ABSTRACT: We report the application of single cell RNA sequencing technology for high-throughput profiling of sham and 3 dpi spinal cords in mice. By obtaining a total of 16051 cells from sham and 14295 cells from 3 dpi tissue, we identified 26 distinct cell clusters and 11 major cell types expressing known markers. These clusters comprised oligodendrocytes (Mbp, Mobp, Mog, Plp1), microglia (Gpr84, Cx3cr1, Csf1r), astrocytes (Gpr37l1, Bcan, Gfap), neutrophils (S100a9, Mmp9, S100a8), fibroblasts (Col1a1, Col1a2, Dcn), pericytes (Pdgfrb, Rgs5), endothelial cells (Flt1, Pecam1, Egfl7), macrophages (Ms4a7), monocytes (Ccr2, Cxcl3), b cells (CD19) and t cells (CD3e). neurons were not included because they were not expected to fit the sequencing protocol. We found that the most abundant cell type in the sham group was oligodendrocytes, accounting for 46.12%, while it decreased to 15.9% in the 3 dpi group. The second was microglia, accounting for 22.41%, which increased in number in the 3 dpi group, making it the most abundant cell in the SCI 3 dpi tissue (26.65%). The number of astrocytes also increased to 9.24% after SCI. Foreign immune cells such as neutrophils, macrophages, and monocytes accounted for 11.15%, 17.74%, and 9.41% of all cells after SCI, respectively. Among these, the percentage of pericytes decreased from 8.64% in the sham group to 1.28% in the 3 dpi group. The number of fibroblasts varied dramatically, rising rapidly from 0.33% in the sham group to 5.65% in the SCI 3 dpi group (Figure 2B). This study provides a framework for the application of single cell sequencing towards characterization of diverse cell populations in the sham and 3 dpi spinal cord.
