Single cell RNA-seq of mouse brain vascular transcriptomes

By analyzing thousands of vascular single cell transcriptomes from adult mouse brain, we provide molecular definitions of the principal vascular (endothelial and mural cells), and vascular-associated cell classes. We used four different transgenic mouse reporter lines with fluorescent expression in different populations of vascular cells, Cldn5(BAC)eGFP mice that strongly labels brain endothelial cells, mice doubly positive for Pdgfrb(BAC)eGFP and NG2dsRed, in which brain vascular mural cells express both markers whereas each single marker are expressed also in other, non-overlapping cell types, and Pdgfra-H2BGFP that we found labeled a perivascular population of cells distinct from mural cells and astrocytes, in addition to the known labeling of cells of the oligendendrocyte lineage. 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