|
| Status |
Public on May 24, 2010 |
| Title |
Viral Microarray - Cultured Virus Set |
| Platform organism |
Viruses |
| Sample organisms |
Chlorocebus aethiops; Human alphaherpesvirus 1; West Nile virus; Vesicular stomatitis Indiana virus; Lassa virus Josiah; Human adenovirus E4; Echovirus E18; Zaire ebolavirus; SARS coronavirus Tor2; Influenza A virus (A/Texas/36/1991(H1N1)) |
| 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.
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|
| 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 various viruses, then RNA was harvested. RNA was converted to cDNA, then amplified, labeled and hybridized to the array.
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| |
|
| 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) |
| GPL10320 |
Virus 45K Microarray - Agilent 2517771 |
|
| Samples (11)
|
| GSM532787 |
Influenza A H1N1 Texas 1991 (FLUA-H1N1) |
| GSM532788 |
Lassa virus strain Josiah (LASV) |
| GSM532789 |
Negative Control (Vero cell tissue culture supernatant) 01 |
| GSM532790 |
Negative Control (Vero cell tissue culture supernatant) 02 |
| GSM532791 |
SARS Human Coronavirus Tor2 (HCoV-SARS) |
| GSM532792 |
Vesicular stomatitis virus Indiana (VSV) |
| GSM532793 |
West Nile virus NY99 (WNV) |
| GSM532794 |
Zaire ebolavirus (ZEBOV) |
|
| This SubSeries is part of SuperSeries: |
|
| Relations |
| BioProject |
PRJNA129469 |
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