Extended Data Fig. 2: Identification of haematopoietic cells in CS14 embryo and extraembryonic tissues.
From: Mapping human haematopoietic stem cells from haemogenic endothelium to birth
(a) Single-cell RNA-seq analysis of different tissues from CS14 (4.5 weeks) conceptus. tSNE clustering indicating the main cell types, and feature plots documenting the expression of selected HSC molecular signature genes RUNX1, HLF and SPINK2+ are shown. Total haematopoietic cells (RUNX1+/CD45+) and HSCs are circled in purple and black, respectively. (b) Presence of HLF+ HSPC in HSC-containing clusters in each CS14 tissue. (c) Nascent HSC scorecard genes evaluated in HLF+ HSPC in each tissue. (d) UMAP analysis of haematopoietic cells from the merge of all indicated tissues from the 4.5 weeks/CS14 embryo, using MAGIC for imputation of gene expression. (e) Feature plots showing MAGIC-imputed expression of the six HSC signature genes RUNX1, HLF, HOXA9, MLLT3, MECOM, HLF and SPINK2. (f) Visualization of HSCs defined by the “HSC signature” module score on MAGIC-imputed expression. (g) Nascent HSC scorecard on HSC signature module -defined HSCs identified in CS14 tissues. (h) Nascent HSC scorecard on all SPINK2+ cells from haematopoietic clusters from CS14 tissues. (i) GO categories and example genes enriched SPINK2+ AGM HSC (top) or in SPINK2+ Liver haematopoietic progenitors (bottom) (Fisher’s exact test). (j) Dot plot of genes enriched in SPINK2+ Liver haematopoietic progenitors in SPINK2+ cells from CS14 tissues. (k) UMAP analysis of CS14 liver haematopoietic clusters, showing 10 clusters and the main cell types. (l) Feature plots of HSPC genes in haematopoietic cells in CS14 liver. SPINK2+ progenitor cells are circled. (m) Feature plots of lineage-specific genes in CS14 liver.
