Single-cell and single-nucleus transcriptome analysis of pattern formation in the early embryo of the spider Parasteatoda tepidariorum

In a cellular field of the early spider embryo, Hedgehog signaling operates to specify a “fuzzy” French-flag-like pattern along the primary axis. We applied single-cell and single-nucleus RNA sequencing to the early spider embryo. We confirmed that these techniques successfully detected three cell population corresponding to germ layers and some known cell types. We showed that the data had sufficient information for reconstruction of a correct global polarity of the presumptive ectoderm. Cells and nuclei were isolated from whole embryos at late germ-disc stage and analyzed using single-cell and single-nucleus RNA-seq.