Evidence map›Paper›PMID 41233368›Full record

ArticleNature communications2025

Ultra-mild bisulfite outperforms existing methods for 5-methylcytosine detection with low input DNA.

Qing Dai, Tanner Baldwin, Ruitu Lyu, Bryan Daniels, Chang Ye, Chen Cao, Chenyou Zhu, Diwen Fan, Liane Lin, Yushuai Liu and 2 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Fluorescent Analysis of KBiomolecules · 2026
    Article
  6. Review
  7. Article
  8. Article
  9. Review
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

12 authors.

Qing Dai *Department of Chemistry, The University of Chicago, Chicago, IL, USA. daiqing@uchicago.edu.ORCID http://orcid.org/0000-0002-8578-1568
Tanner Baldwin *Department of Chemistry, The University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0009-0001-4603-1836
Ruitu Lyu *Department of Chemistry, The University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0003-4597-1604
Bryan Daniels *Department of Chemistry, The University of Chicago, Chicago, IL, USA.
Chang YeDepartment of Chemistry, The University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0003-0236-5671
Chen CaoDepartment of Chemistry, The University of Chicago, Chicago, IL, USA.
Chenyou ZhuDepartment of Chemistry, The University of Chicago, Chicago, IL, USA.
Diwen FanDepartment of Chemistry, The University of Chicago, Chicago, IL, USA.
Liane LinLibertyville High School, Libertyville, IL, USA.ORCID http://orcid.org/0009-0006-6437-8565
Yushuai LiuDepartment of Chemistry, The University of Chicago, Chicago, IL, USA.
Yiding WangCommittee on Genetics, Genomics & System Biology, The University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-7172-8651
Chuan HeDepartment of Chemistry, The University of Chicago, Chicago, IL, USA. chuanhe@uchicago.edu.ORCID http://orcid.org/0000-0003-4319-7424

Funding

Pilot Program CoreP30ES027792 · NIEHS · UNIVERSITY OF CHICAGO · PI Gokhan M. Mutlu · 2017 to 2026
$13.6M
Role of the Non-canonical Inflammasome in SARS-CoV-2-mediated Pathology and CoagulopathyP01AI175399 · NIAID · OHIO STATE UNIVERSITY · PI Amal O Amer, Estelle A Cormet-Boyaka · 2024 to 2026
$12.0M
Labeling and sequencing of 5hmC and 5mC in DNA-RenewalR01HG006827 · NHGRI · UNIVERSITY OF CHICAGO · PI HE, CHUAN · 2012 to 2025
$7.2M
NHGRI NIH HHS R01 HG006827NIAID NIH HHS P01 AI175399NIEHS NIH HHS P30 ES027792U.S. Department of Health & Human Services | National Institutes of Health (NIH) HG006827
6 · The paper itself

Abstract

We present Ultra-Mild Bisulfite Sequencing (UMBS-seq), a method for 5-methylcytosine (5mC) detection that minimizes DNA degradation and background noise. UMBS-seq outperforms conventional bisulfite and enzymatic methyl-sequencing (EM-seq) methods in library yield, complexity, and conversion efficiency when applied to low-input DNA samples. In particular, its effectiveness with low-input cell-free DNA (cfDNA) and hybridization-based target capture highlights its potential for clinical applications, including 5mC biomarker detection and early disease diagnosis.

Indexed as

5-MethylcytosineDNAHigh-Throughput Nucleotide SequencingSequence Analysis, DNASulfitesCell-Free Nucleic AcidsDNA MethylationHumans5-MethylcytosineCell-Free Nucleic AcidsDNAhydrogen sulfiteSulfites

Identifiers

PMID41233368
PMCPMC12615686

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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.