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Status
Public on Oct 25, 2012
Title
08392T1
Sample type
genomic
Source name
08392T1
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_0710-07F_GenomeWideSNP_6_08392T1.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
0.001
1588.780
1530.110
SNP_A-1967418
BB
0.001
288.787
677.808
SNP_A-1969580
BB
0.001
1388.802
4176.127
SNP_A-4263484
BB
0.007
461.131
1209.726
SNP_A-1978185
AA
0.004
1408.338
409.033
SNP_A-4264431
AA
0.002
1250.547
391.229
SNP_A-1980898
BB
0.004
215.507
727.439
SNP_A-1983139
AA
0.004
1513.305
467.158
SNP_A-4265735
AB
0.014
599.853
611.124
SNP_A-1995832
AB
0.003
1483.637
1251.694
SNP_A-1995893
AB
0.002
1416.361
1670.152
SNP_A-1997689
BB
0.004
693.101
3240.528
SNP_A-1997709
AA
0.002
1616.066
270.068
SNP_A-1997896
AA
0.003
1392.625
521.647
SNP_A-1997922
AB
0.001
599.744
565.104
SNP_A-2000230
AB
0.006
1108.545
1810.554
SNP_A-2000332
BB
0.004
928.219
3036.727
SNP_A-2000337
AA
0.007
1400.961
380.005
SNP_A-2000342
AA
0.001
2876.344
827.487
SNP_A-4268173
AA
0.002
1182.621
264.536
909622 35516 Kbytes .Supplementary file Size Download File type/resource GSM742348.CEL.gz
34.3 Mb
(ftp) (http) CEL
GSM742348.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
