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Sample GSM397716 Query DataSets for GSM397716
Status Public on Jul 31, 2010
Title Blood-MND-1062-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 0.004684 AB 3254.673828 3581.369873
SNP_A-1967418 BB 0.001157 BB 255.258514 691.346741
SNP_A-1969580 BB 0.003463 BB 1145.822754 4447.244629
SNP_A-4263484 BB 0.000914 BB 473.485626 2091.213867
SNP_A-1978185 AA 0.007847 AA 1830.128174 358.409271
SNP_A-4264431 AA 0.003677 AA 2109.226807 362.760315
SNP_A-1980898 AB 0.000825 AB 603.779236 549.791687
SNP_A-1983139 AA 0.003028 AA 4538.564941 945.496338
SNP_A-4265735 AB 0.006337 AB 1420.364258 1468.822021
SNP_A-1995832 AB 0.002329 AB 1654.910400 1243.500610
SNP_A-1995893 AB 0.008020 AB 1456.642212 1798.876831
SNP_A-1997689 BB 0.004309 BB 753.905151 4422.606934
SNP_A-1997709 AA 0.000445 AA 2461.890625 322.122650
SNP_A-1997896 AB 0.001201 AB 1052.059448 1669.937378
SNP_A-1997922 AA 0.002624 AA 883.992065 224.902130
SNP_A-2000230 AA 0.001793 AA 2738.805908 1151.200684
SNP_A-2000332 AB 0.004564 AB 2705.354980 2720.356201
SNP_A-2000337 AA 0.001068 AA 1698.437134 267.102966
SNP_A-2000342 AA 0.002735 AA 3896.522461 1004.066589
SNP_A-4268173 AB 0.002410 AB 749.112000 764.857605

Total number of rows: 909622

Table truncated, full table size 46135 Kbytes.

Supplementary file Size Download File type/resource
GSM397716.CEL.gz 29.5 Mb (ftp)(http) CEL
GSM397716.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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