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. 2020 Jan 14;11:247. doi: 10.1038/s41467-019-14118-w

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Schematic of the study design (Methods). b Uniform Manifold Approximation and Projection (UMAP) plot representing 17 color-coded cell clusters identified in merged single-cell transcriptomes of blood (42,969) and CSF (22,357) cells from control (n = 4) and multiple sclerosis (MS; n = 4) patients (Methods). Cluster names were manually assigned. c Dotplot depicting selected marker genes in cell clusters. Dot size encodes percentage of cells expressing the gene, color encodes the average per cell gene expression level. d UMAP plots comparing blood (left) and CSF (right) cell clustering. Please note that the MegaK cluster is disregarded for higher resolution. e Volcano plot depicting differences of cluster abundance in CSF compared to blood plotting fold change (log10) against p value (−log10) based on beta-binomial regression (Methods). Horizontal line indicates significance threshold. Cluster key: pDC, plasmacytoid dendritic cells (DC); mDC1, myeloid DC type 1; Mono1, monocyte cluster 1 preferentially blood-derived; Mono2, monocyte cluster 2 preferentially CSF-derived; gran, granulocytes; Tdg, γδ T cells; CD8na, non-activated CD8⁺ T cells; CD8a, activated CD8⁺ T cells; Tregs, regulatory CD4⁺ T cells; CD4, CD4⁺ T cells; NK, natural killer cells; MegaK, megakaryocytes; B1/B2, B cell subsets; plasma, plasmablasts. Source data for (c) listing the differential expression values for all cells merged are provided in Supplementary Dataset 1. Source data for (d, e) listing the differential expression values for CSF vs. blood are provided in Supplementary Dataset 2.