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Quantifying Viral mRNAs at Different Time Points? - (Nov/26/2012 )

In my research project I want to look at the different viral mRNAs being produced at different times of a Sendai virus infection. I am concerned with identifying the Sendai virus proteins being translated at early time points during infection. I will be infecting LL-MK2 cells, extracting the mRNA and using real-time quantitative RT-PCR to measure the different mRNAs produced at different time points .

Question: In my gene manipulation class the other day, we discussed the topic of “Functional Genomics,” and the use of ‘cluster analysis of microarray data’ came up. The example used to explain this topic resembled what I intend to do for my research experiment (in-class example= microarray data taken at different times looking at what genes were being turned on and off during the course of the cell cycle). I am wondering if I can use ‘Microarray Technology’ instead of ‘Real-Time Quantitative RT-PCR’ for my experiment?
If anyone has any experience with this please let me know!!



Microarrays are used to measure extensive numbers of transcripts at one time, though ale less accurate then qPCR. I seriously doubt your virus has so many genes to measure, that the microarray technology would be of any advantage.
For microarrays you need special reader, sample preparation and chips are expensive (especially when not some common patways).


Okay cool! Thanks for the heads up!
Guess I'll just stick to the Real-Time Quantitative RT-PCR.