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I have a Seurat object

> pbmc
An object of class Seurat 
48608 features across 11709 samples within 2 assays 
Active assay: SCT (22220 features, 3000 variable features)
 1 other assay present: RNA
 2 dimensional reductions calculated: pca, umap
>

I want to plot TCRVδ2

> FeaturePlot(pbmc,"TCRVδ2")
Error: None of the requested features were found: TCRVδ2 in slot data
In addition: Warning message:
In FetchData(object = object, vars = c(dims, "ident", features),  :
  The following requested variables were not found: TCRVδ2
>

This data base is about human TCR genes

https://www.genenames.org/data/genegroup/#!/group/370

But I even can not find this gene here

Do you know what is the corresponding symbol for this gene used in Seurat?

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1 Answer 1

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TCRVδ2 is not a gene, but it defines a specific subset of gamma-delta TCRs. You can look at TRDC (delta chain) and TRGC1 and TRGC2 (gamma chains). TCRVδ2 should have the combo TRDC-TRGC1, while TCRVδ1 should express TRDC-TRGC2. You may need to increase the resolution of your clustering, to avoid clustering the gamma-delta T cells with the NK cells.

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  • $\begingroup$ Thank you so much. I have another question about gene symbols. CD45 is corresponding to PTPRC butler most of CD genes I can not find the corresponding official gene symbols. Please, do you know how I can find corresponding gene symbols for CD genes? $\endgroup$
    – Mahta Mira
    Aug 5, 2021 at 17:05

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