Characterization of CD8 T cells during acute LCMV infection using scRNA-seq

During a viral infection, CD8 T cells encounter a myriad of antigenic and inflammatory signals of variable strength, which sets off each individual T cell on a unique differentiation trajectory. However, the developmental path for each of these cells will ultimately lead to one of only two potential outcomes after clearance of the infection—death or survival and development into memory CD8 T cells. How this cell fate decision is made remains incompletely understood. In this study, we explore the dynamic transcriptional changes during effector and memory CD8 T cell differentiation at the single cell level. Overall design: Three samples (Day 0, 9, and 129) prepared using 10x Genomics Chromium platform