Abstract
Single-cell RNA-seq has been established as a reliable and accessible technique enabling new types of analyses, such as identifying cell types and studying spatial and temporal gene expression variation and change at single-cell resolution. Recently, single-cell RNA-seq has been applied to developing embryos, which offers great potential for finding and characterising genes controlling the course of development along with their expression patterns. In this study, we applied single-cell RNA-seq to the 16-cell stage of the Ciona embryo, a marine chordate and performed a computational search for cell-specific gene expression patterns. We recovered many known expression patterns from our single-cell RNA-seq data and despite extensive previous screens, we succeeded in finding new cell-specific patterns, which we validated by in situ and single-cell qPCR.
Highlights
Single-cell RNA-seq has been established as a reliable and accessible technique enabling new types of analyses, such as identifying cell types and studying spatial and temporal gene expression variation and change at single-cell resolution
Homogenous groups of cells can be clustered to identify novel and rare subtypes[1,2,3,4,5] and cells undergoing differentiation at different rates can be ordered and analysed[6,7,8,9]. This offers great potential for studying developing embryos with their high diversity of cell types[10,11,12,13,14,15,16,17,18,19,20]. Making sense of this diversity is a goal of developmental biology and an important first step is identifying and characterising the relatively few genes controlling the course of development and the subsets of cells they are expressed in, or in other words, their gene expression patterns
Zygotic expression begins around the 8-cell stage[21,22] and many gene expression patterns, both maternal and zygotic, are known from comprehensive in situ screens in Ciona[23] (Fig. 1b, Supplementary Table 1)
Summary
Single-cell RNA-seq has been established as a reliable and accessible technique enabling new types of analyses, such as identifying cell types and studying spatial and temporal gene expression variation and change at single-cell resolution. We applied single-cell RNA-seq (scRNA-seq) to the 16-cell stage of Ciona, a simple chordate, and looked for gene expression patterns using a novel computational approach. Zygotic expression begins around the 8-cell stage[21,22] and many gene expression patterns, both maternal and zygotic, are known from comprehensive in situ screens in Ciona[23] (Fig. 1b, Supplementary Table 1).
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