Single-cell transcriptomic resources for tracing neurogenesis and cell fate specification in sea urchin embryos

We generated a developmental stage-specific single-cell RNA-sequencing atlas of the Western Pacific sea urchin Hemicentrotus pulcherrimus, uncovering new gene modules associated with neurogenesis and identifying Delta/Notch-sensitive regulators of neuronal differentiation. Pharmacological perturbation of this pathway revealed neurogenic genes that are inconspicuous under normal conditions and clarified the roles of regional specifiers in maintaining progenitor states. To promote broader accessibility, we developed an interactive web platform within HpBase with Kana, enabling gene expression exploration even for researchers without computational expertise. Furthermore, we performed a cell-type deconvolution method that links bulk RNA sequencing to the single-cell reference, allowing rapid visualization of cell-type composition changes from bulk data alone. These integrated resources and analytical tools not only provide mechanistic insights into echinoderm neurodevelopment but also establish a generalizable workflow for combining bulk and single-cell transcriptomics in non-model organisms, empowering developmental and evolutionary biologists with practical strategies for cell-type-level resolution in complex systems.