College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
BGI Research, Shenzhen, 518083, China.
Sci Data. 2023 Jul 19;10(1):464. doi: 10.1038/s41597-023-02373-y.
Vertebrate embryogenesis is a remarkable process, during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis-regulatory elements (CREs) and gene expression within the hierarchy of cell fate decisions. Here, we employed single-nucleus ATAC-seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis, including 3.3 hpf, 5.25 hpf, 6 hpf, 10 hpf, 12 hpf, 18 hpf and 24 hpf, obtained 51,620 high-quality nuclei and 23 clusters. Furthermore, by integrating snATAC-seq data with single-cell RNA-seq data, we described the dynamics of chromatin accessibility and gene expression across developmental time points, which validates the accuracy of the chromatin landscape data. Together, our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.
脊椎动物胚胎发生是一个显著的过程，在此过程中，大量不同谱系的细胞类型在很短的时间内出现。理解这一过程的一个巨大挑战是缺乏动态染色质可及性信息，无法在细胞命运决定的层次结构内将顺式调控元件 (CRE) 和基因表达联系起来。在这里，我们利用单核 ATAC-seq 在斑马鱼胚胎发生的第一天生成染色质可及性数据集，包括 3.3 hpf、5.25 hpf、6 hpf、10 hpf、12 hpf、18 hpf 和 24 hpf，获得了 51,620 个高质量的细胞核和 23 个簇。此外，通过将 snATAC-seq 数据与单细胞 RNA-seq 数据整合，我们描述了发育时间点的染色质可及性和基因表达的动态变化，这验证了染色质景观数据的准确性。总之，我们的数据可以作为揭示斑马鱼胚胎发生的表观遗传调控机制的基础资源。
