GEO help: Mouse over screen elements for information.
Status
Public on Oct 25, 2012
Title
32LM7NVG
Sample type
genomic
Source name
32LM7NVG
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_0710-01B_GenomeWideSNP_6_32LM7NVG.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
0.000
1713.593
1568.928
SNP_A-1967418
AB
0.007
447.335
499.229
SNP_A-1969580
BB
0.008
1623.097
5450.937
SNP_A-4263484
AB
0.001
1377.335
1139.311
SNP_A-1978185
AA
0.004
1775.579
343.748
SNP_A-4264431
AA
0.002
1208.970
372.881
SNP_A-1980898
AB
0.004
789.719
658.941
SNP_A-1983139
AA
0.006
1924.116
395.630
SNP_A-4265735
NoCall
0.186
391.312
752.533
SNP_A-1995832
AB
0.008
1069.721
1156.784
SNP_A-1995893
AB
0.007
1195.458
1268.294
SNP_A-1997689
BB
0.005
589.149
2671.772
SNP_A-1997709
AA
0.003
1279.597
238.815
SNP_A-1997896
AA
0.008
972.712
443.860
SNP_A-1997922
AB
0.022
427.180
448.209
SNP_A-2000230
AB
0.002
1509.280
2166.323
SNP_A-2000332
AB
0.003
1720.857
1880.270
SNP_A-2000337
AA
0.007
2380.027
337.932
SNP_A-2000342
AA
0.002
2857.476
792.981
SNP_A-4268173
AA
0.004
1026.271
260.112
909622 35564 Kbytes .Supplementary file Size Download File type/resource GSM742296.CEL.gz
32.9 Mb
(ftp) (http) CEL
GSM742296.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
