|
| Status |
Public on Sep 05, 2013 |
| Title |
sporadic, sample 31 |
| Sample type |
RNA |
| |
|
| Source name |
frozen surgical sample of breast cancer, sporadic
|
| Organism |
Homo sapiens |
| Characteristics |
clinical sample: surgical tumor sample
histopathology: ductal breast ca.
molecular subtype (according to sorlie et al., pnas 100, 8418-23 (2003): basal-like
estrogen receptor status (by immunohistochemistry): ER(-)
brca1/2 mutation: No mutation
brca1 promoter methylation: methylated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Total RNA (8 ug) was used for synthesis of double stranded cDNA according to manufacturer's instructions. Half of the cDNA volume was used for synthesis of biotynylated cRNA with the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics).
|
| |
|
| Hybridization protocol |
Following fragmentation, 16 ug of cRNA were hybridized for 16 hr at 45C on HG U133 Plus 2.0 Gene Chip oligonucleotide arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
|
| Description |
Gene expression data from sporadic breast cancer
|
| Data processing |
Data was acquired using GCOS 1.2 software (Affymetrix). The preprocessing was performed by Robust Multiarray Analysis (RMA, Bioconductor).
|
| |
|
| Submission date |
Sep 04, 2013 |
| Last update date |
Dec 10, 2014 |
| Contact name |
Katarzyna Marta Lisowska |
| E-mail(s) |
klisowska@io.gliwice.pl
|
| Organization name |
MSC Memorial Cancer Center and Institute of Oncology, Gliwice Branch
|
| Department |
Center for Translational Research and Molecular Biology of Cancer
|
| Street address |
ul. Wybrzeże Armii Krajowej 15
|
| City |
Gliwice |
| ZIP/Postal code |
44-101 |
| Country |
Poland |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE50567 |
BRCA1-related gene signature in breast cancer: the role of ER status and molecular type |
|
