I am looking for a protocol or kit for RIP seq in a rare cell population. I am sorting this rare cell population by FACS, but only get around 3K cells per experiment. However, I know that my RBP is highly expressed and that every cell I sort expresses the RBP.  

I have a few additional questions:

1) How many cells are needed for RIP seq considering they would all have the protein of interest? I can combine multiple experiments, but don't want to have to do 300 experiments for one RIP seq. 

2) Is is better to cross link? If so, Tris vs Glycine for quenching?

3) Protein A beads vs Protein G with a mouse monoclonal antibody (against GFP)? I've got protein G but I noticed some kits come with A. Or, does anyone know of  anti-GFP conjugated beads that work well? 

Thanks for your help!

Rosa