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Sample GSM397829 Query DataSets for GSM397829
Status Public on Jul 31, 2010
Title Blood-Ctrl-1948-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 9 / 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 BB 0.003404 BB 628.259399 4884.048828
SNP_A-1967418 BB 0.000431 BB 270.183746 754.049805
SNP_A-1969580 BB 0.007088 BB 1174.043213 3495.384766
SNP_A-4263484 AB 0.004224 AB 1612.789185 1326.690430
SNP_A-1978185 AA 0.004525 AA 922.886047 300.279480
SNP_A-4264431 AA 0.002537 AA 1902.959961 258.714691
SNP_A-1980898 BB 0.003437 BB 209.573303 919.139893
SNP_A-1983139 AA 0.007005 AA 5333.620117 1130.972778
SNP_A-4265735 AB 0.000864 AB 1746.350952 1846.030151
SNP_A-1995832 AA 0.001388 AA 2704.159180 369.843750
SNP_A-1995893 AA 0.001252 AA 3225.630859 1214.192383
SNP_A-1997689 BB 0.003178 BB 854.525146 3947.142334
SNP_A-1997709 AA 0.001708 AA 2667.121094 365.752228
SNP_A-1997896 AA 0.001494 AA 1289.839844 410.089264
SNP_A-1997922 AA 0.000332 AA 1031.478271 253.699020
SNP_A-2000230 AA 0.007647 AA 2319.502930 795.173523
SNP_A-2000332 AA 0.004723 AA 4231.790527 793.253967
SNP_A-2000337 AA 0.002353 AA 1795.488525 235.577972
SNP_A-2000342 AA 0.005401 AA 4652.109863 1218.159546
SNP_A-4268173 AA 0.001363 AA 1269.065186 250.102951

Total number of rows: 909622

Table truncated, full table size 46132 Kbytes.

Supplementary file Size Download File type/resource
GSM397829.CEL.gz 30.6 Mb (ftp)(http) CEL
GSM397829.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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