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Sample GSM397723 Query DataSets for GSM397723
Status Public on Jul 31, 2010
Title Brain-MND-1083-rep1
Sample type genomic
 
Source name MND Brain (Brodmann area 46)
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
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 Brain (Brodmann area 46)
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
ID_REF PROBE SET NAME
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
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 AB 0.001124 AB 2745.081055 2830.019775
SNP_A-1967418 AB 0.000601 AB 563.544739 503.850037
SNP_A-1969580 BB 0.004893 BB 1079.830933 3493.705322
SNP_A-4263484 BB 0.001194 BB 503.082184 2155.293457
SNP_A-1978185 AA 0.001963 AA 1164.284790 359.075500
SNP_A-4264431 AA 0.003160 AA 1587.819458 241.537537
SNP_A-1980898 AB 0.002592 AB 555.750183 433.532806
SNP_A-1983139 AA 0.001681 AA 4365.797852 1051.895386
SNP_A-4265735 AB 0.003001 AB 2133.301514 2164.809326
SNP_A-1995832 AA 0.002751 AA 3275.684570 512.691772
SNP_A-1995893 AA 0.001352 AA 3319.857666 1262.203979
SNP_A-1997689 BB 0.001865 BB 661.302063 3746.531738
SNP_A-1997709 AA 0.010697 AA 3455.003906 360.266266
SNP_A-1997896 AA 0.001088 AA 1266.043457 428.439301
SNP_A-1997922 AA 0.002418 AA 925.977173 260.968628
SNP_A-2000230 AA 0.000829 AA 2651.808105 1007.321594
SNP_A-2000332 AA 0.006313 AA 4401.555176 815.481689
SNP_A-2000337 AA 0.007185 AA 1634.699585 190.571854
SNP_A-2000342 AA 0.001847 AA 4076.133789 1092.296265
SNP_A-4268173 AA 0.002445 AA 1557.127563 283.421356

Total number of rows: 909622

Table truncated, full table size 46124 Kbytes.




Supplementary file Size Download File type/resource
GSM397723.CEL.gz 29.8 Mb (ftp)(http) CEL
GSM397723.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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