Clustering heart data

The single cell were sorted from male and female mouse at 10 weeks old. The cardiac cells and a portion of endothelial cells were filter out.

Look through the data

Violin plot below shows:
- nGene: Number of genes detected (UMI>0) in each cell.
- nUMI: Number of Unique Molecular Identity identified in each cell.
- percent.mito: Percentage of mitochondrial genes UMIs in all total UMIs.
Note that large number of cells express high level of mitochondrial genes. Is it a reasonable phenomenon for cardiac muscle cells?

Seurat clustering

The cells were clustering using Seurat,2016. The top 8 PCs were used as imput. No mitochondrion genes were detected as HVG.

Determine statistically significant principal components. We select top 8 pcs for clustering.

tSNE and UMAP are two non-linear dimention reduction algorithm. The clustering results of Seurat are showed. (Resolution=0.2)

Cardica myoblast markers and hemoglobin

Hematopoietic markers

Find markers in each group

Top 10 markers of each cluster.

Differentially expression stats.

Enrichment

Gene Ontology