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Status
Public on Oct 25, 2012
Title
08410T2
Sample type
genomic
Source name
08410T2
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_0710-05G_GenomeWideSNP_6_08410T2.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
0.008
694.158
1887.070
SNP_A-1967418
AB
0.004
474.097
470.653
SNP_A-1969580
BB
0.006
1694.345
4480.539
SNP_A-4263484
BB
0.002
548.203
1448.396
SNP_A-1978185
AA
0.002
1438.017
368.822
SNP_A-4264431
AA
0.003
1159.135
389.549
SNP_A-1980898
BB
0.005
249.427
660.954
SNP_A-1983139
AA
0.002
1618.008
464.301
SNP_A-4265735
NoCall
0.764
714.988
490.927
SNP_A-1995832
AB
0.008
1503.107
967.692
SNP_A-1995893
AB
0.002
1183.226
1451.609
SNP_A-1997689
BB
0.002
624.094
2982.069
SNP_A-1997709
AA
0.002
1249.617
248.699
SNP_A-1997896
AA
0.002
1341.575
534.818
SNP_A-1997922
AB
0.006
515.953
548.813
SNP_A-2000230
BB
0.003
770.266
2536.026
SNP_A-2000332
BB
0.005
864.554
2468.992
SNP_A-2000337
AA
0.000
1893.903
336.659
SNP_A-2000342
AA
0.004
2807.152
989.561
SNP_A-4268173
AB
0.005
637.559
681.253
909622 35535 Kbytes .Supplementary file Size Download File type/resource GSM742333.CEL.gz
34.1 Mb
(ftp) (http) CEL
GSM742333.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
