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Sample GSM397748 Query DataSets for GSM397748
Status Public on Jul 31, 2010
Title Brain-Ctrl-1673-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 BB 0.002399 BB 633.347229 4131.919922
SNP_A-1967418 BB 0.005902 BB 322.109558 727.302673
SNP_A-1969580 BB 0.003315 BB 1318.850098 4201.402832
SNP_A-4263484 BB 0.004273 BB 547.296204 2332.601074
SNP_A-1978185 AA 0.004713 AA 952.064026 218.219437
SNP_A-4264431 AA 0.003666 AA 1530.391357 311.379272
SNP_A-1980898 BB 0.003244 BB 198.191391 658.704956
SNP_A-1983139 AA 0.000434 AA 4655.033203 1193.438965
SNP_A-4265735 AA 0.001007 AA 2836.729980 633.845093
SNP_A-1995832 BB 0.003769 BB 502.143677 2496.456787
SNP_A-1995893 BB 0.000421 BB 481.283051 2925.479492
SNP_A-1997689 BB 0.001461 BB 763.952637 3803.620605
SNP_A-1997709 AA 0.005718 AA 1844.854614 328.732605
SNP_A-1997896 AA 0.002264 AA 1470.301270 467.421509
SNP_A-1997922 BB 0.004931 BB 396.474792 930.962952
SNP_A-2000230 AA 0.002703 AA 2452.495361 1047.794434
SNP_A-2000332 AA 0.010244 AA 4580.302246 811.262024
SNP_A-2000337 AA 0.006639 AA 1785.327148 190.630524
SNP_A-2000342 AA 0.003468 AA 3951.617676 1106.143921
SNP_A-4268173 AB 0.004451 AB 749.935730 823.111206

Total number of rows: 909622

Table truncated, full table size 46135 Kbytes.

Supplementary file Size Download File type/resource
GSM397748.CEL.gz 30.3 Mb (ftp)(http) CEL
GSM397748.CHP.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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