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Status
Public on Oct 25, 2012
Title
08405T1
Sample type
genomic
Source name
08405T1
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_0710-06F_GenomeWideSNP_6_08405T1.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
834.077
2467.109
SNP_A-1967418
BB
0.002
269.238
648.819
SNP_A-1969580
BB
0.002
1595.630
4751.540
SNP_A-4263484
AA
0.006
1656.901
395.075
SNP_A-1978185
AA
0.005
1302.115
349.752
SNP_A-4264431
AB
0.001
850.872
748.044
SNP_A-1980898
AB
0.002
570.000
559.105
SNP_A-1983139
AA
0.005
1375.857
369.441
SNP_A-4265735
NoCall
0.731
361.877
853.626
SNP_A-1995832
AB
0.001
1315.392
1060.094
SNP_A-1995893
AB
0.004
1265.760
1355.968
SNP_A-1997689
BB
0.001
722.372
2899.833
SNP_A-1997709
AA
0.002
1391.976
289.594
SNP_A-1997896
AA
0.001
1236.635
569.698
SNP_A-1997922
AB
0.004
542.789
511.569
SNP_A-2000230
AA
0.005
2021.314
1172.289
SNP_A-2000332
BB
0.005
740.047
2794.835
SNP_A-2000337
AA
0.002
2051.958
294.992
SNP_A-2000342
AA
0.008
2892.063
1085.394
SNP_A-4268173
AA
0.002
1203.212
267.120
909622 35521 Kbytes .Supplementary file Size Download File type/resource GSM742340.CEL.gz
34.8 Mb
(ftp) (http) CEL
GSM742340.chp.gz
13.2 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
