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Sample GSM397729 Query DataSets for GSM397729
Status Public on Jul 31, 2010
Title Brain-MND-1140-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 0.015523 BB 588.995300 3213.034424
SNP_A-1967418 BB 0.003662 BB 295.451904 693.877319
SNP_A-1969580 BB 0.005043 BB 1123.337524 3537.888184
SNP_A-4263484 BB 0.020116 BB 384.277405 1470.151245
SNP_A-1978185 AA 0.001759 AA 1487.807251 360.710938
SNP_A-4264431 AB 0.005104 AB 1006.980530 778.943359
SNP_A-1980898 BB 0.009210 BB 264.720154 627.591675
SNP_A-1983139 AA 0.003744 AA 4766.836426 1416.847412
SNP_A-4265735 AB 0.003893 AB 1492.011108 1706.025024
SNP_A-1995832 AB 0.000688 AB 1796.432861 1396.223877
SNP_A-1995893 AB 0.003607 AB 1794.344238 1890.959839
SNP_A-1997689 BB 0.005669 BB 891.520752 3780.559570
SNP_A-1997709 AA 0.000787 AA 2289.960449 290.208893
SNP_A-1997896 AA 0.005842 AA 1538.723389 661.371521
SNP_A-1997922 AB 0.004416 AB 848.744690 593.622314
SNP_A-2000230 AA 0.003931 AA 2867.364990 1237.867798
SNP_A-2000332 AB 0.002929 AB 2721.815918 3147.422607
SNP_A-2000337 AA 0.016057 AA 1208.590088 331.709015
SNP_A-2000342 AA 0.004591 AA 3908.975098 1128.582153
SNP_A-4268173 AA 0.000593 AA 1292.274536 231.055664

Total number of rows: 909622

Table truncated, full table size 46134 Kbytes.




Supplementary file Size Download File type/resource
GSM397729.CEL.gz 30.0 Mb (ftp)(http) CEL
GSM397729.CHP.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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