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Sample GSM397720 Query DataSets for GSM397720
Status Public on Jul 31, 2010
Title Blood-MND-1082-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 0.032210 BB 629.719360 6107.240723
SNP_A-1967418 AB 0.029473 AB 908.472107 726.492126
SNP_A-1969580 BB 0.005785 BB 855.976929 3720.615967
SNP_A-4263484 BB 0.005726 BB 554.247131 2383.681641
SNP_A-1978185 AA 0.002117 AA 1472.466553 312.930298
SNP_A-4264431 BB 0.001063 BB 484.402771 1565.504395
SNP_A-1980898 AB 0.009406 AB 827.955872 675.188171
SNP_A-1983139 AA 0.003139 AA 5242.112793 1313.612793
SNP_A-4265735 AB 0.009982 AB 2323.562500 2570.223145
SNP_A-1995832 AB 0.001996 AB 1935.866211 1342.054932
SNP_A-1995893 AB 0.004547 AB 1907.298462 2410.667480
SNP_A-1997689 BB 0.001864 BB 659.140564 3753.885742
SNP_A-1997709 AA 0.001148 AA 2420.525391 297.042694
SNP_A-1997896 AA 0.003120 AA 1359.450562 376.597504
SNP_A-1997922 AB 0.001866 AB 684.996826 548.307495
SNP_A-2000230 AA 0.000529 AA 2661.442139 1030.595093
SNP_A-2000332 AA 0.004902 AA 3721.745117 781.212097
SNP_A-2000337 AA 0.002058 AA 1705.227417 307.063385
SNP_A-2000342 AA 0.011034 AA 4533.591797 802.208252
SNP_A-4268173 AA 0.000409 AA 1333.364502 230.131516

Total number of rows: 909622

Table truncated, full table size 46131 Kbytes.

Supplementary file Size Download File type/resource
GSM397720.CEL.gz 29.1 Mb (ftp)(http) CEL
GSM397720.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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