Evidence map›Paper›PMID 40495257›Full record

ArticleGenome biology2025

Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors.

Jingjing He, Yi Yang, Rui Jiang, Yanying Zheng, Xianfa Yang, Xu Jiang, Xin Xue, Zhongzhou Yang, Naihe Jing, Hailong Cao and 4 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 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Review
  5. Elucidating Gene Functions in Congenital Heart Disease.Current treatment options in cardiovascular medicine · 2026
    Review
  6. Review
  7. 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

14 authors.

Jingjing He *Department of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast University, Nanjing, China.
Yi Yang *Department of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast University, Nanjing, China.
Rui Jiang *Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, China.
Yanying Zheng *Department of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast University, Nanjing, China.
Xianfa YangGuangzhou Laboratory, Guangzhou, China.
Xu JiangDepartment of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast University, Nanjing, China.
Xin XueDepartment of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast University, Nanjing, China.
Zhongzhou YangState Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Model Animal Research Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing, China.
Naihe JingGuangzhou Laboratory, Guangzhou, China.
Hailong CaoDepartment of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast University, Nanjing, China. shuqu_1982@sina.com.
Zhuojuan LuoDepartment of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast University, Nanjing, China. zjluo@seu.edu.cn.
Ke WeiInstitute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, China. kewei@tongji.edu.cn.
Peng XieState Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China. pengx@seu.edu.cn.
Chengqi LinDepartment of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast University, Nanjing, China. cqlin@seu.edu.cn.

Funding

National Key Research and Development Program of China 2018YFA0800100National Key Research and Development Program of China 2018YFA0800103National Key Research and Development Program of China 2018YFA0800104National Natural Science Foundation of China 32030017National Natural Science Foundation of China 32070823National Natural Science Foundation of China 32100529Shenzhen Science and Technology Innovation Program JCYJ20220530160416037Shenzhen Science and Technology Innovation Program JCYJ20220530160417038
6 · The paper itself

Abstract

Obtaining single-cell spatial information remains a challenge in spatial transcriptomics. Here we develop SEU-TCA, a method that leverages transfer component analysis to improve single-cell spatial mapping accuracy. Application to multiple single-cell and spatial transcriptomic datasets shows superior performance in spatial deconvolution and cell mapping. Using SEU-TCA, we explore spatial gene expression and regulon activity during mouse gastrulation and identify anterior second heart field progenitors regulated by Irx1. Functional experiments reveal that Irx1 deletion disrupts anterior second heart field development and causes ventricular septal defects, underscoring SEU-TCA's potential for advancing developmental biology research.

Indexed as

Gene Expression ProfilingHeartSingle-Cell AnalysisStem CellsTranscriptomeAnimalsGastrulationGene Expression Regulation, DevelopmentalHomeodomain ProteinsMiceTranscription FactorsHomeodomain ProteinsTranscription FactorsCardiac progenitorsRegulatory factorsSingle-cell RNA sequencingSpatial transcriptomic

Identifiers

PMID40495257
PMCPMC12150484

What OpenQuestion holds

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LicenceCC BY
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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.