Single Cell RNA Sequencing Data Analysis and Applications in Caenorhabditis Elegans Embryo Development

Single cell RNA sequencing (hereinafter “scRNA-seq”) has become a routine assay in molecular biological research, allowing in-depth assessments of individual cell transcriptome. Here, we used scRNA-seq datasets to study the global cellular communications in the Caenorhabditis elegans (hereinafter “C. elegans”) embryo. As a key genetic model organism, especially for embryo development, this nematode has an invariant cell lineage which was fully mapped, making it the ideal model in which gene expression patterns of individual cells could be used to construct the transcriptomic dynamic during cell differentiation and development. Even though many aspects of C. elegans embryo have been well-characterized, many questions remain. In this work, we highlighted the utility of scRNA-seq in inferring cell-cell interactions (hereinafter “CCI”) in the entire embryo to characterize the coordination between cell populations and the dynamic of signaling pathways throughout embryo development. This study is the first to holistically study the CCI landscape throughout embryo development in C. elegans using scRNA-seq data and should lay the framework for identifying how these different interaction patterns control morphogenesis at the cellular and molecular levels.