Single-cell immune repertoire sequencing of B and T cells following infection and autoimmunity

Single-cell immune repertoire sequencing (gene expression and immune receptor repertoire) was performed under various contexts. This includes CD4 T follicular cells (sorted by surface expression of PD1+ CXCR5+ CD4+) following high dose LCMV clone 13 infection on days 10, 25, and 50 and low dose clone 13 infection on day 10 post infection. We additionally profiled virus-specific CD8 T cells that are specific to either GP33 or NP396. Gp33-specific CD8 T cells were sorted 15 months post infection with either low dose clone 13 LCMV, MCMV-ie2-gp33 or MCMV-m45-gp33. NP396-specific CD8 T cells were isolated either 10 days post challenge or 25 days post challenge using the viral model of dejavu (https://pubmed.ncbi.nlm.nih.gov/16604192/). B and T cells were isolated 14 days post induction of Experimental autoimmune encephalomyelitis (EAE).