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Sample GSM397828 Query DataSets for GSM397828
Status Public on Jul 31, 2010
Title Blood-Ctrl-1932-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 6 / 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 BB 0.015602 BB 1029.468140 4609.598633
SNP_A-1967418 BB 0.005201 BB 246.990997 590.594238
SNP_A-1969580 BB 0.007164 BB 880.161865 3278.956055
SNP_A-4263484 BB 0.016935 BB 432.498230 1559.713013
SNP_A-1978185 AA 0.001171 AA 1174.616577 325.272614
SNP_A-4264431 AB 0.002591 AB 1215.114746 834.887512
SNP_A-1980898 AB 0.000754 AB 621.279968 555.021973
SNP_A-1983139 AA 0.008597 AA 4397.535645 714.465210
SNP_A-4265735 AA 0.015317 AA 2201.639160 588.467834
SNP_A-1995832 AB 0.004900 AB 1585.837524 1066.778564
SNP_A-1995893 AB 0.024626 AB 1159.725952 1259.191406
SNP_A-1997689 BB 0.007131 BB 711.393555 3292.679443
SNP_A-1997709 AA 0.008699 AA 1428.653809 283.392090
SNP_A-1997896 AA 0.005381 AA 1643.017212 552.310120
SNP_A-1997922 AB 0.006188 AB 723.073242 772.081543
SNP_A-2000230 AA 0.015929 AA 3013.444580 713.089050
SNP_A-2000332 AA 0.013660 AA 3628.029297 588.390381
SNP_A-2000337 AA 0.014029 AA 1202.278687 234.807343
SNP_A-2000342 AA 0.001312 AA 4380.052246 1074.798584
SNP_A-4268173 AA 0.002352 AA 1474.657227 307.831085

Total number of rows: 909622

Table truncated, full table size 46141 Kbytes.

Supplementary file Size Download File type/resource
GSM397828.CEL.gz 29.6 Mb (ftp)(http) CEL
GSM397828.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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