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Sample GSM397732 Query DataSets for GSM397732
Status Public on Jul 31, 2010
Title Brain-Ctrl-1169-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 0.011358 BB 974.388550 4597.034180
SNP_A-1967418 BB 0.022705 BB 377.344788 1062.574341
SNP_A-1969580 BB 0.002229 BB 1160.536133 3821.766357
SNP_A-4263484 BB 0.015669 BB 560.816162 2582.092285
SNP_A-1978185 AA 0.003200 AA 1019.522095 254.473709
SNP_A-4264431 AA 0.001577 AA 1731.340210 329.894928
SNP_A-1980898 BB 0.001577 BB 255.095901 911.440063
SNP_A-1983139 AA 0.002597 AA 4823.644531 1378.231079
SNP_A-4265735 AA 0.026329 AA 3298.855225 1130.172852
SNP_A-1995832 AA 0.024727 AA 4260.312988 722.631226
SNP_A-1995893 AA 0.017156 AA 3827.808594 1968.843140
SNP_A-1997689 BB 0.016014 BB 1057.339600 3844.781982
SNP_A-1997709 AA 0.009639 AA 3585.788574 476.030670
SNP_A-1997896 AA 0.003626 AA 1149.394775 351.636810
SNP_A-1997922 AA 0.000817 AA 966.475525 245.241592
SNP_A-2000230 AA 0.001517 AA 2548.748291 1014.919922
SNP_A-2000332 AA 0.002938 AA 4344.327148 1044.928345
SNP_A-2000337 AA 0.024545 AA 1712.226807 448.025391
SNP_A-2000342 AA 0.008995 AA 3807.990234 1205.270386
SNP_A-4268173 AA 0.001673 AA 1215.176880 230.759018

Total number of rows: 909622

Table truncated, full table size 46118 Kbytes.

Supplementary file Size Download File type/resource
GSM397732.CEL.gz 29.6 Mb (ftp)(http) CEL
GSM397732.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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