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Status
Public on Oct 25, 2012
Title
08404T1
Sample type
genomic
Source name
08404T1
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_0710-06H_GenomeWideSNP_6_08404T1.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
0.001
739.741
2474.088
SNP_A-1967418
BB
0.004
265.674
598.531
SNP_A-1969580
BB
0.005
1049.729
3639.153
SNP_A-4263484
AA
0.006
1540.679
323.773
SNP_A-1978185
AA
0.002
1714.754
379.047
SNP_A-4264431
AA
0.001
1202.288
368.155
SNP_A-1980898
BB
0.001
276.709
866.918
SNP_A-1983139
AA
0.003
1497.266
443.834
SNP_A-4265735
AB
0.035
712.341
621.912
SNP_A-1995832
AB
0.000
1321.281
1145.537
SNP_A-1995893
AB
0.002
1373.829
1665.506
SNP_A-1997689
BB
0.001
679.480
2941.697
SNP_A-1997709
AA
0.002
1500.455
251.945
SNP_A-1997896
AB
0.002
878.210
1369.704
SNP_A-1997922
AA
0.002
773.806
298.247
SNP_A-2000230
AA
0.002
2019.661
1058.963
SNP_A-2000332
AB
0.002
1870.127
2203.639
SNP_A-2000337
AA
0.001
1765.423
315.658
SNP_A-2000342
AA
0.006
2675.421
734.488
SNP_A-4268173
AA
0.002
1261.267
236.435
909622 35512 Kbytes .Supplementary file Size Download File type/resource GSM742342.CEL.gz
34.1 Mb
(ftp) (http) CEL
GSM742342.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
