Seurat Cell Cycle Phase Assignments

Question

[ianmw]

Hi Biostars,

I want to estimate cell-cycle phase from some single cell RNA sequencing data. I’ve used the CellCycleScoring function in Seurat to get cell cycle scores and phase assignments. The output gives phase assignments of either G1, G2M, or S. My questions…

1) Which phase correlates with quiescent or non-cycling cells? In the cell-cycle vignette on the Seurat website, it says that “cells expressing neither [G2/M or S markers] are likely not cycling and in G1 phase.” So does the G1 phase assignment represent non-cycling cells? Could you also consider these cells to be in G0?

2) Is it appropriate to use the output of CellCycleScoring to report the fraction of cells in different cell cycle phases?

3) Is there a better way to estimate cell cycle phase from single cell RNA sequencing data?

Any help would be greatly appreciated.

I

Answer 1

[Kristoffer Vitting-Seerup]

I'll attempt to answer the questions in order:

1. None of them. Quiescent cells is a special case of G1 - actually it is mostly described as cells that have exited the cell cycle program and are in G0 - see fx this image or this wiki page. That also means that for a single cell you cannot distinguish G1 and G0 from the Seurat analysis (I am unsure if you can do that at all - and you could it would probably have to be based on genes specific to the cell/tissue type you are analysing.
2. Yes
3. If you have cell-cycle data more specific to your setup probably yes. Seurat uses the genes defined in this article - you can judge yourself whether you have (or can get) better data.

What I have seen done before is that for sets (clusters etc) of cell you can compare the fraction of genes in the different cell cycles. Cell-types which are very proliferative would have a higher fraction of cells in S/G2M whereas the cell types with low S/G2M fraction would be terminally differentiated, slowly dividing or quiescent cells.

[ianmw]

Very helpful answer. Thank you so much Kristoffer !