|
| Status |
Public on Nov 06, 2011 |
| Title |
BR00-0344 |
| Sample type |
genomic |
| |
|
| Source name |
Breast Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
subtype: LumB
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Peripheral blood was collected in EDTA and stored at -40°C. DNA was isolated using phenol/chloroform extraction and ethanol precipitation as described previously (Andersen et al., 1992). Tumor DNA from snap frozen tumors, stored at -80°C, was isolated following the same Phenol/Chloroform extraction procedure.
|
| Label |
biotin
|
| Label protocol |
250 ng of genomic DNA was used as template for WGA, using Illumina proprietary reagents. Following WGA, the amplified DNA was enzymatically fragmented, isopropanol precipitated and resuspended in Illumina resuspension buffer
|
| |
|
| Hybridization protocol |
The samples were loaded onto the Human-1 array, and hybridized overnight for 16h at 48°C. Following hybridization, the beadchips were submerged in buffer, spun dry in a centrifuge, and assembled into a TeFlow hydro-chamber heated to 44°C
|
| Scan protocol |
Within three days, beadchips were imaged on the BeadArray reader using BeadScan software.
|
| Description |
Paired Normal Sample (Rref) came from Normal DNA from Normal Breast
|
| Data processing |
Sample values were derived follwing a 'PairedSample Analysis' from Illumina's BeadStudio Genotyping Module v(3.3.4)
|
| |
|
| Submission date |
Feb 24, 2009 |
| Last update date |
Jul 17, 2015 |
| Contact name |
Charles M. Perou |
| E-mail(s) |
[email protected]
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center
|
| Street address |
12-044 Lineberger Comprehensive Cancer Center CB# 7295
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7264 |
| Country |
USA |
| |
|
| Platform ID |
GPL8864 |
| Series (1) |
| GSE10893 |
Basal-like Breast Cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival |
|
