GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM397687 Query DataSets for GSM397687
Status Public on Jul 31, 2010
Title Blood-MND-0794-rep1
Sample type genomic
Source name MND Blood
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 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 BB 0.022896 BB 935.493958 6359.643555
SNP_A-1967418 BB 0.002919 BB 261.527405 647.041321
SNP_A-1969580 BB 0.042463 BB 1912.578369 5657.615723
SNP_A-4263484 BB 0.002403 BB 489.026733 2193.537842
SNP_A-1978185 AA 0.002866 AA 1527.824707 313.550385
SNP_A-4264431 AB 0.002366 AB 1096.287354 969.523621
SNP_A-1980898 AB 0.004070 AB 720.385010 641.485718
SNP_A-1983139 AA 0.004214 AA 4648.172852 1398.188354
SNP_A-4265735 BB 0.006828 BB 733.241516 2616.104736
SNP_A-1995832 AB 0.045598 AB 3165.096680 2592.014404
SNP_A-1995893 AB 0.001127 AB 1873.222778 2084.081543
SNP_A-1997689 BB 0.009632 BB 671.436157 3146.759277
SNP_A-1997709 AA 0.014486 AA 2335.985352 456.354156
SNP_A-1997896 AA 0.004493 AA 1380.490845 350.335419
SNP_A-1997922 AB 0.001037 AB 679.036743 587.447937
SNP_A-2000230 AA 0.000802 AA 2792.028809 1099.644775
SNP_A-2000332 AB 0.004951 AB 3256.018066 3203.460449
SNP_A-2000337 AA 0.004200 AA 1890.080078 336.676819
SNP_A-2000342 AA 0.012992 AA 4110.375488 1369.500977
SNP_A-4268173 AA 0.014068 AA 1958.531128 315.331543

Total number of rows: 909622

Table truncated, full table size 46130 Kbytes.

Supplementary file Size Download File type/resource
GSM397687.CEL.gz 30.1 Mb (ftp)(http) CEL
GSM397687.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