Evidence map›Paper›PMID 40826097›Full record

ArticleGenome biology2025

Direct and bisulfite-free 5-methylcytosine and 5-hydroxymethylcytosine sequencing at single-cell resolution with scTAPS and scCAPS + .

Xiufei Chen, Jingfei Cheng, Linzhen Kong, Xiao Shu, Haiqi Xu, Masato Inoue, Marion Silvana Fernández-Berrocal, Dagny Sanden Døskeland, Magnar Bjørås, Shivan Sivakumar and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 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

13 authors.

Xiufei Chen *Department of Central Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, China.
Jingfei Cheng *Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7FZ, UK.
Linzhen Kong *Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7FZ, UK.
Xiao ShuNuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7FZ, UK.
Haiqi XuNuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7FZ, UK.
Masato InoueNuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7FZ, UK.
Marion Silvana Fernández-BerrocalDepartment of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.
Dagny Sanden DøskelandDepartment of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.
Magnar BjøråsDepartment of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.
Shivan SivakumarThe Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
Yibin LiuState Key Laboratory of Metabolism and Regulation in Complex Organisms, College of Chemistry and Molecular Sciences, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China. liuyibin@whu.edu.cn.
Jing YeDepartment of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway. jing.ye@ntnu.no.
Chun-Xiao SongNuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7FZ, UK. chunxiao.song@ludwig.ox.ac.uk.ORCID http://orcid.org/0000-0002-7781-6521

Funding

Ludwig Institute for Cancer Research C63763/A26394National science Foundation of China 22307099Research Council of Norway 326101
6 · The paper itself

Abstract

We present direct sequencing methodologies, scTAPS for 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) and scCAPS + specifically for 5hmC, enabling quantitative detection of 5mC and 5hmC at single-base resolution and single-cell level. Achieving approximately 90% mapping efficiency, our plate-based methods accurately recover 5mC and 5hmC profiles in CD8 + T and mouse embryonic stem cells. Notably, scCAPS + reveals a global increase in 5hmC across neuronal and non-neuronal cells in the hippocampus of aging mice. Our methods offer strong potential for seamless integration into high-throughput single-cell multi-omics, facilitating future investigations of epigenomic dynamics in specific biological processes.

Indexed as

5-MethylcytosineCytosineHigh-Throughput Nucleotide SequencingSequence Analysis, DNASingle-Cell AnalysisAnimalsDNA MethylationEpigenomicsHippocampusMiceSulfites5-hydroxymethylcytosine5-MethylcytosineCytosinehydrogen sulfiteSulfites5hmC5mCAgingNeuronscCAPS +scTAPSSingle-cell sequencing

Identifiers

PMID40826097
PMCPMC12359873

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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.