Single cell analysis of innate lymphoid cells in the context of TNF challenge in the intestine

In the gastrointestinal tract, excessive TNF drives cell death in the intestinal epithelium, and blockade of TNF has provided substantial therapeutic benefit to individuals with inflammatory bowel disease. However, the cellular and molecular pathways that control the beneficial versus detrimental impacts of TNF in the gut remain poorly understood. To understand the role of ILCs in regulation of TNF outcome in the intestine, we performed single-cell RNA-sequencing on 11,556 sort-purified ILCs from the small intestine of mice treated with PBS or TNF, identified and classified nine distinct clusters of cells based on expression of signature genes. For each sample, two mice were pooled together, and ILCs (CD45+CD3-epsilon-CD5-CD8-alpha-ΝΚ1.1-ΤCR-gamma-delta-CD11b-CD11c-B220-CD127+) were sort-purified lamina propria of small intestine.