Protocol for in vivo DNA-RNA hybrid immunoprecipitation, sequencing, and analysis from frozen mouse tissues.

Hassan Massalha, Cameron J Chee, Julia S P Mawer, Francesco Puzzo, Magdalena P Crossley

Abstract read

In one paragraph

Article in STAR protocols, 2026. 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

5 authors.

Hassan MassalhaCancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.

Cameron J CheeCancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.

Julia S P MawerCancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.

Francesco PuzzoTelethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy. Electronic address: f.puzzo@tigem.it.

Magdalena P CrossleyCancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK. Electronic address: mpk33@cam.ac.uk.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

DNA-RNA hybrids (R-loops) form transiently on the genome and regulate cellular homeostasis. They also influence genome-editing outcomes, highlighting their therapeutic potential. Here, we present a protocol for high-resolution mapping of DNA-RNA hybrids from frozen mouse tissues, including genomic DNA extraction and isolation of digested DNA-RNA hybrids using the hybrid-specific S9.6 antibody. We detail procedures for processing hybrids for whole-genome sequencing to generate R-loop profiles. For details on the use of this protocol, please refer to Puzzo et al.

Indexed as

AntibodyCell isolationChIPChIPseqChromatin immunoprecipitationGeneticsGenomicsSequencing

Identifiers

PMID42490222

DOI10.1016/j.xpro.2026.104654

PMCPMC13427435

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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.