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Status
Public on Oct 25, 2012
Title
08255T1
Sample type
genomic
Source name
08255T1
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_0711-01D_GenomeWideSNP_6_08255T1.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
676.578
2016.166
SNP_A-1967418
BB
0.006
310.087
944.550
SNP_A-1969580
BB
0.005
1229.329
3616.312
SNP_A-4263484
BB
0.036
725.188
2702.142
SNP_A-1978185
AA
0.001
1525.724
373.821
SNP_A-4264431
AA
0.008
1741.153
368.661
SNP_A-1980898
BB
0.016
282.716
1229.980
SNP_A-1983139
AA
0.006
2006.916
613.782
SNP_A-4265735
AA
0.010
985.605
437.762
SNP_A-1995832
BB
0.003
572.632
1660.780
SNP_A-1995893
BB
0.002
437.762
2117.426
SNP_A-1997689
BB
0.001
718.099
3053.983
SNP_A-1997709
AA
0.001
1480.704
259.114
SNP_A-1997896
AB
0.003
1043.067
1433.284
SNP_A-1997922
AB
0.002
631.080
635.394
SNP_A-2000230
AA
0.003
2473.603
1042.607
SNP_A-2000332
AB
0.003
2106.524
2091.669
SNP_A-2000337
AA
0.004
1530.223
309.200
SNP_A-2000342
AA
0.007
3393.766
949.593
SNP_A-4268173
AB
0.002
906.594
808.216
909622 35518 Kbytes .Supplementary file Size Download File type/resource GSM742392.CEL.gz
34.0 Mb
(ftp) (http) CEL
GSM742392.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
