Hello Everyone, recently I have been working on the scRNA seq analysis of HBV-associated Heptatocellular carcinoma (HCC) cells using Seurat packages. When I used the 20 genes with lowest adjusted p-value in each cluster to plot the violin plots and Feature Plots, I realized that some mitochondrial genes and ribosomal genes are highly enriched in every cluster (as shown in the attached photo). Regarding this, I have several questions:

1. I think It should make sense and be inevitable to see the mitochondrial gene & ribosomal gene enrichment, even in the presence of quality control to filter cells with high % of mitochondrial genes. You know, mitochondrial and ribosomal genes should be present in all the kinds of cells because they serve essential functions.