A resource of single‐cell gene expression profiles in a planarian Dugesia japonica

Abstract

The freshwater planarian Dugesia japonica maintains an abundant heterogeneous cell population called neoblasts, which include adult pluripotent stem cells. Thus, it is an excellent model organism for stem cell and regeneration research. Recently, many single‐cell RNA sequencing (scRNA‐Seq) databases of several model organisms, including other planarian species, have become publicly available; these are powerful and useful resources to search for gene expression in various tissues and cells. However, only one scRNA‐Seq dataset for D. japonica that has limitation in the detected gene number has been available. Herein, we collected D. japonica cells, and conducted scRNA‐Seq analysis. A novel, automatic, iterative cell clustering strategy produced 3,404 cell dataset, which could be classified into 63 cell types based on gene expression profiles. We introduced two kinds of usage examples of the scRNA‐Seq dataset in this study using D. japonica. First, the dataset provided consistent results with previous studies as well as novel functionally relevant insights, i.e., the expression of DjMTA and DjP2X‐A genes in neoblasts that give rise to differentiated cells. Second, we conducted an integrative analysis of the scRNA‐Seq dataset and time‐course bulk RNA‐Seq of irradiated animals, demonstrating that the dataset can help interpret differentially expressed genes captured via bulk RNA‐Seq. Using the R package “Seurat” and GSE223927, researchers can easily access and utilize this dataset. (215/250 words)This article is protected by copyright. All rights reserved.