Question: Mitochondrial genes in single cell nuclear RNAseq data
gravatar for dalhoomist
19 months ago by
dalhoomist10 wrote:

I have done several single cell nuclear RNAseq experiments on human brain tissue. I followed this protocol outlined in Krishnaswami et al 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?

rna-seq mitochondria gene • 1.1k views
ADD COMMENTlink written 19 months ago by dalhoomist10

Since the explanation in this case is likely going to be related to experimental protocol/technique, you may want to post this at SeqAnswers and biology SE.

Informatically you could ignore the counts on mito genes if they are not of interest. But their presence seems to indicate that your nuclear preps were likely not clean or perhaps mitochondrial RNA's get transferred to nuclei? It also looks like mitochondrial genes are found in nuclei so that may also be another explanation?

ADD REPLYlink modified 19 months ago • written 19 months ago by genomax87k
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