Epithelial zonation along the mammalian small intestine defines five discrete metabolic domains [Mouse_bulkRNA-seq]

Longitudinal zonation of epithelial cells across the mammalian small intestine defines five domains of nutrient absorption. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points. Intestinal organoids derived from the distal-most domain of the small intestine from adult Lgr5creERT2; Rosa26 LSL-Cas9-eGFP/+; ROSA26tdTomato mice, in which cas9-GFP is expressed in a tamoxifen-inducible manner. Sequenced organoids are either experimental Ppard (2 mutants) or Cdx1 (1 mutant) knockout organoids lines, which were transduced with dual guide RNAs targeting either gene and CRISPR-mediated gene deletion, or control lines (uninfected with virus containing dual guide RNAs with our without 4-hydroxytamoxifen treatment, or infected with dual guide RNAs but untreated with 4-hydroxytamoxifen).