Fig. 5: Signaling interactions identified by ligand–receptor analysis.

Selected signal pathways regulated by ligand–receptor interactions between AGM niche EC and developing HSCs based on complementary scRNA-seq analysis. HSC Precursor: Indicates receptors expressed in primary AGM V⁺61⁺E⁺ cells classified as “HSC Precursor” types (see Fig. 3h). HSC: Indicates receptors expressed in cells generated following AGM-EC co-culture of V⁺61⁺E⁺ cells classified as “HSC” type (see Fig. 4g, Supplementary Fig 8f–h). Receptors were also classified as to whether they were expressed more highly in early (enriched in HE) or late (enriched in pre-HSC) pseudotime for primary AGM V⁺61⁺E⁺ cells, or expressed more highly in early pseudotime (enriched in HSCs vs HPCs) in cells generated following AGM-EC co-culture. Ligands were classified by whether they were expressed in HSC-supportive AGM-EC (cultured AGM-EC), primary AGM-derived AGM V⁺61⁺E⁺ cells classified as “arterial EC” (primary AGM arterial EC), or both. Signals mediated by ligands differentially expressed in HSC-supportive vs non-supportive AGM-EC are indicated by yellow arrows (see Supplementary Data 1). *indicates exogenous cytokines in AGM-EC culture conditions. (See also Supplementary Data 5 for a complete list of identified ligands, receptors, and ligand–receptor interactions).