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Sample GSM397811 Query DataSets for GSM397811
Status Public on Jul 31, 2010
Title Blood-Ctrl-0834-rep2
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 2 / Father Replicate
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 0.002556 AB 2674.862793 2640.373535
SNP_A-1967418 AB 0.000406 AB 575.970703 522.618042
SNP_A-1969580 BB 0.007593 BB 818.730835 3349.155518
SNP_A-4263484 BB 0.001217 BB 477.820129 2118.733154
SNP_A-1978185 AA 0.002187 AA 1384.764526 408.670227
SNP_A-4264431 AA 0.002360 AA 1783.312134 247.305832
SNP_A-1980898 AB 0.001423 AB 642.711426 503.722107
SNP_A-1983139 AA 0.001716 AA 4590.795410 1254.725098
SNP_A-4265735 AB 0.003305 AB 2154.350098 2189.620850
SNP_A-1995832 AA 0.002199 AA 2904.448486 323.259186
SNP_A-1995893 AA 0.011178 AA 2902.849854 1431.839966
SNP_A-1997689 BB 0.001755 BB 652.095581 3827.132324
SNP_A-1997709 AA 0.013261 AA 3334.362061 313.004730
SNP_A-1997896 AA 0.000344 AA 1308.211060 483.455475
SNP_A-1997922 AA 0.001619 AA 926.823914 239.032089
SNP_A-2000230 AA 0.014655 AA 3031.194336 1467.025024
SNP_A-2000332 AA 0.013307 AA 4038.256836 1264.368408
SNP_A-2000337 AA 0.005832 AA 1750.105591 354.064972
SNP_A-2000342 AA 0.002543 AA 3995.719482 918.614075
SNP_A-4268173 AA 0.005008 AA 1065.040771 232.454468

Total number of rows: 909622

Table truncated, full table size 46122 Kbytes.

Supplementary file Size Download File type/resource
GSM397811.CEL.gz 28.3 Mb (ftp)(http) CEL
GSM397811.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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