GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM397787 Query DataSets for GSM397787
Status Public on Jul 31, 2010
Title Hair-Ctrl-1467-rep1
Sample type genomic
Source name Ctrl Hair
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 3
twin info: Monozygotic Control
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 Hair
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 0.004080 AB 3150.742188 2993.632324
SNP_A-1967418 BB 0.007595 BB 278.699249 928.814148
SNP_A-1969580 BB 0.028384 BB 1758.193115 5506.928223
SNP_A-4263484 AB 0.044922 AB 2744.791748 2358.569336
SNP_A-1978185 AA 0.001131 AA 1171.597046 311.329224
SNP_A-4264431 AB 0.002326 AB 1169.203979 1019.248779
SNP_A-1980898 AB 0.003804 AB 580.476990 412.324219
SNP_A-1983139 AA 0.004222 AA 5384.820312 1418.063110
SNP_A-4265735 AA 0.004645 AA 3168.069824 633.447693
SNP_A-1995832 AB 0.010175 AB 2194.224121 2018.818481
SNP_A-1995893 AB 0.007003 AB 2428.185547 2428.185547
SNP_A-1997689 BB 0.002238 BB 634.944702 3922.041016
SNP_A-1997709 AA 0.037360 AA 2877.853760 591.167603
SNP_A-1997896 AA 0.007163 AA 1143.157715 595.275818
SNP_A-1997922 AB 0.004109 AB 586.519348 586.519348
SNP_A-2000230 AA 0.000284 AA 2720.744141 1035.517456
SNP_A-2000332 AA 0.008394 AA 4700.928223 1004.960632
SNP_A-2000337 AA 0.014877 AA 2272.559814 197.551651
SNP_A-2000342 AA 0.008307 AA 4466.122559 1333.328979
SNP_A-4268173 AB 0.007636 AB 517.426941 462.204742

Total number of rows: 909622

Table truncated, full table size 46114 Kbytes.

Supplementary file Size Download File type/resource
GSM397787.CEL.gz 29.0 Mb (ftp)(http) CEL
GSM397787.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