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Sample GSM397685 Query DataSets for GSM397685
Status Public on Jul 31, 2010
Title Blood-MND-0766-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 BB 0.008927 BB 842.090332 5662.503906
SNP_A-1967418 AB 0.006308 AB 630.095764 655.275269
SNP_A-1969580 BB 0.012099 BB 1401.393555 3775.816406
SNP_A-4263484 AB 0.009747 AB 2517.590088 1868.678589
SNP_A-1978185 AA 0.001518 AA 1135.058594 301.290833
SNP_A-4264431 AB 0.003677 AB 1403.507080 945.309814
SNP_A-1980898 BB 0.002134 BB 265.365906 872.447205
SNP_A-1983139 AA 0.004781 AA 4798.728027 1467.364746
SNP_A-4265735 AA 0.006134 AA 3347.346436 774.937805
SNP_A-1995832 AA 0.022242 AA 3825.768066 396.769287
SNP_A-1995893 AA 0.000849 AA 3291.819824 1376.218750
SNP_A-1997689 BB 0.001060 BB 760.801208 3851.380371
SNP_A-1997709 AA 0.036844 AA 4029.496094 659.430054
SNP_A-1997896 AA 0.001259 AA 1430.898560 507.645782
SNP_A-1997922 AA 0.001159 AA 971.064697 212.815308
SNP_A-2000230 AA 0.002112 AA 2947.427979 1119.867432
SNP_A-2000332 AB 0.001143 AB 2984.053711 3160.471680
SNP_A-2000337 AA 0.006726 AA 2183.076660 275.819458
SNP_A-2000342 AA 0.004590 AA 4613.196289 1195.320435
SNP_A-4268173 AB 0.005294 AB 977.134521 680.205322

Total number of rows: 909622

Table truncated, full table size 46122 Kbytes.

Supplementary file Size Download File type/resource
GSM397685.CEL.gz 30.6 Mb (ftp)(http) CEL
GSM397685.CHP.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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