Protocol to track single-cell-derived clones using DNA barcoding combined with single-cell RNA sequencing

Clonal fitness and plasticity drive tumor heterogeneity contributing to disease progression and treatment resistance. Here, we provide a protocol to track the clonal outputs from uniquely marked cells. We describe steps for constructing and validating lentiviral DNA barcode libraries. We then detail procedures for single-cell RNA sequencing. This approach links clonal growth activity with transcriptomic profiles and enables permanent cellular labeling to track clonal dynamics in various model systems, which can provide insight into molecular processes underlying clone function. For complete details on the use and execution of this protocol, please refer to Nguyen et al.1.