Single-cell characterization of differentiated HepaRG cells

We used scRNA-seq to characterise the differentiation status of HepaRG cells after applying standard differentiation protocols on these cells. For downstream Perturb-seq we also characterised two cell lines of different genotype; Wt and cells transduced with dCas9-KRAB. Overall design: HepaRG cells were harvested in their proliferative state at Day 5 of culturing, after differentiation at Day 28 and after differentiation at Day 42 to control if cells can be kept in their differentiated state. Both Wt and dCas9 cells were captured. Lastly, dCas9-expressing HepaRG cells were transduced with lentiviral vectors carrying sgRNA in a pooled format, which were analysed using the feature barcodes technology from 10X Genomics allowing for pooled CRISPRi screens.