HEART CELL ATLAS

Using single cell technologies, we profiled the transcriptome of 486,134 cells and nuclei from six anatomical cardiac regions. Given the complexity of these data, we integrated them using state-of-the-art machine learning methods. Using this strategy, we identified 11 major cardiac cell types and 62 different cell states.

Donor Demographics

We collected healthy hearts from 14 adult donors, seven male and seven female, within the age range of 40 - 75 years. The hearts were collected in North America and the United Kingdom.

Data Sources

Using a variational autoencoder, we integrated the single nuclei produced in two different institutes, the total single cell and the CD45+enriched single cell into a unified manifold by learning the latent representation of each data source.
Single nucleus and single cell sequencing capture different cell types. Single nuclei captured most of the cardiomyocytes, fibroblasts and adipocytes; whereas single cell/CD45+enriched single cell capture most of the vascular and immune cells.

Cardiac Regions

Unsupervised clustering of the cardiac cells reveal stark regional differences in specific cell types. The most dramatic one being the transcriptional difference between atrial and ventricular cardiomyocytes.
We also observe transcriptional differences by regions for fibroblasts and vascular cells.

Visualisations

Heart Global

Combined single cell and single nuclei RNA-Seq data of 485K cardiac cells with annotations

486,134

cells

14

donors

40-75

age group
Heart Atrial
Cardiomyocytes
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Heart Ventricular
Cardiomyocytes
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Heart Fibroblasts
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Human Adult Skeletal Muscle

Analysis of 52,825 single cells and nuclei from five donors

34,577

cells

18,248

nuclei

5

donors

60-75

age group
HCA Heart RNA Velocity of vascular cells

Object and manifold with RNA Velocity calculated for single cells and CD45+enriched single cells using scVelo for the cardiac vascular compartment.

122,343

cells

7

donors

50-75

age group

Team

Teichmann Lab
Teichmann Lab
Hubner Lab
Hubner Lab
Noseda Lab
Noseda Lab
Seidman Lab
Seidman Lab
Bayraktar Lab
Bayraktar Lab
Heinig Lab
Heinig Lab
CBTM
Cambridge Biorepository for Translational Medicine
University of Alberta
University of Alberta

Funders

Chan Zuckerberg Initiative Wellcome Trust British Heart Fundation Deutsches Zentrum für Herz-Kreislauf-Forschung