PT  - JOURNAL ARTICLE
AU  - Matthew C. Canver
AU  - Maximilian Haeussler
AU  - Daniel E. Bauer
AU  - Stuart H. Orkin
AU  - Neville E. Sanjana
AU  - Ophir Shalem
AU  - Guo-Cheng Yuan
AU  - Feng Zhang
AU  - Jean-Paul Concordet
AU  - Luca Pinello
TI  - Integrated design, execution, and analysis of arrayed and pooled CRISPR genome editing experiments
AID  - 10.1101/125245
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 125245
4099  - http://biorxiv.org/content/early/2017/09/11/125245.short
4100  - http://biorxiv.org/content/early/2017/09/11/125245.full
AB  - CRISPR genome editing experiments offer enormous potential for the evaluation of genomic loci using arrayed single guide RNAs (sgRNAs) or pooled sgRNA libraries. Numerous computational tools are available to help design sgRNAs with optimal on-target efficiency and minimal off-target potential. In addition, computational tools have been developed to analyze deep sequencing data resulting from genome editing experiments. However, these tools are typically developed in isolation and oftentimes not readily translatable into laboratory-based experiments. Here we present a protocol that describes in detail both the computational and 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. This protocol allows for design and execution of arrayed and pooled CRISPR experiments in 4-5 weeks by non-experts as well as computational data analysis in 1-2 days that can be performed by both computational and non-computational biologists alike.