation, 1.875 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene 1.0ST Array. GeneChips were washed and stained in the Affymetrix GeneChip® fluidics station 450 with the FS450-0007 protocol.

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

label_protocol: 150 ng of RNA from each sample was used to synthesize biotinylated probes, with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from between 8x10E5 and 4x10E6 cells for each leukocyte subset with the Qiagen micro RNAeasy kit, with on column DNase digestion, according to the manufacturer protocol.

treatment_protocol: injection of 100 ug of poly(I:C). Cells were isolated from the mouse spleen 3 hours after injection.

tag: agent


title: IFNAR-/- CD8a DC, steady-state, replicate 1

description:
Sample name: MDD_B17
IFNAR-KO spleen CD8a+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.2(pos)


title: WT CD8a DC, p(I:C), replicate 2

description:
Sample name: MDD_15-CD8a
WT spleen CD8a+ dendritic cells (DC) from poly(I:C)-injected mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos)


title: WT CD8a DC, MCMV, replicate 1

description:
Sample name: MDD_B20
WT spleen CD8a+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.1(pos)


title: IFNAR-/- CD8a DC, steady-state, replicate 2

description:
Sample name: MDD_A10
IFNAR-KO spleen CD8a+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.2(pos)


title: WT CD8a DC, steady-state, replicate 1

description:
Sample name: MDD_A3
WT spleen CD8a+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.1(pos)


title: WT CD8a DC, steady-state, replicate 2

description:
Sample name: MDD_11-CD8a
WT spleen CD8a+ dendritic cells (DC) from untreated mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos)


title: IFNAR-/- CD8a DC, MCMV, replicate 1

description:
Sample name: MDD_C33
IFNAR-KO spleen CD8a+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.2(pos)


title: Chi-60216

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: Chi-6002357-244k

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-136


title: FVB_MMTV_Neu_CA05_865A_CHURCHILL

status: Public on Aug 21 2012

description: Mammary Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

source_name: Whole Mouse Reference RNA

extract_protocol: Total RNA isolated using Qiagen RNeasy Kit

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups

tag: tumor

value: Untreated MMTV-Neu mammary tumor


title: FVB_MMTV_Neu_CA05_863A_CHURCHILL

description: Mammary Tumor


title: Chi-63448-244k

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127


title: Chi-6004767-244k

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134


title: Chi-62415-244k

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-133


title: BC00086

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

tag: ose (0=alive, 1=dod or doc)

tag: osm (os in months)

tag: rfse (0=no event, 1=first event and can be local, regiol, distant or death event)

tag: rfsm (rfs in months)

tag: sex_(1 = female, 0 = male)

value: Female

tag: race_(0 = non-black, 1 = black)

value: Black

tag: age_(at breast cancer dx)

value: Basal

tag: estrogen receptor  (negative = 0, positive = 1 by ihc)

tag: tumor size_1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin)

value: II


title: FVB_C57Bl6_C3(1)_Tag_117277T1_HERSCH

description: Mammary Tumor

tag: reference

value: Untreated C3(1)-Tag mammary tumor


title: FVB_C57Bl6_C3(1)_Tag_117218T1_HERSCH

description: Mammary Tumor


title: FVB_C57B6_C3(1)_TAG_117074_HERSC

description: Mammary Tumor


title: FVB_B6_C3(1)_Tag_117200T1_HERSCH

description: Mammary Tumor


title: C3H_Virgin_12351_Chaos3/Chaos3_Schimenti

description: Mammary Tumor

value: Untreated mammary tumor from Chaos3 mouse model


title: FVB_MMTV-Neu_142292_Non-treated

description: Mammary Tumor


title: WT CD8a DC, steady-state, replicate 1

description:
Sample name: MDD_3-CD8a
WT spleen CD8a+ dendritic cells (DC) from untreated mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos)

tag: strain


title: Chi-6005695-244k

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-149

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-148

tag: tissue

value: Breast Tumor


title: C3H_Virgin_14826_Chaos3/Chaos3_Schimenti

description: Mammary Tumor


title: Chi-64562-244k


title: LCCC-9003-BxComb

status: Public on Jul 14 2012

tag: slide name

tag: subtype

tag: study arm

value: Arm 1b Cetuximab+Carboplatin

tag: best response

value: SD

tag: ttp (days)


title: C3H_Virgin_12352_Chaos3/Chaos3_Schimenti

description: Mammary Tumor

tag: tumor


title: LCCC-9006-Bx0

value: Claudin-low

tag: os(mo)

tag: survival status

value: Alive


title: FVB_C3(1)-Tag_142274_Non-treated

description: Mammary Tumor


title: C3H_Virgin_12115_Chaos3/Chaos3_Schimenti

description: Mammary Tumor


title: LCCC-9006-BxComb

value: Arm 2 Cetuximab + Carboplatin

value: PR


title: LCCC-9003-Bx0

value: Dead


title: LCCC-9003-BxSingle

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: Arm 1 Cetuximab

value: PD


title: C3H_Virgin_12353_Chaos3/Chaos3_Schimenti

description: Mammary Tumor

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups


title: B6xC3H_F1_12115_Chaos3/Chaos3_Schimenti

description: Mammary Tumor


title: FVB_MMTV-Neu_133120 Non-treated

description: Mammary Tumor

source_name: FVB_MMTV-Neu_133120 Non-treated

value: Untreated MMTV-Neu mammary tumor


title: LCCC-9002-Bx0

value: Basal


title: FVB_MMTV-Neu_138865 Non-treated

description: Mammary Tumor

source_name: FVB_MMTV-Neu_138865 Non-treated


title: LCCC-9001-BxSingle


title: LCCC-9001-BxComb


title: FVB_C3(1)-Tag_145186_Non-treated

description: Mammary Tumor


title: LCCC-9002-BxComb


title: FVB_MMTV-Neu_126563 Non-treated

description: Mammary Tumor

source_name: FVB_MMTV-Neu_126563 Non-treated


title: FVB_C3(1)-Tag_142157_Non-treated

description: Mammary Tumor


title: LCCC-4012-Bx0


title: LCCC-4006-Bx0

value: Normal


title: LCCC-4004-Bx0


title: LCCC-4005-BxComb


title: LCCC-4012-BxSingle


title: FVB_C3(1)-Tag_142209_Non-treated

description: Mammary Tumor

value: Untreated C3(1)-Tag mammary tumor


title: LCCC-6005-Bx0


title: FVB_C3(1)-Tag_142204_Non-treated

description: Mammary Tumor


title: C3H_Virgin_15259_Chaos3/Chaos3_Schimenti

description: Mammary Tumor

value: Untreated mammary tumor from Chaos3 mouse model


title: LCCC-4005-Bx0

value: Breast Tumor


title: LCCC-3006-Bx0


title: LCCC-3006-BxComb


title: LCCC-4004-BxComb


title: WCE Input RPMI (6/27/11)_ChipSeq

status: Public on Jul 09 2012

type: SRA

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Chromatin IP against WCE Input RPMI (6/27/11).
09162011_C0082ABXX_2.CGATGT
Barcode (already removed): CGATGT

library_source: genomic

data_processing:
Images analysis and base calling were done using the Solexa pipeline.
Reads were aligned to human genome build hg18 using Bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: Aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

molecule: genomic DNA

source_name: T-ALL cell line, WCE input

growth_protocol: Human RPMI-8402 cells were purchased from the German Collection of Microorganisms and Cell Culture (DSMZ), Leibniz, Germany. Cells were maintained under typical conditions in RPMI media with 10% bovine calf serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linking with formaldehyde for 20 min.

extract_protocol: Whole cell extracts (WCEs) were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 4500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing using the Beckman SPRIworks fragment library system with adapters from the Illumina TruSeq DNA kit. DNA fragments were end repaired, ligated and size selected using SPRIworks. DNA was then subjected to 18 cycles of PCR using oligos provided by Illumina.

tag: cell line

tag: cell type

value: T-cell acute lymphoblastic leukemia (T-ALL) cells

tag: chip antibody


title: LCCC-2002-BxComb

value: EPD


title: LCCC-9001-Bx0

value: Claudin-low


title: LCCC-12001-BxSingle


title: FVB_MMTV-Neu_133121 Non-treated

description: Mammary Tumor

source_name: FVB_MMTV-Neu_133121 Non-treated


title: LCCC-13003-Bx0


title: LCCC-1003-Bx0


title: LCCC-1011-BxComb

value: NE


title: LCCC-12001-Bx0


title: LCCC-13003-BxComb

value: Arm 2 Cetuximab + Carboplatin


title: LCCC-1003-BxSingle


title: LCCC-2002-Bx0


title: LCCC-1010-Bx0


title: LCCC-6005-BxComb

value: PR


title: LCCC-1011-Bx0

value: Dead


title: LCCC-9009-Bx0

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: LCCC-4003-Bx0


title: LCCC-4003-BxComb


title: 252550310007-4

status: Public on Jun 30 2012

scan_protocol: Agilent Technologies Scanner G2505C US82800149 Using Feature Extraction Software

source_name: Whole Mouse Reference RNA-2009

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-504

treatment_protocol: described in He et al., 2004. BioTechniques, Vol. 38:464–468

value: Whole Mouse Reference

source_name: tumor: Mouse tumor derived cell line

value: Mouse tumor derived cell line


title: T8_Kp16null

status: Public on Jun 25 2012

description: Tumor

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.1

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups

value: KRAS; p16 null (TKp16L/L)


title: T9_Kp16null_rep

description: Tumor


title: T7_TRIA

description: Tumor

value: TRIA (TRIA)


title: LCCC-1010-BxComb

value: Basal

value: PD


title: T9_Kp16null

description: Tumor


title: T6_TRIA_rep

description: Tumor


title: 252550310009-2


title: T5_KLkb1null

description: Tumor

value: KRAS; Lkb1 null (TKLkb1L/L)


title: T7_TRIA_rep

description: Tumor


title: 252550310009-1


title: 252550310009-3


title: T4_Kp53Lkb1null

description: Tumor

value: KRAS; p53 null, Lkb1 null (TKp53L/LLkb1L/L)


title: T3_Kp53Lkb1null_rep

description: Tumor


title: C6_Kp53null

description: Cell Line

value: KRAS; p53 null; Lkb1 null with Lkb1 add back (TKp53L/LLkb1L/L + pBabe_Lkb1)


title: C8_K

description: Cell Line

value: KRAS; Lkb1 null with Lkb1 add back (TKLkb1L/L + pBabe_Lkb1)


title: T3_Kp53Lkb1null

description: Tumor


title: T1_Kp53Lkb1null

description: Tumor


title: C5_KLkb1null

description: Cell Line


title: C8_KLkb1null

description: Cell Line


title: C4_Kp53null

description: Cell Line


title: C7_Kp53Lkb1null

description: Cell Line

value: KRAS; p53 null; Lkb1 null (TKp53L/LLkb1L/L)


title: C4_Kp53Lkb1null

description: Cell Line


title: C9_Kp53null

description: Cell Line


title: T6_TRIA

description: Tumor


title: C6_Kp53Lkb1null

description: Cell Line


title: T2_KLkb1null

description: Tumor


title: C9_Kp53Lkb1null

description: Cell Line


title: C5_K

description: Cell Line


title: C10_Kp53Lkb1null

description: Cell Line


title: C2_Kp53Lkb1null

description: Cell Line


title: C3_Kp53Lkb1null

description: Cell Line


title: 252550310053-1

status: Public on May 30 2012

source_name: tumor: Mouse mammary adenocarcinoma

value: Mouse mammary adenocarcinoma


title: 252550310055-1


title: 252550310053-2


title: 252550310054-3


title: 252550310053-3


title: C3_Kp53null

description: Cell Line


title: C2_Kp53null

description: Cell Line


title: C7_Kp53null

description: Cell Line


title: C1_KLkb1null

description: Cell Line


title: C10_Kp53null

description: Cell Line


title: 252550310054-1


title: 252550310054-2


title: 252550310051-3


title: 252550310047-1

description: FVB_MMTV-Neu_121575 Non-treated


title: 252550310047-2


title: 252550310012-1


title: 252550310045-2

description: FVB_MMTV-Neu_138865 Non-treated


title: 252550310019-3

description: FVB_MMTV-Neu_126563_untreated_Usary_test-2micrograms_RNA


title: 252550310047-3

description: FVB_MMTV-Neu_123299 Non-treated


title: 252550310020-2

description: FVB_MMTV-Neu_133120_untreated_Usary_test-2micrograms_RNA


title: 252550310052-1


title: 252550310052-3


title: C1_K

description: Cell Line


title: MCF10_WT_DMSO_vs_GFP_DMSO_4Hr_v1.1

status: Public on May 01 2012

description: MCF-10A cells expressing a wild-type PIK3CA expression vector were compared to MCF-10A cells with a GFP control.

hyb_protocol: described in Prat et al., 2010, Breast Cancer Research, 12:R68

label_protocol: Agilent Quick Amp Labeling Kit

tag: genotype/variation

value: GFP

value: WT


title: 252550310023-3

description: FVB_MMTV-Neu_133121 Non-treated


title: MCF10_WT_DMSO_vs_GFP_DMSO_4Hr_v2.0


title: MCF10_H1047R_DMSO_vs_GFP_DMSO_4Hr_v2.0

description: MCF-10A cells with the PIK3CA H1047R mutation were compared to MCF-10A cells with a GFP control.


title: MCF10_WT_DMSO_vs_GFP_DMSO_4Hr_v1.0


title: 252550310051-4


title: 252550310055-2


title: MCF10_H1047R_DMSO_vs_GFP_DMSO_4Hr_v1.0


title: MCF10_H1047R_BAY_vs_H1047R_DMSO_4Hr_v1.1

description: MCF-10A cells with the PIK3CA H1047R mutation were treated with BAY-65-1942 for 4 hours and compared to MCF-10A cells with the PIK3CA H1047R treated with DMSO for 4 hour.


title: MCF10_H1047R_4Hr_vs_H1047R_0Hr_IL6R_Inhibitor_v1.1

description: MCF-10A cells with the PIK3CA H1047R mutation were treated with an IL-6 receptor monoclonal antibody for 4 hours and compared to MCF-10A cells with the PIK3CA H1047R mutation.


title: 252550310008-1

description: FVB_C3(1)-Tag_120157_untreated_Usary_test-2micrograms_RNA


title: MCF10_H1047R_BAY_vs_H1047R_DMSO_4Hr_v2.0


title: 252550310052-2


title: MCF10_H1047R_BAY_vs_H1047R_DMSO_4Hr_v1.0


title: 252550310047-4

description: FVB_MMTV-Neu_121304-2 Non-treated


title: 252550310023-1

description: FVB_MMTV-Neu_126563 Non-treated


title: 252550310022-4

description: FVB_C3(1)-Tag_117517_untreated_Usary_test-2000ngRNA


title: MCF10_H1047R_4Hr_vs_H1047R_0Hr_IL6R_Inhibitor_v1.0


title: MCF10_H1047R_DMSO_vs_GFP_DMSO_4Hr_v1.1


title: 252550310022-3

description: FVB_C3(1)-Tag_117517_untreated_Usary_test-1600ngRNA


title: 252550310021-3

description: FVB_C3(1)-Tag_120157_untreated_Usary_test-1600ngRNA


title: 252550310021-1

description: FVB_C3(1)-Tag_120157_untreated_Usary_test-800ngRNA


title: MCF10_H1047R_4Hr_vs_H1047R_0Hr_IL6R_Inhibitor_v2.0


title: MCF10_H1047R_4Hr_LY_vs_H1047R_0Hr_LY_Treatment_v1.1

description: MCF-10A cells with the PIK3CA H1047R mutation were treated with LY294002 for 4 hours and compared to MCF-10A cells with the PIK3CA H1047R mutation.


title: MCF10_H1047R_4Hr_LY_vs_H1047R_0Hr_LY_Treatment_v1.0


title: MCF10_H1047R_24Hr_vs_H1047R_0Hr_IL6R_Inhibitor_v1.1

description: MCF-10A cells with the PIK3CA H1047R mutation were treated with an IL-6 receptor monoclonal antibody for 24 hours and compared to MCF-10A cells with the PIK3CA H1047R mutation.


title: 252550310022-1

description: FVB_C3(1)-Tag_117517_untreated_Usary_test-800ngRNA


title: MCF10_H1047R_24Hr_vs_H1047R_0Hr_IL6R_Inhibitor_v2.0


title: MCF10_H1047R_24Hr_LY_vs_H1047R_0Hr_LY_Treatment_v1.1

description: MCF-10A cells with the PIK3CA H1047R mutation were treated with LY294002 for 24 hours and compared to MCF-10A cells with the PIK3CA H1047R mutation.


title: 252550310021-2

description: FVB_C3(1)-Tag_120157_untreated_Usary_test-1000ngRNA


title: 252550310023-2

description: FVB_MMTV-Neu_133120 Non-treated


title: 252550310021-4

description: FVB_C3(1)-Tag_120157_untreated_Usary_test-2000ngRNA


title: MCF10_E545K_DMSO_vs_GFP_DMSO_4Hr_v2.0

description: MCF-10A cells with the PIK3CA E545K mutation were compared to MCF-10A cells with a GFP control.


title: MCF10_H1047R_24Hr_LY_vs_H1047R_0Hr_LY_Treatment_v1.0


title: MCF10_H1047R_4Hr_LY_vs_H1047R_0Hr_LY_Treatment_v2.0


title: MCF10_E545K_BAY_vs_E545K_DMSO_4Hr_v2.0

description: MCF-10A cells with the PIK3CA E545K mutation were treated with BAY-65-1942 for 4 hours and compared to MCF-10A cells treated with DMSO for 4 hours.


title: MCF10_E545K_4Hr_vs_E545K_0Hr_IL6R_Inhibitor_v1.1

description: MCF-10A cells with the PIK3CA E545K mutation were treated with an IL-6 receptor monoclonal antibody for 4 hours and compared to MCF-10A cells with the PIK3CA E545K mutation.


title: MCF10_E545K_BAY_vs_E545K_DMSO_4Hr_v1.0


title: MCF10_E545K_4Hr_vs_E545K_0Hr_IL6R_Inhibitor_v2.0


title: MCF10_H1047R_24Hr_LY_vs_H1047R_0Hr_LY_Treatment_v2.0


title: MCF10_E545K_4Hr_LY_vs_E545K_0Hr_LY_Treatment_v1.1

description: MCF-10A cells with the PIK3CA E545K mutation were treated with LY294002 for 4 hours and compared to MCF-10A cells with the PIK3CA E545K mutation.


title: CD161++CD8aa, biological rep 4

status: Public on Jan 25 2012

city: Oxford

first: Natasha

last: Sahgal

address: Old Road Campus

department: Ludwig Institute of Cancer Research

country: United Kingdom

institute: University of Oxford

description: Gene expression data from CD161++CD8aa T cells.

hyb_protocol: Following fragmentation, 5ug of biotinylated cDNA was hybridized to GeneChip Human Genome U133 Plus 2.0 arrays (Affymetrix) for 18 hrs at 45C and stained in the Affymetrix 3 GeneChip® Fluidics Stations F450.

scan_protocol: GeneChip® Scanner 3000 7G with autoloader.

data_processing: Raw data was analyzed using R and Bioconductor packages to generate RMA-normalized intensities.

label: Biotin

source_name: Ex-vivo CD161++CD8aa T cells

label_protocol: Biotinylated cDNA were prepared according to the Ovation Pico WTA system (Nugen) protocol.

extract_protocol: Total RNA was extracted using the RNeasy mini extraction kit (Qiagen) according to the manufacturer's instructions.

value: peripheral blood

value: CD161++CD8aa T cells

tag: disease state

value: healthy


title: CD161++CD8ab, biological rep 3

description: Gene expression data from CD161++CD8ab T cells.

source_name: Ex-vivo CD161++CD8ab T cells

value: CD161++CD8ab T cells


title: MCF10_E545K_24Hr_LY_vs_E545K_0Hr_LY_Treatment_v2.0

description: MCF-10A cells with the PIK3CA E545K mutation were treated with LY294002 for 24 hours and compared to MCF-10A cells with the PIK3CA E545K mutation.


title: MCF10_E545K_24Hr_vs_E545K_0Hr_IL6R_Inhibitor_v1.1

description: MCF-10A cells with the PIK3CA E545K mutation were treated with an IL-6 receptor monoclonal antibody for 24 hours and compared to MCF-10A cells with the PIK3CA E545K mutations.


title: CD161++CD8aa, biological rep 3


title: MCF10_E545K_24Hr_LY_vs_E545K_0Hr_LY_Treatment_v1.1


title: MCF10_E545K_4Hr_LY_vs_E545K_0Hr_LY_Treatment_v1.0


title: MCF10_E545K_4Hr_LY_vs_E545K_0Hr_LY_Treatment_v2.0


title: MCF10_E545K_BAY_vs_E545K_DMSO_4Hr_v1.1


title: MCF10_E545K_24Hr_LY_vs_E545K_0Hr_LY_Treatment_v1.0


title: MCF10_E545K_DMSO_vs_GFP_DMSO_4Hr_v1.0


title: CD161++CD8ab, biological rep 4


title: MCF10_E545K_DMSO_vs_GFP_DMSO_4Hr_v1.1


title: MCF10_E545K_24Hr_vs_E545K_0Hr_IL6R_Inhibitor_v2.0


title: MCF10_E545K_24Hr_vs_E545K_0Hr_IL6R_Inhibitor_v1.0


title: MCF10_E545K_4Hr_vs_E545K_0Hr_IL6R_Inhibitor_v1.0


title: CD161++CD8aa, biological rep 2


title: CD161++CD8ab, biological rep 2


title: 227157-2008

status: Public on Jan 13 2012

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: i-spy id

tag: experiment name

tag: study

value: ISPY

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: Luminal A

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

tag: pathological complete response (pcr)

value: No

tag: rcb class

value: III=RCB index greater than 3.28

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1415

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)

tag: survival status (7=alive; 8=dead, 9=lost)


title: 219373-2008

tag: reference

tag: slide name

tag: i-spy id

tag: experiment name

tag: her2 (0=negative; 1=positive;)

value: Basal-like

value: II=RCB index greater than 1.36 or equal to 3.28

value: local or distant progression or death (time unit is days):524


title: CD161++CD8ab, biological rep 1

tag: tissue

tag: cell type

tag: disease state


title: MCF10_H1047R_24Hr_vs_H1047R_0Hr_IL6R_Inhibitor_v1.0

tag: cell line

tag: genotype/variation


title: 218013-2008

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

value: local or distant progression or death (time unit is days):303


title: CD161++CD8aa, biological rep 1


title: 219392-2008

tag: reference

tag: slide name

tag: i-spy id

tag: experiment name

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:4

tag: pathological complete response (pcr)

tag: rcb class

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):216

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)

tag: survival status (7=alive; 8=dead, 9=lost)


title: 219411-2008

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: her2 (0=negative; 1=positive;)

value: Unavailable

value: local or distant progression or death (time unit is days):369


title: 245509-3

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: Luminal B

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:3

value: local or distant progression or death (time unit is days):1031


title: 219170-2008

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: slide name

tag: i-spy id

tag: experiment name

value: ISPY

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

value: local or distant progression or death (time unit is days):1670


title: 254449-3weak

value: Luminal A

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

tag: pathological complete response (pcr)

value: No

tag: rcb class

value: I=RCB index less than or equal to 1.36

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1155

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 225023-2008

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

value: III=RCB index greater than 3.28

value: local or distant progression or death (time unit is days):298

tag: survival status (7=alive; 8=dead, 9=lost)


title: 235184-2

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: her2 (0=negative; 1=positive;)

value: Basal-like

value: local or distant progression or death (time unit is days):315


title: 244359-3

tag: reference

tag: slide name

tag: i-spy id

tag: experiment name

tag: intrinsic subtype by pam50

value: II=RCB index greater than 1.36 or equal to 3.28

value: local or distant progression or death (time unit is days):1379


title: 226920-2008

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

tag: rcb class

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1928

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 227535-2008

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

value: Luminal B

value: local or distant progression or death (time unit is days):571

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 212062-2008

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

value: Unavailable

value: local or distant progression or death (time unit is days):2266

tag: survival status (7=alive; 8=dead, 9=lost)


title: 244677

tag: reference

tag: slide name

tag: i-spy id

tag: experiment name

value: ISPY

tag: her2 (0=negative; 1=positive;)

value: local or distant progression or death (time unit is days):1197


title: 221152-2008

tag: intrinsic subtype by pam50

value: Luminal A

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

tag: pathological complete response (pcr)

value: No

tag: rcb class

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1876


title: 254890

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

value: local or distant progression or death (time unit is days):185

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 254433

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

value: Basal-like

value: Yes

value: 0=RCB index 0

value: local or distant progression or death (time unit is days):644

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 240236

tag: reference

tag: slide name

tag: i-spy id

tag: experiment name

value: II=RCB index greater than 1.36 or equal to 3.28

value: local or distant progression or death (time unit is days):970

tag: survival status (7=alive; 8=dead, 9=lost)


title: 254900weak

tag: her2 (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:3

tag: pathological complete response (pcr)

tag: rcb class

value: local or distant progression or death (time unit is days):478


title: 219203-2008

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

value: Normal-like

value: Unavailable

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):469


title: 232500-2

value: ISPY

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

value: Luminal B

value: local or distant progression or death (time unit is days):1624

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 254443weak

tag: reference

tag: slide name

tag: i-spy id

tag: experiment name

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

value: local or distant progression or death (time unit is days):1234

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 245829

tag: her2 (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: Basal-like

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: No

value: III=RCB index greater than 3.28

value: local or distant progression or death (time unit is days):510

tag: survival status (7=alive; 8=dead, 9=lost)


title: 254439

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

value: Luminal A

tag: rcb class

value: II=RCB index greater than 1.36 or equal to 3.28

value: local or distant progression or death (time unit is days):1303


title: 242696

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:3

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):644


title: 254435

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: slide name

tag: i-spy id

tag: experiment name

value: Yes

value: 0=RCB index 0

value: local or distant progression or death (time unit is days):1227

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 239357

value: ISPY

tag: her2 (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: local or distant progression or death (time unit is days):1441

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 243504

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:1

value: local or distant progression or death (time unit is days):1183

tag: survival status (7=alive; 8=dead, 9=lost)


title: 231719

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

tag: rcb class

value: local or distant progression or death (time unit is days):1190


title: 238847

tag: reference

tag: slide name

tag: i-spy id

tag: experiment name

value: No

value: III=RCB index greater than 3.28

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1111


title: 239105

tag: her2 (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: Luminal A

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: Unavailable

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 239734

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

value: Basal-like

value: local or distant progression or death (time unit is days):1309

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 238399

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

value: I=RCB index less than or equal to 1.36

value: local or distant progression or death (time unit is days):1000

tag: survival status (7=alive; 8=dead, 9=lost)


title: 232147

tag: reference

tag: slide name

tag: i-spy id

tag: experiment name

value: Normal-like

value: Yes

tag: rcb class

value: 0=RCB index 0

value: local or distant progression or death (time unit is days):384


title: 229951

value: ISPY

tag: intrinsic subtype by pam50

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):718


title: 239010

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: her2 (0=negative; 1=positive;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

value: II=RCB index greater than 1.36 or equal to 3.28

value: local or distant progression or death (time unit is days):1126

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 230572

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: er (0=negative; 1=positive;)

value: local or distant progression or death (time unit is days):371

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 248290

tag: reference

tag: slide name

tag: i-spy id

tag: pgr  (0=negative; 1=positive;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:3

value: local or distant progression or death (time unit is days):953

tag: survival status (7=alive; 8=dead, 9=lost)


title: 244242

tag: experiment name

tag: intrinsic subtype by pam50

value: Luminal A

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: No

tag: rcb class

value: local or distant progression or death (time unit is days):481


title: 231867

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: her2 (0=negative; 1=positive;)

value: Basal-like

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1615


title: 242624-3

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: er (0=negative; 1=positive;)

value: local or distant progression or death (time unit is days):1159

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 238587

tag: reference

tag: slide name

tag: i-spy id

tag: pgr  (0=negative; 1=positive;)

value: local or distant progression or death (time unit is days):1050

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 237951

tag: experiment name

tag: intrinsic subtype by pam50

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: III=RCB index greater than 3.28

value: local or distant progression or death (time unit is days):1425

tag: survival status (7=alive; 8=dead, 9=lost)


title: 232542

tag: study

value: ISPY

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: her2 (0=negative; 1=positive;)

tag: rcb class

value: I=RCB index less than or equal to 1.36

value: local or distant progression or death (time unit is days):1190


title: 235681

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: er (0=negative; 1=positive;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

value: Yes

value: 0=RCB index 0

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):499


title: 230875

tag: reference

tag: slide name

tag: i-spy id

tag: pgr  (0=negative; 1=positive;)

value: Luminal A

value: local or distant progression or death (time unit is days):283

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 225625

tag: experiment name

tag: intrinsic subtype by pam50

value: Luminal B

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: No

value: II=RCB index greater than 1.36 or equal to 3.28

value: local or distant progression or death (time unit is days):1349

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 225347

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

value: local or distant progression or death (time unit is days):1420

tag: survival status (7=alive; 8=dead, 9=lost)


title: 238715

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: her2 (0=negative; 1=positive;)

value: Basal-like

tag: rcb class

value: III=RCB index greater than 3.28

value: local or distant progression or death (time unit is days):274


title: 231660

tag: reference

tag: slide name

tag: i-spy id

value: ISPY

value: Normal-like

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1534


title: 231387

tag: experiment name

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

value: Yes

value: local or distant progression or death (time unit is days):1646

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 230370

tag: study

tag: age

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: 0=RCB index 0

value: local or distant progression or death (time unit is days):1261

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 231480

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

value: Luminal B

value: local or distant progression or death (time unit is days):1617

tag: survival status (7=alive; 8=dead, 9=lost)


title: 231535

tag: reference

tag: slide name

tag: i-spy id

tag: her2 (0=negative; 1=positive;)

value: Luminal A

value: No

tag: rcb class

value: II=RCB index greater than 1.36 or equal to 3.28

value: local or distant progression or death (time unit is days):1544


title: 227624

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: experiment name

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: I=RCB index less than or equal to 1.36

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1887


title: 227022

tag: study

value: ISPY

tag: age

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: local or distant progression or death (time unit is days):1481

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 227838

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

value: Basal-like

value: local or distant progression or death (time unit is days):1375

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 229274

tag: reference

tag: slide name

tag: i-spy id

tag: her2 (0=negative; 1=positive;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

value: III=RCB index greater than 3.28

value: local or distant progression or death (time unit is days):360

tag: survival status (7=alive; 8=dead, 9=lost)


title: 225866

tag: experiment name

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: Yes

tag: rcb class

value: 0=RCB index 0

value: local or distant progression or death (time unit is days):1510


title: 227422

tag: study

tag: age

value: Luminal A

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1652


title: 229433

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

value: local or distant progression or death (time unit is days):1679

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 229141

tag: reference

tag: slide name

tag: i-spy id

tag: her2 (0=negative; 1=positive;)

value: No

value: local or distant progression or death (time unit is days):1596

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 229567

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: experiment name

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: local or distant progression or death (time unit is days):1329

tag: survival status (7=alive; 8=dead, 9=lost)


title: 228257

tag: study

value: ISPY

tag: age

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

tag: rcb class

value: local or distant progression or death (time unit is days):1472


title: 222920

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

value: Luminal B

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1513


title: 216826

tag: reference

tag: slide name

tag: i-spy id

tag: her2 (0=negative; 1=positive;)

value: Basal-like

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:1

value: local or distant progression or death (time unit is days):225

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 215630

tag: experiment name

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

value: II=RCB index greater than 1.36 or equal to 3.28

value: local or distant progression or death (time unit is days):224

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 225635

tag: study

tag: age

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:3

tag: pathological complete response (pcr)

value: Yes

value: 0=RCB index 0

value: local or distant progression or death (time unit is days):1886

tag: survival status (7=alive; 8=dead, 9=lost)


title: 220456

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

value: No

tag: rcb class

value: local or distant progression or death (time unit is days):1981


title: 225737

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: slide name

tag: i-spy id

tag: her2 (0=negative; 1=positive;)

value: Luminal A

value: III=RCB index greater than 3.28

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1802


title: 226662

tag: experiment name

value: ISPY

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: Luminal B

value: local or distant progression or death (time unit is days):1756

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 226342

tag: study

tag: age

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: local or distant progression or death (time unit is days):1516

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 217419

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

value: Basal-like

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

value: local or distant progression or death (time unit is days):663

tag: survival status (7=alive; 8=dead, 9=lost)


title: 218367

tag: reference

tag: slide name

tag: i-spy id

tag: her2 (0=negative; 1=positive;)

tag: rcb class

value: II=RCB index greater than 1.36 or equal to 3.28

value: local or distant progression or death (time unit is days):179


title: 221380

tag: experiment name

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: Normal-like

value: Yes

value: 0=RCB index 0

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1891


title: 218564

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: study

tag: age

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: No

value: local or distant progression or death (time unit is days):1738

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 214699-Repeat

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:1

value: local or distant progression or death (time unit is days):1058

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 217408

tag: reference

tag: slide name

tag: i-spy id

value: ISPY

tag: her2 (0=negative; 1=positive;)

value: III=RCB index greater than 3.28

tag: survival status (7=alive; 8=dead, 9=lost)


title: 211158

tag: experiment name

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

tag: rcb class

value: local or distant progression or death (time unit is days):2370


title: 213782

tag: study

tag: age

value: Luminal A

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):729


title: 226791

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

value: local or distant progression or death (time unit is days):1906

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 211754

tag: reference

tag: slide name

tag: i-spy id

tag: her2 (0=negative; 1=positive;)

value: Basal-like

value: local or distant progression or death (time unit is days):2340

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 210832

tag: experiment name

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: II=RCB index greater than 1.36 or equal to 3.28

value: local or distant progression or death (time unit is days):2355

tag: survival status (7=alive; 8=dead, 9=lost)


title: 213088

tag: study

tag: age

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

tag: rcb class

value: local or distant progression or death (time unit is days):410


title: 212312

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

value: Unavailable

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):273


title: 210891

tag: reference

tag: slide name

tag: i-spy id

tag: her2 (0=negative; 1=positive;)

value: Luminal B

value: No

value: local or distant progression or death (time unit is days):759

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 212619

tag: experiment name

value: ISPY

tag: intrinsic subtype by pam50

value: local or distant progression or death (time unit is days):1555

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 235704

tag: study

tag: age

value: local or distant progression or death (time unit is days):1662

tag: survival status (7=alive; 8=dead, 9=lost)


title: Stri 574-44K

tag: tissue

value: normal breast


title: 211629

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

tag: pathological complete response (pcr)

value: Yes

tag: rcb class

value: 0=RCB index 0

value: local or distant progression or death (time unit is days):2213


title: 215309

tag: reference

tag: slide name

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

value: II=RCB index greater than 1.36 or equal to 3.28

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):2033


title: 222598

tag: i-spy id

tag: experiment name

tag: her2 (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: local or distant progression or death (time unit is days):1766

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 211643

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: er (0=negative; 1=positive;)

value: local or distant progression or death (time unit is days):639

tag: survival status (7=alive; 8=dead, 9=lost)


title: 221399

tag: reference

tag: pgr  (0=negative; 1=positive;)

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

tag: rcb class

value: local or distant progression or death (time unit is days):1926


title: 209389

tag: slide name

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

value: Basal-like

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):2436


title: 214462

tag: i-spy id

tag: experiment name

tag: her2 (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: No

value: I=RCB index less than or equal to 1.36

value: local or distant progression or death (time unit is days):1843

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 212695

tag: study

value: ISPY

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: er (0=negative; 1=positive;)

value: Luminal A

value: local or distant progression or death (time unit is days):1384

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 214474

tag: reference

tag: pgr  (0=negative; 1=positive;)

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

tag: pathological complete response (pcr)

value: local or distant progression or death (time unit is days):1806

tag: survival status (7=alive; 8=dead, 9=lost)


title: 214441

tag: slide name

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: rcb class

value: local or distant progression or death (time unit is days):1924


title: 254438-2008

tag: i-spy id

tag: experiment name

tag: her2 (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:3

value: II=RCB index greater than 1.36 or equal to 3.28

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1148


title: 218521

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: er (0=negative; 1=positive;)

value: Yes

value: 0=RCB index 0

value: local or distant progression or death (time unit is days):1655

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 238178-2008

tag: reference

value: Luminal B

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: local or distant progression or death (time unit is days):1238

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 217568-weak

tag: slide name

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: pgr  (0=negative; 1=positive;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:1

value: No

value: local or distant progression or death (time unit is days):1992

tag: survival status (7=alive; 8=dead, 9=lost)


title: 209534

tag: i-spy id

tag: experiment name

value: ISPY

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: her2 (0=negative; 1=positive;)

tag: rcb class

value: III=RCB index greater than 3.28

value: local or distant progression or death (time unit is days):1043


title: 226962-2008

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: intrinsic subtype by pam50

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1967


title: 209515

tag: reference

tag: er (0=negative; 1=positive;)

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: local or distant progression or death (time unit is days):751

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 225982

tag: slide name

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: pgr  (0=negative; 1=positive;)

value: Normal-like

value: local or distant progression or death (time unit is days):1802

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 221853

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: i-spy id

tag: experiment name

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: her2 (0=negative; 1=positive;)

value: Luminal A

value: II=RCB index greater than 1.36 or equal to 3.28

value: local or distant progression or death (time unit is days):1812

tag: survival status (7=alive; 8=dead, 9=lost)


title: 217144

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: intrinsic subtype by pam50

value: Luminal B

tag: rcb class

value: local or distant progression or death (time unit is days):1679


title: 209633

tag: reference

tag: er (0=negative; 1=positive;)

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: Unavailable

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):2520


title: 233841-2008

tag: slide name

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: pgr  (0=negative; 1=positive;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:3

value: No

value: local or distant progression or death (time unit is days):1289

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 225708-2008

tag: i-spy id

tag: experiment name

value: ISPY

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: her2 (0=negative; 1=positive;)

value: Basal-like

value: local or distant progression or death (time unit is days):1154

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 245424-2008

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: intrinsic subtype by pam50

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

value: local or distant progression or death (time unit is days):1248

tag: survival status (7=alive; 8=dead, 9=lost)


title: 254442-2008

tag: reference

tag: er (0=negative; 1=positive;)

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

tag: rcb class

value: local or distant progression or death (time unit is days):1272


title: 227349-2008

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: slide name

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: pgr  (0=negative; 1=positive;)

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):530


title: 211739

tag: i-spy id

tag: experiment name

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: her2 (0=negative; 1=positive;)

value: II=RCB index greater than 1.36 or equal to 3.28

value: local or distant progression or death (time unit is days):2312

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 212114

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: intrinsic subtype by pam50

value: Luminal B

value: local or distant progression or death (time unit is days):1242

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 216719

tag: reference

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: Yes

value: 0=RCB index 0

value: local or distant progression or death (time unit is days):475

tag: survival status (7=alive; 8=dead, 9=lost)


title: 237516-2008

tag: slide name

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: er (0=negative; 1=positive;)

value: No

tag: rcb class

value: local or distant progression or death (time unit is days):1318


title: 245219-2008

tag: i-spy id

tag: experiment name

value: ISPY

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: pgr  (0=negative; 1=positive;)

value: Normal-like

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:3

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):694


title: 223651-2008

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: her2 (0=negative; 1=positive;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

value: I=RCB index less than or equal to 1.36

value: local or distant progression or death (time unit is days):1959

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 232839-2008

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: intrinsic subtype by pam50

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: local or distant progression or death (time unit is days):1470

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 224298

tag: slide name

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: er (0=negative; 1=positive;)

value: II=RCB index greater than 1.36 or equal to 3.28

value: local or distant progression or death (time unit is days):873

tag: survival status (7=alive; 8=dead, 9=lost)


title: 232340-2008

tag: i-spy id

tag: experiment name

tag: pgr  (0=negative; 1=positive;)

value: Basal-like

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:4

tag: rcb class

value: Unavailable

value: local or distant progression or death (time unit is days):1595


title: 232413-2008

tag: study

tag: age

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

value: No

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1521


title: 235533-2008

tag: reference

value: ISPY

tag: her2 (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

value: Yes

value: 0=RCB index 0

value: local or distant progression or death (time unit is days):855

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: 240415-2008

tag: slide name

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

value: Luminal A

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:3

tag: pathological complete response (pcr)

value: local or distant progression or death (time unit is days):1113

tag: overall survival - time from study chemo start date to death or last follow-up; (time unit is days)


title: 234915-2008

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

tag: i-spy id

tag: experiment name

tag: er (0=negative; 1=positive;)

tag: pgr  (0=negative; 1=positive;)

value: A = doxorubicin, C = Cyclophosphamide, T = taxane:2

value: local or distant progression or death (time unit is days):326

tag: survival status (7=alive; 8=dead, 9=lost)


title: Kidney, high-phosphorus diet administrated for 24d, biological rep3

status: Public on Jan 12 2012

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

data_processing: CEL files were quantified with the distribution free weighted (DFW) method, using the statistical language R and Bioconductor.

organism: Rattus norvegicus

source_name: Kidney, fed 1.2% phosphorus containing diet for 24d

label_protocol: biotinylated aRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen Life Technologies Corp.), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

tag: gender

value: Male

tag: strain

value: Wistar

tag: tissue

value: Kidney

tag: age

value: 8 weeks

tag: diet

value: 1.2% phosphorus containing diet for 24d


title: Kidney, high-phosphorus diet administrated for 24d, biological rep2


title: Kidney, high-phosphorus diet administrated for 24d, biological rep4


title: Kidney, high-phosphorus diet administrated for 24d, biological rep1


title: Kidney, control diet administrated for 24d, biological rep4

source_name: Kidney, fed control AIN-93G diet for 24d

value: control AIN-93G diet for 24d


title: T47D_2

status: Public on Dec 21 2011

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-147

source_name: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

label_protocol: Homo sapiens

growth_protocol: Total RNA isolated by stratagene

tag: reference

value: Human Reference B

source_name: T47D, parental cell lines, Cells were grown in EGM-2 and RNA was collected at 80-90% confluence

tag: exptid

tag: printid

tag: tumor cell line


title: T47D_E_1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-140

source_name: T47D, parental cell lines were grown in mammary glands of nude mice, tumors were extracted and sublines were grown in steroid-depleted media supplemented with 1nM estradiol-17β supplemented media (E)


title: Kidney, control diet administrated for 24d, biological rep3


title: Kidney, control diet administrated for 24d, biological rep1


title: T47D_1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-146


title: T47D_E_3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-142


title: T47D_3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-148


title: SUM149_2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-135

source_name: SUM149, Cells were grown in EGM-2 and RNA was collected at 80-90% confluence


title: Kidney, control diet administrated for 24d, biological rep2


title: SUM159_3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-139

source_name: SUM159, Cells were grown in EGM-2 and RNA was collected at 80-90% confluence


title: T47D_EWD_2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-144

source_name: T47D, parental cell lines were grown in mammary glands of nude mice, tumors were extracted and sublines were grown in steroid-depleted media (EWD)


title: SUM149_1

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134


title: SUM159_1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-137


title: T47D_EWD_1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-143


title: T47D_EWD_3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-145


title: Breast Tumor 247

status: Public on Nov 06 2011

type: genomic

description: Paired Normal Sample (Rref) came from normal DNA from EBV immortalized Lymphocyte

hyb_protocol: The samples were loaded onto the Human-1 array, and hybridized overnight for 16h at 48°C. Following hybridization, the beadchips were submerged in buffer, spun dry in a centrifuge, and assembled into a TeFlow hydro-chamber heated to 44°C

scan_protocol: Within three days, beadchips were imaged on the BeadArray reader using BeadScan software.

data_processing: Sample values were derived follwing a 'PairedSample Analysis' from Illumina's BeadStudio Genotyping Module v(3.3.4)

source_name: Breast Tumor

label_protocol: 250 ng of genomic DNA was used as template for WGA, using Illumina proprietary reagents. Following WGA, the amplified DNA was enzymatically fragmented, isopropanol precipitated and resuspended in Illumina resuspension buffer

extract_protocol: Peripheral blood was collected in EDTA and stored at -40°C. DNA was isolated using phenol/chloroform extraction and ethanol precipitation as described previously (Andersen et al., 1992). Tumor DNA from snap frozen tumors, stored at -80°C, was isolated following the same Phenol/Chloroform extraction procedure.

tag: subtype

value: Claudin


title: MCF7_3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127

source_name: MCF7, Cells were grown in EGM-2 and RNA was collected at 80-90% confluence


title: MDA231_3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130

source_name: MDA231, Cells were grown in EGM-2 and RNA was collected at 80-90% confluence


title: SKBR3_1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131

source_name: SKBR3, Cells were grown in EGM-2 and RNA was collected at 80-90% confluence


title: MDA231_2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129


title: Breast Tumor 709

value: Basal


title: Breast Tumor 221


title: Breast Tumor 71


title: Breast Tumor 42


title: Breast Tumor 185


title: MCF7_1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125


title: SKBR3_3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-133


title: Breast Tumor 67


title: Breast Tumor 298


title: Breast Tumor 722

value: LumB


title: Breast Tumor 197


title: Breast Tumor 246


title: Breast Tumor 630


title: 232061-2008

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

source_name: Human Reference B

tag: slide name

tag: study

value: ISPY

tag: histologic grade (1=grade i (low);  2= grade ii (intermediate); 3= grade iii (high); 4=indeterminate)

tag: histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present;)

tag: clinical tumor size (pre-chemotherapy), cm (-1 = n/a)

tag: clinical t stage (pre-chemotherapy) (1 = <= 2cm; 2 = >2-5 cm; 3 = > 5cm)

tag: her2 (0=negative; 1=positive;)

tag: intrinsic subtype by pam50

value: Luminal B

tag: neoadjuvant chemotherapy* (1 = ac only; 2 = ac + t; 3 = ac + t + herceptin; 4 = ac + t + other;)

tag: pathological complete response (pcr)

value: No

tag: rcb class

value: II=RCB index greater than 1.36 or equal to 3.28

tag: relapse-free survival time – time from chemo start date until earliest

value: local or distant progression or death (time unit is days):1581

tag: relapse-free survival indicator (1=event; local or distant progression or death, 0=censor at last follow-up)


title: Breast Tumor 267


title: Breast Tumor 24


title: Breast Tumor 132


title: Breast Tumor 334

value: Normal-like


title: Breast Tumor 18


title: Breast Tumor 209


title: Breast Tumor 391


title: Breast Tumor 512


title: Breast Tumor 234


title: Breast Tumor 371


title: Breast Tumor 31


title: Breast Tumor 539


title: Breast Tumor 318


title: Breast Tumor 91


title: Breast Tumor 579


title: Breast Tumor 277


title: Breast Tumor 167


title: Breast Tumor 64


title: Breast Tumor 283


title: Breast Tumor 119


title: Breast Tumor 190


title: Breast Tumor 79


title: Breast Tumor 20


title: Breast Tumor 80


title: Breast Tumor 53


title: Breast Tumor 476


title: Breast Tumor 75


title: Breast Tumor 146


title: Breast Tumor 57


title: Breast Tumor 44


title: Breast Tumor 100


title: Breast Tumor 144


title: Breast Tumor 88


title: Breast Tumor 240


title: Breast Tumor 627


title: Breast Tumor 232


title: Breast Tumor 359

value: LumA


title: Breast Tumor 551


title: Breast Tumor 355


title: Breast Tumor 22


title: Breast Tumor 363


title: Breast Tumor 34


title: Breast Tumor 89


title: Breast Tumor 632


title: Breast Tumor 570


title: Breast Tumor 493


title: Breast Tumor 488


title: Breast Tumor 451


title: Breast Tumor 470


title: Breast Tumor 406


title: Breast Tumor 378


title: Breast Tumor 381


title: Breast Tumor 357


title: Breast Tumor 308


title: Breast Tumor 309


title: Breast Tumor 430


title: Breast Tumor 17


title: Breast Tumor 222


title: Breast Tumor 275


title: Breast Tumor 223


title: Breast Tumor 245


title: Breast Tumor 263


title: Breast Tumor 285


title: Breast Tumor 210


title: Breast Tumor 220


title: Breast Tumor 264


title: Breast Tumor 300


title: Breast Tumor 457


title: Breast Tumor 388


title: Breast Tumor 201


title: Breast Tumor 163


title: Breast Tumor 122


title: Breast Tumor 338


title: Breast Tumor 150


title: Breast Tumor 139


title: Breast Tumor 106


title: Breast Tumor 101


title: Breast Tumor 148


title: Breast Tumor 83


title: Breast Tumor 86


title: Breast Tumor 98


title: Breast Tumor 85


title: Breast Tumor 19


title: Breast Tumor 69


title: Breast Tumor 112


title: Breast Tumor 65


title: Breast Tumor 68


title: Breast Tumor 14


title: BR00-0504

description: Paired Normal Sample (Rref) came from Normal DNA from Normal Breast


title: Breast Tumor 15


title: Breast Tumor 23


title: BR97-0137-VIM


title: BR00-0344


title: BR01-0349


title: BR00-0572-VIM


title: BR95-0184


title: BR95-0017


title: BR00-0284


title: BR00-0587-GATA3


title: Breast Tumor 3


title: BC00094T


title: BC00086


title: BC00085


title: BC00097


title: BR00-0387


title: BC00043T


title: A8-Lung-Met

description: Paired Normal Sample (Rref) came from Normal DNA from Met Site

source_name: Autopsy patient #8 Lung metastasis from breast


title: BC00014


title: BC00041


title: A7-LN-Met

source_name: Autopsy patient #7 Lymph Node metastasis from breast


title: 9830-030562B

source_name: Breast Tumor, tamoxifen-treated patient


title: A1-17-Left-Primary-VIM

source_name: Autopsy patient #1 breast primary tumor


title: BC00054

value: Claudin-low


title: BC00017-T


title: BC00033-T


title: A5-Skin-Left-Met

source_name: Autopsy patient #5 skin metastasis from breast foci B


title: A6-Liver-Met

source_name: Autopsy patient #6 metastasis from breast to Liver


title: 9830-020461B