Single cell analysis of antigen-presenting cells in the large intestine

Antigen-presenting cells are responsible for the initiation of T cell responses and critically shape tolerogenic or inflammatory immune responses to the gut microbiota. Here, we employed the pathobiont Helicobacter hepaticus, and performed single-cell RNA sequencing for all antigen-presenting cells in the large intestine in various contexts. MHCII+ cells were sorted from the large intestine of naïve C57BL/6J mice, C57BL/6J mice colonized with Helicobacter hepaticus, and Il10-/- mice colonized with Helicobacter hepaticus. We mixed a 9:1 ratio of CD19- cells to CD19+ cells, to enrich for non-B cell populations. Cells were pooled from two mice for each sample.