Evidence map›Paper›PMID 38351457›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2024

Mapping Meiotic DNA Breaks: Two Fully-Automated Pipelines to Analyze Single-Strand DNA Sequencing Data, hotSSDS and hotSSDS-extra.

Pauline Auffret, Bernard de Massy, Julie A J Clément

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Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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

3 authors.

Pauline AuffretIfremer, IRSI, SeBiMER Service de Bioinformatique de l'Ifremer, Plouzané, France.
Bernard de MassyInstitut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, UnivMontpellier, Montpellier, France.
Julie A J ClémentInstitut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, UnivMontpellier, Montpellier, France. julie.clement@univ-perp.fr.ORCID 0000-0002-3243-9718

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Molecular approaches are required to detect DNA double-strand break (DSB) events and to map and quantify them at high resolution. One of the most popular molecular methods in the field of meiotic recombination is the ChIP-SSDS (Chromatin immuno-precipitation and single-strand DNA sequencing). Here, we present two fully-automated Nextflow-based pipelines to analyze the sequencing data generated by this method. The first one identifies highly reproducible DSB sites, while the second provides a characterization of recovered DSB sites, including the description of the hotspot distribution and intensity along the genome and the overlap with specific regions such as gene features or known DSB hotspots. Finally, we discuss limitations/advantages and key points to consider when applying this method to specific genotypes or unconventional species.

Indexed as

DNA Breaks, Double-StrandedHomologous RecombinationDNA, Single-StrandedGenomeMeiosisSequence Analysis, DNADNA, Single-StrandedChIP single-strand DNA sequencingComputational pipelinesDouble-strand break mappingMeiotic hotspot

Identifiers

PMID38351457

What OpenQuestion holds

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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.