HCA Gut Cell Atlas v1 Lymphoid Lineage

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Cell Metadata

T GammaDelta

Ontology Term: gamma-delta T cellCL:0000798
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: gamma delta T cell, Tgd
Category Class of which the cell type is a subclass.: Unconventional T cell
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: unconventional T cell category would be useful to encapsulate non-CD8/CD4 t cell subclasses. https://doi.org/10.1038/ni.3298
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: TRGC1, TRDC, TRDV1, TRDV2, TRDV3, KLRK1
Canonical Marker Genes: TRDC, TRGC2, TRDV1
Rationale: TRDC, TRGC2 and SOX4 point to gamma delta T cells, but these do not show the canonical TRGC9, TRDC2 variants.

Set of Labels Description: Cell annotations (Prelim annotation) are based on the finest possible label that could be used to describe each of the ~500 clusters found during integration and subclustering
Annotation Method: both
Algorithm Name: scVI
Algorithm Version: 1.3.2
Algorithm URL: https://github.com/scverse/scvi-tools

Ontology Term: gamma-delta T cellCL:0000798
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: gamma delta T cell, Tgd
Category Class of which the cell type is a subclass.: Unconventional T cell
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: unconventional T cell category would be useful to encapsulate non-CD8/CD4 t cell subclasses. https://doi.org/10.1038/ni.3298
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: TRGC1, TRDC, TRDV1, TRDV2, TRDV3, KLRK1
Canonical Marker Genes: TRDC, TRGC2, TRDV1
Rationale: TRDC, TRGC2 and SOX4 point to gamma delta T cells, but these do not show the canonical TRGC9, TRDC2 variants.

Set of Labels Description: Cell annotations (Prelim annotation) are based on the finest possible label that could be used to describe each of the ~500 clusters found during integration and subclustering
Annotation Method: both
Algorithm Name: scVI
Algorithm Version: 1.3.2
Algorithm URL: https://github.com/scverse/scvi-tools