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Status
Public on Oct 25, 2012
Title
IM3FENUT
Sample type
genomic
Source name
IM3FENUT
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_0710-03D_GenomeWideSNP_6_IM3FENUT.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
AB
0.001
1708.914
1493.471
SNP_A-1967418
AB
0.006
648.131
485.744
SNP_A-1969580
BB
0.005
1431.249
5030.120
SNP_A-4263484
AA
0.003
1809.419
331.262
SNP_A-1978185
AA
0.006
1310.596
408.638
SNP_A-4264431
AB
0.042
973.661
933.515
SNP_A-1980898
BB
0.003
248.188
730.119
SNP_A-1983139
AB
0.001
1164.122
959.674
SNP_A-4265735
AB
0.053
517.993
742.570
SNP_A-1995832
AB
0.001
1342.733
1088.314
SNP_A-1995893
AB
0.007
1487.004
1366.013
SNP_A-1997689
BB
0.004
634.236
2689.891
SNP_A-1997709
AA
0.005
1158.252
292.413
SNP_A-1997896
AA
0.002
1348.535
567.872
SNP_A-1997922
NoCall
0.687
436.875
639.523
SNP_A-2000230
AA
0.002
2035.027
958.952
SNP_A-2000332
AB
0.001
1858.606
2007.887
SNP_A-2000337
AA
0.002
2051.119
336.417
SNP_A-2000342
AA
0.004
2619.380
888.101
SNP_A-4268173
AA
0.011
1046.237
140.206
909622 35562 Kbytes .Supplementary file Size Download File type/resource GSM742314.CEL.gz
33.2 Mb
(ftp) (http) CEL
GSM742314.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
