Is the upregulation of ribosome genes in scRNA-seq reliable?

Question

[tujuchuanli]

Hi all,

I am analyzing the scRNA-seq data in Breast cancer. I find that there are 7 clusters in my dataset. I determined cells in these 7 clusters as luminal epithelial cells by expression of marker genes. In one of these clusters, I find that some of ribosome genes are up-regulated when comparing to the other clusters. I have reads some papers and threads on net and find that someone considered the ribosome and MT genes as quality control and excluded them from subsequent analysis.

My question is whether the upregulation of ribosome genes in scRNA-seq is reliable?

Thanks

[Diedes]

Hey,

Sorry for the late reply, did not see you post earlier. I did see something very similar in data where they gated for only a subset of tcells. I made the assumption that this has to do with the fact the cells are very similar to the others on transcription level. This similarity causes that ribosomal proteins to somehow be the most significantly differential expressed. I even saw actin pop up somewhere as 3rd highest differential expressed in a cluster compared to other clusters.

In your case of all 7 clusters being luminal epithelial cells, I guess it is the same. I do not think this is a bad thing and it can mean a lot of things depending on your experiment.

What you can do aswell, is compare cluster 1 vs cluster 4 and 5 for example, to exclude all other clusters.