Evidence map›Paper›PMID 40666962›Full record

ArticlebioRxiv : the preprint server for biology2025

Non-disruptive 3D profiling of combinations of epigenetic marks in single cells.

Yanbo Chen, Jonathan S D Radda, Myles H Alderman, Shengyan Jin, Yubao Cheng, Yuan Zhang, Miao Liu, Andrew Z Xiao, Siyuan Wang

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 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

9 authors.

Yanbo ChenDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
Jonathan S D RaddaDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
Myles H AldermanDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
Shengyan JinDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
Yubao ChengDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
Yuan ZhangDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
Miao LiuDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
Andrew Z XiaoDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
Siyuan WangDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.

Funding

PREDOCTORAL TRAINING PROGRAM IN GENETICST32GM007499 · NIGMS · YALE UNIVERSITY · PI CARLSON, JOHN R, REINKE, VALERIE J · 1985 to 2022
$13.9M
DNA Methylation at N6-Adenine in Placental Trophoblast DevelopmentR01HD102533 · NICHD · UNIVERSITY OF FLORIDA · PI JIANG, ZONGLIANG, XIAO, ZHUO ANDREW · 2020 to 2024
$3.1M
A novel epigenetic mechanism in early embryogenesisR35GM136346 · NIGMS · YALE UNIVERSITY · PI XIAO, ZHUO ANDREW · 2020 to 2024
$2.5M
Spatial omics technologies to map the senescent cell microenvironmentUH3CA268202 · NCI · BROWN UNIVERSITY · PI MA, JIAN, NERETTI, NICOLA · 2023 to 2025
$2.2M
Integrative single-cell spatial genomic, transcriptomic, and epigenetic imaging in mammalian tissueR01HG011245 · NHGRI · YALE UNIVERSITY · PI WANG, SIYUAN · 2020 to 2023
$2.1M
High Performance Computing Instrumentation for the Yale Center for Genome AnalysisS10OD030363 · OD · YALE UNIVERSITY · PI MANE, SHRIKANT M · 2022 to 2022
$1.2M
NCI NIH HHS UH3 CA268202NHGRI NIH HHS R01 HG011245NICHD NIH HHS R01 HD102533NIGMS NIH HHS R35 GM136346NIGMS NIH HHS T32 GM007499NIH HHS S10 OD030363
6 · The paper itself

Abstract

Recent advancements in single-cell sequencing and spatial omics technologies have enhanced our understanding of diverse cellular identities, compositions, architectures, and functions. However, the single-cell three-dimensional (3D) organization of the epigenome is still not well understood, due to an absence of spatial single-cell methods that allow high-resolution, locus-specific detection of combinations of epigenetic marks while maintaining the 3D organization of the genome. Here, we develop Epigenetic Proximity Hybridization Reaction (Epi-PHR), a non-disruptive image-based single-cell spatial epigenetic profiling technology. Epi-PHR enables locus-specific and high-resolution

Identifiers

PMID40666962
PMCPMC12262473

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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 Socratic graph.