RNA-seq analysis of two common T cell models, HUT78 and JURKAT E6.1: Project 5 of Open Targets - Epigenomes of Cell Lines

The aim of this experiment was to characterize the gene expression of two common immortalized T cell lines (HUT78 and JURKAT E6.1) with and without activating stimuli. Two independent cultures were carried out for each of the cell lines. Cells were cultured according to supplier recommendations and either left untreated or stimulated with Dynabeads human T-activator CD4/CD28 beads (Invitrogen, UK) at a ratio of 1 bead:3 cells for 48 hours. This RNA-seq experiment is being carried out as part of the Open Targets project to identify a gene expression signature of common immortalised 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.