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Sample GSM397682 Query DataSets for GSM397682
Status Public on Jul 31, 2010
Title Brain-MND-0556-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 0.005530 BB 663.317627 5166.135742
SNP_A-1967418 AB 0.008133 AB 514.941528 383.304657
SNP_A-1969580 AB 0.001723 AB 2282.184326 2493.972412
SNP_A-4263484 BB 0.007679 BB 601.177124 2481.768066
SNP_A-1978185 AA 0.006823 AA 817.620361 210.296066
SNP_A-4264431 AA 0.006368 AA 1351.999023 250.685364
SNP_A-1980898 BB 0.010957 BB 209.605988 501.110840
SNP_A-1983139 AA 0.010748 AA 5671.975586 1225.139526
SNP_A-4265735 BB 0.003507 BB 724.858948 3244.578857
SNP_A-1995832 AA 0.000665 AA 2804.067383 391.011627
SNP_A-1995893 AA 0.013491 AA 3703.762695 1207.076660
SNP_A-1997689 BB 0.005868 BB 616.395630 3382.283447
SNP_A-1997709 AA 0.008993 AA 3553.995850 419.981293
SNP_A-1997896 AA 0.005328 AA 1031.483398 355.077118
SNP_A-1997922 AA 0.067224 AA 690.507202 250.685364
SNP_A-2000230 AA 0.008494 AA 2278.533691 782.795044
SNP_A-2000332 AA 0.013520 AA 4797.582520 888.095825
SNP_A-2000337 AA 0.002935 AA 2001.348511 265.618439
SNP_A-2000342 AA 0.006350 AA 4661.582520 975.979004
SNP_A-4268173 AB 0.003399 AB 626.762329 584.421631

Total number of rows: 909622

Table truncated, full table size 46114 Kbytes.

Supplementary file Size Download File type/resource
GSM397682.CEL.gz 29.4 Mb (ftp)(http) CEL
GSM397682.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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