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Status
Public on Oct 25, 2012
Title
08418T1
Sample type
genomic
Source name
08418T1
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_0710-05D_GenomeWideSNP_6_08418T1.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
0.002
723.478
2627.821
SNP_A-1967418
BB
0.006
264.024
538.035
SNP_A-1969580
BB
0.007
1621.580
4217.318
SNP_A-4263484
AB
0.003
1720.837
1370.561
SNP_A-1978185
AA
0.002
1618.340
332.020
SNP_A-4264431
AB
0.005
1072.041
677.292
SNP_A-1980898
BB
0.007
262.927
646.075
SNP_A-1983139
AB
0.029
532.766
356.922
SNP_A-4265735
BB
0.020
404.870
1221.575
SNP_A-1995832
BB
0.002
586.869
1677.177
SNP_A-1995893
BB
0.005
490.509
1822.143
SNP_A-1997689
BB
0.000
724.133
2967.664
SNP_A-1997709
AA
0.003
1229.328
247.162
SNP_A-1997896
AB
0.005
799.124
1243.741
SNP_A-1997922
AB
0.004
540.117
513.400
SNP_A-2000230
AA
0.001
2152.428
1007.724
SNP_A-2000332
AB
0.002
1860.963
2250.617
SNP_A-2000337
AA
0.004
2238.589
358.851
SNP_A-2000342
AA
0.000
2939.138
890.387
SNP_A-4268173
AB
0.003
891.498
878.872
909622 35538 Kbytes .Supplementary file Size Download File type/resource GSM742330.CEL.gz
34.4 Mb
(ftp) (http) CEL
GSM742330.chp.gz
13.2 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
