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A SIMPLE ATAC-SEQ PROTOCOL FOR POPULATION EPIGENETICS [VERSION 2; PEER REVIEW: 2 APPROVED]
10.12688/wellcomeopenres.15552.2
Author
Augusto, Ronaldo de Carvalho
Rey, Oliver
Cosseau, Céline
Chaparro, Cristian
Vidal-Dupiol, Jérémie
Allienne, Jean-François
Duva, David
Pinaud, Silvain
Tönges, Sina
Andriantsoa, Ranja
Luquet, Emilien
Aubret, Fabien
Sow, Mamadou Dia
David, Patrice
Thomson, Vicki
Joly, Dominique
Lima, Mariana Gomes
Federico, Déborah
Danchin, Etienne
Minoda, Aki
Grunau, Christoph
Rey, Oliver
Cosseau, Céline
Chaparro, Cristian
Vidal-Dupiol, Jérémie
Allienne, Jean-François
Duva, David
Pinaud, Silvain
Tönges, Sina
Andriantsoa, Ranja
Luquet, Emilien
Aubret, Fabien
Sow, Mamadou Dia
David, Patrice
Thomson, Vicki
Joly, Dominique
Lima, Mariana Gomes
Federico, Déborah
Danchin, Etienne
Minoda, Aki
Grunau, Christoph
Affilliation
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France / LBMC, Laboratoire de Biologie et Modélisation de la Cellule Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1210, Lyon, 69007, France.
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France.
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France.
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France.
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France.
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France.
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France / Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK,
Division of Epigenetics, DKFZ ZMBH Alliance, German Cancer Research Center. Heidelberg, 69120, Germany.
Division of Epigenetics, DKFZ ZMBH Alliance, German Cancer Research Center. Heidelberg, 69120, Germany.
Univ Lyon, Université Claude Bernard Lyon 1, CNRS.Villeurbanne, 69622, France.
CNRS,Station d'Ecologie Théorique et Expérimentale, Université Paul Sabatier. Moulis, 09200, France / School of Molecular and Life Sciences, Curtin University. Bentley, Australia.
LBLGC, INRA, Université d’Orléans. Orléans, France.
Univ. Montpellier, CNRS, CEFE, F-34293. Montpellier, France.
School of Biological Sciences, University of Adelaide. Adelaide, 5005, Australia.
Laboratoire Evolution, Génomes Comportement, Ecologie, CNRS Université Paris Sud UMR 9191. Gif sur Yvette, 91198, France.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Malacologia. Rio de janeiro, RJ, Brasil.
Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse; CNRS. Toulouse, 31062, France.
Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse; CNRS. Toulouse, 31062, France.
RIKEN Center for Integrative Medical Sciences, Epigenome Technology Exploration Unit, Tsurumi.Kanagawa, 230-0045, Japan.
LBMC, Laboratoire de Biologie et Modélisation de la Cellule Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1210, Lyon, 69007, France.
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France.
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France.
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France.
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France.
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France.
Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095. Montpellier, France / Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK,
Division of Epigenetics, DKFZ ZMBH Alliance, German Cancer Research Center. Heidelberg, 69120, Germany.
Division of Epigenetics, DKFZ ZMBH Alliance, German Cancer Research Center. Heidelberg, 69120, Germany.
Univ Lyon, Université Claude Bernard Lyon 1, CNRS.Villeurbanne, 69622, France.
CNRS,Station d'Ecologie Théorique et Expérimentale, Université Paul Sabatier. Moulis, 09200, France / School of Molecular and Life Sciences, Curtin University. Bentley, Australia.
LBLGC, INRA, Université d’Orléans. Orléans, France.
Univ. Montpellier, CNRS, CEFE, F-34293. Montpellier, France.
School of Biological Sciences, University of Adelaide. Adelaide, 5005, Australia.
Laboratoire Evolution, Génomes Comportement, Ecologie, CNRS Université Paris Sud UMR 9191. Gif sur Yvette, 91198, France.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Malacologia. Rio de janeiro, RJ, Brasil.
Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse; CNRS. Toulouse, 31062, France.
Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse; CNRS. Toulouse, 31062, France.
RIKEN Center for Integrative Medical Sciences, Epigenome Technology Exploration Unit, Tsurumi.Kanagawa, 230-0045, Japan.
LBMC, Laboratoire de Biologie et Modélisation de la Cellule Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1210, Lyon, 69007, France.
Abstract
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.
Publisher
F1000Research
Citation
AUGUSTO, Ronaldo de Carvalho et al. A simple ATAC-seq protocol for population epigenetics [version 2; peer review: 2 approved]. Wellcome Open Research, v. 5, n. 121, p. 1-24, Jan. 2021.DOI
10.12688/wellcomeopenres.15552.110.12688/wellcomeopenres.15552.2
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