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Sample GSM397797 Query DataSets for GSM397797
Status Public on Jul 31, 2010
Title Blood-Ctrl-1927-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 0.002591 BB 635.111755 4814.783691
SNP_A-1967418 BB 0.002067 BB 289.318329 807.875061
SNP_A-1969580 BB 0.004395 BB 943.219849 4019.056641
SNP_A-4263484 BB 0.018358 BB 500.857300 2547.200928
SNP_A-1978185 AA 0.003140 AA 1095.311035 368.107727
SNP_A-4264431 AA 0.016000 AA 2494.416992 272.752502
SNP_A-1980898 BB 0.016516 BB 234.228180 1238.549194
SNP_A-1983139 AA 0.002188 AA 4404.710449 977.666931
SNP_A-4265735 AB 0.002016 AB 1637.911377 1826.349976
SNP_A-1995832 AB 0.003914 AB 1541.085815 1326.146851
SNP_A-1995893 AB 0.001254 AB 1845.246826 2100.473389
SNP_A-1997689 BB 0.006513 BB 863.818054 4541.212402
SNP_A-1997709 AA 0.002741 AA 2037.301270 238.762024
SNP_A-1997896 AB 0.001426 AB 1047.954346 1696.792236
SNP_A-1997922 AA 0.002663 AA 1156.375610 244.156662
SNP_A-2000230 AA 0.002988 AA 2976.138428 1012.781433
SNP_A-2000332 AB 0.004612 AB 2607.442627 2790.936523
SNP_A-2000337 AA 0.002672 AA 1909.525024 241.482590
SNP_A-2000342 AA 0.003802 AA 4321.500488 902.295593
SNP_A-4268173 AA 0.024442 AA 1870.554688 184.601593

Total number of rows: 909622

Table truncated, full table size 46132 Kbytes.

Supplementary file Size Download File type/resource
GSM397797.CEL.gz 30.1 Mb (ftp)(http) CEL
GSM397797.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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