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Jan 05, 2024;52 (D1): D882-D890.

CROST: a comprehensive repository of spatial transcriptomics.

Guoliang Wang, Song Wu, Zhuang Xiong, Hongzhu Qu, Xiangdong Fang, Yiming Bao
Author Information
  1. Guoliang Wang: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, Beijing 100101, China. ORCID
  2. Song Wu: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, Beijing 100101, China. ORCID
  3. Zhuang Xiong: Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou 350002, China. ORCID
  4. Hongzhu Qu: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, Beijing 100101, China.
  5. Xiangdong Fang: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, Beijing 100101, China. ORCID
  6. Yiming Bao: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, Beijing 100101, China.
PMID: 37791883 DOI: 10.1093/nar/gkad782

Abstract

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.

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Grants

  1. 2021YFF0703701/National Key Research and Development Program of China
  2. 82270126/National Natural Science Foundation of China

MeSH Term

Humans
Gene Expression Profiling
Genome
Neoplasms
Transcriptome
Databases, Genetic
Journal Article

Links to CNCB-NGDC Resources

Database Commons: DBC009040 (CROST)

Word Cloud

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