Ribosome profiling is a method that determines genome-wide mRNA translation through measuring ribosome-protected mRNA fragments by deep sequencing. This method can be used to quantify gene expression at the translational level and precisely pinpoint ribosome loading onto mRNA with codon-level resolution. Genome-wide regulation of mRNA translation can also be determined if RNA-Sequencing (RNA-Seq) is carried out in parallel. Here, we describe a protocol for simultaneously performing ribosome profiling and RNA-Seq in cells infected with vaccinia virus.
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