integrative cluster analysis - proliverative cardiomyocytes

This study includes the single snRNA-seq in whole adult murine hearts from an inbred (C57BL/6NRj) and an outbred (Fzt:DU) mouse strain in comparison to publicly available scRNA-seq data of the tabula muris project.

DOI: 10.15490/

Zenodo URL: None

Created at: 4th May 2020 at 09:47


integrative cluster analysis of single cell and single nuclei data

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Top100 transcripts

This file contains the top 100 transcripts for the identified cell types in the integrated dataset.

  • transcripts_top100.xlsx

number of cells per cluster

The file contains the absolute and relative cell/nuclei numbers per cluster for each individual dataset used in the integrated analysis.
Subpopulations were grouped together for the representation of relative cell/nuclei numbers.

  • cells per cluster by datasets.xlsx

FeaturePlot of cardiomyocyte markers

The file contains FeaturePlots of 4 different cardiomyocyte markers (Actn2, Tnnc1, Actc1 and Ryr2) to demonstrate how annotation of clusters needs to be based on several markers and approaches, which in the aggregate allow for more reliable conclusions/results.

  • cardiomyocyte_annotation.pdf

Figures Galow et al.

This pdf file contains all figures of the article "Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mice" in high resolution.

  • Figures Galow et al.pdf

top10 marker for cell clusters

This pdf contains the top 10 markers for each identified cell type as a dot-plot.

  • top10marker_per_cluster.pdf

CD34 expression across clusters

The file contains an UMAP representation illustrating the expression of the stem cell marker Cd34 in all identified cell clusters.

  • UMAP_Cd34.pdf

Nuclei isolation for single nuclei RNA-seq

This file contains the detailed experimental protocol to isolate nuclei from murine hearts.

  • nuclei isolation_english.pdf

R-Script for integrative clusteranalysis of single cell and single nuclei data

This file contains the R-script to analyse single nuclei and single cell data of Bl6 and Fzt:DU mice previously processed with cellranger. The analyses utilizes the Seurat and harmony package to integrate three datasets before subsequent downstream analysis characterizing proliferative cardiomyocytes.

  • proliferative cardiomyocytes.R

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Galow, A.-M., & Wolfien, M. (2020). integrative cluster analysis - proliverative cardiomyocytes. FAIRDOMHub.
Snapshot 1 (4th May 2020) DOI

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Created: 4th May 2020 at 09:47

Last updated: 4th May 2020 at 09:48

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