I am going to compare miRNA profiling of different cells infected with H1N1 virus. I will fix them using a MOI of 10. Is there a problem using a high MOI, if I use it in all experiments?
It depends of what you want to see.Whit a high MOI the effects you will see are of cells infected but it will be difficult to see effects derived of reinfections(virus produced in your cells infecting others). If you have any idea of when the miRNA are produce you will have an idea of which MOI is best in your experiment. the course of the infection will be really different between MOI of 0.1 and 10. Maybe the best is try to use more than 1 MOI or refer to the literature to see what others have done. example: If you are studying the antiviral effect of a protein that affects budding you will see a better result with smaller MOI
I agree with Domingo, "it depends on what you want to see." It will also depend on when you deside to "stop" the infection. If you are doing a short incubation (less than 12 hrs) with the virus then harvesting RNA or fixing with formalin, then an MOI of 10 isn't so bad but you could probably get away with a lower MOI. If you are doing anything longer than 24 hrs i don't think your cells would hold up with a high MOI (really for flu anything above 1). Influenza causes a significant amount of CPE, even with an MOI of 0.01 I see CPE after 24 hrs.
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