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Status
Public on Oct 25, 2012
Title
08274T1
Sample type
genomic
Source name
08274T1
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_0710-12B_GenomeWideSNP_6_08274T1.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
0.005
849.484
2803.811
SNP_A-1967418
BB
0.003
326.688
768.420
SNP_A-1969580
BB
0.008
1698.616
4306.913
SNP_A-4263484
AB
0.012
2110.434
1712.178
SNP_A-1978185
AA
0.004
1407.254
410.065
SNP_A-4264431
BB
0.009
532.726
1465.937
SNP_A-1980898
BB
0.012
383.485
1253.131
SNP_A-1983139
AA
0.006
2299.538
582.636
SNP_A-4265735
AA
0.005
1287.094
432.283
SNP_A-1995832
AB
0.002
1332.170
1050.648
SNP_A-1995893
AB
0.001
1369.653
1605.032
SNP_A-1997689
BB
0.005
858.215
3070.750
SNP_A-1997709
AA
0.017
1829.416
355.005
SNP_A-1997896
AA
0.011
1341.522
719.315
SNP_A-1997922
AB
0.002
643.277
618.410
SNP_A-2000230
AA
0.009
2769.346
1330.510
SNP_A-2000332
AB
0.009
1505.169
1784.614
SNP_A-2000337
AA
0.007
2309.850
258.560
SNP_A-2000342
AA
0.006
2541.188
872.316
SNP_A-4268173
AA
0.003
986.521
229.032
909622 35516 Kbytes .Supplementary file Size Download File type/resource GSM742384.CEL.gz
33.5 Mb
(ftp) (http) CEL
GSM742384.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
