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Status
Public on Oct 25, 2012
Title
08255T2
Sample type
genomic
Source name
08255T2
Organism
Homo sapiens Characteristics
tissue: Tumor
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_0711-01C_GenomeWideSNP_6_08255T2.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
672.889
2264.482
SNP_A-1967418
BB
0.014
359.720
1052.417
SNP_A-1969580
BB
0.003
1503.547
4188.879
SNP_A-4263484
BB
0.024
910.150
2650.020
SNP_A-1978185
AA
0.019
2055.001
547.254
SNP_A-4264431
AA
0.010
1777.318
431.029
SNP_A-1980898
BB
0.007
328.446
1147.362
SNP_A-1983139
AA
0.016
2678.449
705.523
SNP_A-4265735
AA
0.014
1430.758
617.981
SNP_A-1995832
BB
0.004
780.666
1918.115
SNP_A-1995893
BB
0.031
462.243
2783.484
SNP_A-1997689
BB
0.000
712.303
2999.413
SNP_A-1997709
AA
0.005
1762.250
262.195
SNP_A-1997896
AB
0.023
1122.585
1962.062
SNP_A-1997922
AB
0.024
899.272
630.934
SNP_A-2000230
AA
0.008
2800.595
1286.340
SNP_A-2000332
AB
0.063
2213.500
3250.443
SNP_A-2000337
AA
0.002
2012.666
379.641
SNP_A-2000342
AA
0.011
3324.001
1108.959
SNP_A-4268173
AB
0.016
1200.978
840.398
909622 35614 Kbytes .Supplementary file Size Download File type/resource GSM742391.CEL.gz
34.1 Mb
(ftp) (http) CEL
GSM742391.chp.gz
13.2 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
