Comprehensive study of immune cells transcriptome and TCR clonotype diversity in mouse lung at different time points following one or two consecutive bacterial infections

Using single-cell transcriptomic analysis, we comprehensively described the immune composition of C57 Black 6 mouse lung following a bacterial infection at different time points, uninfected (day 0), on-going infection (day 1 and day 3) and infection cured (day 7). Seven days after a first lung bacterial infection, i.e. in cured mice, consequences of a second lung bacterial infection was investigated with the same strategy. Alongside a study of the TCR repertoire of Alpha/Beta T cells, a focus was placed on the transcriptome of Cxcr6 positive T cells following either primary or secondary pneumonia.