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Status
Public on Oct 25, 2012
Title
08384T2
Sample type
genomic
Source name
08384T2
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_0710-08C_GenomeWideSNP_6_08384T2.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
AB
0.003
1491.211
1517.337
SNP_A-1967418
AB
0.003
537.622
555.824
SNP_A-1969580
BB
0.003
1131.475
4090.412
SNP_A-4263484
BB
0.002
411.089
1417.022
SNP_A-1978185
AA
0.001
1522.072
334.910
SNP_A-4264431
AA
0.001
1220.414
343.865
SNP_A-1980898
BB
0.001
285.166
802.248
SNP_A-1983139
AA
0.001
1894.337
465.979
SNP_A-4265735
AB
0.017
599.896
694.307
SNP_A-1995832
AB
0.002
1344.005
1266.096
SNP_A-1995893
AB
0.001
1391.887
1526.069
SNP_A-1997689
BB
0.004
617.485
2653.163
SNP_A-1997709
AA
0.001
1405.692
256.647
SNP_A-1997896
AA
0.005
1317.488
442.523
SNP_A-1997922
AB
0.011
667.406
461.713
SNP_A-2000230
AA
0.003
2097.193
906.112
SNP_A-2000332
AA
0.010
2762.342
562.627
SNP_A-2000337
AA
0.003
1627.588
344.917
SNP_A-2000342
AA
0.004
2702.029
784.506
SNP_A-4268173
AB
0.001
873.449
794.967
909622 35517 Kbytes .Supplementary file Size Download File type/resource GSM742353.CEL.gz
32.7 Mb
(ftp) (http) CEL
GSM742353.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
