To better understand the transcriptional heterogeneity and clonal diversity among CD4 T cells responding to chronic viral infection, we performed paired scRNA-seq and scTCR-seq on splenic GP66-77 (GP66)-specific CD4 T cells that were isolated from two individual mice on day 10 post-LCMV Clone 13 (Cl13) infection, a timepoint in which the endogenous GP66-specific T cell response is approximately at its peak (Crawford et al., 2014). The gene discussed is CD4; the disease is viral infectious disease.