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Status
Public on Oct 25, 2012
Title
08269T1
Sample type
genomic
Source name
08269T1
Organism
Homo sapiens Characteristics
tissue: Normal
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_0710-12D_GenomeWideSNP_6_08269T1.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.
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
2545.155
498.640
SNP_A-1967418
BB
0.003
311.184
875.847
SNP_A-1969580
BB
0.004
1074.948
3764.298
SNP_A-4263484
AA
0.013
3035.166
485.743
SNP_A-1978185
AA
0.006
1844.557
444.351
SNP_A-4264431
NoCall
0.171
1368.208
1015.206
SNP_A-1980898
AA
0.004
1324.655
257.729
SNP_A-1983139
AA
0.005
1678.406
357.108
SNP_A-4265735
AB
0.053
996.871
1006.380
SNP_A-1995832
AA
0.001
1847.267
491.851
SNP_A-1995893
AA
0.002
1895.804
767.768
SNP_A-1997689
BB
0.003
653.231
2711.951
SNP_A-1997709
AA
0.008
1835.560
316.583
SNP_A-1997896
AA
0.004
1433.609
610.862
SNP_A-1997922
AA
0.007
963.196
346.509
SNP_A-2000230
AA
0.054
3664.405
1187.612
SNP_A-2000332
AA
0.003
2400.011
718.034
SNP_A-2000337
AA
0.003
2121.832
392.213
SNP_A-2000342
AA
0.018
3705.959
963.317
SNP_A-4268173
AA
0.022
1735.785
238.074
909622 35515 Kbytes .Supplementary file Size Download File type/resource GSM742386.CEL.gz
32.4 Mb
(ftp) (http) CEL
GSM742386.chp.gz
13.0 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
