Cell cycle arrest analysis using bulk RNA-seq

Question

[Apex92]

Dear all.

Here I have a general question and would appreciate your input.

I have bulk RNA-seq data (3 control and 3 KD samples) from mouse embryonic stem cells (mESCs) - what I want to do is to see if cell cycle arrest is happening in the KD condition by looking at the levels of the cell cycle marker genes. With that said, is there any tool (except Seurat which is suitable for scRNA-seq data) that I can work with? And what are the most reliable marker genes for this analysis?

Thank you in advance.

Answer 1

[ATpoint]

The scran package implements the cyclone classifier for such analysis, see http://bioconductor.org/books/3.15/OSCA.advanced/cell-cycle-assignment.html#using-the-cyclone-classifier

It was developed for single-cell data but the input is simply an expression matrix and I think conceptually you could apply it basically to any count data experiment. Marker genes for this analysis are provided via the package, see the link. It is based on this paper . The advantage here is that the method is generic and you do not have to squeeze your data into this custom Seurat format.

[Apex92]

That was quite helpful - thank you for your input @ATpoint