Troubleshooting off-target CRISPR in mammalian cells: RNP vs plasmid delivery

[Natalie.S]

I'm a graduate student in molecular biology, and my thesis project involves using CRISPR gene editing to knock out a specific regulatory gene in a mammalian cell line, but I'm consistently getting off-target effects despite using a high-fidelity Cas9 variant and carefully designed sgRNAs. For researchers with hands-on CRISPR experience, what troubleshooting steps proved most effective for you in minimizing off-target activity? I'm particularly interested in your practical insights on optimizing delivery methods, whether you've had better success with ribonucleoprotein complexes versus plasmid vectors, and if you recommend specific in silico prediction tools or experimental validation assays like GUIDE-seq or CIRCLE-seq that are feasible for an academic lab with a moderate budget.