State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
Nucleic Acids Res. 2023 Jan 6;51(D1):D924-D932. doi: 10.1093/nar/gkac848.
The emerging importance of embryonic development research rapidly increases the volume for a professional resource related to multi-omics data. However, the lack of global embryogenesis repository and systematic analysis tools limits the preceding in stem cell research, human congenital diseases and assisted reproduction. Here, we developed the EmAtlas, which collects the most comprehensive multi-omics data and provides multi-scale tools to explore spatiotemporal activation during mammalian embryogenesis. EmAtlas contains data on multiple types of gene expression, chromatin accessibility, DNA methylation, nucleosome occupancy, histone modifications, and transcription factors, which displays the complete spatiotemporal landscape in mouse and human across several time points, involving gametogenesis, preimplantation, even fetus and neonate, and each tissue involves various cell types. To characterize signatures involved in the tissue, cell, genome, gene and protein levels during mammalian embryogenesis, analysis tools on these five scales were developed. Additionally, we proposed EmRanger to deliver extensive development-related biological background annotations. Users can utilize these tools to analyze, browse, visualize, and download data owing to the user-friendly interface. EmAtlas is freely accessible at http://bioinfor.imu.edu.cn/ematlas.
胚胎发育研究的重要性日益凸显，相关多组学数据的专业资源需求也迅速增加。然而，缺乏全球性的胚胎发生数据库和系统分析工具，限制了干细胞研究、人类先天性疾病和辅助生殖领域的发展。在这里，我们开发了 EmAtlas，它汇集了最全面的多组学数据，并提供多尺度工具来探索哺乳动物胚胎发生过程中的时空激活。EmAtlas 包含了多种类型的基因表达、染色质可及性、DNA 甲基化、核小体占有率、组蛋白修饰和转录因子的数据，展示了跨越多个时间点的小鼠和人类完整的时空景观，涉及配子发生、着床前，甚至胎儿和新生儿，每个组织都涉及多种细胞类型。为了描述哺乳动物胚胎发生过程中组织、细胞、基因组、基因和蛋白质水平上涉及的特征，我们在这五个尺度上开发了分析工具。此外，我们还提出了 EmRanger 来提供广泛的与发育相关的生物学背景注释。用户可以通过友好的界面利用这些工具进行分析、浏览、可视化和下载数据。EmAtlas 可在 http://bioinfor.imu.edu.cn/ematlas 免费获取。
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