Extended Data Fig. 6: DC subpopulations.

a, Bar plot represents the proportion of DCs among all myeloid cells for each patient (Ctrl n = 3, EuE n = 9, EcP n = 8, EcPA n = 6, EcO n = 4). Patient-to-patient variability was observed in DC proportions within the myeloid population and across different tissue types. The box represents the interquartile range with median and minimum/maximum represented by box centerline and whiskers, respectively. b, PAGA and RNA velocity trajectory analyses suggest that pre-cDC2 differentiate towards cDC2 and DC3 in Ctrl and EuE. Red arrows indicate that some cDC2 and DC3 cells derive from a smaller intermediate cell population. c, Cell cycle analysis for pre-cDC2, cDC2 and DC3 populations. d, Expression of DC progenitor markers FLT3, AXL, and SIGLEC6. e, Phagocytosis pathway is enriched in cDC2 subpopulations of peritoneal lesions. Bar plot shows the Normalized Enrichment Score (NES) for the top 10- GSEA pathways in cDC2 cells of EuE and EcPA (FDR < 0.1). Related to Fig. 5.