Extended Data Fig. 8: Relationship of intra- and extraembryonic haematopoietic cells.

(a) UMAP analysis of haematopoietic and erythroid cells in embryonic and extraembryonic tissues from CS10 to 15 weeks concepti (CS14/15 AGM, CS14 placenta, yolk sac, vitelline vessels, umbilical cord, head, heart, CS14 to 15 weeks livers) (n = 19 biologically independent samples), using MAGIC imputed gene expression. (b) Feature plots displaying MAGIC imputed expression of HSC signature genes. (c) Visualization of HSCs defined based on the “HSC signature” module score on MAGIC imputed expression. (d) Quantification of module-selected HSCs in CS10 to 15 weeks concepti. (e) Mature HSC and Immature HSC module scores in module-defined HSCs. (f) UMAP analysis showing relative similarity of HLF+ HSPCs from each tissue and stage (CS14/15 AGM, CS14 placenta, yolk sac, vitelline vessels and umbilical cord, CS17 to 15 weeks livers, 40 weeks cord blood) (n = 12 biologically independent samples). (g) “HSPC waves scorecard” documenting the expression of wave-specific genes in HLF+ HSPCs. (h) “HSC maturation scorecard” documenting the maturation stage. (i) Feature plots show the expression of HSC signature genes, nascent HSC genes and maturation genes in HLF+ HSPC in the indicated tissues over time. (j) UMAP analysis including haematopoietic (RUNX1+PTPRC+) and erythroid (RUNX1-GYPA+) clusters from the indicated tissues and stages (CS14–17 AGM, CS14 other haematopoietic tissues, CS17 to 15 weeks livers, n = 19 biologically independent samples. Colours show the contribution of each tissue to haematopoietic cell types (top). Selected tissues highlighted in black on the UMAP plot display HSC and progenitor populations and their differentiation trajectories in each tissue (bottom). (k) Feature plots show the expression of HSPC signature genes and lineage markers at different ages. HLF+ HSC are circled in black.