Interpretting mitochondrial reads

[14zac2]

Hello!

I recently used scVelo to analyze my scRNA-seq data. One interesting pattern I noticed was that one of my clusters that was downstream of another cluster had very high mitochondrial content (~50% of all reads were encoded by the mitochondria). I filtered out the mitochondrial genes and reran scVelo, finding the same pattern. My current thought is that perhaps the upstream cluster contains cells that are replacing the dying, downstream cluster.

I was hoping I could get your thoughts on the above interpretation of scVelo results, considering I am not looking at two clusters that are hypothesized to have a developmental gradient between them (these are unknown cell types in a species that is not looked at very often). I have not found any resources describing how RNA-velocity may relate to cell death or mitochondrial content, so any insight you may have on this would be much appreciated.

Many thanks for your time, and please let me know if you'd like any further details!