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Sample GSM397789 Query DataSets for GSM397789
Status Public on Jul 31, 2010
Title Blood-MND-1900-rep2
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 4 Replicate
twin info: Monozygotic Discordant for MND
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 0.016576 AB 1892.877563 1886.460449
SNP_A-1967418 AB 0.009807 AB 767.332153 607.520630
SNP_A-1969580 BB 0.009217 BB 969.786926 3149.336914
SNP_A-4263484 AB 0.002471 AB 2023.014771 1337.091919
SNP_A-1978185 AB 0.010007 AB 1130.553833 1901.626709
SNP_A-4264431 AB 0.000494 AB 1245.465454 953.814880
SNP_A-1980898 AB 0.004552 AB 697.627930 496.570496
SNP_A-1983139 AB 0.005181 AB 2892.300781 2974.822021
SNP_A-4265735 AA 0.002130 AA 2627.538574 577.794617
SNP_A-1995832 BB 0.003307 BB 595.453613 2091.903076
SNP_A-1995893 BB 0.002149 BB 536.241516 3215.881348
SNP_A-1997689 BB 0.007142 BB 535.448669 3452.716797
SNP_A-1997709 AA 0.006099 AA 1409.990967 229.494400
SNP_A-1997896 AA 0.009333 AA 1769.525513 566.390991
SNP_A-1997922 BB 0.002114 BB 539.931274 1236.068604
SNP_A-2000230 AA 0.001972 AA 2864.291016 996.359680
SNP_A-2000332 AB 0.002174 AB 2933.616455 3252.265625
SNP_A-2000337 AA 0.003798 AA 1564.632202 240.310440
SNP_A-2000342 AA 0.020151 AA 5247.284180 1340.887329
SNP_A-4268173 AA 0.004133 AA 1654.232300 313.578461

Total number of rows: 909622

Table truncated, full table size 46125 Kbytes.

Supplementary file Size Download File type/resource
GSM397789.CEL.gz 29.9 Mb (ftp)(http) CEL
GSM397789.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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