GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM397838 Query DataSets for GSM397838
Status Public on Jul 31, 2010
Title Blood-Ctrl-2247-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 12 / 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 BB 0.006608 BB 431.774811 3756.419189
SNP_A-1967418 BB 0.002328 BB 256.006409 806.349426
SNP_A-1969580 BB 0.001866 BB 1047.377930 4078.662109
SNP_A-4263484 AB 0.005535 AB 2041.965088 1254.211792
SNP_A-1978185 AA 0.001178 AA 1221.476685 352.817474
SNP_A-4264431 AB 0.003162 AB 1027.241089 900.635498
SNP_A-1980898 BB 0.008398 BB 186.170090 976.211853
SNP_A-1983139 AA 0.004083 AA 4031.437744 939.138367
SNP_A-4265735 AB 0.002540 AB 1664.178833 1692.931152
SNP_A-1995832 BB 0.013656 BB 521.769592 1624.042480
SNP_A-1995893 BB 0.001267 BB 490.458038 2869.685059
SNP_A-1997689 BB 0.002929 BB 638.347351 4087.071045
SNP_A-1997709 AA 0.003377 AA 1768.697266 273.942291
SNP_A-1997896 AA 0.008293 AA 1284.044434 674.640076
SNP_A-1997922 BB 0.004378 BB 431.757416 953.092407
SNP_A-2000230 AA 0.003688 AA 3073.315430 1143.546021
SNP_A-2000332 AA 0.006413 AA 3564.841309 844.372925
SNP_A-2000337 AA 0.007804 AA 2117.039795 342.676819
SNP_A-2000342 AA 0.000387 AA 4258.368652 1036.621216
SNP_A-4268173 AA 0.002456 AA 1151.270630 212.831085

Total number of rows: 909622

Table truncated, full table size 46128 Kbytes.

Supplementary file Size Download File type/resource
GSM397838.CEL.gz 28.3 Mb (ftp)(http) CEL
GSM397838.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