Evidence map›Paper›PMID 40924578›Full record

ArticleSTAR protocols2025

Small-scale in situ Hi-C protocol for early embryos to resolve the three-dimensional genome structure.

Linjie Song, Jingcheng Zhang, Linqian Pan, Shengjie Sun, Binqiang Shi, Hexu Zhang, Hengkuan Li, Zixiao Liu, Linmi Li, Yong Zhang and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 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

11 authors.

Linjie SongCollege of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
Jingcheng ZhangKey Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China; College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
Linqian PanCollege of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
Shengjie SunCollege of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
Binqiang ShiCollege of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
Hexu ZhangCollege of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
Hengkuan LiCollege of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
Zixiao LiuCollege of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
Linmi LiKey Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China; College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
Yong ZhangKey Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China; College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China. Electronic address: zhangyong1956@nwafu.edu.cn.
Gang RenCollege of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China. Electronic address: rengang666@nwafu.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

High-throughput chromosome conformation capture (Hi-C) provides genome-wide insights into chromatin interactions within the three-dimensional structure of the nucleus, making it a powerful tool for studying genome architecture. Here, we provide a modified in situ Hi-C protocol for small cell numbers, utilizing 50-100 embryonic cells at the 8-cell stage to investigate chromatin organization during bovine early embryonic development. This protocol overcomes the challenges of limited sample availability and offers valuable insights into chromatin dynamics during bovine early embryogenesis. For complete details on the use and execution of this protocol, please refer to Zhang et al.

Indexed as

Embryo, MammalianGenomeAnimalsCattleChromatinChromosomesEmbryonic DevelopmentChromatincell biologycell culturedevelopmental biologyGenomicsSystems biology

Identifiers

PMID40924578
PMCPMC12451162

What OpenQuestion holds

Textmetadata
LicenceCC BY
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 OpenQuestion graph.