Dataset for transcriptomic, H3K9ac and H3K9me3 profiles during cardiac regeneration

Xuelong Wang; Huiping Guo; Feifei Yu; Hui Zhang; Ying Peng; Chenghui Wang; Gang Wei; Jizhou Yan

doi:10.1016/j.dib.2022.108569

Dataset for transcriptomic, H3K9ac and H3K9me3 profiles during cardiac regeneration

Data Brief. 2022 Sep 2:45:108569. doi: 10.1016/j.dib.2022.108569. eCollection 2022 Dec.

Authors

Xuelong Wang^{1

2

3}, Huiping Guo^{2

4}, Feifei Yu², Hui Zhang², Ying Peng², Chenghui Wang⁵, Gang Wei³, Jizhou Yan²

Affiliations

¹ Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
² Department of Developmental Biology, and Institute for Marine Biosystem and Neurosciences, Shanghai Ocean University, Shanghai, China.
³ CAS Key Laboratory of Computational Biology, Chinese Academy of Sciences, Shanghai, China.
⁴ Present address: School of Life Sciences and Technology, Tongji University, Shanghai, China.
⁵ Department of Aquaculture, Shanghai Ocean University, Shanghai, China.

Abstract

Acetylation and tri-methylation of histone H3 lysine 9 (H3K9ac and H3K9me3) play an interactive regulatory role in the epigenetic regulation of gene expression during heart development and cardiovascular disease, but little is known about their possible role in heart regeneration. 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.

Keywords: Blastema; ChIP-seq; Epigenetics; H3K9ac; H3K9me3; RNA-seq.