Single cell analysis of RORgt-expressing immune cells in the large intestine of healthy mice

RORgt is a lineage-specifying transcription factor expressed among immune cells that are enriched in the gastrointestinal tract and critically orchestrate immunity, inflammation, and tissue homeostasis. However, the spectrum of cellular heterogeneity among these cell types, the mechanisms controlling their tissue protective versus inflammatory roles, and their functional redundancy, are not fully understood. To address these fundamental gaps in knowledge, we performed single-cell RNA sequencing on RORgt-expressing immune cells of the large intestine of healthy mice and identified 10 distinct clusters of cells based on expression of signature genes. Overall design: RORgt+ immune cells were sorted from the large intestine lamina propria of RORgt-EGFP mice and mixed at a 1:1 ratio of TCRb+ cells to TCRb- cells, to enrich the non-T cell population. Cells were pooled from two mice.