Evidence map›Paper›PMID 40418446›Full record

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

Imaging Nuclear Clusters in Live Zebrafish Embryos.

Shivali Dongre, Lennart Hilbert, Nadine L Vastenhouw

Abstract read
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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. 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

3 authors.

Shivali DongreCenter for Integrative Genomics, University of Lausanne, Quartier Sorge, Lausanne, Switzerland.
Lennart HilbertDepartment of Systems Biology/Bioinformatics, Zoological Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
Nadine L VastenhouwCenter for Integrative Genomics, University of Lausanne, Quartier Sorge, Lausanne, Switzerland. nadine.vastenhouw@unil.ch.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The transcriptional machinery of a cell is often not homogenously distributed but rather forms clusters in the nucleus. These clusters are important for gene expression, but how they form and function is often not clear. The zebrafish embryo provides an excellent system to study these clusters of transcriptional machinery, because embryos are transparent and develop rapidly, making it easy to track proteins as they cluster and perform their function. Here, we provide a protocol for how to image nuclear clusters in living zebrafish embryos. The protocol includes information on the selection and encoding of proteins and fluorophores, embryo-embedding for live-cell microscopy, the use of a spinning disk microscope, staging of embryos post image acquisition, and image analysis. While the protocol is written in the context of our work with early zebrafish embryos, many of the tools will be useful in other contexts.

Indexed as

Cell NucleusEmbryo, NonmammalianZebrafishAnimalsImage Processing, Computer-AssistedMicroscopy, FluorescenceClustersGene expressionImage analysisImagingTranscription bodiesTranscription factorsZebrafish

Identifiers

PMID40418446

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.