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Sample GSM397695 Query DataSets for GSM397695
Status Public on Jul 31, 2010
Title Blood-MND-0870-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: M
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 Blood
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 0.019857 BB 1090.707764 4716.210449
SNP_A-1967418 BB 0.003595 BB 223.464874 759.206604
SNP_A-1969580 BB 0.028045 BB 1502.248169 3532.803711
SNP_A-4263484 AA 0.017826 AA 4245.727539 716.321411
SNP_A-1978185 AA 0.010932 AA 632.326965 243.359818
SNP_A-4264431 AA 0.006613 AA 1410.810913 325.935150
SNP_A-1980898 AB 0.010704 AB 364.161499 374.126160
SNP_A-1983139 AA 0.013736 AA 5171.937988 1794.806030
SNP_A-4265735 AA 0.014465 AA 2951.883545 927.646667
SNP_A-1995832 AB 0.002960 AB 2049.841309 1705.537598
SNP_A-1995893 AB 0.012397 AB 2163.856201 2809.770264
SNP_A-1997689 BB 0.027524 BB 879.248474 2844.464111
SNP_A-1997709 AA 0.003880 AA 2884.307373 327.674225
SNP_A-1997896 AA 0.006659 AA 1111.599854 566.319580
SNP_A-1997922 AB 0.006247 AB 559.362061 451.985870
SNP_A-2000230 AA 0.009296 AA 2543.150391 1318.674927
SNP_A-2000332 AA 0.004628 AA 4494.336914 1046.016968
SNP_A-2000337 AA 0.003300 AA 2008.219482 301.694916
SNP_A-2000342 AA 0.015313 AA 3923.737549 1353.872803
SNP_A-4268173 AA 0.006413 AA 1005.269897 225.018478

Total number of rows: 909622

Table truncated, full table size 46114 Kbytes.

Supplementary file Size Download File type/resource
GSM397695.CEL.gz 30.7 Mb (ftp)(http) CEL
GSM397695.CHP.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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