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Status
Public on Oct 25, 2012
Title
08246T1
Sample type
genomic
Source name
08246T1
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_0711-01F_GenomeWideSNP_6_08246T1.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
BB
0.001
752.149
2512.916
SNP_A-1967418
AB
0.007
650.739
464.422
SNP_A-1969580
BB
0.009
915.470
3173.134
SNP_A-4263484
AA
0.021
3290.595
517.581
SNP_A-1978185
AA
0.001
1577.341
395.989
SNP_A-4264431
AA
0.008
1756.090
389.949
SNP_A-1980898
BB
0.017
314.918
1282.989
SNP_A-1983139
AA
0.006
2215.520
509.671
SNP_A-4265735
AA
0.005
1266.736
506.164
SNP_A-1995832
AB
0.003
1267.059
997.258
SNP_A-1995893
AB
0.004
1448.628
1458.817
SNP_A-1997689
BB
0.004
652.783
3214.750
SNP_A-1997709
AA
0.003
1641.544
286.740
SNP_A-1997896
AA
0.005
1450.200
539.980
SNP_A-1997922
AB
0.016
761.494
758.027
SNP_A-2000230
AA
0.006
2716.292
1233.446
SNP_A-2000332
AA
0.002
2468.573
819.294
SNP_A-2000337
AA
0.002
1661.717
357.134
SNP_A-2000342
AA
0.005
3294.049
863.400
SNP_A-4268173
AA
0.011
1523.124
225.217
909622 35516 Kbytes .Supplementary file Size Download File type/resource GSM742394.CEL.gz
33.0 Mb
(ftp) (http) CEL
GSM742394.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
