Loading…
CROST: a comprehensive repository of spatial transcriptomics
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...
Saved in:
| Published in: | Nucleic acids research 2024-01, Vol.52 (D1), p.D882-D890 |
|---|---|
| Main Authors: | , , , , , |
| Format: | Article |
| Language: | English |
| Subjects: | |
| Citations: | Items that this one cites Items that cite this one |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| cited_by | cdi_FETCH-LOGICAL-c343t-d5f3129023b8f5c0c791a9bdbacd947e966c3f7b1dfcce5196e9cf689c4123e03 |
|---|---|
| cites | cdi_FETCH-LOGICAL-c343t-d5f3129023b8f5c0c791a9bdbacd947e966c3f7b1dfcce5196e9cf689c4123e03 |
| container_end_page | D890 |
| container_issue | D1 |
| container_start_page | D882 |
| container_title | Nucleic acids research |
| container_volume | 52 |
| creator | Wang, Guoliang Wu, Song Xiong, Zhuang Qu, Hongzhu Fang, Xiangdong Bao, Yiming |
| description | 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.
Graphical Abstract
Graphical Abstract |
| doi_str_mv | 10.1093/nar/gkad782 |
| format | article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10773281</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/nar/gkad782</oup_id><sourcerecordid>2872804606</sourcerecordid><originalsourceid>FETCH-LOGICAL-c343t-d5f3129023b8f5c0c791a9bdbacd947e966c3f7b1dfcce5196e9cf689c4123e03</originalsourceid><addsrcrecordid>eNp9kEtLw0AUhQdRbK2u3EtWIkjsPJJ5iCBSfEGhoHU9TCaTdjTJxJmk0H9vpLXoxtVd3I_vHA4ApwheISjIuFZ-vPhQOeN4DwwRoThOBMX7YAgJTGMEEz4ARyG8Q4gSlCaHYEAYE4hzMgQ3k5fZ6_w6UpF2VePN0tTBrkzkTeOCbZ1fR66IQqNaq8qo9aoO2tumdZXV4RgcFKoM5mR7R-Dt4X4-eYqns8fnyd001iQhbZynBUFYQEwyXqQa6j5ciSzPlM5FwoygVJOCZSgvtDYpEtQIXVAudIIwMZCMwO3G23RZZXJt6r5IKRtvK-XX0ikr_35qu5QLt5IIMkYwR73hYmvw7rMzoZWVDdqUpaqN64LEnGEOEwppj15uUO1dCN4UuxwE5ffgsh9cbgfv6bPf1Xbsz8I9cL4BXNf8a_oCD22Lxg</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2872804606</pqid></control><display><type>article</type><title>CROST: a comprehensive repository of spatial transcriptomics</title><source>Open Access: Oxford University Press Open Journals</source><source>PubMed Central</source><creator>Wang, Guoliang ; Wu, Song ; Xiong, Zhuang ; Qu, Hongzhu ; Fang, Xiangdong ; Bao, Yiming</creator><creatorcontrib>Wang, Guoliang ; Wu, Song ; Xiong, Zhuang ; Qu, Hongzhu ; Fang, Xiangdong ; Bao, Yiming</creatorcontrib><description>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.
Graphical Abstract
Graphical Abstract</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkad782</identifier><identifier>PMID: 37791883</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Database Issue ; Databases, Factual ; Gene Expression Profiling ; Genome ; Humans ; Neoplasms - genetics ; Transcriptome</subject><ispartof>Nucleic acids research, 2024-01, Vol.52 (D1), p.D882-D890</ispartof><rights>The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. 2024</rights><rights>The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c343t-d5f3129023b8f5c0c791a9bdbacd947e966c3f7b1dfcce5196e9cf689c4123e03</citedby><cites>FETCH-LOGICAL-c343t-d5f3129023b8f5c0c791a9bdbacd947e966c3f7b1dfcce5196e9cf689c4123e03</cites><orcidid>0000-0003-4941-8283 ; 0000-0001-8360-9417 ; 0000-0002-0923-639X ; 0000-0002-1335-3708</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10773281/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10773281/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,1603,27923,27924,53790,53792</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37791883$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Guoliang</creatorcontrib><creatorcontrib>Wu, Song</creatorcontrib><creatorcontrib>Xiong, Zhuang</creatorcontrib><creatorcontrib>Qu, Hongzhu</creatorcontrib><creatorcontrib>Fang, Xiangdong</creatorcontrib><creatorcontrib>Bao, Yiming</creatorcontrib><title>CROST: a comprehensive repository of spatial transcriptomics</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>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.
Graphical Abstract
Graphical Abstract</description><subject>Database Issue</subject><subject>Databases, Factual</subject><subject>Gene Expression Profiling</subject><subject>Genome</subject><subject>Humans</subject><subject>Neoplasms - genetics</subject><subject>Transcriptome</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><recordid>eNp9kEtLw0AUhQdRbK2u3EtWIkjsPJJ5iCBSfEGhoHU9TCaTdjTJxJmk0H9vpLXoxtVd3I_vHA4ApwheISjIuFZ-vPhQOeN4DwwRoThOBMX7YAgJTGMEEz4ARyG8Q4gSlCaHYEAYE4hzMgQ3k5fZ6_w6UpF2VePN0tTBrkzkTeOCbZ1fR66IQqNaq8qo9aoO2tumdZXV4RgcFKoM5mR7R-Dt4X4-eYqns8fnyd001iQhbZynBUFYQEwyXqQa6j5ciSzPlM5FwoygVJOCZSgvtDYpEtQIXVAudIIwMZCMwO3G23RZZXJt6r5IKRtvK-XX0ikr_35qu5QLt5IIMkYwR73hYmvw7rMzoZWVDdqUpaqN64LEnGEOEwppj15uUO1dCN4UuxwE5ffgsh9cbgfv6bPf1Xbsz8I9cL4BXNf8a_oCD22Lxg</recordid><startdate>20240105</startdate><enddate>20240105</enddate><creator>Wang, Guoliang</creator><creator>Wu, Song</creator><creator>Xiong, Zhuang</creator><creator>Qu, Hongzhu</creator><creator>Fang, Xiangdong</creator><creator>Bao, Yiming</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-4941-8283</orcidid><orcidid>https://orcid.org/0000-0001-8360-9417</orcidid><orcidid>https://orcid.org/0000-0002-0923-639X</orcidid><orcidid>https://orcid.org/0000-0002-1335-3708</orcidid></search><sort><creationdate>20240105</creationdate><title>CROST: a comprehensive repository of spatial transcriptomics</title><author>Wang, Guoliang ; Wu, Song ; Xiong, Zhuang ; Qu, Hongzhu ; Fang, Xiangdong ; Bao, Yiming</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c343t-d5f3129023b8f5c0c791a9bdbacd947e966c3f7b1dfcce5196e9cf689c4123e03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Database Issue</topic><topic>Databases, Factual</topic><topic>Gene Expression Profiling</topic><topic>Genome</topic><topic>Humans</topic><topic>Neoplasms - genetics</topic><topic>Transcriptome</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Guoliang</creatorcontrib><creatorcontrib>Wu, Song</creatorcontrib><creatorcontrib>Xiong, Zhuang</creatorcontrib><creatorcontrib>Qu, Hongzhu</creatorcontrib><creatorcontrib>Fang, Xiangdong</creatorcontrib><creatorcontrib>Bao, Yiming</creatorcontrib><collection>Open Access: Oxford University Press Open Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Guoliang</au><au>Wu, Song</au><au>Xiong, Zhuang</au><au>Qu, Hongzhu</au><au>Fang, Xiangdong</au><au>Bao, Yiming</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>CROST: a comprehensive repository of spatial transcriptomics</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2024-01-05</date><risdate>2024</risdate><volume>52</volume><issue>D1</issue><spage>D882</spage><epage>D890</epage><pages>D882-D890</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>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.
Graphical Abstract
Graphical Abstract</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>37791883</pmid><doi>10.1093/nar/gkad782</doi><orcidid>https://orcid.org/0000-0003-4941-8283</orcidid><orcidid>https://orcid.org/0000-0001-8360-9417</orcidid><orcidid>https://orcid.org/0000-0002-0923-639X</orcidid><orcidid>https://orcid.org/0000-0002-1335-3708</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0305-1048 |
| ispartof | Nucleic acids research, 2024-01, Vol.52 (D1), p.D882-D890 |
| issn | 0305-1048 1362-4962 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10773281 |
| source | Open Access: Oxford University Press Open Journals; PubMed Central |
| subjects | Database Issue Databases, Factual Gene Expression Profiling Genome Humans Neoplasms - genetics Transcriptome |
| title | CROST: a comprehensive repository of spatial transcriptomics |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-10T21%3A41%3A44IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=CROST:%20a%20comprehensive%20repository%20of%20spatial%20transcriptomics&rft.jtitle=Nucleic%20acids%20research&rft.au=Wang,%20Guoliang&rft.date=2024-01-05&rft.volume=52&rft.issue=D1&rft.spage=D882&rft.epage=D890&rft.pages=D882-D890&rft.issn=0305-1048&rft.eissn=1362-4962&rft_id=info:doi/10.1093/nar/gkad782&rft_dat=%3Cproquest_pubme%3E2872804606%3C/proquest_pubme%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c343t-d5f3129023b8f5c0c791a9bdbacd947e966c3f7b1dfcce5196e9cf689c4123e03%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2872804606&rft_id=info:pmid/37791883&rft_oup_id=10.1093/nar/gkad782&rfr_iscdi=true |