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Sample GSM770987 Query DataSets for GSM770987
Status Public on Feb 10, 2012
Title Gastric primary tumor sample 980097T SNP6
Sample type genomic
 
Source name Gastric primary tumor sample 980097T
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 02, 2011
Last update date Aug 11, 2016
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
Relations
Reanalyzed by GSE85466

Data table header descriptions
ID_REF
VALUE CN STATE
CHROMOSOME
POSITION
LOG2 RATIO
SMOOTH SIGNAL
LOH
ALLELE DIFFERENCE

Data table
ID_REF VALUE CHROMOSOME POSITION LOG2 RATIO SMOOTH SIGNAL LOH ALLELE DIFFERENCE
CN_473963 3.000000 1 51586 0.046203 2.880798 nan nan
CN_473964 3.000000 1 51659 0.185231 2.880897 nan nan
CN_473965 3.000000 1 51674 0.200767 2.880917 nan nan
CN_473981 3.000000 1 52771 -0.092165 2.882387 nan nan
CN_473982 3.000000 1 52788 0.378557 2.882409 nan nan
CN_497981 3.000000 1 62627 0.817284 2.895236 nan nan
CN_502615 3.000000 1 75787 0.275518 2.911263 nan nan
CN_502613 3.000000 1 75849 0.310293 2.911335 nan nan
CN_502614 3.000000 1 76175 0.386922 2.911713 nan nan
CN_502616 3.000000 1 76192 0.587202 2.911733 nan nan
CN_502843 3.000000 1 88453 0.144807 2.925269 nan nan
CN_466171 2.000000 1 218557 -0.551765 1.597836 nan nan
CN_468414 2.000000 1 218926 0.913601 1.597757 nan nan
CN_468412 2.000000 1 219009 -0.095007 1.597739 nan nan
CN_468413 2.000000 1 219024 -0.523952 1.597736 nan nan
CN_470565 2.000000 1 219470 -0.358183 1.597641 nan nan
CN_468424 2.000000 1 225521 -0.281753 1.596340 nan nan
CN_468425 2.000000 1 225579 -0.365894 1.596327 nan nan
CN_460512 2.000000 1 346294 -0.126648 1.543586 nan nan
CN_460513 2.000000 1 346393 -0.288789 1.543585 nan nan

Total number of rows: 1813441

Table truncated, full table size 114234 Kbytes.




Supplementary file Size Download File type/resource
GSM770987_GC-980097T_V6.CEL.gz 28.3 Mb (ftp)(http) CEL
GSM770987_GC-980097T_V6.def.CN5.CNCHP.gz 34.9 Mb (ftp)(http) CNCHP
Processed data included within Sample table
Processed data provided as supplementary file

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