Codon and amino acid identity are major determinants of mRNA stability in humans

To investigate the effects of the coding sequence on mRNA decay, we globally analyzed the stability of endogenous mRNAs as well as those derived from the human ORFeome collection, which contains full-length coding sequences in the context of invariant UTRs. HEK293T cell lines expressing subsets of the human ORFeome collection were generated. Cell lines were either left untreated, treated with DMSO, or treated with translation inhibitor 4EGI-1, and then subjected to 4SU based metabolic labeling. RNA sequencing libraries were prepared using TruSeq Stranded mRNA Sample Preparation Kit (Illumina). Sequenced reads that passed quality filters were mapped to the reference genome using STAR aligner, and quantified at the gene level using HT-seq.