Single cell transcriptional analysis reveals the effects of mucosal vaccination on mouse lung CD4 T cell compartments

We report the results of single cell RNA sequencing (scRNA-seq) analysis on CD4+ T cells sorted from the lungs of mice vaccinated with a TB vaccine and infected with M. tuberculosis. To gain a more detailed understanding of the characteristics of the CD4 T cell response during M. tuberculosis infection and after mucosal vaccination, we performed scRNA-seq on CD4 T cells sorted from naïve and i.n. H1/ML-RR-cGAMP vaccinated infected mouse lungs at the peak of the T cell response, 3 weeks post infection. Subsets of CD4 T cells were manually annotated based on signature expression of lineage-specific transcription factor, cytokine, and cell surface markers. Mouse lung CD4 T cells pooled from mock (PBS control) or mucosally vaccinated with H1/ML-RR-cGAMP vaccine (IN vacc) 3 weeks post M. tuberculosis infection, 3 mice pooled per sample.