Cargando…
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...
Autores principales: | , , , , , , , |
---|---|
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 |
_version_ | 1784682607767715840 |
---|---|
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. |
format | Online Article Text |
id | pubmed-8986790 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT raineamanda scsplatascalableplatebasedprotocolforsinglecellwgbslibrarypreparation AT lundmarkanders scsplatascalableplatebasedprotocolforsinglecellwgbslibrarypreparation AT annettalva scsplatascalableplatebasedprotocolforsinglecellwgbslibrarypreparation AT wimanannchristin scsplatascalableplatebasedprotocolforsinglecellwgbslibrarypreparation AT cavallimarco scsplatascalableplatebasedprotocolforsinglecellwgbslibrarypreparation AT wadeliusclaes scsplatascalableplatebasedprotocolforsinglecellwgbslibrarypreparation AT berginclaudia scsplatascalableplatebasedprotocolforsinglecellwgbslibrarypreparation AT nordlundjessica scsplatascalableplatebasedprotocolforsinglecellwgbslibrarypreparation |