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Related Experiment Video

Updated: Jun 27, 2026

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

ProbeST: a custom probe design pipeline for dual host-pathogen Spatial Transcriptomics.

Sofia Rouot1, Ireen van Dolderen1,2, Patrick Rosendahl Andreassen3,4

  • 1SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.

BMC Genomics
|June 25, 2026
PubMed
Summary

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This summary is machine-generated.

ProbeST is an open-source pipeline enabling custom probe design for spatial transcriptomics in any organism. This expands the technique to non-model organisms and host-pathogen interaction studies.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Probe-based Spatial Transcriptomics (ST) offers spatially-resolved transcriptome profiling.
  • Current commercial probe sets limit ST applications primarily to human and mouse studies.
  • A need exists for adaptable methods to apply ST to diverse organisms.

Purpose of the Study:

  • To develop an open-source computational pipeline, ProbeST, for designing custom gene-specific probe sets.
  • To enable the application of probe-based ST to non-model organisms.
  • To facilitate studies of host-pathogen interactions using ST.

Main Methods:

  • ProbeST pipeline development for custom probe set design.
  • Validation using Formalin-fixed paraffin-embedded (FFPE) mouse enteroid models infected with Salmonella Typhimurium.
Keywords:
Salmonella TyphimuriumColocalization analysisDualSTFormalin-fixed paraffin-embedded (FFPE) tissuesHost–pathogen interactionsMouse EnteroidsPipelineProbe DesignSpatial Transcriptomics

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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
14:58

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

Related Experiment Videos

Last Updated: Jun 27, 2026

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

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
14:58

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

  • Simultaneous detection of host and pathogen transcripts using custom and existing probe panels.

    • Main Results:

    • ProbeST successfully designed custom pathogen probes for Salmonella Typhimurium.
    • Simultaneous detection of host (Mefv, Tnf, Anxa1) and pathogen transcripts was achieved.
    • High probe specificity and low sensitivity were observed, with identified host genes colocalizing with pathogen genes.

    Conclusions:

    • The ProbeST workflow is reproducible and expands probe-based ST capabilities.
    • This computational tool democratizes ST for non-model organisms.
    • ProbeST facilitates detailed spatial analysis of host-pathogen interactions.