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Sample GSM397835 Query DataSets for GSM397835
Status Public on Jul 31, 2010
Title Blood-Ctrl-2123-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 10 / 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 0.002672 BB 637.807495 4832.512695
SNP_A-1967418 BB 0.003559 BB 274.850677 650.864807
SNP_A-1969580 BB 0.007130 BB 1325.846069 4847.137207
SNP_A-4263484 BB 0.001698 BB 566.795532 2247.977539
SNP_A-1978185 AA 0.003506 AA 1056.166748 227.555664
SNP_A-4264431 AA 0.003107 AA 2093.869629 317.956543
SNP_A-1980898 BB 0.001817 BB 260.706818 856.696838
SNP_A-1983139 AA 0.011088 AA 5416.708496 1048.710083
SNP_A-4265735 AB 0.000675 AB 1769.161255 1862.986450
SNP_A-1995832 AB 0.002218 AB 2121.628662 1610.805786
SNP_A-1995893 AB 0.002852 AB 2137.529053 2469.323730
SNP_A-1997689 BB 0.000638 BB 704.682190 3867.351318
SNP_A-1997709 AA 0.008158 AA 2806.538330 458.773987
SNP_A-1997896 AB 0.015626 AB 1242.753906 2272.428711
SNP_A-1997922 AA 0.003693 AA 1128.691895 198.279495
SNP_A-2000230 AA 0.012740 AA 2425.199463 670.546021
SNP_A-2000332 AB 0.009019 AB 2398.187256 2979.346436
SNP_A-2000337 AA 0.006786 AA 1546.208130 203.847794
SNP_A-2000342 AA 0.000747 AA 4238.181641 1084.186279
SNP_A-4268173 AA 0.003810 AA 1500.161133 335.157196

Total number of rows: 909622

Table truncated, full table size 46123 Kbytes.

Supplementary file Size Download File type/resource
GSM397835.CEL.gz 30.9 Mb (ftp)(http) CEL
GSM397835.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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