GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM397836 Query DataSets for GSM397836
Status Public on Jul 31, 2010
Title Blood-Ctrl-2124-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 10 / 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 AB 0.001991 AB 3078.754883 3237.967285
SNP_A-1967418 AB 0.001140 AB 591.529785 494.883667
SNP_A-1969580 BB 0.007956 BB 960.169434 3213.422119
SNP_A-4263484 BB 0.003635 BB 668.840576 2400.644775
SNP_A-1978185 AA 0.003226 AA 1022.916687 327.756866
SNP_A-4264431 AA 0.004238 AA 1465.033691 259.463989
SNP_A-1980898 AB 0.016042 AB 444.742401 240.095657
SNP_A-1983139 AA 0.005325 AA 5354.409180 1225.983032
SNP_A-4265735 AA 0.004092 AA 2536.439697 587.569885
SNP_A-1995832 AB 0.002858 AB 1670.203369 1443.514038
SNP_A-1995893 AB 0.008418 AB 2510.798096 2604.336670
SNP_A-1997689 BB 0.019156 BB 1001.799316 3402.913086
SNP_A-1997709 AA 0.006211 AA 3156.276123 349.166443
SNP_A-1997896 AB 0.010179 AB 708.150085 1038.162354
SNP_A-1997922 NC 0.485007 AB 738.876404 360.595032
SNP_A-2000230 AA 0.003939 AA 2468.040527 1141.138184
SNP_A-2000332 AA 0.001944 AA 4130.549316 1034.681519
SNP_A-2000337 AA 0.001834 AA 1920.429688 294.908417
SNP_A-2000342 AA 0.002006 AA 3993.363281 1050.841431
SNP_A-4268173 AA 0.036142 AA 665.331726 178.829437

Total number of rows: 909622

Table truncated, full table size 46106 Kbytes.

Supplementary file Size Download File type/resource
GSM397836.CEL.gz 28.8 Mb (ftp)(http) CEL
GSM397836.chp.gz 12.9 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