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Sample GSM397724 Query DataSets for GSM397724
Status Public on Jul 31, 2010
Title Blood-MND-1095-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 AB 0.008531 AB 3515.786133 3725.976562
SNP_A-1967418 BB 0.007475 BB 188.868637 725.835083
SNP_A-1969580 BB 0.004343 BB 902.490417 3672.873291
SNP_A-4263484 AB 0.001630 AB 1800.817505 1243.272583
SNP_A-1978185 AA 0.003666 AA 980.088257 254.472305
SNP_A-4264431 AA 0.002752 AA 1558.310791 278.396179
SNP_A-1980898 BB 0.008107 BB 149.422302 738.806519
SNP_A-1983139 AA 0.005310 AA 5361.241699 1232.501953
SNP_A-4265735 AA 0.008539 AA 3052.129883 471.753784
SNP_A-1995832 AB 0.004903 AB 1458.526978 1239.239868
SNP_A-1995893 AB 0.005005 AB 2160.689453 2096.887695
SNP_A-1997689 BB 0.001962 BB 762.138672 3739.645996
SNP_A-1997709 AA 0.005306 AA 2608.727295 264.187469
SNP_A-1997896 AA 0.006807 AA 1006.363281 478.501923
SNP_A-1997922 AB 0.002945 AB 610.224731 541.086365
SNP_A-2000230 AA 0.001900 AA 2899.715088 1024.423340
SNP_A-2000332 AB 0.003774 AB 3192.981934 3123.894287
SNP_A-2000337 AA 0.000250 AA 1802.573975 272.105560
SNP_A-2000342 AA 0.001139 AA 4189.892578 974.545959
SNP_A-4268173 AA 0.003669 AA 1305.222046 165.336060

Total number of rows: 909622

Table truncated, full table size 46124 Kbytes.

Supplementary file Size Download File type/resource
GSM397724.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM397724.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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