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Status
Public on Oct 25, 2012
Title
N8FM1ANF
Sample type
genomic
Source name
N8FM1ANF
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_0710-03G_GenomeWideSNP_6_N8FM1ANF.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
2504.857
597.078
SNP_A-1967418
BB
0.005
231.977
680.098
SNP_A-1969580
BB
0.004
1628.353
4454.248
SNP_A-4263484
BB
0.001
472.153
1643.703
SNP_A-1978185
AB
0.002
1051.046
1569.729
SNP_A-4264431
AB
0.003
753.073
665.615
SNP_A-1980898
BB
0.002
288.439
790.848
SNP_A-1983139
AB
0.001
1095.043
936.614
SNP_A-4265735
AB
0.060
663.460
579.694
SNP_A-1995832
BB
0.002
702.875
1582.848
SNP_A-1995893
BB
0.001
373.743
1889.840
SNP_A-1997689
BB
0.001
749.222
2920.897
SNP_A-1997709
AA
0.007
1214.041
215.517
SNP_A-1997896
AA
0.007
998.658
461.901
SNP_A-1997922
NoCall
0.305
413.844
639.463
SNP_A-2000230
AA
0.003
1973.972
1080.406
SNP_A-2000332
AB
0.004
1760.568
1794.476
SNP_A-2000337
AA
0.001
1949.818
298.595
SNP_A-2000342
AA
0.002
3079.942
933.326
SNP_A-4268173
AA
0.005
902.265
213.953
909622 35575 Kbytes .Supplementary file Size Download File type/resource GSM742317.CEL.gz
34.5 Mb
(ftp) (http) CEL
GSM742317.chp.gz
13.2 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
