You should use global profiling like miRNA sequencing or microarray if you want to screen some miRNA. Then you can go for reverse transcriptase PCR for selective miRNAs. Using FISH in TMA will also helpful for expression study but not for screening. If you have limited funds then you select some miRNAs on the basis of published articles of related study, but in that case you should select only those miRNA which have experimentally validated targets of pathways of your interest. Transfection studies in cell lines using siRNAs as positive controls can validate the function of miRNAs relevant to metabolic pathways of your interest.

thanks niley. actually i am testing the regulation (up or down) of only two miRNA, so i dont need the microarray right? i have limited time ( few months) so wonder if reverse transcriptase would be useful only. using taq man

Yes, it will be best for this. And taqman is most accurate. 

Hello Heba,

Do you have certain miRNAs in mind? It is always good to have a set of miRNAs in mind, if you have limited time.

Also, what is the sample you are working on? This is important, because it will help you avoid external circulatory miRNAs. We recently published an article on this.

Warm regards,

Venk

Article Are We Eating Our Way to Prostate Cancer—A Hypothesis Based ...