Evidence map›Paper›PMID 40845850›Full record

ArticleStem cell reports2025

Toti: An integrated multi-omics database to decipher the epigenetic regulation of gene expression in totipotent stem cells.

Yi Chai, Ruiying Zhang, Shunze Jia, Danfei Zhu, Siyi Chen, Shuai Liu, Na Kong, Xudong Fu, Xin Sheng

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Stem cell reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
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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.

Yi ChaiDepartment of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, Zhejiang 311121, China; Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, Singapore 117597, Singapore.
Ruiying ZhangLiangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, Zhejiang 311121, China; Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China.
Shunze JiaLiangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, Zhejiang 311121, China; Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China.
Danfei ZhuDepartment of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, Zhejiang 311121, China; Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
Siyi ChenDepartment of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, Zhejiang 311121, China; Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
Shuai LiuLiangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, Zhejiang 311121, China.
Na KongLiangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, Zhejiang 311121, China; Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
Xudong FuLiangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, Zhejiang 311121, China; Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China. Electronic address: xudongfu@zju.edu.cn.
Xin ShengDepartment of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, Zhejiang 311121, China; Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China. Electronic address: shengxin@zju.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Totipotent stem cells (TSCs), the origin of mammalian life and the foundation of early embryogenesis, possess the highest differentiation capacity and extensive developmental potential. However, none of the existing embryonic databases have provided epigenetic and transcriptomic resources on totipotency, greatly limiting our understanding of its establishment and exit mechanisms. Here, we present Toti, a pioneering multi-omics database developed to investigate transcriptional and epigenetic factors governing totipotency, encompassing in vivo, in vitro, and genome-edited human and mouse embryonic TSCs, TSC-like cells, pluripotent stem cells, and embryos spanning preimplantation stages, with a total of 8,284 samples. Toti enables flexible keyword-based search, comparative visualization of transcriptomic and epigenetic features, motif and pathway enrichment analysis across diverse cell types, and single-cell resolution investigation of totipotency by offering Search, Browse, and Analysis modules, available at http://toti.zju.edu.cn/. Toti thus serves as a valuable resource for exploring the molecular underpinnings of totipotency.

Indexed as

Databases, GeneticEmbryonic Stem CellsEpigenesis, GeneticGene Expression Regulation, DevelopmentalAnimalsCell DifferentiationHumansMiceMultiomicsPluripotent Stem CellsTranscriptomeATAC-seqChIP-seqdatabaseembryonic cellsmulti-omicsRNA-seqscRNA-seqTotitotipotencytotipotent stem cells

Identifiers

PMID40845850
PMCPMC12447336

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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.