Question: I have ribosomal and mitochondrial genes in my nuclei data. Do I need to filter them?
Answer: This is a common nuclei observation of having mitochondrial clouds because as the cell membrane is broken open, there is a release of all the organelles into a solution that includes a few cells with high GEM encapsulated mitochondria along with the background. These cells have enough transcripts to make it through the cell calling threshold. Illustrated below is a QC plot for filtering cells using certain criteria that includes >5% mitochondrial content between cellular and nuclei datasets.
In cells and nuclei, high ribosomal genes might be an indication of sample quality and therefore high background. For samples that truly indicate poor quality, this can try to be filtered out using the filtering and reclustering option on Loupe Browser or using Cell Ranger on filtered results as Illustrated here.
Products: Single Cell Gene Expression