RNA seq gene expression profile of SUM159PT cells sorted for TM4SF1 (high vs bulk).

Cancer is a heterogeneous disease, where multiple, phenotypically distinct subpopulations co-exist. Tumour evolution is a result of a complex interplay of genetic and epigenetic factors. To predict the molecular drivers of distinct cancer responses, we apply single-cell lineage tracing (scRNA-Seq of barcoded cells) on a triple-negative breast cancer model. We propose GALILEO, a framework providing lineage tracing, transcriptomic, and chromatin accessibility information simultaneously at single-cell resolution (Multiome ATAC + gene expression on barcoded cells). The combination of single-cell lineage tracing with phenotypic assays allows to link a cell state with its fate. Overall design: SUM159PT cells were sorted according to the surface marker TM4SF1 (high or bulk) and then immediately processed by RNA-seq or cultivated for the indicated number of passages (P4, P19) and processed by RNA-seq.