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Sample GSM397696 Query DataSets for GSM397696
Status Public on Jul 31, 2010
Title Brain-MND-0870-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 0.003021 BB 590.482788 4024.376953
SNP_A-1967418 BB 0.006229 BB 334.443756 804.238464
SNP_A-1969580 BB 0.004793 BB 1185.776001 3657.645264
SNP_A-4263484 AA 0.048138 AA 4166.902344 418.476196
SNP_A-1978185 AA 0.004572 AA 1554.993652 461.265045
SNP_A-4264431 AA 0.003543 AA 1622.678467 344.237030
SNP_A-1980898 AB 0.002973 AB 507.919373 448.569855
SNP_A-1983139 AA 0.005306 AA 5057.809570 1543.560669
SNP_A-4265735 AA 0.002118 AA 2998.176025 702.985229
SNP_A-1995832 AB 0.000880 AB 1837.519165 1480.648804
SNP_A-1995893 AB 0.019745 AB 2231.079346 2981.210693
SNP_A-1997689 BB 0.001523 BB 728.048584 4149.272949
SNP_A-1997709 AA 0.002334 AA 2697.179443 381.160370
SNP_A-1997896 AA 0.004134 AA 1298.926758 602.492249
SNP_A-1997922 AB 0.003003 AB 814.036987 732.973816
SNP_A-2000230 AA 0.012691 AA 2695.886963 1412.539795
SNP_A-2000332 AA 0.024696 AA 3823.505127 1337.979736
SNP_A-2000337 AA 0.009488 AA 1478.566162 354.056122
SNP_A-2000342 AA 0.016067 AA 4615.918457 1462.332642
SNP_A-4268173 AA 0.019908 AA 868.940613 261.841125

Total number of rows: 909622

Table truncated, full table size 46117 Kbytes.

Supplementary file Size Download File type/resource
GSM397696.CEL.gz 29.3 Mb (ftp)(http) CEL
GSM397696.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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