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Sample GSM782537 Query DataSets for GSM782537
Status Public on Sep 13, 2011
Title Triple-negative breast cancer_015
Sample type RNA
 
Source name primary breast cancer tissue
Organism Homo sapiens
Characteristics tissue: triple-negative breast cancer
lymph node status (0: negative, 1: positive): 0
grade (12: G1 or G2, 3: G3): 12
tumor size (1: up to 1 cm, 2: >1cm): 2
event-free interval (months): 77
event (1: yes, 0: no): 0
cohort: FRA
biopsy type (1: surgical, 2: core needle): 1
chemotherapy treatment (yes/no): YES
neoadjuvant chemotherapy (yes/no): NO
Treatment protocol Samples were snap frozen and stored at -80°C.
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy kit according to the manufacturer's instructions.
Label biotin
Label protocol Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kits according to the manufacturer's instructions.
 
Hybridization protocol Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45°C on the GeneChip HG-U133A array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description TNBC_015
Gene expression data from primary breast tumors.
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Aug 18, 2011
Last update date Sep 23, 2011
Contact name Thomas Karn
E-mail(s) t.karn@em.uni-frankfurt.de
Organization name J.W.Goethe-University
Street address Theodor-Stern-Kai 7
City Frankfurt
ZIP/Postal code 60590
Country Germany
 
Platform ID GPL96
Series (1)
GSE31519 A Clinically Relevant Gene Signature in Triple-Negative and Basal-Like Breast Cancer

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity

Data table
ID_REF VALUE
1007_s_at 3265.7
1053_at 197.6
117_at 190.4
121_at 640.8
1255_g_at 7.8
1294_at 439.1
1316_at 109.1
1320_at 13.9
1405_i_at 1229
1431_at 50.7
1438_at 1661.8
1487_at 452.5
1494_f_at 106.7
1598_g_at 2270.4
160020_at 903.8
1729_at 755.9
177_at 165.8
1773_at 174.1
179_at 471.9
1861_at 284.5

Total number of rows: 22283

Table truncated, full table size 358 Kbytes.




Supplementary file Size Download File type/resource
GSM782537.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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