|
| Status |
Public on Sep 22, 2020 |
| Title |
BC5462: primary breast cancer patient 174 |
| Sample type |
RNA |
| |
|
| Source name |
primary breast cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary breast cancer
age: 59
node: 0
grade: 2
t-size (mm): 30
t.dmfs: 173
e.dmfs: 0
adjuvant treatment: tamoxifen
intrinsic subtype: 2
|
| 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 |
GSM663989 |
