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Sample GSM742299 Query DataSets for GSM742299
Status Public on Oct 25, 2012
Title 3ENVAAQV
Sample type genomic
 
Source name 3ENVAAQV
Organism Homo sapiens
Characteristics tissue: Tumor
Extracted molecule genomic DNA
Extraction protocol Acquired from Tissue Solutions Ltd
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 EA09054_0710-01E_GenomeWideSNP_6_3ENVAAQV.birdseed-v2.chp
Data processing CEL files were generated with GCOS, and further processed using default algorithms for normalization and genotype calling in Affymetrix Genotyping Consol.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Confidence' = strengh of the call (smaller is better); 'Signal A' = Summarized signal for allele A; 'Signal B' = Summarized signal for allele B;
 
Submission date Jun 15, 2011
Last update date Oct 25, 2012
Contact name Joanna Dawn Holbrook
E-mail(s) Joanna_Holbrook@sics.a-star.edu.sg
Organization name Singapore Institute of Clinical Sciences
Street address 30 Medical Drive
City Singapore
ZIP/Postal code 117609
Country Singapore
 
Platform ID GPL6801
Series (2)
GSE29996 Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine [Affymetrix SNP array data]
GSE29999 Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine

Data table header descriptions
ID_REF
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
Confidence strengh of the call (smaller is better)
Signal A Summarized signal for allele A
Signal B Summarized signal for allele B

Data table
ID_REF VALUE Confidence Signal A Signal B
SNP_A-2131660 AA 0.004 2164.672 691.674
SNP_A-1967418 AB 0.004 616.027 470.981
SNP_A-1969580 BB 0.009 1669.972 5545.980
SNP_A-4263484 AA 0.002 2252.518 526.460
SNP_A-1978185 AA 0.007 1892.157 432.462
SNP_A-4264431 AA 0.003 1268.251 404.035
SNP_A-1980898 BB 0.003 355.459 890.729
SNP_A-1983139 AA 0.003 1689.637 382.827
SNP_A-4265735 AB 0.046 446.185 504.608
SNP_A-1995832 AB 0.003 1387.824 1277.672
SNP_A-1995893 AB 0.008 1553.056 1843.574
SNP_A-1997689 BB 0.003 770.505 2784.066
SNP_A-1997709 AA 0.009 1325.502 325.735
SNP_A-1997896 AA 0.007 1058.811 597.089
SNP_A-1997922 AB 0.005 672.232 673.583
SNP_A-2000230 AA 0.002 2282.793 1164.247
SNP_A-2000332 AB 0.007 1709.870 1686.057
SNP_A-2000337 AA 0.007 2195.208 458.293
SNP_A-2000342 AA 0.004 2852.887 739.719
SNP_A-4268173 AA 0.004 926.218 225.748

Total number of rows: 909622

Table truncated, full table size 35610 Kbytes.




Supplementary file Size Download File type/resource
GSM742299.CEL.gz 32.8 Mb (ftp)(http) CEL
GSM742299.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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