|
| Status |
Public on Jun 30, 2013 |
| Title |
MDACC 20107 |
| Sample type |
genomic |
| |
|
| Source name |
STAG2-mutant urothelial carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
patient gender: female
patient age at specimen collection: 76
procedure at collection: transurethral resection
pathologic stage at collection: pTa
stag2 mutation present in tumor: 3642delC; 1045R>frameshift (deletion)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was prepared directly from snap-frozen urothelial carcinoma primary tumor samples using Qiagen QIAamp DNA Extraction Kits.
|
| 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 |
Urothelial carcinoma with STAG2 mutation
TW06
|
| Data processing |
.CEL files were generated from the scanned array image files by the Affymetrix GeneChip Command Console Software and were imported into the Affymetrix Chromosome Analysis Suite v1.2.2 Software. Copy number data files (.CYCHP files) were generated using the ChAS Analysis Files for the CytoScan HD Array version NA32.1 as a reference
The copy number data files (.CYCHP files) contain the whole genome copy number data for the 12 STAG2-mutant urothelial carcinomas of the bladder accessible using Affymetrix Chromosome Analysis Suite v1.2.2 Software.
|
| |
|
| Submission date |
Oct 15, 2012 |
| Last update date |
Jun 30, 2013 |
| Contact name |
David A. Solomon |
| E-mail(s) |
david.solomon@ucsfmedctr.org
|
| Organization name |
University of California, San Francisco
|
| Department |
Pathology
|
| Street address |
513 Parnassus Ave, HSW 450
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL16131 |
| Series (1) |
| GSE41581 |
Frequent truncating mutations of STAG2 in bladder cancer |
|
