Below please find links to resources of interest to researchers in the genome editing field. Included are sources for reporter animals, reagents, analysis tools and data submission repositories. We encourage all investigators to submit data to the appropriate repositories for use by the wider research community.

Awesome-CRISPR (Wei Li github)

  • Guide design tools
  • Off-target prediction algorithms
  • Editing outcomes and predictions
  • Analysis algorithms

Sanger Institute Genome Editing (WGE)

  • CRISPR Finder tool for human and mouse – search by gene or sequence
  • Off Target Finder – by sequence
  • Gibson Designer – finds the oligos in either Human or Mouse genomes that can be used to create targeting vectors by Gibson assembly
  • WGE API

CRISPR RGEN Tools

  • RNA-Guided endonuclease tools
    • Cas-OFFinder – searches for potential off-target sites
    • Cas-Designer – Guide RNA designer for CRISPR/Cas derived RNA-Guided endonucleases
    • Analyzer tools

CRISPOR

  • Design and evaluate guide sequences for many organisms

CRISPick

  • Ranks and picks candidate CRISPRko/a/i sgRNA sequences
    to maximize on-target activity for target(s) provided.

CRISPR-FOCUS

  • Guide Design tool for human and mouse

CRISPRDB

  • Online database for genome-wide CRISPR/Cas9 gRNA design

BiooTools

  • Guide design tools

CRISPRdirect

  • Tool to design CRISPR/Cas target for multiple organisms

CRISPR MultiTargeter

  • Find guide RNA targets for multiple organisms

CCTop-CRISPR/Cas9 Target Online Predictor

  • Target prediction for many organisms

CHOPCHOP

  • Tool for selecting target sites for many organisms

CrisprGE

  • Contains sequence and modifications for target genes for multiple organisms linked to publications

CRISPscan

  • Search for or predict guides for multiple species
  • Off target predictions for guides

CRISPRdirect

  • Tool to design CRISPR/Cas target for multiple organisms

CRISPR MultiTargeter

  • Find guide RNA targets for multiple organisms

CCTop-CRISPR/Cas9 Target Online Predictor

  • Target prediction for many organisms

CHOPCHOP

  • Tool for selecting target sites for many organisms

CrisprGE

  • Contains sequence and modifications for target genes for multiple organisms linked to publications

CRISPscan

  • Search for or predict guides for multiple species
  • Off target predictions for guides

Sanger FORECasT

  • Predicts mutational outcomes from double stranded breaks induced by CRISPR/Cas9

CRISPResso2

  • Analysis of genome editing outcomes from deep sequencing data – Cas9, Cpf1, Base editors

Sanger WGE-CRISPR Design Tool

  • Web based Visual tool with embedded genome browser and database
  • CRISPR Analyser tool – finds off targets for CRISPR site for any species

Sprout

  • Machine learning tool predicting DNA repair outcome in CRISPR-Cas9

inDelphi

  • Machine learning algorithm to predict heterogeneous mixture of indels from MMEJ and NHEJ

BioGRID Open Repository of CRISPR Screens (ORCS)

  • Screens for human, mouse, fly curated from publications

GenomeCRISPR

  • Tool to compare screens across experiments

CRISPRCloud2

  • Analysis platform for deconvolution of CRISPR pooled screening data

Plasmids and Vectors

ADDGENE

Cell Lines

Cellosaurus

  • Provides catalog of 117636 cell lines (human, mouse, rat) used in biomedical research includes accession numbers for catalog and unique identifiers (RRID).

ATCC

WiCell

  • Provides catalog of 1503 stem Cell lines

Fluorescent Proteins

Fluorescent Protein Database

  • Provides catalogue of fluorescent proteins including data on organism, sequence, mutations, structure and references.
  • Data Submission

MOUSE

Mutant Mouse Resource and Research Centers (MMRRC) – distributes and cryopreserves genetically engineered mouse strains and mouse ES cell lines and provides unique identifiers and official nomenclature for strains.

International Mouse Strain Resource (IMSR) – Database of inbred, mutant, and genetically engineered mouse strains available worldwide.

Mouse Genome Informatics (MGI) – Comprehensive gene data

SWINE

National Swine Resource and Research Center – provides a database of model swine including descriptions and availability and creates genetically modified swine, cryopreserves embryos and somatic cells and stores tissues and organs.

Animal QTL Database – QTLs/associations for 688 traits.

RHESUS MACAQUE

The Macaque Genotype and Phenotype Resource (mGAP) – provides DNA variant catalogue, predicted damaging variants, and raw sequence data for colony at the Oregon National Primate Research Center (ONPRC)

MARMOSET

Marmoset Gene Atlas – In situ hybridization gene expression database for marmoset.

Marmoset Brain Connectivity Atlas – Digital repository for data on connections between different cortical areas