Early-life RNA sequencing of colon stromal cells and iNKT cells

The early-life intestinal microenvironment plays a pivotal role in shaping immune cell development, yet the mechanisms regulating colonic invariant natural killer T (iNKT) cells remain incompletely understood. To investigate how embryonic macrophages regulate iNKT cells during early life, we collected Day 9 whole-colon lamina propria cells after embryonic macrophage depletion and performed both bulk RNA sequencing and single-cell RNA sequencing. We also performed bulk RNA sequencing on distinct colonic stromal cell populations, conventional αβT cells, and iNKT cells under homeostatic early-life conditions to identify factors that directly imprint iNKT cells during this developmental period.