Single-cell and single-nucleus transcriptome analysis of stripe pattern formation in the embryo of the spider Parasteatoda tepidariorum
Segmented body plans are a hallmark of arthropods, yet their underlying developmental processes vary widely. We applied single-cell and single-nucleus RNA sequencing of Parasteatoda tepidariorum embryos at late stage 5 and stage 7, a critical period of emergence of segmental units along the anterior-posterior (AP) axis. Single-nucleus RNA sequencing yielded high-quality quantitative data, and subsequent clustering analysis reconstructed an axial alignment of ectoderm cells, reflecting the differing cell states along the segmenting AP axis. This enabled us to generate genome-wide quantitative gene expression profiles along the reconstructed axis.  Employing unbiassed statistical methods, we comprehensively identified pattern elements. These data lay the groundwork for exploring the origins of developmental diversity for arthropod body plans. Overall design: Cells and nuclei were isolated from whole embryos at an early germ-band stage (stage 7) and analyzed using single-cell and single-nucleus RNA-seq. The data GSM6069861 in the series GSE201705, single-nucleus RNA-seq data at a late germ-disc stage (late stage 5), were reanalyzed to generate filtered and normalized count matrices. *************************************************************** The table below lists GEO accessions reused/reanalyzed for this study. ***************************************************************