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Sample GSM397721 Query DataSets for GSM397721
Status Public on Jul 31, 2010
Title Brain-MND-1082-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
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 0.015797 BB 364.795654 3051.431152
SNP_A-1967418 AB 0.004294 AB 694.785828 577.253357
SNP_A-1969580 BB 0.002630 BB 1199.042725 3862.000732
SNP_A-4263484 BB 0.003102 BB 574.935486 2023.476807
SNP_A-1978185 AA 0.008065 AA 1803.988281 325.330109
SNP_A-4264431 BB 0.001792 BB 356.725281 1583.262085
SNP_A-1980898 AB 0.003801 AB 675.663635 646.850525
SNP_A-1983139 AA 0.001421 AA 4408.614746 1092.764160
SNP_A-4265735 AB 0.000401 AB 1807.369751 1892.262085
SNP_A-1995832 AB 0.002332 AB 1671.444214 1233.387085
SNP_A-1995893 AB 0.004688 AB 1707.526489 2187.948242
SNP_A-1997689 BB 0.009605 BB 462.182037 3730.104004
SNP_A-1997709 AA 0.005599 AA 1700.694580 300.885254
SNP_A-1997896 AA 0.008593 AA 1695.110596 462.366180
SNP_A-1997922 AB 0.018035 AB 1051.812988 924.500427
SNP_A-2000230 AA 0.002570 AA 2988.049316 1064.383789
SNP_A-2000332 AA 0.006223 AA 3834.412842 1085.893311
SNP_A-2000337 AA 0.012724 AA 1226.281982 294.701996
SNP_A-2000342 AA 0.003541 AA 4521.776855 1180.187866
SNP_A-4268173 AA 0.009690 AA 1772.237549 408.297974

Total number of rows: 909622

Table truncated, full table size 46136 Kbytes.

Supplementary file Size Download File type/resource
GSM397721.CEL.gz 29.6 Mb (ftp)(http) CEL
GSM397721.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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