A simple ATAC-seq protocol for population epigenetics

We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a stre...

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Bibliographic Details
Published in:Wellcome open research 2020, Vol.5, p.121
Main Authors: Augusto, Ronaldo de Carvalho, Rey, Oliver, Cosseau, Céline, Chaparro, Cristian, Vidal-Dupiol, Jérémie, Allienne, Jean-François, Duval, David, Pinaud, Silvain, Tönges, Sina, Andriantsoa, Ranja, Luquet, Emilien, Aubret, Fabien, Dia Sow, Mamadou, David, Patrice, Thomson, Vicki, Joly, Dominique, Gomes Lima, Mariana, Federico, Déborah, Danchin, Etienne, Minoda, Aki, Grunau, Christoph
Format: Article
Language:English
Subjects:
Animal populations
Deoxyribonucleic acid
DNA
Ecology
Epigenetics
Gene expression
Genomes
Laboratories
Molecular biology
Peer review
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Summary:We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.
ISSN:2398-502X
2398-502X
DOI:10.12688/WELLCOMEOPENRES.15552.1