title: BLCA_Cx_298

status: Public on Mar 13 2017

city: Lund

first: Pontus

last: Eriksson

state: Select:

address: Scheelevägen 2

department: Department of Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor R package Affy. Probe intensities were normalized in labeling batches of 24 using RMA. Batches were combined and RMA normalized.
The file Processed_Data_Supplement.txt contains ready-to-use median centered gene expression data for 307 tumor samples, with EntrezID and GeneSymbol. Sample order is derived from ConsensusClusterPlus, performed on the top 50% variance genes (n=7031) and matches the Sjodahl 2017 publication. Metadata: CEL Filename, GEO_SampleName, Labeling Batch, Hybridisation Number, TURB Stage, TURB Grade, Lund 2012 Taxonomy By Centroid Correlation, ConsensusClusterPlus Cluster, Sjodahl 2017 mRNA-cluster/Phenotype, Publication Heatmap Order.

source_name: FFPE tissue specimen

label_protocol: SensationPlus FFPE Amplification and WT labeling kit

extract_protocol: High Pure FFPET RNA isolation kit (Roche)

value: bladder cancer

tag: stage and grade

value: pT2   Gx

tag: labeling batch


title: Breast Cancer Array_Patient ID_21009_BL

status: Public on Jan 04 2017

type: RNA

city: st louis

first: Cynthia

last: Ma

state: Missouri

address: 4515 Mckinley, 4515 Mckinley

department: Medical Oncology

country: USA

institute: Washington University

hyb_protocol: Agilent 60-mer oligo microarray processing protocol

scan_protocol: Microarrays were scanned with an Agilent Scanner.

data_processing: txt files from Agilent Feature Extraction software were loaded into the UNC-CH Microarray Database. Final loess, normalized log2 ratios (Cy5-sample/Cy3-control) for each probe were retrieved after applying default quality control filters.

molecule: total RNA

organism: Homo sapiens

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

label_protocol: Agilent Low Input Linear Amplification Kit and protocol

growth_protocol: patient biopsies were frozen and stored in oct compound

extract_protocol: Trizol extractions followed by Dnase treatment and column purification.

tag: rna source

value: Total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.

source_name: Primary Breast Tumor_Patient ID_21009_BL

tag: tissue

value: breast cancer tissue

tag: biopsy type

value: oct blocks from fine needle biopsies which contained at least 50% tumor cellularity

tag: study id

tag: studynum

tag: bl  ki67

tag: eot ki67

tag: endocrine therapy response group

value: sensitive

tag: treatment course

value: continue AI


title: Breast Cancer Array_Patient ID_18155_w2

source_name: Primary Breast Tumor_Patient ID_18155_w2


title: Breast Cancer Array_Patient ID_18161_BL

source_name: Primary Breast Tumor_Patient ID_18161_BL


title: Breast Cancer Array_Patient ID_18161_w2

source_name: Primary Breast Tumor_Patient ID_18161_w2


title: Breast Cancer Array_Patient ID_21072_M_Redo

source_name: Primary Breast Tumor_Patient ID_21072_M_Redo


title: Breast Cancer Array_Patient ID_18183_BL

source_name: Primary Breast Tumor_Patient ID_18183_BL


title: BLCA_Cx_188

label: biotin

value: pT2   G3


title: BLCA_Cx_229


title: Breast Cancer Array_Patient ID_18156_BL_Redo

source_name: Primary Breast Tumor_Patient ID_18156_BL_Redo


title: Breast Cancer Array_Patient ID_18189_BL

source_name: Primary Breast Tumor_Patient ID_18189_BL


title: Breast Cancer Array_Patient ID_18184_W2

source_name: Primary Breast Tumor_Patient ID_18184_W2


title: BLCA_Cx_167

value: pTa   G2


title: Breast Cancer Array_Patient ID_18197_BL

source_name: Primary Breast Tumor_Patient ID_18197_BL


title: Breast Cancer Array_Patient ID_203_C1D15

status: Public on Apr 07 2017

description:
pd991
Sample name: 203_C1D15
Generated labeled cRNA.

hyb_protocol: Agilent 60-mer oligo microarray processing protocol.

data_processing:
Text files from Agilent Feature Extraction software were loaded into the UNC-CH Microarray Database. Final Loess, normalized log2 ratios (Cy5-sample/Cy3-control) for each probe were retrieved after applying default quality control filters.
Probes were excluded if the microarray spot: a) was not found in either channel, b) is a non-uniform outlier, c) background is a non-uniform outlier, d) is a non-uniform outlier for the population, e) background is a non-uniform outlier for the population, or f) is not a positive and significant signal in either channel.

source_name: Stratagene Human Universal Reference spiked with MCF7 and ME16C mRNA

label_protocol: Agilent Low Input Linear Amplification Kit and protocol.

extract_protocol: Trizol extractions followed by DNase treatment and column purification.

tag: cell line

value: 10 human cell lines (1_Adenocarcinoma, mammary gland; 2_Hepatoblastoma, liver; 3_Adenocarcinoma, cervix; 4_Embryonal carcinoma, testis; 5_Glioblastoma, brain; 6_Melanoma; 7_Liposarcoma; 8_Histiocytic Lymphoma; macrophage; histocyte; 9_ Lymphoblastic leukemia, T lymphoblast; 10_Plasmacytoma; myeloma; B lymphocyte). Also, mRNA spiked in from MCF7 and ME16C.

tag: sample type

value: reference

source_name: Primary Breast Tumor_Patient ID_203_C1D15

growth_protocol: Patient biopsies were frozen and stored in oct compound.

treatment_protocol: The treatment time course is BL - C1D1 - C1D15 - Surgery.

tag: disease state

value: breast cancer

value: oct blocks from fine needle breast tumor biopsies which contained at least 50% tumor cellularity

tag: treatment

tag: patient id


title: BLCA_Cx_64


title: Breast Cancer Array_Patient ID_18156_W2

source_name: Primary Breast Tumor_Patient ID_18156_W2


title: Breast Cancer Array_Patient ID_18115_BL

source_name: Primary Breast Tumor_Patient ID_18115_BL


title: Breast Cancer Array_Patient ID_18145_M

source_name: Primary Breast Tumor_Patient ID_18145_M

value: resistant

value: chose to continue on AI


title: Breast Cancer Array_Patient ID_18145_BL

source_name: Primary Breast Tumor_Patient ID_18145_BL


title: Breast Cancer Array_Patient ID_18025_BL

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_18025_BL

value: switch to NAC


title: Breast Cancer Array_Patient ID_18025_w2

source_name: Primary Breast Tumor_Patient ID_18025_w2


title: Breast Cancer Array_Patient ID_18052_w2

source_name: Primary Breast Tumor_Patient ID_18052_w2


title: Breast Cancer Array_Patient ID_18091_BL

source_name: Primary Breast Tumor_Patient ID_18091_BL


title: Breast Cancer Array_Patient ID_17881_BL

source_name: Primary Breast Tumor_Patient ID_17881_BL


title: Breast Cancer Array_Patient ID_18091_M

source_name: Primary Breast Tumor_Patient ID_18091_M


title: Breast Cancer Array_Patient ID_17946_w2

source_name: Primary Breast Tumor_Patient ID_17946_w2


title: Breast Cancer Array_Patient ID_18115_w2

source_name: Primary Breast Tumor_Patient ID_18115_w2


title: Breast Cancer Array_Patient ID_17902_M

source_name: Primary Breast Tumor_Patient ID_17902_M


title: Breast Cancer Array_Patient ID_17868_w2_Redo

source_name: Primary Breast Tumor_Patient ID_17868_w2_Redo


title: Breast Cancer Array_Patient ID_18052_BL

source_name: Primary Breast Tumor_Patient ID_18052_BL


title: Breast Cancer Array_Patient ID_17913_w2

source_name: Primary Breast Tumor_Patient ID_17913_w2


title: Breast Cancer Array_Patient ID_17860_BL

source_name: Primary Breast Tumor_Patient ID_17860_BL


title: Breast Cancer Array_Patient ID_17946_BL

source_name: Primary Breast Tumor_Patient ID_17946_BL


title: Breast Cancer Array_Patient ID_18074_w2

source_name: Primary Breast Tumor_Patient ID_18074_w2


title: Breast Cancer Array_Patient ID_17910_BL

source_name: Primary Breast Tumor_Patient ID_17910_BL


title: Breast Cancer Array_Patient ID_17835_BL

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_17835_BL


title: Breast Cancer Array_Patient ID_17881_M

source_name: Primary Breast Tumor_Patient ID_17881_M


title: Breast Cancer Array_Patient ID_17860_w2

source_name: Primary Breast Tumor_Patient ID_17860_w2


title: Breast Cancer Array_Patient ID_17835_w2

source_name: Primary Breast Tumor_Patient ID_17835_w2


title: Breast Cancer Array_Patient ID_17868_BL

source_name: Primary Breast Tumor_Patient ID_17868_BL


title: Breast Cancer Array_Patient ID_17823_w2

source_name: Primary Breast Tumor_Patient ID_17823_w2


title: Breast Cancer Array_Patient ID_17910_W2

source_name: Primary Breast Tumor_Patient ID_17910_W2


title: Breast Cancer Array_Patient ID_17913_BL

source_name: Primary Breast Tumor_Patient ID_17913_BL


title: Breast Cancer Array_Patient ID_17818_BL

source_name: Primary Breast Tumor_Patient ID_17818_BL


title: Breast Cancer Array_Patient ID_17818_W2

source_name: Primary Breast Tumor_Patient ID_17818_W2


title: Breast Cancer Array_Patient ID_17807_w2

source_name: Primary Breast Tumor_Patient ID_17807_w2


title: Breast Cancer Array_Patient ID_17807_BL

source_name: Primary Breast Tumor_Patient ID_17807_BL


title: Breast Cancer Array_Patient ID_17902_BL

source_name: Primary Breast Tumor_Patient ID_17902_BL


title: Breast Cancer Array_Patient ID_17787_w2

source_name: Primary Breast Tumor_Patient ID_17787_w2


title: Breast Cancer Array_Patient ID_17762_M

source_name: Primary Breast Tumor_Patient ID_17762_M


title: Breast Cancer Array_Patient ID_17787_BL

source_name: Primary Breast Tumor_Patient ID_17787_BL


title: Breast Cancer Array_Patient ID_17738_w2

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_17738_w2


title: Breast Cancer Array_Patient ID_17738_BL

source_name: Primary Breast Tumor_Patient ID_17738_BL


title: Breast Cancer Array_Patient ID_17733_w2

source_name: Primary Breast Tumor_Patient ID_17733_w2


title: Breast Cancer Array_Patient ID_17823_BL

source_name: Primary Breast Tumor_Patient ID_17823_BL


title: Breast Cancer Array_Patient ID_17746_BL

source_name: Primary Breast Tumor_Patient ID_17746_BL


title: Breast Cancer Array_Patient ID_17739_w2

source_name: Primary Breast Tumor_Patient ID_17739_w2


title: Breast Cancer Array_Patient ID_17675_w2

source_name: Primary Breast Tumor_Patient ID_17675_w2


title: Breast Cancer Array_Patient ID_17746_W2_Redo

source_name: Primary Breast Tumor_Patient ID_17746_W2_Redo


title: Breast Cancer Array_Patient ID_17762_BL

source_name: Primary Breast Tumor_Patient ID_17762_BL


title: Breast Cancer Array_Patient ID_17674_BL

source_name: Primary Breast Tumor_Patient ID_17674_BL


title: Breast Cancer Array_Patient ID_17739_BL

source_name: Primary Breast Tumor_Patient ID_17739_BL


title: Breast Cancer Array_Patient ID_17776_w2

source_name: Primary Breast Tumor_Patient ID_17776_w2

value: NP

value: off study


title: Breast Cancer Array_Patient ID_17675_BL

source_name: Primary Breast Tumor_Patient ID_17675_BL


title: Breast Cancer Array_Patient ID_17714_w2

source_name: Primary Breast Tumor_Patient ID_17714_w2


title: Breast Cancer Array_Patient ID_17674_w2

source_name: Primary Breast Tumor_Patient ID_17674_w2


title: Breast Cancer Array_Patient ID_17733_BL

source_name: Primary Breast Tumor_Patient ID_17733_BL


title: Breast Cancer Array_Patient ID_17688_M

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_17688_M


title: Breast Cancer Array_Patient ID_17776_BL

source_name: Primary Breast Tumor_Patient ID_17776_BL


title: Breast Cancer Array_Patient ID_17688_BL

source_name: Primary Breast Tumor_Patient ID_17688_BL


title: Breast Cancer Array_Patient ID_17714_BL

source_name: Primary Breast Tumor_Patient ID_17714_BL


title: Breast Cancer Array_Patient ID_18074_BL

source_name: Primary Breast Tumor_Patient ID_18074_BL


title: Breast Cancer Array_Patient ID_17646_BL

source_name: Primary Breast Tumor_Patient ID_17646_BL


title: Breast Cancer Array_Patient ID_17646_w2

source_name: Primary Breast Tumor_Patient ID_17646_w2


title: Breast Cancer Array_Patient ID_17636_w2

source_name: Primary Breast Tumor_Patient ID_17636_w2


title: Breast Cancer Array_Patient ID_17636_BL

source_name: Primary Breast Tumor_Patient ID_17636_BL


title: Breast Cancer Array_Patient ID_17612_BL

source_name: Primary Breast Tumor_Patient ID_17612_BL


title: Breast Cancer Array_Patient ID_17612_w2

source_name: Primary Breast Tumor_Patient ID_17612_w2


title: Breast Cancer Array_Patient ID_17611_w2

source_name: Primary Breast Tumor_Patient ID_17611_w2


title: Breast Cancer Array_Patient ID_17586_w2

source_name: Primary Breast Tumor_Patient ID_17586_w2


title: Breast Cancer Array_Patient ID_17601_w2

source_name: Primary Breast Tumor_Patient ID_17601_w2


title: Breast Cancer Array_Patient ID_17566_BL_Redo

source_name: Primary Breast Tumor_Patient ID_17566_BL_Redo


title: Breast Cancer Array_Patient ID_17584_w2

source_name: Primary Breast Tumor_Patient ID_17584_w2


title: Breast Cancer Array_Patient ID_17611_BL

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_17611_BL


title: Breast Cancer Array_Patient ID_17522_w2

source_name: Primary Breast Tumor_Patient ID_17522_w2


title: Breast Cancer Array_Patient ID_17518_BL

source_name: Primary Breast Tumor_Patient ID_17518_BL

value: surgery


title: Breast Cancer Array_Patient ID_17586_BL

value: Total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.

source_name: Primary Breast Tumor_Patient ID_17586_BL


title: Breast Cancer Array_Patient ID_17521_BL

source_name: Primary Breast Tumor_Patient ID_17521_BL

value: breast cancer tissue


title: Breast Cancer Array_Patient ID_17494_w2

source_name: Primary Breast Tumor_Patient ID_17494_w2

value: oct blocks from fine needle biopsies which contained at least 50% tumor cellularity


title: Breast Cancer Array_Patient ID_17584_BL

source_name: Primary Breast Tumor_Patient ID_17584_BL

value: sensitive


title: Breast Cancer Array_Patient ID_17522_BL Redo

source_name: Primary Breast Tumor_Patient ID_17522_BL Redo

value: continue AI


title: Breast Cancer Array_Patient ID_17521_W2

source_name: Primary Breast Tumor_Patient ID_17521_W2


title: Breast Cancer Array_Patient ID_17502_w2

source_name: Primary Breast Tumor_Patient ID_17502_w2


title: Breast Cancer Array_Patient ID_17490_BL

source_name: Primary Breast Tumor_Patient ID_17490_BL


title: Breast Cancer Array_Patient ID_17467_w2

source_name: Primary Breast Tumor_Patient ID_17467_w2


title: Breast Cancer Array_Patient ID_17502_BL

source_name: Primary Breast Tumor_Patient ID_17502_BL


title: Breast Cancer Array_Patient ID_17494_BL

source_name: Primary Breast Tumor_Patient ID_17494_BL


title: Breast Cancer Array_Patient ID_17490_M

source_name: Primary Breast Tumor_Patient ID_17490_M


title: Breast Cancer Array_Patient ID_17601_BL

source_name: Primary Breast Tumor_Patient ID_17601_BL


title: Breast Cancer Array_Patient ID_17518_w2

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_17518_w2


title: Breast Cancer Array_Patient ID_17467_BL

source_name: Primary Breast Tumor_Patient ID_17467_BL


title: Breast Cancer Array_Patient ID_17566_M

source_name: Primary Breast Tumor_Patient ID_17566_M


title: Breast Cancer Array_Patient ID_17423_W2

source_name: Primary Breast Tumor_Patient ID_17423_W2


title: Breast Cancer Array_Patient ID_17423_BL

source_name: Primary Breast Tumor_Patient ID_17423_BL


title: Breast Cancer Array_Patient ID_17409_W2

source_name: Primary Breast Tumor_Patient ID_17409_W2


title: Breast Cancer Array_Patient ID_17412_BL

source_name: Primary Breast Tumor_Patient ID_17412_BL


title: Breast Cancer Array_Patient ID_17412_w2

source_name: Primary Breast Tumor_Patient ID_17412_w2


title: Breast Cancer Array_Patient ID_17409_BL

source_name: Primary Breast Tumor_Patient ID_17409_BL


title: Breast Cancer Array_Patient ID_17407_w2

source_name: Primary Breast Tumor_Patient ID_17407_w2


title: Breast Cancer Array_Patient ID_17407_BL

source_name: Primary Breast Tumor_Patient ID_17407_BL


title: Breast Cancer Array_Patient ID_18155_BL_Redo

source_name: Primary Breast Tumor_Patient ID_18155_BL_Redo


title: Breast Cancer Array_Patient ID_17384_BL

source_name: Primary Breast Tumor_Patient ID_17384_BL


title: Breast Cancer Array_Patient ID_17384_w2

source_name: Primary Breast Tumor_Patient ID_17384_w2


title: Breast Cancer Array_Patient ID_17383_W2_Redo

source_name: Primary Breast Tumor_Patient ID_17383_W2_Redo


title: Breast Cancer Array_Patient ID_17329_w2

source_name: Primary Breast Tumor_Patient ID_17329_w2


title: Breast Cancer Array_Patient ID_17445_BL

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_17445_BL


title: Breast Cancer Array_Patient ID_17383_BL_Redo

source_name: Primary Breast Tumor_Patient ID_17383_BL_Redo


title: Breast Cancer Array_Patient ID_17331_w2

source_name: Primary Breast Tumor_Patient ID_17331_w2


title: Breast Cancer Array_Patient ID_17327_W2

source_name: Primary Breast Tumor_Patient ID_17327_W2


title: Breast Cancer Array_Patient ID_17329_BL

source_name: Primary Breast Tumor_Patient ID_17329_BL


title: Breast Cancer Array_Patient ID_17328_w2

source_name: Primary Breast Tumor_Patient ID_17328_w2


title: Breast Cancer Array_Patient ID_17328_BL

source_name: Primary Breast Tumor_Patient ID_17328_BL


title: Breast Cancer Array_Patient ID_17445_w2

source_name: Primary Breast Tumor_Patient ID_17445_w2


title: Breast Cancer Array_Patient ID_17331_BL

source_name: Primary Breast Tumor_Patient ID_17331_BL


title: Breast Cancer Array_Patient ID_17327_BL

source_name: Primary Breast Tumor_Patient ID_17327_BL


title: Breast Cancer Array_Patient ID_17292_w2

source_name: Primary Breast Tumor_Patient ID_17292_w2


title: Breast Cancer Array_Patient ID_17278_w2

source_name: Primary Breast Tumor_Patient ID_17278_w2


title: Breast Cancer Array_Patient ID_17277_w2

source_name: Primary Breast Tumor_Patient ID_17277_w2


title: Breast Cancer Array_Patient ID_17278_BL

source_name: Primary Breast Tumor_Patient ID_17278_BL


title: Breast Cancer Array_Patient ID_17292_BL

source_name: Primary Breast Tumor_Patient ID_17292_BL


title: Breast Cancer Array_Patient ID_17277_BL

source_name: Primary Breast Tumor_Patient ID_17277_BL


title: Breast Cancer Array_Patient ID_17233_BL

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_17233_BL


title: Breast Cancer Array_Patient ID_17250_BL

source_name: Primary Breast Tumor_Patient ID_17250_BL


title: Breast Cancer Array_Patient ID_17240_M

source_name: Primary Breast Tumor_Patient ID_17240_M


title: Breast Cancer Array_Patient ID_17196_w2

source_name: Primary Breast Tumor_Patient ID_17196_w2


title: Breast Cancer Array_Patient ID_17233_W2

source_name: Primary Breast Tumor_Patient ID_17233_W2


title: Breast Cancer Array_Patient ID_17250_w2

source_name: Primary Breast Tumor_Patient ID_17250_w2


title: Breast Cancer Array_Patient ID_17157_w2

source_name: Primary Breast Tumor_Patient ID_17157_w2


title: Breast Cancer Array_Patient ID_17240_BL

source_name: Primary Breast Tumor_Patient ID_17240_BL


title: Breast Cancer Array_Patient ID_17232_M

source_name: Primary Breast Tumor_Patient ID_17232_M


title: Breast Cancer Array_Patient ID_17170_w2

source_name: Primary Breast Tumor_Patient ID_17170_w2


title: Breast Cancer Array_Patient ID_17143_w2

source_name: Primary Breast Tumor_Patient ID_17143_w2


title: Breast Cancer Array_Patient ID_17157_BL

source_name: Primary Breast Tumor_Patient ID_17157_BL


title: Breast Cancer Array_Patient ID_17143_BL

source_name: Primary Breast Tumor_Patient ID_17143_BL


title: Breast Cancer Array_Patient ID_17232_BL

source_name: Primary Breast Tumor_Patient ID_17232_BL


title: Breast Cancer Array_Patient ID_17070_BL

source_name: Primary Breast Tumor_Patient ID_17070_BL


title: Breast Cancer Array_Patient ID_17124_re-analyzed

description:
Z1031B
GSM863200

source_name: Primary Breast Tumor_Patient ID_17124_BL


title: Breast Cancer Array_Patient ID_17196_BL

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_17196_BL


title: Breast Cancer Array_Patient ID_17124_W2

source_name: Primary Breast Tumor_Patient ID_17124_W2


title: Breast Cancer Array_Patient ID_17070_w2

source_name: Primary Breast Tumor_Patient ID_17070_w2


title: Breast Cancer Array_Patient ID_16998_W2

source_name: Primary Breast Tumor_Patient ID_16998_W2


title: Breast Cancer Array_Patient ID_17170_re-analyzed

description:
Z1031B
GSM863201

source_name: Primary Breast Tumor_Patient ID_17170_BL


title: Breast Cancer Array_Patient ID_17032_w2

source_name: Primary Breast Tumor_Patient ID_17032_w2


title: Breast Cancer Array_Patient ID_17066_BL

source_name: Primary Breast Tumor_Patient ID_17066_BL


title: Breast Cancer Array_Patient ID_17032_BL

source_name: Primary Breast Tumor_Patient ID_17032_BL


title: Breast Cancer Array_Patient ID_16994_w2

source_name: Primary Breast Tumor_Patient ID_16994_w2


title: Breast Cancer Array_Patient ID_16998_BL

source_name: Primary Breast Tumor_Patient ID_16998_BL


title: Breast Cancer Array_Patient ID_16994_BL

source_name: Primary Breast Tumor_Patient ID_16994_BL


title: Breast Cancer Array_Patient ID_16992_re-analyzed

description:
Z1031B
GSM863198

source_name: Primary Breast Tumor_Patient ID_16992_BL


title: Breast Cancer Array_Patient ID_17066_W2

source_name: Primary Breast Tumor_Patient ID_17066_W2


title: Breast Cancer Array_Patient ID_16970_w2

source_name: Primary Breast Tumor_Patient ID_16970_w2


title: Breast Cancer Array_Patient ID_16993_w2 Redo

source_name: Primary Breast Tumor_Patient ID_16993_w2 Redo


title: Breast Cancer Array_Patient ID_16970_re-analyzed

description:
Z1031B
GSM863196

source_name: Primary Breast Tumor_Patient ID_16970_BL


title: Breast Cancer Array_Patient ID_16982_W2_Redo

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_16982_W2_Redo


title: Breast Cancer Array_Patient ID_16959_BL

source_name: Primary Breast Tumor_Patient ID_16959_BL


title: Breast Cancer Array_Patient ID_16982_BL_Redo

source_name: Primary Breast Tumor_Patient ID_16982_BL_Redo


title: Breast Cancer Array_Patient ID_16959_W2

source_name: Primary Breast Tumor_Patient ID_16959_W2


title: Breast Cancer Array_Patient ID_16993_BL

source_name: Primary Breast Tumor_Patient ID_16993_BL


title: Breast Cancer Array_Patient ID_16965_w2

source_name: Primary Breast Tumor_Patient ID_16965_w2


title: Breast Cancer Array_Patient ID_16992_W2

source_name: Primary Breast Tumor_Patient ID_16992_W2


title: Breast Cancer Array_Patient ID_16965_re-analyzed

description:
Z1031B
GSM863195

source_name: Primary Breast Tumor_Patient ID_16965_BL


title: Breast Cancer Array_Patient ID_16956_W2

source_name: Primary Breast Tumor_Patient ID_16956_W2


title: Breast Cancer Array_Patient ID_16984_BL

source_name: Primary Breast Tumor_Patient ID_16984_BL


title: Breast Cancer Array_Patient ID_16984_w2

source_name: Primary Breast Tumor_Patient ID_16984_w2


title: Breast Cancer Array_Patient ID_16956_re-analyzed

description:
Z1031B
GSM863194

source_name: Primary Breast Tumor_Patient ID_16956_BL


title: Breast Cancer Array_Patient ID_16949_BL

source_name: Primary Breast Tumor_Patient ID_16949_BL


title: Breast Cancer Array_Patient ID_16949_w2

source_name: Primary Breast Tumor_Patient ID_16949_w2


title: Breast Cancer Array_Patient ID_16934_BL

source_name: Primary Breast Tumor_Patient ID_16934_BL


title: Breast Cancer Array_Patient ID_16934_w2

source_name: Primary Breast Tumor_Patient ID_16934_w2


title: Breast Cancer Array_Patient ID_16921_w2

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_16921_w2


title: Breast Cancer Array_Patient ID_16921_BL

source_name: Primary Breast Tumor_Patient ID_16921_BL


title: Breast Cancer Array_Patient ID_16918_w2

source_name: Primary Breast Tumor_Patient ID_16918_w2


title: Breast Cancer Array_Patient ID_16917_w2

source_name: Primary Breast Tumor_Patient ID_16917_w2


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16918_re-analyzed

description:
Z1031B
GSM728815

source_name: Primary Breast Tumor_Patient ID_16918_BL


title: Breast Cancer Array_Patient ID_16917_BL

source_name: Primary Breast Tumor_Patient ID_16917_BL


title: Breast Cancer Array_Patient ID_16895_BL

source_name: Primary Breast Tumor_Patient ID_16895_BL


title: Breast Cancer Array_Patient ID_16895_w2

source_name: Primary Breast Tumor_Patient ID_16895_w2


title: Breast Cancer Array_Patient ID_16880_w2

source_name: Primary Breast Tumor_Patient ID_16880_w2


title: Breast Cancer Array_Patient ID_16889_re-analyzed

description:
Z1031B
GSM863193

source_name: Primary Breast Tumor_Patient ID_16889_BL


title: Breast Cancer Array_Patient ID_16858_BL

source_name: Primary Breast Tumor_Patient ID_16858_BL


title: Breast Cancer Array_Patient ID_16847_w2

source_name: Primary Breast Tumor_Patient ID_16847_w2


title: Breast Cancer Array_Patient ID_16886_w2

source_name: Primary Breast Tumor_Patient ID_16886_w2


title: Breast Cancer Array_Patient ID_16889_w2

source_name: Primary Breast Tumor_Patient ID_16889_w2


title: Breast Cancer Array_Patient ID_16880_re-analyzed

description:
Z1031B
GSM863192

source_name: Primary Breast Tumor_Patient ID_16880_BL


title: Breast Cancer Array_Patient ID_16779_re-analyzed

description:
Z1031B
GSM863190

source_name: Primary Breast Tumor_Patient ID_16779_BL


title: Breast Cancer Array_Patient ID_16745_re-analyzed

description:
Z1031B
GSM863187

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_16745_BL


title: Breast Cancer Array_Patient ID_16757_re-analyzed

description:
Z1031B
GSM863189

source_name: Primary Breast Tumor_Patient ID_16757_BL


title: Breast Cancer Array_Patient ID_16757_w2

source_name: Primary Breast Tumor_Patient ID_16757_w2


title: Breast Cancer Array_Patient ID_16886_BL

source_name: Primary Breast Tumor_Patient ID_16886_BL


title: Breast Cancer Array_Patient ID_16825_re-analyzed

description:
Z1031B
GSM863191

source_name: Primary Breast Tumor_Patient ID_16825_BL


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16754_re-analyzed

description:
Z1031B
GSM859838

source_name: Primary Breast Tumor_Patient ID_16754_BL


title: Breast Cancer Array_Patient ID_16754_w2

source_name: Primary Breast Tumor_Patient ID_16754_w2


title: Breast Cancer Array_Patient ID_16825_w2

source_name: Primary Breast Tumor_Patient ID_16825_w2


title: Breast Cancer Array_Patient ID_16779_w2

source_name: Primary Breast Tumor_Patient ID_16779_w2


title: Breast Cancer Array_Patient ID_16751_M

source_name: Primary Breast Tumor_Patient ID_16751_M


title: Breast Cancer Array_Patient ID_16745_w2

source_name: Primary Breast Tumor_Patient ID_16745_w2


title: Breast Cancer Array_Patient ID_16858_w2

source_name: Primary Breast Tumor_Patient ID_16858_w2


title: Breast Cancer Array_Patient ID_16744_re-analyzed

description:
Z1031B
GSM863186

source_name: Primary Breast Tumor_Patient ID_16744_BL


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16847_re-analyzed

description:
Z1031B
GSM859842

source_name: Primary Breast Tumor_ Patient ID_16847_BL


title: Breast Cancer Array_Patient ID_16723_BL

source_name: Primary Breast Tumor_Patient ID_16723_BL


title: Breast Cancer Array_Patient ID_16751_re-analyzed

description:
Z1031B
GSM863188

source_name: Primary Breast Tumor_Patient ID_16751_BL


title: Breast Cancer Array_Patient ID_16744_w2

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_16744_w2


title: Breast Cancer Array_Patient ID_16723_W2

source_name: Primary Breast Tumor_Patient ID_16723_W2


title: PBMC_mild asthma_stim_subject14

status: Public on Nov 14 2016

city: Bethesda

first: Gabriela

middle: A

last: Ferreyra

state: MD

address: 9000 Rockville Pike - Building 10 room 4D03

department: CCMD

institute: Clinical Center

hyb_protocol: 5 ug of fragmented biotin labeled aRNA was used with hybridization cocktails on GeneChip PrimeView Human Gene Expression Array(Affymetrix) following manufacturer protocols.

scan_protocol: GeneChip PrimeView Human Gene Expression Array (Affymetrix) chips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: Raw data were normalized using RMA in Affymetrix Expression Console and presented as log transformed signal intensity; One way ANOVA and contrasts to test the significance of individual comparisons between groups were performed using R statistical package.

label: Biotin

source_name: PBMC_mild asthma_stim_6h

label_protocol: AffymetrixGeneChip IVT Express Kit  was used for the synthesis of cDNA and cRNA an biotin-labeled cRNA. 100 ng of tRNA was utilized as starting material following manufacturer protocol.

growth_protocol: Blood specimens from patients with mild-to moderate asthma and severe asthma, and control subjects were drawn after obtaining informed consent. Blood samples were processed immediately using lymphocyte separation medium (LSM) (Lonza, Walkersville, MD), according to the manufacturer’s protocol to obtain peripheral blood monuclear cells (PBMCs). 4x106 PBMCs were resuspended in 1 ml of RPMI 1640 medium with 2 mM of L-glutamine, supplemented with 10% heat-inactivated FBS and treated immediately after purification.

extract_protocol: Total RNA was extracted from cells using QIAshredder columns and RNeasy mini kit and treated with DNase (Qiagen). Total RNA concentration was measured by the Nanodrop ND-1000 spectophotometer (NanoDrop Technologies, Wilmington, DE) and the quality of RNA was confirmed by OD 260/280 ratio.

treatment_protocol: 4x106 PBMCs were resuspended in 1 ml of RPMI 1640 medium with 2 mM of L-glutamine, supplemented with 10% heat-inactivated FBS and treated with purified LMW HA (MP Biomedicals; Solon, OH) (stimulated samples) or vehicle (unstimulated samples) for 6 h. Each experiment was performed in duplicates. LMW HA used in this study was a purified mixture of fragments between 50 kDa to 600 kDa. Each experiment was performed in the presence of polymyxin B sulfate (Calbiochem) (10 ug/ml) to exclude an effect of LPS contamination. Supernatants were collected and kept frozen in -80oC before further analyses. Cell pellets were lysed in RLT buffer, homogenized using QIAshredder columns (Qiagen, Valencia, CA) and stored at  -80oC before total RNA extraction.

value: Hyaluronan

value: mild asthma

tag: gender

value: male

tag: ethnicity

value: black

tag: cell type

value: PBMC


title: PBMC_mild asthma_unstim_subject14

source_name: PBMC_mild asthma_unstim_6h


title: Breast Cancer Array_Patient ID_410

status: Public on Dec 31 2016

description: pol

data_processing: txt files from Agilent Feature Extraction software were loaded into the UNC-CH Microarray Database. Final loess, normalized log2 ratios (Cy5-sample/Cy3-control) for each probe were retrieved.

tag: tag

value: Total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C

value: reference sample

source_name: Primary Breast Tumor_Patient ID_410

tag: erbl

tag: baselinesubtype

value: Normal

tag: baselinerorp

value: med

tag: baselinerors

value: low

tag: studyid

value: POL


title: PBMC_healthy_unstim_subject13

value: healthy

value: white


title: PBMC_severe asthma_stim_subject19

source_name: PBMC_severe asthma_stim_6h

value: severe asthma

value: female


title: PBMC_healthy_stim_subject13


title: PBMC_severe asthma_unstim_subject18

source_name: PBMC_severe asthma_unstim_6h

value: asian


title: PBMC_mild asthma_stim_subject11


title: PBMC_healthy_unstim_subject10


title: PBMC_healthy_unstim_subject15


title: PBMC_severe asthma_stim_subject18


title: PBMC_mild asthma_stim_subject12


title: PBMC_mild asthma_unstim_subject11


title: PBMC_mild asthma_unstim_subject9


title: PBMC_severe asthma_unstim_subject16


title: PBMC_mild asthma_unstim_subject17


title: PBMC_healthy_stim_subject15


title: PBMC_healthy_stim_subject10


title: PBMC_mild asthma_unstim_subject12


title: PBMC_severe asthma_unstim_subject3


title: PBMC_mild asthma_stim_subject17


title: PBMC_severe asthma_stim_subject3


title: PBMC_healthy_stim_subject8


title: PBMC_severe asthma_stim_subject16


title: PBMC_severe asthma_unstim_subject19


title: PBMC_mild asthma_stim_subject9


title: PBMC_healthy_unstim_subject8


title: PBMC_mild asthma_stim_subject7


title: PBMC_severe asthma_stim_subject2


title: PBMC_mild asthma_unstim_subject7


title: PBMC_severe asthma_unstim_subject2


title: PBMC_healthy_stim_subject6


title: PBMC_healthy_stim_subject4


title: PBMC_healthy_unstim_subject4


title: PBMC_severe asthma_unstim_subject1


title: PBMC_severe asthma_stim_subject1


title: PBMC_healthy_unstim_subject6


title: MR expression with DOC stimulation, biological replicate 3

status: Public on Sep 20 2016

description: mineralocorticoid receptor with deoxycorticosterone acetate stimulation

hyb_protocol: Fragmented labeled cRNA (65 ug per sample) were hybridized for 16 hr at 45C on PrimeView Human Gene  Expression  Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 400 following manufacturer protocols.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: Raw data were normalized using RMA in Affymetrix Expression Console and presented as log transformed signal intensity. The probe set results were all within bounds.

source_name: Embryonic kidney cells (HEK293)

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNAusing genechip 3' IVT express kit (Affymetrix) following manufacturer protocol

growth_protocol: Human embryonic kidney cells (HEK293) were grown in high glucose DMEM supplemented with 10% heat-inactivated FBS

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) and  quality was evaluated using RNA 6000 Nano LabChip

treatment_protocol: 5x105 HEK293 cells were stransfected using lipofectamine 2000  with 500 ng/well of  MR vector expression plasmids for 24 h followed by 4h treatment with vehicle, DOC (100 nM), PMA (10 nM) or DOC plus PMA.

value: DOC (100 nM)


title: MR expression with DOC stimulation, biological replicate 1


title: MR expression with PMA stimulation, biological replicate 4

description: mineralocorticoid receptor with PMA stimulation

value: PMA (10 nM)


title: MR expression with PMA stimulation, biological replicate 3


title: PBMC_mild asthma_stim_subject5

value: Hyaluronan

value: mild asthma


title: MR expression, biological replicate 4

description: mineralocorticoid receptor control


title: MR expression with DOC and PMA stimulation, biological replicate 2

description: mineralocorticoid receptor with PMA and deoxycorticosterone acetate stimulation

value: DOC (100 nM) and PMA (10 nM)


title: MR expression, biological replicate 3

description: mineralocorticoid receptor control


title: MR expression with DOC stimulation, biological replicate 2


title: MR expression with DOC and PMA stimulation, biological replicate 1


title: MR expression with DOC stimulation, biological replicate 4


title: MR expression with PMA stimulation, biological replicate 1


title: MR expression, biological replicate 2

description: mineralocorticoid receptor control


title: MR expression with DOC and PMA stimulation, biological replicate 3


title: MR expression, biological replicate 1

description: mineralocorticoid receptor control


title: total RNA of FFPE sample from patient H&N#9

status: Public on Apr 01 2016

city: St. John's

first: Jessica

middle: L

last: Esseltine

state: NL

address: 300 Prince Philip Drive

department: Division of Biomedical Sciences

country: Canada

institute: Memorial University of Newfoundland

description: matches with fresh frozen sample 273s1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner settings.

data_processing: BeadStudio software v3.2

source_name: primary oral cavity SCC from patient H&N#9

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

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: worst pattern of invasion (wpoi)


title: total RNA of FFPE sample from patient H&N#8

description: matches with fresh frozen sample 227s1

source_name: primary oral cavity SCC from patient H&N#8


title: MR expression with PMA stimulation, biological replicate 2


title: total RNA of FFPE sample from patient H&N#5

description: matches with fresh frozen sample 139s1

source_name: primary oral cavity SCC from patient H&N#5


title: total RNA of FFPE sample from patient H&N#17

description: matches with fresh frozen sample 212s1

source_name: primary oral cavity SCC from patient H&N#17


title: total RNA of fresh frozen sample 139s1

description: matches with FFPE sample H&N#5

source_name: primary oral cavity SCC sample 139s1


title: MR expression with DOC and PMA stimulation, biological replicate 4


title: total RNA of fresh frozen sample 273s1

description: matches with FFPE sample H&N#9

source_name: primary oral cavity SCC sample 273s1


title: total RNA of FFPE sample from patient H&N#3

description: matches with fresh frozen sample 77s1

source_name: primary oral cavity SCC from patient H&N#3


title: total RNA of FFPE sample from patient H&N#2

description: matches with fresh frozen sample 160s1

source_name: primary oral cavity SCC from patient H&N#2


title: total RNA of fresh frozen sample 227s1

description: matches with FFPE sample H&N#8

source_name: primary oral cavity SCC sample 227s1


title: total RNA of FFPE sample from patient H&N#23

description: matches with fresh frozen sample 180s1

source_name: primary oral cavity SCC from patient H&N#23


title: total RNA of fresh frozen sample 181s1

description: matches with FFPE sample H&N#12

source_name: primary oral cavity SCC sample 181s1


title: total RNA of fresh frozen sample 160s1

description: matches with FFPE sample H&N#2

source_name: primary oral cavity SCC sample 160s1


title: total RNA of FFPE sample from patient H&N#7

description: matches with fresh frozen sample 187s1

source_name: primary oral cavity SCC from patient H&N#7


title: total RNA of FFPE sample from patient H&N#12

description: matches with fresh frozen sample 181s1

source_name: primary oral cavity SCC from patient H&N#12


title: total RNA of fresh frozen sample 180s1

description: matches with FFPE sample H&N#23

source_name: primary oral cavity SCC sample 180s1


title: PBMC_mild asthma_unstim_subject5

source_name: PBMC_mild asthma_unstim_6h

value: PBMC


title: total RNA of fresh frozen sample 187s1

description: matches with FFPE sample H&N#7

source_name: primary oral cavity SCC sample 187s1


title: total RNA of fresh frozen sample 77s1

description: matches with FFPE sample H&N#3

source_name: primary oral cavity SCC sample 77s1


title: total RNA of fresh frozen sample 212s1

description: matches with FFPE sample H&N#17

source_name: primary oral cavity SCC sample 212s1


title: siBMPR2 plus PMA, biological rep2

status: Public on Dec 04 2015

source_name: Primary HPAECs from female donor

growth_protocol: HPAECs were cultured in endothelial basal growth medium-2 (EBM™-2) supplemented with growth factors (EGM™-2 SingleQuot kit)

treatment_protocol: HPAEC cells were treated with targeted knockdown or control siRNA for 48 h followed by 4 h treatment with or without 10 nM PMA

value: human pulmonary artery endothelial cells


title: Input_LSD1 3T3-L1_LSD1 cells day 7

status: Public on Jun 10 2014

type: SRA

city: ILLKIRCH

first: Delphine

last: Duteil

address: 1 rue Laurent Fries

country: France

institute: IGBMC

library_source: genomic

data_processing:
peak finding algorithm MACS 1.41
All peaks with FDR greater than 1 % were excluded from further analysis
ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 2
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: Input_LSD1 3T3-L1_LSD1 cells day 7

growth_protocol: Mouse 3T3-L1 preadipocytes were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % FBS and glutamine.

extract_protocol:
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 8
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).

treatment_protocol: Differentiation of 3T3-L1 cells was induced by treatment of confluent cells (designated day 0) with an adipogenic mixture consisting of 10 µg/ml insulin (Gibco), 1 µM dexamethasone (Calbiochem), 10 µM rosiglitazone (Cayman) and 500 µM isobutylmethylxanthine (Serva) in the presence of 10 % FBS. The differentiation medium was replaced 3 days later (day 3) with medium supplemented with 10 % FBS and 10 µg/ml insulin for 2 days. Subsequently, the cells were cultured in the same medium for 2 more days (day 7).

tag: differentiation stage

value: Day 7, 7 days after induction of differentiation

tag: genotype

value: LSD1 overexpression

tag: passages

tag: chip antibody


title: siBMPR2, biological rep1


title: Input_Nrf1 3T3-L1 cells day 0

source_name: Input_Nrf1 3T3-L1 cells day 0

extract_protocol:
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 10
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).

tag: cell line

value: Day 0, undifferentiated

value: Control


title: Input_Nrf1 3T3-L1_LSD1 cells day 7

source_name: Input_Nrf1 3T3-L1_LSD1 cells day 7

extract_protocol:
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 12
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).


title: siBMPR2, biological rep4


title: Nrf1_ChIPseq 3T3-L1_LSD1 cells day 7

source_name: Nrf1_ChIPseq 3T3-L1_LSD1 cells day 7

extract_protocol:
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 13
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).

value: Nrf1 (ab55744, Abcam)


title: siBMPR2, biological rep3


title: LSD1_ChIPseq 3T3-L1_LSD1 cells day 0

source_name: LSD1_ChIPseq 3T3-L1_LSD1 cells day 0

extract_protocol:
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 7
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).

value: LSD1 (20752, homemade, Schüle lab)


title: LSD1_ChIPseq 3T3-L1 cells day 7

source_name: LSD1_ChIPseq 3T3-L1 cells day 7

extract_protocol:
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 5
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).


title: Input_LSD1 3T3-L1 cells day 7

source_name: Input_LSD1 3T3-L1 cells day 7

extract_protocol:
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 4
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).


title: siBMPR2 plus PMA, biological rep1


title: siControl plus PMA, biological rep3


title: siBMPR2, biological rep2


title: siControl, biological rep1


title: siControl plus PMA, biological rep2


title: siControl plus PMA, biological rep4


title: siControl plus PMA, biological rep1


title: siBMPR2 plus PMA, biological rep3


title: siBMPR2 plus PMA, biological rep4


title: LSD1_ChIPseq 3T3-L1_LSD1 cells day 7

source_name: LSD1_ChIPseq 3T3-L1_LSD1 cells day 7

extract_protocol:
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 9
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).


title: siControl, biological rep4


title: Nrf1_ChIPseq 3T3-L1 cells day 0

source_name: Nrf1_ChIPseq 3T3-L1 cells day 0

extract_protocol:
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 11
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).


title: 3T3-L1_LSD1 cells day 7, biological replicate 2

library_source: transcriptomic

data_processing:
We aligned these reads to the mm10 build of the mouse genome using TopHat version 2
The aligned reads were counted with the homer software (analyze RNA) and DEG’s were identified using EdgeR and DESeq version 1.8.3.
Genome_build: mm10

source_name: 3T3-L1_LSD1 cells day 7

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files).


title: LSD1_ChIPseq 3T3-L1 cells day 0

source_name: LSD1_ChIPseq 3T3-L1 cells day 0

extract_protocol:
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 3
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).


title: Input_LSD1 3T3-L1_LSD1 cells day 0

source_name: Input_LSD1 3T3-L1_LSD1 cells day 0

extract_protocol:
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 6
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).


title: Input_LSD1 3T3-L1 cells day 0

source_name: Input_LSD1 3T3-L1 cells day 0

extract_protocol:
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 2
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).


title: 3T3-L1_LSD1 cells day 7, biological replicate 3


title: siControl, biological rep3


title: siControl, biological rep2


title: 3T3-L1_LSD1 cells day 7, biological replicate 1


title: 3T3-L1_LSD1 cells day 0, biological replicate 3

source_name: 3T3-L1_LSD1 cells day 0


title: 3T3-L1 cells day 7, biological replicate 3

source_name: 3T3-L1 cells day 7


title: 3T3-L1 cells day 7, biological replicate 2


title: 3T3-L1 cells day 0, biological replicate 2

source_name: 3T3-L1 cells day 0


title: 3T3-L1 cells day 0, biological replicate 1


title: 3T3-L1 cells day 0, biological replicate 3


title: 3T3-L1_LSD1 cells day 0, biological replicate 2


title: 3T3-L1_LSD1 cells day 0, biological replicate 1


title: 3T3-L1 cells day 7, biological replicate 1


title: genomic DNA from sample 911Tu

status: Public on Jun 07 2014

type: genomic

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

label: Cy5 and Cy3

source_name: primary oropharygeal SCC from patient 911

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tissue samples using Qiagen DNeasy Kit according to standard instructions

value: F

tag: disease state

value: primary tumor

tag: hpv status

value: Negative

tag: p16 ihc


title: genomic DNA from sample 990Tu

source_name: primary oropharygeal SCC from patient 990

tag: gender

value: M

value: Positive


title: genomic DNA from sample 923NL

source_name: normal adjacent mucosa from patient 923

value: normal mucosa


title: genomic DNA from sample 923Tu

source_name: primary oropharygeal SCC from patient 923


title: genomic DNA from sample 847NL

source_name: normal adjacent mucosa from patient 847


title: genomic DNA from sample 920NL

source_name: normal adjacent mucosa from patient 920


title: genomic DNA from sample 892NL

source_name: normal adjacent mucosa from patient 892


title: genomic DNA from sample 920Tu

source_name: primary oropharygeal SCC from patient 920


title: genomic DNA from sample 847Tu

source_name: primary oropharygeal SCC from patient 847


title: genomic DNA from sample 841Tu

source_name: primary oropharygeal SCC from patient 841


title: genomic DNA from sample 990NL

source_name: normal adjacent mucosa from patient 990


title: genomic DNA from sample 892Tu

source_name: primary oropharygeal SCC from patient 892


title: genomic DNA from sample 997Tu

source_name: primary oropharygeal SCC from patient 997


title: genomic DNA from sample 848NL

source_name: normal adjacent mucosa from patient 848


title: genomic DNA from sample 941Tu

source_name: primary oropharygeal SCC from patient 941


title: genomic DNA from sample 848Tu

source_name: primary oropharygeal SCC from patient 848


title: genomic DNA from sample 941NL

source_name: normal adjacent mucosa from patient 941


title: genomic DNA from sample 838NL

source_name: normal adjacent mucosa from patient 838


title: genomic DNA from sample 911NL

source_name: normal adjacent mucosa from patient 911


title: genomic DNA from sample 828Tu

source_name: primary oropharygeal SCC from patient 828


title: genomic DNA from sample 828NL

source_name: normal adjacent mucosa from patient 828


title: genomic DNA from sample 810Tu

source_name: primary oropharygeal SCC from patient 810


title: genomic DNA from sample 841NL

source_name: normal adjacent mucosa from patient 841


title: genomic DNA from sample 997NL

source_name: normal adjacent mucosa from patient 997


title: genomic DNA from sample 824NL

source_name: normal adjacent mucosa from patient 824


title: genomic DNA from sample 838Tu

source_name: primary oropharygeal SCC from patient 838

value: Indeterminate


title: genomic DNA from sample 754Tu

source_name: primary oropharygeal SCC from patient 754

value: Unknown


title: genomic DNA from sample 810NL

source_name: normal adjacent mucosa from patient 810


title: genomic DNA from sample 824Tu

source_name: primary oropharygeal SCC from patient 824


title: genomic DNA from sample 754NL

source_name: normal adjacent mucosa from patient 754


title: genomic DNA from sample 694Tu

source_name: primary oropharygeal SCC from patient 694


title: genomic DNA from sample 73NL

source_name: normal adjacent mucosa from patient 73


title: genomic DNA from sample 673NL

source_name: normal adjacent mucosa from patient 673


title: genomic DNA from sample 694NL

source_name: normal adjacent mucosa from patient 694


title: genomic DNA from sample 73Tu

source_name: primary oropharygeal SCC from patient 73


title: genomic DNA from sample 611Tu

source_name: primary oropharygeal SCC from patient 611


title: genomic DNA from sample 648Tu

source_name: primary oropharygeal SCC from patient 648


title: genomic DNA from sample 673Tu

source_name: primary oropharygeal SCC from patient 673


title: genomic DNA from sample 566NL

source_name: normal adjacent mucosa from patient 566


title: genomic DNA from sample 638NL

source_name: normal adjacent mucosa from patient 638


title: genomic DNA from sample 566Tu

source_name: primary oropharygeal SCC from patient 566


title: genomic DNA from sample 517NL

source_name: normal adjacent mucosa from patient 517


title: genomic DNA from sample 638Tu

source_name: primary oropharygeal SCC from patient 638


title: genomic DNA from sample 583Tu

source_name: primary oropharygeal SCC from patient 583


title: genomic DNA from sample 532NL

source_name: normal adjacent mucosa from patient 532


title: genomic DNA from sample 583NL (2)

source_name: normal adjacent mucosa from patient 583


title: genomic DNA from sample 611NL

source_name: normal adjacent mucosa from patient 611


title: genomic DNA from sample 583NL


title: genomic DNA from sample 504Tu

source_name: primary oropharygeal SCC from patient 504


title: genomic DNA from sample 648NL

source_name: normal adjacent mucosa from patient 648


title: genomic DNA from sample 590Tu

source_name: primary oropharygeal SCC from patient 590


title: genomic DNA from sample 583Tu (2)


title: genomic DNA from sample 590NL

source_name: normal adjacent mucosa from patient 590


title: genomic DNA from sample 456NL

source_name: normal adjacent mucosa from patient 456


title: genomic DNA from sample 504NL

source_name: normal adjacent mucosa from patient 504


title: genomic DNA from sample 483Tu

source_name: primary oropharygeal SCC from patient 483


title: genomic DNA from sample 483NL

source_name: normal adjacent mucosa from patient 483


title: genomic DNA from sample 517Tu

source_name: primary oropharygeal SCC from patient 517


title: genomic DNA from sample 456Tu

source_name: primary oropharygeal SCC from patient 456


title: genomic DNA from sample 44NL

source_name: normal adjacent mucosa from patient 44


title: genomic DNA from sample 532Tu

source_name: primary oropharygeal SCC from patient 532


title: genomic DNA from sample 413Tu

source_name: primary oropharygeal SCC from patient 413


title: genomic DNA from sample 400NL

source_name: normal adjacent mucosa from patient 400


title: genomic DNA from sample 38Tu

source_name: primary oropharygeal SCC from patient 38


title: genomic DNA from sample 393Tu

source_name: primary oropharygeal SCC from patient 393


title: genomic DNA from sample 44Tu

source_name: primary oropharygeal SCC from patient 44


title: genomic DNA from sample 37Tu

source_name: primary oropharygeal SCC from patient 37


title: genomic DNA from sample 37NL

source_name: normal adjacent mucosa from patient 37


title: genomic DNA from sample 393NL

source_name: normal adjacent mucosa from patient 393


title: genomic DNA from sample 32Tu

source_name: primary oropharygeal SCC from patient 32


title: genomic DNA from sample 413NL

source_name: normal adjacent mucosa from patient 413


title: genomic DNA from sample 335NL

source_name: normal adjacent mucosa from patient 335


title: genomic DNA from sample 32NL

source_name: normal adjacent mucosa from patient 32


title: genomic DNA from sample 261Tu

source_name: primary oropharygeal SCC from patient 261


title: genomic DNA from sample 303NL

source_name: normal adjacent mucosa from patient 303


title: genomic DNA from sample 261NL

source_name: normal adjacent mucosa from patient 261


title: genomic DNA from sample 303Tu

source_name: primary oropharygeal SCC from patient 303


title: genomic DNA from sample 205Tu

source_name: primary oropharygeal SCC from patient 205


title: genomic DNA from sample 391NL

source_name: normal adjacent mucosa from patient 391


title: genomic DNA from sample 336Tu

source_name: primary oropharygeal SCC from patient 336


title: genomic DNA from sample 233NL

source_name: normal adjacent mucosa from patient 233


title: genomic DNA from sample 233Tu

source_name: primary oropharygeal SCC from patient 233


title: genomic DNA from sample 391Tu

source_name: primary oropharygeal SCC from patient 391


title: genomic DNA from sample 336NL

source_name: normal adjacent mucosa from patient 336


title: genomic DNA from sample 400Tu

source_name: primary oropharygeal SCC from patient 400


title: genomic DNA from sample 2Tu

source_name: primary oropharygeal SCC from patient 2


title: genomic DNA from sample 170NL

source_name: normal adjacent mucosa from patient 170


title: genomic DNA from sample 38NL

source_name: normal adjacent mucosa from patient 38


title: genomic DNA from sample 2NL

source_name: normal adjacent mucosa from patient 2


title: genomic DNA from sample 170Tu

source_name: primary oropharygeal SCC from patient 170


title: genomic DNA from sample 205NL

source_name: normal adjacent mucosa from patient 205


title: H_0C4

status: Public on Mar 01 2014

hyb_protocol: 20 μg of fragmented biotin-labeled cRNA was used in hybridization cocktails on 430 2.0 Mouse Genome Arrays (Affymetrix) following manufacturer protocols.

scan_protocol: Affymetrix 430 2.0 array chips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: Data were generated using the Mas 5.0 algorithm in the Affymetrix Expression Console software

source_name: Heart Control 0h Animal # 100

label_protocol: Affymetrix GeneChip Expression 3'-Amplification One-Cycle Target Labeling and Control Kit was used for the synthesis of cDNA and cRNA and biotin-labeled cRNA. 2 μg of tRNA was utilized as starting material following manufacturer protocol.

growth_protocol: Male C3H/HeJ, weighing ~ 20 g each (7-10 weeks old), were housed in conventional micro isolator cages.  Food and water were freely available at all times.

extract_protocol: PBMC were isolated by gradient (Nycoprep) from blood collected in EDTA-treated tubes and lysed in RLT buffer.  Tissues were thinly sliced and preserved in RNAlater reagent at -80 C.  tRNA was obtained using RNeasy kit (Qiagen) following manufacturer protocols. tRNA concentration was measure by nanodrop and tRNA quality was evaluated by Bioanalyzer.

treatment_protocol: Animals were anesthetized and SEB toxin (treatment) or saline (control) was administered i.n. (5 μg SEB/ 50 μl) followed by and i.p. (2 μg SEB/200 μ-l) dose 2h later. PBMC, spleen, lung, liver, kidney, and heart were harvest for tRNA purification from SEB and  saline control groups  at 0, 2.75, 5 and 24 h after treatment .

tag: background strain

value: Male

tag: tissue

value: Heart


title: H_2S3

source_name: Heart SEB  2h45m Animal # 94


title: H_24C3

source_name: Heart Control  24h Animal # 99


title: H_24C2

source_name: Heart Control  24h Animal # 92


title: H_5C4

source_name: Heart Control  5h Animal # 104


title: H_2C4

source_name: Heart Control  2h45m Animal # 102


title: H_2S4

source_name: Heart SEB  2h45m Animal # 101


title: H_5S2

source_name: Heart SEB  5h Animal # 89


title: H_2C2

source_name: Heart Control  2h45m Animal # 88


title: genomic DNA from sample 335Tu

source_name: primary oropharygeal SCC from patient 335


title: H_2C3

source_name: Heart Control  2h45m Animal # 95


title: H_24C4

source_name: Heart Control  24h Animal # 106


title: H_0C3

source_name: Heart Control 0h Animal # 93


title: H_5S4

source_name: Heart SEB  5h Animal # 103


title: H_5C2

source_name: Heart Control  5h Animal # 90


title: H_24S3

source_name: Heart SEB  24h Animal # 98


title: H_5C3

source_name: Heart Control  5h Animal # 97


title: H_24S2

source_name: Heart SEB  24h Animal # 91


title: H_2S2

source_name: Heart SEB  2h45m Animal # 87


title: H_24C1

source_name: Heart Control  24h Animal # 85


title: H_0C2

source_name: Heart Control 0h Animal # 86


title: H_5S3

source_name: Heart SEB  5h Animal # 96


title: H_24S1

source_name: Heart SEB  24h Animal # 84


title: H_5S1

source_name: Heart SEB  5h Animal # 82


title: H_2C1

source_name: Heart Control  2h45m Animal # 81


title: H_5C1

source_name: Heart Control  5h Animal # 83


title: H_0C1

source_name: Heart Control 0h Animal # 79


title: S_24C5

source_name: Spleen Control  24h Animal # 78

value: Spleen


title: H_2S1

source_name: Heart SEB  2h45m Animal # 80


title: S_5C5

source_name: Spleen Control  5h Animal # 76


title: S_2S5

source_name: Spleen SEB  2h45m Animal # 73


title: S_24S5

source_name: Spleen SEB  24h Animal # 77


title: S_5S5

source_name: Spleen SEB  5h Animal # 75


title: S_2C5

source_name: Spleen Control  2h45m Animal # 74


title: S_24S4

source_name: Spleen SEB  24h Animal # 105


title: S_24C4

source_name: Spleen Control  24h Animal # 106


title: S_0C4

source_name: Spleen Control 0h Animal # 100


title: S_2C4

source_name: Spleen Control  2h45m Animal # 102


title: S_5C1

source_name: Spleen Control  5h Animal # 83


title: S_2S1

source_name: Spleen SEB  2h45m Animal # 80


title: S_5C4

source_name: Spleen Control  5h Animal # 104


title: S_24S1

source_name: Spleen SEB  24h Animal # 84


title: S_5S4

source_name: Spleen SEB  5h Animal # 103


title: S_2C1

source_name: Spleen Control  2h45m Animal # 81


title: S_0C5

source_name: Spleen Control 0h Animal # 72


title: S_24C1

source_name: Spleen Control  24h Animal # 85


title: S_24S2

source_name: Spleen SEB  24h Animal # 91


title: S_2S4

source_name: Spleen SEB  2h45m Animal # 101


title: S_0C1

source_name: Spleen Control 0h Animal # 79


title: Li_24C4

source_name: Liver Control  24h Animal # 106

value: Liver


title: S_0C2

source_name: Spleen Control 0h Animal # 86


title: Li_5S4

source_name: Liver SEB  5h Animal # 103


title: Li_2S4

source_name: Liver SEB  2h45m Animal # 101


title: S_5S1

source_name: Spleen SEB  5h Animal # 82


title: Li_0C4

source_name: Liver Control 0h Animal # 100


title: Li_2C4

source_name: Liver Control  2h45m Animal # 102


title: Li_24C3

source_name: Liver Control  24h Animal # 99


title: Li_5C3

source_name: Liver Control  5h Animal # 97


title: Li_24S3

source_name: Liver SEB  24h Animal # 98


title: Li_24C2

source_name: Liver Control  24h Animal # 92


title: Li_24S2

source_name: Liver SEB  24h Animal # 91


title: Li_2C3

source_name: Liver Control  2h45m Animal # 95


title: Li_2S3

source_name: Liver SEB  2h45m Animal # 94


title: Li_5S1

source_name: Liver SEB  5h Animal # 82


title: Li_24S1

source_name: Liver SEB  24h Animal # 84


title: Li_2C1

source_name: Liver Control  2h45m Animal # 81


title: Li_5C1

source_name: Liver Control  5h Animal # 83


title: Li_5C2

source_name: Liver Control  5h Animal # 90


title: K_5S4

source_name: Kidney SEB  5h Animal # 103

value: kidney


title: Li_0C2

source_name: Liver Control 0h Animal # 86


title: K_2S4

source_name: Kidney SEB  2h45m Animal # 101


title: K_2C3

source_name: Kidney Control  2h45m Animal # 95


title: K_5S3

source_name: Kidney SEB  5h Animal # 96


title: Li_0C1

source_name: Liver Control 0h Animal # 79


title: Li_2S1

source_name: Liver SEB  2h45m Animal # 80


title: Li_5S2

source_name: Liver SEB  5h Animal # 89


title: K_24C4

source_name: Kidney Control  24h Animal # 106


title: K_24C2

source_name: Kidney Control  24h Animal # 92


title: K_24S3

source_name: Kidney SEB  24h Animal # 98


title: K_5C4

source_name: Kidney Control  5h Animal # 104


title: K_5C3

source_name: Kidney Control  5h Animal # 97


title: Li_5S3

source_name: Liver SEB  5h Animal # 96


title: K_0C3

source_name: Kidney Control 0h Animal # 93


title: K_2C4

source_name: Kidney Control  2h45m Animal # 102


title: K_2S3

source_name: Kidney SEB  2h45m Animal # 94


title: K_24C3

source_name: Kidney Control  24h Animal # 99


title: Li_24C1

source_name: Liver Control  24h Animal # 85


title: Li_2C2

source_name: Liver Control  2h45m Animal # 88


title: Li_2S2

source_name: Liver SEB  2h45m Animal # 87


title: K_0C4

source_name: Kidney Control 0h Animal # 100


title: K_24S2

source_name: Kidney SEB  24h Animal # 91


title: K_5C2

source_name: Kidney Control  5h Animal # 90


title: K_24C1

source_name: Kidney Control  24h Animal # 85


title: K_2C2

source_name: Kidney Control  2h45m Animal # 88


title: K_5S2

source_name: Kidney SEB  5h Animal # 89


title: K_0C2

source_name: Kidney Control 0h Animal # 86


title: Lu_5S4

source_name: Lung SEB  5h Animal # 103

value: Lung


title: Lu_2C3

source_name: Lung Control  2h45m Animal # 95


title: Lu_5C4

source_name: Lung Control  5h Animal # 104


title: Lu_24C4

source_name: Lung Control  24h Animal # 106


title: Lu_24S2

source_name: Lung SEB  24h Animal # 91


title: Lu_24C3

source_name: Lung Control  24h Animal # 99


title: K_0C1

source_name: Kidney Control 0h Animal # 79


title: K_2S2

source_name: Kidney SEB  2h45m Animal # 87


title: K_24S1

source_name: Kidney SEB  24h Animal # 84


title: Lu_0C4

source_name: Lung Control 0h Animal # 100


title: Lu_0C3

source_name: Lung Control 0h Animal # 93


title: K_5C1

source_name: Kidney Control  5h Animal # 83


title: K_2S1

source_name: Kidney SEB  2h45m Animal # 80


title: Lu_5C3

source_name: Lung Control  5h Animal # 97


title: Lu_24S3

source_name: Lung SEB  24h Animal # 98


title: Lu_2S4

source_name: Lung SEB  2h45m Animal # 101


title: Lu_5C2

source_name: Lung Control  5h Animal # 90


title: Lu_5S3

source_name: Lung SEB  5h Animal # 96


title: Lu_5S2

source_name: Lung SEB  5h Animal # 89


title: Lu_2S3

source_name: Lung SEB  2h45m Animal # 94


title: Lu_24C2

source_name: Lung Control  24h Animal # 92


title: K_5S1

source_name: Kidney SEB  5h Animal # 82


title: K_2C1

source_name: Kidney Control  2h45m Animal # 81


title: Lu_2C4

source_name: Lung Control  2h45m Animal # 102


title: Lu_2S2

source_name: Lung SEB  2h45m Animal # 87


title: Lu_24S1

source_name: Lung SEB  24h Animal # 84


title: Lu_24C1

source_name: Lung Control  24h Animal # 85


title: Lu_0C2

source_name: Lung Control 0h Animal # 86


title: P_24C3

source_name: PBMC Control  24h

value: PBMC


title: Lu_5C1

source_name: Lung Control  5h Animal # 83


title: Lu_2C1

source_name: Lung Control  2h45m Animal # 81


title: Lu_0C1

source_name: Lung Control 0h Animal # 79


title: P_24S4

source_name: PBMC SEB  24h


title: P_5S3

source_name: PBMC SEB  5h


title: P_24C4


title: P_24S2


title: P_2C2

source_name: PBMC Control  2h45m


title: P_0C2

source_name: PBMC Control 0h


title: P_24S1


title: P_5S4


title: P_2S2

source_name: PBMC SEB  2h45m


title: P_2S4


title: P_0C3


title: P_2S3


title: P_5C3

source_name: PBMC Control  5h


title: P_5C2


title: P_5C4


title: Lu_5S1

source_name: Lung SEB  5h Animal # 82


title: P_24C1


title: P_5S2


title: P_24C2


title: P_24S3


title: P_2C4


title: P_2C3


title: P_5S1


title: P_5C1


title: P_2S1


title: WHIM 25_human counterpart

status: Public on Oct 10 2013

description:
homo sapiens
25Hu

scan_protocol: Microarrays were scanned with an Agilent B Scanner using 5um, single pass scanning mode and eXtended dynamic range.

data_processing: txt files and tif images generated by Agilent's Feature Extraction, v9.5.3.1, were uploaded into the UNC Microarray database.

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

extract_protocol: Trizol extractions followed by Dnase treatment and column purification.

tag: sample type

value: Total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.

source_name: primary breast tumor_him25_human counterpart

value: oct blocks

tag: subtype

value: PAM50 BASAL Subtype

tag: clin er

tag: clin pgr


title: P_2C1


title: WHIM 25_mouse passage3

description:
xenograft
25C

organism:
Homo sapiens
Mus musculus

source_name: primary breast tumor_him25_xenograft passage3


title: WHIM 24_human counterpart

description:
homo sapiens
24Hu

source_name: primary breast tumor_him24_human counterpart

value: PAM50 LUMA Subtype


title: WHIM 24_mouse passage1

description:
xenograft
24A

source_name: primary breast tumor_him24_xenograft passage1

value: PAM50 LUMB Subtype

value: Negative


title: WHIM 22_mouse passage1

description:
xenograft
22A

source_name: primary breast tumor_him22_xenograft passage1

value: Positive


title: WHIM 26_mouse passage2

description:
xenograft
26B

source_name: primary breast tumor_him26_xenograft passage2


title: WHIM 21_mouse passage2

description:
xenograft
21B

source_name: primary breast tumor_him21_xenograft passage2


title: WHIM 18_mouse passage3

description:
xenograft
18C

source_name: primary breast tumor_him18_xenograft passage3


title: WHIM 18_human counterpart

description:
homo sapiens
18Hu

source_name: primary breast tumor_him18_human counterpart


title: WHIM 18_mouse passage1

description:
xenograft
18A

source_name: primary breast tumor_him18_xenograft passage1


title: WHIM 23_mouse passage1

description:
xenograft
23A

source_name: primary breast tumor_him23_xenograft passage1


title: WHIM 26_mouse passage1

description:
xenograft
26A

source_name: primary breast tumor_him26_xenograft passage1


title: WHIM 26_human counterpart

description:
homo sapiens
26Hu

source_name: primary breast tumor_him26_human counterpart


title: WHIM 25_mouse passage1

description:
xenograft
25A

source_name: primary breast tumor_him25_xenograft passage1


title: WHIM 24_mouse passage2

description:
xenograft
24B

source_name: primary breast tumor_him24_xenograft passage2


title: P_0C1

source_name: PBMC Control 0h


title: WHIM 20_mouse passage2

description:
xenograft
20B

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: primary breast tumor_him20_xenograft passage2


title: WHIM 20_mouse passage1

description:
xenograft
20A

source_name: primary breast tumor_him20_xenograft passage1


title: WHIM 20_human counterpart

description:
homo sapiens
20Hu

source_name: primary breast tumor_him20_human counterpart


title: WHIM 22_mouse passage2

description:
xenograft
22B

source_name: primary breast tumor_him22_xenograft passage2


title: WHIM 22_human counterpart

description:
homo sapiens
22Hu

source_name: primary breast tumor_him22_human counterpart


title: WHIM 21_human counterpart

description:
homo sapiens
21Hu

source_name: primary breast tumor_him21_human counterpart


title: WHIM 21_mouse passage1

description:
xenograft
21A

source_name: primary breast tumor_him21_xenograft passage1


title: WHIM 9_mouse passage2

description: xenograft

data_processing: txt files and tif images generated by Agilent's Feature Extraction, v9.5.3.1, were uploaded into the UNC Microarray database. VALUE in tables is log(base2) of R/G Lowess Normalized Ratio (Mean).

source_name: Stratagene Human Universal Reference spiked with MCF7 and ME16C mRNA

tag: cell type

value: Total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte. Also, mRNA spiked in from MCF7 and ME16C.

value: oct block from human:mouse xenograft which contained at least 50% tumor cellularity

tag: clin her2


title: WHIM 9_mouse passage4

description: xenograft


title: WHIM 8_human counterpart

description: homo sapiens

value: oct blocks from biopsy which contained at least 50% tumor cellularity


title: WHIM 9_human counterpart

description: homo sapiens


title: WHIM 6_human counterpart

description: homo sapiens

source_name: primary breast tumor_him6_human counterpart


title: WHIM 8_mouse passage5

description: xenograft


title: WHIM 9_mouse passage1

description: xenograft


title: WHIM 8_mouse passage1

description: xenograft

source_name: primary breast tumor_him8_xenograft passage1


title: WHIM 6_mouse passage1

description: xenograft

source_name: primary breast tumor_him6_xenograft passage1


title: WHIM 6_mouse passage3

description: xenograft

source_name: primary breast tumor_him6_xenograft passage3


title: WHIM 2_mouse passage1

description: xenograft

source_name: primary breast tumor_him2_xenograft passage1


title: WHIM 2_mouse passage5

description: xenograft

source_name: primary breast tumor_him2_xenograft passage5


title: WHIM 6_mouse passage5

description: xenograft

source_name: primary breast tumor_him6_xenograft passage5


title: WHIM 16_human counterpart

description: homo sapiens

source_name: primary breast tumor_him16_human counterpart


title: WHIM 2_human counterpart

description: homo sapiens

source_name: primary breast tumor_him2_human counterpart


title: WHIM 16_mouse passage2

description: xenograft

source_name: primary breast tumor_him16_xenograft passage2


title: WHIM 2_mouse passage3

description: xenograft

source_name: primary breast tumor_him2_xenograft passage3


title: WHIM 14_human counterpart

description: homo sapiens

source_name: primary breast tumor_him14_human counterpart


title: WHIM 16_mouse passage1

description: xenograft

source_name: primary breast tumor_him16_xenograft passage1


title: WHIM 14_mouse passage1

description: xenograft

source_name: primary breast tumor_him14_xenograft passage1


title: WHIM 12_mouse passage3

description: xenograft

source_name: primary breast tumor_him12_xenograft passage3


title: WHIM 13_mouse passage2

description: xenograft

source_name: primary breast tumor_him13_xenograft passage2


title: WHIM 12_human counterpart

description: homo sapiens

source_name: Stratagene Human Universal Reference spiked with MCF7 and ME16C mRNA

source_name: primary breast tumor_him12_human counterpart

value: oct block from biopsy which contained at least 50% tumor cellularity


title: WHIM 13_mouse passage1

description: xenograft

source_name: primary breast tumor_him13_xenograft passage1


title: WHIM 13_human counterpart

description: homo sapiens

source_name: primary breast tumor_him13_human counterpart


title: WHIM 11_human counterpart

description: homo sapiens

source_name: primary breast tumor_him11_human counterpart


title: WHIM 14_mouse passage2

description: xenograft

source_name: primary breast tumor_him14_xenograft passage2


title: WHIM 12_mouse passage1

description: xenograft

source_name: primary breast tumor_him12_xenograft passage1


title: WHIM 11_mouse passage2

description: xenograft

source_name: primary breast tumor_him11_xenograft passage2


title: WHIM 11_mouse passage1

description: xenograft

source_name: primary breast tumor_him11_xenograft passage1


title: WHIM 11_mouse passage4

description: xenograft

source_name: primary breast tumor_him11_xenograft passage4


title: CD11b+CD8a- with vehicle control replicate 3

status: Public on Aug 16 2013

description: Gene expresion data from splenic CD11b+CD8a- cells control

hyb_protocol: 1.8 ug of labeled and fragmented SS DNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST arrays , following Affymetrix protocol.GeneChips arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix Expression Console using default settings for median polish RMA summarization and Sketch-Quantile as the normalization method.

source_name: CD11b+CD8a- with vehicle control

label_protocol: Ambion WT  Expression kit was used for the synthesis of cDNA. 140 ng of tRNA were utilized as starting material following manufacturer protocol.  cDNA was labeled  with Affymetrix GeneChip® WT Terminal Labeling Kit.

growth_protocol: FACS-sorted splenic cDC subsets were processed directly after isolation without additional culturing or treatment of the cells.

extract_protocol: tRNA was obtained using Rnaesy kit (Qiagen) following manufacturer protocols. tRNA concentration was measure by nanodrop and tRNA quality was evaluated by Bioanalyzer.

treatment_protocol: Splenic cDC subsets which reconstituted in vivo in mice treated with total body irradiation alone or in combination with exogenous retinoic acid were directly FACS-sorted into RNAprotect reagent.

tag: strain

tag: tissue origin

value: spleen


title: CD11b+CD8a- with vehicle control replicate 4


title: CD11b+CD8a- with exogenous RA replicate 3

description: Gene expresion data from splenic CD11b+CD8a- cells with RA treatment

source_name: CD11b+CD8a- with exogenous RA


title: CD11b+CD8a- with vehicle control replicate 1


title: CD11b+CD8a- with vehicle control replicate 2


title: CD11b-CD8a+ with exogenous RA replicate 4

description: Gene expresion data from splenic CD11b-CD8a+ cells with RA treatment

source_name: CD11b-CD8a+ with exogenous RA


title: CD11b+CD8a- with exogenous RA replicate 4


title: CD11b-CD8a+ with exogenous RA replicate 3


title: CD11b-CD8a+ with vehicle control replicate 4

description: Gene expresion data from splenic CD11b-CD8a+ cells control

source_name: CD11b-CD8a+ with vehicle control


title: CD11b-CD8a+ with vehicle control replicate 3


title: CD11b-CD8a+ with exogenous RA replicate 1


title: CD11b+CD8a- with exogenous RA replicate 2


title: CD11b-CD8a+ with vehicle control replicate 2


title: CD11b+CD8a- with exogenous RA replicate 1


title: CD11b-CD8a+ with vehicle control replicate 1


title: CD11b-CD8a+ with exogenous RA replicate 2


title: WU-BC5, mouse passage5

status: Public on Oct 10 2012

description: PAM50 Basal Subtype

data_processing: txt files and tif images generated by Agilent's Feature Extraction, v9.5.3.1, were uploaded into the UNC Microarray database. Final loess, normalized log2 ratios (Cy5-sample/Cy3-control) for each probe were retrieved.

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

tag: reference

value: Stratagene Human Reference total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.

source_name: primary breast tumor, WU-BC5, xenograft passage5

tag: tissue type

value: primary breast tumor

tag: clinical er

tag: clinical pgr

tag: clinical her2


title: WU-BC5, mouse passage3

description: PAM50 Basal Subtype

source_name: primary breast tumor, WU-BC5, xenograft passage3


title: WU-BC3, mouse passage5

description: PAM50 HER2-E Subtype

source_name: primary breast tumor, WU-BC3, xenograft passage5


title: WU-BC5, human counterpart

description: PAM50 Basal Subtype

source_name: primary breast tumor, WU-BC5, human counterpart


title: WU-BC4, mouse passage4

description: PAM50 Basal Subtype

source_name: primary breast tumor, WU-BC4, xenograft passage4


title: WU-BC5, mouse passage1

description: PAM50 Basal Subtype

source_name: primary breast tumor, WU-BC5, xenograft passage1


title: WU-BC3, mouse passage2

description: PAM50 HER2-E Subtype

source_name: primary breast tumor, WU-BC3, xenograft passage2


title: WU-BC5, mouse passage3, ovary metastasis

description: PAM50 Basal Subtype

source_name: ovary metastasis, WU-BC5, xenograft passage3

value: ovary metastasis


title: WU-BC4, mouse passage5

description: PAM50 Basal Subtype

source_name: primary breast tumor, WU-BC4, xenograft passage5


title: WU-BC4, mouse passage3

description: PAM50 Basal Subtype

source_name: primary breast tumor, WU-BC4, xenograft passage3


title: WU-BC4, human counterpart

description: PAM50 Basal Subtype

source_name: primary breast tumor, WU-BC4, human counterpart


title: Breast Cancer Array_Patient ID_17170

status: Public on Jun 21 2012

tag: components

value: Generated labeled cRNA from reference sample

source_name: Primary Breast Tumor_Patient ID_17170

tag: comment

value: oct blocks from fine needle biopsies which contained at least 50% tumor cellularity

tag: ki67 surg

tag: er bl

tag: baseline subtype

value: LumB

tag: baseline ror p

tag: baseline ror s

value: mod

tag: studyid

value: breast cancer tumor


title: WU-BC4, mouse passage1

description: PAM50 Basal Subtype

source_name: primary breast tumor, WU-BC4, xenograft passage1

tag: sample type


title: Breast Cancer Array_Patient ID_16992

value: Total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.

source_name: Primary Breast Tumor_Patient ID_16992

value: triaged to chemo

tag: tissue


title: Breast Cancer Array_Patient ID_17208

source_name: Primary Breast Tumor_Patient ID_17208


title: WU-BC3, mouse passage1

description: PAM50 HER2-E Subtype

source_name: primary breast tumor, WU-BC3, xenograft passage1

value: Negative


title: Breast Cancer Array_Patient ID_17124

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_17124


title: Breast Cancer Array_Patient ID_16965

source_name: Primary Breast Tumor_Patient ID_16965

value: high


title: Breast Cancer Array_Patient ID_16986

source_name: Primary Breast Tumor_Patient ID_16986


title: Breast Cancer Array_Patient ID_16970

source_name: Primary Breast Tumor_Patient ID_16970

value: LumA

value: low


title: Breast Cancer Array_Patient ID_16880

source_name: Primary Breast Tumor_Patient ID_16880

value: moderate


title: Breast Cancer Array_Patient ID_16825

source_name: Primary Breast Tumor_Patient ID_16825


title: Breast Cancer Array_Patient ID_16889

source_name: Primary Breast Tumor_Patient ID_16889


title: Breast Cancer Array_Patient ID_17123

source_name: Primary Breast Tumor_Patient ID_17123


title: Breast Cancer Array_Patient ID_16956

source_name: Primary Breast Tumor_Patient ID_16956

value: y

value: Moderate


title: Breast Cancer Array_Patient ID_16757

source_name: Primary Breast Tumor_Patient ID_16757


title: Breast Cancer Array_Patient ID_16751

source_name: Primary Breast Tumor_Patient ID_16751


title: Breast Cancer Array_Patient ID_16745

source_name: Primary Breast Tumor_Patient ID_16745


title: Breast Cancer Array_Patient ID_16004

source_name: Primary Breast Tumor_Patient ID_16004

value: med


title: Breast Cancer Array_Patient ID_16702

source_name: Primary Breast Tumor_Patient ID_16702


title: Breast Cancer Array_Patient ID_15892

source_name: Primary Breast Tumor_Patient ID_15892


title: Breast Cancer Array_Patient ID_16598

source_name: Primary Breast Tumor_Patient ID_16598


title: Breast Cancer Array_Patient ID_308

description: pol

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_308

value: pol


title: Breast Cancer Array_Patient ID_16744

source_name: Primary Breast Tumor_Patient ID_16744

value: High


title: Breast Cancer Array_Patient ID_16779

value: Generated labeled cRNA from reference sample

source_name: Primary Breast Tumor_Patient ID_16779


title: Breast Cancer Array_Patient ID_15870

source_name: Primary Breast Tumor_Patient ID_15870

value: oct blocks from fine needle biopsies which contained at least 50% tumor cellularity


title: Breast Cancer Array_Patient ID_16579

source_name: Primary Breast Tumor_Patient ID_16579


title: Breast Cancer Array_Patient ID_16590

source_name: Primary Breast Tumor_Patient ID_16590


title: Breast Cancer Array_Patient ID_811

description: pol

source_name: Primary Breast Tumor_Patient ID_811

value: LumB


title: Breast Cancer Array_Patient ID_409

description: pol

source_name: Primary Breast Tumor_Patient ID_409


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16315

description:
Z1031_16315_BL
baseline expression array

source_name: Primary breast tumor

tag: patient id

value: primary breast tumor

value: oct block from fine needle biopsy which contained at least 50% tumor cellularity


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16837

description:
Z1031_16837_BL
baseline expression array

value: Total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16847

description:
Z1031_16847_BL
baseline expression array


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16846

description:
Z1031_16846_BL
baseline expression array


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16727

description:
Z1031_16727_BL
baseline expression array


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16786

description:
Z1031_16786_BL
baseline expression array


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16202

description:
Z1031_16202_BL
baseline expression array


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16912

description:
Z1031_16912_BL
baseline expression array


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16754

description:
Z1031_16754_BL
baseline expression array


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16216

description:
Z1031_16216_BL
baseline expression array


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16947

description:
Z1031_16947_BL
baseline expression array


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_15980

description:
Z1031_15980_BL
baseline expression array


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_16326

description:
Z1031_16326_BL
baseline expression array


title: Breast Cancer Array_Patient ID_16566

value: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor Patient ID 16566

tag: study id

value: breast cancer tumor

tag: treatment

value: Z1031 screening study


title: Breast Cancer Array_Pre-treatment_Z1031 Patient ID_15952

description:
Z1031_15952_BL
baseline expression array

tag: reference

value: 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.


title: Breast Cancer Array_Patient ID_16561

source_name: Primary Breast Tumor Patient ID 16561

value: LumA


title: Breast Cancer Array_Patient ID_16495

source_name: Primary Breast Tumor Patient ID 16495

value: low


title: Breast Cancer Array_Patient ID_16439

source_name: Primary Breast Tumor Patient ID 16439


title: Breast Cancer Array_Patient ID_16531

source_name: Primary Breast Tumor Patient ID 16531


title: Breast Cancer Array_Patient ID_16442

source_name: Primary Breast Tumor Patient ID 16442


title: Breast Cancer Array_Patient ID_16364

source_name: Primary Breast Tumor Patient ID 16364


title: Breast Cancer Array_Patient ID_16402

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor Patient ID 16402

value: high


title: Breast Cancer Array_Patient ID_16398

source_name: Primary Breast Tumor Patient ID 16398


title: Breast Cancer Array_Patient ID_16368

source_name: Primary Breast Tumor Patient ID 16368


title: Breast Cancer Array_Patient ID_16376

source_name: Primary Breast Tumor Patient ID 16376


title: Breast Cancer Array_Patient ID_16486

source_name: Primary Breast Tumor Patient ID 16486

value: mod


title: Breast Cancer Array_Patient ID_16392

source_name: Primary Breast Tumor Patient ID 16392


title: Breast Cancer Array_Patient ID_16492

source_name: Primary Breast Tumor Patient ID 16492


title: Breast Cancer Array_Patient ID_16365

source_name: Primary Breast Tumor Patient ID 16365

value: med


title: Breast Cancer Array_Patient ID_16171

source_name: Primary Breast Tumor Patient ID 16171


title: Breast Cancer Array_Patient ID_16224

source_name: Primary Breast Tumor Patient ID 16224


title: Breast Cancer Array_Patient ID_16148

source_name: Primary Breast Tumor Patient ID 16148


title: Breast Cancer Array_Patient ID_16290

source_name: Primary Breast Tumor Patient ID 16290


title: Breast Cancer Array_Patient ID_16237

source_name: Primary Breast Tumor Patient ID 16237


title: Breast Cancer Array_Patient ID_16170

source_name: Primary Breast Tumor Patient ID 16170


title: Breast Cancer Array_Patient ID_16136

source_name: Primary Breast Tumor Patient ID 16136


title: Breast Cancer Array_Patient ID_16165

source_name: Primary Breast Tumor Patient ID 16165


title: Breast Cancer Array_Patient ID_16256

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor Patient ID 16256


title: Breast Cancer Array_Patient ID_16292

source_name: Primary Breast Tumor Patient ID 16292


title: Breast Cancer Array_Patient ID_16342

source_name: Primary Breast Tumor Patient ID 16342


title: Breast Cancer Array_Patient ID_16270

source_name: Primary Breast Tumor Patient ID 16270


title: Breast Cancer Array_Patient ID_16313

source_name: Primary Breast Tumor Patient ID 16313


title: Breast Cancer Array_Patient ID_16295

source_name: Primary Breast Tumor Patient ID 16295


title: Breast Cancer Array_Patient ID_16135

source_name: Primary Breast Tumor Patient ID 16135


title: Breast Cancer Array_Patient ID_16099

source_name: Primary Breast Tumor Patient ID 16099


title: Breast Cancer Array_Patient ID_16092

source_name: Primary Breast Tumor Patient ID 16092


title: Breast Cancer Array_Patient ID_16093

source_name: Primary Breast Tumor Patient ID 16093


title: Breast Cancer Array_Patient ID_16105

source_name: Primary Breast Tumor Patient ID 16105


title: Breast Cancer Array_Patient ID_16063

source_name: Primary Breast Tumor Patient ID 16063


title: Breast Cancer Array_Patient ID_16070

source_name: Primary Breast Tumor Patient ID 16070


title: Breast Cancer Array_Patient ID_16127

source_name: Primary Breast Tumor Patient ID 16127


title: Breast Cancer Array_Patient ID_16054

source_name: Primary Breast Tumor Patient ID 16054


title: Breast Cancer Array_Patient ID_16064

source_name: Primary Breast Tumor Patient ID 16064


title: Breast Cancer Array_Patient ID_16074

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor Patient ID 16074


title: Breast Cancer Array_Patient ID_16067

source_name: Primary Breast Tumor Patient ID 16067


title: Breast Cancer Array_Patient ID_16069

source_name: Primary Breast Tumor Patient ID 16069


title: Breast Cancer Array_Patient ID_16084

source_name: Primary Breast Tumor Patient ID 16084


title: Breast Cancer Array_Patient ID_16042

source_name: Primary Breast Tumor Patient ID 16042


title: Breast Cancer Array_Patient ID_16052

source_name: Primary Breast Tumor Patient ID 16052


title: Breast Cancer Array_Patient ID_16007

source_name: Primary Breast Tumor Patient ID 16007


title: Breast Cancer Array_Patient ID_16031

source_name: Primary Breast Tumor Patient ID 16031


title: Breast Cancer Array_Patient ID_15950

source_name: Primary Breast Tumor Patient ID 15950


title: Breast Cancer Array_Patient ID_15977

source_name: Primary Breast Tumor Patient ID 15977


title: Breast Cancer Array_Patient ID_15913

source_name: Primary Breast Tumor Patient ID 15913


title: Breast Cancer Array_Patient ID_15901

source_name: Primary Breast Tumor Patient ID 15901


title: Breast Cancer Array_Patient ID_15931

source_name: Primary Breast Tumor Patient ID 15931


title: Breast Cancer Array_Patient ID_16016

source_name: Primary Breast Tumor Patient ID 16016


title: Breast Cancer Array_Patient ID_16043

source_name: Primary Breast Tumor Patient ID 16043


title: Breast Cancer Array_Patient ID_15976

source_name: Primary Breast Tumor Patient ID 15976


title: Breast Cancer Array_Patient ID_15858

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor Patient ID 15858


title: Breast Cancer Array_Patient ID_15882

source_name: Primary Breast Tumor Patient ID 15882

value: moderate


title: Breast Cancer Array_Patient ID_15776

source_name: Primary Breast Tumor Patient ID 15776


title: Breast Cancer Array_Patient ID_15867

source_name: Primary Breast Tumor Patient ID 15867


title: Breast Cancer Array_Patient ID_15797

source_name: Primary Breast Tumor Patient ID 15797


title: Breast Cancer Array_Patient ID_15816

source_name: Primary Breast Tumor Patient ID 15816


title: Breast Cancer Array_Patient ID_15832

source_name: Primary Breast Tumor Patient ID 15832


title: Breast Cancer Array_Patient ID_15757

source_name: Primary Breast Tumor Patient ID 15757


title: Breast Cancer Array_Patient ID_15830

source_name: Primary Breast Tumor Patient ID 15830


title: Breast Cancer Array_Patient ID_15866

source_name: Primary Breast Tumor Patient ID 15866


title: Breast Cancer Array_Patient ID_15770

source_name: Primary Breast Tumor Patient ID 15770


title: Breast Cancer Array_Patient ID_15838

source_name: Primary Breast Tumor Patient ID 15838


title: Breast Cancer Array_Patient ID_15660

source_name: Primary Breast Tumor Patient ID 15660


title: Breast Cancer Array_Patient ID_15715

source_name: Primary Breast Tumor Patient ID 15715


title: Breast Cancer Array_Patient ID_15616

source_name: Primary Breast Tumor Patient ID 15616


title: Breast Cancer Array_Patient ID_15574

source_name: Primary Breast Tumor Patient ID 15574


title: Breast Cancer Array_Patient ID_15565

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor Patient ID 15565


title: Breast Cancer Array_Patient ID_15547

source_name: Primary Breast Tumor Patient ID 15547


title: Breast Cancer Array_Patient ID_15462

source_name: Primary Breast Tumor Patient ID 15462


title: Breast Cancer Array_Patient ID_15654

source_name: Primary Breast Tumor Patient ID 15654


title: Breast Cancer Array_Patient ID_15571

source_name: Primary Breast Tumor Patient ID 15571


title: Breast Cancer Array_Patient ID_15921

source_name: Primary Breast Tumor Patient ID 15921


title: Breast Cancer Array_Patient ID_15681

source_name: Primary Breast Tumor Patient ID 15681


title: Breast Cancer Array_Patient ID_826

description: pol

source_name: Primary Breast Tumor Patient ID 826

value: POL

value: Pre-Operative Letrozole


title: Breast Cancer Array_Patient ID_15829

value: Generated labeled cRNA from reference sample

source_name: Primary Breast Tumor Patient ID 15829

value: oct blocks from fine needle biopsies which contained at least 50% tumor cellularity


title: Breast Cancer Array_Patient ID_831

description: pol

source_name: Primary Breast Tumor Patient ID 831

value: LumB


title: Breast Cancer Array_Patient ID_15544

source_name: Primary Breast Tumor Patient ID 15544


title: Breast Cancer Array_Patient ID_829

description: pol

source_name: Primary Breast Tumor Patient ID 829


title: Breast Cancer Array_Patient ID_841

description: pol

source_name: Primary Breast Tumor Patient ID 841


title: Breast Cancer Array_Patient ID_15669

source_name: Primary Breast Tumor Patient ID 15669


title: Breast Cancer Array_Patient ID_15894

source_name: Primary Breast Tumor Patient ID 15894


title: Breast Cancer Array_Patient ID_839

description: pol

source_name: Primary Breast Tumor Patient ID 839


title: Breast Cancer Array_Patient ID_15445

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: Primary Breast Tumor Patient ID 15445


title: Breast Cancer Array_Patient ID_15386

source_name: Primary Breast Tumor Patient ID 15386


title: Breast Cancer Array_Patient ID_818

description: pol

source_name: Primary Breast Tumor Patient ID 818


title: Breast Cancer Array_Patient ID_823

description: pol

source_name: Primary Breast Tumor Patient ID 823


title: Breast Cancer Array_Patient ID_122

description: pol

source_name: Primary Breast Tumor Patient ID 122