Summary

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.

Raw reads for the study are now available in the Data Coordination Platform for the Human Cell Atlas.

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

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  	Summary	Cells	Nuclei	Donors	Age Group	H5AD	Interactive view
  Heart Global	Combined single cell and single nuclei RNA-Seq data of 485K cardiac cells with annotations	486,134		14	40-75	file_download	pageview
  Heart Atrial Cardiomyocytes						file_download	pageview
  Heart Ventricular Cardiomyocytes						file_download	pageview
  Heart Vascular						file_download	pageview
  Heart Fibroblasts						file_download	pageview
  Heart Immune						file_download	pageview
  Heart Neuronal						file_download	pageview
  Heart Adipocytes						file_download	pageview
  Human Adult Skeletal Muscle	Analysis of 52,825 single cells and nuclei from five donors	34,577	18,248	5	60-75	file_download	pageview
  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		7	50-75	file_download