Extended Data Fig. 1: Perfusion is not sufficient to deplete intra-vascular leukocytes in the meninges.
a, Graph depicting the percentage of remaining peripheral blood leukocytes of all leukocytes isolated from CNS-associated border tissues (CNS, SDM, Dura, choroid plexus (CP)) after intracardial perfusion as shown in Fig. 1b. Four healthy C57BL/6 mice were intravenously injected with a fluorescent coupled antibody against CD45 (CD45iv). 10 minutes later, blood was taken, mice were intracardially perfused and leukocytes were isolated from the CNS-associated border tissues and blood. Leukocytes were then stained with a second CD45 antibody and were measured on a flow cytometer. Data represented as mean ± SD, n = 4 (b) Dotplot of marker genes defining the different tissue-resident leukocyte (TRL) cell cluster in the merged dataset from Fig. 1c. Dot size encodes percentage of cells expressing the gene, color encodes the average per cell gene expression level. c, Feature plots of selected marker genes used to identify cluster identities in the merged dataset from Fig. 1c. d, Uniform Manifold Approximation and Projection (UMAP) plots of the merged dataset from Fig. 1c split by tissue of origin. Corresponding cluster frequencies are shown in Fig. 1d.
