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Sample GSM397727 Query DataSets for GSM397727
Status Public on Jul 31, 2010
Title Brain-Ctrl-1105-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 0.006675 AB 2238.716064 2403.036133
SNP_A-1967418 BB 0.000463 BB 259.108154 751.354858
SNP_A-1969580 BB 0.004845 BB 1329.881958 4032.147705
SNP_A-4263484 AB 0.003697 AB 1528.019653 1168.725098
SNP_A-1978185 AA 0.000843 AA 1303.627930 362.195038
SNP_A-4264431 AA 0.009689 AA 1293.136475 324.990387
SNP_A-1980898 AB 0.004354 AB 521.841797 570.084473
SNP_A-1983139 AA 0.001431 AA 4935.971680 1192.301636
SNP_A-4265735 AA 0.004870 AA 2352.893799 472.617737
SNP_A-1995832 AB 0.006130 AB 2014.007812 1831.700317
SNP_A-1995893 AB 0.003037 AB 1712.240112 2047.088379
SNP_A-1997689 BB 0.002136 BB 654.588440 3718.585205
SNP_A-1997709 AA 0.003933 AA 2612.195557 401.801025
SNP_A-1997896 AB 0.001296 AB 920.921570 1450.436157
SNP_A-1997922 AA 0.003948 AA 872.727417 246.000580
SNP_A-2000230 AA 0.003744 AA 2462.056885 896.569580
SNP_A-2000332 AB 0.001951 AB 3078.627686 3130.226562
SNP_A-2000337 AA 0.005704 AA 2025.892090 221.875992
SNP_A-2000342 AA 0.003398 AA 4372.040527 932.436829
SNP_A-4268173 AA 0.001541 AA 1211.909912 212.395279

Total number of rows: 909622

Table truncated, full table size 46129 Kbytes.

Supplementary file Size Download File type/resource
GSM397727.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM397727.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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