RT Journal Article
SR Electronic
T1 On the optimal design of metabolic RNA labeling experiments
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 428862
DO 10.1101/428862
A1 Alexey Uvarovskii
A1 Isabel S. Naarmann-de Vries
A1 Christoph Dieterich
YR 2018
UL http://biorxiv.org/content/early/2018/11/14/428862.abstract
AB 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 asymptotic theory of optimal design. Specifically, we derive the optimal labeling time for any given degradation rate and show that sub-optimal time points yield better rate estimates if they precede the optimal time point. Subsequently, we show that an increase in sample numbers should be preferred over an increase in sequencing depth. Lastly, we provide some guidance on use cases when laborious biochemical separation outcompetes recent nucleotide conversion based methods (such as SLAMseq).