|
| Status |
Public on Oct 10, 2015 |
| Title |
P-19 |
| Sample type |
genomic |
| |
|
| Source name |
tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Patient sample
preservation method: FFPE
|
| Growth protocol |
Samples were grown according to standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumor areas within samples were marked by the Pathologist on an H&E stained slide. These areas were used to guide the acquisition of a 0.6mm core biopsy from the FFPE block. The FFPE tissue sections were extracted with xylene, washed with ethanol, and DNA was isolated using the Recover All Total Nucleic Acid Isolation kit for FFPE (Life Technologies, catalog-AM1975). The average DNA recovered was 36.6ng/mL (range 2.6-203.3)
|
| 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 |
a520780-00-941870-103115-4214911-83944
a520780-00-941995-103115-4214911-70977
|
| Data processing |
Affymetrix OncoScan Console 1.1 software was acquired to yield log R ratios (LRR) and B allele frequencies (BAF) for each SNP in each sample using the TuScan algorithm. Computations were performed relative to the normal reference provided by Affymetrix
|
| |
|
| Submission date |
Oct 09, 2015 |
| Last update date |
Oct 10, 2015 |
| Contact name |
LI SHEN |
| E-mail(s) |
lishen@mdanderson.org
|
| Organization name |
MD Anderson Cancer Center
|
| Street address |
1400 Pressler Street
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL18602 |
| Series (1) |
| GSE73902 |
Affymetrix Oncoscan array data for aggressive variant prostate cancer (AVPC) samples |
|
