Mapping the thymic hematopoietic antigen presenting cell network

To characterize thymic APCs in an unbiased manner, we generated a scRNA-seq atlas of thymic antigen presenting cells (APCs) isolated from thymic rosettes, cellular complexes of physically interacting thymocytes and APCs. Around 8,000 APCs were captured, mostly haematopoietic in origin, consisting of B cell, dendritic cell and macrophage lineages. Thymic rosettes were isolated from three C57Bl/6 female mice and dissociated into single cell suspension using trypsin. CD11b+CD11c+EpCAM+B220+Gr-1+SiglecH+F4/80+ cells and remaining CD90.2- non-thymocytes were sorted by fluorescence activated cell sorting (FACS) for single cell RNA sequencing on the 10X Genomics platform.