|
| Status |
Public on Feb 10, 2012 |
| Title |
Gastric primary tumor sample 2000242T SNP6 |
| Sample type |
genomic |
| |
|
| Source name |
Gastric primary tumor sample 2000242T
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Gastric primary tumor tissue
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from flash-frozen gastric tumors and matched non-maligant gastric tissues using a Qiagen genomic DNA extraction kit.
|
| 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 SNP6 array
|
| Data processing |
Analysis of raw cel files was performed by Affymetrix Genotyping Console 4.0 software. A reference Model File was created based on 98 non-malignant samples (included as Gastric Normal.REF in the submission). Gastric non-malignant samples and tumors samples were then processed separately using this referenece file by median normalization and GC correlation to obtain the CHP files.
|
| |
|
| Submission date |
Aug 01, 2011 |
| Last update date |
Feb 10, 2012 |
| Contact name |
Niantao Deng |
| Organization name |
Duke NUS Graduate Medical School
|
| Street address |
Center for Computational Biology, level 6, 8 College Road
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE31168 |
Genetic Landscape of Copy Number Alterations in Gastric Cancer |
|
