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.