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Sample GSM397783 Query DataSets for GSM397783
Status Public on Jul 31, 2010
Title Blood-MND-0573-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 1
twin info: Monozygotic Concordant 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 0.003851 AB 2437.140381 2561.539307
SNP_A-1967418 AB 0.005771 AB 435.983093 448.870300
SNP_A-1969580 BB 0.003436 BB 1318.149170 4171.154785
SNP_A-4263484 BB 0.000336 BB 505.417664 2068.285889
SNP_A-1978185 AA 0.014186 AA 2053.247803 387.379395
SNP_A-4264431 AA 0.001843 AA 1638.315308 301.648743
SNP_A-1980898 BB 0.004646 BB 269.638794 748.044495
SNP_A-1983139 AA 0.004101 AA 4939.795898 1035.967163
SNP_A-4265735 AA 0.013221 AA 2136.523438 513.409424
SNP_A-1995832 AB 0.003846 AB 1708.895752 1137.113159
SNP_A-1995893 AB 0.007688 AB 1488.868286 1944.461914
SNP_A-1997689 BB 0.002822 BB 841.794434 4168.760254
SNP_A-1997709 AA 0.005267 AA 2858.799805 432.746674
SNP_A-1997896 AA 0.047439 AA 1276.213745 836.871521
SNP_A-1997922 AB 0.001370 AB 745.233643 687.087280
SNP_A-2000230 AA 0.003690 AA 3029.329102 1015.141357
SNP_A-2000332 BB 0.003857 BB 1318.911865 4921.070312
SNP_A-2000337 AA 0.005325 AA 1562.859131 217.422958
SNP_A-2000342 AA 0.007021 AA 4476.070312 1304.114990
SNP_A-4268173 AA 0.001883 AA 1412.795532 217.422958

Total number of rows: 909622

Table truncated, full table size 46134 Kbytes.

Supplementary file Size Download File type/resource
GSM397783.CEL.gz 30.9 Mb (ftp)(http) CEL
GSM397783.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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