Single cell RNA and TCR profiling of tetramer sorted mouse mLN and IELs.

We utilized H2-I-Ab tetramers to isolate CD4 T cells from mice to characterize the functional characteristics of ileal intraepithelial T cells and their lymphoid counterparts in the corresponding draining lymph nodes (mLN). Non-CD4 T cells (B220+, CD11b+, CD11c+, F4/80+, CD8a+) were excluded before FACS-sorting of CD45+CD3+CD4+ tetramer-specific T cells discriminated by double-positive staining with dual-labeled tetramer fluorophores. We recovered tetramer+ and tetramer- IELs and mLN T cells, and profiled them by single-cell RNA and TCR sequencing. Overall design: FACS sort of tetramer positive and tetramer negative cells in mLN and IELs.