GEO help: Mouse over screen elements for information.
Status
Public on Oct 25, 2012
Title
3ENVAAQV
Sample type
genomic
Source name
3ENVAAQV
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_0710-01E_GenomeWideSNP_6_3ENVAAQV.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. 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;
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
0.004
2164.672
691.674
SNP_A-1967418
AB
0.004
616.027
470.981
SNP_A-1969580
BB
0.009
1669.972
5545.980
SNP_A-4263484
AA
0.002
2252.518
526.460
SNP_A-1978185
AA
0.007
1892.157
432.462
SNP_A-4264431
AA
0.003
1268.251
404.035
SNP_A-1980898
BB
0.003
355.459
890.729
SNP_A-1983139
AA
0.003
1689.637
382.827
SNP_A-4265735
AB
0.046
446.185
504.608
SNP_A-1995832
AB
0.003
1387.824
1277.672
SNP_A-1995893
AB
0.008
1553.056
1843.574
SNP_A-1997689
BB
0.003
770.505
2784.066
SNP_A-1997709
AA
0.009
1325.502
325.735
SNP_A-1997896
AA
0.007
1058.811
597.089
SNP_A-1997922
AB
0.005
672.232
673.583
SNP_A-2000230
AA
0.002
2282.793
1164.247
SNP_A-2000332
AB
0.007
1709.870
1686.057
SNP_A-2000337
AA
0.007
2195.208
458.293
SNP_A-2000342
AA
0.004
2852.887
739.719
SNP_A-4268173
AA
0.004
926.218
225.748
Total number of rows: 909622 Table truncated, full table size 35610 Kbytes .Supplementary file
Size
Download
File type/resource
GSM742299.CEL.gz
32.8 Mb
(ftp) (http)
CEL
GSM742299.chp.gz
13.1 Mb
(ftp) (http)
CHP
Processed data included within Sample table
Processed data provided as supplementary file