ArticleNature communications2021
Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
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Who cites it
142 citing papers in PubMed, 199 citations in OpenAlex.
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- ProST: an image prompt-guided multimodal representation learning framework for spatial domain identification.Bioinformatics (Oxford, England) · 2026Article
- st2traj: deconvolution-informed trajectory inference for multi-timepoint spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Advances in Poultry RNA-Omics Research: Technologies, RNA Information Layers, and Applications in Complex Traits.Animals : an open access journal from MDPI · 2026Review
- Deciphering spatial heterogeneity by multimodal spatial transcriptomics modelling with SpatialModal.Bioinformatics (Oxford, England) · 2026Article
- Article
- Alternative Developmental Toxicity Screening Methods Using Chick Embryo-Based Models.Journal of applied toxicology : JAT · 2026Review
- Cross-Propagative Graph Learning Reveals Spatial Tissue Domains in Multi-Modal Spatial Transcriptomics.Small methods · 2026Article
- Decoding Cardiac Development and Maturation at Single-Cell and Spatial Transcriptomic Resolution.Circulation research · 2026Review
- An efficient method for tissue-specific protoplast isolation suitable for single-cell RNA sequencing and transient gene expression analysis in saffron (Crocus sativus L.).BMC biotechnology · 2026Article
- Myocardial Immune Niches in Homeostasis and Inflammation.Immunological reviews · 2026Review
- IntegrateRigor: annotation-free integration optimization for cell identity recovery reveals cancer-immune interface niches.bioRxiv : the preprint server for biology · 2026Article
- SECTOR: structural entropy-based learning of spatiotemporal organisation in spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Kinemomics: spatiotemporal morphodynamic mapping of ventricular kinematic subpopulations in organotypic fetal heart slices.bioRxiv : the preprint server for biology · 2026Article
- Robust identification of cell-cell communication heterogeneity in single cells.bioRxiv : the preprint server for biology · 2026Article
- Single-cell transcriptomics reveals targeted modulation of inflammatory repertoire by SOCE blockers.Human immunology · 2026Article
- Pan-3D Genome Analysis Reveals the Roles of Structural Variation in Chicken Chromatin Architectures, Domestication and Production Traits.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Simultaneous spatial transcriptomics and morphology profiling as tools to explore how microglia change with age.Nature aging · 2026Article
- Single-Cell Multi-Omics Reveal Gene Regulatory Mechanisms Underlying Cardiac Embryonic Development.Genes · 2026Review
82 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
Single-cell RNA sequencing is a powerful tool to study developmental biology but does not preserve spatial information about tissue morphology and cellular interactions. Here, we combine single-cell and spatial transcriptomics with algorithms for data integration to study the development of the chicken heart from the early to late four-chambered heart stage. We create a census of the diverse cellular lineages in developing hearts, their spatial organization, and their interactions during development. Spatial mapping of differentiation transitions in cardiac lineages defines transcriptional differences between epithelial and mesenchymal cells within the epicardial lineage. Using spatially resolved expression analysis, we identify anatomically restricted expression programs, including expression of genes implicated in congenital heart disease. Last, we discover a persistent enrichment of the small, secreted peptide, thymosin beta-4, throughout coronary vascular development. Overall, our study identifies an intricate interplay between cellular differentiation and morphogenesis.
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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.