ArticleScientific data2023
Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow by Oxford Nanopore sequencing.
Article in Scientific data, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 8 citations in OpenAlex.
- DNA methylation profiles of quail blood cells by whole-genome bisulfite and Oxford Nanopore sequencing.Scientific data · 2026Article
- Environmental DNA Epigenetics Accurately Predicts the Age of Cultured Fish Larvae.Ecology and evolution · 2025Article
- Chromosome-level genome assembly and methylome profile yield insights for the conservation of endangered loggerhead sea turtles.GigaScience · 2025Article
- Giraffe: A tool for comprehensive processing and visualization of multiple long-read sequencing data.Computational and structural biotechnology journal · 2024Article
- Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications.Genome research · 2024Article
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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