Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Video

Updated: Jul 29, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

5.0K

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
PubMed
Summary

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A Human-specific Protein Regulated by Alternative Polyadenylation Shapes Uniqueness of Human Brain Development.

Genomics, proteomics & bioinformatics·2025
Same author

Tumors with microsatellite instability upregulate TREX1 to escape antitumor immunity.

The Journal of experimental medicine·2025
Same author

Interpretable niche-based cell‒cell communication inference using multi-view graph neural networks.

Nature computational science·2025
Same author

Author Correction: Activation of GPR81 by lactate drives tumour-induced cachexia.

Nature metabolism·2024
Same author

Long-range alternative splicing contributes to neoantigen specificity in glioblastoma.

Briefings in bioinformatics·2024
Same author

A germline-to-soma signal triggers an age-related decline of mitochondrial stress response.

Nature communications·2024
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles
This summary is machine-generated.

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.

More Related Videos

Transcriptome Analysis of Single Cells
07:27

Transcriptome Analysis of Single Cells

Published on: April 25, 2011

30.0K
Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis
07:40

Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis

Published on: May 16, 2025

380

Related Experiment Videos

Last Updated: Jul 29, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

5.0K
Transcriptome Analysis of Single Cells
07:27

Transcriptome Analysis of Single Cells

Published on: April 25, 2011

30.0K
Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis
07:40

Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis

Published on: May 16, 2025

380

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.