RNA from murine intestines or organoids for bulk sequencing was isolated using TRIZOL. RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was ≥7.7. DNA libraries suitable for sequencing were prepared from 300 ng of total RNA for four samples and appx 200 ng for two samples with lower concentrations, with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq.