Zebrafish Plasmids and Resources

The zebrafish (Danio rerio), named for the horizontal stripes on the sides of the adult body, is a tropical freshwater fish in the minnow family. It has long been established as a powerful vertebrate model organism for the study of genetics and developmental biology. With its rapid development (embryogenesis is complete in ~3 days), short generation time (~3 months), ease of care and breeding, and transparency of the embryo and larvae, it is easy to culture large populations that are amenable to genetics, high-throughput screening and non-invasive live imaging. A standard toolbox of genetic methods, such as Tol2 transposons, Cre-mediated site-specific recombination, morpholinos, zinc finger nucleases, TALENS, and CRISPR/Cas9-based gene editing make the zebrafish a stalwart research model. With more than 70% of human disease genes having an ortholog in zebrafish, this species has more recently emerged as a model system for human disease and translational research, including the study of cancer, inflammation and infection, regeneration, human neurological disorders, microbiota studies, and drug discovery and development. Here we highlight some of the plasmids and tools available at Addgene for use in zebrafish.

Browse Plasmids

Plasmid Tools for Use in Zebrafish

Looking for plasmids containing your zebrafish gene of interest? Search Addgene's collection for plasmids that contain a zebrafish gene or sequence.

The table below highlights plasmids that contain tools for use in zebrafish research. This includes plasmids for genome editing, empty backbones, fluorescent proteins, reporters, biosensors, and Cre expression plasmids. Large collections or kits are described below.

Highlights of Zebrafish Tools in our Collection

CRISPR

Please refer to Addgene's CRISPR Guide for a general introduction to CRISPR technology or the zebrafish CRISPR resources for a full selection of plasmids expressing Cas9 and empty gRNA backbones. A few examples of useful zebrafish CRISPR resources can be found below:

• UFlip CRISPR targeted integration vectors for cell-type specific conditional gene inactivation - Jeffrey Essner Lab
• GeneWeld Vectors for Targeted Integration Using CRISPR/Cas9 - Jeffrey Essner Lab
• CRISPR-Cas/RNA-Guided Nuclease (RGN) expression plasmids - Keith Joung Lab
• CRISPR/Cas9-based conditional mutagenesis in zebrafish - Wenbiao Chen Lab
• A CRISPR/Cas9 Vector System for Tissue-Specific Gene Disruption in Zebrafish - Leonard Zon Lab
• Programmable base editing of zebrafish genome using a modified CRISPR-Cas9 system - Shuo Lin Lab
• Re-purposed Ac/Ds transgenic system enabling CRISPR/dCas9-interference (CRISPRi) modulation of enhancers and non-coding RNAs in zebrafish - Tatjana Sauka-Spengler Lab

Lineage Tracing

Cell lineage tracing in multicellular systems typically relies on genetic markers, somatic mutations, or labeling with fluorescent proteins to visualize and track clones of cells over time. Examples of useful tools for studying cells that share clonal origin in zebrafish can be found below:

• Optimized QF-binary expression system for use in zebrafish - Bret Pearson Lab
• MAZe: a tool for mosaic analysis of gene function in zebrafish - Julian Lewis Lab
• PhOTO Zebrafish: A Transgenic Resource for In Vivo Lineage Tracing during Development and Regeneration - Periklis Pantazis Lab
• Multibow: digital spectral barcodes for cell tracing - Sean Megason Lab
• Zebrabow - Albert Pan and Alex Schier Labs. Multicolor fluorescent labeling in zebrafish
• Whole organism lineage tracing by combinatorial and cumulative genome editing - Jay Shendure Lab
• Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain - Alex Schier Lab

Other Tools of Interest

A few examples of popular tools to use in zebrafish, ranging from optogenetics to tools for studying diseases, are listed below:

• Lipid droplet reporters - Richard White Lab. An imaging platform to study lipid dynamics in vivo.
• Bimolecular fluorescence complementation (BiFC) tools - Marco Morsch Lab. A vertebrate model to study ALS-linked aggregates in real time.
• Live imaging of astroctyes - Kelly Monk Lab. Live imaging tools to study the development and function of zebrafish astrocytes.
• Knock-in tagging - Michel Bagnat lab. Targeting cassettes encoding fluorescent proteins for tagging genes at endogenous genomic loci in zebrafish.
• NTR 2.0 - Jeff Mumm Lab. NTR 2.0/MTZ-based cell ablation system that allows sustained cell loss and ablation of previously resistant cell types.
• CreLite - George Eisenhoffer Lab. An optogenetically controlled Cre/loxP system that enables precise temporal and spatial control of gene expression in zebrafish using red light.
• LipoGlo - Steven Farber Lab. A reporter system that allows direct assessment of lipoprotein abundance, size, and localization in high-throughput.
• MAZERATI platform - Leonard Zon Lab. A platform to rapidly model potential cancer drivers in vivo.
• Biotagging toolkit - Tatjana Sauka-Spengler Lab. A genetic binary system for cell- and compartment-specific biotin labeling in zebrafish.
• pGCS Vector Kit - Hai-Ning Du Lab. A set of pCS2+ backbone-based Gateway destination vectors (pGCS), bearing either amino- or carboxyl-terminal tags, including Myc, HA, Flag, GST and eGFP epitopes.
• Zebrafish Tol2 Gateway-compatible Kit for Neurodegenerative Disorders - Nicholas Cole Lab. A kit consisting of plasmids with four promoters, six fluorophores, and empty vectors designed to streamline the production of transgenic zebrafish for studying neurodegenerative disorders.
• Fluorescent Protein Fusion Construct Set - Amro Hamdoun Lab. A useful “starter kit” for screening fluorescent protein fusion expression in organisms or cells in which an exogenous mRNA can be injected and expressed.
• EXPRESs Plasmids for Zebrafish Receptors and Zebrafish Monoclonal Antibody plasmids - Gavin Wright Lab. Collections of plasmids that encode zebrafish receptors or monoclonal antibodies to zebrafish cell surface receptors and secreted proteins.

Other Resources

Addgene Blog Posts

• Advancing Biology with Zebrafish: Genetic Tools for Developmental Studies and More
• Zebrafish as a Model for Behavior: Swimming into the Optogenetic Spotlight

External Resources

• Zebrafish Genome Project - Access the latest reference sequence assembly for the zebrafish genome.
• Zebrafish Model Organism Database (ZFIN) - A curated database of genetic, genomic, and developmental data for zebrafish biology.
• Zebrafish International Resource Center (ZIRC) - A US-based repository for zebrafish strains and materials and information about zebrafish research.
• China Zebrafish Resource Center (CZRC) - A resource center based in China focused on collecting existing zebrafish resources and developing new lines and technology.
• European Zebrafish Resource Center (EZRC) - A repository at the Karlsruhe Institute of Technology (KIT) for the distribution of zebrafish lines from European researchers.
• International Zebrafish Society (IZFS) - An organization that promotes and advocates for zebrafish research in the international research community.
• The Latin American Zebrafish Network (LAZEN) - LAZEN aims to increase the use of zebrafish as a model organism and to foster advanced training of young scientists in Latin America.
• The Zebrafish Book - A guide for the laboratory use of zebrafish.
• CRISPRz - A database of CRISPR/Cas9 target sequences that have been experimentally validated in zebrafish.
• Zebrafish expression atlas - A zebrafish-specific gene expression database that provides information about when genes are active in developing embryos.
• zfRegeneration - A database for gene expression profiling during regeneration.
• Seurat - R package for analyzing single cell genomics in zebrafish.