STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization

• Published in: Nucleic acids research Vol. 52; no. D1; pp. D1053 - D1061
• Main Authors: Xu, Zhicheng, Wang, Weiwen, Yang, Tao, Li, Ling, Ma, Xizheng, Chen, Jing, Wang, Jieyu, Huang, Yan, Gould, Joshua, Lu, Huifang, Du, Wensi, Sahu, Sunil Kumar, Yang, Fan, Li, Zhiyong, Hu, Qingjiang, Hua, Cong, Hu, Shoujie, Liu, Yiqun, Cai, Jia, You, Lijin, Zhang, Yong, Li, YuXiang, Zeng, Wenjun, Chen, Ao, Wang, Bo, Liu, Longqi, Chen, Fengzhen, Ma, Kailong, Xu, Xun, Wei, Xiaofeng
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 05.01.2024
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkad933

Abstract Recent technological developments in spatial transcriptomics allow researchers to measure gene expression of cells and their spatial locations at the single-cell level, generating detailed biological insight into biological processes. A comprehensive database could facilitate the sharing of spatial transcriptomic data and streamline the data acquisition process for researchers. Here, we present the Spatial TranscriptOmics DataBase (STOmicsDB), a database that serves as a one-stop hub for spatial transcriptomics. STOmicsDB integrates 218 manually curated datasets representing 17 species. We annotated cell types, identified spatial regions and genes, and performed cell-cell interaction analysis for these datasets. STOmicsDB features a user-friendly interface for the rapid visualization of millions of cells. To further facilitate the reusability and interoperability of spatial transcriptomic data, we developed standards for spatial transcriptomic data archiving and constructed a spatial transcriptomic data archiving system. Additionally, we offer a distinctive capability of customizing dedicated sub-databases in STOmicsDB for researchers, assisting them in visualizing their spatial transcriptomic analyses. We believe that STOmicsDB could contribute to research insights in the spatial transcriptomics field, including data archiving, sharing, visualization and analysis. STOmicsDB is freely accessible at https://db.cngb.org/stomics/. Graphical Abstract Graphical Abstract