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Series GSE21317 Query DataSets for GSE21317
Status Public on May 24, 2010
Title Viral Microarray - Control Set
Platform organism Viruses
Sample organisms Homo sapiens; West Nile virus; artificial sequences
Experiment type Expression profiling by array
Summary Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy.
 
Overall design A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with West Nile Virus, then RNA was harvested. RNA was converted to cDNA, then copy number was quantified by quantatative real-time PCR. RNA stocks were diluted to 10^4 or 10^6 copies per microliter then converted to cDNA, amplified, labeled and hybridized to the array. Human Lung RNA was used as a control and spiked in at 10ng or 200ng.
 
Contributor(s) Jabado OJ, Lipkin WI
Citation(s) 20584331
Submission date Apr 12, 2010
Last update date Mar 22, 2012
Contact name Omar Jabado
Organization name Columbia University
Department Epidemiology
Lab Lipkin
Street address 722 W 168 Street 17th Fl
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platforms (1)
GPL10319 Virus 45K Microarray - Agilent 25161471
Samples (29)
GSM532755 Negative Control (10ng Human Lung RNA)
GSM532756 Negative Control (200ng Human Lung RNA) 01
GSM532757 Negative Control (200ng Human Lung RNA) 02
This SubSeries is part of SuperSeries:
GSE21319 Viral Microarray
Relations
BioProject PRJNA129467

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE21317_RAW.tar 193.4 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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