A Guide for Designing and Analyzing RNA-Seq Data

Methods in Molecular Biology
Aniruddha ChatterjeeMichael R Eccles

Abstract

The identity of a cell or an organism is at least in part defined by its gene expression and therefore analyzing gene expression remains one of the most frequently performed experimental techniques in molecular biology. The development of the RNA-Sequencing (RNA-Seq) method allows an unprecedented opportunity to analyze expression of protein-coding, noncoding RNA and also de novo transcript assembly of a new species or organism. However, the planning and design of RNA-Seq experiments has important implications for addressing the desired biological question and maximizing the value of the data obtained. In addition, RNA-Seq generates a huge volume of data and accurate analysis of this data involves several different steps and choices of tools. This can be challenging and overwhelming, especially for bench scientists. In this chapter, we describe an entire workflow for performing RNA-Seq experiments. We describe critical aspects of wet lab experiments such as RNA isolation, library preparation and the initial design of an experiment. Further, we provide a step-by-step description of the bioinformatics workflow for different steps involved in RNA-Seq data analysis. This includes power calculations, setting up a computational envir...Continue Reading

Citations

Sep 13, 2019·Bioinformatics·Wei Vivian Li, Jingyi Jessica Li
Aug 20, 2020·Fluids and Barriers of the CNS·David M F FranciscoRémy Bruggmann
Dec 22, 2020·Adipocyte·Mohamed Al-SayeghMohamed Abu-Farha
Dec 6, 2020·Journal of Hematology & Oncology·Mingye HongHua Zhang

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