Extended Data Fig. 2: RNA-seq analysis of granuloma-associated crypt epithelium.

a, Representative gating example of epithelia, crypt cells, Lgr5–GFP and Sca-1 in biopsied tissue six days after H. polygyrus infection. Unfractionated tissue preps (as in Extended Data Fig. 3a) were gated similarly. b–e, Crypt epithelium was sorted from granuloma and non-granuloma biopsies and subjected to RNA-seq analysis as indicated in the Methods. b, The data were filtered for ≥100 reads average in either group, FDR ≤ 0.05, and fold-change comparison of ≥ 2. The 277 genes that passed were compiled into a heat map demonstrating high (red) and low (blue) relative expression. c, GSEA for Lgr5⁺ signature genes⁹. FDR <0.01. ES, enrichment score. d, Lgr5⁺ intestinal stem cell signature genes⁹ were cross-referenced to the RNA-seq dataset. Data were filtered as in (b) except no fold-change requirement was applied. Clca4 is also known as Clca3b e, The unfiltered RNA-seq dataset was analysed for upstream regulators using Ingenuity Pathways Analysis. The activation Z score indicates the extent of enrichment of targets within the RNA-seq dataset downstream of the indicated regulator, with a positive score indicating enrichment. IFN-related pathways are highlighted in orange. n = 4 independently sorted samples (b–e, granuloma, 20 mice total), or 5 independently sorted samples (b–e, non-granuloma, 25 mice total).