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Status
Public on Oct 25, 2012
Title
08359T2
Sample type
genomic
Source name
08359T2
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_0710-10C_GenomeWideSNP_6_08359T2.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
0.003
663.418
2653.061
SNP_A-1967418
AB
0.007
437.947
439.799
SNP_A-1969580
BB
0.001
1454.598
4561.295
SNP_A-4263484
AA
0.003
1910.644
441.014
SNP_A-1978185
AA
0.003
1631.471
299.747
SNP_A-4264431
AA
0.006
1093.293
270.801
SNP_A-1980898
BB
0.003
232.093
750.277
SNP_A-1983139
AA
0.004
1672.674
365.837
SNP_A-4265735
NoCall
0.122
713.345
348.956
SNP_A-1995832
AA
0.002
1779.526
455.486
SNP_A-1995893
AA
0.009
1620.087
753.914
SNP_A-1997689
BB
0.007
631.018
2492.251
SNP_A-1997709
AA
0.002
1391.894
243.517
SNP_A-1997896
AA
0.010
933.029
440.092
SNP_A-1997922
AA
0.001
777.662
267.218
SNP_A-2000230
AA
0.003
2009.414
1093.841
SNP_A-2000332
AB
0.005
1617.578
1942.500
SNP_A-2000337
AA
0.002
1990.143
285.933
SNP_A-2000342
AA
0.003
2711.064
859.812
SNP_A-4268173
AA
0.006
914.094
248.485
909622 35516 Kbytes .Supplementary file Size Download File type/resource GSM742369.CEL.gz
34.1 Mb
(ftp) (http) CEL
GSM742369.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
