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Sample GSM397791 Query DataSets for GSM397791
Status Public on Jul 31, 2010
Title Sperm-MND-1900-rep1
Sample type genomic
Source name MND Sperm
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 4
twin info: Monozygotic Discordant for MND
gender: M
phenotype: MND
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 MND Sperm
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 0.001995 AB 2862.174561 2806.719727
SNP_A-1967418 AB 0.009572 AB 760.757141 596.926819
SNP_A-1969580 BB 0.008741 BB 1194.790527 4835.357422
SNP_A-4263484 AB 0.001034 AB 1950.253662 1347.068359
SNP_A-1978185 AB 0.005238 AB 949.483521 1514.512695
SNP_A-4264431 AB 0.001061 AB 1135.027344 915.772583
SNP_A-1980898 AB 0.000658 AB 599.687561 497.252869
SNP_A-1983139 AB 0.002807 AB 2584.793945 2176.179688
SNP_A-4265735 AA 0.001014 AA 2659.718018 508.192352
SNP_A-1995832 BB 0.008437 BB 558.254517 1816.877197
SNP_A-1995893 BB 0.000982 BB 448.435211 2952.765625
SNP_A-1997689 BB 0.003869 BB 581.761169 3801.646729
SNP_A-1997709 AA 0.004624 AA 1577.114380 212.004959
SNP_A-1997896 AA 0.001921 AA 1401.976074 430.757660
SNP_A-1997922 BB 0.017046 BB 445.666107 889.194458
SNP_A-2000230 AA 0.018315 AA 3662.298096 1197.909912
SNP_A-2000332 AB 0.004232 AB 2680.922119 3196.902588
SNP_A-2000337 AA 0.005136 AA 2012.881592 226.177353
SNP_A-2000342 AA 0.003419 AA 4477.298340 980.492126
SNP_A-4268173 AA 0.001559 AA 1396.234619 286.240143

Total number of rows: 909622

Table truncated, full table size 46125 Kbytes.

Supplementary file Size Download File type/resource
GSM397791.CEL.gz 28.6 Mb (ftp)(http) CEL
GSM397791.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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