Bulk RNA Sequencing of SUM159PT cells grown in 2D or from tumors formed in NOD mice

Cancer is a heterogeneous disease, where multiple, phenotypically distinct subpopulations co-exist. Tumor 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. SUM159PT cells were cultivated in 2D dishes (N=6) or transplanted (100k cells) in vivo in the mammary fat pad of NOD mice and collected when the tumors (N=5) reached 1.2 cm (with a typical latency of 30 days). Bulk RNA-seq was used to compare the transcriptome of SUM159 derived tumors compared to cells grown in 2D