Protocol for quantifying silent ribosome induction in yeast and mammalian cells using polysome profiling

Translationally silent ribosomes lack bound mRNA and are difficult to quantify. Here, we present a protocol to measure silent ribosome induction under diverse conditions in yeast and mammalian cells. We describe steps to isolate polysome-profiling fractions, analyze ribosome-associated RNA by RNA sequencing with identification and removal of anomalously amplified rRNAs, and validate measurements by qPCR. For complete details on the use and execution of this protocol, please refer to Rahaman et al.¹.