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?