Entering edit mode
2.9 years ago
david.f.stein ▴ 10
I have some scRNA-seq data from developing mouse limbs that I've analyzed in Seurat. My PI has suggested some cell-type marker genes to use for identifying the cell types of my clusters. However, I'm looking for a database of mouse marker genes that I can use to further identify the cell types. Does anyone know of a resource like this?
Cell type markers are more complicated than most people initially assume. What defines a good marker depends on all the cell types that are present in your experiment. Same cell types can also have different markers in different contexts (for example, during different stages of development).
Anyway, here is another possible solution: https://cran.r-project.org/package=clustermole/vignettes/clustermole-intro.html
What kind of markers do you need? It differs if you need markers for in silico analysis which would then simply be a set of genes that in its union defines a cluster or if you want to really FACS-out these cells, in which case in would need to be genes expressed as proteins on the cell surface.