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Sample GSM1039135 Query DataSets for GSM1039135
Status Public on Apr 19, 2013
Title 51T_mRNA
Sample type RNA
 
Source name Breast tissue
Organism Homo sapiens
Characteristics tissue: Breast
status: primary triple negative cancer
gender: Female
age at diagnosis: 63
best stage: 2B
grade: 2
Extracted molecule total RNA
Extraction protocol RNA was isolated from FFPE tissue using Recover ALL kit (Ambion)
Label n/a
Label protocol RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol by the Ohio State Microarray Core Facility
 
Hybridization protocol RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.
Scan protocol Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.
Data processing Data were collected as NanoString RCC files and provided as an Excel spreadsheet. The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using quantile normalization.
Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system.
 
Submission date Nov 19, 2012
Last update date Apr 19, 2013
Contact name Luciano Cascione
E-mail(s) luciano.cascione@ior.usi.ch
Organization name IOR
Department Lymphoma & Genomics Research Program
Street address Via Chiesa 5
City Bellinzona
State/province Ticino
ZIP/Postal code 6500
Country Switzerland
 
Platform ID GPL16299
Series (2)
GSE41970 Integrated microRNA and mRNA Signatures Associated with Survival in Triple Negative Breast Cancer
GSE45498 Integrated microRNA and mRNA Signatures Associated with Survival in Triple Negative Breast Cancer II

Data table header descriptions
ID_REF
VALUE quantile normalized

Data table
ID_REF VALUE
POS_A(128) 6921.939155
POS_B(32) 2288.382394
POS_C(8) 502.2192019
POS_D(2) 124.7196244
POS_E(0.5) 18.93065728
POS_F(0.125) 26.7256338
NEG_A(0) 4.4542723
NEG_B(0) 11.13568075
NEG_C(0) 8.908544601
NEG_D(0) 6.681408451
NEG_E(0) 8.908544601
NEG_F(0) 10.02211268
NEG_G(0) 7.794976526
NEG_H(0) 11.13568075
ABCB1 41.33597039
ABL1 164.4807214
AKT1 14.34534003
AKT2 231.9572973
APC 56.51819997
AR 22.77991202

Total number of rows: 250

Table truncated, full table size 4 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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