scRNA sequencing of total CD4+ T cells in spinal cord of EAE mice and SILP of SFB-colonized mice

There are two aims in this study – (1) To figure out the pathogenic sub-populations of CD4+ T cells in the spinal cord of EAE model; and (2) by comparing the gene expression profile of pathogenic Th17 cells in EAE model to that of the non-pathogenic Th17 cells induced by SFB in SILP, to identify genes candidates that are potentially selectively essential to pathogenic ones. Overall design: Il23r is essential for the pathogenicity of CD4+ T cells in the EAE model. We generated chimera mice reconstituted with Il23RGfp/+ CD45.1/2 and Il23rGfp/Gfp CD45.1/1 bone marrow cells, and induced EAE or inoculate SFB for isolating CD4+ T cells from EAE spinal cord or SFB SILP for scRNAseq analysis. We used Smart-seq2 protocol to generate scRNA library. By comparing Il23rGfp/+ and Il23rGfp/Gfp clusters, we identified the pathogenic Th17 populations in the EAE model. By comparing gene expression profile of the pathogenic EAE Th17 cells to that of the SFB Th17 cells, we identified genes only expressed in the pathogenic ones, the function of which were further studied in genetic mouse models.