Extended Data Figure 9: Pericyte definition, organotypicity and transporter transcript expression.

a, Bar plot showing the expression of the highly abundant endothelial marker Cldn5 across the BackSPIN clusters; note the abundant and specific expression in EC clusters. The arrow points to a small group of cells in the PC cluster showing Cldn5 expression. The BackSPIN range of 1,088 pericytes is shown at larger magnification in the lower panels. An additional seven high abundant endothelial markers (Pecam1, Ly6a, Ly6c1, Podxl, Ptprb, Slc2a1 and Slco1c1) all show a peak of expression in the same roughly 10 cells, suggesting endothelial contamination of these pericytes. The high abundance markers for fibroblast-like cells (Lum) and astrocytes (Aqp4) do not reveal signs of contamination of the pericytes by these cell types. b, Annotation of lung vascular cell BackSPIN clusters and identification of lung pericytes. The PC cluster was identified according to the expression of known and/or shared markers with brain pericytes, combined with the absence of markers for vascular smooth muscle cells (VSMC), fibroblasts (FB), chondrocytes/perichondrium (CP), or endothelial cells (EC). The mixed cluster contains markers for epithelial cells together with markers for fibroblasts and probably represents contaminated cells. Among the endothelial cells (EC), several clusters were identified, including arterial (a), capillary (c/capil) and lymphatic (LEC). c, t-SNE analysis of brain and lung cells shows separation of brain and lung pericytes, as well as of brain and lung fibroblast-like cells, into distinct clusters suggesting organotypic differences for both cell classes. d, Bar plot of expression of the transporter transcript Atp13a5 in brain shows that it is highly specific for pericytes and vSMCs. e, Heat map illustrating the expression (red, high; blue, low) of the 200 most variable transporter transcripts across the brain vascular and vessel-associated cell types. Hierarchical clustering divides the patterns of transporter distribution into approximately 13 groups (separated by hatched lines). The identity of the transcripts in each group is provided to the right of the heat map. Note the abundance of transporters that are pericyte-specific.