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RNA Sequencing and Analysis in Microorganisms for Metabolic Network Reconstruction

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Metabolic Network Reconstruction and Modeling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1716))

Abstract

There is a strict interplay between metabolic networks and transcriptional regulation in bacteria; indeed, the transcriptome regulation, affecting the expression of large gene sets, can be used to predict the likely “on” or “off” state of metabolic genes as a function of environmental factors. Up to date, many bacterial transcriptomes have been studied by RNAseq, hundreds of experiments have been performed, and Giga bases of sequences have been produced. All this transcriptional information could potentially be integrated into metabolic networks in order to obtain a more comprehensive view of their regulation and to increase their prediction power.

To get high-quality transcriptomic data, to be integrated into metabolic networks, it is paramount to clearly know how to produce highly informative RNA sequencing libraries and how to manage RNA sequencing data.

In this chapter, we will get across the main steps of an RNAseq experiment: from removal of ribosomal RNAs, to strand-specific library preparation, till data analysis and integration. We will try to share our experience and know-how, to give you a precise protocol to follow, and some useful recommendations or tips and tricks to adopt in order to go straightforward toward a successful RNAseq experiment.

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Authors and Affiliations

  1. Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Fratelli Cervi 93, 20090 Segrate, Milan, Italy

    Eva Pinatel

  2. Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, Humanitas Clinical and Research Center, Via Manzoni 56, 20089, Milan, Italy

    Clelia Peano

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  1. Eva Pinatel
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  2. Clelia Peano
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Correspondence to Clelia Peano .

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Editors and Affiliations

  1. Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy

    Marco Fondi

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Pinatel, E., Peano, C. (2018). RNA Sequencing and Analysis in Microorganisms for Metabolic Network Reconstruction. In: Fondi, M. (eds) Metabolic Network Reconstruction and Modeling. Methods in Molecular Biology, vol 1716. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7528-0_11

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  • DOI: https://doi.org/10.1007/978-1-4939-7528-0_11

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