GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM397730 Query DataSets for GSM397730
Status Public on Jul 31, 2010
Title Brain-Ctrl-1167-rep1
Sample type genomic
Source name Ctrl Brain (Brodmann area 46)
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: M
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 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 BB 0.006994 BB 768.359802 5462.218262
SNP_A-1967418 BB 0.007411 BB 228.774536 549.747192
SNP_A-1969580 BB 0.008119 BB 1211.166504 4823.659180
SNP_A-4263484 BB 0.012667 BB 599.914978 2578.630615
SNP_A-1978185 AA 0.006521 AA 817.104065 229.259750
SNP_A-4264431 AA 0.004921 AA 1456.534912 308.117432
SNP_A-1980898 AB 0.006133 AB 435.376312 411.433838
SNP_A-1983139 AA 0.022907 AA 6345.929688 1436.406738
SNP_A-4265735 AB 0.008039 AB 2408.706787 2329.988281
SNP_A-1995832 BB 0.002047 BB 627.182312 2529.190918
SNP_A-1995893 AB 0.005420 AB 2356.681885 2386.821289
SNP_A-1997689 BB 0.000846 BB 764.409668 3900.353760
SNP_A-1997709 AA 0.004877 AA 3093.953857 427.462524
SNP_A-1997896 AA 0.009503 AA 917.476685 449.251312
SNP_A-1997922 AB 0.013611 AB 472.824371 535.017151
SNP_A-2000230 AB 0.002295 AB 2018.901245 2437.958740
SNP_A-2000332 AB 0.005813 AB 3223.709229 3394.944092
SNP_A-2000337 AA 0.002498 AA 1634.633179 247.315399
SNP_A-2000342 AA 0.004804 AA 3985.388916 832.134460
SNP_A-4268173 AB 0.002948 AB 644.163452 642.479248

Total number of rows: 909622

Table truncated, full table size 46113 Kbytes.

Supplementary file Size Download File type/resource
GSM397730.CEL.gz 28.7 Mb (ftp)(http) CEL
GSM397730.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