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STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data
Xiangshang Li1, Chunfu Xiao1, Juntian Qi1
1Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China.
Nucleic Acids Research
|May 24, 2023
Summary
STellaris assigns spatial information to single-cell RNA sequencing (scRNA-seq) data using public spatial transcriptomics (ST) datasets. This enables the study of cell-cell interactions and spatial features in various biological contexts.
Area of Science:
- Genomics
- Bioinformatics
- Spatial Biology
Background:
- Single-cell RNA sequencing (scRNA-seq) reveals cellular heterogeneity but lacks spatial context.
- Understanding spatially related features like cell-cell interactions is crucial for biological insights.
Purpose of the Study:
- To present STellaris, a web server for assigning spatial information to scRNA-seq data.
- To enable the analysis of spatially resolved intercellular communications and regulatory networks.
Main Methods:
- STellaris utilizes transcriptomic similarity between scRNA-seq data and a curated database of 101 spatial transcriptomics (ST) datasets.
- Input includes raw count matrix and cell type annotation; output maps cells to spatial locations in matched ST sections.
- Analysis of spatial distances and ligand-receptor interactions (LRIs) between annotated cell types is performed.
Main Results:
- STellaris successfully maps scRNA-seq data onto spatial tissue architecture.
- Spatially resolved intercellular communications, including LRIs, are characterized.
- The tool demonstrates utility in spatial annotation of multiomics data and provides insights in case studies.
Conclusions:
- STellaris effectively integrates spatial information into scRNA-seq data, enhancing biological interpretation.
- The platform facilitates the study of spatial biology and cell-cell interactions.
- STellaris adds significant value to scRNA-seq datasets by providing a spatial dimension.
