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Sample GSM397799 Query DataSets for GSM397799
Status Public on Jul 31, 2010
Title Blood-MND-1954-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 6
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 BB 0.005205 BB 516.887512 3774.089111
SNP_A-1967418 BB 0.001004 BB 272.663483 718.765808
SNP_A-1969580 BB 0.006836 BB 912.343567 4140.117676
SNP_A-4263484 BB 0.001214 BB 442.302155 2044.696899
SNP_A-1978185 AA 0.005145 AA 1652.118652 308.120117
SNP_A-4264431 AA 0.004767 AA 1624.001221 206.812515
SNP_A-1980898 BB 0.001517 BB 216.703842 731.580811
SNP_A-1983139 AA 0.004797 AA 4481.927734 856.099304
SNP_A-4265735 AB 0.001540 AB 1840.764038 2046.424194
SNP_A-1995832 AB 0.002430 AB 1718.728149 1471.836182
SNP_A-1995893 AB 0.009001 AB 1764.075562 2421.783203
SNP_A-1997689 BB 0.006033 BB 644.089355 4388.149414
SNP_A-1997709 AA 0.001908 AA 2205.082764 262.595093
SNP_A-1997896 AA 0.004120 AA 1118.201782 501.774628
SNP_A-1997922 AA 0.016040 AA 839.598511 286.667236
SNP_A-2000230 AA 0.001860 AA 2907.929199 1035.193481
SNP_A-2000332 AA 0.002453 AA 3961.246826 1015.776672
SNP_A-2000337 AA 0.002176 AA 1703.107544 308.708771
SNP_A-2000342 AA 0.005095 AA 3995.719482 823.060486
SNP_A-4268173 BB 0.010016 BB 270.648438 1452.486938

Total number of rows: 909622

Table truncated, full table size 46132 Kbytes.

Supplementary file Size Download File type/resource
GSM397799.CEL.gz 28.1 Mb (ftp)(http) CEL
GSM397799.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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