Protocol for identifying recirculating thymic regulatory T cells and characterizing the role of Eos in their function using scRNA-seq and TCR-seq

Previous studies on the characterization of regulatory T cells (Tregs) in the thymus have proven to be simplistic. Here, we present a protocol for identifying recirculating thymic Tregs in mice and characterizing the role of Eos in their function. We describe steps for thymic dissection, magnetic cell separator (autoMACS) and fluorescence-activated cell sorting (FACS), single-cell sequencing, and downstream computational analysis. This protocol details a refined classification based on analysis of gene expression from single-cell RNA sequencing (scRNA-seq) and TCR sequencing data. For details on the use of this protocol, refer to Xie et al. 1