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.
| ID | Plasmid | Purpose | Gene/Insert | PI | |
|---|---|---|---|---|---|
| 17095 | pCS2P+ | Kirschner | |||
| 26125 | I-SceI pB 5UAS::ZfSyGCaMP2 | Synaptophysin GCaMP2 (Danio rerio) | Lagnado | ||
| 27320 | pENTR5'_ubi | zebrafish ubiquitin promoter (Danio rerio) | Zon | ||
| 27321 | pENTR/D_creERt2 | creERt2 | Zon | ||
| 27322 | pENTR5'_ubi:loxP-EGFP-loxP | ubiquitin:loxP-EGFP-loxP (Danio rerio) | Zon | ||
| 27323 | pDestTol2pA2_ubi:EGFP | ubiquitin:EGFP reporter (Danio rerio) | Zon | ||
| 29574 | tol2-mpx-Dendra2 | mpx-Dendra 2 | Huttenlocher | ||
| 29585 | tol2-mpx-mCherry | mpx-mCherry | Huttenlocher | ||
| 31241 | pSCAC-69 | Mitochondrial localization of EGFP, for real-time imaging of mitochondria in transgenic zebrafish | mitochondrial localization enhanced green fluorescent protein (Danio rerio) | Choi | |
| 32359 | pBH-UAS-secA5-YFP | Live imaging of apoptotic cells in zebrafish | secreted human annexin 5 (Homo sapiens) | Peterson | |
| 32673 | pISce1-memGFP | Tsang | |||
| 32674 | pISce1-D2EGFP | Tsang | |||
| 37845 | E1b-GFP-Tol2 | Ahituv | |||
| 37846 | E1b-GFP-Tol2-Gateway | Ahituv | |||
| 41878 | tol2-4xnr UAS-PA Rac1-mCherry | photoactivatable Rac1 (Homo sapiens) | Huttenlocher | ||
| 42250 | DR274 | guide RNA (gRNA) expression vector used to create a gRNA to a specific sequence; uses T7 promoter for in vitro transcription | Joung | ||
| 42252 | MLM3639 | Streptococcus pyogenes Cas9-3X Flag | Joung | ||
| 45246 | Tol2-mpx:Lifeact-Ruby | lifeact-ruby | Huttenlocher | ||
| 45247 | mpx:UtrCH-GFP | utrophin (Homo sapiens) | Huttenlocher | ||
| 45509 | Tol2 Krt4 Src (YF)-uniRapR-cerulean | Src (YF)-uniRapR-cerulean | Huttenlocher | ||
| 46138 | pFT1.0 | mCherry | Chen | ||
| 46139 | pFT1.1 | mCherry | Chen | ||
| 46140 | pFT1.2 | mCherry | Chen | ||
| 46144 | pT2-eab2-[GTR] | EGFP/mCherry | Chen | ||
| 46759 | pT7-gRNA | gRNA cloning vector for in vitro transcription of target gRNA | gRNA core (Synthetic) | Chen | |
| 47322 | pCS2-Cas9 | For in vivo expression of Cas9 or generation of Cas9 mRNA | Cas9 (Other) | Schier | |
| 47929 | pCS2-nCas9n | expression of an optimized Cas9 for genome-editing in zebrafish | nls-zcas9-nls (Synthetic) | Chen | |
| 51815 | pCS2+hSpCas9 | Encode hSpCas9 for in vitro transcription with Sp6 | humanized S.pyogenes Cas9 | Kinoshita | |
| 53616 | Zebrafish ArcLight Q175 | Genetically encoded voltage sensor ArcLight with improved kinetics | Zebrafish ArcLight-Q175 (Danio rerio) | Pieribone | |
| 58890 | p5'Entry-lck-5.5kb | provides zebrafish lck promoter (5.5 kb) for GateWay construction of Tol2 transgenes | zebrafish lymphocyte-specific protein tyrosine kinase (lck) promoter, 5.5 kb (Danio rerio) | Yoder | |
| 58891 | p5'Entry-lck-7.4kb | provides zebrafish lck promoter (7.4 kb) for GateWay construction of Tol2 transgenes | zebrafish lymphocyte-specific protein tyrosine kinase (lck) promoter, 7.4 kb (Danio rerio) | Yoder | |
| 59530 | Tol2-elavl3-H2B-GCaMP6s | Expressed nuclear-localized GCaMP6-slow, a calcium indicator, in neurons in zebrafish larva. The plasmid is in Tol2 transposon backbone | elavl3 promoter (Danio rerio), H2B (Homo sapiens), GCaMP6s (Synthetic) | Ahrens | |
| 59531 | Tol2-elavl3-GCaMP6s | Expressed GCaMP6-slow, a calcium indicator, in neurons in zebrafish larva. The plasmid is in Tol2 transposon backbone | elavl3 promoter (Danio rerio), GCaMP6s (Synthetic) | Ahrens | |
| 60877 | pMAZe | Reporter construct for lineage tracing and mosaic analysis in zebrafish. | hsp70l promoter, Cre, dTomato, UAS promoter, Gal4VP16 | Lewis | |
| 61069 | eGFPbait-E2A-KalTA4-pA donor vector | for CRISPR/Cas9 mediated insertion of E2A-KalTA4; to be used in combination with a eGFP specific sgRNA (e.g. Plasmid 61051) | eGFPbait (Synthetic), KalTA4 (Synthetic) | Del Bene | |
| 61387 | pCS2-NfsB.zf1 | mRNA synthesis of bacterial nitroreductase NfsB codon modified for zebrafish | nfsB.zf1 (Synthetic) | Burgess | |
| 61388 | pCS2-Tol1.zf1 | mRNA synthesis of tol1 transposase codon modified for zebrafish | tol1.zf1 (Synthetic) | Burgess | |
| 61389 | pCS2-Cer.zf1 | mRNA synthesis of cerulean codon modified for zebrafish | Cer.zf1 (Synthetic) | Burgess | |
| 61390 | pCS2-TagRFPT.zf1 | mRNA synthesis of TagRFPT codon modified for zebrafish | TagRFPT.zf1 (Synthetic) | Burgess | |
| 61391 | pCS2-Cre.zf1 | mRNA synthesis of Cre recombinase codon modified for zebrafish | Cre.zf1 (Synthetic) | Burgess | |
| 61392 | pCS2-Gal4ff.zf1 | mRNA synthesis of Gal4ff codon modified for zebrafish | Gal4ff.zf1 (Synthetic) | Burgess | |
| 61394 | pBS-Isce1-eno2:egfp | Expresses GFP in neurons of transgenic zebrafish | eno2 regulatory element (Danio rerio) | Burton | |
| 62213 | pCS2-epNTR | epNTR (zebrafish optimized nitroreductase, T41L, N71S, F124W) in pCS2 | epNTR (Synthetic) | Burgess | |
| 62215 | pT1UciMP | UAS transgenesis vector | Burgess | ||
| 62216 | pT1QciMP | QUAS transgenesis vector | Burgess | ||
| 62542 | pCS2-nCas9n-nanos 3’UTR | expression of a germ-line targeted, codon optimized Cas9 for genome-editing in zebrafish | nanos 3' UTR (Danio rerio) | Giraldez | |
| 63154 | pME-Cas9 | Middle Entry clone for Gateway containing a zebrafish codon-optimized Cas9 flanked by 2 NLS | Cas9 (Danio rerio) | Zon | |
| 63155 | pME-Cas9-T2A-GFP | Middle Entry clone for Gateway containing a zebrafish codon-optimized Cas9 flanked by 2 NLS and followed by inframe GFP. Cas9 and GFP are separated by the sequence of a T2A self-cleaving peptide. | Cas9-T2A-GFP (Danio rerio) | Zon | |
| 63156 | pDestTol2CG2-U6:gRNA | Destination vector for Gateway based on vector #395 from the Tol2Kit, containing a gRNA scaffold under the control of a zebrafish U6 promoter, and cmlc2:GFP as a transgenesis marker. | Zon | ||
| 63157 | pDestTol2pA2-U6:gRNA | Destination vector for Gateway based on vector #394 from the Tol2Kit, containing a gRNA scaffold under the control of a zebrafish U6 promoter. | Zon | ||
| 64020 | p5E_unc503 | 5' Gateway entry vector with muscle-specific promoter of zebrafish unc-45b | muscle-specific promoter of zebrafish unc-45b (Danio rerio) | Currie | |
| 64021 | punc503GFP | 503-bp promoter of zebrafish unc-45b drives muscle-specific GFP expression | unc-45b: GFP (Danio rerio) | Currie | |
| 64022 | pDestTol2pACryGFP | Gateway destination vector with zebrafish aA-crystallin promoter driving GFP in lens | GFP (Danio rerio) | Currie | |
| 64023 | pDESTtol2pACrymCherry | Gateway destination vector with zebrafish aA-crystallin promoter driving mCherry GFP in lens | mCherry (Danio rerio) | Currie | |
| 64237 | pME-Cas9 | expresses codon optimized Cas9 in zebrafish | codon optimized Cas9 (Other) | Chen | |
| 65562 | th-P2A-EGFP donor | Intron targeting-mediated EGFP knockin at the zebrafish th locus. | th-P2A-EGFP (Danio rerio) | Du | |
| 65563 | th-P2A-Gal4 donor | Intron targeting-mediated Gal4 knockin at the zebrafish th locus. | th-P2A-Gal4 (Danio rerio) | Du | |
| 65564 | gfap-EGFP donor | Intron targeting-mediated EGFP knockin at the zebrafish gfap locus | gfap-EGFP (Danio rerio) | Du | |
| 65565 | pT7-th-sgRNA | in vitro trancription of sgRNA targeting the zebrafish th locus | th sgRNA (Danio rerio) | Du | |
| 65566 | pT7-gfap-sgRNA | in vitro trancription of sgRNA targeting the zebrafish gfap locus | gfap sgRNA (Danio rerio) | Du | |
| 66593 | ins:CFP-NTR | Specific and conditional cell ablation of beta cells in the zebrafish pancreas | Insulin promotor driving CFP-nitroreductase (Danio rerio) | Stainier | |
| 67568 | DF-UAS-spa-GCaMP6f | Zebrafish expression of a photoactivatable fluorescent calcium reporter | spa-GCaMP6f (Synthetic) | Isacoff | |
| 67569 | DF-UAS-sspa-GCaMP6f | Zebrafish expression of a short photoactivatable fluorescent calcium reporter | sspa-GCaMP6f (Synthetic) | Isacoff | |
| 67668 | Bact2-APEX2-GBP in pDEST-Tol2-pA2-acrys-cherry | Zebrafish expression vector for ubiquitous expression of APEX2-GBP | APEX2-GBP (Synthetic) | Parton | |
| 68310 | pcDNA3.1 phiC31 | In vitro transcription vector to generate phiC31 mRNA (i.e. for zebrafish injection). | phiC31 (Other) | Basler | |
| 68313 | pDestattB (pCM268) | Multisite Gateway destination vector to create transgenes for phiC31-mediated transgenesis in zebrafish | Mosimann | ||
| 68339 | pDestattB_ubi:EGFP (pCM272) | Multisite Gateway destination vector for phiC31-mediated transgenesis in zebrafish, harbors ubiquitin promoter (ubi)-driven EGFP. | EGFP (Other) | Mosimann | |
| 68341 | pDestattB/CY (pCM327) | Multisite Gateway destination vector to create transgenes for phiC31-mediated transgenesis in zebrafish, contains an attB site and alpha-cystallin:YFP (CY) transgenesis marker in backbone. | Mosimann | ||
| 69542 | pmtb-t7-alpha-bungarotoxin | For in vitro transcription of alpha-bungarotoxin mRNA that can be injected into embryos. | alpha-bungarotoxin (Synthetic) | Megason | |
| 70052 | p5E-mfap4 | 5' Entry vector containing the zebrafish mfap4 promoter. Used with Gateway Recombination to generate transgenic constructs exhibiting macrophage-restricted expression of transgenes. | mfap4 promoter (Danio rerio) | Tobin | |
| 71282 | HSP70l-APEX2-GBP in pDEST-Tol2-pA2-acrys-mCherry | Zebrafish expression vector for heat-shock inducible expression of APEX2-GBP | APEX2-GBP (Synthetic) | Parton | |
| 72433 | pCS2+_Myr-mIFP | Expression of Myr-mIFP in Zebrafish | Mry-mIFP | Shu | |
| 72640 | p5E-elavl3 | Gateway p5E 5'entry clone with elavl3 (HuC) enhancer/promoter for pan-neuronal expression in zebrafish | elavl3 enhancer (Danio rerio) | Bonkowsky | |
| 73198 | pBS-TarHom-Tol2-FRT-GalK-cryaa-YFP | BAC targeting cassette for pTARBAC2 with GalK selection marker and lens-specific transgenesis marker Citrine | YFP (Synthetic) | Knaut | |
| 73200 | pBS-TarHom-Tol2-FRT-GalK-cryaa-CFP | BAC targeting cassette for pTARBAC2 with GalK selection marker and lens-specific transgenesis marker Cerulean | CFP (Synthetic) | Knaut | |
| 73202 | pBS-TarHom-Tol2-TetR-cryaa-YFP | BAC targeting cassette for pTARBAC2 with tetR selection marker and lens-specific transgenesis marker Citrine | YFP (Synthetic) | Knaut | |
| 73203 | pBS-IndHom-Tol2-FRT-GalK-cryaa-dsRed | BAC targeting cassette for pIndigoBAC-536 with GalK selection marker and lens-specific transgenesis marker dsRed | dsRed (Synthetic) | Knaut | |
| 73204 | pBS-IndHom-Tol2-TetR-cryaa-dsRed | BAC targeting cassette for pIndigoBAC-536 with tetR selection marker and lens-specific transgenesis marker dsRed | dsRed (Synthetic) | Knaut | |
| 74009 | pUAS:Cas9T2AGFP;U6:sgRNA1;U6:sgRNA2 | Tissue-specific knock-out in zebrafish, Cas9 and GFP driven by a UAS promoter | 5x UAS (Saccharomyces cerevisiae), Cas9 (Other), T2A, GFP, U6 promoter (Danio rerio) | Del Bene | |
| 74010 | pUAS:Cas9T2ACre;U6:sgRNA1;U6:sgRNA2 | Tissue-specific knock-out in zebrafish, Cas9 and Cre driven by a UAS promoter | 5xUAS, Cas9, Cre, U6 promoter | Del Bene | |
| 74116 | pCS2+ MBIC5-mCer3 | For generating mRNA for zebrafish injection of cytoplasmic fluorogen-activating protein (FAP) | MBIC5-mCer3 (Synthetic) | Tsang | |
| 74117 | pISceI-myl7:MBIC5-mCer3 | Zebrafish transgenic construct | MBIC5-mCer3 (Synthetic) | Tsang | |
| 74302 | pDestTol2CG2-Neurog1-Magneto2.0-p2A-mCherry-pA | Expression of Magneto2.0-p2A-mCherry in Rohon-Beard sensory neurons of the zebrafish | Magneto2.0 (Homo sapiens) | Guler | |
| 74314 | 14UAS zfPSD95:GFP | A fusion of zebrafish PSD95 to GFP under control of 14 UAS repeats | zebrafish PSD95 (Danio rerio) | Smith | |
| 74315 | 14UAS PSD95:GFP 5UAS DSRedExpress | Encodes a PSD95:GFP fusion protein and DsRedExpress from separate UAS cassettes; for long-term two-photon time-lapse imaging of dendrite growth and synaptogenesis in zebrafish | zebrafish PSD95 (Danio rerio), DsRedExpress (Other) | Smith | |
| 74316 | 5UAS zfSynaptophysin:GFP | A fusion of zebrafish synaptophysin to GFP under the control of 5UAS repeats | synaptophysin (Danio rerio) | Smith | |
| 74317 | 5UAS zfSynaptophysin:GFP-5UAS DsRedExpress | A fusion of zebrafish synaptophysin to GFP and DsRedExpress under the control of separate UAS cassettes; for dual-labeling of retinal ganglion cell (RGC) axon arbors in zebrafish | synaptophysin (Danio rerio), DsRedExpress (Other) | Smith | |
| 74592 | pKHR4 | an ampR plasmid built from pBluescript: the multiple cloning site (mcs) flanked by inverted head-to-head oriented I-SceI sites. Genbank accession number is KU144822. | Grunwald | ||
| 74593 | pKHR5 | an alpha-crystallin::Venus (green lens) reporter cassette flanked by FRT sites and with a single loxP site at the 3’ end was inserted in the middle of pKHR4 mcs. Genbank accession number is KU144823. | FRT-alpha-crystallin::Venus-FRT-loxP reporter cassette (Danio rerio) | Grunwald | |
| 74624 | pKHR7 | a cmlc2::mCherry (red heart) reporter gene was inserted at the 3’end of pKHR4 mcs, that resides within donor fragments produced by I-SceI digestion. Genbank accession number is KU144824. | cmlc2::mCherry (Danio rerio) | Grunwald | |
| 74625 | pKHR8 | a plasmid derived from pKHR5: in addition to Venus reporter gene, it also contains cmlc2::mCherry (red heart) reporter gene at 3’ end of the mcs as pKHR7. Genbank accession number is KU144825. | FRT-alpha-crystallin::Venus-FRT-loxP reporter cassette (Danio rerio), cmlc2::mCherry (Danio rerio) | Grunwald | |
| 74632 | p5E--3mnx1 | Can be used to drive expression specifically in zebrafish motor neurons | motor neuron and pancreas homeobox 1 promoter (Danio rerio) | Cole | |
| 74736 | pDestTol2pA2-9xGRE | GRE-dependent EGFP reporter construct flanked by the minimal Tol2 transposon elements | EGFP (Other) | Dalla Valle | |
| 78627 | pTol2-DRv7 | GESTALT V7 barcode for zebrafish | GESTALT lineage tracing target V7 (Danio rerio) | Shendure | |
| 78628 | pTol2-DRv6 | GESTALT V6 barcode for zebrafish | GESTALT lineage tracing target V6 (Danio rerio) | Shendure | |
| 80904 | pMT-HuC:Dendra2 | Injection into Zebrafish larvae together with Tol2-Transposase to achieve pan-neuronal expression of the photoconvertible fluorescent protein Dendra2 | Dendra2 (Synthetic) | Pantazis | |
| 81234 | p5E-mitfa2.1 | zebrafish mitfa promoter entry vector for multisite Gateway cloning | mitfa promoter (Danio rerio) | Lister | |
| 82400 | p5E-elavl3 | Gateway-compatible zebrafish elavl3 promoter | elavl3 promoter (Danio rerio) | Eisen | |
| 82401 | p5E-gfap | Gateway-compatible zebrafish gfap promoter | gfap promoter (Danio rerio) | Eisen | |
| 82402 | p5E-mnx1 | Gateway-compatible zebrafish mnx1 promoter | mnx1 promoter (Danio rerio) | Eisen | |
| 82583 | p5E-EF1a/b-actin | 5' entry vector containing the EF1a/B-globin fused to zebrafish b-actin 2 enhancer/promoter for strong semi-ubiquitous expression | EF1a/b-globin fused to zebrafish b-actin 2 enhancer/promoter | Stankunas | |
| 82584 | p5E-dusp6 | 5' entry vector containing FGF-responsive regulatory element of the zebrafish dusp6 promoter for FGF-responding cells | FGF-responsive element of the dusp6 promoter (Danio rerio) | Stankunas | |
| 82585 | p5E-krt5 | 5' entry vector containing the zebrafish krt5 promoter for epidermis-specific expression | zebrafish krt5 promoter (Danio rerio) | Stankunas | |
| 84032 | pHD066 | Vector for creating transgenic zebrafish. Expresses mCherry-Cre fusion protein under the elastase promoter and Venus under the crystalin promoter in zebrafish | Cre (Other), Venus (Other) | Stainier | |
| 84033 | pHD157 | Vector for creating transgenic zebrafish. Expresses mCherry-Cre fusion protein under the fabp10 promoter and Venus under the crystalin promoter in zebrafish | Cre (Other), Venus (Other) | Stainier | |
| 84603 | 8xGliBS-IVS2-mCherry-NLS-Odc1-polyA-Tol2 | Tol2-based hedgehog signal reporter plasmid for zebrafish transgenesis | mCherry (Synthetic) | Chen | |
| 84604 | 8xGliBS-IVS2-mCherry-NLS-polyA-Tol2 | Tol2-based hedgehog signal reporter plasmid for zebrafish transgenesis | mCherry (Synthetic) | Chen | |
| 85418 | Dat - EGFP - Tol2 | for making transgenic zebrafish expressing GFP under the control of cis-regulatory elements of the dopamine transporter (dat) gene | dopamine transporter (Danio rerio) | Ekker | |
| 86248 | pTol-Promoter:NLS-tdMCP-eGFP | For generating transgenic lines that ubiquitously expressing the fluorescent MCP reporter | beta Actin promoter:NLS-tdMCPeGFP | Marlow | |
| 86371 | pUAS-MmTFP13xmyc | membrane targeted Tfp1 expression in zebrafish | mTfp1 (Other) | Wong | |
| 86372 | pUAS-MEYFP | membrane targeted EYFP expression in zebrafish | EYFP (Other) | Wong | |
| 86373 | pCx55.5-TrpR | for zebrafish transgenesis, expression of TrpR from Cx55.5 promoter, also expresses mCherry | TrpR (Other) | Wong | |
| 86374 | pME-nfsB-CFP | expression of nfsB-CFP | nitroreductase (Other) | Wong | |
| 86375 | pSws1-nfsB-CFP | for zebrafish transgenesis, expression of nfsB-CFP, also expresses EGFP | nitroreductase (Other) | Wong | |
| 89886 | pCrysβ:ECFP-LexOP:mCherry-NRasQ61K | Human NRasQ61K fused to mCherry downstream of LexOP, placed within a non-autonomous maize dissociation (Ds) element for integration in zebrafish. Contains pCrysB-ECFP for screening. | mCherry-NRasQ61K (Homo sapiens) | Sauka-Spengler | |
| 89887 | pCrysβ:ECFP-LexOP:mCherry-HrasG12V | Human HRasG12V fused to mCherry downstream of LexOP, placed within a non-autonomous maize dissociation (Ds) element for integration in zebrafish. Contains pCrysB-ECFP for screening. | mCherry-HRasG12V (Homo sapiens) | Sauka-Spengler | |
| 89888 | pCrysβ:ECFP-LexOP:mCherry-KrasG12V | Human KRasG12V fused to mCherry downstream of LexOP, placed within a non-autonomous maize dissociation (Ds) element for integration in zebrafish. Contains pCrysB-ECFP for screening. | mCherry-KRasG12V (Homo sapiens) | Sauka-Spengler | |
| 92388 | pTol2pA2-ubb:secHsa.ANNEXINV-mVenus, cryaa:RFP | Cell death reporter | ANNEXINV (Homo sapiens) | Cole | |
| 92400 | PhOTO-N (pMTB:memb-Cerulean-2A-H2B-Dendra2) | Constitutive expression of nuclear green-to-red photoconvertible Dendra2 and the membrane blue fluorescent protein Cerulean. | Dendra2 (Synthetic), Cerulean (Synthetic) | Pantazis | |
| 92401 | PhOTO-M (pMTB:memb-Dendra2-2A-H2B-Cerulean) | Constitutive expression of membrane green-to-red photoconvertible Dendra2 and the nuclear blue fluorescent protein Cerulean. | Dendra2 (Synthetic), Cerulean (Synthetic) | Pantazis | |
| 92402 | PhOTO-C (pMTB:cyto-Dendra2-2A-H2B-Cerulean) | Constitutive expression of cytosolic green-to-red photoconvertible Dendra2 and the nuclear blue fluorescent protein Cerulean. | Dendra2 (Synthetic), Cerulean (Synthetic) | Pantazis | |
| 101739 | pCMV-BE-zCas9 | expression of an optimized Cas9 for base-editing in zebrafish | rAPOBEC1-XTEN-zCas9-UGI-NLS (Rattus norvegicus) | Lin | |
| 101740 | pCMV-BE-VQRCas9 | expression of an optimized Cas9 for base-editing in zebrafish | rAPOBEC1-XTEN-zCas9(VQR)-UGI-NLS (Rattus norvegicus) | Lin | |
| 102417 | pVC-Ds-E1b:eGFP-Ds | Fluorescent vector for screening enhancer elements in zebrafish | E1b:eGFP (Danio rerio) | Sauka-Spengler | |
| 105127 | pKE4-I-SceI-fabp10a:Xpt-β-cat, cryaa:Venus | Used along with I-SceI enzyme to generate transgenic zebrafish expressing hepatocyte-specific Xenopus activated beta-catenin and lens-specific Venus fluorescent protein | Zebrafish fabp10a promoter:Xenopus pt-beta-catenin coding sequence, polyA (Xenopus laevis), Zebrafish cryaa promoter:Venus fluorescent protein coding sequence (Danio rerio) | Stainier | |
| 105664 | Tol2-BetaActin-SecA5-YFP | Ubiquitously expresses a secreted and fluorescently tagged Annexin5 for in-vivo apoptosis reporter | Secreted Annexin5-EYFP (Homo sapiens) | Deng | |
| 106425 | Tol2-ngn1-Trpa1b-2A-mCherry | For expressing Trpa1b-2A-mCherry in zebrafish Rohon-Beard neurons. | cmlc2 promoter (Danio rerio), Trpa1b (Danio rerio) | Peterson | |
| 107185 | pT3TS-zAsCpf1 | plasmid to carry out IVT of AsCpf1 (zebrafish codon optimized) | AsCpf1 (Danio rerio) | Giraldez | |
| 107590 | Tol2-lyzC-mito-Dendra2 | Expresses mitochondria localized Dendra2 in zebrafish neutrophils | mito-Dendra2 (Danio rerio) | Deng | |
| 108356 | UAS:iGluSnfr.zf1 | UAS driven variant of iGluSnFR for zebrafish expression | UAS:[GlyRa1 secretion sequence]-[iGluSnFR] (Synthetic) | Burgess | |
| 108415 | pTol2-UAS-zmiRFP | Codon-optimized monomeric near-infrared fluorescent protein miRFP in zebrafish expression plasmid | zmiRFP (Synthetic) | Boyden | |
| 108427 | pTol2-UAS-zArchon1-KGC-EGFP-ER2 | Codon-optimized Archon1 fluorescent voltage reporter in zebrafish expression plasmid | zArchon1-KGC-EGFP-ER2 (Synthetic) | Boyden | |
| 108428 | pTol2-UAS-zArchon2-KGC-EGFP-ER2 | Codon-optimized Archon2 fluorescent voltage reporter in zebrafish expression plasmid | zArchon2-KGC-EGFP-ER2 (Synthetic) | Boyden | |
| 108870 | pTol2-hspDRv7_scGstlt | scGESTALT V7 lineage barcode for zebrafish | scGESTALT lineage tracing target V7 (Synthetic) | Schier | |
| 108871 | pTol2-hsp70l:Cas9-t2A-GFP, 5xU6:sgRNA | Expression of heat shock inducible Cas9-GFP and U6-driven 5 individual gRNAs for scGESTALT in zebrafish | 5xU6:sgRNA (Danio rerio), Cas9-t2A-GFP (Danio rerio) | Schier | |
| 109490 | actc1b-mKate2-GPI-pA | Muscle specific zebrafish expression of mKate2 fused to the 5' and 3' sequences from zebrafish folate receptor 1 | actc1b-mKate2-GPI-pA (Synthetic) | Parton | |
| 109542 | pME-mKate2-GPI-pA | Multisite gateway vector for expression of mKate2 fused to the 5' and 3' sequences from zebrafish folate receptor 1 | mKate2 fused to the 5' and 3' sequences from zebrafish folate receptor 1 (Synthetic) | Parton | |
| 109768 | pT3TS_Transposase | Codon optimised transposase sequence in an optimal vector for in vitro transcription. Contains the T3 promoter and synthetic polyA tract. | Tol2 Transposase (Synthetic) | Parton | |
| 109769 | p3E-rev_U6_MCS | Multisite gateway vector for 3' expression of a guide RNA from the U6 promoter (cassette in the reverse orientation). Contains BseRI sites for insertion of gRNA sequence | U6-gRNA cassette (Synthetic) | Parton | |
| 110282 | ins:MCS; cryaa:RFP | A zebrafish insulin promoter containing vector with multiple cloning sites. Contains red eye marker, and is flanked with I-SceI sites. | Ninov | ||
| 110283 | ins:BB1.0L; cryaa:RFP | A zebrafish insulin promoter driving the Brainbow (BB1.0L) cassette. Contains red eye marker, and is flanked with I-SceI sites. | Brainbow1.0L (Synthetic) | Ninov | |
| 110285 | ins:GCaMP6s; cryaa:RFP | A zebrafish insulin promoter driving the calcium indicator, GCaMP6s. Contains red eye marker, and is flanked with I-SceI sites. | GCaMP6s (Other) | Ninov | |
| 110286 | ins:MCS2; cryaa:RFP | A zebrafish insulin promoter containing vector with a second multiple cloning sites. Contains red eye marker, and is flanked with I-SceI sites. | Ninov | ||
| 112205 | pBS-I-Sce1-eno2:Tau-IRES-egfp | Used to make transgenic zebrafish expressing human 4R/0N Tau under the neuronal eno2 promoter | MAPT (Homo sapiens) | Burton | |
| 112225 | pMTB | Expression of membrane-tagged super folder GFP from zebrafish beta-actin promoter. | Super-folder GFP (Other) | Megason | |
| 115515 | pTol2pA2-mnx1:MLS-KillerRed | Plasmid driving expression of membrane bound KillerRed fluorophore in zebrafish motor neurons | MLS-KillerRed (Other) | Morsch | |
| 115516 | 4xnrUAS:MLS-KillerRed in pTol2pA2-acrys-EGFP- | Plasmid driving expression of membrane bound KillerRed fluorophore under UAS response element, with a green lens reporter | MLS-KillerRed (Other) | Morsch | |
| 115517 | pME-MLS-KillerRed | Middle entry plasmid containing membrane bound KillerRed fluorophore | MLS-KillerRed (Other) | Morsch | |
| 118844 | MiniCoopR 2xU6:gRNA, mitfa:Cas9 | Targets 2 genes and expresses zebrafish mitfa specifically in zebrafish melanocytes | Zon | ||
| 119037 | pTol2-elavl3-Voltron | Pan neuronal expression of Voltron in zebrafish | Voltron (Synthetic) | Schreiter | |
| 119038 | pTol2-elavl3-Voltron-ST | Pan neuronal expression of soma-localized Voltron in zebrafish | Voltron-ST (Synthetic) | Schreiter | |
| 119039 | pTol2-10xUAS-Voltron | UAS-driven expresion of Voltron in zebrafish | Voltron (Synthetic) | Schreiter | |
| 119040 | pTol2-10xUAS-Voltron-ST | UAS-driven expresion of soma-localized Voltron in zebrafish | Voltron-ST (Synthetic) | Schreiter | |
| 119716 | pCS2(+)-zGrad | Plasmid to generate zGrad mRNA to inactivate proteins in zebrafish | zGrad (Danio rerio) | Knaut | |
| 121987 | pDestTol2-ubi-ASAP1 | ubiqutously express ASAP1 voltage biosensor | ASAP1 (Synthetic) | Zhang | |
| 122129 | pTol2-elavl3_NES-rsCaMPARI-mRuby3 | Pan-neuronal expression of rsCaMPARI in zebrafish, nucleus excluded | rsCaMPARI (Synthetic) | Schreiter | |
| 124231 | pTol1-UAS:ChrimsonR-tdTomato | Zebrafish Tol1 construct for UAS-mediated expression of the optogenetic opsin ChrimsonR fused to the red fluorescent protein tdTomato | ChrimsonR-tdTomato (Other) | Bianco | |
| 124232 | pTol1-UAS:Chronos-tdTomato | Zebrafish Tol1 construct for UAS-mediated expression of the optogenetic opsin Chronos fused to the red fluorescent protein tdTomato | Chronos-tdTomato (Other) | Bianco | |
| 124233 | pTol1-UAS:CoChR-tdTomato | Zebrafish Tol1 construct for UAS-mediated expression of the optogenetic opsin CoChR fused to the red fluorescent protein tdTomato | CoChR-tdTomato (Other) | Bianco | |
| 124234 | pTol1-UAS:CheRiff-tdTomato | Zebrafish Tol1 construct for UAS-mediated expression of the optogenetic opsin CheRiff fused to the red fluorescent protein tdTomato | CheRiff-tdTomato (Other) | Bianco | |
| 124235 | pTol1-UAS:GtACR1-tdTomato | Zebrafish Tol1 construct for UAS-mediated expression of the optogenetic opsin GtACR1 fused to the red fluorescent protein tdTomato | GtACR1-tdTomato (Other) | Bianco | |
| 124236 | pTol1-UAS:GtACR2-tdTomato | Zebrafish Tol1 construct for UAS-mediated expression of the optogenetic opsin GtACR2 fused to the red fluorescent protein tdTomato | GtACR2-tdTomato (Other) | Bianco | |
| 124237 | pTol1-UAS:ChR2(H134R)-tdTomato | Zebrafish Tol1 construct for UAS-mediated expression of the optogenetic opsin ChR2(H134R) fused to the red fluorescent protein tdTomato | ChR2(H134R)-tdTomato (Other) | Bianco | |
| 124431 | PCS2-FlipGFP(Casp3 cleavage seq) T2A mCherry | Expresses FlipGFP (caspase-3 cleavage sequence) protease reporter and T2A mCherry in zebrafish | FlipGFP(Casp3 cleavage seq) T2A mCherry (Synthetic) | Shu | |
| 124432 | PCS2-FlipGFP(Casp3 cleavage seq) | Expresses FlipGFP (caspase-3 cleavage sequence) protease reporter in zebrafish (verified) | FlipGFP(Casp3 cleavage seq) (Synthetic) | Shu | |
| 124433 | pCS2-GFP1-9 | Expresses GFP1-9 in zebrafish | GFP1-9 (Synthetic) | Shu | |
| 125690 | pT2-5xERE:GFP | Transgene to report estrogen receptor activity in zebrafish | 5xERE:GFP (Synthetic) | Halpern | |
| 125697 | pT2-bactin:QF2,crybb:CFP | Expresses QF2 ubiquitously in zebrafish, with selectable marker CFP in eye lens | bactin:QF2 (Danio rerio) | Gorelick | |
| 127591 | pBT2-4xUAS:P2A-EGFP | This vector is used for cloning a gene driven by 4xnrUAS, to be co-expressed with EGFP through P2A self-cleaving peptides. | Fang | ||
| 127592 | pBT2-4xUAS:P2A-mCerulean3 | This vector is used for cloning a gene driven by 4xnrUAS, to be co-expressed with mCerulean3 through P2A self-cleaving peptides. | Fang | ||
| 127594 | pBT2-4xUAS:NICD-P2A-mRFP | Zebrafish NICD was driven by 4xnrUAS, to be co-expressed with mRFP through P2A self-cleaving peptides. | NICD (Danio rerio) | Fang | |
| 128838 | Tg(lyz:EGFP-Mmu.Rpl10a) | RNA isolation from neutrophils via TRAP | EGFP-L10a | Huttenlocher | |
| 128839 | Tg(krt4:EGFP-Mmu.Rpl10a) | RNA isolation from keratinocytes via TRAP | EGFP-L10a | Huttenlocher | |
| 128840 | Tg(mpeg1:EGFP-Mmu.Rpl10a) | RNA isolation from machrophages via TRAP | EGFP-L10a | Huttenlocher | |
| 129265 | pTol2-Huc-Positron-ST | pan neuronal expression of soma-localized Positron in zebrafish | Positron-ST (Synthetic) | Schreiter | |
| 129266 | pT2-Tbait-UAS-Positron-ST | UAS-driven expression of Positron in zebrafish | Positron-ST (Synthetic) | Schreiter | |
| 129590 | pCMV-15F11-HA-mEGFP | The encoded protein is the anti-HA scFv (anti-HA frankenbody) fused with the mEGFP. It can be used to track mature and nascent HA tagged proteins in living organism. | Anti-HA frankenbody-mEGFP (15F11-HA scFv-mEGFP) (Homo sapiens) | Stasevich | |
| 129591 | pCMV-15F11-HA-mCh | The encoded protein is the anti-HA scFv (anti-HA frankenbody) fused with the mCherry. It can be used to track mature and nascent HA tagged proteins in living organism. | Anti-HA frankenbody-mCherry (15F11-HA scFv-mCh) (Homo sapiens) | Stasevich | |
| 129592 | pCMV-15F11-HA-Halo | The encoded protein is the anti-HA scFv (anti-HA frankenbody) fused with the HaloTag. It can be used to track mature and nascent HA tagged proteins in living organism. | Anti-HA frankenbody-HaloTag (15F11-HA scFv-HaloTag) (Homo sapiens) | Stasevich | |
| 129595 | pCMV-2E2-HA-mEGFP | The encoded protein is the anti-HA frankenbody variant fused with the mEGFP. It can be used to track mature and nascent HA tagged proteins in living organism. | Anti-HA frankenbody variant-mEGFP (2E2-HA scFv-mEGFP) (Homo sapiens) | Stasevich | |
| 129596 | pCMV-2E2-HA-mCh | The encoded protein is the anti-HA frankenbody variant fused with the mCherry. It can be used to track mature and nascent HA tagged proteins in living organism. | Anti-HA frankenbody variant-mCherry (2E2-HA scFv-mCherry) (Homo sapiens) | Stasevich | |
| 131780 | pCS2+PIF6CreN | Mammalian, Zebrafish, or Xenopus expression of PIF6CreN, one half of the CreLite system | PIF6CreN (Arabidopsis thaliana) | Eisenhoffer | |
| 131781 | pCS2+PhyBΔCreC | Mammalian, Zebrafish, or Xenopus expression of PhyBΔCreC, one half of the CreLite system. | PhyBCreC (Arabidopsis thaliana) | Eisenhoffer | |
| 131783 | pTol2-CreLite | Tol2 destination vector carrying Ubi:CreLite with mTagBFP2 as a visual marker. | PhyBCreC, PIF6CreN, and mTagBFP2 (Arabidopsis thaliana) | Eisenhoffer | |
| 131787 | pTol2-PcyA-IRES-HO1 | Tol2 bicistronic vector expressing PcyA and HO1 for Phycocyanobilin (PCB) synthesis, driven by heatshock promoter hsp70. | PcyA and HO1 (Homo sapiens) | Eisenhoffer | |
| 135214 | pDEST mfap4:tdTomato | Red tagged macrophages | mfap4 promoter and tdTomato (Danio rerio) | Tobin | |
| 135215 | pDEST mpeg1:tomato-CAAX | Red tagged macrophages | mpeg1 and tdTomato (Danio rerio) | Tobin | |
| 135217 | pDEST mfap4:icre-p2a-tomato | Cre coexpressed with tdTomato in macrophages | mfap4 promoter with iCre and Tomato (Danio rerio) | Tobin | |
| 135218 | pDEST mfap4:turquoise2 | Cyan tagged macrophages | mfap4 promoter and mTurquoise2 (Danio rerio) | Tobin | |
| 137185 | pTol2-HuC(elavl3)-CaMPARI2 | pan-neuronal expression of CaMPARI2 in zebrafish, used to generate the CaMPARI2 zebrafish line at ZIRC (ZL13801) | HuC(elavl3)-CaMPARI2-FLAG-HA-myc-polyA (Rattus norvegicus) | Schreiter |
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:
- 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:
- 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:
- 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.
Do you have suggestions for other plasmids that should be added to this list?
Fill out our Suggest a Plasmid form or e-mail [email protected] to help us improve this resource!