Fig 2: Transcriptomic identification of major myeloid subtypes acutely after SCI. (A) UMAP plot of all myeloid cells from uninjured spinal cord and 1, 3, and 7 dpi. Neutrophils, monocytes, macrophages, microglia, div-myeloid, and dendritic cells (Fig. 1 A) were extracted, reclustered, and re-embedded in new UMAP coordinates. Cells are colored by myeloid subtype as shown in legend on right. Cell counts in parentheses. Subtypes were annotated using a combination of DEGs, GO enrichment analyses, and previously published data. (B) UMAP of myeloid cells split by each time point. Cells are colored by neighborhood density in UMAP space to illustrate shifts over time. Darker red colors indicate greater cell density in the UMAP or gray if not from indicated time point. (C) Expression pattern of canonical marker genes, DEGs, and genes implicated in disease from previous studies. Cells are colored by expression value. Values are log-transformed normalized expression counts. The large cluster on the left was identified as microglia by the expression of P2ry12, Tmem119, and Siglech. The large cluster on the right was identified as peripheral myeloid cells by the expression of Ccr2 and Ly6c2. Homeostatic microglia (H-microglia) were identified by high expression of P2ry12, Siglech, and Tmem119. Inflammatory microglia were identified by Igf1, and migrating microglia were identified by Msr1 and Igf1. Dividing myeloid cells were identified by Mki67 and Top2a. Monocytes were identified by Ccr2 and Ly6c2. Macrophages (Mac) were identified by Cd63 and the reduced expression of monocyte markers. BA, border-associated; Div, dividing.