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Sample GSM397816 Query DataSets for GSM397816
Status Public on Jul 31, 2010
Title Blood-Ctrl-1421-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 4 / Father
twin #: NA
twin info: NA
gender: M
phenotype: Ctrl
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 Ctrl 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 0.004139 AB 2721.533936 3365.842773
SNP_A-1967418 BB 0.001064 BB 276.266693 726.837341
SNP_A-1969580 BB 0.000794 BB 1078.575928 3962.680176
SNP_A-4263484 AB 0.006985 AB 1825.149170 1090.911499
SNP_A-1978185 AA 0.001657 AA 1175.248291 352.318634
SNP_A-4264431 AB 0.008837 AB 1175.248291 1169.319580
SNP_A-1980898 BB 0.006488 BB 243.183334 1085.192261
SNP_A-1983139 AA 0.001668 AA 4375.197754 1042.160278
SNP_A-4265735 AA 0.000791 AA 2688.639893 520.257874
SNP_A-1995832 AB 0.003837 AB 2062.662109 1755.501221
SNP_A-1995893 AB 0.001104 AB 2017.286499 2155.791016
SNP_A-1997689 BB 0.005303 BB 811.304016 4497.893555
SNP_A-1997709 AA 0.001431 AA 2048.156738 289.653290
SNP_A-1997896 AA 0.006187 AA 1668.270752 533.051025
SNP_A-1997922 AB 0.011412 AB 945.513916 890.499451
SNP_A-2000230 AA 0.003268 AA 3018.070557 1033.454834
SNP_A-2000332 AA 0.002551 AA 3923.977783 1004.119568
SNP_A-2000337 AA 0.003455 AA 1547.582153 288.942596
SNP_A-2000342 AA 0.000838 AA 4098.625488 1035.543579
SNP_A-4268173 AA 0.008828 AA 1808.319824 288.942596

Total number of rows: 909622

Table truncated, full table size 46129 Kbytes.

Supplementary file Size Download File type/resource
GSM397816.CEL.gz 30.4 Mb (ftp)(http) CEL
GSM397816.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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