(A) The tSNE maps presented in Figure 4C are portrayed as heatmaps showing expression levels of CD27, CD69, PD1, CXCR5, TIGIT, and ICOS. Regions with the highest density of kNN latent cells shown in Figure 4C are circled in red. Dot plot and pie graph depictions of the same datasets are presented in Figure 4D. (B) Dot plots comparing the expression patterns of CD27, CD69, CXCR5, PD1, CTLA4, and CCR6 on kNN latent cells from the gut and blood. In the dot plots, kNN latent cells are depicted in red and atlas cells in gray. The proportions of kNN latent cells that fall within each quadrant are depicted as pie charts beneath each dot plot. Top: Most kNN latent cells from the gut reside in quadrant 3 (Q3), corresponding to cells expressing high levels of CD69 and low levels of CD27. Middle: Most kNN latent cells from the gut reside in Q3, corresponding to cells expressing high levels of PD1 and low levels of CXCR5. Bottom: Most kNN latent cells from the gut reside in quadrant 2 (Q2), corresponding to cells expressing high levels of CTLA4 and CCR6. (C) kNN latent cells from FNAs but not the gut include naïve CD4+ T cells. Dot plots showing kNN latent cells (red) and atlas cells (gray) for two FNA and four gut specimens. Events were pre-gated on CD4+ T cells (CD3+CD8-CD19-). Naïve cells are visualized as those expressing high levels of CD45RA and low levels of CD45RO. These naïve cells also expressed high levels of CD27 and CCR7 (not shown). Red numbers indicate the number of kNN latent cells in each plot.