Single-cell RNA-seq profiling of ARID1A-loss-associated transcriptional heterogeneity and clonal diversification in pancreatic cancer cells

The shPseuMO-Tag system couples genetic perturbation with clonal lineage tracing. The datasets include an initial epigenetic-modifier screen, an ARID1A knockdown time course, a large-scale pooled five-shRNA experiment, acute SMARCA4 degradation, independent experiments in multiple PDAC cell lines, and matched pre-injection and lung-colonization samples.

In the independent multi-cell-line experiment, BxPC3, HPAC, SW1990, and SUIT-2 were profiled using independently derived clones, whereas HPAFII was analyzed as a pooled population because stable single-cell-derived HPAFII clones could not be established.