Multimodal T Cell Analysis with CoNGA

Advances in single-cell technologies have made it possible to simultaneously quantify gene expression and immune receptor sequence across thousands of individual T or B cells in a single experiment. Data from such experiments are advancing our understanding of the relationship between adaptive immune receptor sequence and transcriptional profile. We recently reported a software tool, CoNGA, specifically developed to detect correlation between receptor sequence and transcriptional profile. Here we describe in detail how CoNGA can be applied to analyze a large and diverse T cell dataset featuring multiple donors and batch annotations. Our workflow illustrates new analysis modes for the detection of TCR sequence convergence into similarity clusters and of matches to literature-derived TCR databases, as well as processing of gamma-delta T cells.