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Sample GSM397725 Query DataSets for GSM397725
Status Public on Jul 31, 2010
Title Brain-MND-1095-rep1
Sample type genomic
 
Source name MND Brain (Brodmann area 46)
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
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 Brain (Brodmann area 46)
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 0.009485 AB 3388.199951 3963.706787
SNP_A-1967418 BB 0.012480 BB 265.730225 975.816833
SNP_A-1969580 BB 0.003260 BB 1011.003113 3589.616943
SNP_A-4263484 AB 0.000805 AB 1887.853149 1406.483154
SNP_A-1978185 AA 0.001426 AA 1456.156250 346.471558
SNP_A-4264431 AA 0.001248 AA 1682.066895 288.270935
SNP_A-1980898 BB 0.011049 BB 216.774429 511.102997
SNP_A-1983139 AA 0.001815 AA 5054.224609 1270.671875
SNP_A-4265735 AA 0.001982 AA 3017.576660 689.771545
SNP_A-1995832 AB 0.011152 AB 2594.522217 1941.520020
SNP_A-1995893 AB 0.001743 AB 2138.893799 2367.573486
SNP_A-1997689 BB 0.005324 BB 896.003601 4346.544922
SNP_A-1997709 AA 0.001208 AA 2624.959961 348.613770
SNP_A-1997896 AA 0.001868 AA 1251.807739 396.345764
SNP_A-1997922 AB 0.000810 AB 724.070862 662.754089
SNP_A-2000230 AA 0.000795 AA 2625.800049 1029.127197
SNP_A-2000332 AB 0.002258 AB 3100.821045 3119.346436
SNP_A-2000337 AA 0.001265 AA 1680.398071 281.607300
SNP_A-2000342 AA 0.002253 AA 4426.064941 1011.003113
SNP_A-4268173 AA 0.003018 AA 1400.623413 194.611298

Total number of rows: 909622

Table truncated, full table size 46128 Kbytes.




Supplementary file Size Download File type/resource
GSM397725.CEL.gz 29.3 Mb (ftp)(http) CEL
GSM397725.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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