CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, Beijing 100101, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Nucleic Acids Res. 2024 Jan 5;52(D1):D882-D890. doi: 10.1093/nar/gkad782.
The development of spatial transcriptome sequencing technology has revolutionized our comprehension of complex tissues and propelled life and health sciences into an era of spatial omics. However, the current availability of databases for accessing and analyzing spatial transcriptomic data is limited. In response, we have established CROST (https://ngdc.cncb.ac.cn/crost), a comprehensive repository of spatial transcriptomics. CROST encompasses high-quality samples and houses 182 spatial transcriptomic datasets from diverse species, organs, and diseases, comprising 1033 sub-datasets and 48 043 tumor-related spatially variable genes (SVGs). Additionally, it encompasses a standardized spatial transcriptome data processing pipeline, integrates single-cell RNA sequencing deconvolution spatial transcriptomics data, and evaluates correlation, colocalization, intercellular communication, and biological function annotation analyses. Moreover, CROST integrates the transcriptome, epigenome, and genome to explore tumor-associated SVGs and provides a comprehensive understanding of their roles in cancer progression and prognosis. Furthermore, CROST provides two online tools, single-sample gene set enrichment analysis and SpatialAP, for users to annotate and analyze the uploaded spatial transcriptomics data. The user-friendly interface of CROST facilitates browsing, searching, analyzing, visualizing, and downloading desired information. Collectively, CROST offers fresh and comprehensive insights into tissue structure and a foundation for understanding multiple biological mechanisms in diseases, particularly in tumor tissues.
空间转录组测序技术的发展彻底改变了我们对复杂组织的理解，并将生命和健康科学推向了空间组学时代。然而，目前可用于访问和分析空间转录组数据的数据库有限。有鉴于此，我们建立了 CROST（https://ngdc.cncb.ac.cn/crost），这是一个全面的空间转录组学数据库。CROST 包含高质量的样本，收纳了来自不同物种、器官和疾病的 182 个空间转录组数据集，包含 1033 个子数据集和 48043 个与肿瘤相关的空间可变基因（SVGs）。此外，它还包含标准化的空间转录组数据处理流程，集成了单细胞 RNA 测序去卷积空间转录组数据，并评估了相关性、共定位、细胞间通讯和生物学功能注释分析。此外，CROST 整合了转录组、表观基因组和基因组，以探索与肿瘤相关的 SVGs，并全面了解它们在癌症进展和预后中的作用。此外，CROST 提供了两个在线工具，即单样本基因集富集分析和 SpatialAP，供用户对上传的空间转录组数据进行注释和分析。CROST 的用户友好界面方便浏览、搜索、分析、可视化和下载所需信息。总之，CROST 为理解组织结构和多种疾病的生物学机制提供了新的、全面的视角，特别是在肿瘤组织中。
