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Sample GSM397745 Query DataSets for GSM397745
Status Public on Jul 31, 2010
Title Brain-Ctrl-1667-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 0.004935 AB 3154.408203 3655.892578
SNP_A-1967418 BB 0.003151 BB 233.059174 777.862244
SNP_A-1969580 BB 0.004943 BB 1330.087524 4022.780762
SNP_A-4263484 AA 0.003511 AA 3348.261475 581.042053
SNP_A-1978185 AA 0.001476 AA 1146.582397 291.404144
SNP_A-4264431 AA 0.011009 AA 1172.348633 255.922287
SNP_A-1980898 BB 0.004999 BB 194.088028 592.358521
SNP_A-1983139 AA 0.002488 AA 4829.350098 1373.808960
SNP_A-4265735 AB 0.006084 AB 2319.881592 2313.016846
SNP_A-1995832 AB 0.005772 AB 2244.793945 1463.033325
SNP_A-1995893 AB 0.004520 AB 2239.663818 2224.328857
SNP_A-1997689 BB 0.013821 BB 1058.076782 4354.389648
SNP_A-1997709 AA 0.009869 AA 3033.860352 486.488068
SNP_A-1997896 AA 0.014629 AA 848.217041 469.715790
SNP_A-1997922 AB 0.002731 AB 625.071045 533.418579
SNP_A-2000230 AA 0.011230 AA 2447.225586 1324.483032
SNP_A-2000332 AA 0.004544 AA 3826.643555 1033.688965
SNP_A-2000337 AA 0.000977 AA 1728.215576 289.874115
SNP_A-2000342 AA 0.007542 AA 4110.095215 1275.015869
SNP_A-4268173 AA 0.013118 AA 740.744324 124.321510

Total number of rows: 909622

Table truncated, full table size 46121 Kbytes.

Supplementary file Size Download File type/resource
GSM397745.CEL.gz 30.0 Mb (ftp)(http) CEL
GSM397745.CHP.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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