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).被囊动物（tunicates）的内胚层索（endodermal strand）在胚胎中的拓扑位置与脊椎动物的下脊索（hypochord）完全一致；后者由单列单细胞排列而成，紧邻脊索（notochord）的腹侧正下方。脊椎动物的下脊索与神经底板（floor plate）共享多个基因的表达谱，包括音猬因子（Sonic Hedgehog, Shh）和叉头框A（FoxA），并在背主动脉发育中发挥作用。全胚胎单细胞转录组分析在A型柄海鞘（Ciona intestinalis type A）的中尾芽期胚胎中，鉴定出一批同时在神经底板与内胚层索中特异性表达的基因。本研究采用Loupe Cell Browser 3.1.1软件（10x Genomics公司，加利福尼亚州）完成了t分布邻域嵌入（t-distributed stochastic neighbor embedding, t-SNE）分析。经处理的数据集已以Loupe Cell Browser文件格式（.cloupe）存档并提交。