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Sample GSM397683 Query DataSets for GSM397683
Status Public on Jul 31, 2010
Title Blood-MND-0754-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: F
phenotype: MND
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 MND 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 0.004113 BB 743.241943 5195.138184
SNP_A-1967418 AB 0.001787 AB 523.341003 500.319244
SNP_A-1969580 BB 0.003682 BB 1338.857422 4466.516602
SNP_A-4263484 AB 0.002371 AB 1718.199463 1185.437378
SNP_A-1978185 AA 0.001889 AA 1480.525513 383.662140
SNP_A-4264431 AA 0.002644 AA 1996.802124 362.577698
SNP_A-1980898 AB 0.001684 AB 627.264709 482.275635
SNP_A-1983139 AA 0.001796 AA 4822.331543 1100.168579
SNP_A-4265735 AA 0.025422 AA 3382.752930 462.622101
SNP_A-1995832 BB 0.011270 BB 537.993225 2833.004639
SNP_A-1995893 BB 0.002354 BB 588.583740 3123.421387
SNP_A-1997689 BB 0.000108 BB 737.254944 3953.863525
SNP_A-1997709 AA 0.004090 AA 1655.839478 217.313583
SNP_A-1997896 AB 0.004280 AB 1092.469727 1370.387817
SNP_A-1997922 AB 0.024582 AB 574.076233 700.914612
SNP_A-2000230 AA 0.000578 AA 2754.550293 1026.592651
SNP_A-2000332 AA 0.002342 AA 3984.506592 825.722656
SNP_A-2000337 AA 0.000738 AA 1829.672119 288.901215
SNP_A-2000342 AA 0.006658 AA 3666.230469 1038.742798
SNP_A-4268173 AB 0.003227 AB 869.692017 855.635742

Total number of rows: 909622

Table truncated, full table size 46132 Kbytes.

Supplementary file Size Download File type/resource
GSM397683.CEL.gz 28.6 Mb (ftp)(http) CEL
GSM397683.CHP.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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