Repertoire-based scRNA-Seq phenotyping delineates responding helper T cell subsets

Here we aimed to create an integrated reference scRNA-seq dataset of peripheral blood CD4 T cells.Furthermore, we provided scRNA-seq datasets of effector-memory peripheral CD4 T cells collected during the two COVID-19 breakthrough infections from one individual. We identified SARS-CoV-2 specific TCR clonotypes from this donor with the help of longitudinal bulk TCRbeta profiling, as well as with the help of functional T cell assay coupled with TCRbeta profiling. Finally, we delineated the phenotype of SARS-CoV-2-specific CD4 T cells in this donor making use of our reference scRNA-seq dataset.