Hi everyone,

I am interested in the RNA interactors of a specific protein but I am struggling a bit with the RNA extraction from the dynabeads (invitrogen) after CLIP. What I did until now was putting trizol on the beads and continuing with the RNA extraction ( chloroform etc).

The problem is that the yield is very low and I think it might be due to a loss of RNA still bound to the protein (and then precipitated during the RNA extraction). To overcome this issue, I wanted to de-crosslink putting proteinase K directly on the beads and after digestion, add trizol. In this way I should remove all the RNA bound directly to the protein.

Do you think it will work? Do you have any protocol or suggestion to successfully extract RNA after CLIP that is suitable for RNA-seq?

Any help would be really appreciated.

Thanks in advance