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Sample GSM397813 Query DataSets for GSM397813
Status Public on Jul 31, 2010
Title Blood-MND-0895-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 3 / Child
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 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 0.007540 BB 655.290710 3725.133057
SNP_A-1967418 BB 0.004452 BB 211.270248 736.012390
SNP_A-1969580 BB 0.005307 BB 875.066162 3536.295898
SNP_A-4263484 AB 0.003639 AB 1546.218506 1210.111328
SNP_A-1978185 AA 0.002456 AA 1326.114746 256.391174
SNP_A-4264431 AB 0.043235 AB 1893.863037 1389.221191
SNP_A-1980898 BB 0.004964 BB 256.173584 1059.089478
SNP_A-1983139 AA 0.006448 AA 3791.348877 912.619873
SNP_A-4265735 AA 0.006443 AA 2238.699463 421.323517
SNP_A-1995832 BB 0.005571 BB 467.537811 1830.275269
SNP_A-1995893 BB 0.001100 BB 435.253723 2890.755371
SNP_A-1997689 BB 0.005374 BB 639.094849 3399.761963
SNP_A-1997709 AA 0.007288 AA 1352.342651 242.023132
SNP_A-1997896 AB 0.004526 AB 1108.181152 1900.597290
SNP_A-1997922 AB 0.005378 AB 862.934021 791.354370
SNP_A-2000230 AA 0.001751 AA 2533.077637 996.651306
SNP_A-2000332 AA 0.001959 AA 3964.363770 995.906494
SNP_A-2000337 AA 0.011781 AA 1438.867798 178.448929
SNP_A-2000342 AA 0.007914 AA 4257.383301 784.143555
SNP_A-4268173 AB 0.009999 AB 964.796448 1022.810303

Total number of rows: 909622

Table truncated, full table size 46137 Kbytes.

Supplementary file Size Download File type/resource
GSM397813.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM397813.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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