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Sample GSM397782 Query DataSets for GSM397782
Status Public on Jul 31, 2010
Title Brain-MND-2146-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 AB 0.004249 AB 2387.462646 2577.814453
SNP_A-1967418 BB 0.003928 BB 213.952820 726.099548
SNP_A-1969580 BB 0.002644 BB 1048.318115 3659.219727
SNP_A-4263484 BB 0.014935 BB 529.185730 2535.246094
SNP_A-1978185 AA 0.002804 AA 1519.831665 311.323669
SNP_A-4264431 AA 0.003056 AA 1653.470337 234.870239
SNP_A-1980898 AB 0.001825 AB 569.485657 455.882904
SNP_A-1983139 AA 0.000767 AA 4869.214844 1228.286621
SNP_A-4265735 AB 0.001060 AB 1848.997559 2023.098145
SNP_A-1995832 AB 0.001106 AB 1873.614502 1355.527100
SNP_A-1995893 AB 0.003575 AB 1936.227417 1956.304688
SNP_A-1997689 BB 0.004918 BB 580.643250 4074.466309
SNP_A-1997709 AA 0.004275 AA 2774.350830 301.121246
SNP_A-1997896 AA 0.001152 AA 1381.891968 450.216217
SNP_A-1997922 AB 0.000521 AB 727.185181 618.599976
SNP_A-2000230 AA 0.000543 AA 2666.119629 1063.502441
SNP_A-2000332 AA 0.004323 AA 3813.395264 1019.059998
SNP_A-2000337 AA 0.001490 AA 1912.572266 285.102295
SNP_A-2000342 AA 0.001984 AA 4450.393066 1093.049072
SNP_A-4268173 AA 0.002329 AA 1184.795166 234.870239

Total number of rows: 909622

Table truncated, full table size 46124 Kbytes.

Supplementary file Size Download File type/resource
GSM397782.CEL.gz 29.4 Mb (ftp)(http) CEL
GSM397782.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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