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Status |
Public on Feb 10, 2012 |
Title |
Gastric primary tumor sample 980029T SNP6 |
Sample type |
genomic |
|
|
Source name |
Gastric primary tumor sample 980029T
|
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)
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|
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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.
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|
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Submission date |
Aug 02, 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 |
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