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Zebrafish

Zebrafish

Danio rerio

A popular vertebrate model organism for studying development, genetics, regeneration, and human diseases.

Dataset Statistics

1418
Bulk runs
8.3 T
Bulk bases
120
SC sample groups
3.2 M
Cells

Overview

Zebrafish (Danio rerio) is a premier model organism for developmental biology, genetics, and regenerative medicine research. This portal provides comprehensive genomic resources including bulk RNA-seq, ATAC-seq, ChIP-seq, single-cell RNA-seq and single-cell ATAC-seq datasets spanning embryonic development, organogenesis, and regeneration processes.

Research Areas Covered

  • Embryonic Development: Cell fate determination, pluripotency regulation, maternal-to-zygotic transition
  • Organogenesis: Heart, brain, pancreas, retina, gonad, and other organ development
  • Hematopoiesis: Stem cell expansion, lineage specification, blood cell development
  • Regeneration: Heart, fin, brain, retinal, and muscle regeneration mechanisms
  • Disease Models: Cancer, cardiovascular disease, toxicology, environmental stress responses
  • Epigenetics: DNA methylation, histone modifications, chromatin accessibility, 3D genome organization
  • Single-cell Analysis: Cell-type identification, developmental trajectories, lineage tracing, cell state transitions

Reference Genome and Annotation

ItemValue
Genome assemblyGRCz11
Gene annotationEnsembl 100

Data Sources

Single cell data
StudyIDYearJournalTitlePMIDSampleGeneID handling
2025_Elife_Chung2025ElifeSingle-cell transcriptomes of zebrafish germline reveal progenitor types and feminization by Foxl2l40497446Germ cellsRebuilt
2025_DevCell_Xiong2025Dev CellCloche/Npas4l is a pro-regenerative platelet factor during zebrafish heart regeneration40602409HeartConverted
2024_NatCellBiol_Lan2024Nat Cell BiolMapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq38977847Embryo, scATACConverted
2024_Development_Gagnon2024DevelopmentGerm cell progression through zebrafish spermatogenesis declines with age39470160Germ cellsRebuilt
2024_Cell_Royer2024CellA multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors39454574EmbryoConverted
2024_BiolOpen_Gagnon2024Biol OpenDistinct features of the regenerating heart uncovered through comparative single-cell profiling38526188HeartConverted
2023_Nature_Trapnell2023NatureEmbryo-scale reverse genetics at single-cell resolution37968389EmbryoConverted
2023_DevCell_Farrell2023Dev CellSingle-cell analysis of shared signatures and transcriptional diversity during zebrafish development37995681EmbryoConverted
2022_NatCommun_Crump2022Nat CommunLifelong single-cell profiling of cranial neural crest diversification in zebrafish35013168Cranial neural crest-derived cells (CNCCs), scRNA+scATACConverted
2022_FrontiersinGenetics_Xie2022Front GenetSingle cell transcriptome sequencing of zebrafish testis revealed novel spermatogenesis marker genes and stronger leydig-germ cell paracrine interactions35360857TestisRebuilt
2022_Elife_Draper2022ElifeSingle-cell transcriptome reveals insights into the development and function of the zebrafish ovary35588359Germ cellsRebuilt
2020_Science_Blackshaw2020ScienceGene regulatory networks controlling vertebrate retinal regeneration33004674RetinaConverted
2020_EnvironSciTechnol_Wu2020Environ Sci TechnolSingle-cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development32644799EmbryoConverted
2020_EMBORep_Sumeet2020EMBO RepSingle-cell transcriptome analysis reveals thyrocyte diversity in the zebrafish thyroid gland33140917ThyroidConverted
2020_DevCell_Riley2020Dev CellFunctional heterogeneity within the developing zebrafish epicardium32084358EpicardiumConverted
2020_DevBiol_Miller2020Dev BiolA single-cell transcriptome atlas for zebrafish development31782996EmbryoConverted
2019_CellRep_Liu2019Cell RepA 3D atlas of hematopoietic stem and progenitor cell expansion by multi-dimensional RNA-seq analysis31042481Caudal hematopoietic tissue (CHT)Converted
2018_Science_Schier2018ScienceSingle-cell reconstruction of developmental trajectories during zebrafish embryogenesis29700225EmbryoConverted
2018_Science_Klein2018ScienceSingle-cell mapping of gene expression landscapes and lineage in the zebrafish embryo29700229EmbryoConverted
2018_NatBiotechnol_Schier2018Nat BiotechnolSimultaneous single-cell profiling of lineages and cell types in the vertebrate brain29608178BrainConverted

GeneID handling describes how single-cell gene identifiers are connected to the current portal database:

  • Original: keeps the author’s original identifier system.
  • Converted: keeps the author matrix but converts gene identifiers to the current database when a stable mapping is available. Some features may be omitted from public display when no confident mapping exists, and renamed or merged annotations can introduce small differences relative to the author’s original feature set.
  • Rebuilt: regenerates the matrix from raw reads against the current reference. This keeps identifiers consistent with the current database, but expression values, detected features, and cell annotations can differ from the author’s original workflow.
Bulk data
StudyIDYearJournalTitlePMIDSample
2024_DevCell_Simoes2024Dev CellDistinct epicardial gene regulatory programs drive development and regeneration of the zebrafish heart38237592Epicardium control, larval, sham and cryoinjury states in tbx18 and tcf21 lineages
2022_NatCommun_Onichtchouk2022Nat CommunPluripotency factors determine gene expression repertoire at zygotic genome activation35145080Embryo 2.5 to 6 hpf, dome and oblong
2022_NatCommun_Bessa2022Nat CommunMultidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers35410466Endocrine, exocrine, muscle and pancreas
2022_Development2022DevelopmentWt1 transcription factor impairs cardiomyocyte specification and drives a phenotypic switch from myocardium to epicardium35312773Heart tube, proepicardium, pericardium and wt1b overexpression
2022_BMCGenomics2022BMC GenomicsHigh-throughput transcriptome sequencing reveals the key stages of cardiovascular development in zebrafish embryos35964013Embryo 18, 24 and 42 hpf
2021_Development2021DevelopmentExtensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish33298460Embryo 0 hpf to 10 dpf and PGC RNA fractions
2021_DevCell2021Dev CellGerm cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization33651978PGC, soma and brain from 256-cell to prim5 and 10 somites
2020_iScience2020iScienceDemarcation of topologically associating domains is uncoupled from enriched CTCF binding in developing zebrafish32334414Embryo 24 hpf
2020_eLife_Zhu2020eLifeAn improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes32831172Nr2f2/Y1 and pdgfrb positive and negative cell populations
2020_eLife_Cornell2020eLifeAnalysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/1832031521krt4-GFP positive and negative embryo cells at 11 hpf
2020_Science_SanchezAlvarado2020ScienceChanges in regeneration-responsive enhancers shape regenerative capacities in vertebrates32883834Fin regeneration 0 and 1 dpa, RNA and chromatin marks
2020_Nature2020NatureA map of cis-regulatory elements and 3D genome structures in zebrafish33239788Adult tissues plus embryonic brain and trunk
2020_GenomeBiol2020Genome BiolRegenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility32106888Fin 0, 1, 2 and 4 dpa, sp7-positive and sp7-negative subsets
2020_CirculationRes2020Circ ResAP-1 contributes to chromatin accessibility to promote sarcomere disassembly and cardiomyocyte protrusion during zebrafish heart regeneration32312172Heart 4 dpci A-Fos and gata4 states, uninjured overexpression controls
2019_PLoSOne2019PLoS OneTranscriptomic profile of early zebrafish PGCs by single cell sequencing31412047PGC 6, 11 and 24 hpf
2019_NatCommun_Tena2019Nat CommunPioneer and repressive functions of p63 during zebrafish embryonic ectoderm specification31296872Embryo 24 and 36 hpf, 8 somites, 80% epiboly
2019_NatCommun_Bogdanovic2019Nat CommunRetention of paternal DNA methylome in the developing zebrafish germline31296860PGC and soma at 4 to 36 hpf, adult liver
2019_InvestOphthalmolVisSci2019Invest Ophthalmol Vis SciParadoxical changes underscore epigenetic reprogramming during adult zebrafish extraocular muscle regeneration31794598Muscle control, 18 hpi, 9 dpi
2019_GenomeRes2019Genome ResDynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development30760547Heart GFP positive and negative cells, 24 to 72 hpf, mutants
2019_Development2019DevelopmentH3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration31427288Heart and cardiomyocytes, injured and uninjured
2019_DevBiol2019Dev Biolfoxc1 is required for embryonic head vascular smooth muscle differentiation in zebrafish31199900acta2 and kdrl positive and negative vascular cells
2019_BMCBiol2019BMC BiolFoxH1 represses miR-430 during early embryonic development of zebrafish via non-canonical regulation31362746Embryo 6 hpf
2018_PLoSGenet2018PLoS GenetCooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation30080860Hindbrain and posterior tissues at 5 and 15 ss, 95% epiboly
2018_Nature2018NatureAmphioxus functional genomics and the origins of vertebrate gene regulation30464347Embryo 2 to 72 hpf
2018_GenomeRes2018Genome ResInherited DNA methylation primes the establishment of accessible chromatin during genome activation29844026Embryo 64-cell to oblong, dome, 1k-cell
2018_FrontEndocrinol_Lausanne2018Front Endocrinol (Lausanne)Transcriptomic analysis for differentially expressed genes in ovarian follicle activation in the zebrafish30364302Ovary PG and PV follicles
2018_Development2018DevelopmentCohesin facilitates zygotic genome activation in zebrafish29158440Embryo 2.5 to 10 hpf
2018_Cell2018CellPlaceholder nucleosomes underlie germline-to-embryo DNA methylation reprogramming29456083Pre-ZGA and post-ZGA embryo, sperm
2017_eLife_Stainier2017eLifeReciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration28632131Heart regeneration 0 h to 5 dpci/dps, 6 hpci/hps
2017_eLife_Giraldez2017eLifeA high-resolution mRNA expression time course of embryonic development in zebrafish29144233Embryo 0 hpf to 5 dpf
2017_Development2017DevelopmentHeart morphogenesis gene regulatory networks revealed by temporal expression analysis28807900Heart 30 to 72 hpf
2017_DevCell2017Dev CellThe vertebrate protein dead end maintains primordial germ cell fate by inhibiting somatic differentiation29257950PGC 13 hpf
2017_CellRep2017Cell RepRobust identification of developmentally active endothelial enhancers in zebrafish using FANS-assisted ATAC-seq28723572fli1a-GFP positive and negative cells at 24 hpf
2017_BMCGenomics2017BMC GenomicsHistological and transcriptomic effects of 17α-methyltestosterone on zebrafish gonad development28738802Ovary and testis at 40 and 60 dpf
2016_NatCommun2016Nat CommunRepulsive cues combined with physical barriers and cell-cell adhesion determine progenitor cell positioning during organogenesis27088892PGC and soma at 7 and 36 hpf
2015_PNAS2015Proc Natl Acad Sci U S ADeep conservation of wrist and digit enhancers in fish25535365Embryo 24 hpf, fin 60 hpf
2015_GenomicsData2015Genom DataGenome-wide epigenetic cross-talk between DNA methylation and H3K27me3 in zebrafish embryos26697317Embryo dome, 24 and 48 hpf
2014_BMCBiol2014BMC BiolGlobal identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression25277163Embryo blastula
2013_StemCellReports2013Stem Cell ReportsA Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis24286030Embryo bud stage
2013_Science2013SciencePou5f1 transcription factor controls zygotic gene activation in vertebrates23950494Embryo 2.75 and 5 hpf
2013_PLoSGenet2013PLoS GenetGenome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish24204288Embryo 8 and 24 hpf
2013_Cell2013CellReprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern23663776Early embryo, egg, sperm, muscle
2013_BMCGenomics2013BMC GenomicsDifferential transcript isoform usage pre- and post-zygotic genome activation in zebrafish23676078Embryo post-MBT
2012_GenomeRes_Schier2012Genome ResSystematic identification of long noncoding RNAs expressed during zebrafish embryogenesis22110045Embryo 0.75 hpf to 5 dpf
2012_GenomeRes_GomezSkarmeta2012Genome ResDynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis22593555Embryo dome, 80% epiboly, 24 and 48 hpf
2012_GenomeRes_Bartel2012Genome ResExtensive alternative polyadenylation during zebrafish development22722342Embryo 1-cell to 72 hpf, adult brain, ovary, testis
2012_DevCell2012Dev CellNanog-like regulates endoderm formation through the Mxtx2-Nodal pathway22421047Embryo 3.5 and 4.5 hpf
2012_DevBiol2012Dev BiolZebrafish globin switching occurs in two developmental stages and is controlled by the LCR22537494Adult erythroid cells and whole extract
2011_DevBiol2011Dev BiolIdentification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites21435340Embryo 24 hpf
2011_Cell2011CellConserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution22196729Embryo 24 and 72 hpf, adult

Genome Browser

Interactive genomic data visualization and exploration using JBrowse 2

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Gene Browser

Interactive gene expression analysis and multi-omics data exploration using Dash

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BLAST Search

Find similar sequences in the Zebrafish database using SequenceServer

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