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Sample GSM397819 Query DataSets for GSM397819
Status Public on Jul 31, 2010
Title Blood-MND-1522-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 6 / 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 BB 0.003680 BB 567.355164 3938.961182
SNP_A-1967418 BB 0.001762 BB 270.100830 688.207031
SNP_A-1969580 BB 0.002733 BB 973.661438 3872.239014
SNP_A-4263484 AB 0.001719 AB 1812.181274 1243.019043
SNP_A-1978185 AA 0.006850 AA 1807.894165 397.646057
SNP_A-4264431 AB 0.000935 AB 1276.052246 959.703552
SNP_A-1980898 BB 0.001935 BB 205.887985 826.717529
SNP_A-1983139 AA 0.009375 AA 5280.912598 1021.750916
SNP_A-4265735 AA 0.003534 AA 2867.214600 484.137573
SNP_A-1995832 AB 0.002284 AB 1639.999512 1276.052246
SNP_A-1995893 AB 0.004012 AB 1654.106323 1912.824463
SNP_A-1997689 BB 0.005464 BB 543.153198 3849.335938
SNP_A-1997709 AA 0.000671 AA 2267.219727 316.701508
SNP_A-1997896 AA 0.003684 AA 1564.664795 509.683136
SNP_A-1997922 AB 0.002493 AB 711.182861 706.559143
SNP_A-2000230 AA 0.014477 AA 3474.836670 1003.253784
SNP_A-2000332 AA 0.007363 AA 4209.536133 1189.779419
SNP_A-2000337 AA 0.004830 AA 1822.781494 207.743073
SNP_A-2000342 AA 0.011549 AA 4838.676270 938.090393
SNP_A-4268173 AA 0.005923 AA 1547.330444 200.354599

Total number of rows: 909622

Table truncated, full table size 46133 Kbytes.

Supplementary file Size Download File type/resource
GSM397819.CEL.gz 28.4 Mb (ftp)(http) CEL
GSM397819.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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