Single-cell RNA sequencing of developing mouse small intestine. Single-cell RNA sequencing of developing mouse small intestine

The mammalian intestine is a self-renewing organ that processes ingested food, absorbing nutrients from a sea of biochemical, mechanical, and pathogenic insults. To understand the developmental specification of diverse cell types in the small intestine, we performed time-resolved single-cell transcriptomics across five stages intestinal development: embryonic days (E) 12.5, 14.5, 16.5, and 18.5, and postnatal day (P) 1.5. By dissociating cells from whole organ preparations, we captured the full range of cellular diversity across all intestinal cell lineages. This allowed us to reconstruct the mesenchymal differentiation trajectory and identify the specific genetic programs that give rise to the diverse musculature of the gut wall and villus stroma. Overall design: Time-resolved single-cell transcriptomics across five stages during intestinal development: embryonic days (E) 12.5, 14.5, 16.5, and 18.5, and postnatal day (P) 1.5.