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Compared to traditional sequencing, spatial transcriptomics reserves the spatial information of each captured location and provides novel insights into diverse spatially related biological contexts. Even though two spatial transcriptomics databases exist, they provide limited analytical information. Information such as spatial heterogeneity of genes and cells, cell-cell communication activities in space, and the cell type compositions in the microenvironment are critical clues to unveil the mechanism of tumorigenesis and embryo differentiation. Therefore, we constructed a new spatial transcriptomics database, named SPASCER (https:\/\/ccsm.uth.edu\/SPASCER), designed to help understand the heterogeneity of tissue organizations, region-specific microenvironment, and intercellular interactions across tissue architectures at multiple levels. SPASCER contains datasets from 43 studies, including 1082 sub-datasets from 16 organ types across four species. scRNA-seq was integrated to deconvolve\/map spatial transcriptomics, and processed with spatial cell-cell interaction, gene pattern and pathway enrichment analysis. Cell\u2013cell interactions and gene regulation network of scRNA-seq from matched spatial transcriptomics were performed as well. The application of SPASCER will provide new insights into tissue architecture and a solid foundation for the mechanistic understanding of many biological processes in healthy and diseased tissues.<\/jats:p>","DOI":"10.1093\/nar\/gkac889","type":"journal-article","created":{"date-parts":[[2022,10,16]],"date-time":"2022-10-16T09:59:29Z","timestamp":1665914369000},"page":"D1138-D1149","source":"Crossref","is-referenced-by-count":49,"title":["SPASCER: spatial transcriptomics annotation at single-cell resolution"],"prefix":"10.1093","volume":"51","author":[{"given":"Zhiwei","family":"Fan","sequence":"first","affiliation":[{"name":"West China School of Public Health and West China Fourth Hospital, Sichuan University , Chengdu \u00a0610041, China"},{"name":"Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston , TX \u00a077030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yangyang","family":"Luo","sequence":"additional","affiliation":[{"name":"West China Hospital, Sichuan University , Chengdu \u00a0610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huifen","family":"Lu","sequence":"additional","affiliation":[{"name":"West China Hospital, Sichuan University , Chengdu \u00a0610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiangang","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, Xidian University , Xi\u2019an \u00a0710126,\u00a0 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"YuZhou","family":"Feng","sequence":"additional","affiliation":[{"name":"West China Hospital, Sichuan University , Chengdu \u00a0610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiling","family":"Zhao","sequence":"additional","affiliation":[{"name":"Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston , TX \u00a077030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8321-6864","authenticated-orcid":false,"given":"Pora","family":"Kim","sequence":"additional","affiliation":[{"name":"Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston , TX \u00a077030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7191-6495","authenticated-orcid":false,"given":"Xiaobo","family":"Zhou","sequence":"additional","affiliation":[{"name":"Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston , TX \u00a077030, USA"},{"name":"McGovern Medical School, The University of Texas Health Science Center at Houston , Houston ,\u00a0 TX \u00a077030, USA"},{"name":"School of Dentistry, The University of Texas Health Science Center at Houston , Houston ,\u00a0 TX \u00a077030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,10,16]]},"reference":[{"key":"2023010804312902800_B1","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1126\/science.aaf2403","article-title":"Visualization and analysis of gene expression in tissue sections by spatial transcriptomics","volume":"353","author":"St\u00e5hl","year":"2016","journal-title":"Science"},{"key":"2023010804312902800_B2","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1016\/j.cell.2020.06.038","article-title":"Spatial transcriptomics and in situ sequencing to study alzheimer's disease","volume":"182","author":"Chen","year":"2020","journal-title":"Cell"},{"key":"2023010804312902800_B3","doi-asserted-by":"crossref","first-page":"19490","DOI":"10.1073\/pnas.1912459116","article-title":"Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression","volume":"116","author":"Xia","year":"2019","journal-title":"Proc. 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