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Sample GSM397833 Query DataSets for GSM397833
Status Public on Jul 31, 2010
Title Blood-Ctrl-2114-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 11 / Father
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 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 0.007969 AB 3427.547363 3811.985352
SNP_A-1967418 BB 0.004244 BB 224.188553 782.030457
SNP_A-1969580 BB 0.036968 BB 1271.663574 5681.493164
SNP_A-4263484 AB 0.005924 AB 2277.478516 1736.050171
SNP_A-1978185 AA 0.006600 AA 825.938416 305.671478
SNP_A-4264431 AA 0.006277 AA 2266.839600 370.699982
SNP_A-1980898 BB 0.002470 BB 269.065094 923.873718
SNP_A-1983139 AA 0.004515 AA 5287.177246 1222.633057
SNP_A-4265735 AA 0.008418 AA 3083.060059 490.087952
SNP_A-1995832 BB 0.001584 BB 530.095276 2397.895020
SNP_A-1995893 BB 0.013404 BB 658.180176 3790.957031
SNP_A-1997689 BB 0.011071 BB 658.273560 4684.166504
SNP_A-1997709 AA 0.003266 AA 1746.564209 234.930908
SNP_A-1997896 AA 0.017578 AA 1661.986938 292.230225
SNP_A-1997922 BB 0.001769 BB 535.045715 1216.053101
SNP_A-2000230 AA 0.004275 AA 2478.182861 869.565491
SNP_A-2000332 AB 0.000580 AB 2900.885742 3114.134521
SNP_A-2000337 AA 0.001721 AA 1645.444580 267.896332
SNP_A-2000342 AA 0.005635 AA 4597.868164 961.221985
SNP_A-4268173 AA 0.001125 AA 1398.603882 228.962677

Total number of rows: 909622

Table truncated, full table size 46123 Kbytes.

Supplementary file Size Download File type/resource
GSM397833.CEL.gz 29.9 Mb (ftp)(http) CEL
GSM397833.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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