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Sample GSM397837 Query DataSets for GSM397837
Status Public on Jul 31, 2010
Title Blood-MND-2215-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 12 / Child
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 0.008293 BB 572.441589 3548.851318
SNP_A-1967418 BB 0.002230 BB 284.859497 819.908569
SNP_A-1969580 BB 0.003779 BB 1063.046753 4321.500488
SNP_A-4263484 AA 0.002636 AA 2715.859619 351.783325
SNP_A-1978185 AA 0.002484 AA 1526.437012 331.194794
SNP_A-4264431 AB 0.000259 AB 1201.227173 923.480103
SNP_A-1980898 AB 0.002123 AB 528.717834 489.555389
SNP_A-1983139 AA 0.005731 AA 4977.650391 989.093018
SNP_A-4265735 BB 0.001959 BB 618.283142 2791.808838
SNP_A-1995832 BB 0.019633 BB 553.862061 1536.876831
SNP_A-1995893 BB 0.003970 BB 447.177521 2635.275146
SNP_A-1997689 BB 0.003574 BB 590.190613 3838.604980
SNP_A-1997709 AA 0.003367 AA 1727.949219 234.573792
SNP_A-1997896 AB 0.002698 AB 848.265747 1541.045166
SNP_A-1997922 AB 0.000888 AB 685.979004 592.472961
SNP_A-2000230 AA 0.012042 AA 3453.853760 1077.980347
SNP_A-2000332 AB 0.002620 AB 2691.719482 3046.948975
SNP_A-2000337 AA 0.002391 AA 1601.448242 281.429626
SNP_A-2000342 AA 0.014411 AA 4708.220215 814.013611
SNP_A-4268173 AA 0.002319 AA 1159.546997 193.976288

Total number of rows: 909622

Table truncated, full table size 46135 Kbytes.

Supplementary file Size Download File type/resource
GSM397837.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM397837.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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