RT Journal
A1 Huang, Xin
A1 Tang, Xiaohan
A1 Bai, Xuemei
A1 Li, Honglei
A1 Tao, Huan
A1 Wang, Junting
A1 Li, Yaru
A1 Sun, Yu
A1 Zheng, Yang
A1 Xu, Xiang
A1 Wang, Longteng
A1 Ding, Yang
A1 Lu, Meisong
A1 Zhou, Pingkun
A1 Bo, Xiaochen
A1 Li, Hao
A1 Chen, Hebing
T1 dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development
JF Genome Research 
JO Genome Research 
YR 2022 
FD August 01 
VO 32 
IS 8 
SP 1612 
OP 1625 
DO 10.1101/gr.276744.122 
UL http://genome.cshlp.org/content/32/8/1612.abstract 
AB During early mammalian embryo development, different epigenetic marks undergo reprogramming and play crucial roles in the mediation of gene expression. Currently, several databases provide multi-omics information on early embryos. However, how interconnected epigenetic markers function together to coordinate the expression of the genetic code in a spatiotemporal manner remains difficult to analyze, markedly limiting scientific and clinical research. Here, we present dbEmbryo, an integrated and interactive multi-omics database for human and mouse early embryos. dbEmbryo integrates data on gene expression, DNA methylation, histone modifications, chromatin accessibility, and higher-order chromatin structure profiles for human and mouse early embryos. It incorporates customized analysis tools, such as “multi-omics visualization,” “Gene&Peak annotation,” “ZGA gene cluster,” “cis-regulation,” “synergistic regulation,” “promoter signal enrichment,” and “3D genome.” Users can retrieve gene expression and epigenetic profile patterns to analyze synergistic changes across different early embryo developmental stages. We showed the uniqueness of dbEmbryo among extant databases containing data on early embryo development and provided an overview. Using dbEmbryo, we obtained a phase-separated model of transcriptional control during early embryo development. dbEmbryo offers web-based analytical tools and a comprehensive resource for biologists and clinicians to decipher molecular regulatory mechanisms of human and mouse early embryo development.