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Status
Public on Oct 25, 2012
Title
336MHN76
Sample type
genomic
Source name
336MHN76
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_0710-01D_GenomeWideSNP_6_336MHN76.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
0.016
1606.364
499.118
SNP_A-1967418
BB
0.002
309.201
832.589
SNP_A-1969580
BB
0.001
1520.270
4635.722
SNP_A-4263484
AB
0.001
1393.099
1110.500
SNP_A-1978185
AB
0.006
1001.092
1210.277
SNP_A-4264431
AB
0.003
850.520
655.138
SNP_A-1980898
BB
0.001
258.689
858.121
SNP_A-1983139
AA
0.004
1445.617
391.591
SNP_A-4265735
AB
0.086
569.339
830.774
SNP_A-1995832
BB
0.001
666.384
1654.606
SNP_A-1995893
BB
0.003
344.242
1851.826
SNP_A-1997689
BB
0.004
680.058
2601.045
SNP_A-1997709
AA
0.011
1026.378
204.342
SNP_A-1997896
AA
0.006
1024.961
541.469
SNP_A-1997922
BB
0.022
353.098
666.384
SNP_A-2000230
AB
0.003
1272.209
1837.768
SNP_A-2000332
BB
0.002
835.225
2619.568
SNP_A-2000337
AA
0.003
2187.588
348.687
SNP_A-2000342
AA
0.002
2766.513
854.953
SNP_A-4268173
AA
0.003
981.390
197.848
909622 35553 Kbytes .Supplementary file Size Download File type/resource GSM742298.CEL.gz
34.9 Mb
(ftp) (http) CEL
GSM742298.chp.gz
13.2 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
