ScRNAseq-How to correctly choose cell type marker genes

Question

[Francesco]

Hello! I’m new to the field of single-cell RNA sequencing, and I need to analyze some datasets consisting of 10 samples across 2 different conditions. I’m facing challenges in the cell type classification step because my data are derived from cerebrospinal fluid (CSF), whereas the canonical reference-based classification models are trained on blood-derived data. I’m considering using marker-based methods like cellAssign, but this requires obtaining marker genes for each cell type from the literature. However, after an extensive search, I’ve found that there isn’t a strong consensus on the most important markers for accurately defining every cellular type. Therefore, I have the following questions:

1. Is CSF similar to blood, and can I simply use reference-based models in my situation?
2. If not, how can I achieve correct cell type classification?

Thank you a lot

Answer 1

[Bioinfotec]

In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. For example, you can first use singleR and celldex for reference-based automatic annotation and then manually check the results with marker gene from literature.

[Francesco]

Thank you for your valuable suggestion!