GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM397832 Query DataSets for GSM397832
Status Public on Jul 31, 2010
Title Blood-MND-2113-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 11 / Child
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 Blood
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 0.003035 AB 3143.286621 3125.804688
SNP_A-1967418 BB 0.006753 BB 233.658127 857.258240
SNP_A-1969580 BB 0.016579 BB 1658.054077 4950.803223
SNP_A-4263484 AB 0.002334 AB 1965.610229 1513.983276
SNP_A-1978185 AA 0.005529 AA 885.262695 317.146271
SNP_A-4264431 AA 0.022986 AA 2754.479004 409.782043
SNP_A-1980898 BB 0.012115 BB 273.417023 1227.589478
SNP_A-1983139 AA 0.002414 AA 4420.079590 962.183899
SNP_A-4265735 AB 0.002499 AB 1738.597900 1719.613525
SNP_A-1995832 AB 0.002633 AB 1822.517090 1239.267212
SNP_A-1995893 AB 0.002566 AB 2209.989990 2356.818848
SNP_A-1997689 BB 0.006571 BB 927.803833 4366.953613
SNP_A-1997709 AA 0.002679 AA 2020.911865 239.192566
SNP_A-1997896 AA 0.021878 AA 1929.783936 453.269073
SNP_A-1997922 AB 0.006770 AB 935.575500 739.870422
SNP_A-2000230 AA 0.003499 AA 3067.608154 1110.462891
SNP_A-2000332 AB 0.049866 AB 1913.442505 2056.349609
SNP_A-2000337 AA 0.021245 AA 2532.424805 288.958435
SNP_A-2000342 AA 0.008913 AA 3917.177979 731.657471
SNP_A-4268173 AA 0.002121 AA 1505.490723 250.154892

Total number of rows: 909622

Table truncated, full table size 46131 Kbytes.

Supplementary file Size Download File type/resource
GSM397832.CEL.gz 30.2 Mb (ftp)(http) CEL
GSM397832.chp.gz 13.1 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