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.

哺乳动物肠道是一类具有自我更新能力的器官，负责消化摄入的食物，并从充斥着生化、机械与病原性损伤的复杂环境中摄取营养物质。为解析小肠内多种细胞类型的发育特化机制，我们针对肠道发育的五个阶段开展了时间分辨率单细胞转录组学（time-resolved single-cell transcriptomics）分析，分别为胚胎期（embryonic days, E）12.5、14.5、16.5、18.5天，以及出生后（postnatal day, P）1.5天。通过从完整器官组织中解离细胞，我们完整捕获了所有肠道细胞谱系的全部细胞多样性，借此成功重构间充质分化轨迹，并鉴定出调控肠壁肌肉层与绒毛间质多样化形成的特异性基因表达程序。
实验整体设计：覆盖肠道发育五个阶段的时间分辨率单细胞转录组学分析，阶段分别为胚胎期E12.5、E14.5、E16.5、E18.5天，以及出生后P1.5天。