SI organoids were stimulated with ENR (control) or ENR + Hpb-CM medium for 24 h from the start of culture. RNA was extracted using Trizol reagent (Sigma-Aldrich), and quality was checked with the Bioanalyzer RNA 6000 kit. Libraries were prepared using the NEB mRNA stranded library prep Kit (New England Biolabs) and paired-end sequenced on the NovaSeq 6000 at 25 million reads per sample. RNA-seq reads were aligned to the mm10 reference genome using STAR (Dobin et al., 2013 (link)). Read counts were calculated using the strand-specific exonic reads of each gene, and duplicate genes were merged using HOMER (Heinz et al., 2010 (link)). Transcripts per million were used to evaluate the correlation among replicates for quality control. Differential gene expression was calculated from the raw read counts using edgeR (Robinson et al., 2009 (link)). Data sets presented in the manuscript can be found at GEO, accession no. GSE199227.