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Sample GSM397736 Query DataSets for GSM397736
Status Public on Jul 31, 2010
Title Brain-MND-1221-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: F
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
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 0.005216 BB 552.565613 4797.291016
SNP_A-1967418 BB 0.003763 BB 297.232758 696.390930
SNP_A-1969580 BB 0.004089 BB 1059.486938 3533.689209
SNP_A-4263484 AB 0.002606 AB 1649.621094 1283.654541
SNP_A-1978185 AA 0.002022 AA 1510.568726 358.541809
SNP_A-4264431 AA 0.005206 AA 1411.430908 278.966797
SNP_A-1980898 BB 0.002859 BB 217.299408 670.485718
SNP_A-1983139 AA 0.003970 AA 4044.394775 983.319824
SNP_A-4265735 AB 0.007221 AB 1396.060791 1789.570801
SNP_A-1995832 AB 0.005284 AB 1684.002319 1066.084961
SNP_A-1995893 AB 0.003108 AB 1928.050537 2364.967041
SNP_A-1997689 BB 0.007515 BB 719.247437 4597.034180
SNP_A-1997709 AA 0.003274 AA 2656.114014 296.024811
SNP_A-1997896 AB 0.003099 AB 828.834656 1379.175171
SNP_A-1997922 AA 0.000926 AA 1022.381958 222.438690
SNP_A-2000230 AA 0.001660 AA 2559.079590 1072.834961
SNP_A-2000332 AA 0.015549 AA 3740.129150 1217.159668
SNP_A-2000337 AA 0.000993 AA 1796.241943 296.024811
SNP_A-2000342 AA 0.008892 AA 4477.682617 823.467468
SNP_A-4268173 AB 0.000768 AB 760.960388 667.240540

Total number of rows: 909622

Table truncated, full table size 46129 Kbytes.

Supplementary file Size Download File type/resource
GSM397736.CEL.gz 29.4 Mb (ftp)(http) CEL
GSM397736.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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