Tools & Reagents

To help make CRISPR genome engineering accessible to other researchers, we share our protocols and reagents whenever possible. We also maintain a list of computational tools that may be useful in setting up CRISPR experiments, analyzing data, and more.

Protocols

Detailed protocols for an assortment of techniques related to CRISPR-Cas9 gene editing are available for free at protocols.io. Browse IGI-generated protocols, including:

Protocols used by our CRISPR screening facility can be found here, including:

  • Cloning, sequencing, and re-amplifying gRNA libraries
  • Generating stable cell lines expressing Cas9
  • Large-scale lentivirus production and transfection
  • Screening adherent and suspension cells

Larger collections of protocols are also available:

CRISPR-Cas: A laboratory manual. Edited by Doudna JA and Mali P. Cold Spring Harbor Laboratory Press (2016).
Contains a variety of protocols for genome manipulation with Cas9, including genome editing, troubleshooting in specific organisms, how to detect editing, guide RNA library construction, and CRISPR inhibition or activation screening.

CRISPR Methods and Protocols. Edited by Lundgren M, Charpentier E, and Fineran PC. Methods in Molecular Biology (2015).
Features protocols for studying the mechanisms of CRISPR-Cas immunity from genetic, genomic, molecular, biochemical, and structural perspectives.

Plasmids & Libraries

A variety of plasmids and pooled guide RNA libraries for CRISPR-mediated genome manipulation generated by IGI member labs and others can be acquired through AddGene. Our CRISPR screening facility also distributes certain gRNA libraries.

Cell Lines

Published CRISPR interference, activation, or knockout cell lines may be provided upon request from the cell culture facility at UC Berkeley. Browse available lines here and contact Alison Killilea to learn more: ankillilea (at) berkeley.edu.

Guide RNA Design

*You may wish to use a tool designed specifically for the organism you want to edit.*

“How to Make a Guide RNA for a Cas9 Knockout” tutorial (IGI)

CHOPCHOP (University of Bergen & Harvard Medical School)

CRISPR Design (MIT)
Good for predicting off-target sites in human cells.

CRISPR RGEN Suite (Institute for Basic Science, Korea; Seoul National University; Hanyang University)
Contains tools for identifying potential off-target sites (Cas-OFFinder) and microhomology regions (Microhomology-Predictor), as well as a guide RNA design tool that incorporates these parameters (Cas-Designer).

E-CRISP (DKFZ)

sgRNA Designer (CRISPRko) (Broad)
Works only for S. pyogenes Cas9 (PAMNGG); uses Doench cutting frequency determination (CFD) score to evaluate off-targets.

High-throughput CRISPR Screen Design

cld (CRISPR library designer) (Ontario Institute for Cancer Research)
Design multispecies sgRNA libraries.

CRISPRiaDesign scripts (UCSF)
Offers basic sgRNA machine learning scripts used to generate next-generation CRISPRi and CRISPRa libraries from IGI co-executive director Jonathan Weissman’s lab.

A primer on CRISPRi/a cell line production (UCSF)
The Weissman lab's handy guide on how to generate and validate stably-expressing CRISPRi and CRISPRa cell lines.

Sequencing Data Analysis

CasAnalyzer (Institute for Basic Science, Korea; Seoul National University; Hanyang University)
Offers JavaScript-based instant assessment of genome editing NGS data.

CRISPResso (Mass General Hospital & Harvard)
Analyze deep sequencing data to determine CRISPR-Cas9 genome editing outcomes.

 

caRpools (Ontario Institute for Cancer Research)
Analyze raw NGS data from pooled CRISPR screens.

MAGeCK (Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout) (Dana-Farber & Harvard)
Analyze data from genome-wide CRISPR knockout screens.

ScreenProcessing (UCSF)
Analyze sequencing data from pooled CRISPR screens.

CRISPRAnalyzeR (DKFZ)
User-friendly, web-based analysis suite for pooled CRISPR-Cas9 screens.

Databases & Other Tools

CRISPRdb & CRISPRFinder (University of Paris-Saclay)
Find CRISPR arrays in a prokaryotic species of interest from a database of analyzed genomes (db) or in a user-uploaded sequence (Finder).

GenomeCRISPR (DKFZ)
This database compiles results from CRISPR–Cas9 high-throughput screening studies, featuring data from over half a million sgRNAs in 48 human cell lines.

Addgene’s List of CRISPR Resources