Single-cell intracellular epitope and transcript detection revealing signal transduction dynamics

To further our understanding of how biochemical information flows through cells upon external stimulation, we require single-cell multi-omics methods that concurrently map changes in (phospho)protein levels across signaling networks and the associated gene expression profiles. Here, we present Quantification of RNA and Intracellular Epitopes by sequencing (QuRIE-seq), a droplet-based platform for single-cell RNA and intra- and extracellular (phospho)protein quantification through sequencing. We applied QuRIE-seq to quantify cell-state changes of 6976 cells, at both the signaling and transcriptome level following 2, 4, 6, 60, and 180-minute stimulation of the B-cell receptor pathway (BCR) in Burkitt lymphoma cells (BJABs). Using the recently developed multi-factor omics analysis (MOFA+) framework we delineated changes in single-cell (phospho)protein and gene expression patterns over multiple timescales and revealed the effect of an inhibitory drug (Ibrutinib) on signaling and gene expression landscape. Overall design: We used our novel technology QuRIE-seq for simultaneous quantification of RNA and (phospho) proteins at a single-cell level. The deposited data contains the quantification of gene expression profiles as well as a set of 80 proteins for individual BJAB cells upon different durations of aIg stimulation (0, 2, 4, 6, 60, 180 min) with previous ibrutinib inhibition (for 6, 180 min)