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Sample GSM397788 Query DataSets for GSM397788
Status Public on Jul 31, 2010
Title Blood-MND-1900-rep1
Sample type genomic
Source name MND Blood
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 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 0.000988 AB 2748.989746 3078.549561
SNP_A-1967418 AB 0.003868 AB 478.707642 443.542572
SNP_A-1969580 BB 0.002885 BB 987.814087 3656.693848
SNP_A-4263484 AB 0.004669 AB 1544.699829 1058.311401
SNP_A-1978185 AB 0.010169 AB 1361.504639 2093.319336
SNP_A-4264431 AB 0.002131 AB 1074.966187 905.732544
SNP_A-1980898 AB 0.002561 AB 688.385559 529.488281
SNP_A-1983139 AB 0.003430 AB 2892.598145 2354.493164
SNP_A-4265735 AA 0.009126 AA 2132.626465 414.480347
SNP_A-1995832 BB 0.001523 BB 469.247284 2102.049316
SNP_A-1995893 BB 0.011092 BB 384.042297 2289.906494
SNP_A-1997689 BB 0.002524 BB 833.328918 3935.471680
SNP_A-1997709 AA 0.003858 AA 1750.697510 215.259567
SNP_A-1997896 AA 0.001962 AA 1330.617432 401.530182
SNP_A-1997922 BB 0.000272 BB 468.290741 1133.841675
SNP_A-2000230 AA 0.000630 AA 2753.185791 1093.785522
SNP_A-2000332 AB 0.002014 AB 2832.656250 2867.609863
SNP_A-2000337 AA 0.006877 AA 2170.985596 308.056274
SNP_A-2000342 AA 0.006277 AA 3932.545410 792.550781
SNP_A-4268173 AA 0.003550 AA 1514.797485 222.690018

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.

Supplementary file Size Download File type/resource
GSM397788.CEL.gz 31.4 Mb (ftp)(http) CEL
GSM397788.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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