We acquired single-cell transcriptomic data from multiple time points during chronic infection, covering the very early phases (day 1-4), peak phase (day 7), contraction phase (day 14), and late phase (day 21) (Fig 2A), to capture an increased spectrum of the transcriptional landscape during the course of the infection that would allow a time-resolved analysis of single-cell heterogeneity and possibly more accurate inference of differentiation trajectories of virus-specific CD8 T cells. Here, CD8A is linked to infection.