Identification of major cell types using expression pattern of canonical genes and SingleR. (A and B) Cell type identification based on SingleR using the reference data from Rosenberg et al. (2018) (A) or Sathyamurthy et al. (2018) (B). The cell type names used in A and B are those from corresponding references. (C) Expression pattern of previously annotated marker genes used to identify major cell types on the combined UMAP in Fig. 1. Cx3cr1 and Tmem119 identified microglia. Itgam and Ptprc identified leukocytes. Ly6c2 and Ccr1 identified monocytes. Ly6g identified neutrophils. Cd3e identified lymphocytes. Mki67 and Cdk1 identified dividing cells. Pecam1 and Cldn5 identified endothelial cells. Col1a1 identified fibroblasts. Combined expression of Cspg4 and Pdgfrb identified pericytes. Foxj1 identified ependymal cells. Combined expression of Aqp4 and Gfap identified astrocytes. Plp1 and Opalin identified oligodendrocytes. Combined expression of Pdgfra and Olig2 identified OPCs. Snap25 identified neurons. Expression values are log-normalized counts. (D) Immunohistochemical analysis of 7 dpi spinal cord from Postn-CreER/Rosa26-EYFP mice shows genetically labeled EYFP⁺ fibroblasts exclusively located in the fibrotic area delineated by dense PDGFRβ⁺ region as well as only in meningeal fibroblasts that overlie the injury site. Arrowheads denote activated fibroblasts that are EYFP⁺/PDGFRβ⁺. PDGFRβ⁺ fibroblasts in the fibrotic scar that do not express EYFP are due to low recombination efficiency in these mice. Arrows indicate perivascular PDGFRβ⁺ cells in uninjured regions that do not express EYFP. Boxed regions are magnified in the right panels. Scale bars, 100 µm (left) and 30 µm (right). Astro, astrocyte; Endo/endothe, endothelial; Oligo, oligodendrocyte; OPC, oligodendrocyte progenitor cell.