GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM397726 Query DataSets for GSM397726
Status Public on Jul 31, 2010
Title Brain-MND-1100-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 AB 0.006121 AB 2265.310791 2710.798096
SNP_A-1967418 BB 0.001972 BB 264.718475 807.776428
SNP_A-1969580 BB 0.003371 BB 1010.081909 4144.849121
SNP_A-4263484 AB 0.000448 AB 1866.171387 1370.862427
SNP_A-1978185 AA 0.002075 AA 1491.291626 389.718628
SNP_A-4264431 AA 0.002747 AA 1561.729858 289.848206
SNP_A-1980898 AB 0.002810 AB 510.845184 455.395874
SNP_A-1983139 AA 0.000541 AA 4706.291992 1221.695312
SNP_A-4265735 AA 0.001397 AA 2913.567627 664.846436
SNP_A-1995832 AB 0.007468 AB 2378.489990 1922.864502
SNP_A-1995893 AB 0.004362 AB 1984.675781 2465.454346
SNP_A-1997689 BB 0.000598 BB 747.637634 4038.607910
SNP_A-1997709 AA 0.003287 AA 2206.401123 242.034317
SNP_A-1997896 AA 0.001595 AA 1453.911987 504.203644
SNP_A-1997922 AB 0.004733 AB 809.860596 788.966003
SNP_A-2000230 AA 0.005175 AA 2407.256348 853.022766
SNP_A-2000332 AA 0.005239 AA 4197.975586 1141.084473
SNP_A-2000337 AA 0.002857 AA 1574.598145 283.037231
SNP_A-2000342 AA 0.004710 AA 4652.568848 1054.658081
SNP_A-4268173 AA 0.000192 AA 1347.064209 237.481232

Total number of rows: 909622

Table truncated, full table size 46125 Kbytes.

Supplementary file Size Download File type/resource
GSM397726.CEL.gz 27.6 Mb (ftp)(http) CEL
GSM397726.CHP.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap