Evidence map›Paper›PMID 39644494›Full record

ArticleSTAR protocols2024

Protocol for open-source automated universal high-content multiplex fluorescence for RNA in situ analysis.

Jean Descarpentrie, Florian Bernard, Wilfried Souleyreau, Lucie Brisson, Thomas Mathivet, Ioannis S Pateras, Océane C B Martin, Maria Lopez Chiloeches, Teresa Frisan

Abstract read
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In one paragraph

Article in STAR protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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.

Jean DescarpentrieDepartment of Molecular Biology, 90187 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 90187 Umeå, Sweden. Electronic address: jean.descarpentrie@umu.se.
Florian BernardUniversity of Bordeaux, INSERM, U1212, Nucleic Acids: Natural and Artificial Regulations Laboratory, 33000 Bordeaux, France.
Wilfried SouleyreauUniversity of Bordeaux, INSERM, U1312 BRIC, Tumor and Vascular Biology Laboratory, 33000 Bordeaux, France.
Lucie BrissonUniversity of Bordeaux, INSERM, U1312 BRIC, Tumor and Vascular Biology Laboratory, 33000 Bordeaux, France.
Thomas MathivetUniversity of Bordeaux, INSERM, U1312 BRIC, Tumor and Vascular Biology Laboratory, 33000 Bordeaux, France.
Ioannis S Pateras2nd Department of Pathology, "Attikon" University Hospital, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece.
Océane C B MartinUniversity of Bordeaux, CNRS, IBGC, UMR 5095, 33000 Bordeaux, France.
Maria Lopez ChiloechesDepartment of Molecular Biology, 90187 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 90187 Umeå, Sweden.
Teresa FrisanDepartment of Molecular Biology, 90187 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 90187 Umeå, Sweden. Electronic address: teresa.frisan@umu.se.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In situ hybridization visualizes RNA in cells, but image analysis is complex. We present a protocol based on open-source software for automated high-content multiplex fluorescence in situ transcriptomics analysis. Steps include nuclei segmentation with a Fiji macro and quantification of up to 14 mRNA probes per image. We describe procedures for storing raw data, quality control images, and the use of a Python app to summarize all the results in one spreadsheet detailing the number of single or co-positive cells.

Indexed as

In Situ Hybridization, FluorescenceRNASoftwareHumansImage Processing, Computer-AssistedRNAcell biologyhealth sciencesin situ hybridization

Identifiers

PMID39644494
PMCPMC11667704

What OpenQuestion holds

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LicenceCC BY
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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.