We are using CRISPR/Cas9 to introduce small indels to KO genes in immortalized MEFs and are finding that in almost all clones and different gene KOs that the null cells transfect very poorly. This is not linked to any particular gene but appears to be the result of going through the selection and cloning (by limited dilution) process. We use Lipofectamine or PEI and our WT cells are low (20-40%) but manageable. But clones obtained after CRISPR we are lucky to find a single cell expressing our protein, making rescue experiements dependent upon virus expression, which is much more costly. Anyone know the issue here and a work around?