Single-cell transcriptomic analysis of 36 hpf Zebrafish etv2 and jam2b positive cells

We performed single-cell RNAseq analysis of FACs sorted etv2 and jam2b psoitive cells from etv2Gt(2A-Venus) ; jam2bGt(2A-Gal4);UAS:NTR-mCherry zebrafish embryos at 36 hpf using 10x Genomics' Chromium platform. 18 distinct cell populations were identified including vascular endothelial cells and LPM cells. Transgenic etv2Gt(2A-Venus) fish were crossed to jam2bGt(2A-Gal4);UAS:NTR-mCherry fish. Whole embryos at 36 hpf were then dissociated into a single-cell suspension by cold protease tissue dissociation protocol. Cells expressing Venus only, mCherry only, and both (Venus and mCherry) were sorted using a BD/FACSAria II flow cytometer cell sorter. After sorting, cells expressing both Venus and mCherry were equally divided and added into the Venus only and mCherry only populations manually. Barcoding of cells and and cDNA library construction was carried out using 10X Genomics' Chromium platform.