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Sample GSM397814 Query DataSets for GSM397814
Status Public on Jul 31, 2010
Title Blood-Ctrl-0896-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 3 / Mother
twin #: NA
twin info: NA
gender: F
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 0.005115 BB 574.986694 3791.823242
SNP_A-1967418 BB 0.002392 BB 295.071533 810.237671
SNP_A-1969580 BB 0.002259 BB 1015.514282 4015.916016
SNP_A-4263484 AB 0.003673 AB 1749.490234 1142.887817
SNP_A-1978185 AA 0.001174 AA 1244.644897 360.438690
SNP_A-4264431 AB 0.004434 AB 1296.616699 1104.779663
SNP_A-1980898 BB 0.011259 BB 224.565155 1143.867554
SNP_A-1983139 AA 0.003640 AA 4082.201660 982.690552
SNP_A-4265735 AA 0.005028 AA 2347.676025 474.931885
SNP_A-1995832 BB 0.005907 BB 425.312988 1784.154053
SNP_A-1995893 BB 0.012526 BB 454.851471 3476.226074
SNP_A-1997689 BB 0.001303 BB 749.707825 3793.779785
SNP_A-1997709 AA 0.005542 AA 1449.122559 218.750107
SNP_A-1997896 AB 0.005789 AB 1254.565796 1703.605225
SNP_A-1997922 AB 0.006326 AB 859.069824 819.649536
SNP_A-2000230 AA 0.005014 AA 2618.135742 1238.197998
SNP_A-2000332 AA 0.002721 AA 4103.522949 1060.072754
SNP_A-2000337 AA 0.011707 AA 1268.086792 230.359726
SNP_A-2000342 AA 0.000417 AA 4252.825684 1062.896240
SNP_A-4268173 AB 0.001575 AB 870.386475 693.488098

Total number of rows: 909622

Table truncated, full table size 46134 Kbytes.

Supplementary file Size Download File type/resource
GSM397814.CEL.gz 30.0 Mb (ftp)(http) CEL
GSM397814.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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