Evidence map›Paper›PMID 39527218›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2025

Homebuilt Imaging-Based Spatial Transcriptomics: Tertiary Lymphoid Structures as a Case Example.

Thomas Defard, Auxence Desrentes, Charles Fouillade, Florian Mueller

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. 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

4 authors.

Thomas DefardInstitut Pasteur, Université Paris Cité, Photonic Bio-Imaging, Centre de Ressources et Recherches Technologiques (UTechS-PBI, C2RT), Paris, France.
Auxence DesrentesUMRS1135 Sorbonne University, Paris, France.
Charles FouilladeInstitut Curie, Inserm U1021-CNRS UMR 3347, University Paris-Saclay, PSL Research University, Centre Universitaire, Orsay, France.
Florian MuellerInstitut Pasteur, Université Paris Cité, Photonic Bio-Imaging, Centre de Ressources et Recherches Technologiques (UTechS-PBI, C2RT), Paris, France. fmueller@pasteur.fr.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Spatial transcriptomics methods provide insight into the cellular heterogeneity and spatial architecture of complex, multicellular systems. Combining molecular and spatial information provides important clues to study tissue architecture in development and disease. Here, we present a comprehensive do-it-yourself (DIY) guide to perform such experiments at reduced costs leveraging open-source approaches. This guide spans the entire life cycle of a project, from its initial definition to experimental choices, wet lab approaches, instrumentation, and analysis. As a concrete example, we focus on tertiary lymphoid structures (TLS), which we use to develop typical questions that can be addressed by these approaches.

Indexed as

Gene Expression ProfilingTertiary Lymphoid StructuresTranscriptomeAnimalsHumansSoftwareHomebuiltOpen-sourceSpatial biologySpatial transcriptomicTertiary lymphoid structure

Identifiers

PMID39527218

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.