Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos

We applied single-cell RNA-sequencing (scRNA-seq) of vascular endothelial cells isolated from zebrafish embryos at the 24 hours post fertilization (hpf) stage. Six distinct clusters or subclusters related to vascular endothelial cells were identified which include arterial, two venous, cranial, endocardial and endothelial progenitor cell subtypes We crossed previously established Tg(kdrl:mCherry) and etv2ci32Gt; UAS:GFP lines. GFP and mCherry positive embryos were collected at 24 hpf. GFP+mCherry+ and GFP+mCherry- cell populations were isolated by FACS (fluorescent activated cell sorting) and subjected to single-cell RNA-seq analysis using Chromium Controller (10x Genomics) followed by the next-generation sequencing.