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Sample GSM397792 Query DataSets for GSM397792
Status Public on Jul 31, 2010
Title Blood-Ctrl-1901-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 4
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
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 AB 0.007425 AB 2177.108154 2468.113770
SNP_A-1967418 AB 0.005981 AB 519.564819 600.038452
SNP_A-1969580 BB 0.001923 BB 1019.169861 3961.181152
SNP_A-4263484 AB 0.005133 AB 1439.520874 1145.415283
SNP_A-1978185 AB 0.047592 AB 720.954590 1664.437744
SNP_A-4264431 AB 0.006872 AB 1484.381714 1109.028198
SNP_A-1980898 AB 0.016427 AB 648.877441 797.319336
SNP_A-1983139 AB 0.008778 AB 2237.108887 1764.942993
SNP_A-4265735 AA 0.005087 AA 2299.308105 412.484955
SNP_A-1995832 BB 0.000310 BB 531.072327 2270.370850
SNP_A-1995893 BB 0.001828 BB 406.687561 2799.389160
SNP_A-1997689 BB 0.004602 BB 874.396851 3822.866699
SNP_A-1997709 AA 0.008414 AA 1281.095947 241.996338
SNP_A-1997896 AA 0.007704 AA 1623.549927 416.780792
SNP_A-1997922 BB 0.002362 BB 469.349731 1246.733276
SNP_A-2000230 AA 0.006027 AA 2688.200928 814.804260
SNP_A-2000332 AB 0.015755 AB 2516.815918 3488.181396
SNP_A-2000337 AA 0.001503 AA 1704.033569 253.491913
SNP_A-2000342 AA 0.006650 AA 3623.875977 913.756226
SNP_A-4268173 AA 0.010022 AA 1855.415161 302.760590

Total number of rows: 909622

Table truncated, full table size 46137 Kbytes.

Supplementary file Size Download File type/resource
GSM397792.CEL.gz 30.0 Mb (ftp)(http) CEL
GSM397792.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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