Extended Data Fig. 5: Transcriptome profiles of Ciona notochord cells during development.

a, t-SNE plot of notochord cells. Cells are coloured by developmental stage. The dashed line shows the separation between the primary (n = 3,123 cells) and secondary lineages (n = 627 cells). b, c, The single-cell transcriptome trajectory (top) and pseudotemporal gene-expression profiles (bottom) of the primary notochord and the secondary notochord. Cells were ordered along the trajectory across pseudotime. Only significantly expressed genes (likelihood ratio test) with q < 1 × 10⁻¹⁰⁰ (primary notochord) and q < 1 × 10⁻²⁰ (secondary notochord) are shown. Selected transcription factors and signalling molecules are labelled in orange. d, Heat map of differentially expressed genes between the primary and secondary notochord. Genes are clustered by Euclidean distance. e, Expression of a Casq1/2 fog>GFP reporter gene in a late-tailbud-stage embryo (left, one optical plane; right, maximum intensity projection). n = 3 electroporation experiments. GFP (green) was present in the muscle and in the secondary notochord (arrow), but no expression was observed in the primary notochord (arrowhead). f, Expression of KH.C9.405>mChCAAX reporter gene in late tailbud II stage embryo. mChCAAX (red) was present in the secondary notochord but not the primary notochord. n = 3 electroporation experiments. Scale bars, 20 μm.