Multimodal Single-Cell Profiling of Immune Cells

A specimen from the meninges and at least one specimen from peripheral blood or spleen were collected from each individual at autopsy. Whole blood was first centrifuged to remove the plasma, after which peripheral blood mononuclear cells (PBMC) were isolated by Ficoll separation (Sigma Millipore). Splenic and meningeal tissues were processed into single-cell suspensions, prior to cell sorting. CD3⁺ T cells and CD14⁺ macrophage lineage cells were isolated by sequential positive selection (CD3⁺ then CD14⁺) from PBMC and splenic or meningeal single-cell suspensions using magnetic activated cell sorting (MACS), per the manufacturer’s protocol (Miltenyi). The estimated number of cells (cell genome equivalents [CGE]) was calculated based on the amount of DNA used for amplifications using the ratio of 6 pg DNA/cell (50 (link), 51 (link)).