The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline

Bisulfite sequencing is a widely used technique for determining DNA methylation and its relationship with epigenetics, genetics, and environmental parameters. Various techniques were implemented for epigenome-wide association studies (EWAS) to reveal meaningful associations; however, there are only...

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Autores principales: Can, Sultan Nilay, Nunn, Adam, Galanti, Dario, Langenberger, David, Becker, Claude, Volmer, Katharina, Heer, Katrin, Opgenoorth, Lars, Fernandez-Pozo, Noe, Rensing, Stefan A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594691/
https://www.ncbi.nlm.nih.gov/pubmed/34968299
http://dx.doi.org/10.3390/epigenomes5020012
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author Can, Sultan Nilay
Nunn, Adam
Galanti, Dario
Langenberger, David
Becker, Claude
Volmer, Katharina
Heer, Katrin
Opgenoorth, Lars
Fernandez-Pozo, Noe
Rensing, Stefan A.
author_facet Can, Sultan Nilay
Nunn, Adam
Galanti, Dario
Langenberger, David
Becker, Claude
Volmer, Katharina
Heer, Katrin
Opgenoorth, Lars
Fernandez-Pozo, Noe
Rensing, Stefan A.
author_sort Can, Sultan Nilay
collection PubMed
description Bisulfite sequencing is a widely used technique for determining DNA methylation and its relationship with epigenetics, genetics, and environmental parameters. Various techniques were implemented for epigenome-wide association studies (EWAS) to reveal meaningful associations; however, there are only very few plant studies available to date. Here, we developed the EpiDiverse EWAS pipeline and tested it using two plant datasets, from P. abies (Norway spruce) and Q. lobata (valley oak). Hence, we present an EWAS implementation tested for non-model plant species and describe its use.
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spelling pubmed-85946912021-12-28 The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline Can, Sultan Nilay Nunn, Adam Galanti, Dario Langenberger, David Becker, Claude Volmer, Katharina Heer, Katrin Opgenoorth, Lars Fernandez-Pozo, Noe Rensing, Stefan A. Epigenomes Article Bisulfite sequencing is a widely used technique for determining DNA methylation and its relationship with epigenetics, genetics, and environmental parameters. Various techniques were implemented for epigenome-wide association studies (EWAS) to reveal meaningful associations; however, there are only very few plant studies available to date. Here, we developed the EpiDiverse EWAS pipeline and tested it using two plant datasets, from P. abies (Norway spruce) and Q. lobata (valley oak). Hence, we present an EWAS implementation tested for non-model plant species and describe its use. MDPI 2021-05-04 /pmc/articles/PMC8594691/ /pubmed/34968299 http://dx.doi.org/10.3390/epigenomes5020012 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Can, Sultan Nilay
Nunn, Adam
Galanti, Dario
Langenberger, David
Becker, Claude
Volmer, Katharina
Heer, Katrin
Opgenoorth, Lars
Fernandez-Pozo, Noe
Rensing, Stefan A.
The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline
title The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline
title_full The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline
title_fullStr The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline
title_full_unstemmed The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline
title_short The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline
title_sort epidiverse plant epigenome-wide association studies (ewas) pipeline
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594691/
https://www.ncbi.nlm.nih.gov/pubmed/34968299
http://dx.doi.org/10.3390/epigenomes5020012
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