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Related Experiment Video

Updated: Mar 25, 2026

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Published on: October 31, 2025

SMIntegration: A web tool for comprehensive spatial metabolomics and transcriptomics integrated analysis and

Haoke Deng¹, Xiaolian Ning², Xun Lin¹

¹Department of Mass Spectrometry, BGI, No. 146, Beishan Road, Yantian District, Shenzhen 518083, Guangdong Province, China.

|March 24, 2026

Summary

This summary is machine-generated.

SMIntegration is a new web platform for integrated spatial transcriptomics and metabolomics analysis. It enables researchers to explore gene-metabolite interactions in tissues, aiding biological discovery.

Keywords:

differential expression network gene–metabolite co-localization spatial differential analysis spatial multi-omics spatial pattern analysis

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Last Updated: Mar 25, 2026

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

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Published on: May 27, 2014

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Area of Science:

Spatial omics
Multi-omics integration
Bioinformatics

Background:

Existing spatial omics tools struggle with integrated transcriptomics and metabolomics analysis.
In-depth biological interpretation and user-friendly operation are often lacking.

Purpose of the Study:

To introduce SMIntegration, a novel web-based graphical platform for integrated spatial metabolomics and transcriptomics analysis.
To provide a user-friendly, zero-code solution for exploring gene-metabolite interactions in microenvironments.

Main Methods:

Developed SMIntegration using R/Shiny and Docker containerization.
Implemented automated spatial registration, cross-modal pattern recognition, flexible differential analysis, and network construction.
Utilized adjacent mouse brain sections with Stereo-seq transcriptomics and AFADESI-MS metabolomics data.

Main Results:

SMIntegration successfully identified specific brain regions missed by single-modality clustering.
Revealed associations between astrocyte GABA metabolism and Slc6a11.
Dissected glutamatergic and cannabinoid signaling pathways by comparing distinct brain regions.

Conclusions:

SMIntegration offers a comprehensive workflow for integrated spatial omics analysis.
The platform empowers researchers to investigate complex gene-metabolite interactions in various biological contexts.