Tracking of CD4+ T cells during CNS autoimmunity

Here, we use in vivo labeling at defined anatomical sites for "provance" tracking of immune cells across compartmental borders in the context of experimental autoimmune encephalomyelitis (EAE). Specifically, we labeled T cells in mesenteric or inguinal lymph nodes (LNs) of T cell conditional mitoDendra2 reporter mice via photoconversion at disease onset and re-isolated photoconverted T cells form the LNs, spleen and CNS two days later and we performed scRNA-seq on them. Our experimental system will help to better understand the phenotype and function of T cells migration into the CNS as a consequence of priming in a distinct peripheral immune compartment. Two single-cell RNA experiments were performed. In the first, scRNA-seq and Cell Hashing libraries were prepared using the 10x Chromium Single Cell 3' Solution (Chromium Single Cell 3' v3 combined with Cell Hashing as per established protocols (doi: 10.1186/s13059-018-1603-1). In the second, scRNA-seq, scTCR-seq and Cell Hashing libraries were prepared using the 10x Chromium Single Cell 5' Solution (Chromium Next GEM Single Cell VDJ v1.1 with Feature Barcoding technology for Cell Surface Protein)