I have done several single cell nuclear RNAseq experiments on human brain tissue. I followed this protocol outlined in Krishnaswami et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941947/. The percentage of viable (intact) cells out of the total nuclei suspension is less than 5% - and these cells can be excluded in the analysis. The nuclear specific transcripts are enriched (for example MALAT-1). However, some mitochondrial specific genes like MT-ND1, MT-ND2, MT-ND3, MT-CO1, MT-CO2, and MT-CO3 are still detected at high levels (And often differentially expressed between clusters). Given that the RNA sequenced is nuclear RNA, how can I explain the presence of mitochondria-encoded RNA in my data?
I've read in some papers that use single nucleus datasets that mitochondrial genes are ignored for downstream analysis.
"Mitochondrial RNA genes were filtered out as well to exclude transcripts originating from outside the nucleus and avoid biases introduced by the isolation of nuclei and ultracentrifugation."