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Sample GSM397734 Query DataSets for GSM397734
Status Public on Jul 31, 2010
Title Brain-MND-1188-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 0.001011 BB 629.526611 4549.352051
SNP_A-1967418 BB 0.002075 BB 262.906372 669.580444
SNP_A-1969580 BB 0.002729 BB 988.003845 3970.561035
SNP_A-4263484 BB 0.003263 BB 443.404175 1865.158691
SNP_A-1978185 AA 0.004095 AA 1608.226318 435.026764
SNP_A-4264431 AB 0.010701 AB 815.945618 901.010681
SNP_A-1980898 BB 0.002835 BB 190.563141 730.917358
SNP_A-1983139 AA 0.001355 AA 4592.213867 1051.564209
SNP_A-4265735 BB 0.008797 BB 571.691772 2383.896973
SNP_A-1995832 BB 0.002712 BB 566.693115 2086.033447
SNP_A-1995893 BB 0.004364 BB 376.412170 2556.508789
SNP_A-1997689 BB 0.002568 BB 682.573730 4184.057129
SNP_A-1997709 AA 0.001761 AA 1970.476807 271.313293
SNP_A-1997896 BB 0.001787 BB 475.415405 2133.602539
SNP_A-1997922 AA 0.005224 AA 1121.959595 169.047485
SNP_A-2000230 AA 0.003134 AA 2423.404541 960.414734
SNP_A-2000332 AA 0.004423 AA 3837.720947 1034.953735
SNP_A-2000337 AA 0.006808 AA 1771.515015 362.940918
SNP_A-2000342 AA 0.003397 AA 4560.518066 1145.330688
SNP_A-4268173 AA 0.003863 AA 1063.184937 182.233841

Total number of rows: 909622

Table truncated, full table size 46133 Kbytes.

Supplementary file Size Download File type/resource
GSM397734.CEL.gz 28.3 Mb (ftp)(http) CEL
GSM397734.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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