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SMTdb: A comprehensive spatial meta-transcriptome resource in cancer

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Vydáno v:bioRxiv (Jan 25, 2025)
Hlavní autor: Li, Yongsheng
Další autoři: Xu, Juan, Zhou, Weiwei, Yang, Qingyi, Guo, Jiyu
Vydáno:
Cold Spring Harbor Laboratory Press
Témata:
Cancer
Transcriptomes
Tumor microenvironment
Tumors
Spatial distribution
Spatial discrimination
Transcriptomics
Microbiota
Microbiomes
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Abstrakt:Microbes have been found in various tumors and the research of tumor microbiome has been garnering increased attention. However, it remains challenge to investigate the microbiome in cancer at spatial resolution. The rapid advent of spatially resolved transcriptomics techniques has given rise to map transcripts at single-cell resolution in various types of cancer. Here, we constructed a comprehensive spatial meta-transcriptome resource by manually curating 203 fresh frozen (FF) slices from 20 cancers encompassing 334,253 spots and 1,908,646 cells. SMTdb (http://bio-bigdata.hrbmu.edu.cn/SMTdb/) was constructed to provide comprehensive insights into the abundance, distribution and enriched TME regions of 1218 microbiota in spatial tissue slices. SMTdb enables vast interactive data exploration of spatial distribution and expression of microbiota, host gene modules associated with certain microbiota and co-occurrence between microbiota and immune cells within tumor microenvironment. The atlas resource serves as a one-stop and time-effective platform to investigate the interactions among microbial ecosystems and hosts in cancer.Competing Interest StatementThe authors have declared no competing interest.
ISSN:2692-8205
DOI:10.1101/2025.01.22.634407
Zdroj:Biological Science Database