GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM397831 Query DataSets for GSM397831
Status Public on Jul 31, 2010
Title Blood-Ctrl-2006-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 9 / Mother
twin #: NA
twin info: NA
gender: F
phenotype: Ctrl
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 Ctrl 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 AA 0.006594 AA 4979.388184 887.018250
SNP_A-1967418 BB 0.000857 BB 258.297485 702.873108
SNP_A-1969580 BB 0.007915 BB 1362.278809 4900.616699
SNP_A-4263484 BB 0.008695 BB 491.762695 1761.518677
SNP_A-1978185 AA 0.002562 AA 1427.538330 279.111816
SNP_A-4264431 AA 0.006182 AA 2208.583496 285.645447
SNP_A-1980898 AB 0.000796 AB 643.052795 548.342773
SNP_A-1983139 AA 0.003273 AA 4131.230469 972.289368
SNP_A-4265735 AB 0.002779 AB 1660.145020 1676.596069
SNP_A-1995832 BB 0.002936 BB 492.098175 2430.026367
SNP_A-1995893 BB 0.002728 BB 380.392090 2708.255859
SNP_A-1997689 BB 0.006298 BB 814.253662 3480.891113
SNP_A-1997709 AA 0.009475 AA 1243.743286 248.541901
SNP_A-1997896 AB 0.004700 AB 768.871277 1328.606079
SNP_A-1997922 AB 0.008168 AB 533.768005 575.995422
SNP_A-2000230 AA 0.002527 AA 2605.463135 1147.791138
SNP_A-2000332 AA 0.002956 AA 3782.503662 893.087952
SNP_A-2000337 AA 0.002802 AA 1998.744141 270.401825
SNP_A-2000342 AA 0.001815 AA 4183.462402 1125.417114
SNP_A-4268173 AA 0.002794 AA 1515.986694 237.980988

Total number of rows: 909622

Table truncated, full table size 46135 Kbytes.

Supplementary file Size Download File type/resource
GSM397831.CEL.gz 30.6 Mb (ftp)(http) CEL
GSM397831.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