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Sample GSM397722 Query DataSets for GSM397722
Status Public on Jul 31, 2010
Title Blood-MND-1083-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 0.006006 AB 2893.080078 2521.833984
SNP_A-1967418 AB 0.044628 AB 344.268066 214.519043
SNP_A-1969580 BB 0.001846 BB 1216.322510 3996.261230
SNP_A-4263484 BB 0.010860 BB 537.902405 1773.981445
SNP_A-1978185 AA 0.002434 AA 1362.516113 264.438660
SNP_A-4264431 AA 0.001848 AA 1672.210205 261.966980
SNP_A-1980898 AB 0.004069 AB 548.537537 591.226746
SNP_A-1983139 AA 0.003032 AA 5221.551758 1298.229614
SNP_A-4265735 AB 0.007399 AB 2197.144287 1951.614868
SNP_A-1995832 AA 0.006419 AA 2325.887207 347.826691
SNP_A-1995893 AA 0.007872 AA 3024.980713 905.770386
SNP_A-1997689 BB 0.006145 BB 649.450928 3339.863281
SNP_A-1997709 AA 0.015548 AA 4001.459229 477.520172
SNP_A-1997896 AA 0.007345 AA 1155.866089 605.496216
SNP_A-1997922 NC 0.195318 AA 560.190613 222.207733
SNP_A-2000230 AA 0.003089 AA 3017.640869 1048.958252
SNP_A-2000332 AA 0.009144 AA 4730.049805 1076.243652
SNP_A-2000337 AA 0.003570 AA 1619.012085 231.547241
SNP_A-2000342 AA 0.001384 AA 4319.821289 1114.970703
SNP_A-4268173 AA 0.001352 AA 1251.458862 203.915222

Total number of rows: 909622

Table truncated, full table size 46131 Kbytes.

Supplementary file Size Download File type/resource
GSM397722.CEL.gz 27.9 Mb (ftp)(http) CEL
GSM397722.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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