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Sample GSM397698 Query DataSets for GSM397698
Status Public on Jul 31, 2010
Title Brain-MND-0899-rep1
Sample type genomic
Source name MND Brain (Brodmann area 46)
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: F
phenotype: MND
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 MND 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 0.005166 AB 2332.282715 2490.311523
SNP_A-1967418 AB 0.014323 AB 762.872070 568.003174
SNP_A-1969580 BB 0.003819 BB 925.676270 3664.667725
SNP_A-4263484 AB 0.008283 AB 2516.093994 1642.850952
SNP_A-1978185 AA 0.003527 AA 990.202454 313.517395
SNP_A-4264431 AA 0.001614 AA 1667.806763 271.586823
SNP_A-1980898 BB 0.022006 BB 290.076996 617.560486
SNP_A-1983139 AA 0.007546 AA 5524.057617 1645.959595
SNP_A-4265735 AB 0.014080 AB 2617.986816 2573.517578
SNP_A-1995832 AB 0.004151 AB 1545.833008 1358.595093
SNP_A-1995893 AB 0.002988 AB 2130.145752 2162.210693
SNP_A-1997689 BB 0.001714 BB 654.891174 3816.423340
SNP_A-1997709 AA 0.002136 AA 2489.298828 288.929840
SNP_A-1997896 AB 0.003595 AB 802.502136 1396.132568
SNP_A-1997922 AA 0.003308 AA 875.014282 236.165558
SNP_A-2000230 AA 0.001844 AA 2931.112305 1098.430054
SNP_A-2000332 AB 0.006684 AB 2762.635498 2606.764648
SNP_A-2000337 AA 0.001728 AA 1925.236572 288.929840
SNP_A-2000342 AA 0.001531 AA 4344.747559 1119.101929
SNP_A-4268173 AA 0.019534 AA 899.373901 276.156586

Total number of rows: 909622

Table truncated, full table size 46115 Kbytes.

Supplementary file Size Download File type/resource
GSM397698.CEL.gz 29.5 Mb (ftp)(http) CEL
GSM397698.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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