Whole transcriptome profiles and ribosome profiling of thapsigargin- and tunicamycin-treated LN308 cells

Accumulation of unfolded proteins in the endoplasmic reticulum triggers the unfolded protein response (UPR), an adaptive signal transduction pathway aimed at reinstating cellular homeostasis, or, if that fails, at triggering of apoptosis. To gain a comprehensive and systems-wide understanding of the UPR, we have pursued a multi-omics approach that, upon chemical induction of the UPR with two different compounds, monitors in parallel several parameters in the astrocytoma cell line LN-308. Changes to the cellular transcriptome (by high throughput sequencing) and altered translation status (by ribosome profiling) were measured after 2h and 6h of treatment. Overall design: Whole transcriptome profiles and ribosome profiling libraries were generated for thapsigargin- and tunicamycin-treated LN308 cell lines by next generation sequencing (Illumina Next Seq 500). Samples were taken after 0, 2 and 6 hours of pharmacological treatment.