Thank you, I was thinking about Trizol but was wondering about the protein part as usually it is used for RNA/DNA.

If you recover the flow though from quiagen RNa isolation kit, the protein is in there. but be carefull using a protein titration method compatible with the guanidine present in the RLT buffer

Thanks, I was thinking about that, but the RLT buffer is denaturating and I need CoIP 2 proteins.

So I have no choice but do 2 dishes.

Better you can use the Norgen kit. You could get both RNA and Protein. By using this kit you will get less amounts of RNA as well as Protein compared to Trizol/RIPA buffer separately.

From my experience, at least 200,000 cells were enough for RNA extraction using Trizol.

Question for Benjamin: In which buffer and how would you re-suspend the protein after acetone precipitation from the flow-through of the RNeasy column (if you've ever done it and it worked) ?

I tried RIPA buffer and sample buffer (SDS, Tris, Glycerol), heating at 95C, vortexing, pipetting, but the pellet is quite resistant.

Any idea ?

If you want get RNA and protein from the same dish you can trypsinized the cells and divide in two diferent tubes and treat them separantely.

Not enough cells, I'm working in 12 wells.

Acetone precipitation from the RNeasy flow-through and re-suspension in sample buffer followed by 10 min at 95C seams to work quite well for what I'm looking for so all is good now :-)

Thanks everybody for all your ideas