I am trying to cleave 2 targets for multiplex genome engineering, which method would you recommend I use.

Answer

Use 2 gRNA simultaneously co-transfected with Cas9. If using a robust work horse cell line like 293 you could directly use the U6 synthetic DNA fragment. For more difficult to transfect cell lines we recommend using complete RNA format (Cas9 mRNA+ in vitro transcribed gRNA synthesized from T7 promoter containing DNA template).