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Sample GSM397817 Query DataSets for GSM397817
Status Public on Jul 31, 2010
Title Blood-Ctrl-1422-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 4 / Mother
twin #: NA
twin info: NA
gender: F
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 0.005807 BB 589.447144 4981.282227
SNP_A-1967418 BB 0.004459 BB 248.091522 842.447571
SNP_A-1969580 BB 0.003362 BB 1245.559814 4528.530762
SNP_A-4263484 AB 0.007529 AB 1545.563354 965.189392
SNP_A-1978185 AA 0.001975 AA 1498.079102 340.570435
SNP_A-4264431 AB 0.002655 AB 1311.858765 1046.716553
SNP_A-1980898 AB 0.010248 AB 836.890137 660.987000
SNP_A-1983139 AA 0.004260 AA 4134.460938 1131.751465
SNP_A-4265735 AB 0.006219 AB 1357.085205 1577.248535
SNP_A-1995832 BB 0.002279 BB 515.718201 2056.072998
SNP_A-1995893 BB 0.009563 BB 527.993591 2569.979736
SNP_A-1997689 BB 0.001341 BB 750.980835 3791.390137
SNP_A-1997709 AA 0.004090 AA 1627.370361 225.020126
SNP_A-1997896 AA 0.003080 AA 1198.316040 359.176117
SNP_A-1997922 BB 0.017660 BB 468.785889 905.255920
SNP_A-2000230 AA 0.003222 AA 2707.655029 1202.223267
SNP_A-2000332 AA 0.006553 AA 4423.722168 819.581177
SNP_A-2000337 AA 0.004970 AA 1694.941528 207.105362
SNP_A-2000342 AA 0.005438 AA 4508.527832 920.745605
SNP_A-4268173 AA 0.005750 AA 1724.239258 300.830902

Total number of rows: 909622

Table truncated, full table size 46138 Kbytes.

Supplementary file Size Download File type/resource
GSM397817.CEL.gz 31.2 Mb (ftp)(http) CEL
GSM397817.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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