ArticleeLife2020
An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes.
Article in eLife, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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Who cites it
90 citing papers in PubMed.
- Comutation of asxl1 and IDH2R172K enhances leukemogenesis and correlates with epigenetic activation of MAPK and AP-1 in zebrafish.Blood advances · 2026Article
- In vivo screen for osteoclast derived osteogenic factors using non-resorptive osteoclasts in zebrafish bone.G3 (Bethesda, Md.) · 2026Article
- Sulf1 regulates inflammation via modulation of TGF-β dependent epicardial activation.EMBO reports · 2026Article
- Evolutionarily Conserved Epigenetic Regulation of Transcriptional Cell States During Vertebrate Pancreatic Tumorigenesis.Cellular and molecular gastroenterology and hepatology · 2026Article
- Fibroblast response to burn injury in larval zebrafish mirrors developmental maturation and is inhibited by infiltrating neutrophils.Development (Cambridge, England) · 2026Article
- Review
- Lineage-specific change in craniofacial gene regulatory networks of syngnathid fishes revealed by integrating multiomics across fishes.bioRxiv : the preprint server for biology · 2026Article
- Whole-body single-cell atlas of an adult vertebrate in homeostasis and regeneration.bioRxiv : the preprint server for biology · 2026Article
- Elevated phagocytic capacity directs innate spinal cord repair.Cell reports · 2026Article
- Intracellular pH dynamics promotes zebrafish larval tail regeneration.bioRxiv : the preprint server for biology · 2026Article
- Molecular and functional dissection using CaMPARI-seq reveals the neuronal organization for dissociating optic flow-dependent behaviors.Nature communications · 2026Article
- MIC-Drop-seq: scalable single-cell phenotyping of mutant vertebrate embryos.Nature communications · 2026Article
- Hb-EGF directs systemic muscle repair.Development (Cambridge, England) · 2026Article
- Gli3R-mediated inhibition of hedgehog signaling alters the embryonic transcriptome in zebrafish.G3 (Bethesda, Md.) · 2026Article
- Attenuation of epicardial activation and myofibroblast abundance via the Fbln2-Nupr1b axis stimulates cardiac regeneration in zebrafish.Nature cardiovascular research · 2026Article
- Zebrafish screen of schizophrenia risk genes reveals convergent dysregulation of cholesterol metabolism.bioRxiv : the preprint server for biology · 2026Article
- Vertebrate-wide transcriptomic screening identifies immune cell-specific expression of the conserved OR-κ gene.Zoological letters · 2026Article
- Article
- Developmental single-cell atlas of coronary vessel growth and cardiomyocyte interaction in zebrafish.Development (Cambridge, England) · 2026Article
- Impact of maternal compensation on developmental phenotypes in a zebrafish model of severe congenital muscular dystrophy.PLoS genetics · 2026Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
The zebrafish is ideal for studying embryogenesis and is increasingly applied to model human disease. In these contexts, RNA-sequencing (RNA-seq) provides mechanistic insights by identifying transcriptome changes between experimental conditions. Application of RNA-seq relies on accurate transcript annotation for a genome of interest. Here, we find discrepancies in analysis from RNA-seq datasets quantified using Ensembl and RefSeq zebrafish annotations. These issues were due, in part, to variably annotated 3' untranslated regions and thousands of gene models missing from each annotation. Since these discrepancies could compromise downstream analyses and biological reproducibility, we built a more comprehensive zebrafish transcriptome annotation that addresses these deficiencies. Our annotation improves detection of cell type-specific genes in both bulk and single cell RNA-seq datasets, where it also improves resolution of cell clustering. Thus, we demonstrate that our new transcriptome annotation can outperform existing annotations, providing an important resource for zebrafish researchers.
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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.