Fig. 3: Subclustering of CD8 T Cells.

a UMAP plot showing the subclustering of CD8 T cells, and corresponding cluster designations. b Violin plots showing the distribution of representative markers for the identified cell types. c Stacked bar plot demonstrating the relative enrichment of each CD8 T cell subset by cohort designation. d Boxplots showing the per-patient proportional differences from each of the subtypes. The proportions shown are relative to the number of all CD8 T cells for each patient. Significance was calculated using scCODA—n.s. indicates the MC proportions are not significantly different from controls, and an asterisk (*) indicates significance at an FDR level of 0.05. Number of patients in each cohort: MC (n = 16); chronic diarrhea (n = 13); unaffected controls (n = 15). Patients with no cells in a given identity class were not plotted. Boxplot center line represents the median; the box bounds span from the first to the third quartile; whiskers extend from the box to the largest value no further than 1.5 * inter-quartile-range from the box. e RNAscope images of a representative patient from each cohort. Number of slides examined for each cohort: n = 8 for active MC, n = 8 for CD, n = 9 for unaffected controls. The fluorescent images are colored as follows: DAPI: blue; CD8: white; BATF: green; GZMB: magenta. Quantitation of all patient slides and individual channels is shown separately in Supplementary Fig. S11. Source data are provided as a Source Data file.