HCA Gut Cell Atlas v1 Lymphoid Lineage

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Cell Metadata

CD4 Th17

Ontology Term: T-helper 17 cellCL:0000899
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: Th17 CD4 T cell, Th17
Category Class of which the cell type is a subclass.: CD4-positive, alpha-beta T cellCL:0000624
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: RORC, IL17A, IL22, IL21, CSF2, IL23R
Canonical Marker Genes: RORC, IL17A, CCR6
Rationale: Since both ILC3s and Th17 express RORC and IL7R, these can be difficult to separate. Th17 were annotated when larger clusters of naive T cells showed a clear IL7R and RORC expressing subcluster

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: T-helper 17 cellCL:0000899
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: Th17 CD4 T cell, Th17
Category Class of which the cell type is a subclass.: CD4-positive, alpha-beta T cellCL:0000624
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: RORC, IL17A, IL22, IL21, CSF2, IL23R
Canonical Marker Genes: RORC, IL17A, CCR6
Rationale: Since both ILC3s and Th17 express RORC and IL7R, these can be difficult to separate. Th17 were annotated when larger clusters of naive T cells showed a clear IL7R and RORC expressing subcluster

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