I am currently doing siRNA experiments and getting 80% knockdown at RNA level, however no effect is seen at the protein level even at higher concentrations tested. What more should i try?
You're not alone, it's a common observation! Try later time-points, changes in protein levels typically take days to observe 3, 5, sometimes even 8 days or more! It also depends on the cell line, we've seen protein half-lives vary drastically between cell lines for the same gene.