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Status
Public on Oct 25, 2012
Title
08335T2
Sample type
genomic
Source name
08335T2
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_0710-11A_GenomeWideSNP_6_08335T2.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
0.001
744.137
2383.386
SNP_A-1967418
BB
0.004
276.529
580.746
SNP_A-1969580
BB
0.004
1386.897
3905.353
SNP_A-4263484
AB
0.003
1392.000
991.859
SNP_A-1978185
AA
0.013
1933.930
291.123
SNP_A-4264431
AB
0.002
842.004
692.598
SNP_A-1980898
BB
0.004
275.425
717.020
SNP_A-1983139
AA
0.002
1761.298
413.524
SNP_A-4265735
AB
0.016
533.841
582.031
SNP_A-1995832
BB
0.003
556.013
1580.181
SNP_A-1995893
BB
0.003
328.687
1839.544
SNP_A-1997689
BB
0.004
730.399
2653.061
SNP_A-1997709
AA
0.003
1165.015
265.388
SNP_A-1997896
AB
0.003
849.043
1328.188
SNP_A-1997922
AA
0.015
622.094
297.541
SNP_A-2000230
AA
0.001
2123.727
964.925
SNP_A-2000332
AB
0.001
1965.952
2069.531
SNP_A-2000337
AA
0.004
2222.788
287.935
SNP_A-2000342
AA
0.003
2786.746
773.914
SNP_A-4268173
AA
0.005
913.297
240.705
909622 35523 Kbytes .Supplementary file Size Download File type/resource GSM742375.CEL.gz
34.0 Mb
(ftp) (http) CEL
GSM742375.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
