Bulk RNA sequencing of TCM, TEM, and TRM from CD8+CD44+GP33+ T cells after LCMV infection

During acute infections, CD8+ T cells form various memory subpopulations to provide long-lasting protection against reinfection. Central memory (TCM), Effector memory (TEM), and long-lived effector (LLE) cells are circulating memory populations with distinct plasticity, migration patterns, and effector functions. Tissue-resident memory (TRM) cells permanently reside in the frontline sites of pathogen entry and provide tissue-specific protection upon reinfection. Here, using scRNA-seq and bulk RNA-seq, we examined the different and shared transcriptomes and regulators of TRMs with other circulating memory populations. Furthermore, we identified heterogeneity within the TRM pool from small intestine and novel transcriptional regulators that may control the phenotypic and functional heterogeneity of TRM cells during acute infection. Our findings provide a resource for future studies to identify novel pathways for enhancing vaccination and immunotherapeutic approaches. There are three CD8 memory groups, TEM, TCM, and TRM. CD8+CD44+GP33+ cells were sorted from LCMV infected mice at day 30 post infection. TEM and TCM cells are sorted from spleen, seperated by CD62L. TRM cells are sorted from intraepithelial lymphocytes from small intestine. There are 2-3 replicates for each cell group.