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Status
Public on Oct 25, 2012
Title
08405T2
Sample type
genomic
Source name
08405T2
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_0710-06E_GenomeWideSNP_6_08405T2.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
781.663
2232.282
SNP_A-1967418
BB
0.004
323.917
693.001
SNP_A-1969580
BB
0.002
1381.810
4085.173
SNP_A-4263484
AA
0.002
1971.884
432.563
SNP_A-1978185
AA
0.001
1542.815
331.647
SNP_A-4264431
AB
0.022
631.857
850.731
SNP_A-1980898
AB
0.006
632.273
428.494
SNP_A-1983139
AA
0.014
2072.455
369.188
SNP_A-4265735
NoCall
0.712
329.482
820.271
SNP_A-1995832
AB
0.002
1213.070
1065.497
SNP_A-1995893
AB
0.002
1164.799
1480.221
SNP_A-1997689
BB
0.001
694.623
2872.173
SNP_A-1997709
AA
0.002
1241.022
251.484
SNP_A-1997896
AA
0.002
1383.880
567.785
SNP_A-1997922
AB
0.015
515.722
604.791
SNP_A-2000230
AA
0.001
2140.814
1032.603
SNP_A-2000332
BB
0.002
814.522
2840.443
SNP_A-2000337
AA
0.001
1873.868
360.701
SNP_A-2000342
AA
0.004
2974.893
753.736
SNP_A-4268173
AA
0.002
1008.239
209.451
909622 35520 Kbytes .Supplementary file Size Download File type/resource GSM742339.CEL.gz
34.2 Mb
(ftp) (http) CEL
GSM742339.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
