Evaluation of RNA extraction and rRNA depletion protocols for RNA-Seq in eleven edible seaweed species from brown, red, and green algae

Rob J. Dekker; Wim A. Ensink; Marina F. van Olst; Selina M. van Leeuwen; Wim C. de Leeuw; Martijs J. Jonker; Timo M. Breit

doi:10.1371/journal.pone.0339896

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Open Access

Peer-reviewed

Research Article

Evaluation of RNA extraction and rRNA depletion protocols for RNA-Seq in eleven edible seaweed species from brown, red, and green algae

Rob J. Dekker,

Roles Conceptualization, Supervision, Visualization, Writing – original draft, Writing – review & editing

Affiliation RNA Biology research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands

https://orcid.org/0000-0002-2662-8715

⨯
Wim A. Ensink,

Roles Conceptualization, Investigation

Affiliation RNA Biology research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
⨯
Marina F. van Olst,

Roles Investigation

Affiliation RNA Biology research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
⨯
Selina M. van Leeuwen,

Roles Investigation, Project administration

Affiliation RNA Biology research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
⨯
Wim C. de Leeuw,

Roles Formal analysis, Software

Affiliation RNA Biology research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
⨯
Martijs J. Jonker,

Roles Supervision, Writing – review & editing

Affiliation RNA Biology research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
⨯
Timo M. Breit

Roles Conceptualization, Supervision, Writing – review & editing

* E-mail: T.M.Breit@uva.nl

Affiliation RNA Biology research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
⨯

Evaluation of RNA extraction and rRNA depletion protocols for RNA-Seq in eleven edible seaweed species from brown, red, and green algae

Rob J. Dekker,
Wim A. Ensink,
Marina F. van Olst,
Selina M. van Leeuwen,
Wim C. de Leeuw,
Martijs J. Jonker,
Timo M. Breit

Published: January 2, 2026
https://doi.org/10.1371/journal.pone.0339896

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Seaweed
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Ribosomal RNA
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RNA extraction
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RNA sequencing
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RNA isolation
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Algae
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Transcriptome analysis
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Polysaccharides
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