scDOT：空间转录组学中绘制衰老细胞图谱的最佳传输方式

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-11-08 DOI:10.1186/s13059-024-03426-0

Nam D. Nguyen, Lorena Rosas, Timur Khaliullin, Peiran Jiang, Euxhen Hasanaj, Jose A. Ovando-Ricardez, Marta Bueno, Irfan Rahman, Gloria S. Pryhuber, Dongmei Li, Qin Ma, Toren Finkel, Melanie Königshoff, Oliver Eickelberg, Mauricio Rojas, Ana L. Mora, Jose Lugo-Martinez, Ziv Bar-Joseph

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引用次数: 0

摘要

空间转录组学数据的分辨率较低，需要额外的信息才能得到最佳利用。我们开发的 scDOT 结合了空间转录组学和单细胞 RNA 测序，提高了重建单细胞解析空间图和识别衰老细胞的能力。scDOT 在肺部空间转录组学数据中的应用改进了之前的方法，并能识别衰老细胞的空间组织、其邻近细胞以及参与细胞-细胞相互作用的新基因，而细胞-细胞相互作用可能是衰老的驱动因素。

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scDOT: optimal transport for mapping senescent cells in spatial transcriptomics

The low resolution of spatial transcriptomics data necessitates additional information for optimal use. We developed scDOT, which combines spatial transcriptomics and single cell RNA sequencing to improve the ability to reconstruct single cell resolved spatial maps and identify senescent cells. scDOT integrates optimal transport and expression deconvolution to learn non-linear couplings between cells and spots and to infer cell placements. Application of scDOT to lung spatial transcriptomics data improves on prior methods and allows the identification of the spatial organization of senescent cells, their neighboring cells and novel genes involved in cell-cell interactions that may be driving senescence.

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.