Understanding how a fertilized egg develops into a complex organism requires tracking how individual cells change over time. During embryonic development, cells gradually specialize into different types, such as muscle cells, neurons, or skin cells. Studying these transitions can reveal how organisms build tissues and organs and how genetic programs control development.

Researchers at Chiba University in Japan created a detailed map of gene activity during the early development of the Western Pacific sea urchin Hemicentrotus pulcherrimus. They used single cell RNA sequencing, a technology that measures gene expression in individual cells instead of averaging signals across thousands or millions of cells.

Cells expressing neural-specific genes are shown in darker shades. Developmental stages progress from left to right. The increase in neural cells can be seen in the later stages of development.

Traditional bulk RNA sequencing measures gene activity across large groups of cells. While useful, this approach can hide important differences between cell types. Single cell RNA sequencing solves this problem by analyzing cells one at a time, allowing scientists to see how specific cell populations form and change as development progresses.

Using this approach, the research team built a developmental atlas of sea urchin embryos covering several stages of development. The atlas captures gene expression patterns from 24 to 96 hours after fertilization, allowing researchers to follow how cells shift into different developmental pathways. By analyzing these data, the scientists identified groups of genes that are active during the formation of neurons.

The study also explored the role of the Delta Notch signaling pathway, a well known communication system that helps cells decide what type of cell they will become. By pharmacologically inhibiting this pathway, the researchers were able to reveal additional genes involved in neuronal development that are normally difficult to detect. This helped clarify how certain regulatory genes maintain populations of neural precursor cells before they differentiate into mature neurons.

To make these results widely accessible, the team developed an interactive web platform within the HpBase database. The platform allows users to explore gene expression patterns directly through a graphical interface. Importantly, it was designed so that scientists without advanced bioinformatics skills can still investigate the dataset.

Another key feature of the project connects bulk RNA sequencing data with single cell data. The researchers implemented a cell type deconvolution method that allows bulk datasets to be interpreted using the single cell atlas as a reference. This makes it possible to estimate which cell types are present in bulk samples and how their proportions change over time.

Beyond sea urchin biology, the work provides a useful framework for combining bulk and single cell transcriptomic data in organisms that lack extensive genomic resources. Such strategies could help researchers study development, evolution, and cell type diversity across a wide range of species.

By integrating single cell RNA sequencing, pathway perturbation experiments, and accessible data tools, the researchers have created a valuable resource for understanding how neurons form during early development and how complex cell populations emerge in living organisms.

Availability – https://cell-innovation.nig.ac.jp/Hpul/