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scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation

DNA methylation is a central epigenetic mark that has diverse roles in gene regulation, development, and maintenance of genome integrity. 5 methyl cytosine (5mC) can be interrogated at base resolution in single cells by using bisulfite sequencing (scWGBS). Several different scWGBS strategies have be...

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Autores principales: Raine, Amanda, Lundmark, Anders, Annett, Alva, Wiman, Ann-Christin, Cavalli, Marco, Wadelius, Claes, Bergin, Claudia, Nordlund, Jessica
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8986790/
https://www.ncbi.nlm.nih.gov/pubmed/35388090
http://dx.doi.org/10.1038/s41598-022-09798-2
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author Raine, Amanda
Lundmark, Anders
Annett, Alva
Wiman, Ann-Christin
Cavalli, Marco
Wadelius, Claes
Bergin, Claudia
Nordlund, Jessica
author_facet Raine, Amanda
Lundmark, Anders
Annett, Alva
Wiman, Ann-Christin
Cavalli, Marco
Wadelius, Claes
Bergin, Claudia
Nordlund, Jessica
author_sort Raine, Amanda
collection PubMed
description DNA methylation is a central epigenetic mark that has diverse roles in gene regulation, development, and maintenance of genome integrity. 5 methyl cytosine (5mC) can be interrogated at base resolution in single cells by using bisulfite sequencing (scWGBS). Several different scWGBS strategies have been described in recent years to study DNA methylation in single cells. However, there remain limitations with respect to cost-efficiency and yield. Herein, we present a new development in the field of scWGBS library preparation; single cell Splinted Ligation Adapter Tagging (scSPLAT). scSPLAT employs a pooling strategy to facilitate sample preparation at a higher scale and throughput than previously possible. We demonstrate the accuracy and robustness of the method by generating data from 225 single K562 cells and from 309 single liver nuclei and compare scSPLAT against other scWGBS methods.
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spelling pubmed-89867902022-04-08 scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation Raine, Amanda Lundmark, Anders Annett, Alva Wiman, Ann-Christin Cavalli, Marco Wadelius, Claes Bergin, Claudia Nordlund, Jessica Sci Rep Article DNA methylation is a central epigenetic mark that has diverse roles in gene regulation, development, and maintenance of genome integrity. 5 methyl cytosine (5mC) can be interrogated at base resolution in single cells by using bisulfite sequencing (scWGBS). Several different scWGBS strategies have been described in recent years to study DNA methylation in single cells. However, there remain limitations with respect to cost-efficiency and yield. Herein, we present a new development in the field of scWGBS library preparation; single cell Splinted Ligation Adapter Tagging (scSPLAT). scSPLAT employs a pooling strategy to facilitate sample preparation at a higher scale and throughput than previously possible. We demonstrate the accuracy and robustness of the method by generating data from 225 single K562 cells and from 309 single liver nuclei and compare scSPLAT against other scWGBS methods. Nature Publishing Group UK 2022-04-06 /pmc/articles/PMC8986790/ /pubmed/35388090 http://dx.doi.org/10.1038/s41598-022-09798-2 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Raine, Amanda
Lundmark, Anders
Annett, Alva
Wiman, Ann-Christin
Cavalli, Marco
Wadelius, Claes
Bergin, Claudia
Nordlund, Jessica
scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation
title scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation
title_full scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation
title_fullStr scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation
title_full_unstemmed scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation
title_short scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation
title_sort scsplat, a scalable plate-based protocol for single cell wgbs library preparation
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8986790/
https://www.ncbi.nlm.nih.gov/pubmed/35388090
http://dx.doi.org/10.1038/s41598-022-09798-2
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