STOmicsDB: a database of Spatial Transcriptomic data

Zhicheng Xu; Weiwen Wang; Tao Yang; Ling Li; Xizheng Ma; Jing Chen; Jieyu Wang; Yan Huang; Joshua Gould; Huifang Lü; Wensi Du; Sunil Kumar Sahu; Fan Yang; Zhiyong Li; Qingjiang Hu; Cong Hua; Shoujie Hu; Yiqun Liu; Jia Cai; Lijin You; Yong Zhang; Yuxiang Li; Wenjun Zeng; Ao Chen; Bo Wang; Longqi Liu; Fengzhen Chen; Kailong Ma; Xun Xu; Xiaofeng Wei

doi:10.1093/nar/gkad933

GenomicsNucleic Acids ResearchNov 11, 2023

Peer-reviewed journal article

STOmicsDB: a database of Spatial Transcriptomic data

Zhicheng Xu iD, Weiwen Wang iD, Tao Yang iD, Ling Li iD, Xizheng Ma iD, Jing Chen iD, Jieyu Wang iD, Yan Huang iD, Joshua Gould iD, Huifang Lü, Wensi Du, Sunil Kumar Sahu iD, Fan Yang iD, Zhiyong Li iD, Qingjiang Hu iD, Cong Hua, Shoujie Hu, Yiqun Liu iD, Jia Cai, Lijin You, Yong Zhang iD, Yuxiang Li iD, Wenjun Zeng iD, Ao Chen iD, Bo Wang, , Xiaofeng Wei iD

Abstract

Recent technological development in spatial transcriptomics allows researchers to measure gene expression of cells and their spatial locations at the almost single-cell level, which generates detailed biological insight into biological processes. However, specialized spatial transcriptomics databases are rare. Here, we present the Spatial TranscriptOmics DataBase (STOmicsDB), a user-friendly database with multifunctions including search of relevant publications and tools, public dataset visualization, customized specialized databases, new data archive, and online analysis. The current version of STOmicsDB consists of 141 curated spatial transcript datasets covering 12 species, and includes 5,618 spatial multi-omics publications and 674 tools. STOmicsDB is freely accessible at https://db.cngb.org/stomics/.

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