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Sample GSM397686 Query DataSets for GSM397686
Status Public on Jul 31, 2010
Title Brain-MND-0766-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 0.003115 BB 597.581421 4015.371094
SNP_A-1967418 AB 0.003241 AB 555.983215 580.950012
SNP_A-1969580 BB 0.006885 BB 1386.238281 4051.325684
SNP_A-4263484 AB 0.006037 AB 2424.431152 1706.420288
SNP_A-1978185 AA 0.002441 AA 1056.109985 298.328186
SNP_A-4264431 AB 0.007150 AB 889.803528 865.196472
SNP_A-1980898 BB 0.003767 BB 199.829346 633.875183
SNP_A-1983139 AA 0.033852 AA 6291.656738 2212.054932
SNP_A-4265735 AA 0.012119 AA 3628.045898 901.281494
SNP_A-1995832 AA 0.001458 AA 2795.392090 448.192871
SNP_A-1995893 AA 0.007680 AA 3730.104004 1728.081909
SNP_A-1997689 BB 0.000300 BB 721.776123 3976.916992
SNP_A-1997709 AA 0.003293 AA 2903.694336 344.746277
SNP_A-1997896 AA 0.005066 AA 1046.438965 456.939423
SNP_A-1997922 AA 0.001285 AA 1082.236694 279.062012
SNP_A-2000230 AA 0.005449 AA 2486.228760 1204.943726
SNP_A-2000332 AB 0.001129 AB 3006.080566 3132.537109
SNP_A-2000337 AA 0.002198 AA 1623.649780 259.222382
SNP_A-2000342 AA 0.013866 AA 4518.471191 1431.077881
SNP_A-4268173 AB 0.017401 AB 343.220612 326.373016

Total number of rows: 909622

Table truncated, full table size 46114 Kbytes.

Supplementary file Size Download File type/resource
GSM397686.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM397686.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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