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Coupled Transcriptomics for Differential Expression Analysis and Determination of Transcription Start Sites: Design and Bioinformatics

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Antimicrobial Therapies

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2296))

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Abstract

The term coupled transcriptomics is coined to describe a design of an RNA-seq experiment intended for both differential expression analysis and genome-wide determination of the transcription start sites (TSS). The minimal requirements for the first analysis are two experimental conditions with at least two biological replicates enabling statistical tests. The second analysis involves the bioinformatics comparison of the data generated from a control RNA-seq library with another library enriched in primary transcripts using Terminator™ 5′-phosphate-dependent exonuclease, in an experiment denominated differential RNA-seq (dRNA-seq). Usually, dRNA-seq is carried out with specific protocols for library construction, different of those used for common differential expression analysis. Our experimental design allows to use the same data for both analyses, reducing the number of libraries to be generated and sequenced. This is a guide for designing a coupled transcriptomics experiment and for the subsequent bioinformatics procedures. The proposed methods can be applied to the detection and study of small RNA genes.

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Acknowledgments

This work has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement No. 720793 TOPCAPI—Thoroughly Optimised Production Chassis for Advanced Pharmaceutical Ingredients. The authors also wish to acknowledge Spanish Government (MINECO) for funding the application of these methods to Streptomyces tsukubaensis, part of the collaborative ERA-IB TACRODRUGS project, ref. PCIN-2016-012.

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Authors and Affiliations

  1. Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, León, Spain

    Antonio Rodríguez-García, Alberto Sola-Landa & Rosario Pérez-Redondo

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  1. Antonio Rodríguez-García
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  2. Alberto Sola-Landa
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  3. Rosario Pérez-Redondo
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Correspondence to Antonio Rodríguez-García .

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Editors and Affiliations

  1. INBIOTEC (Instituto de Biotecnología de León), Parque Científico de León, León, Spain

    Carlos Barreiro

  2. Department of Biotechnology, Crystal Pharma A Subsidiary of Albany Molecular Research Inc. (AMRI) Parque Tecnológico de León, León, Spain

    José-Luis Barredo

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Rodríguez-García, A., Sola-Landa, A., Pérez-Redondo, R. (2021). Coupled Transcriptomics for Differential Expression Analysis and Determination of Transcription Start Sites: Design and Bioinformatics. In: Barreiro, C., Barredo, JL. (eds) Antimicrobial Therapies. Methods in Molecular Biology, vol 2296. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1358-0_16

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  • DOI: https://doi.org/10.1007/978-1-0716-1358-0_16

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1357-3

  • Online ISBN: 978-1-0716-1358-0

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