Experimental design for time-series RNA-seq analysis of gene expression and alternative splicing

Tzioutziou, N. A., James, A. B. , Guo, W., Calixto, C. P.G., Zhang, R., Nimmo, H. G. and Brown, J. W.S. (2021) Experimental design for time-series RNA-seq analysis of gene expression and alternative splicing. In: Staiger, D., Davis, S. and Davis, A. M. (eds.) Plant Circadian Networks: Methods and Protocols. Series: Methods in molecular biology (2398). Humana: New York, pp. 173-188. ISBN 9781071619117 (doi: 10.1007/978-1-0716-1912-4_14)

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Abstract

RNA-sequencing (RNA-seq) is currently the method of choice for analysis of differential gene expression. To fully exploit the wealth of data generated from genome-wide transcriptomic approaches, the initial design of the experiment is of paramount importance. Biological rhythms in nature are pervasive and are driven by endogenous gene networks collectively known as circadian clocks. Measuring circadian gene expression requires time-course experiments which take into account time-of-day factors influencing variability in expression levels. We describe here an approach for characterizing diurnal changes in expression and alternative splicing for plants undergoing cooling. The method uses inexpensive everyday laboratory equipment and utilizes an RNA-seq application (3D RNA-seq) that can handle complex experimental designs and requires little or no prior bioinformatics expertise.

Item Type:Book Sections
Keywords:Experimental design, RNA-seq, primer design, time course, data validation.
Status:Published
Glasgow Author(s) Enlighten ID:Nimmo, Professor Hugh and James, Dr Allan
Authors: Tzioutziou, N. A., James, A. B., Guo, W., Calixto, C. P.G., Zhang, R., Nimmo, H. G., and Brown, J. W.S.
College/School:College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
Journal Name:Methods in molecular biology (Clifton, N.J.)
Publisher:Humana
ISSN:1940-6029
ISBN:9781071619117
Published Online:01 October 2021

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