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Status
Public on Oct 25, 2012
Title
PGRZ1AR6
Sample type
genomic
Source name
PGRZ1AR6
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_0710-04A_GenomeWideSNP_6_PGRZ1AR6.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
0.002
2322.871
648.820
SNP_A-1967418
BB
0.004
289.960
607.162
SNP_A-1969580
BB
0.008
1491.055
5289.258
SNP_A-4263484
AB
0.002
1313.493
998.978
SNP_A-1978185
AB
0.004
1115.249
1823.747
SNP_A-4264431
BB
0.011
492.986
1053.442
SNP_A-1980898
BB
0.004
299.931
729.806
SNP_A-1983139
AA
0.004
1429.602
352.633
SNP_A-4265735
AB
0.037
577.768
563.203
SNP_A-1995832
AB
0.003
1481.142
1265.764
SNP_A-1995893
AB
0.011
1118.769
1172.159
SNP_A-1997689
BB
0.011
798.342
2430.000
SNP_A-1997709
AA
0.004
1152.730
278.447
SNP_A-1997896
AA
0.003
1143.724
458.169
SNP_A-1997922
AB
0.008
509.723
472.397
SNP_A-2000230
AA
0.011
2012.634
1274.822
SNP_A-2000332
BB
0.002
845.617
2632.476
SNP_A-2000337
AA
0.001
2000.046
332.328
SNP_A-2000342
AA
0.008
2952.060
1088.121
SNP_A-4268173
AA
0.005
1015.965
180.667
909622 35592 Kbytes .Supplementary file Size Download File type/resource GSM742319.CEL.gz
33.6 Mb
(ftp) (http) CEL
GSM742319.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
