|
| Status |
Public on Sep 18, 2008 |
| Title |
Tumor (T-04_FFPE_03) |
| Sample type |
genomic |
| |
|
| Source name |
Human tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
Female, primary breast tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Protocol 1 and 2 are new DNA extraction protocols, protocol 3 is modified Qiagen extraction protocol and 4 is Qiagen DNA extraction protocol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated DNA were prepared according to the standard Affymetrix protocol from 90 ug total DNA (250K StyI Mapping Asssay Technical Manual, 2006, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 90 ug of DNA were hybridized for 16 hr at 49C on 250K StyI mapping Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Scanner 7000.
|
| Description |
formalin fixed parafin embedded tissue
|
| Data processing |
The data were analyzed with CNAG v2.0, AsCNAR and CNATv4.0.1.
|
| |
|
| Submission date |
Sep 25, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Ralf Krahe |
| E-mail(s) |
rkrahe@mdanderson.org
|
| Phone |
(713) 834-6345
|
| Fax |
(713) 834-6319
|
| Organization name |
University of Texas M.D. Anderson Cancer Center
|
| Department |
Cancer Genetics
|
| Lab |
Krahe Lab
|
| Street address |
1515 Holcombe Blvd., Unit #1010
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL3720 |
| Series (1) |
| GSE9154 |
Optimizations of DNA isolation and copy number analysis identifies regions of genomic gain/loss in early breast cancer |
|
