Figure S4.

CyTOF dynamics of T cell cluster frequencies. (A) Heatmap showing the normalized median expression values of all markers used for clustering in each of the 49 T cell clusters identified in VAC063C. Names were assigned manually using activation, lineage, and memory markers to broadly categorize each T cell cluster; when more than one cluster was placed into the same category (e.g., activated effector memory [EM] CD4) clusters were given an accessory label to highlight their unique phenotype or property (e.g., T-bet^lo Eomes^neg). The order of features was determined by unsupervised hierarchical clustering. (B) All T cell clusters that were differentially abundant at any time point (relative to baseline) during VAC063C. Each cluster is shown as a proportion of total CD45^pos CD3^pos T cells and clusters are shown in the same order as the heatmap in part (A) (left to right and top to bottom). Box (median and IQR) and whisker (1.5× upper or lower IQR) plots are shown (with outliers as dots) and significance (FDR < 0.05 and >2 fold-change) is indicated by color (dark blue for first infection and bright blue for third). In all plots, n = 3 for the first infection and n = 6 for the third infection. CM, central memory; MAIT, mucosal-associated invariant T cell; NK, natural killer; TEMRA, terminally differentiated effector memory cell re-expressing CD45RA; Treg, regulatory T cell.