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利用 CytoSPACE 实现单细胞和空间转录组的高分辨率比对。

High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE.

机构信息

Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.

出版信息

Nat Biotechnol. 2023 Nov;41(11):1543-1548. doi: 10.1038/s41587-023-01697-9. Epub 2023 Mar 6.

DOI:10.1038/s41587-023-01697-9
PMID:36879008
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10635828/
Abstract

Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE, an optimization method for mapping individual cells from a single-cell RNA sequencing atlas to spatial expression profiles. Across diverse platforms and tissue types, we show that CytoSPACE outperforms previous methods with respect to noise tolerance and accuracy, enabling tissue cartography at single-cell resolution.

摘要

最近的研究强调了单细胞空间生物学的重要性，但现有的空间转录组学检测方法存在基因回收率有限或空间分辨率低的问题。在这里，我们介绍了 CytoSPACE，这是一种将单细胞 RNA 测序图谱中的单个细胞映射到空间表达图谱的优化方法。在不同的平台和组织类型中，我们表明 CytoSPACE 在噪声容忍度和准确性方面优于以前的方法，从而能够以单细胞分辨率进行组织绘图。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0dfb/10635828/6cd7de3a32bc/41587_2023_1697_Fig12_ESM.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0dfb/10635828/6cd7de3a32bc/41587_2023_1697_Fig12_ESM.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0dfb/10635828/5b76ec354745/41587_2023_1697_Fig3_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0dfb/10635828/1e75fbc92d6c/41587_2023_1697_Fig4_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0dfb/10635828/5ec56d86302c/41587_2023_1697_Fig5_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0dfb/10635828/8b3f66369941/41587_2023_1697_Fig6_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0dfb/10635828/4ae5cd6a4a76/41587_2023_1697_Fig7_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0dfb/10635828/a7af71e88a10/41587_2023_1697_Fig8_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0dfb/10635828/e6dc644381be/41587_2023_1697_Fig9_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0dfb/10635828/090f9f76f102/41587_2023_1697_Fig10_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0dfb/10635828/0ea790219cfb/41587_2023_1697_Fig11_ESM.jpg
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