NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4797088 Query DataSets for GSM4797088
Status Public on Sep 22, 2020
Title BC6082: primary breast cancer patient 275
Sample type RNA
 
Source name primary breast cancer tissue
Organism Homo sapiens
Characteristics tissue: primary breast cancer
age: 66
node: 0
grade: 2
t-size (mm): 1
t.dmfs: 241
e.dmfs: 0
adjuvant treatment: none
intrinsic subtype: 3
Treatment protocol For all tumors, samples were snap frozen and stored at -80°C. Tumor cell content exceeded 40% in all samples.
Extracted molecule total RNA
Extraction protocol Approximately 50 mg of frozen breast tumor tissue was crushed in liquid nitrogen. RLT-Buffer was added and the homogenate was centrifuged through a QIAshredder column (QIAGEN, Hilden, Germany). RNeasy extraction (QIAGEN) of total RNA was performed 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 Kit, according to the manufacturer’s instructions
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on 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.
Data processing Raw expression data (CEL files) were normalized using frozen robust multiarray analysis (fRMA)
 
Submission date Sep 21, 2020
Last update date Sep 22, 2020
Contact name Marcus Schmidt
E-mail(s) Marcus.Schmidt@unimedizin-mainz.de
Organization name Universitätsmedizin Mainz
Department Universitäres Centrum für Tumorerkrankungen
Street address Langenbeckstr. 1
City Mainz
ZIP/Postal code 55131
Country Germany
 
Platform ID GPL96
Series (1)
GSE158309 Prognostic significance of interferon-γ and its signaling pathway in early breast cancer depends on the molecular subtypes
Relations
Reanalysis of GSM282449

Data table header descriptions
ID_REF
VALUE log2 frozen RMA signal

Data table
ID_REF VALUE
1007_s_at 10.728
1053_at 6.891
117_at 7.805
121_at 9.457
1255_g_at 5.117
1294_at 8.632
1316_at 7.079
1320_at 5.353
1405_i_at 7.325
1431_at 5.360
1438_at 8.158
1487_at 8.144
1494_f_at 7.152
1598_g_at 9.576
160020_at 10.256
1729_at 8.826
177_at 6.011
1773_at 6.250
179_at 10.071
1861_at 6.730

Total number of rows: 22283

Table truncated, full table size 370 Kbytes.




Supplementary file Size Download File type/resource
GSM4797088_BC6082.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap