Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing

Nikoleta A. Tzioutziou; Allan B. James; Wenbin Guo; Cristiane P. G. Calixto; Runxuan Zhang; Hugh G. Nimmo; John W. S. Brown

doi:10.1007/978-1-0716-1912-4_14

Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing

Nikoleta A. Tzioutziou, Allan B. James, Wenbin Guo, Cristiane P. G. Calixto, Runxuan Zhang, Hugh G. Nimmo, John W. S. Brown (Lead / Corresponding author)

Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed) › peer-review

1 Citation (Scopus)

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.

Original language	English
Title of host publication	Plant Circadian Networks
Subtitle of host publication	Methods and Protocols
Editors	Dorothee Staiger, Seth Davis, Amanda Melaragno Davis
Place of Publication	New York
Publisher	Humana Press
Pages	173-188
Number of pages	16
ISBN (Electronic)	9781071619124
ISBN (Print)	9781071619117 , 9781071619148
DOIs	https://doi.org/10.1007/978-1-0716-1912-4_14
Publication status	Published - 2022

Publication series

Name	Methods in Molecular Biology
Volume	2398
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Keywords

Data validation
Experimental design
Primer design
RNA-seq
Time course

ASJC Scopus subject areas

Molecular Biology
Genetics

Access to Document

10.1007/978-1-0716-1912-4_14

Cite this

Tzioutziou, N. A., James, A. B., Guo, W., Calixto, C. P. G., Zhang, R., Nimmo, H. G., & Brown, J. W. S. (2022). Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing. In D. Staiger, S. Davis, & A. Melaragno Davis (Eds.), Plant Circadian Networks: Methods and Protocols (pp. 173-188). (Methods in Molecular Biology; Vol. 2398). Humana Press. https://doi.org/10.1007/978-1-0716-1912-4_14

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title = "Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing",

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.",

keywords = "Data validation, Experimental design, Primer design, RNA-seq, Time course",

author = "Tzioutziou, {Nikoleta A.} and James, {Allan B.} and Wenbin Guo and Calixto, {Cristiane P. G.} and Runxuan Zhang and Nimmo, {Hugh G.} and Brown, {John W. S.}",

note = "Funding Information: This work was supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) [BB/P009751/1 to JWSB; BB/K006835/1 to HGN] and the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to JWSB and RZ]. Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",

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doi = "10.1007/978-1-0716-1912-4_14",

language = "English",

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Tzioutziou, NA, James, AB, Guo, W, Calixto, CPG, Zhang, R, Nimmo, HG & Brown, JWS 2022, Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing. in D Staiger, S Davis & A Melaragno Davis (eds), Plant Circadian Networks: Methods and Protocols. Methods in Molecular Biology, vol. 2398, Humana Press, New York, pp. 173-188. https://doi.org/10.1007/978-1-0716-1912-4_14

Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing. / Tzioutziou, Nikoleta A.; James, Allan B.; Guo, Wenbin et al.
Plant Circadian Networks: Methods and Protocols. ed. / Dorothee Staiger; Seth Davis; Amanda Melaragno Davis. New York: Humana Press, 2022. p. 173-188 (Methods in Molecular Biology; Vol. 2398).

Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed) › peer-review

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T1 - Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing

AU - Tzioutziou, Nikoleta A.

AU - James, Allan B.

AU - Guo, Wenbin

AU - Calixto, Cristiane P. G.

AU - Zhang, Runxuan

AU - Nimmo, Hugh G.

AU - Brown, John W. S.

N1 - Funding Information: This work was supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) [BB/P009751/1 to JWSB; BB/K006835/1 to HGN] and the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to JWSB and RZ]. Publisher Copyright: © 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - Data validation

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BT - Plant Circadian Networks

A2 - Staiger, Dorothee

A2 - Davis, Seth

A2 - Melaragno Davis, Amanda

PB - Humana Press

CY - New York

ER -

Tzioutziou NA, James AB, Guo W, Calixto CPG, Zhang R, Nimmo HG et al. Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing. In Staiger D, Davis S, Melaragno Davis A, editors, Plant Circadian Networks: Methods and Protocols. New York: Humana Press. 2022. p. 173-188. (Methods in Molecular Biology). Epub 2021 Oct 22. doi: 10.1007/978-1-0716-1912-4_14

Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing

Abstract

Publication series

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Dynamic Re-programming of the Cold Transcriptome in Arabidopsis (Joint with JHI)

Cite this

Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing

Abstract

Publication series

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Projects

Dynamic Re-programming of the Cold Transcriptome in Arabidopsis (Joint with JHI)

Cite this