Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX

Abstract

Ribosome profiling provides the opportunity to evaluate translation kinetics at codon level resolution. Here, we describe ribosome profiling data, generated from two HEK293T cell lines. The ribosome profiling data are composed of Ribo-seq (mRNA sequencing data from ribosome protected fragments) and RNA-seq data (total RNA sequencing). The two HEK293T cell lines each express a version of the F9 gene, both of which are translated into identical proteins in terms of their amino acid sequences. However, these F9 genes vary drastically in their codon usage and predicted mRNA structure. We also provide the pipeline that we used to analyze the data. Further analyzing this dataset holds great potential as it can be used i) to unveil insights into the composition and regulation of the transcriptome, ii) for comparison with other ribosome profiling datasets, iii) to measure the rate of protein synthesis across the proteome and identify differences in elongation rates, iv) to discover previously unidentified translation of peptides, v) to explore the effects of codon usage or codon context in translational kinetics and vi) to investigate cotranslational folding. Importantly, a unique feature of this dataset, compared to other available ribosome profiling data, is the presence of the F9 gene in two very distinct coding sequences.

RiboDoc: A Docker-based package for ribosome profiling analysis

“…As we only implemented the published RiboWaltz package into RiboDoc we did not use this option here to demonstrate how RiboDoc works. We selected the trip option for the following analysis applied to two datasets: a previously published dataset for human cells [24] and an unpublished dataset for yeast from our own group. The human dataset was selected because quality controls had been rigorously performed, making it possible for us to compare RiboDoc with data analyzed with different scripts.…”