Dataset for transcriptomic, H3K9ac and H3K9me3 profiles during cardiac regeneration.

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Here we utilized genome-wide high-throughput RNA sequencing (RNA-seq) and chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) for H3K9ac and H3K9me3, carried out on regenerative cardiac tissues at different days post amputation in zebrafish (Danio rerio) to investigate dynamic changes in gene expression and the epigenetic landscape of H3K9ac and H3K9me3. The STAR, Bowtie2, MACS2, and deepTools2 were mainly used for RNA-Seq or ChIP-seq data analysis. In this article, we present detailed information on experiment design, data generation, quality assessment and processing pipeline. Raw reads of the RNA-seq and ChIP-seq data have been deposited at the NCBI GEO repository with the accession number GSE158104. Our data will be a valuable resource for the elucidation of H3K9ac and H3K9me3 involvement in the regulation of gene transcription during cardiac regeneration.", "claims": [{"id": "claim-method", "statement": "Differential expression genes (DEGs) were filtered for a P value < 0.05, the absolute value of fold change (FC) >= 1.5 and the average FPKM >= 3 in at least one of the two groups based on R package edgeR.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36131949", "locator": "sections[8] \"RNA-seq data analysis\" paragraph 2", "quote": "Differential expression genes (DEGs) were filtered for a P value < 0.05, the absolute value of fold change (FC) >= 1.5 and the average FPKM >= 3 in at least one of the two groups based on R package edgeR."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Dataset for transcriptomic, H3K9ac and H3K9me3 profiles during cardiac regeneration in zebrafish (Original data) (NCBI GEO repository).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36131949", "locator": "sections[17] \"Data Availability\" paragraph 2", "quote": "Dataset for transcriptomic, H3K9ac and H3K9me3 profiles during cardiac regeneration in zebrafish (Original data) (NCBI GEO repository)."}], "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:36131949"], "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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