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Sample GSM397684 Query DataSets for GSM397684
Status Public on Jul 31, 2010
Title Brain-MND-0754-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: 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 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 0.002841 BB 560.768127 4536.953125
SNP_A-1967418 AB 0.002930 AB 547.380554 445.527374
SNP_A-1969580 BB 0.001033 BB 1163.929810 4226.959961
SNP_A-4263484 AB 0.001283 AB 1852.845215 1406.083252
SNP_A-1978185 AA 0.001266 AA 1344.192871 293.804871
SNP_A-4264431 AA 0.002859 AA 1815.215942 241.014236
SNP_A-1980898 AB 0.001585 AB 547.380554 482.384979
SNP_A-1983139 AA 0.001888 AA 4696.189453 1046.410400
SNP_A-4265735 AA 0.003382 AA 2859.829834 484.815002
SNP_A-1995832 BB 0.001768 BB 518.641296 2095.840576
SNP_A-1995893 BB 0.002852 BB 416.444214 2672.061768
SNP_A-1997689 BB 0.004062 BB 684.615479 4325.056152
SNP_A-1997709 AA 0.007202 AA 1925.223633 177.990524
SNP_A-1997896 AB 0.001456 AB 1065.119263 1535.204102
SNP_A-1997922 AB 0.012867 AB 733.224548 825.863708
SNP_A-2000230 AA 0.011204 AA 3445.488037 1130.385864
SNP_A-2000332 AA 0.007091 AA 3747.907471 701.767090
SNP_A-2000337 AA 0.005240 AA 1959.844727 215.616562
SNP_A-2000342 AA 0.005784 AA 3849.343262 816.696411
SNP_A-4268173 AB 0.006732 AB 1049.923462 955.709351

Total number of rows: 909622

Table truncated, full table size 46131 Kbytes.

Supplementary file Size Download File type/resource
GSM397684.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM397684.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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