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Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity

1
Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
2
Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
3
Reference and Translation Center for Cardiac Stem Cell therapy (RTC), Department of Cardiac Surgery, Rostock University Medical Center, 18057 Rostock, Germany
4
Department of Life, Light, and Matter of the Interdisciplinary Faculty at Rostock University, 18059 Rostock, Germany
5
Molecular Biology and Fish Genetics, Faculty of Agriculture and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
6
Stellenbosch Institute of Advanced Study, Wallenberg Research Centre, Stellenbosch University, 7602 Stellenbosch, South Africa
*
Authors to whom correspondence should be addressed.
These authors contributed equally.
Cells 2020, 9(2), 318; https://doi.org/10.3390/cells9020318 (registering DOI)
Received: 23 December 2019 / Revised: 24 January 2020 / Accepted: 25 January 2020 / Published: 28 January 2020
(This article belongs to the Special Issue Single Cell Analysis)
Analyses on the cellular level are indispensable to expand our understanding of complex tissues like the mammalian heart. Single-nucleus sequencing (snRNA-seq) allows for the exploration of cellular composition and cell features without major hurdles of single-cell sequencing. We used snRNA-seq to investigate for the first time an entire adult mammalian heart. Single-nucleus quantification and clustering led to an accurate representation of cell types, revealing 24 distinct clusters with endothelial cells (28.8%), fibroblasts (25.3%), and cardiomyocytes (22.8%) constituting the major cell populations. An additional RNA velocity analysis allowed us to study transcription kinetics and was utilized to visualize the transitions between mature and nascent cellular states of the cell types. We identified subgroups of cardiomyocytes with distinct marker profiles. For example, the expression of Hand2os1 distinguished immature cardiomyocytes from differentiated cardiomyocyte populations. Moreover, we found a cell population that comprises endothelial markers as well as markers clearly related to cardiomyocyte function. Our velocity data support the idea that this population is in a trans-differentiation process from an endothelial cell-like phenotype towards a cardiomyocyte-like phenotype. In summary, we present the first report of sequencing an entire adult mammalian heart, providing realistic cell-type distributions combined with RNA velocity kinetics hinting at interrelations. View Full-Text
Keywords: snRNA-seq; RNA velocity; cluster analysis; cardiomyocytes; seurat snRNA-seq; RNA velocity; cluster analysis; cardiomyocytes; seurat
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Wolfien, M.; Galow, A.-M.; Müller, P.; Bartsch, M.; Brunner, R.M.; Goldammer, T.; Wolkenhauer, O.; Hoeflich, A.; David, R. Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity. Cells 2020, 9, 318.

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