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Status
Public on Oct 25, 2012
Title
08274T2
Sample type
genomic
Source name
08274T2
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_0710-12A_GenomeWideSNP_6_08274T2.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
627.458
2644.907
SNP_A-1967418
BB
0.000
288.238
721.756
SNP_A-1969580
BB
0.001
1403.210
4319.739
SNP_A-4263484
AB
0.007
2027.166
1542.351
SNP_A-1978185
AA
0.002
1610.837
323.212
SNP_A-4264431
BB
0.009
437.503
1420.533
SNP_A-1980898
BB
0.001
273.215
904.137
SNP_A-1983139
AA
0.005
2240.500
545.652
SNP_A-4265735
AA
0.009
1410.247
433.951
SNP_A-1995832
AB
0.009
1276.505
815.820
SNP_A-1995893
AB
0.003
1430.291
1691.921
SNP_A-1997689
BB
0.000
696.334
2973.122
SNP_A-1997709
AA
0.006
1807.632
260.720
SNP_A-1997896
AA
0.004
1441.561
549.802
SNP_A-1997922
AB
0.007
750.593
636.355
SNP_A-2000230
AA
0.013
3040.186
1225.024
SNP_A-2000332
AB
0.003
2027.766
2247.001
SNP_A-2000337
AA
0.003
2078.816
286.882
SNP_A-2000342
AA
0.004
3235.801
862.608
SNP_A-4268173
AA
0.009
1554.331
263.517
909622 35504 Kbytes .Supplementary file Size Download File type/resource GSM742383.CEL.gz
33.7 Mb
(ftp) (http) CEL
GSM742383.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
