Fig. 1.

Temporal analysis of resident and infiltrating peripheral immune cells in the brain after TBI. A Graphical workflow of the mass cytometry experiment including the isolation of immune cells from the brains of 7 experimental groups, the staining and processing of the cells, and the R packages used to analyze the data. B A lineage UMAP showing a total of 42,000 cells (1000 per sample) plotted based on the expression of lineage markers. Four versions are shown color-coded respectively by the experimental group, the time point after traumatic brain injury, the 40 lineage clusters returned by the FlowSOM algorithm, and the 13 immune cell types derived from the manual annotation of the 40 lineage clusters (see also Additional file 1: Fig. S1). C Heatmap showing lineage marker expression of the 13 identified cell types. D Lineage UMAP depicting cells from the sham and PBS-treated groups at days 3, 7, and 28 in separate subpanels, color-coded by the immune cell type. E Quantification of the cell count (green) and the percentage (red) of each of the 13 immune cell types in the sham and PBS-treated groups at days 3, 7, and 28. Data are represented as mean. Significant changes compared to the sham group are in green and red dots; non-significant changes are in gray. N = 6 per group. False discovery rate was used to adjust the p-value. Abbreviations: cDC = conventional dendritic cell, pDC = plasmacytoid dendritic cell, MdC = monocyte-derived cell