scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Single-cell DNA methylation profiling currently suffers from excessive noise and/or limited cellular throughput. We developed scTAM-seq, a targeted bisulfite-free method for profiling up to 650 CpGs in up to 10,000 cells per experiment, with a dropout rate as low as 7%. We demonstrate that scTAM-seq...

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Autores principales: Bianchi, Agostina, Scherer, Michael, Zaurin, Roser, Quililan, Kimberly, Velten, Lars, Beekman, Renée
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9615163/
https://www.ncbi.nlm.nih.gov/pubmed/36307828
http://dx.doi.org/10.1186/s13059-022-02796-7
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author Bianchi, Agostina
Scherer, Michael
Zaurin, Roser
Quililan, Kimberly
Velten, Lars
Beekman, Renée
author_facet Bianchi, Agostina
Scherer, Michael
Zaurin, Roser
Quililan, Kimberly
Velten, Lars
Beekman, Renée
author_sort Bianchi, Agostina
collection PubMed
description Single-cell DNA methylation profiling currently suffers from excessive noise and/or limited cellular throughput. We developed scTAM-seq, a targeted bisulfite-free method for profiling up to 650 CpGs in up to 10,000 cells per experiment, with a dropout rate as low as 7%. We demonstrate that scTAM-seq can resolve DNA methylation dynamics across B-cell differentiation in blood and bone marrow, identifying intermediate differentiation states that were previously masked. scTAM-seq additionally queries surface-protein expression, thus enabling integration of single-cell DNA methylation information with cell atlas data. In summary, scTAM-seq is a high-throughput, high-confidence method for analyzing DNA methylation at single-CpG resolution across thousands of single cells. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02796-7.
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spelling pubmed-96151632022-10-29 scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells Bianchi, Agostina Scherer, Michael Zaurin, Roser Quililan, Kimberly Velten, Lars Beekman, Renée Genome Biol Method Single-cell DNA methylation profiling currently suffers from excessive noise and/or limited cellular throughput. We developed scTAM-seq, a targeted bisulfite-free method for profiling up to 650 CpGs in up to 10,000 cells per experiment, with a dropout rate as low as 7%. We demonstrate that scTAM-seq can resolve DNA methylation dynamics across B-cell differentiation in blood and bone marrow, identifying intermediate differentiation states that were previously masked. scTAM-seq additionally queries surface-protein expression, thus enabling integration of single-cell DNA methylation information with cell atlas data. In summary, scTAM-seq is a high-throughput, high-confidence method for analyzing DNA methylation at single-CpG resolution across thousands of single cells. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02796-7. BioMed Central 2022-10-28 /pmc/articles/PMC9615163/ /pubmed/36307828 http://dx.doi.org/10.1186/s13059-022-02796-7 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Bianchi, Agostina
Scherer, Michael
Zaurin, Roser
Quililan, Kimberly
Velten, Lars
Beekman, Renée
scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells
title scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells
title_full scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells
title_fullStr scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells
title_full_unstemmed scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells
title_short scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells
title_sort sctam-seq enables targeted high-confidence analysis of dna methylation in single cells
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9615163/
https://www.ncbi.nlm.nih.gov/pubmed/36307828
http://dx.doi.org/10.1186/s13059-022-02796-7
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