Protocol for isolating stromal cells from lymphoid tissue for performing scRNA-seq

Stromal cells constitute less than 2% of cells in lymph nodes and are technically difficult to isolate and analyze. Here, we present a protocol to purify fibroblasts from lymphoid tissues in preparation for single-cell RNA sequencing (scRNA-seq) analysis. We describe steps for lymph node dissection and digestion, cell staining, and magnetic separation and also detailed procedures for checking purity and viability. This protocol can be applied to other tissues, including tumors. For complete details on the use and execution of this protocol, please refer to Makris et al.¹.