Massively multiplex multi-modal chemical screens at single-cell resolution with icCITE-plex

We present icCITE-plex, a novel cellular barcoding systems that enable multiplexed analysis of multiple independent samples within a single experiment through a combination of viral barcodes and antibody-based plate-barcodes. Using this platform, we successfully profiled 360 drug-dose responses across 475 surface proteins, 64 intracellular epitopes, and the whole transcriptome in human and mouse T cells treated with 56 different kinase inhibitors, demonstrating the method's ability to capture multi-modal cellular responses to chemical perturbations.