Integrated computational guide design, execution, and analysis of arrayed and pooled CRISPR genome editing experiments

ABSTRACT

CRISPR genome editing experiments offer enormous potential for evaluation of genomic loci using arrayed or pooled lentiviral libraries of single guide RNAs (sgRNAs). Numerous computational tools are available to help design sgRNAs with optimal on-target efficiency and minimal off-target effects. In addition, a few computational tools have been developed to analyze data resulting from genome editing experiments. However, these tools are typically developed in isolation and oftentimes are not readily translatable into laboratory-based experiments. Here we present a protocol that describes in detail both the computational and the benchtop implementation of an arrayed and/or pooled CRISPR genome editing experiment. This protocol provides instructions for sgRNA design with CRISPOR, experimental implementation, and analysis of the resulting high-throughput sequencing data with CRISPResso.