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Sample GSM397739 Query DataSets for GSM397739
Status Public on Jul 31, 2010
Title Blood-MND-1438-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: M
phenotype: MND
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from leukocytes using the phenol chloroform method or Qiamp blood kits (Qiagen Pty Ltd, Doncaster, Vic, Australia), hair using the phenol chloroform method, and from sperm using Pure Sperm 100 kits (Nidacom, Gothenburg, Sweden).
Label biotin
Label protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia), Affymetrix dsDNA terminal label.
Hybridization protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)
Scan protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)
Description Affy 6.0 MND Blood
Data processing Data processed using Affymetrix Command Console software and Affymetrix Genotyping Console 3.0.2 software using the Birdseed version 2 algorithm and default settings.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
Submission date Apr 25, 2009
Last update date Jun 26, 2012
Contact name Roger Pamphlett
Organization name University of Sydney
Street address Blackburn Bld
City University of Sydney
ZIP/Postal code 2006
Country Australia
Platform ID GPL6801
Series (1)
GSE15826 Affymetrix 6.0 study of sporadic motor neuron disease patients and controls.

Data table header descriptions
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
CONFIDENCE A value in the range [0,1] with lower values corresponding to greater confidence
FORCED CALL This value is the genotyping call that would be made if the calling algorithm were tuned to the least stringency. Providing this value allows for determining what the calls would have been at a stringency different to that applied to the calls in the second field, without having to re-run the genotyping algorithm
SIGNAL A Summarized signal A
SIGNAL B Summarized signal B

Data table
SNP_A-2131660 BB 0.003097 BB 716.043579 5054.897949
SNP_A-1967418 AB 0.006679 AB 527.949402 615.873291
SNP_A-1969580 BB 0.004654 BB 1100.282104 4462.188477
SNP_A-4263484 AB 0.008808 AB 1237.141602 989.224182
SNP_A-1978185 AB 0.003795 AB 1375.727539 1860.315430
SNP_A-4264431 AB 0.001225 AB 1225.112305 997.153748
SNP_A-1980898 BB 0.005019 BB 175.854645 808.268311
SNP_A-1983139 AA 0.004649 AA 4169.313965 827.641541
SNP_A-4265735 AA 0.003543 AA 2404.549072 434.140411
SNP_A-1995832 AB 0.002685 AB 1789.434570 1222.479248
SNP_A-1995893 AB 0.000685 AB 1902.858276 2134.240967
SNP_A-1997689 BB 0.000296 BB 726.391113 3900.099609
SNP_A-1997709 AA 0.003887 AA 3002.403320 356.920227
SNP_A-1997896 AB 0.003310 AB 814.695557 1483.789795
SNP_A-1997922 AA 0.004075 AA 928.992737 285.843536
SNP_A-2000230 AA 0.002097 AA 2841.471436 1165.653198
SNP_A-2000332 AB 0.002343 AB 2729.158447 2888.936523
SNP_A-2000337 AA 0.022829 AA 2537.516357 325.581818
SNP_A-2000342 AA 0.006938 AA 3630.136475 870.436951
SNP_A-4268173 AA 0.001506 AA 1482.741455 259.232208

Total number of rows: 909622

Table truncated, full table size 46136 Kbytes.

Supplementary file Size Download File type/resource
GSM397739.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM397739.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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