Next generation sequencing (NGS) application in multiparameter gene expression analysis

Degeng Wang, Andrey L. Karamychev

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

1 Scopus citations

Abstract

Next generation sequencing (NGS) is routinely used in gene expression analyses. In particular, RNA-seq has been the method of choice for highly sensitive genome-wide quantification of RNA expression. The method can be used in a wide variety of model systems, including studies to gain insight into underlying mechanisms of toxicologic processes and disease development induced by environmental toxicants. RNA-seq has also been coupled to many other molecular biology protocols to monitor specific aspects of the gene expression process. Here, we describe two such coupling—(a) global run-on sequencing (GRO-seq) that coupled it to the nuclear run-on (NRO), and (b) polysome profiling that coupled it to sucrose-gradient-based polysome isolation. Simultaneous RNA-seq, GRO-seq, and polysome profiling analyses enabled genome-wide analysis of the mode of stability control of individual RNA molecules.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages17-34
Number of pages18
DOIs
StatePublished - 2020

Publication series

NameMethods in Molecular Biology
Volume2102
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • GRO-seq
  • Gene expression regulation
  • Next generation sequencing
  • Nuclear run-on
  • Polysome profiling
  • Polysomes
  • RNA-seq
  • Ribosomes
  • Sucrose gradient
  • Translation

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