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Sample GSM397717 Query DataSets for GSM397717
Status Public on Jul 31, 2010
Title Brain-MND-1062-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 AB 0.001281 AB 2855.743164 3218.556641
SNP_A-1967418 BB 0.005303 BB 206.079575 609.890686
SNP_A-1969580 BB 0.014352 BB 1167.813843 3177.221924
SNP_A-4263484 BB 0.002145 BB 542.530273 2017.444214
SNP_A-1978185 AA 0.000506 AA 1238.734375 319.462250
SNP_A-4264431 AA 0.011642 AA 1193.741821 301.269348
SNP_A-1980898 AB 0.003381 AB 492.773926 467.769348
SNP_A-1983139 AA 0.002150 AA 5036.424805 1369.392334
SNP_A-4265735 AB 0.003270 AB 1785.714844 1708.256470
SNP_A-1995832 AB 0.001161 AB 1956.466309 1414.938599
SNP_A-1995893 AB 0.001415 AB 1833.064453 2117.794189
SNP_A-1997689 BB 0.020250 BB 1029.998291 3468.884521
SNP_A-1997709 AA 0.019150 AA 3397.557861 562.871765
SNP_A-1997896 AB 0.001803 AB 886.914917 1545.589111
SNP_A-1997922 AA 0.005374 AA 849.561401 245.154266
SNP_A-2000230 AA 0.003994 AA 2366.794922 940.076477
SNP_A-2000332 AB 0.006545 AB 3324.546387 3157.085449
SNP_A-2000337 AA 0.015070 AA 1189.191040 226.459198
SNP_A-2000342 AA 0.012229 AA 4423.351562 1402.394531
SNP_A-4268173 AB 0.010068 AB 547.570190 747.830200

Total number of rows: 909622

Table truncated, full table size 46125 Kbytes.

Supplementary file Size Download File type/resource
GSM397717.CEL.gz 30.3 Mb (ftp)(http) CEL
GSM397717.CHP.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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