ArticleDevelopmental biology2020
A single-cell transcriptome atlas for zebrafish development.
Article in Developmental biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 172 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
172 citing papers in PubMed, 312 citations in OpenAlex.
- PAICS mediates DNA damage and cerebellar neuronal loss in C9orf72 amyotrophic lateral sclerosis.Brain : a journal of neurology · 2026Article
- Mycn regulates vascular development through PI3K signaling pathway in zebrafish.Developmental dynamics : an official publication of the American Association of Anatomists · 2026Article
- Laminin α5 and integrins α3 and α6 coordinately regulate collective cell migration in vivo.Development (Cambridge, England) · 2026Article
- Distinct transcriptional programs define cranial motor neuron subtypes during vertebrate development.bioRxiv : the preprint server for biology · 2026Article
- Lineage-specific change in craniofacial gene regulatory networks of syngnathid fishes revealed by integrating multiomics across fishes.bioRxiv : the preprint server for biology · 2026Article
- Remote homology and functional genetics unmask deeply preserved Scm3/HJURP orthologs in metazoans.Science advances · 2026Article
- Comparison of Human Melanoma Single Cell Profiles to Evolutionary Medicine Model Xiphophorus Provides Insights in Disease Control.Pigment cell & melanoma research · 2026Article
- Molecular Basis of Color Variation in Taiwanese Loach Revealed by Early Developmental Transcriptome Analysis.Animals : an open access journal from MDPI · 2026Article
- Myosin light chain proteins cooperatively promote sarcomere growth in fast-twitch muscle.Nature communications · 2026Article
- Heme oxygenase 1 activity mediates red blood cell clearance and tail fin regeneration in zebrafish larvae.Scientific reports · 2026Article
- Flow-mediated endothelial remodeling and inflammation drive developmental vascular susceptibility in ldlr loss of function.Nature communications · 2026Article
- A comparative brain atlas in the Mexican cavefish identifies widespread changes in cellular composition and gene expression.bioRxiv : the preprint server for biology · 2026Article
- Mutation of Tubgcp6 induces hematopoietic stem and progenitor cell exhaustion in zebrafish.Communications biology · 2026Article
- Modern Mining: The Role of Single-cell RNA Sequencing in Advancing Neuroscience Research.BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Remote homology and functional genetics unmask deeply preserved Scm3/HJURP orthologs in metazoans.bioRxiv : the preprint server for biology · 2026Article
- Loss of MITF activity leads to emergent cell states from the melanocyte stem cell lineage.bioRxiv : the preprint server for biology · 2026Article
- Transcriptional profiling of extraocular motor neurons revealsbioRxiv : the preprint server for biology · 2026Article
- A transcription regulator atlas identifies TOX3 as an Atoh1 coactivator in cerebellar development and tumorigenesis.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- LMO1 expression in neuroblastoma cells reprograms tumor-associated macrophages to promote metastasis.iScience · 2026Article
- ROME, an Ancient Gene with a Novel Function in Vertebrates, Is a Key Modulator of Embryonal Development and Cancer Metastasis.Cancer research communications · 2026Article
112 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge, we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap, we produced an atlas using single-cell RNA-sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single-cell transcriptome atlas encompasses transcriptional profiles from 44,102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single-cell resolution. Furthermore, we highlight the power of this analysis to assign new cell-type or developmental stage-specific expression information to many genes, including those that are currently known only by sequence and/or that lack expression information altogether. The resulting atlas is a resource for biologists to generate hypotheses for functional analysis, which we hope integrates with existing efforts to define the diversity of cell-types during zebrafish organogenesis, and to examine the transcriptional profiles that produce each cell type over developmental time.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.