Extended Data Figure 2. Transcriptomic analysis of H. poly-infected TM.

(a) Experimental design for bulk RNAseq of EGCs from the TM of naïve and H. poly-infected (7 dpi) Sox10|tdT mice. tdT⁺ and tdT^- cell populations of dissociated TM were separated using FACS and subjected to RNAseq. (b) Sorting strategy for tdT⁺ EGCs and tdT^- non-glia cells. (c, d) Volcano plot showing mean log₂-transformed fold change (x-axis) and significance (-log₁₀(adjusted Pvalue)) of differentially expressed genes between tdT^- and tdT⁺ cells from naïve mice (c) and in tdT^- cells from naïve and H. poly-infected animals (d). Coloured dots in (c) indicate genes specific to EGCs (Sox10, Plp1, S100b, Foxd3, Erbb3, Sox2; red), enteric neurons (Ret, Tubb3, Sst, Elavl3, Elavl4; green), immune cells (Ptprc; cyan), interstitial cells of Cajal (Kit; orange), smooth muscle cells (Acgt2; pink), fibroblasts (Pdgfra; purple) and in (d) genes specific to type II immune response (Arg1, Retnla, Chil3) and T_H2 cytokines (Il13).n=4. (e) Quantification of IFN-γ in the TM of naïve and H. poly-infected animals (7 dpi). Mean±SD; n=6. Two-tailed Mann-Whitney test. (f) UMAP of sequenced EGCs from the TM of naïve and H. poly infected mice. Cells are color-coded according to experimental batches. (g) Violin plots showing normalized expression of representative EGC marker genes in EGC1 and EGC2 clusters in Fig. 1g. (h, i) Top 20 up-regulated and top 20 down-regulated genes in EGCs from H. poly-infected mice (h) and in EGC2 relative to EGC1 (i). IFN-γ-target genes shown in bold (h). Dot size indicates proportion of expressing cells and fill colour indicates mean normalized, centred and scaled expression level. (j, k) GO terms significantly enriched among the differentially expressed genes in EGC1 and EGC2 clusters shown in Fig. 1g (j) and in hEGC1 and hEGC2 clusters shown in Fig. 1j (k).