Hello. I am isolating single nuclei from snap-frozen samples. The RNA integrity from whole tissue/bulk RNA extraction is good with clear 28S/18S bands on bleach gel. However, after performing single nuclei isolation, the extracted RNA is degraded.

Are there any improvements to the "Frankenstein" single nuclei protocol that can be suggested to improve downstream RNA quality? I am already working on ice and as quickly as possible.

Has anyone else struggled with RNA degradation during nuclei isolations?

Thank you