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Status
Public on Oct 25, 2012
Title
B38W6ANP
Sample type
genomic
Source name
B38W6ANP
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_0710-02A_GenomeWideSNP_6_B38W6ANP.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
AA
0.004
2589.223
609.446
SNP_A-1967418
AA
0.001
858.800
260.124
SNP_A-1969580
BB
0.005
1695.844
5167.765
SNP_A-4263484
AB
0.001
1558.592
1266.567
SNP_A-1978185
AA
0.006
1290.797
366.582
SNP_A-4264431
AB
0.003
720.381
686.695
SNP_A-1980898
BB
0.005
365.916
833.091
SNP_A-1983139
AA
0.003
2010.669
486.941
SNP_A-4265735
NoCall
0.131
796.572
438.397
SNP_A-1995832
AA
0.023
1545.615
593.196
SNP_A-1995893
AA
0.014
1597.798
534.668
SNP_A-1997689
BB
0.006
750.353
2570.052
SNP_A-1997709
AA
0.012
1658.901
343.095
SNP_A-1997896
AA
0.011
928.178
549.708
SNP_A-1997922
AA
0.015
745.276
365.298
SNP_A-2000230
AA
0.002
2380.108
1173.948
SNP_A-2000332
AA
0.002
2492.370
712.248
SNP_A-2000337
AA
0.008
2420.194
291.356
SNP_A-2000342
AA
0.003
2932.931
769.388
SNP_A-4268173
AA
0.013
677.288
187.424
909622 35562 Kbytes .Supplementary file Size Download File type/resource GSM742303.CEL.gz
32.7 Mb
(ftp) (http) CEL
GSM742303.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
