Can the eluted (incompletely enriched) mRNA be used again as starting material for another kit like say, Ribo Zero, or do I need to use a different set of total RNA altogether?
Hi
Theoretically you can use another kit to deplete resting rRNA.
However I would not recommend using RiboZero after MicrobeExpress. Firstly because RiboZero is very efficient in depletion (if it is compatible) and there is only a very small quantity obtained after the depletion (I suppose that even some mRNA material is depleted as well).
It is better to use RiboZero from the beginning. Again, before using RiboZero kit you can go on the Epicenter web site and blast the rRNA of your bacterium to check in the oligos of the kit are compatible for the depletion.
So, I would suggest you to do a second run with MicrobeExpress (I have done it for my samples) but you have to precipitate RNA to concentrate you material till 10 µl (so you will lose a part of RNA). Whatever decision you’ll take remember to prepare all your samples (control and test) in the same way for RNA-seq.
I hope it helps
Thanks a lot for your input! It definitely helped. It is true that Ribo Zero is pretty efficient in rRNA removal and the final volume of the elute obtained after mRNA enrichment is just 10ul. My initial RNA sample will not have enough left after the Microbexpress treatment.
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