Single Cell Core

Abstract The Single Cell Core will provide state-of-the-art experimental technology for single-cell multi-omic profiling. Two major limitations of conventional scRNA-seq for immunophenotyping include the lack of correlation between mRNA levels and surface protein expression and the lack of clonal identity from immune receptor sequence. The Core will provide access to technologies for simultaneous profiling of mRNA, immune receptor sequence, and surface protein expression from individual cells at scale. For experiments with limited cell numbers, we will also provide scPLATE-seq, a fully automated platform for index sorting and scRNA-seq that is cost-effective for low cell numbers. Given the focus on analyzing virus-specific immune responses longitudinally and across tissues, the ability to associate immunophenotypes such as surface protein expression, the transcriptome, and TCR sequence with antigen specificity is also highly desirable. This information will allow us to determine the phenotypic subset and clonal identity of each cell in a virus-specific T cell population, to anchor virus-specific T cells from different individuals, ages, and tissue sites to our reference map, and to investigate their functional capacities with single-cell resolution. The Core will provide scalable technology for associating antigen specificity and T cell receptor sequence with targeted mRNA and surface protein profiles of individual cells (TetTCR- seqHD). We will develop and optimize barcoded tetramer pools for a broad range of viruses and vaccines including CMV, influenza, and SARS-CoV-2 for joint analysis T cell receptor antigen recognition, clonotype, and immunophenotype in individual T cells.