ArticleDevelopment (Cambridge, England)2021
Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo.
Article in Development (Cambridge, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Deciphering Gamete Differentiation in Ostrea edulis using Laser Capture Microdissection and RNA-seq.Marine biotechnology (New York, N.Y.) · 2026Article
- Distinct cell states define larval and adult body plans in a hemichordate.Nature communications · 2026Article
- BMP signaling regulates dorsal skeletal growth in the sea urchin embryo.Development (Cambridge, England) · 2026Article
- Extreme conservation of cnidarian stinging cell identity despite 600 million years of evolution.bioRxiv : the preprint server for biology · 2026Article
- Metamorphosis of the purple sea urchin Heliocidaris crassispina: Single-cell transcriptomic datasets.Scientific data · 2026Article
- Wnt dynamics at the blastopore and stomodeum during sea urchin gastrulation.Development (Cambridge, England) · 2026Article
- Parameter-free representations outperform single-cell foundation models on downstream benchmarks.ArXiv · 2026Article
- Parameter-free representations outperform single-cell foundation models on downstream benchmarks.bioRxiv : the preprint server for biology · 2026Article
- A Field-Friendly, Non-Toxic Fixative for Integrated Morphological and Molecular Research in Non-Model Invertebrates.Ecology and evolution · 2026Article
- Skeletogenic Expression of Integrin Alpha, Talin and Npnt Genes and Npnt Role in Sea Urchin Skeletogenesis.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2026Article
- Non-visual photoreceptive brain specification in sea urchin larvae.Nature communications · 2025Article
- Single-nucleus profiling highlights the all-brain echinoderm nervous system.Science advances · 2025Article
- Primordial germ cell specification and early developmental cell states in Pacific oyster.BMC genomics · 2025Article
- Genetically tractable embryonic cell lines from sea urchins Lytechinus variegatus and Strongylocentrotus purpuratus.Communications biology · 2025Article
- Applications and techniques of single-cell RNA sequencing across diverse species.Briefings in bioinformatics · 2025Review
- The Cell States of Sea Urchin During Metamorphosis Revealed by Single-Cell RNA Sequencing.International journal of molecular sciences · 2025Article
- Single-Cell Transcriptomics Reveals Evolutionary Reconfiguration of Embryonic Cell Fate Specification in the Sea Urchin Heliocidaris erythrogramma.Genome biology and evolution · 2025Article
- Article
- Reprogramming of cells during embryonic transfating: overcoming a reprogramming block.Development (Cambridge, England) · 2024Article
- An RNA interference approach for functional studies in the sea urchin and its use in analysis of nodal signaling gradients.Developmental biology · 2024Article
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Authors and funding
7 authors.
Funding
Abstract
Using scRNA-seq coupled with computational approaches, we studied transcriptional changes in cell states of sea urchin embryos during development to the larval stage. Eighteen closely spaced time points were taken during the first 24 h of development of Lytechinus variegatus (Lv). Developmental trajectories were constructed using Waddington-OT, a computational approach to 'stitch' together developmental time points. Skeletogenic and primordial germ cell trajectories diverged early in cleavage. Ectodermal progenitors were distinct from other lineages by the 6th cleavage, although a small percentage of ectoderm cells briefly co-expressed endoderm markers that indicated an early ecto-endoderm cell state, likely in cells originating from the equatorial region of the egg. Endomesoderm cells also originated at the 6th cleavage and this state persisted for more than two cleavages, then diverged into distinct endoderm and mesoderm fates asynchronously, with some cells retaining an intermediate specification status until gastrulation. Seventy-nine out of 80 genes (99%) examined, and included in published developmental gene regulatory networks (dGRNs), are present in the Lv-scRNA-seq dataset and are expressed in the correct lineages in which the dGRN circuits operate.
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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 Socratic graph.