Whole-embryo single-cell RNA-seq data for genes expressed in the midline tissues of Ciona intestinalis type A embryos

The endodermal strand of tunicates occupies the same topographic position of the embryo as does the vertebrate hypochord, which consists of a row of single cells lined up immediately ventral to the notochord. The vertebrate hypochord shares expression of several genes with the floor plate, including Shh and FoxA, and play a role in dorsal aorta development. Whole-embryo single-cell transcriptome analysis identified a number of genes specifically expressed in both the floor plate and the endodermal strand in Ciona intestinalis type A mid-tailbud embryos. The t-distributed stochastic neighbor embedding (t-SNE) analysis was performed using the Loupe Cell Browser 3.1.1 software (10x Genomics, CA). The processed data are deposited as a Loupe Cell Browser file (.cloupe).