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Sample GSM397693 Query DataSets for GSM397693
Status Public on Jul 31, 2010
Title Blood-MND-0868-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: F
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 0.003321 BB 513.952393 4202.980957
SNP_A-1967418 AB 0.002030 AB 592.512817 479.297333
SNP_A-1969580 BB 0.004051 BB 944.210144 3976.916992
SNP_A-4263484 BB 0.014252 BB 423.403381 1588.667480
SNP_A-1978185 AA 0.000343 AA 1270.371948 335.578888
SNP_A-4264431 AB 0.002615 AB 1121.493408 827.162292
SNP_A-1980898 AB 0.001853 AB 614.324890 469.242706
SNP_A-1983139 AA 0.003057 AA 4160.653809 1024.023438
SNP_A-4265735 AB 0.002762 AB 1630.937134 1891.359497
SNP_A-1995832 BB 0.012879 BB 565.137085 1696.620850
SNP_A-1995893 BB 0.003406 BB 353.273773 2727.411133
SNP_A-1997689 BB 0.003499 BB 650.719421 4196.735840
SNP_A-1997709 AA 0.005549 AA 1566.144165 269.299622
SNP_A-1997896 BB 0.002162 BB 437.602966 2335.306885
SNP_A-1997922 AA 0.007444 AA 828.142273 246.447372
SNP_A-2000230 AA 0.001252 AA 2771.271240 1127.979614
SNP_A-2000332 AB 0.000953 AB 2827.986084 2971.328857
SNP_A-2000337 AA 0.000928 AA 1819.067993 259.431793
SNP_A-2000342 AA 0.004715 AA 3747.158691 994.009155
SNP_A-4268173 AA 0.001463 AA 1427.065796 231.056824

Total number of rows: 909622

Table truncated, full table size 46131 Kbytes.

Supplementary file Size Download File type/resource
GSM397693.CEL.gz 29.8 Mb (ftp)(http) CEL
GSM397693.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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