Visualization of all cells and identification of cell types

After creating an integrated data set, we next utilized uniform manifold approximation and projection (34) to visualize cells from all samples in a low-dimensional embedding. Cell types (i.e., the major immune lineages CD8⁺ T cells, CD4⁺ T cells, CD4⁺ regulatory T cells, NK cells, B cells, plasmablasts, monocytes, macrophages, and plasmacytoid dendritic cells) were identified as described previously (31).