I performed CRISPR/Cas9 genome editing on my cells. As a pool, they were mixed and depletion did not seem that good. I decided to do single cell cloning. After that, I checked the depletion on those single cells in both mRNA and protein level. In mRNA level, there is 90% depletion but in protein level, they exactly look like control cells. What is the logic behind of this or did anybody have the same problem before?

Thanks for your help in advance!

Beste