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

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• dc.contributor.author Bianchi, Agostina
• dc.contributor.author Scherer, Michael
• dc.contributor.author Zaurín Quer, Roser
• dc.contributor.author Quililan, Kimberly
• dc.contributor.author Velten, Lars
• dc.contributor.author Beekman, Renée
• dc.date.accessioned 2023-01-23T07:34:00Z
• dc.date.available 2023-01-23T07:34:00Z
• dc.date.issued 2022
• dc.description.abstract 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.
• dc.description.sponsorship We acknowledge support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the CERCA Programme/Generalitat de Catalunya. We acknowledge support from the CRG/CNAG/UPF core facilities (cytometry and genomics unit). A.B. was supported by an FPI fellowship from the Spanish Ministry of Science and Innovation (PRE2019-087574), R.B. was supported by a Junior Leader Fellowship from the la Caixa foundation. M.S. was supported through the Walter Benjamin Fellowship funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 493935791. This work was supported by grants from the Spanish Ministry of Science and Innovation (RTI2018-096359-A-I00) and the European Hematology Association (EHA, Advanced Research Grants to L.V. and R.B.).
• dc.format.mimetype application/pdf
• dc.identifier.citation Bianchi A, Scherer M, Zaurin R, Quililan K, Velten L, Beekman R. scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells. Genome Biol. 2022 Oct 28;23(1):229. DOI: 10.1186/s13059-022-02796-7
• dc.identifier.doi http://dx.doi.org/10.1186/s13059-022-02796-7
• dc.identifier.issn 1474-7596
• dc.identifier.uri http://hdl.handle.net/10230/55374
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.ispartof Genome Biol. 2022 Oct 28;23(1):229
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PRE2019-087574
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/RTI2018-096359-A-I00
• dc.rights © The Author(s) 2022. 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data ma
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword DNA methylation
• dc.subject.keyword Epigenetics
• dc.subject.keyword Hematopoiesis
• dc.subject.keyword Multi-omic analysis
• dc.subject.keyword Single-cell profiling
• dc.title scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion