Tracking the differentiation of Xenopus epithelia using single-cell RNA sequencing

Abstract

During Xenopus development, cells in the animal cap can differentiate into various type of epithelial cells, including ciliated cell, ionocyte, mucus-secreting goblet cell, and serotonin-secreting cells. To understand the details of cell differentiation in this system, we performed single-cell RNA sequencing (scRNA-Seq) to analyze the cell populations changes and their gene expression through the differentiation of Xenopus epithelia (from embryonic stage 8 to stage 27). As a result, we observed that in the early stage, cells in the animal cap show similar gene expression and clustered in one big cluster. However, as the epithelia are differentiated, several different cell clusters emerged. By tracking each cell cluster based on their expression patterns, we could see the history of cell differentiation in the population level. For example, ciliated cell cluster is distinct from other cell clusters in the early stage, while ionocyte and secretory cell clusters start to show in the late stage. We also identified the single-cell level marker genes for each group of the cell population, which can be useful to study the cells in each cluster. This result will expand our knowledge to understand the development of mucociliary epithelia.