To explore the temporal and developmental relationships between naïve, effector, and memory T cells, and the role of environmental cues versus TCR specificity in driving these distinct cell fates, we deployed paired single-cell RNA and TCR sequencing (scRNA/scTCR-seq) combined with trajectory analyses to reconstruct naïve CD4+ T cell differentiation during acute bacterial infection (Nowotschin et al., 2019). The gene discussed is CD4; the disease is bacterial infectious disease.