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Status
Public on Oct 25, 2012
Title
08259T2
Sample type
genomic
Source name
08259T2
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_0710-12E_GenomeWideSNP_6_08259T2.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
0.004
856.871
2456.553
SNP_A-1967418
BB
0.002
294.816
827.363
SNP_A-1969580
BB
0.003
1185.647
3805.022
SNP_A-4263484
AB
0.005
1955.491
1445.300
SNP_A-1978185
AA
0.001
1652.421
378.437
SNP_A-4264431
AA
0.010
1802.772
365.559
SNP_A-1980898
AB
0.026
1082.410
680.492
SNP_A-1983139
AA
0.004
2167.223
553.592
SNP_A-4265735
NoCall
0.204
800.261
1063.486
SNP_A-1995832
BB
0.008
555.823
1351.020
SNP_A-1995893
BB
0.001
411.772
2078.625
SNP_A-1997689
BB
0.004
655.263
3208.152
SNP_A-1997709
AA
0.001
1437.811
284.147
SNP_A-1997896
AA
0.004
1426.485
575.909
SNP_A-1997922
BB
0.002
440.175
884.721
SNP_A-2000230
AA
0.017
3109.727
1384.451
SNP_A-2000332
AA
0.007
2205.239
764.089
SNP_A-2000337
AA
0.001
2002.026
334.712
SNP_A-2000342
AA
0.002
3117.267
850.661
SNP_A-4268173
AB
0.002
837.101
849.933
909622 35512 Kbytes .Supplementary file Size Download File type/resource GSM742387.CEL.gz
33.0 Mb
(ftp) (http) CEL
GSM742387.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
