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Sample GSM397749 Query DataSets for GSM397749
Status Public on Jul 31, 2010
Title Brain-Ctrl-1674-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: F
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 0.001301 BB 678.563599 4768.525391
SNP_A-1967418 BB 0.002121 BB 254.281906 661.254333
SNP_A-1969580 BB 0.006470 BB 1240.857178 4761.209961
SNP_A-4263484 BB 0.001802 BB 448.250519 1937.468750
SNP_A-1978185 AA 0.005164 AA 927.358459 338.023804
SNP_A-4264431 AA 0.003253 AA 1546.418213 305.887146
SNP_A-1980898 BB 0.004582 BB 225.959305 626.148254
SNP_A-1983139 AA 0.004386 AA 5092.978516 1100.597412
SNP_A-4265735 AB 0.008421 AB 1747.337402 2230.507812
SNP_A-1995832 BB 0.003227 BB 443.103241 1945.725952
SNP_A-1995893 BB 0.001159 BB 470.147461 3040.206543
SNP_A-1997689 BB 0.000197 BB 733.222717 3919.588379
SNP_A-1997709 AA 0.006157 AA 1777.758179 180.432068
SNP_A-1997896 AB 0.008151 AB 819.490723 1064.951172
SNP_A-1997922 AB 0.004910 AB 573.601807 482.055908
SNP_A-2000230 AA 0.002923 AA 2855.621338 948.176819
SNP_A-2000332 AB 0.019856 AB 3519.460205 3756.291748
SNP_A-2000337 AA 0.002095 AA 1670.282837 247.612747
SNP_A-2000342 AA 0.005589 AA 3826.695801 828.472839
SNP_A-4268173 AA 0.001704 AA 1204.318970 222.647507

Total number of rows: 909622

Table truncated, full table size 46118 Kbytes.

Supplementary file Size Download File type/resource
GSM397749.CEL.gz 29.1 Mb (ftp)(http) CEL
GSM397749.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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