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Sample GSM397710 Query DataSets for GSM397710
Status Public on Jul 31, 2010
Title Blood-MND-1011-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 0.001393 BB 710.577515 4417.304199
SNP_A-1967418 BB 0.004375 BB 232.813446 602.977051
SNP_A-1969580 BB 0.001162 BB 1073.797974 4058.165527
SNP_A-4263484 AB 0.001135 AB 1823.035645 1276.053833
SNP_A-1978185 AA 0.002445 AA 1085.825317 261.111572
SNP_A-4264431 AB 0.006937 AB 1039.130005 717.581238
SNP_A-1980898 AB 0.001268 AB 557.351746 498.568054
SNP_A-1983139 AA 0.004754 AA 5339.092285 1250.528687
SNP_A-4265735 AA 0.000499 AA 2830.511475 609.009277
SNP_A-1995832 AB 0.002436 AB 1665.765259 1402.326294
SNP_A-1995893 AB 0.001251 AB 1999.713135 2128.952393
SNP_A-1997689 BB 0.004122 BB 675.308105 4312.197266
SNP_A-1997709 AA 0.003603 AA 2453.377197 384.434479
SNP_A-1997896 AB 0.000260 AB 971.699402 1549.156250
SNP_A-1997922 AA 0.000128 AA 1016.639893 248.303024
SNP_A-2000230 AA 0.002396 AA 2912.878418 1165.491089
SNP_A-2000332 AA 0.005478 AA 4553.127441 979.192017
SNP_A-2000337 AA 0.005817 AA 1571.169312 210.330475
SNP_A-2000342 AA 0.002145 AA 4108.666016 1118.606812
SNP_A-4268173 AB 0.002089 AB 839.432983 646.869263

Total number of rows: 909622

Table truncated, full table size 46125 Kbytes.

Supplementary file Size Download File type/resource
GSM397710.CEL.gz 28.6 Mb (ftp)(http) CEL
GSM397710.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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