PROJECT ID: PRJNA610520

Data source SRA: PRJNA610520
Description To profile the developmental landscape of fetal HSPCs and their local niche, here, by using single-cell RNA-sequencing, we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg (kdrl:mCherry/CD41:GFP) embryos were collected and digested with 2.5% trypsin for dissociation.The 50,000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting (FACS) for 10× Genomics analysis (CapitalBio Technology Corporation). Please note that the GSE120503 (GSM3402061 55hpf CHT single cell RNA seq data) raw data been re-analyzed in the current study.
Key word zebrafish; HSPC expansion; single-cell RNA-seq; caudal hematopoietic tissue; Gpr182
Publication Xia J, Kang Z, Xue Y, Ding Y et al. A single-cell resolution developmental atlas of hematopoietic stem and progenitor cell expansion in zebrafish. Proc Natl Acad Sci U S A 2021 Apr 6;118(14). PMID: 33785593
Abstract During vertebrate embryogenesis, fetal hematopoietic stem and progenitor cells (HSPCs) exhibit expansion and differentiation properties in a supportive hematopoietic niche. To profile the developmental landscape of fetal HSPCs and their local niche, here, using single-cell RNA-sequencing, we deciphered a dynamic atlas covering 28,777 cells and 9 major cell types (23 clusters) of zebrafish caudal hematopoietic tissue (CHT). We characterized four heterogeneous HSPCs with distinct lineage priming and metabolic gene signatures. Furthermore, we investigated the regulatory mechanism of CHT niche components for HSPC development, with a focus on the transcription factors and ligand-receptor networks involved in HSPC expansion. Importantly, we identified an endothelial cell-specific G protein-coupled receptor 182, followed by in vivo and in vitro functional validation of its evolutionally conserved role in supporting HSPC expansion in zebrafish and mice. Finally, comparison between zebrafish CHT and human fetal liver highlighted the conservation and divergence across evolution. These findings enhance our understanding of the regulatory mechanism underlying hematopoietic niche for HSPC expansion in vivo and provide insights into improving protocols for HSPC expansion in vitro.


Dataset Information

Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. PRJNA610520 (3.5dpf) Danio rerio caudal hematopoietic tissue baseline 3.5dpf, the mixture of same amount of kdrl:mCherry+ cells, CD41:GFP+ cells and double negative cells. SRA: SRR11243177
2. PRJNA610520 (4.5dpf) Danio rerio caudal hematopoietic tissue baseline 4.5dpf, the mixture of same amount of kdrl:mCherry+ cells, CD41:GFP+ cells and double negative cells. SRA: SRR11243184

Clustering Result

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Monocytes ENSDARG00000042725 (cebpb) marker DOI:10.1016/j.cell.2008.01.025
2 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1016/j.cell.2008.01.025
2 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1016/j.cell.2008.01.025
2 HSPCs ENSDARG00000078004 (drl) marker DOI:10.1016/j.cell.2008.01.025
3 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1016/j.cell.2008.01.025
3 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1016/j.cell.2008.01.025
3 HSPCs ENSDARG00000078004 (drl) marker DOI:10.1016/j.cell.2008.01.025
4 Erythroid cells ENSDARG00000089124 (hbae1.3) marker DOI:10.1016/j.cell.2008.01.025
4 Erythroid cells ENSDARG00000096667 (hemgn) marker DOI:10.1016/j.cell.2008.01.025
4 Erythroid cells ENSDARG00000038643 (alas2) marker DOI:10.1016/j.cell.2008.01.025
5 Endothelium ENSDARG00000054632 (fli1a) marker DOI:10.1038/srep44644
6 Myeloid cells ENSDARG00000036074 (cebpa) marker DOI:10.1016/j.cell.2008.01.025
6 Myeloid cells ENSDARG00000057789 (lyz) marker DOI:10.1016/j.cell.2008.01.025
7 Neuron ENSDARG00000055216 (tuba1c) marker DOI:10.1016/j.cell.2008.01.02
7 Neuron ENSDARG00000006497 (rtn1a) marker DOI:10.1016/j.cell.2008.01.025
7 Neuron ENSDARG00000045639 (elavl4) marker DOI:10.1016/j.cell.2008.01.025
7 Neuron ENSDARG00000038574 (scg2b) marker DOI:10.1016/j.cell.2008.01.025
8 Myeloid cells ENSDARG00000036074 (cebpa) marker DOI:10.1016/j.cell.2008.01.025
8 Myeloid cells ENSDARG00000057789 (lyz) marker DOI:10.1016/j.cell.2008.01.025
9 Epidermal cells ENSDARG00000090783 (mfap4) marker DOI:10.1016/j.cell.2008.01.025
9 Epidermal cells ENSDARG00000032849 (ndrg1a) marker DOI:10.1016/j.cell.2008.01.025
9 Epidermal cells ENSDARG00000016691 (cd9b) marker DOI:10.1016/j.cell.2008.01.025
11 Endothelium ENSDARG00000054632 (fli1a) marker DOI:10.1038/srep44644
12 Epithelial cells ENSDARG00000040534 (epcam) marker DOI:10.1016/j.cell.2008.01.025
12 Epithelial cells ENSDARG00000055514 (icn2) marker DOI:10.1016/j.cell.2008.01.025
12 Epithelial cells ENSDARG00000092947 (cyt1) marker DOI:10.1016/j.cell.2008.01.025
12 Epithelial cells ENSDARG00000017624 (krt4) marker DOI:10.1016/j.cell.2008.01.025
13 Neuron ENSDARG00000055216 (tuba1c) marker DOI:10.1016/j.cell.2008.01.02
13 Neuron ENSDARG00000006497 (rtn1a) marker DOI:10.1016/j.cell.2008.01.025
13 Neuron ENSDARG00000045639 (elavl4) marker DOI:10.1016/j.cell.2008.01.025
13 Neuron ENSDARG00000038574 (scg2b) marker DOI:10.1016/j.cell.2008.01.025
14 Macrophages ENSDARG00000077809 (il13) marker DOI:10.1016/j.cell.2008.01.025
15 Neuron ENSDARG00000038574 (scg2b) marker DOI:10.1016/j.cell.2008.01.025
16 Fibroblasts ENSDARG00000069093 (col2a1a) marker DOI:10.1016/j.cell.2008.01.025
17 Muscle cells ENSDARG00000053254 (mylpfa) marker DOI:10.1016/j.cell.2008.01.025
17 Muscle cells ENSDARG00000099197 (actc1b) marker DOI:10.1016/j.cell.2008.01.025
17 Muscle cells ENSDARG00000017441 (mylz3) marker DOI:10.1016/j.cell.2008.01.025

Cluster Cell type Gene id (symbol) Marker class Evidence
1 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1016/j.cell.2008.01.025
1 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1016/j.cell.2008.01.025
1 HSPCs ENSDARG00000078004 (drl) marker DOI:10.1016/j.cell.2008.01.025
2 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1016/j.cell.2008.01.025
2 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1016/j.cell.2008.01.025
2 HSPCs ENSDARG00000078004 (drl) marker DOI:10.1016/j.cell.2008.01.025
3 Erythroid cells ENSDARG00000089475 (hbae1.1) marker DOI:10.1016/j.cell.2008.01.025
3 Erythroid cells ENSDARG00000089124 (hbae1.3) marker DOI:10.1016/j.cell.2008.01.025
3 Erythroid cells ENSDARG00000038643 (alas2) marker DOI:10.1016/j.cell.2008.01.025
4 Myeloid cells ENSDARG00000036074 (cebpa) marker DOI:10.1016/j.cell.2008.01.025
4 Myeloid cells ENSDARG00000057789 (lyz) marker DOI:10.1016/j.cell.2008.01.025
5 Endothelium ENSDARG00000054632 (fli1a) marker DOI:10.1038/srep44644
6 Monocytes ENSDARG00000042725 (cebpb) marker DOI:10.1016/j.cell.2008.01.025
7 Myeloid cells ENSDARG00000036074 (cebpa) marker DOI:10.1016/j.cell.2008.01.025
7 Myeloid cells ENSDARG00000090783 (mfap4) marker DOI:10.1016/j.cell.2008.01.025
8 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1016/j.cell.2008.01.025
8 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1016/j.cell.2008.01.025
8 HSPCs ENSDARG00000078004 (drl) marker DOI:10.1016/j.cell.2008.01.025
9 Epithelial cells ENSDARG00000040534 (epcam) marker DOI:10.1016/j.cell.2008.01.025
9 Epithelial cells ENSDARG00000017624 (krt4) marker DOI:10.1016/j.cell.2008.01.025
10 Neuron ENSDARG00000055216 (tuba1c) marker DOI:10.1016/j.cell.2008.01.025
10 Neuron ENSDARG00000006497 (rtn1a) marker DOI:10.1016/j.cell.2008.01.025
10 Neuron ENSDARG00000045639 (elavl4) marker DOI:10.1016/j.cell.2008.01.025
10 Neuron ENSDARG00000038574 (scg2b) marker DOI:10.1016/j.cell.2008.01.025
11 Endothelium ENSDARG00000054632 (fli1a) marker DOI:10.1038/srep44644
12 Erythroid cells ENSDARG00000089475 (hbae1.1) marker DOI:10.1016/j.cell.2008.01.025
12 Erythroid cells ENSDARG00000089124 (hbae1.3) marker DOI:10.1016/j.cell.2008.01.025
12 Erythroid cells ENSDARG00000038643 (alas2) marker DOI:10.1016/j.cell.2008.01.025
13 Macrophages ENSDARG00000077809 (il13) marker DOI:10.1016/j.cell.2008.01.025
14 Fibroblasts ENSDARG00000069093 (col2a1a) marker DOI:10.1016/j.cell.2008.01.025
15 Epithelial cells ENSDARG00000040534 (epcam) marker DOI:10.1016/j.cell.2008.01.025
15 Epithelial cells ENSDARG00000017624 (krt4) marker DOI:10.1016/j.cell.2008.01.025
16 Epidermal cells ENSDARG00000032849 (ndrg1a) marker DOI:10.1016/j.cell.2008.01.025
16 Epidermal cells ENSDARG00000016691 (cd9b) marker DOI:10.1016/j.cell.2008.01.025
17 Neuron ENSDARG00000055216 (tuba1c) marker DOI:10.1016/j.cell.2008.01.025
17 Neuron ENSDARG00000006497 (rtn1a) marker DOI:10.1016/j.cell.2008.01.025