On the optimal design of metabolic RNA labeling experiments.

ABSTRACT: Massively parallel RNA sequencing (RNA-seq) in combination with metabolic labeling has become the de facto standard approach to study alterations in RNA transcription, processing or decay. Regardless of advances in the experimental protocols and techniques, every experimentalist needs to specify the key aspects of experimental design: For example, which protocol should be used (biochemical separation vs. nucleotide conversion) and what is the optimal labeling time? In this work, we provide approximate answers to these questions using the asymptotic theory of optimal design. Specifically, we investigate, how the variance of degradation rate estimates depends on the time and derive the optimal time for any given degradation rate. Subsequently, we show that an increase in sample numbers shoul

SUBMITTER: Uvarovskii A 

PROVIDER: S-EPMC6699717 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature