Evidence map›Paper›PMID 42351013›Full record

ArticleBMC genomics2026

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

Sofia Rouot, Ireen van Dolderen, Patrick Rosendahl Andreassen, Solène Frapard, Sybil A Herrera-Foessel, Hailey Sounart, Sami Saarenpää, Julia A Vorholt, Stefania Giacomello

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In one paragraph

Article in BMC genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Sofia Rouot *SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
Ireen van Dolderen *SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
Patrick Rosendahl Andreassen *Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.
Solène FrapardSciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
Sybil A Herrera-FoesselSciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
Hailey SounartSciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
Sami SaarenpääSciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
Julia A VorholtInstitute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.
Stefania GiacomelloSciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden. stefania.giacomello@scilifelab.se.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Probe-based Spatial Transcriptomics profiles spatially-resolved transcriptomes using gene-specific probe pairs for both Formalin-fixed paraffin-embedded (FFPE) and Fresh Frozen samples. However, its applicability is restricted to human and mouse studies, due to commercial probe set availability. Here, we present ProbeST, an open-source computational pipeline for designing custom probe sets for genes of interest of a given organism. We validated ProbeST on FFPE mouse enteroid-derived monolayers infected with Salmonella enterica serovar Typhimurium, using custom pathogen probes with the available mouse probe panel. We simultaneously detected host and pathogen transcripts, with high probe specificity and low sensitivity against mCherry imaging, enabling identification of inflammatory response host genes Mefv, Tnf, and Anxa1 colocalizing to pathogen genes. The reproducible ProbeST workflow expands probe-based Spatial Transcriptomics to studies of non-model organisms and host-pathogen interactions.

Indexed as

Gene Expression ProfilingHost-Pathogen InteractionsTranscriptomeAnimalsMiceSalmonella typhimuriumSpatial TranscriptomicsColocalization analysisDualSTFormalin-fixed paraffin-embedded (FFPE) tissuesHost–pathogen interactionsMouse EnteroidsPipelineProbe DesignSalmonella TyphimuriumSpatial Transcriptomics

Identifiers

PMID42351013
PMCPMC13295851

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.