GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM397697 Query DataSets for GSM397697
Status Public on Jul 31, 2010
Title Blood-MND-0899-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: F
phenotype: MND
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 MND 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 0.001326 AB 2709.955811 3069.122559
SNP_A-1967418 AB 0.014453 AB 420.806732 316.196564
SNP_A-1969580 BB 0.012601 BB 730.309204 3054.629395
SNP_A-4263484 AB 0.005517 AB 1422.974731 1043.749878
SNP_A-1978185 AA 0.016171 AA 2060.515625 339.905060
SNP_A-4264431 AA 0.002383 AA 2044.757324 318.993286
SNP_A-1980898 BB 0.005214 BB 250.221069 662.775757
SNP_A-1983139 AA 0.001628 AA 4383.825684 1105.434570
SNP_A-4265735 AB 0.004465 AB 1457.311768 1619.412842
SNP_A-1995832 AB 0.005412 AB 2335.155273 1657.576294
SNP_A-1995893 AB 0.002835 AB 1723.378662 1989.921875
SNP_A-1997689 BB 0.001402 BB 696.147705 3753.885742
SNP_A-1997709 AA 0.001649 AA 2713.728271 357.124420
SNP_A-1997896 AB 0.001723 AB 1095.538208 1662.603394
SNP_A-1997922 AA 0.000434 AA 1002.992676 233.672165
SNP_A-2000230 AA 0.005141 AA 2615.281738 832.313110
SNP_A-2000332 AB 0.001993 AB 2950.489014 3241.752441
SNP_A-2000337 AA 0.013113 AA 1283.335327 205.132294
SNP_A-2000342 AA 0.002564 AA 3978.454590 922.245667
SNP_A-4268173 AA 0.007026 AA 1741.293823 276.997131

Total number of rows: 909622

Table truncated, full table size 46134 Kbytes.

Supplementary file Size Download File type/resource
GSM397697.CEL.gz 29.6 Mb (ftp)(http) CEL
GSM397697.CHP.gz 13.0 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