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Sample GSM397681 Query DataSets for GSM397681
Status Public on Jul 31, 2010
Title Blood-MND-0556-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 BB 0.005252 BB 508.746826 3774.517334
SNP_A-1967418 AB 0.000404 AB 578.477478 524.537231
SNP_A-1969580 AB 0.008606 AB 2794.321289 2541.890869
SNP_A-4263484 BB 0.000531 BB 477.927002 2056.731689
SNP_A-1978185 AA 0.001848 AA 1190.556885 262.669037
SNP_A-4264431 AA 0.002786 AA 2072.316162 317.519653
SNP_A-1980898 BB 0.000640 BB 235.791489 796.732666
SNP_A-1983139 AA 0.000219 AA 4658.017578 1152.612183
SNP_A-4265735 BB 0.001147 BB 668.725830 2877.236816
SNP_A-1995832 AA 0.003219 AA 2562.939453 388.801575
SNP_A-1995893 AA 0.001643 AA 3168.088623 1174.795776
SNP_A-1997689 BB 0.002875 BB 611.265564 3847.735107
SNP_A-1997709 AA 0.006824 AA 3174.855957 344.202515
SNP_A-1997896 AA 0.006670 AA 1643.942749 466.117950
SNP_A-1997922 AA 0.000130 AA 1008.553589 247.861816
SNP_A-2000230 AA 0.004928 AA 2336.854248 897.689087
SNP_A-2000332 AA 0.004998 AA 3669.637939 810.912354
SNP_A-2000337 AA 0.002426 AA 1929.810547 306.461548
SNP_A-2000342 AA 0.007846 AA 4814.783691 1237.295532
SNP_A-4268173 AB 0.002771 AB 755.810974 582.699646

Total number of rows: 909622

Table truncated, full table size 46136 Kbytes.

Supplementary file Size Download File type/resource
GSM397681.CEL.gz 30.1 Mb (ftp)(http) CEL
GSM397681.CHP.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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