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Sample GSM397740 Query DataSets for GSM397740
Status Public on Jul 31, 2010
Title Brain-MND-1438-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 BB 0.006124 BB 461.380859 3735.072021
SNP_A-1967418 AB 0.003789 AB 473.404205 479.118896
SNP_A-1969580 BB 0.000655 BB 1141.911255 4154.647949
SNP_A-4263484 AB 0.002860 AB 1596.060303 1215.087769
SNP_A-1978185 AB 0.004895 AB 967.446960 1513.895996
SNP_A-4264431 AB 0.002181 AB 1075.400635 883.278931
SNP_A-1980898 BB 0.001692 BB 205.732712 800.223511
SNP_A-1983139 AA 0.002907 AA 4422.250000 932.609192
SNP_A-4265735 AA 0.002895 AA 2544.211670 408.965668
SNP_A-1995832 AB 0.001975 AB 1672.809937 1280.590576
SNP_A-1995893 AB 0.004360 AB 1636.980591 1889.909790
SNP_A-1997689 BB 0.001135 BB 689.143433 4013.818848
SNP_A-1997709 AA 0.001376 AA 2661.037109 341.249847
SNP_A-1997896 AB 0.002899 AB 848.960876 1570.040527
SNP_A-1997922 AA 0.001001 AA 953.455322 239.051605
SNP_A-2000230 AA 0.001673 AA 2533.459229 1035.194458
SNP_A-2000332 AB 0.006342 AB 2540.034424 2725.133545
SNP_A-2000337 AA 0.005477 AA 2122.855957 300.623932
SNP_A-2000342 AA 0.000925 AA 4300.872559 1019.493652
SNP_A-4268173 AA 0.000124 AA 1356.518799 241.220505

Total number of rows: 909622

Table truncated, full table size 46131 Kbytes.




Supplementary file Size Download File type/resource
GSM397740.CEL.gz 29.7 Mb (ftp)(http) CEL
GSM397740.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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