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Sample GSM397818 Query DataSets for GSM397818
Status Public on Jul 31, 2010
Title Blood-MND-1483-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 7 / Child
twin #: NA
twin info: NA
gender: M
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 0.008224 BB 546.072021 3526.850586
SNP_A-1967418 AB 0.001293 AB 542.298340 486.131927
SNP_A-1969580 BB 0.002805 BB 1115.750854 4343.654785
SNP_A-4263484 AB 0.001350 AB 1761.828857 1252.905029
SNP_A-1978185 AA 0.001824 AA 1122.284790 328.020569
SNP_A-4264431 AA 0.008073 AA 2355.496338 360.492828
SNP_A-1980898 BB 0.005121 BB 275.335480 1062.600830
SNP_A-1983139 AA 0.005370 AA 4017.077881 803.358398
SNP_A-4265735 AA 0.001080 AA 2646.514160 531.394775
SNP_A-1995832 AB 0.007400 AB 1320.302612 1131.740356
SNP_A-1995893 AB 0.004989 AB 1602.670532 1991.865356
SNP_A-1997689 BB 0.003006 BB 609.549500 3767.693359
SNP_A-1997709 AA 0.003320 AA 1740.585083 261.163055
SNP_A-1997896 AB 0.006499 AB 1268.241821 1839.313843
SNP_A-1997922 AA 0.007758 AA 1311.575195 237.403656
SNP_A-2000230 AA 0.005116 AA 3149.768799 1187.367920
SNP_A-2000332 AB 0.003567 AB 3182.950195 3176.948486
SNP_A-2000337 AA 0.004126 AA 1630.259644 222.139404
SNP_A-2000342 AA 0.005982 AA 3765.315674 832.661377
SNP_A-4268173 AA 0.011837 AA 1844.663940 265.949341

Total number of rows: 909622

Table truncated, full table size 46134 Kbytes.

Supplementary file Size Download File type/resource
GSM397818.CEL.gz 30.1 Mb (ftp)(http) CEL
GSM397818.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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