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Status
Public on Oct 25, 2012
Title
N8FM1NI2
Sample type
genomic
Source name
N8FM1NI2
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_0710-03H_GenomeWideSNP_6_N8FM1NI2.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
0.003
2455.638
487.545
SNP_A-1967418
BB
0.011
211.000
787.831
SNP_A-1969580
BB
0.003
1555.516
4992.203
SNP_A-4263484
BB
0.001
568.718
1771.232
SNP_A-1978185
AB
0.004
1288.847
1911.042
SNP_A-4264431
AB
0.007
915.477
862.446
SNP_A-1980898
BB
0.002
296.252
953.852
SNP_A-1983139
AB
0.002
1102.317
949.597
SNP_A-4265735
NoCall
0.635
644.663
428.159
SNP_A-1995832
BB
0.000
707.661
1711.691
SNP_A-1995893
BB
0.005
394.725
2232.095
SNP_A-1997689
BB
0.002
766.660
3127.086
SNP_A-1997709
AA
0.004
1374.948
232.783
SNP_A-1997896
AA
0.004
1240.129
449.025
SNP_A-1997922
BB
0.009
362.744
704.036
SNP_A-2000230
AA
0.002
2161.032
952.791
SNP_A-2000332
AB
0.001
2003.555
2132.880
SNP_A-2000337
AA
0.000
1884.687
334.124
SNP_A-2000342
AA
0.004
3085.267
773.629
SNP_A-4268173
AA
0.002
1295.705
259.643
909622 35550 Kbytes .Supplementary file Size Download File type/resource GSM742318.CEL.gz
34.5 Mb
(ftp) (http) CEL
GSM742318.chp.gz
13.2 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
