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Sample GSM397731 Query DataSets for GSM397731
Status Public on Jul 31, 2010
Title Brain-Ctrl-1168-rep1
Sample type genomic
Source name Ctrl Brain (Brodmann area 46)
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: M
phenotype: Ctrl
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 Ctrl 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 0.005794 AB 2332.725342 2886.981445
SNP_A-1967418 AB 0.003743 AB 683.587952 566.382202
SNP_A-1969580 BB 0.002208 BB 1183.155151 4378.606934
SNP_A-4263484 AB 0.010100 AB 2505.085693 1881.252075
SNP_A-1978185 AA 0.002532 AA 1133.348755 365.418182
SNP_A-4264431 AA 0.003025 AA 1596.448853 323.819794
SNP_A-1980898 BB 0.003021 BB 197.821457 671.157776
SNP_A-1983139 AA 0.017567 AA 6207.652344 1859.265381
SNP_A-4265735 AA 0.005162 AA 3141.657227 596.169556
SNP_A-1995832 AB 0.000467 AB 1831.796997 1434.875732
SNP_A-1995893 AB 0.020388 AB 2732.682617 3063.116943
SNP_A-1997689 BB 0.002972 BB 640.563660 3629.185791
SNP_A-1997709 AA 0.002013 AA 2319.813965 270.854492
SNP_A-1997896 AA 0.001610 AA 1206.327271 459.869995
SNP_A-1997922 AB 0.006942 AB 907.879883 600.825500
SNP_A-2000230 AA 0.006444 AA 2221.043701 909.598755
SNP_A-2000332 AA 0.001710 AA 4050.588135 1013.598083
SNP_A-2000337 AA 0.002647 AA 1584.391235 279.732605
SNP_A-2000342 AA 0.020849 AA 4982.634766 1486.421143
SNP_A-4268173 AA 0.008209 AA 921.052368 203.178024

Total number of rows: 909622

Table truncated, full table size 46117 Kbytes.

Supplementary file Size Download File type/resource
GSM397731.CEL.gz 29.6 Mb (ftp)(http) CEL
GSM397731.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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