{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE307nnn/GSE307505/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Methylation profiling"],"species":["Danio rerio"," Homo sapiens"],"gds_type":["Methylation profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE307505"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"FINE-EM-seq: a rapid isothermal amplification method enabling comprehensive methylome profiling of zebrafish early embryos","description":"DNA methylation plays a crucial role in development and disease. Bisulfite-free methods such as enzymatic methyl sequencing (EM-seq) offer gentle approaches for whole-genome analysis, but they typically depend on PCR-based library amplification, which distorts coverage and methylation quantification. Here, we introduce FINE (Fast Isothermal amplification via Nicking Enzyme), a robust isothermal amplification strategy that leverages a nicking enzyme-assisted strand displacement reaction and can amplify methylation libraries from sub-nanogram inputs in 20 minutes. FINE-EM-seq increases library efficiency and coverage uniformity compared to PCR-based approaches, minimizing amplification bias and improving methylation calling accuracy. Applied to zebrafish embryos at four early developmental stages, FINE-EM-seq characterized stage-associated methylation dynamics through blastulation and early gastrulation. Furthermore, our analysis revealed blastulation-associated differentially methylated regions (DMRs) overlapping with AT-rich regions that were previously under-covered. These results illustrate that FINE-EM-seq is a rapid, robust solution for low-input whole-genome methylation sequencing with broad utility in developmental biology and clinical epigenomics.","dates":{"publication":"2026/04/09"},"accession":"GSE307505","cross_references":{"GSM":["GSM9225697","GSM9225696","GSM9225695","GSM9590057","GSM9590058","GSM9590055","GSM9590056","GSM9590053","GSM9225711","GSM9590054","GSM9225710","GSM9225699","GSM9225698","GSM9225709","GSM9225708","GSM9225707","GSM9225706","GSM9590060","GSM9590061","GSM9225705","GSM9225704","GSM9225703","GSM9590066","GSM9225702","GSM9590064","GSM9225701","GSM9225700","GSM9590065","GSM9590062","GSM9590063","GSM9590059"],"GPL":["34693","34281"],"GSE":["307505"],"taxon":["Danio rerio"," Homo sapiens"],"PMID":["[42058509]"]}}