CROST: a comprehensiv e reposit ory of spatial tr anscript omics

Abstract

The de v elopment of spatial transcriptome sequencing technology has re v olutioniz ed our comprehension of complex tissues and propelled life and health sciences into an era of spatial omics. Ho w e v er, the current a v ailability of databases for accessing and analyzing spatial transcriptomic data is limited. In response, w e ha v e established CR OS T ( https:// ngdc.cncb.ac.cn/ crost ), a comprehensive repository of spatial transcriptomics. CR OS T encompasses high-quality samples and houses 182 spatial transcriptomic datasets from diverse species, organs, and diseases, compris- ing 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 decon v olution spatial transcriptomics data, and e v aluates correlation, colocal- ization, intercellular communication, and biological function annotation analy ses. Moreo v er, CR OS T 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, CR OS T pro vides tw o online tools, single-sample gene set enrichment analy sis and SpatialAP, f or users to annotate and analyze the uploaded spatial transcriptomics data. The user-friendly interface of CROST facilit ates browsing , searching , analyzing , visualizing , and download- ing desired inf ormation. Collectiv ely, CR OS T offers fresh and comprehensiv e insights into tissue str uct ure and a f oundation f or understanding multiple biological mechanisms in diseases, particularly in tumor tissues.