has anybody ever used a negative control which does not rely on scrambled, non-targeting principles? I am thinking of using guides against "safe harbour" locus ROSA26 or else against a non-coding area of the genome, so that they shouldn't exert any effect. Do you think that's feasible?
I am doing CRISPR interference with dCas-KRAB. Two different scrambled controls turned out to strongly reduce the viability and growth of my cells (one of them is the one by origene which has been suggested in this forum). I am quite at a loss why this happens, so if someone made similar experiences, you are also very welcome to comment on that.