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Sample GSM397776 Query DataSets for GSM397776
Status Public on Jul 31, 2010
Title Blood-MND-1895-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 0.006852 AB 3207.817627 3807.342529
SNP_A-1967418 BB 0.001330 BB 255.430573 776.036926
SNP_A-1969580 BB 0.008305 BB 814.933960 3268.314209
SNP_A-4263484 AB 0.013204 AB 1682.893921 1577.396362
SNP_A-1978185 AA 0.001559 AA 1378.544922 389.638031
SNP_A-4264431 AA 0.001592 AA 1747.792236 261.878113
SNP_A-1980898 BB 0.006437 BB 206.280960 999.642151
SNP_A-1983139 AA 0.002793 AA 4711.193359 1004.206787
SNP_A-4265735 AB 0.001260 AB 1936.582153 2079.210693
SNP_A-1995832 BB 0.006221 BB 479.405975 2578.460449
SNP_A-1995893 BB 0.010017 BB 494.193054 3486.778320
SNP_A-1997689 BB 0.013050 BB 910.755493 4860.831055
SNP_A-1997709 AA 0.005177 AA 1512.260498 240.994675
SNP_A-1997896 AA 0.002643 AA 1278.072998 556.700378
SNP_A-1997922 BB 0.002779 BB 523.489197 1279.608032
SNP_A-2000230 AA 0.005406 AA 2667.514648 1261.133057
SNP_A-2000332 AA 0.000648 AA 4004.302490 920.366516
SNP_A-2000337 AA 0.005531 AA 1633.160889 342.268738
SNP_A-2000342 AA 0.001518 AA 4217.439941 961.582092
SNP_A-4268173 AA 0.001734 AA 1210.327637 229.828400

Total number of rows: 909622

Table truncated, full table size 46132 Kbytes.

Supplementary file Size Download File type/resource
GSM397776.CEL.gz 28.6 Mb (ftp)(http) CEL
GSM397776.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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