A simple ATAC-seq protocol for population epigenetics [version 2; peer review: 2 approved]

Detalhes bibliográficos
Autor(a) principal: Augusto, Ronaldo de Carvalho
Data de Publicação: 2021
Outros Autores: 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
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/46015
Resumo: 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.
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spelling Augusto, Ronaldo de CarvalhoRey, OliverCosseau, CélineChaparro, CristianVidal-Dupiol, JérémieAllienne, Jean-FrançoisDuva, DavidPinaud, SilvainTönges, SinaAndriantsoa, RanjaLuquet, EmilienAubret, FabienSow, Mamadou DiaDavid, PatriceThomson, VickiJoly, DominiqueLima, Mariana GomesFederico, DéborahDanchin, EtienneMinoda, AkiGrunau, Christoph2021-02-09T15:04:29Z2021-02-09T15:04:29Z2021AUGUSTO, 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. 2021.2398-502Xhttps://www.arca.fiocruz.br/handle/icict/4601510.12688/wellcomeopenres.15552.110.12688/wellcomeopenres.15552.2engF1000ResearchSchistosoma mansoniEpigenéticaEpigenomiaDaphnia pulexATAC-seqEpigeneticsEpigenomicsATAC-seqDaphnia pulexSchistosoma mansoniA simple ATAC-seq protocol for population epigenetics [version 2; peer review: 2 approved]info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleUniv. 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, FranceUniv. 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.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.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/46015/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALMarianaGomes_Lima_etal_IOC_2021.pdfMarianaGomes_Lima_etal_IOC_2021.pdfapplication/pdf3957304https://www.arca.fiocruz.br/bitstream/icict/46015/2/MarianaGomes_Lima_etal_IOC_2021.pdfe6510c6a6815575d729534d4533c0615MD52TEXTMarianaGomes_Lima_etal_IOC_2021.pdf.txtMarianaGomes_Lima_etal_IOC_2021.pdf.txtExtracted 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dc.title.pt_BR.fl_str_mv A simple ATAC-seq protocol for population epigenetics [version 2; peer review: 2 approved]
title A simple ATAC-seq protocol for population epigenetics [version 2; peer review: 2 approved]
spellingShingle A simple ATAC-seq protocol for population epigenetics [version 2; peer review: 2 approved]
Augusto, Ronaldo de Carvalho
Schistosoma mansoni
Epigenética
Epigenomia
Daphnia pulex
ATAC-seq
Epigenetics
Epigenomics
ATAC-seq
Daphnia pulex
Schistosoma mansoni
title_short A simple ATAC-seq protocol for population epigenetics [version 2; peer review: 2 approved]
title_full A simple ATAC-seq protocol for population epigenetics [version 2; peer review: 2 approved]
title_fullStr A simple ATAC-seq protocol for population epigenetics [version 2; peer review: 2 approved]
title_full_unstemmed A simple ATAC-seq protocol for population epigenetics [version 2; peer review: 2 approved]
title_sort A simple ATAC-seq protocol for population epigenetics [version 2; peer review: 2 approved]
author Augusto, Ronaldo de Carvalho
author_facet 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
author_role author
author2 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
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv 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
dc.subject.other.pt_BR.fl_str_mv Schistosoma mansoni
Epigenética
Epigenomia
Daphnia pulex
ATAC-seq
topic Schistosoma mansoni
Epigenética
Epigenomia
Daphnia pulex
ATAC-seq
Epigenetics
Epigenomics
ATAC-seq
Daphnia pulex
Schistosoma mansoni
dc.subject.en.pt_BR.fl_str_mv Epigenetics
Epigenomics
ATAC-seq
Daphnia pulex
Schistosoma mansoni
description 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.
publishDate 2021
dc.date.accessioned.fl_str_mv 2021-02-09T15:04:29Z
dc.date.available.fl_str_mv 2021-02-09T15:04:29Z
dc.date.issued.fl_str_mv 2021
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
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status_str publishedVersion
dc.identifier.citation.fl_str_mv 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.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/46015
dc.identifier.issn.pt_BR.fl_str_mv 2398-502X
dc.identifier.doi.none.fl_str_mv 10.12688/wellcomeopenres.15552.1
10.12688/wellcomeopenres.15552.2
identifier_str_mv 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.
2398-502X
10.12688/wellcomeopenres.15552.1
10.12688/wellcomeopenres.15552.2
url https://www.arca.fiocruz.br/handle/icict/46015
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv F1000Research
publisher.none.fl_str_mv F1000Research
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