Fig. 1: Single-cell transcriptomic analysis reveals molecular heterogeneity in the Hensen’s node.

a Schematic representation of the experimental design: 38 Hensen′s nodes were dissected from stage HH4 embryos and subjected to single-cell RNA-seq analysis. b UMAP visualization of all clusters from the dataset, colored by cell identity, depicting 8134 individual cells. c Dot plot showing the expression levels and percent expression of key marker genes for each cluster, indicating specific gene expression in each cell population. d UMAP displaying the expression of CDH11 in the epiblast cluster. e HCR-FISH showing CDH11 expression in the anterior epiblast around the Hensen′s node (n = 3/3 biological replicates with similar results). f UMAP displaying the expression of SOX17 in the endoderm cluster. g HCR-FISH showing SOX17 expression in the Hensen′s node and surrounding endoderm at HH4+ stage (n = 3/3 biological replicates with similar results). h UMAP displaying the expression of CHRD in the anterior and posterior node clusters. i HCR-FISH showing CHRD expression in the Hensen′s node at stage HH4 (arrow, n = 10/10 biological replicates with similar results). j UMAP displaying the expression of GSC, an organizer-specific gene, in the anterior node cluster. k HCR-FISH showing GSC expression in the Hensen’s node at stage HH4 (n = 10/10 biological replicates with similar results). l UMAP displaying the expression of LMO1 in the posterior node cells. m HCR-FISH showing LMO1 expression in the Hensen′s node at stage HH4 (n = 10/10 biological replicates with similar results). Scale bar = 200 μm.