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Sample GSM397737 Query DataSets for GSM397737
Status Public on Jul 31, 2010
Title Blood-MND-1267-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 0.001451 BB 696.108032 4823.659180
SNP_A-1967418 BB 0.003533 BB 297.093262 851.562439
SNP_A-1969580 BB 0.004450 BB 1127.003906 3583.938965
SNP_A-4263484 AA 0.000331 AA 3038.739258 404.063843
SNP_A-1978185 AA 0.006053 AA 1553.414795 241.847198
SNP_A-4264431 AA 0.004472 AA 2182.406982 330.545471
SNP_A-1980898 BB 0.012993 BB 232.646851 1187.613647
SNP_A-1983139 AA 0.012411 AA 3666.744141 1139.092896
SNP_A-4265735 AB 0.000549 AB 1841.190552 1897.989624
SNP_A-1995832 BB 0.000582 BB 597.483765 2358.361572
SNP_A-1995893 BB 0.008938 BB 488.069183 3443.586670
SNP_A-1997689 BB 0.005710 BB 621.216614 4306.707031
SNP_A-1997709 AA 0.003509 AA 1833.299438 293.965973
SNP_A-1997896 AB 0.003601 AB 1127.840088 1472.638306
SNP_A-1997922 AB 0.001276 AB 693.397217 661.216492
SNP_A-2000230 AA 0.004054 AA 2431.844238 892.821716
SNP_A-2000332 AB 0.005971 AB 2785.210449 2638.622314
SNP_A-2000337 AA 0.000152 AA 1772.848511 276.669159
SNP_A-2000342 AA 0.002576 AA 3996.811523 916.668701
SNP_A-4268173 AB 0.003033 AB 872.699707 850.723816

Total number of rows: 909622

Table truncated, full table size 46132 Kbytes.

Supplementary file Size Download File type/resource
GSM397737.CEL.gz 30.3 Mb (ftp)(http) CEL
GSM397737.CHP.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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