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Sample GSM397830 Query DataSets for GSM397830
Status Public on Jul 31, 2010
Title Blood-MND-1982-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 9 / Child
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 0.006968 AB 2753.111572 2355.706055
SNP_A-1967418 BB 0.002804 BB 225.473389 661.944153
SNP_A-1969580 BB 0.004495 BB 928.049744 3963.696289
SNP_A-4263484 AB 0.002840 AB 1604.500366 1233.229980
SNP_A-1978185 AA 0.002116 AA 1303.688477 261.400055
SNP_A-4264431 AA 0.010636 AA 1837.190430 457.171143
SNP_A-1980898 AB 0.002244 AB 526.389893 468.462067
SNP_A-1983139 AA 0.008677 AA 5542.702148 1207.096802
SNP_A-4265735 AB 0.005304 AB 1987.779907 1792.837280
SNP_A-1995832 AB 0.009620 AB 1305.686646 892.672607
SNP_A-1995893 AB 0.005049 AB 1593.517944 1962.774292
SNP_A-1997689 BB 0.012399 BB 578.099426 3041.622070
SNP_A-1997709 AA 0.004220 AA 1652.498779 213.349243
SNP_A-1997896 AA 0.008278 AA 921.837524 347.684448
SNP_A-1997922 AB 0.003431 AB 627.220886 501.910309
SNP_A-2000230 AA 0.016162 AA 3594.342041 1125.484985
SNP_A-2000332 AA 0.008836 AA 4530.246582 1197.513428
SNP_A-2000337 AA 0.003803 AA 1793.291870 335.053680
SNP_A-2000342 AA 0.007132 AA 4789.767578 1217.106689
SNP_A-4268173 AA 0.005854 AA 1037.974121 233.666351

Total number of rows: 909622

Table truncated, full table size 46127 Kbytes.

Supplementary file Size Download File type/resource
GSM397830.CEL.gz 27.6 Mb (ftp)(http) CEL
GSM397830.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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