HemAtlas
Mapping developmental
hematopoiesis across stages, species and models
In zebrafish embryos, definitive hematopoietic stem and progenitor cells (HSPCs) arise from hemogenic endothelial cells via endothelial-to-hematopoietic transition within the ventral wall of dorsal aorta at 36–48 hours post fertilization (hpf). Then, the nascent HSPCs arrive at caudal hematopoietic tissue (CHT) for expansion and differentiation at 48 hpf. Finally, the HSPCs colonize into the kidney marrow to support lifelong hematopoiesis after 96 hpf.
AGM (aorta-gonad-mesonephros) region is an evolutionarily-conserved hematopoietic site for definitive hematopoietic stem and progenitor cell (HSPC) generation. A specialized population of endothelial cells (ECs) in the ventral wall of dorsa aorta acquire hematopoietic fate to specify into hemogenic endothelial cells (HECs), and then produce HSPCs via endothelial-to-hematopoietic transition. AGM region also consists of perivascular cells, mesenchymal cells, and other niche cells.
Related Dataset(s)
| Accession | Omics | Omics Detail | Publication |
|---|---|---|---|
| HemBK00000002 | Bulk RNA-seq | Bulk RNA-seq | OLB-PM-26358189 |
| HemBK00000026 | Bulk RNA-seq | Bulk RNA-seq | OLB-PM-32756943 |
| HemAT00000027 | Epigenomics | ATAC-seq | OLB-PM-32756943 |
| HemCP00000029 | Epigenomics | ChIP-seq | OLB-PM-32756943 |
| HemSC00000044 | Single cell RNA-seq | 10x Genomics | OLB-PM-33273096 |
| HemSC00000059 | Single cell RNA-seq | 10x Genomics | OLB-PM-37016019 |
| HemAT00000060 | Epigenomics | scATAC | OLB-PM-37016019 |
| HemBK00000071 | Bulk RNA-seq | Bulk RNA seq | OLB-PM-37874038 |
| HemSC01000084 | Single cell RNA-seq | 10x Genomics | OLB-PM-37016019;33273096 |
| HemSC01000087 | Single cell RNA-seq | 10x Genomics | OLB-PM-37016019;33273096;31042481;33785593;38497789;28878000 |
CHT (caudal hematopoietic tissue) is a transient hematopoietic site for HSPC expansion and differentiation in zebrafish embryos. Nascent HSPCs are transferred to the CHT via blood circulation and guided into a specialized vascular niche by macrophages. The specialized vascular niche is constituted by vascular endothelial cells and stromal cells, and enriched with cytokines, chemokines, and growth factors.
Related Dataset(s)
| Accession | Omics | Omics Detail | Publication |
|---|---|---|---|
| HemST00000013 | Spatial transcriptome | GEO-seq | OLB-PM-31042481 |
| HemBK00000014 | Bulk RNA-seq | Bulk RNA-seq | OLB-PM-31042481 |
| HemAT00000028 | Epigenomics | ATAC-seq | OLB-PM-32756943 |
| HemSC00000033 | Single cell RNA-seq | 10x Genomics | OLB-PM-33785593 |
| HemSC00000048 | Single cell RNA-seq | 10x Genomics | OLB-PM-31042481 |
| HemBK00000070 | Bulk RNA-seq | Bulk RNA-seq | OLB-PM-38605226 |
| HemSC01000085 | Single cell RNA-seq | 10x Genomics | OLB-PM-31042481;33785593 |
| HemSC01000087 | Single cell RNA-seq | 10x Genomics | OLB-PM-37016019;33273096;31042481;33785593;38497789;28878000 |
KM (kidney marrow) is a hematopoietic site for adult HSPC maintenance in zebrafish. The cell components of kidney marrow include hematopoietic cells, endothelial cells, renal tubular cells, nephron epithelial cells, mucin secreting cells, multi-ciliated cells, and kidney progenitor cells. HSPCs are maintained in a highly vascularized niche and are protected from irradiation by a layer of melanocytes. In the kidney, HSPCs self-renew and differentiate into multilineage hematopoietic cells for the lifetime of the animal.
Related Dataset(s)
| Accession | Omics | Omics Detail | Publication |
|---|---|---|---|
| HemBK00000005 | Bulk RNA-seq | Bulk RNA-seq | OLB-PM-28878000 |
| HemSC00000043 | Single cell RNA-seq | InDrops | OLB-PM-28878000 |
| HemSC00000065 | Single cell RNA-seq | 10x Genomics | OLB-PM-38497789 |
| HemSC00000066 | Single cell RNA-seq | 10x Genomics | OLB-PM-35938989 |
| HemSC01000086 | Single cell RNA-seq | 10x Genomics | OLB-PM-38497789;28878000 |
| HemSC01000087 | Single cell RNA-seq | 10x Genomics | OLB-PM-37016019;33273096;31042481;33785593;38497789;28878000 |