Coupling live-cell imaging and in situ isolation of the same single cell to profile the transient states of predicted drug-tolerant cells.

Cell response variability is a starting point in cancer drug resistance that has been difficult to analyze because the tolerant cell states are short lived. Here, we present fate-seq, an approach to isolate single cells in their transient states of drug sensitivity or tolerance before profiling. The drug response is predicted in live cells, which are laser-captured by microdissection before any drug-induced change can alter their states. This framework enables the identification of the cell-state signatures causing differential cell decisions upon treatment. For complete details on the use and execution of this protocol, please refer to Meyer et al. (2020).