Single-cell RNA-seq of aortic CD3+ T cells

We dissected the changes in the infiltrating T cell population in the aorta of cDC1-impaired mice compared with control mice in atheroprone Ldlr-/- mice by scRNAseq. To this aim, lethally irradiated Ldlr-/- CD45.1 mice were grafted with cDC1-impaired Xcr1Cre-DTA or control Xcr1Cre bone marrow (BM) and fed high cholesterol diet (HCD) for 8 weeks. At the endpoint, 10 mice per group were pooled and aortic CD45+ CD3+ CD11c- I-A/I-E– F4/80- Ly6C- Ly6G- NK1.1- were sorted and sequenced. A number of 6259 CD3+ T cells were sequenced in Xcr1Cre control chimeric mice, while 4072 cells were sequenced in cDC1-impaired Xcr1Cre-DTA chimeric mice. Nine different clusters were identified based on the following gene expression profile.