Srivatsan, S. R. et al. Science 367, 45–51 (2020).

High-throughput screens have been widely used in drug discovery. Yet the typical phenotypic readout, cell viability, often fails to quantify the small changes in cell state that may be attributable to gene expression, epigenetic state or other factors. Srivatsan et al. incorporate ‘nuclear hashing’ into a single-cell combinatorial indexing (sci-RNA-seq) workflow. The resulting ‘sci-Plex’ workflow offers a cost-effective high-throughput screen approach for quantifying cellular responses to chemical compounds at single-cell resolution. To this end, the perturbed cells are lysed in-well and subjected to nuclear hashing, meaning their nuclei are labeled with well-specific polyadenylated oligonucleotides. The polyadenylated hashing oligos allow combinatorial indexing together with endogenous mRNAs so that both hash oligos and endogenous mRNA can be recovered. The sci-Plex screening enables profiling thousands of perturbations in a single experiment, and it uncovered dose-dependent responses of a cancer cells line to 188 chemical compounds.