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Entry level Bioinformatician here. I am trying to map my single cell data with standard annotation file or assign my Seurat cluster to cell types. I have used the singleR and celldex package to map it but my problem is the single cell only consist of endothelial cells. I haven't found paper that only consist of rats endothelial cells. The single cell data is for rats. I am stuck. What is the best thing that could be done here?

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    $\begingroup$ Given that it sounds like you already have a Seurat object, can you please show a UMAP of the cells that is coloured based on clusters identified in FindClusters? This will help us to understand the heterogeneity of the cells you are looking at. $\endgroup$
    – gringer
    Commented Jun 7, 2023 at 21:33

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It seems like you can annotate all your cells as endothelial cells, problem solved ;) But seriously, not clear what your expected cell types are (subtypes of endothelial cells perhaps) or the tissue type. If you can't find a suitable reference dataset for the reference mapping approach, then you can always resort to the 'old fashioned' way of unsupervised clustering (e.g leiden) plus checking marker gene expression to annotate the clusters.

An alternative approach, could be finding a suitable human/mouse reference and then converting the gene ids to rat (ideally via 1:1 ortholog mapping) but this could get messy, so I suggest the former simpler way, at least as a starting point

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  • $\begingroup$ Thanks, this seems to clarify the question. Is this what you mean @appleball? $\endgroup$
    – M__
    Commented Jun 7, 2023 at 20:58
  • $\begingroup$ Hello. thanks for the comments and concerns. For sequencing the data, only endothelial cells were selected so the expected cell types would be the subtypes of endothelial cells, venous capillary or arterial. I have not had any luck in finding the annotation file for the endothelial cells. $\endgroup$
    – Apple Ball
    Commented Jun 8, 2023 at 5:39
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    $\begingroup$ Note that many cell selection methods are imperfect, so for your first pass you should start with confirming their identity by looking at the expression of markers of endothelial cells, and markers of other cells types (pericytes, muscle, ...). $\endgroup$
    – Alexlok
    Commented Jun 8, 2023 at 20:53

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