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Approaches for Displaying Complete Transcriptomes of Environmental Bacteria

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Hydrocarbon and Lipid Microbiology Protocols

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

Genome-wide approaches, and specially high-throughput sequencing technologies, have changed the way biotechnology projects are planned and interpreted. Results are no more restricted to a family of genes but a whole transcriptome or more. Similarly, DNA analyses would not be focused on a small genomic region. Instead, complete chromosomes can be inspected on a single experiment. Therefore, current DNA or RNA sequence-related projects require appropriate ways of storing, visualizing, and integrating both intermediate data files and final results, what made them strongly dependent on specific computational tools. The workflow protocol presented in this chapter describes how to convert raw sequence data obtained with deep-sequencing technologies into standard genomic data file formats, ready to be used with popular genomic visualization programs. Methods to integrate bacterial genomic annotation tables with quantitative differential gene expression results are explained. Finally, a simple yet helpful procedure to sort and filter relevant quantitative results and to qualitatively (graphically) evaluate them is presented. All methods described can be applied using free and widely available software tools.

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Author information

Authors and Affiliations

  1. Computational Genomics Service, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049, Madrid, Spain

    Juan Carlos Oliveros

Authors
  1. Juan Carlos Oliveros
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Corresponding author

Correspondence to Juan Carlos Oliveros .

Editor information

Editors and Affiliations

  1. School of Biological Sciences, University of Essex Dept. Biological Sciences, Colchester, Essex, United Kingdom

    Terry J. McGenity

  2. Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany

    Kenneth N. Timmis

  3. Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

    Balbina Nogales

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© 2015 Springer-Verlag Berlin Heidelberg

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Oliveros, J.C. (2015). Approaches for Displaying Complete Transcriptomes of Environmental Bacteria. In: McGenity, T., Timmis, K., Nogales , B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_59

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  • DOI: https://doi.org/10.1007/8623_2015_59

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-50433-8

  • Online ISBN: 978-3-662-50435-2

  • eBook Packages: Springer Protocols

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