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Sample GSM397711 Query DataSets for GSM397711
Status Public on Jul 31, 2010
Title Brain-MND-1011-rep1
Sample type genomic
Source name MND Brain (Brodmann area 46)
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 Brain (Brodmann area 46)
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 0.000838 BB 731.900574 4635.724121
SNP_A-1967418 BB 0.002532 BB 249.386932 800.318298
SNP_A-1969580 BB 0.003273 BB 945.553833 3759.579590
SNP_A-4263484 AB 0.001829 AB 1781.300415 1227.500244
SNP_A-1978185 AA 0.000987 AA 1404.460938 360.412598
SNP_A-4264431 AB 0.001970 AB 1225.544067 858.718689
SNP_A-1980898 AB 0.002853 AB 565.930786 427.611908
SNP_A-1983139 AA 0.001695 AA 5032.217285 1260.119141
SNP_A-4265735 AA 0.003655 AA 2397.604980 409.894745
SNP_A-1995832 AB 0.001479 AB 1732.423462 1406.302979
SNP_A-1995893 AB 0.001830 AB 1823.963257 2021.124023
SNP_A-1997689 BB 0.001977 BB 666.854431 4065.291992
SNP_A-1997709 AA 0.006322 AA 2143.146729 378.321259
SNP_A-1997896 AB 0.002796 AB 904.923218 1681.663696
SNP_A-1997922 AA 0.005025 AA 1168.422241 192.099564
SNP_A-2000230 AA 0.006330 AA 3240.296143 1133.818726
SNP_A-2000332 AA 0.008642 AA 3984.925781 1181.429443
SNP_A-2000337 AA 0.013812 AA 1742.104004 405.986786
SNP_A-2000342 AA 0.005109 AA 4621.462402 999.238037
SNP_A-4268173 AB 0.002029 AB 683.258667 644.251404

Total number of rows: 909622

Table truncated, full table size 46126 Kbytes.

Supplementary file Size Download File type/resource
GSM397711.CEL.gz 27.9 Mb (ftp)(http) CEL
GSM397711.CHP.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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