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[期刊论文]

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

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author:

Wang, G. (Wang, G..) [1] | Wu, S. (Wu, S..) [2] | Xiong, Z. (Xiong, Z..) [3] | Unfold

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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. © The Author(s) 2023.

Community:

  • [ 1 ] [Wang G.]CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
  • [ 2 ] [Wang G.]University of Chinese Academy of Sciences, Beijing, 100049, China
  • [ 3 ] [Wu S.]CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
  • [ 4 ] [Wu S.]University of Chinese Academy of Sciences, Beijing, 100049, China
  • [ 5 ] [Wu S.]National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
  • [ 6 ] [Xiong Z.]Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou, 350002, China
  • [ 7 ] [Qu H.]CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
  • [ 8 ] [Qu H.]University of Chinese Academy of Sciences, Beijing, 100049, China
  • [ 9 ] [Fang X.]CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
  • [ 10 ] [Fang X.]University of Chinese Academy of Sciences, Beijing, 100049, China
  • [ 11 ] [Bao Y.]CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
  • [ 12 ] [Bao Y.]University of Chinese Academy of Sciences, Beijing, 100049, China
  • [ 13 ] [Bao Y.]National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China

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Source :

Nucleic Acids Research

ISSN: 0305-1048

Year: 2024

Issue: D1

Volume: 52

Page: D882-D890

1 6 . 7 0 0

JCR@2023

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SCOPUS Cited Count: 5

30 Days PV: 0

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