Fig. 3

Characterizing rare cell populations in the integrated CSF cell dataset in MS. A Dot plot of selected genes for smaller subclusters of innate lymphoid cell (ILC) and natural killer cell (NK) in merged control (Ctrl) and MS. FDR > 0.1. To better visualize the differences, the right dot plot shows a zoom-in of selected genes with an adjusted scale. B Precomputed differential expressed genes by cellxgene VIP of selected genes of ILCs in MS compared to Ctrl. Color coding shows significant up- (red) or downregulation (blue), dot size encodes the fold change. FDR > 0.1. C Left stacked bar plot showing the total number of depicted T cell clusters in Ctrl vs MS. Right stacked bar plot shows the relative distribution of T cell subclusters in Ctrl compared to MS. Each cluster is set to 100% irrespective of its abundance. D Dot plot of selected genes characterizing the Treg cluster compared to CD4 naïve cluster in merged Ctrl and MS. FDR > 0.1. E Volcano plot of precomputed differential expressed genes by cellxgene VIP of Treg cells in MS compared to Ctrl. The horizontal line depicts the significance threshold (FDR, false discovery rate = 0.05). F Dot plot of selected signature genes of mucosal associated invariant T cells (MAIT) and double-negative T cells (dnT) in merged Ctrl and MS. G Stacked bar plot showing the relative distribution of MAIT cells and dnT cells in MS compared to Ctrl. H Volcano plot of precomputed differential expressed genes by cellxgene VIP of dnT cells in MS compared to Ctrl. Please note that yellow highlighted genes are higher expressed in the Ctrl and are only applied to significantly upregulated genes. The horizontal line depicts the significance threshold (FDR, false discovery rate = 0.05). I Volcano plot of differential expressed genes in MAIT cells in MS compared to Ctrl; no gene identified. FDR > 0.1