Question: In search of Mouse limb cell type markers database
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gravatar for david.f.stein
4 weeks ago by
david.f.stein10 wrote:

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?

rna-seq next-gen gene genome • 88 views
ADD COMMENTlink written 4 weeks ago by david.f.stein10

https://panglaodb.se/markers.html

ADD REPLYlink written 4 weeks ago by genomax87k

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

ADD REPLYlink written 4 weeks ago by igor11k

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.

ADD REPLYlink written 4 weeks ago by ATpoint36k
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