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Sample GSM397781 Query DataSets for GSM397781
Status Public on Jul 31, 2010
Title Blood-MND-2146-rep1
Sample type genomic
Source name MND Blood
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 Blood
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 0.003273 AB 3167.877930 3442.439209
SNP_A-1967418 BB 0.002639 BB 299.897278 753.138489
SNP_A-1969580 BB 0.005226 BB 1404.233276 4442.243652
SNP_A-4263484 BB 0.001915 BB 552.221558 2246.088867
SNP_A-1978185 AA 0.002074 AA 1399.633911 284.367737
SNP_A-4264431 AA 0.001576 AA 1967.623169 333.890503
SNP_A-1980898 AB 0.001314 AB 655.487915 525.568115
SNP_A-1983139 AA 0.001620 AA 4684.609863 1058.201782
SNP_A-4265735 AB 0.009535 AB 2437.000732 2257.106934
SNP_A-1995832 AB 0.014200 AB 2701.529297 1937.576050
SNP_A-1995893 AB 0.007731 AB 2477.249756 2517.012451
SNP_A-1997689 BB 0.012712 BB 544.926025 4499.123047
SNP_A-1997709 AA 0.005884 AA 2960.929688 444.197174
SNP_A-1997896 AA 0.004681 AA 1170.213379 557.635559
SNP_A-1997922 AB 0.002703 AB 620.198303 603.627686
SNP_A-2000230 AA 0.003402 AA 2493.077148 903.068848
SNP_A-2000332 AA 0.001831 AA 4277.853027 933.186523
SNP_A-2000337 AA 0.002114 AA 1913.002686 252.298080
SNP_A-2000342 AA 0.006577 AA 3907.038330 786.201721
SNP_A-4268173 AA 0.000155 AA 1368.824951 246.534637

Total number of rows: 909622

Table truncated, full table size 46123 Kbytes.

Supplementary file Size Download File type/resource
GSM397781.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM397781.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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