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Sample GSM782535 Query DataSets for GSM782535
Status Public on Sep 13, 2011
Title Triple-negative breast cancer_013
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): 1
grade (12: G1 or G2, 3: G3): 3
tumor size (1: up to 1 cm, 2: >1cm): 2
event-free interval (months): 16
event (1: yes, 0: no): 1
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_013
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 2242.8
1053_at 296.8
117_at 218.4
121_at 812.1
1255_g_at 47.7
1294_at 540
1316_at 89.9
1320_at 71.1
1405_i_at 1513.4
1431_at 59.5
1438_at 527
1487_at 380.6
1494_f_at 177
1598_g_at 3036.9
160020_at 2601.1
1729_at 775.6
177_at 239.2
1773_at 202.5
179_at 656.8
1861_at 279.9

Total number of rows: 22283

Table truncated, full table size 358 Kbytes.




Supplementary file Size Download File type/resource
GSM782535.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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