PRDM16 Functions as A Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle (Spatial Transcriptomics)(Dataset ID: STDS0000102)

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442
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Spots: 1,330
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Genes: 32,285
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PMID: 34915728
Summary
Visualization
Data
Analysis results
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Contributors
Accessions
How to cite
Dataset information
Summary:
The loss of compact myocardial cardiomyocyte (compact CM) identity suggests that PRDM16 deficiency may dramatically alter the cellular composition in left ventricular (LV) compact myocardium. To test this hypothesis, we performed single-cell RNA-seq (scRNA-seq) to examine gene dysreulation in Prdm16cKO heart. We also performed Visium Spatial Transcriptomics (ST) to facilitate mapping CM clusters to their original locations in the heart. As a result, we were able to demonstrate gene misregulation in Prdm16cKO mouse mainly occurred in LV compact CM.
Overall design:
Two pairs of Prdm16cKO/WT E13.5 mouse hearts and two pairs of Prdm16cKO/control E15.5 mouse hearts were used for Visium Spatial Transcriptomics (ST).
Technology:
10x Visium
Platform:
Illumina NovaSeq 6000
Species:
Mus musculus(mm10)
Tissues:
Heart
Development stage:
E13.5,E15.5
Submission date: 2021-07-03Update date: 2021-12-21
Sample number: 4
DOI: To be continue
Contributors
Tongbin Wu,Zhengyu Liang,Ju Chen
Contact: juchen@health.ucsd.edu
Accessions
GEO Series Accessions: GSE179392
scRNA-seq GEO Series Accessions: GSE179390
How to cite
  • Cite database of STOmicsDB:
    [1] Xu, Zhicheng et al. "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization." Nucleic acids research vol. 52,D1 (2024): D1053-D1061. doi: 10.1093/nar/gkad933'
  • Cite visualization dataset:
    [2] Tongbin Wu,Zhengyu Liang,Ju Chen. PRDM16 Functions as A Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle (Spatial Transcriptomics)[DS/OL]. STOmicsDB, 2021[2021-07-03]. https://db.cngb.org/stomics/datasets/STDS0000102/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    Citation: Wu, Tongbin et al. “PRDM16 Is a Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle.” Circulation vol. 145,8 (2022): 586-602. doi:10.1161/CIRCULATIONAHA.121.056666