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Sample GSM397793 Query DataSets for GSM397793
Status Public on Jul 31, 2010
Title Blood-Ctrl-1901-rep2
Sample type genomic
 
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 4 Replicate
twin info: Monozygotic Discordant for MND
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
ID_REF PROBE SET NAME
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
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 AB 0.006605 AB 2322.564209 2296.976807
SNP_A-1967418 AB 0.009452 AB 548.438782 660.153992
SNP_A-1969580 BB 0.012987 BB 826.389587 2934.317139
SNP_A-4263484 AB 0.004214 AB 2087.252197 1324.668823
SNP_A-1978185 AB 0.019696 AB 1313.581909 2150.385986
SNP_A-4264431 AB 0.003356 AB 1183.244507 1056.663818
SNP_A-1980898 AB 0.000750 AB 615.111633 500.886353
SNP_A-1983139 AB 0.003872 AB 2969.252686 2920.523682
SNP_A-4265735 AA 0.000684 AA 2745.746826 585.645630
SNP_A-1995832 BB 0.002421 BB 530.426270 2060.803711
SNP_A-1995893 BB 0.000376 BB 507.321991 3026.259766
SNP_A-1997689 BB 0.001366 BB 672.763733 3810.881836
SNP_A-1997709 AA 0.009353 AA 1201.809326 234.142395
SNP_A-1997896 AA 0.011984 AA 1033.105347 593.355286
SNP_A-1997922 BB 0.003580 BB 576.560547 1287.905640
SNP_A-2000230 AA 0.008525 AA 3327.043945 1080.572754
SNP_A-2000332 AB 0.001884 AB 2940.677734 3232.504639
SNP_A-2000337 AA 0.013394 AA 1596.681396 395.271759
SNP_A-2000342 AA 0.008471 AA 4714.202637 1308.812866
SNP_A-4268173 AA 0.001176 AA 1307.609131 208.812286

Total number of rows: 909622

Table truncated, full table size 46125 Kbytes.




Supplementary file Size Download File type/resource
GSM397793.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM397793.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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