HCA Gut Cell Atlas v1 Lymphoid Lineage

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Cell Metadata

CD8 Memory/Exhausted

Ontology Term: exhausted T cellCL:0011025
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: exhausted CD8 T cell, Tex
Category Class of which the cell type is a subclass.: CD8-positive, alpha-beta T cellCL:0000625
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: LAG3, HAVCR2, PDCD1, LAYN, CTLA4, BATF
Canonical Marker Genes: PDCD1, HAVCR2, TOX
Rationale: TOX, CD27, GZM pointed to CD8 memory here, and HAVCR2 pointed to an exhausted signature

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: exhausted T cellCL:0011025
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: exhausted CD8 T cell, Tex
Category Class of which the cell type is a subclass.: CD8-positive, alpha-beta T cellCL:0000625
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: LAG3, HAVCR2, PDCD1, LAYN, CTLA4, BATF
Canonical Marker Genes: PDCD1, HAVCR2, TOX
Rationale: TOX, CD27, GZM pointed to CD8 memory here, and HAVCR2 pointed to an exhausted signature

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