In contrast, CLs in the early-stage had a higher expression of transcription factors FOS and JUN, and memory-like associated genes (IL7R, TCF7, CCR7), which also persisted in the late-stage of infection where cells had higher expression of transcription factor BACH2 and of S1PR1 (encoding sphingosine-1-phosphate receptor-1), which is known to promote T cell retention in non-lymphoid tissues30. Here, JUN is linked to infection.