MCSeEd (Methylation Context Sensitive Enzyme ddRAD): A New Method to Analyze DNA Methylation
- 23 February 2020
- book chapter
- protocol
- Published by Springer Science and Business Media LLC
- Vol. 2093, 47-64
- https://doi.org/10.1007/978-1-0716-0179-2_4
Abstract
Methylation context sensitive enzyme ddRAD (MCSeEd) is a NGS-based method for genome-wide investigations of DNA methylation at different contexts requiring only low to moderate sequencing depth. It is particularly useful for identifying methylation changes in experimental systems challenged by biotic or abiotic stresses or at different developmental stages.Keywords
This publication has 25 references indexed in Scilit:
- The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNAGenome Research, 2013
- Rainbow: an integrated tool for efficient clustering and assembling RAD-seq readsBioinformatics, 2012
- Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model SpeciesPLOS ONE, 2012
- methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profilesGenome Biology, 2012
- Conserved role of intragenic DNA methylation in regulating alternative promotersNature, 2010
- Genome-Wide Evolutionary Analysis of Eukaryotic DNA MethylationScience, 2010
- Establishing, maintaining and modifying DNA methylation patterns in plants and animalsNature Reviews Genetics, 2010
- BEDTools: a flexible suite of utilities for comparing genomic featuresBioinformatics, 2010
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Highly Integrated Single-Base Resolution Maps of the Epigenome in ArabidopsisCell, 2008