labelling the clusters from the CD4 T cell scRNAseq data

Question

[Sara]

I have some scRNAseq data from only CD4 T cell and clustered them using existing algorithms. Now I am trying to label these clusters to see which subsets of CD4 T cells I have in my data. First I decided to use label transfer method but there should be a reference for that and I did not find it. Therefore I decided to do it manually and look at the top 20 genes of each cluster but except for one cluster in which I found only one gene as marker of one of the CD4 T cell subsets, for the rest I did not see any major gene. Do you have any experience how to label the clusters from such scRNAseq data or do you know any reference file for such question?

[ATpoint]

If you have only gene names as a reference for the subsets you can use UCell from Bioconductor to give each cell a per-signature score and then simply see whether certain signatures are enriched in clusters.

[fracarb8]

Which tissue are you working on? The answer to question might change based on tissue, markers you are using, reference datset you are using for transfering labels,.... For example in pbmc CD4 is mainly expressed by myeloid cells, and to identify TCD4 is better to look for T cell not expressing CD8 (e.g. CD3E+ CD3D+ CD8A- CD8B-)

[Sara]

fracarb8 CD4 T cells are isolated from PBMC.