I am designing a nuclear fractionation experiment and will be looking at RNA in the fractions. To confirm the quality of the fractions I intend on using nucleic acid markers for negative and positive controls (as this is what I'll be studying).
As a positive and negative control for the nuclear and cytoplasmic fraction respectively, genomic DNA will probably be the ideal marker.
However, I have trouble finding a good negative control for the nuclear fraction and a good postive control for the cytoplasmic fraction.
I was thinking along the lines of ribosomal RNA, however this also exists in the nucleus. Perhaps focusing on RNA that has undergone extensive post-transcriptional modification could be another alternative.
Nucleic acid markers for Nuclear Fractionation?
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