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Status
Public on Oct 25, 2012
Title
08393T2
Sample type
genomic
Source name
08393T2
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_0710-07C_GenomeWideSNP_6_08393T2.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. 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;
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
0.003
768.078
2242.341
SNP_A-1967418
AB
0.005
515.894
565.739
SNP_A-1969580
BB
0.002
1238.085
3933.535
SNP_A-4263484
AB
0.006
1018.733
824.175
SNP_A-1978185
AA
0.002
1460.026
390.560
SNP_A-4264431
AA
0.001
1360.746
380.003
SNP_A-1980898
BB
0.003
254.115
721.348
SNP_A-1983139
AA
0.001
1637.621
445.745
SNP_A-4265735
AB
0.014
616.798
677.271
SNP_A-1995832
BB
0.005
658.245
1927.963
SNP_A-1995893
BB
0.005
367.396
2223.596
SNP_A-1997689
BB
0.004
610.949
3114.226
SNP_A-1997709
AA
0.004
1344.006
304.775
SNP_A-1997896
BB
0.002
489.379
2151.172
SNP_A-1997922
AA
0.031
679.173
349.704
SNP_A-2000230
AA
0.001
2073.326
1000.119
SNP_A-2000332
AA
0.004
2591.915
644.208
SNP_A-2000337
AA
0.005
1476.453
312.757
SNP_A-2000342
AA
0.001
2876.201
868.997
SNP_A-4268173
AB
0.003
686.400
718.718
Total number of rows: 909622 Table truncated, full table size 35519 Kbytes .Supplementary file
Size
Download
File type/resource
GSM742345.CEL.gz
33.8 Mb
(ftp) (http)
CEL
GSM742345.chp.gz
13.1 Mb
(ftp) (http)
CHP
Processed data included within Sample table
Processed data provided as supplementary file