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Fig. 1 | Journal of Neuroinflammation

Fig. 1

From: Integrated single-cell transcriptomics of cerebrospinal fluid cells in treatment-naïve multiple sclerosis

Fig. 1

Integrated analysis facilitates characterizing the CSF immunome in treatment-naïve multiple sclerosis. A Schematic representation of sample cohorts, data processing, and bioinformatic analysis. Dataset 1 incorporates the data of Schafflick et al. [11], dataset 2 consists of a new muenster cohort [17] and dataset 3 incorporates the data of Ramesh et al. [13] B Uniform Manifold Approximation and Projection (UMAP) plot of level 1 clustering with automatic annotation based on canonical marker genes [18] (Additional file 6: Tab. S2) in the merged data set. C Dot plot depicting selected signature genes of level 1 clustering in merged control (Ctrl) and MS. Dot color encodes the mean expression, dot size visualizes the fraction of cells expressing the respective gene. Vertical bars on the top show the number of cells in the respective group. D Stacked bar plot showing the proportion of the level 1 cell types in Ctrl and in MS. E Split UMAP plots comparing level 1 clustering in Ctrl (left) and MS (right). F Volcano plot depicting differences of cluster abundance in MS compared to Ctrl. Clusters highlighted in blue are higher expressed in MS, yellow ones are more expressed in the Ctrl group. Fold change (log2) is plotted against t-test p value (-log10). The horizontal line visualizes the significance threshold of p = 0.05. Cluster key: Mono, monocyte cluster; DC, dendritic cell cluster; Bc, B cell cluster; CD4 Tc, CD4+ T cell cluster; CD8 Tc, CD8+ T cell cluster; other Tc, other T cell cluster. Un_assigned and other, cells lacking definitive assignment

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