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Article: Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow by Oxford Nanopore sequencing

TitleUnraveling the whole genome DNA methylation profile of zebrafish kidney marrow by Oxford Nanopore sequencing
Authors
Issue Date10-Aug-2023
PublisherNature Research
Citation
Scientific Data, 2023, v. 10, n. 1 How to Cite?
Abstract

Zebrafish is a widely used model organism for investigating human diseases, including hematopoietic disorders. However, a comprehensive methylation baseline for zebrafish primary hematopoietic organ, the kidney marrow (KM), is still lacking. We employed Oxford Nanopore Technologies (ONT) sequencing to profile DNA methylation in zebrafish KM by generating four KM datasets, with two groups based on the presence or absence of red blood cells. Our findings revealed that blood contamination in the KM samples reduced read quality and altered methylation patterns. Compared with whole-genome bisulfite sequencing (WGBS), the ONT-based methylation profiling can cover more CpG sites (92.4% vs 70%–80%), and exhibit less GC bias with more even genomic coverage. And the ONT methylation calling results showed a high correlation with WGBS results when using shared sites. This study establishes a comprehensive methylation profile for zebrafish KM, paving the way for further investigations into epigenetic regulation and the development of targeted therapies for hematopoietic disorders.


Persistent Identifierhttp://hdl.handle.net/10722/338932
ISSN
2023 Impact Factor: 5.8
2023 SCImago Journal Rankings: 1.937
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorLiu, XD-
dc.contributor.authorNi, Y-
dc.contributor.authorWang, DD-
dc.contributor.authorYe, SL-
dc.contributor.authorYang, MS-
dc.contributor.authorSun, X-
dc.contributor.authorLeung, AYH-
dc.contributor.authorLi, RS-
dc.date.accessioned2024-03-11T10:32:38Z-
dc.date.available2024-03-11T10:32:38Z-
dc.date.issued2023-08-10-
dc.identifier.citationScientific Data, 2023, v. 10, n. 1-
dc.identifier.issn2052-4463-
dc.identifier.urihttp://hdl.handle.net/10722/338932-
dc.description.abstract<p>Zebrafish is a widely used model organism for investigating human diseases, including hematopoietic disorders. However, a comprehensive methylation baseline for zebrafish primary hematopoietic organ, the kidney marrow (KM), is still lacking. We employed Oxford Nanopore Technologies (ONT) sequencing to profile DNA methylation in zebrafish KM by generating four KM datasets, with two groups based on the presence or absence of red blood cells. Our findings revealed that blood contamination in the KM samples reduced read quality and altered methylation patterns. Compared with whole-genome bisulfite sequencing (WGBS), the ONT-based methylation profiling can cover more CpG sites (92.4% vs 70%–80%), and exhibit less GC bias with more even genomic coverage. And the ONT methylation calling results showed a high correlation with WGBS results when using shared sites. This study establishes a comprehensive methylation profile for zebrafish KM, paving the way for further investigations into epigenetic regulation and the development of targeted therapies for hematopoietic disorders.</p>-
dc.languageeng-
dc.publisherNature Research-
dc.relation.ispartofScientific Data-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.titleUnraveling the whole genome DNA methylation profile of zebrafish kidney marrow by Oxford Nanopore sequencing-
dc.typeArticle-
dc.identifier.doi10.1038/s41597-023-02431-5-
dc.identifier.scopuseid_2-s2.0-85167675683-
dc.identifier.volume10-
dc.identifier.issue1-
dc.identifier.eissn2052-4463-
dc.identifier.isiWOS:001048676300004-
dc.identifier.issnl2052-4463-

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