|
| Status |
Public on Jan 17, 2017 |
| Title |
Primary Breast Cancer1930-250ksty |
| Sample type |
genomic |
| |
|
| Source name |
genomic [email protected]
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary Breast Cancer
mutation: BRCAX
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from fresh frozen primary breast cancer tissue using Qiagen Dneasy kit . DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to 250K_Sty
|
| Data processing |
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). .CEL files were imported in Partek Genomics Suite v.6.5. Copy number estimates were calculated in Partek against a reference baseline consisting of 90 female CEPH samples. Copy number segmentation was performed by Parteks Genomic segmentation tool with a minumum number of markers of 20. Threshold for calling gains and losses set to -0.25 < 2 > +25. Signal to noise 0.45.
|
| |
|
| Submission date |
Jan 17, 2014 |
| Last update date |
Jan 17, 2017 |
| Contact name |
Marcel Smid |
| Organization name |
Erasmus MC
|
| Department |
Medical Oncology
|
| Street address |
Dr. Molewaterplein 50
|
| City |
Rotterdam |
| ZIP/Postal code |
PO Box 2040, 3000CA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL3720 |
| Series (2) |
| GSE54193 |
Proper genomic profiling of (BRCA1-mutated) basal-like breast carcinomas requires prior removal of tumor infiltrating lymphocytes |
| GSE54219 |
Molecular genomic and transcriptomic profiling of familial breast cancer. |
|
