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Sample GSM397810 Query DataSets for GSM397810
Status Public on Jul 31, 2010
Title Blood-Ctrl-0834-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 2 / 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 0.002816 AB 2564.113281 2615.771240
SNP_A-1967418 NC 0.290054 AA 679.732666 354.054932
SNP_A-1969580 BB 0.001797 BB 1104.779663 4224.007812
SNP_A-4263484 BB 0.013442 BB 473.169067 1654.398315
SNP_A-1978185 AA 0.000789 AA 1383.005859 328.767120
SNP_A-4264431 AA 0.005367 AA 2212.939697 372.117371
SNP_A-1980898 AB 0.003255 AB 568.630371 590.558472
SNP_A-1983139 AA 0.003963 AA 4060.595215 1021.912781
SNP_A-4265735 AB 0.003189 AB 1545.833130 1764.160156
SNP_A-1995832 AA 0.005256 AA 2459.833252 405.466858
SNP_A-1995893 AA 0.009539 AA 2624.110840 937.025818
SNP_A-1997689 BB 0.004925 BB 792.430115 3531.732910
SNP_A-1997709 AA 0.001628 AA 2014.887451 266.050995
SNP_A-1997896 AA 0.005388 AA 1139.990601 301.005402
SNP_A-1997922 AA 0.001454 AA 938.830261 245.765686
SNP_A-2000230 AA 0.006411 AA 3106.177246 1279.268433
SNP_A-2000332 AA 0.010817 AA 4701.643066 880.795471
SNP_A-2000337 AA 0.000243 AA 1781.222534 281.253510
SNP_A-2000342 AA 0.001717 AA 4421.432617 1058.837646
SNP_A-4268173 AA 0.003404 AA 1528.221069 230.858459

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.

Supplementary file Size Download File type/resource
GSM397810.CEL.gz 30.4 Mb (ftp)(http) CEL
GSM397810.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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