Single cell RNA-seq of mouse lung vascular transcriptomes

By analyzing about 1500 vascular single cell transcriptomes from adult mouse lung, we provide molecular definitions of the principal vascular (endothelial and mural cells), and vascular-associated cell classes. Overall design: We used different transgenic mouse reporter lines with fluorescent expression in different populations of vascular cells, Cldn5(BAC)eGFP mice that strongly labels lung endothelial cells, mice positive for Pdgfrb(BAC)eGFP and NG2dsRed. We chose to focus our efforts to adult mice 10 to 19 weeks old in order to primarily define fully differentiated and quiescent vascular cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs