10X Single cell RNAseq (scRNAseq) analysis of intestinal epithelial cells (IECs) from murine small intestinal organoids treated with vehicle (DMSO) or LXR agonist GW3965.

Intestinal organoids are a good model of in vitro tissue regeneration that faithfully recapitulates majority of cell types of the intestine. To analyze the impact of LXR activation in intestinal regeneration and overall cellular composition, organoids established from WT mice were treated with either vehicle (DMSO) or GW3965 and were analyzed using 10X scRNAseq platform. Small intestinal crypts isolated from WT mice were used for establishing organoids. Starting from the seeding organoids were either treated with vehicle (DMSO) or 1uM GW3965 for a period of 5 days. Organoid medium was changed every 48 hours when the treatment was refreshed. On day5, organoids were removed from the matrigel and single cell suspensions were prepared by TrpLE digestion. Further, Epcam+ IECs were sorted by flow cytometry and processed according to 10x Genomics protocol for Chromium Single cell 3’ kit (version 3.1) and submitted for sequencing.