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Sample GSM397798 Query DataSets for GSM397798
Status Public on Jul 31, 2010
Title Blood-Ctrl-1928-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 5
twin info: Monozygotic Control
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 0.010678 BB 921.214844 4373.899902
SNP_A-1967418 BB 0.002555 BB 285.033630 830.403015
SNP_A-1969580 BB 0.002116 BB 1111.130493 4269.930176
SNP_A-4263484 BB 0.001054 BB 576.484375 2133.593506
SNP_A-1978185 AA 0.002681 AA 1037.537598 295.179504
SNP_A-4264431 AA 0.009671 AA 2372.597168 303.243835
SNP_A-1980898 BB 0.008119 BB 210.468094 1050.841797
SNP_A-1983139 AA 0.005162 AA 4487.071777 843.365540
SNP_A-4265735 AB 0.005363 AB 1403.393188 1635.857178
SNP_A-1995832 AB 0.007166 AB 1348.918213 1029.958740
SNP_A-1995893 AB 0.001830 AB 1806.668701 2033.630249
SNP_A-1997689 BB 0.000468 BB 750.773987 3922.041016
SNP_A-1997709 AA 0.001441 AA 2048.211426 290.210297
SNP_A-1997896 AB 0.002373 AB 855.444580 1511.694458
SNP_A-1997922 AA 0.001873 AA 1114.939819 289.346130
SNP_A-2000230 AA 0.001679 AA 2747.984863 1147.127075
SNP_A-2000332 AB 0.009760 AB 2679.030029 2493.038330
SNP_A-2000337 AA 0.002305 AA 1867.229858 313.665344
SNP_A-2000342 AA 0.007179 AA 4652.568848 941.908203
SNP_A-4268173 AA 0.002139 AA 1480.457886 236.943329

Total number of rows: 909622

Table truncated, full table size 46132 Kbytes.

Supplementary file Size Download File type/resource
GSM397798.CEL.gz 29.9 Mb (ftp)(http) CEL
GSM397798.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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