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单细胞和空间转录组学能够对细胞类型拓扑进行概率推断。

Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography.

机构信息

Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.

出版信息

Commun Biol. 2020 Oct 9;3(1):565. doi: 10.1038/s42003-020-01247-y.


DOI:10.1038/s42003-020-01247-y
PMID:33037292
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7547664/
Abstract

The field of spatial transcriptomics is rapidly expanding, and with it the repertoire of available technologies. However, several of the transcriptome-wide spatial assays do not operate on a single cell level, but rather produce data comprised of contributions from a - potentially heterogeneous - mixture of cells. Still, these techniques are attractive to use when examining complex tissue specimens with diverse cell populations, where complete expression profiles are required to properly capture their richness. Motivated by an interest to put gene expression into context and delineate the spatial arrangement of cell types within a tissue, we here present a model-based probabilistic method that uses single cell data to deconvolve the cell mixtures in spatial data. To illustrate the capacity of our method, we use data from different experimental platforms and spatially map cell types from the mouse brain and developmental heart, which arrange as expected.

摘要

空间转录组学领域正在迅速发展,可用技术的种类也在不断增加。然而,有几种全转录组空间检测方法并非在单细胞水平上进行,而是产生的数据来自于可能存在异质性的细胞混合物。尽管如此,当研究具有多种细胞群体的复杂组织样本时,这些技术仍然具有吸引力,因为需要完整的表达谱才能正确捕捉它们的丰富度。受将基因表达置于背景中并描绘组织内细胞类型空间排列的兴趣的驱使,我们在此提出了一种基于模型的概率方法,该方法使用单细胞数据来对空间数据中的细胞混合物进行去卷积。为了说明我们方法的能力,我们使用了来自不同实验平台的数据,并对来自小鼠大脑和发育心脏的细胞类型进行了空间映射,结果符合预期。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d35c/7547664/e9e7e47f7e31/42003_2020_1247_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d35c/7547664/753b3b0dd153/42003_2020_1247_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d35c/7547664/c93868a18ee8/42003_2020_1247_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d35c/7547664/e9e7e47f7e31/42003_2020_1247_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d35c/7547664/753b3b0dd153/42003_2020_1247_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d35c/7547664/c93868a18ee8/42003_2020_1247_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d35c/7547664/e9e7e47f7e31/42003_2020_1247_Fig3_HTML.jpg

相似文献

[1]
Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography.

Commun Biol. 2020-10-9

[2]
Single-cell multiomics: technologies and data analysis methods.

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[3]
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Nat Genet. 2023-1

[4]
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Mol Cells. 2020-7-31

[5]
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[6]
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[7]
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Nat Commun. 2022-12-10

[8]
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[9]
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Nat Methods. 2021-1

[10]
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Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data.

NPJ Precis Oncol. 2025-9-9

[2]
Scvi-hub: an actionable repository for model-driven single-cell analysis.

Nat Methods. 2025-9-8

[3]
Accurately Predicting Cell Type Abundance from Spatial Histology Image Through HPCell.

Interdiscip Sci. 2025-9-3

[4]
ST-deconv: an accurate deconvolution approach for spatial transcriptome data utilizing self-encoding and contrastive learning.

NAR Genom Bioinform. 2025-8-27

[5]
Improving cell-type composition inference in spatial transcriptomics with SpaDAMA.

PLoS Comput Biol. 2025-8-21

[6]
A Meta-Review of Spatial Transcriptomics Analysis Software.

Cells. 2025-7-10

[7]
A cluster-based cell-type deconvolution of spatial transcriptomic data.

Nucleic Acids Res. 2025-7-19

[8]
Enhancing and accelerating cell type deconvolution of large-scale spatial transcriptomics slices with dual network model.

Bioinformatics. 2025-8-2

[9]
Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms.

Nucleic Acids Res. 2025-7-19

[10]
GraphCellNet: A deep learning method for integrated single-cell and spatial transcriptomic analysis with applications in development and disease.

J Mol Med (Berl). 2025-7-21

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