Mitochondrial genes filtration

Question

[sunshine]

Hello,

I've learned that mitochondrial genes form a contamination reason to samples (due to cell damage or death), which results in low-quality samples. My questions are:

1. Is there a predefined list of all mitochondrial genes to consider during filtration?
2. How to detect mitochondrial genes in the case of the following datasets:

Thank you in advance.

Answer 1

[ATpoint]

For mitochondrial genes it is simple by using grep("^mt-", rownames(your.data)) as these genes are prefixed by mt-. For other genes such as ribosomal ones you probably will need to obtain the GTF reference file and then filter based on the gene_type field.

[sunshine]

Thank you so much for your help.

The grep() will work on "mt-" or "MT-" labeled genes, but I still face a problem with datasets that aren't labeled with "mt-" or "MT-" prefix nor has a gene_type identity, especially that these datasets aren't provided with their GTF file, as I downloaded them as (.rds) files [SingleCellExperiment object].

[ATpoint]

Where are they from, any dataset has some kind of annotation it is based on, one only has to find them ;-)