Multimodal profiling of 500,000 memory T cells from a tuberculosis cohort

We profiled peripheral memory T cells from donors with prior TB disease or latent infection to identify cell states associated with disease or other demographic and environmental variables. For higher-resolution definition of T cell states, we performed CITE-seq to measure single-cell mRNA and surface expression of 31 key memory T cell proteins, integrated these modalities, and quantified asssociations with variables of interest. PBMCs were collected from 259 donors, including former progressors (cases) and non-progressors (controls). Technical replicates were included across separate batches for 12. We isolated memory T cells and profiled 500,089 high-quality cells with CITE-seq (using a surface marker panel of 31 antibodies). Raw sequencing data for human samples will be available on dbGAP.