Single cell RNA sequencing of small intestinal dendritic cells from C57BL/6, RORgt-/- and RORgt-Cre x Ltb-flox mice

Cryptopatches (CP) and isolated lymphoid follicles (ILF) are evolutionary ancient lymphoid structures found in the intestines of all vertebrates. These structures are demarcated by a poorly characterised subset of mononuclear phagocytes (MPh), called CP/ILF-associated (CIA)-MPh. We could demonstrate that CIA-MPh derive from a pre-DC from the bone marrow and thus are boafide dendritic cells. We called these newly identified cDC cells : cryptopatch and ILF associated dendritic cells (CIA-DC). To obtain unbiased insights into how CIA-DC are integrated into the intestinal cDC landscape, we performed single cell RNA-sequencing (scRNA-seq) of purified CD45+ CD64- I-A/I-E+ CD11chigh cells from C57BL/6 mice using the 10X Genomics droplet-based technology. Finally, to study the role of ILC3 in the final differentiation of CIA-DC, we performed single cell RNA-sequencing (scRNA-seq) of cDC from Rorc(γt)-/- and Ltb∆ILC3,T mice, using the 10X Genomics droplet-based technology.