SRA

The aim of this experiment was to characterize the gene expression of several in vitro cellular models of hepatocyte function: primary hepatocytes and common immortalized liver cell lines (HepG2, Hep3B and Huh7), cultured in parallel in both 2D and 3D configurations. Two independent cultures were carried out for each of the cell lines. For primary cultures, cells were obtained from three independent donors and cultured in parallel in both conditions. For the 2D culture, cell lines were grown using standard culture methods and harvested sub-confluence in exponential growth phase. For the 2D culture of primary hepatocytes, cells were grown in sandwich configuration between two layers of extracellular matrix (collagen coated plates and medium containing 0.25mg/ml Matrigel) and harvested at day 9 post seeding. For 3D cultures, cells were seeded at 1500 cells per well in ultra-low adherence multi-well plates to facilitate cellular aggregation and spheroid formation. Cell line spheroids aggregated rapidly and were harvested 4-5 days post seeding. Primary cell spheroids formed more slowly and were harvested 14-17 days post seeding. This RNA-seq experiment is being carried out as part of the Open Targets project to identify a gene expression signature of common immortalized cell lines/models. This signature will be used in combination with data from ChIP-seq experiments from the same cell lines against primary cells and tissues. The overall aim of the Open Targets Cell Line Epigenome project is to establish a systematic approach for the determination of human biological and disease relevance through the generation of transcriptomic and epigenomic data in cell lines of interest. Comparison of cell line mRNA expression and epigenome data with existing and newly generated reference data from human tissue and cell types will identify assay systems that will provide greater confidence in translating target biology and compound pharmacology to patients.