Fig. 1: Single-cell transcriptomics of chick trunk development.

a, Summary of chicken embryo dissections to generate scRNA-seq datasets. Tissue caudal to the third somite pair in embryos with 4S, 7S, 10S and 13S (HH8–HH11) was dissociated and sequenced. b, 2D embedding (uniform manifold approximation and projection) of single-cell data highlighting the different cell populations present during early vertebrate trunk formation. The plot shows 27,379 single cells from all developmental stages. c,d, Embedding of chick trunk (4S–13S) coloured by expression of different marker genes of the paraxial and lateral plate mesodermal (LPM) compartment (c) and of notochord (Noto), neural, endoderm (Endo) and surface ectoderm (SE) (d). e,f, Embedding showing the expression of several genes in the PXM, NMPs and neural cell populations (e) and the NMPs and notochord (f) cell populations. Scale is linear and shows a maximum count of 4. g, Overview of gene expression levels and percentage of cells positive for marker gene expression used to distinguish cell types present in the trunk. FP, floorplate; IntM, intermediate mesoderm; NC, neural crest; PreSomM, presomitic mesoderm.