Single cell transcriptional profiles of islet1-derived ECs and the other ECs in the tail of 48 hpf zebrafish embryos

We report transcriptional heterogeneity of venous endothelial cells (ECs) in the tail of zebrafish embryos, which consist of HSPC-niche-constituting ECs and caudal vessel (CV)-constituting ECs. To characterize isl1-derived ECs which derive from the endoderm and mainly constitute the HSPC niche in the caudal hematopoietic tissue (CHT), we performed single cell RNA sequencing (scRNA-seq) of isl1-derived ECs and the other ECs separately isolated from the tails of zebrafish embryos. Our analyses revealed that tail venous ECs were split into 5 distinct sub-clusters where isl1-derived ECs and the other ECs were similarly distributed to all venous EC clusters, and further revealed that genes whose expression levels are different between isl1-derived ECs and the other ECs tend to show similar changes across all of the clusters even after their diversification. We isolated live TagRFP+/EGFP+ cells (for isl1-derived ECs) and TagRFP-/EGFP+ cells (for the other ECs) separately by FACS sorting from the tails of TgBAC(isl1:TagRFP);Tg(dab2:EGFP) embryos at 48 hpf. Then, barcoded single-cell cDNA libraries were prepared using the Chromium Single Cell 3’ Reagents Kits v3.1 and were then sequenced using Illumina NovaSeq6000.