HCA Gut Cell Atlas v1 Lymphoid Lineage

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Cell Metadata

CD4 Th1

Ontology Term: T-helper 1 cellCL:0000545
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: Th1 CD4 T cell, Th1
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.: CD4, TBX21, IFNG, TNF
Canonical Marker Genes: TBX21, IFNG, CXCR3
Rationale: Th1 are annotated when CD4 cells show IFNG or TNF program signatures and especially IL7R. Thelper cytotoxic dual signatures point then to Th1

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 1 cellCL:0000545
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: Th1 CD4 T cell, Th1
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.: CD4, TBX21, IFNG, TNF
Canonical Marker Genes: TBX21, IFNG, CXCR3
Rationale: Th1 are annotated when CD4 cells show IFNG or TNF program signatures and especially IL7R. Thelper cytotoxic dual signatures point then to Th1

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