What is the control for miRNA qPCR (eg. something like a housekeeping gene -GAPDH, beta actin ). Endogenous reference genes like U6 seem longer than a usual miRNA, and cannot be used. What is the best bet? Is there a defined standard? or Can I use any miRNA that is consistant in both treated and control samples?
We have used U6 before, which was suggested by a collaborator who is a miRNA expert.
Thanks for the information, In my previous paper I used U6 and but now some say it is longer than usual miRNA and cannot be considered as a control.
Hi, Probably by now you've already reached a decision about what endogenous control to use, but I'd recommend any miRNA that shows constant expression between conditions. Of course the use of endogenous control will depend on number of miRNAs assessed and normalization approach, but in my experience (at least in neuronal tissue) neither of traditionally used U6, RNU43, 44 or 48 have performed satisfactory. Personally, i do a descr. stats on the raw data and select the miRNA gene with lowest SD and/ CV to normalize rest of them.
Thank you all for the informations, I used a miRNA that was more consistent in all the expreriments.
Hi, Sreekumar, which miRNA did you select as the housekeeping gene finally?
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