Methylome data derived from maternal-zygotic DNA methyltransferase 3aa-/- zebrafish.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36034642", "kind": "science-record", "revision": 4, "content_hash": "sha256:d9850836b64e8c5e3db0def8c9964bab4b27bcd0ee7e55c288458941cd7b95b8", "created_at": "2026-11-01T18:15:12Z", "updated_at": "2026-11-01T22:07:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Methylome data derived from maternal-zygotic DNA methyltransferase 3aa-/- zebrafish.", "doi": "10.1016/j.dib.2022.108514", "pmid": "36034642", "authors": ["Masaki Shirai", "Kazuya Takayama", "Haruko Takahashi", "Yudai Hirose", "Masashi Fujii", "Akinori Awazu", "Nobuyoshi Shimoda", "Yutaka Kikuchi"], "journal": "Data in brief", "year": 2022, "abstract": "Genomic DNA methylation is an epigenetic marker mediated by DNA methyltransferases (Dnmts); in vertebrates, it comprises of a maintenance DNA methyltransferase, Dnmt1, and two de novo DNA methyltransferases (Dnmt3a and Dnmt3b). In zebrafish, there are two homologs of the mammalian Dnmt3a: Dnmt3aa and Dnmt3ab. A knockout (KO) mutant of zebrafish dnmt3aa was generated using the CRISPR/Cas9 genome-editing system as a new model for DNA methylation research. Since zebrafish dnmt3aa KO mutants were viable and fertile, a maternal-zygotic dnmt3aa deficient mutant (MZdnmt3aa) was generated. We performed whole-genome bisulfite sequencing (WGBS) to reveal the DNA methylation profile using this mutant and identified genomic regions with altered CpG methylation as differentially methylated regions (DMRs) in this mutant compared to those in the wild-type fish. We provided novel raw and processed datasets using the MZdnmt3aa KO mutant, and the raw data of WGBS are available through the Gene Expression Omnibus (GEO), accession number GSE178690.", "claims": [{"id": "claim-method", "statement": "The samples were compared using Fisher's test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36034642", "locator": "sections[9] \"Identification of differentially methylated regions (DMRs)\" paragraph 2", "quote": "The samples were compared using Fisher's test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates [WGBS] (Original data) (NCBI Gene Expression Omnibus (GEO) repository under GEO accession GSE178690)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36034642", "locator": "sections[17] \"Data Availability\" paragraph 2", "quote": "Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates [WGBS] (Original data) (NCBI Gene Expression Omnibus (GEO) repository under GEO accession GSE178690)"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:36034642"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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We performed whole-genome bisulfite sequencing (WGBS) to reveal the DNA methylat", "l Design, Materials and Methods Whole-genome bisulfite library preparation and sequencing of zebraf", "00:1. DNA samples (100 ng) were subjected to bisulfite treatment using an EZ DNA Methylation-Gold K", "EZ DNA Methylation-Gold Kit (Zymo Research). Bisulfite-treated DNA samples (50 ng) were subjected t"], "order_basis": "paper_text_order:655", "id": "assay:2"}, {"role": "analysis", "definition_id": "sequence_alignment", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["sequence_align", "alignment_identity"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Bowtie"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}