which conclusion can get from the cell cycle analysis of scRNAseq data

Question

[alwayshope]

Dear guys,

May I have your guidance that what the conclusion can you get from the cell cycle analysis of scRNAseq data?

Can I say the cells near 1/2 or partial cells are going through the proliferation? Is there a way to get the ratio of the cell numbers of G1, S, G2M? Why G2M, not seperated G2 and M?

Thanks a lot!

Answer 1

[rfran010]

G2/M can be hard to separate, and the genes you might use to separe them could give unreliable results. By counting cells annotated as S, G1, or G2/M you can get the ratios. cells near the G1 group may be early S or late G2M, while further separated cells could be later S, earlier G2M. However, there are always caveats. In terms of proliferation, I'm not sure you could say a lot since you don't know if G1 cells are arrested or preparing for S phase. If the cell is in G1 but preparing for S, I would still consider it proliferating.

Answer 2

[shiyang_bio]

Totally agree with rfran010. The cell cycle analysis does not quite make sense. I'd rather compute the cycling score and see which cell (or cluster) has the highest score.