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Sample GSM397691 Query DataSets for GSM397691
Status Public on Jul 31, 2010
Title Blood-MND-0862-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 0.002614 BB 747.467163 5035.672852
SNP_A-1967418 BB 0.003083 BB 218.932861 693.543457
SNP_A-1969580 BB 0.001534 BB 1059.284424 4069.165527
SNP_A-4263484 AB 0.006298 AB 1785.070312 1086.248779
SNP_A-1978185 AA 0.000567 AA 1368.997925 339.478455
SNP_A-4264431 AA 0.001229 AA 1759.827637 327.686584
SNP_A-1980898 BB 0.001615 BB 207.047913 748.810608
SNP_A-1983139 AA 0.001185 AA 4467.368652 1133.754517
SNP_A-4265735 AA 0.001423 AA 2712.902344 490.679474
SNP_A-1995832 AB 0.004281 AB 1893.457764 1701.168945
SNP_A-1995893 AB 0.001643 AB 1882.938477 2234.468262
SNP_A-1997689 BB 0.001651 BB 806.848877 3974.905762
SNP_A-1997709 AA 0.003246 AA 2681.467285 300.524719
SNP_A-1997896 AA 0.005978 AA 993.962463 387.980255
SNP_A-1997922 AB 0.007536 AB 682.059143 748.810608
SNP_A-2000230 AA 0.008221 AA 2944.283936 823.858948
SNP_A-2000332 AA 0.003984 AA 3956.218506 1066.819946
SNP_A-2000337 AA 0.003305 AA 1788.649292 329.266541
SNP_A-2000342 AA 0.005208 AA 4246.955078 1246.548706
SNP_A-4268173 AA 0.000790 AA 1341.164551 221.912170

Total number of rows: 909622

Table truncated, full table size 46133 Kbytes.

Supplementary file Size Download File type/resource
GSM397691.CEL.gz 28.5 Mb (ftp)(http) CEL
GSM397691.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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