digital droplet PCR. Maybe too expensive if you don't have access to the device. Nevertheless it gives absolute copy numbers and works also with low concentration. You just need primers. I don't how if there are some available for your target.

Other options could be qPCR or northern Plot.

You'd first have to isolate nuclear and cytoplasmic RNA. Then you can use any quantitative method for the determination of RNA levels. These include Northern blot, RNase protection, quantitative PCR, NCounter analysis or digital droplet PCR. For any PCR based method, you first have to do a reverse transcription.

Problems with absolute quantitation in two fractions of very different composition (such as nuclear and cytoplasmic RNA) include different efficiencies of recovery in the RNA isolation step and differences in RT efficiency for any PCR based method. Normally you correct for this by comparing to a housekeeping RNA, but this won't be the same level in these fractions. Only NCounter and Northern blot don't use RT and avoid this problem. In theory, in situ hybridization would be an alternative, but it is very hard to get this quantitative.

If you just want to see if there is a change in the amount of RNA in nucleus and cytoplasm, you can just pick a control RNA to normalize to and see if the nuclear/cytoplasmic ratio changes. You can see an example of this in our paper in RNA (Kondrashov et al. 2012, Fig 6, method described on p 2247).

All the best of luck!

@ Karin Glaser, Thank you for your kindly advice. Unfortunately, I cannot used digital droplet PCR. I think qPCR is the second best in our research condition.

@ Cornelia H de Moor, Thank you for your kindly advice. Your paper is very useful for me.

Hi Gyeoung-Jin Kang ·, Could you please tell me in more detail how did you calculate your target enrichment in the nuclear and cytoplasmic fractions with qPCR?