Quantitative and multiplexed chemical-genetic phenotyping in mammalian cells using QMAP-Seq

Here, we develop Quantitative and Multiplexed Analysis of Phenotype by Sequencing (QMAP-Seq), which leverages next-generation sequencing for pooled high-throughput chemical-genetic profiling. We apply QMAP-Seq to investigate how cellular stress response factors affect therapeutic response in cancer. Using minimal automation, we treat pools of 60 cell types—comprising 12 genetic perturbations in five cell lines—with 1,440 compound-dose combinations, generating 86,400 chemical-genetic measurements. Overall design: Targeted sequencing of sgRNAs and cell line barcodes from samples consisting of 5 cell lines x 12 sgRNAs + cell spike-in standards. Sequencing run was composed of 1,536 samples, each representing a unique compound-dose-replicate combination. 96 samples were DMSO-treated (control), and 1,440 samples were compound-treated.