Mitochondrial Gene percentage threshold in single cell RNA-Seq

Question

[hkarakurt]

Hello everyone, I am working on scRNA-Seq data analysis. As most of you know high mitochondrial gene percentage indicates low quality (damaged or dead cells etc.) and we need to filter that. Is this threshold for identify the low quality cell data dependent? Because for each data set we see a different QC plot. In general, if 20 percent of all expressed genes are mitochondrial genes, is it acceptable?

Thank you in advance.

Answer 1

[GenoMax]

There is a section on mitochondrial genes in this paper with references.

For example, 30% of total mRNA in the heart is mitochondrial due to high energy needs of cardiomyocytes, compared with 5% or less in tissues with low energy demands. For instance, 30% mitochondrial mRNA is representative of a healthy heart muscle cell, but would represent a stressed lymphocyte.