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Sample GSM397746 Query DataSets for GSM397746
Status Public on Jul 31, 2010
Title Brain-Ctrl-1669-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
ID_REF PROBE SET NAME
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
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 BB 0.003017 BB 552.997192 4046.438721
SNP_A-1967418 BB 0.004515 BB 251.885849 605.865234
SNP_A-1969580 BB 0.003673 BB 1306.718872 4543.373047
SNP_A-4263484 BB 0.004658 BB 642.304382 2430.549316
SNP_A-1978185 AA 0.005308 AA 871.193115 256.655090
SNP_A-4264431 AA 0.007310 AA 1343.036743 215.452713
SNP_A-1980898 AB 0.005998 AB 447.561920 390.131348
SNP_A-1983139 AA 0.007764 AA 5264.877441 1062.881348
SNP_A-4265735 AA 0.017760 AA 3310.028320 492.003143
SNP_A-1995832 BB 0.000256 BB 536.949829 2253.853027
SNP_A-1995893 BB 0.001089 BB 438.092285 2914.752930
SNP_A-1997689 BB 0.006259 BB 792.073853 3439.991211
SNP_A-1997709 AA 0.008811 AA 1520.215332 303.377319
SNP_A-1997896 AB 0.010888 AB 725.923096 996.721130
SNP_A-1997922 AB 0.014687 AB 486.567047 380.432800
SNP_A-2000230 AA 0.004690 AA 2715.027832 854.540527
SNP_A-2000332 AB 0.006682 AB 3229.576904 3448.188721
SNP_A-2000337 AA 0.002178 AA 1681.290039 305.356354
SNP_A-2000342 AA 0.001966 AA 3970.812988 978.449402
SNP_A-4268173 AA 0.004638 AA 1224.701172 141.598572

Total number of rows: 909622

Table truncated, full table size 46114 Kbytes.




Supplementary file Size Download File type/resource
GSM397746.CEL.gz 28.7 Mb (ftp)(http) CEL
GSM397746.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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