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Sample GSM397690 Query DataSets for GSM397690
Status Public on Jul 31, 2010
Title Brain-MND-0844-rep1
Sample type genomic
Source name MND Brain (Brodmann area 46)
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 Brain (Brodmann area 46)
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 0.004926 BB 877.716492 5256.630859
SNP_A-1967418 BB 0.007753 BB 321.653442 683.791870
SNP_A-1969580 BB 0.009852 BB 1313.282715 3646.586670
SNP_A-4263484 AA 0.003330 AA 3385.273438 458.449707
SNP_A-1978185 AA 0.008789 AA 714.267761 266.258667
SNP_A-4264431 BB 0.020676 BB 383.712524 1041.952148
SNP_A-1980898 BB 0.004887 BB 225.884460 618.069214
SNP_A-1983139 AA 0.019123 AA 3401.440918 1123.340698
SNP_A-4265735 AA 0.010343 AA 3414.952881 671.719849
SNP_A-1995832 AB 0.003405 AB 2157.467041 1733.270386
SNP_A-1995893 AB 0.006802 AB 2428.927490 2451.949463
SNP_A-1997689 BB 0.006307 BB 744.609802 3369.343750
SNP_A-1997709 AA 0.006018 AA 3309.890869 418.678925
SNP_A-1997896 AB 0.005288 AB 808.898926 1206.663818
SNP_A-1997922 AA 0.018311 AA 783.800659 257.071838
SNP_A-2000230 AA 0.005387 AA 2410.295898 844.236023
SNP_A-2000332 AB 0.007979 AB 3381.828857 3264.994141
SNP_A-2000337 AA 0.001440 AA 1912.956787 277.235931
SNP_A-2000342 AA 0.018252 AA 3202.672119 964.534485
SNP_A-4268173 AB 0.002445 AB 866.491577 656.230225

Total number of rows: 909622

Table truncated, full table size 46111 Kbytes.

Supplementary file Size Download File type/resource
GSM397690.CEL.gz 29.7 Mb (ftp)(http) CEL
GSM397690.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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