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Sample GSM397713 Query DataSets for GSM397713
Status Public on Jul 31, 2010
Title Brain-MND-1016-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 0.001688 BB 583.193726 4370.224121
SNP_A-1967418 BB 0.002818 BB 251.962585 641.904602
SNP_A-1969580 BB 0.006242 BB 1164.869629 4664.401855
SNP_A-4263484 BB 0.007790 BB 453.153625 1739.631958
SNP_A-1978185 AA 0.002096 AA 1438.086670 297.413147
SNP_A-4264431 AA 0.002670 AA 1928.666382 261.288086
SNP_A-1980898 BB 0.004537 BB 261.288086 717.776001
SNP_A-1983139 AA 0.002902 AA 4522.125488 948.372498
SNP_A-4265735 AB 0.000498 AB 1903.463257 1981.687134
SNP_A-1995832 AB 0.006830 AB 2327.877930 1524.460449
SNP_A-1995893 AB 0.002736 AB 1916.685547 1985.207275
SNP_A-1997689 BB 0.002694 BB 635.726990 4038.879883
SNP_A-1997709 AA 0.005821 AA 2755.531982 279.730377
SNP_A-1997896 AA 0.004286 AA 1367.495117 350.618225
SNP_A-1997922 AB 0.008010 AB 770.276672 485.990997
SNP_A-2000230 AA 0.001823 AA 2926.046387 1065.231689
SNP_A-2000332 AB 0.006047 AB 2671.673584 2648.284912
SNP_A-2000337 AA 0.012260 AA 2306.843018 235.998978
SNP_A-2000342 AA 0.006556 AA 3637.586670 894.660339
SNP_A-4268173 AA 0.002067 AA 1320.006958 192.873688

Total number of rows: 909622

Table truncated, full table size 46130 Kbytes.

Supplementary file Size Download File type/resource
GSM397713.CEL.gz 29.1 Mb (ftp)(http) CEL
GSM397713.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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