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Sample GSM397738 Query DataSets for GSM397738
Status Public on Jul 31, 2010
Title Brain-MND-1267-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 0.007033 BB 955.859619 5049.343750
SNP_A-1967418 BB 0.001602 BB 288.968567 769.118958
SNP_A-1969580 BB 0.007870 BB 1146.875244 3409.372559
SNP_A-4263484 AA 0.004735 AA 2734.290771 424.669250
SNP_A-1978185 AA 0.004010 AA 991.778381 340.205566
SNP_A-4264431 AA 0.008042 AA 1277.653564 250.763565
SNP_A-1980898 BB 0.006873 BB 249.475204 624.318115
SNP_A-1983139 AA 0.005728 AA 5242.698242 1578.761353
SNP_A-4265735 AB 0.001799 AB 1964.621216 2126.653564
SNP_A-1995832 BB 0.005572 BB 578.072693 2686.487793
SNP_A-1995893 BB 0.003541 BB 555.483337 2878.885986
SNP_A-1997689 BB 0.003113 BB 848.994141 3915.957031
SNP_A-1997709 AA 0.005739 AA 1970.535645 348.805634
SNP_A-1997896 AB 0.006362 AB 758.336853 1188.790771
SNP_A-1997922 AB 0.003876 AB 587.926331 579.489990
SNP_A-2000230 AA 0.008082 AA 2153.444092 1051.566284
SNP_A-2000332 AB 0.001999 AB 3063.126953 3034.354248
SNP_A-2000337 AA 0.005699 AA 1597.911377 339.200287
SNP_A-2000342 AA 0.005098 AA 3823.317627 1098.126465
SNP_A-4268173 AB 0.008401 AB 497.235657 450.250854

Total number of rows: 909622

Table truncated, full table size 46118 Kbytes.

Supplementary file Size Download File type/resource
GSM397738.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM397738.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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