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Sample GSM397790 Query DataSets for GSM397790
Status Public on Jul 31, 2010
Title Hair-MND-1900-rep1
Sample type genomic
Source name MND Hair
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 4
twin info: Monozygotic Discordant for MND
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 Hair
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 0.020128 AB 1990.979248 1628.857666
SNP_A-1967418 AB 0.009219 AB 734.280640 559.400513
SNP_A-1969580 BB 0.005267 BB 950.677185 4138.021973
SNP_A-4263484 AB 0.001241 AB 1783.139648 1261.472656
SNP_A-1978185 NC 0.407331 BB 1898.479736 3180.919189
SNP_A-4264431 AB 0.003368 AB 1390.980957 943.853210
SNP_A-1980898 AB 0.048458 AB 859.497925 569.193542
SNP_A-1983139 AB 0.002246 AB 2493.960205 2218.492432
SNP_A-4265735 AA 0.016415 AA 2075.504395 518.132446
SNP_A-1995832 BB 0.011470 BB 648.353943 1851.910278
SNP_A-1995893 BB 0.007964 BB 408.663727 3239.736816
SNP_A-1997689 BB 0.008121 BB 488.510193 3794.407227
SNP_A-1997709 AA 0.007631 AA 1246.268188 188.071014
SNP_A-1997896 AA 0.040058 AA 2083.622559 925.474121
SNP_A-1997922 BB 0.041262 BB 471.044037 1802.065186
SNP_A-2000230 AA 0.002165 AA 2811.088379 1170.942505
SNP_A-2000332 AB 0.009112 AB 2882.666504 3556.505615
SNP_A-2000337 AA 0.005816 AA 1437.656982 252.361588
SNP_A-2000342 AA 0.005095 AA 4621.462402 999.910278
SNP_A-4268173 AA 0.004090 AA 1618.376953 263.272339

Total number of rows: 909622

Table truncated, full table size 46138 Kbytes.

Supplementary file Size Download File type/resource
GSM397790.CEL.gz 29.4 Mb (ftp)(http) CEL
GSM397790.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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