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Sample GSM397742 Query DataSets for GSM397742
Status Public on Jul 31, 2010
Title Brain-MND-1568-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: 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 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 BB 0.008418 BB 588.472473 5162.283691
SNP_A-1967418 BB 0.004585 BB 251.619141 604.395630
SNP_A-1969580 BB 0.002077 BB 1093.645020 4230.467773
SNP_A-4263484 AB 0.003718 AB 1726.239502 1407.799072
SNP_A-1978185 AA 0.001990 AA 1302.896606 396.627960
SNP_A-4264431 AB 0.002024 AB 1081.989380 890.436768
SNP_A-1980898 BB 0.005140 BB 209.973618 592.401367
SNP_A-1983139 AA 0.003570 AA 5191.473145 1211.348877
SNP_A-4265735 AB 0.001232 AB 1765.765015 1957.726074
SNP_A-1995832 BB 0.005978 BB 548.196899 1896.464478
SNP_A-1995893 BB 0.004309 BB 415.287140 2581.356934
SNP_A-1997689 BB 0.002933 BB 690.853333 4237.878418
SNP_A-1997709 AA 0.003399 AA 1783.171631 278.885895
SNP_A-1997896 AB 0.006558 AB 829.213562 1725.691284
SNP_A-1997922 AB 0.000720 AB 736.135071 658.284851
SNP_A-2000230 AA 0.002090 AA 2922.544678 1029.734741
SNP_A-2000332 AB 0.000517 AB 2927.231934 3112.148438
SNP_A-2000337 AA 0.007112 AA 1378.626709 264.142761
SNP_A-2000342 AA 0.007350 AA 4823.659180 1097.582275
SNP_A-4268173 AB 0.005635 AB 835.121765 552.228821

Total number of rows: 909622

Table truncated, full table size 46128 Kbytes.




Supplementary file Size Download File type/resource
GSM397742.CEL.gz 27.8 Mb (ftp)(http) CEL
GSM397742.CHP.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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