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Sample GSM397718 Query DataSets for GSM397718
Status Public on Jul 31, 2010
Title Blood-MND-1081-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 0.006948 AB 2202.750977 2498.934814
SNP_A-1967418 BB 0.023450 BB 215.939148 991.350830
SNP_A-1969580 BB 0.007306 BB 1204.776245 4773.715820
SNP_A-4263484 AB 0.004673 AB 2177.078857 1384.448975
SNP_A-1978185 AA 0.027706 AA 2349.841553 421.774780
SNP_A-4264431 BB 0.010564 BB 420.656250 1926.458130
SNP_A-1980898 BB 0.014007 BB 268.215881 1253.407837
SNP_A-1983139 AA 0.002688 AA 4207.570801 1019.137939
SNP_A-4265735 BB 0.003067 BB 846.158142 3355.197266
SNP_A-1995832 AB 0.003092 AB 1626.241211 1179.290894
SNP_A-1995893 AB 0.002814 AB 2039.898926 2430.699463
SNP_A-1997689 BB 0.016163 BB 477.633057 4430.266113
SNP_A-1997709 AA 0.004399 AA 1786.332764 300.123169
SNP_A-1997896 AB 0.017240 AB 1253.407837 2309.006592
SNP_A-1997922 AA 0.073585 AA 1917.352539 233.433151
SNP_A-2000230 AA 0.012863 AA 3347.252686 1373.303101
SNP_A-2000332 AB 0.004455 AB 2620.238281 3117.408447
SNP_A-2000337 AA 0.007849 AA 1352.421387 265.754578
SNP_A-2000342 AA 0.013558 AA 5095.929199 1200.944336
SNP_A-4268173 AA 0.016307 AA 2043.797363 372.182220

Total number of rows: 909622

Table truncated, full table size 46141 Kbytes.

Supplementary file Size Download File type/resource
GSM397718.CEL.gz 29.1 Mb (ftp)(http) CEL
GSM397718.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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