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Status
Public on Oct 25, 2012
Title
PGRZ1NVF
Sample type
genomic
Source name
PGRZ1NVF
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_0710-04B_GenomeWideSNP_6_PGRZ1NVF.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
2085.205
627.103
SNP_A-1967418
BB
0.001
302.963
781.038
SNP_A-1969580
BB
0.005
1513.525
5135.248
SNP_A-4263484
AB
0.002
1253.352
1038.463
SNP_A-1978185
AB
0.004
1124.203
1816.064
SNP_A-4264431
BB
0.005
489.238
1336.079
SNP_A-1980898
BB
0.003
282.595
736.650
SNP_A-1983139
AA
0.002
1586.437
424.457
SNP_A-4265735
AB
0.033
555.129
726.451
SNP_A-1995832
AB
0.003
1286.401
1279.740
SNP_A-1995893
AB
0.002
1189.376
1455.169
SNP_A-1997689
BB
0.002
784.263
3023.462
SNP_A-1997709
AA
0.010
1215.419
326.688
SNP_A-1997896
AA
0.003
1226.651
614.520
SNP_A-1997922
AB
0.003
562.357
534.301
SNP_A-2000230
AA
0.004
2360.350
1221.905
SNP_A-2000332
BB
0.006
1066.011
2998.079
SNP_A-2000337
AA
0.001
1882.851
366.843
SNP_A-2000342
AA
0.001
2823.820
878.960
SNP_A-4268173
AA
0.010
744.704
188.848
909622 35593 Kbytes .Supplementary file Size Download File type/resource GSM742320.CEL.gz
33.6 Mb
(ftp) (http) CEL
GSM742320.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
