Human PBMC atlas - TCD4 effector and nonnaive cells

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Cell Metadata

T CD4 naive/CM Treg

Full Name: naive, central memory regulatory T cell
Closest Ontology Term: regulatory T cellCL:0000815
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: unknown
Category Class of which the cell type is a subclass.: regulatory T cellCL:0000815
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Regulatory T cells have been reported previously, but we differentiate subtypes, here defined by canonical naive and central memory genes
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CCR7, LEF1
Canonical Marker Genes: CD4, FOXP3
Rationale: Regulatory T cells have been reported previously, but we differentiate subtypes, here defined by canonical naive and central memory genes

Set of Labels Description: Cell annotations were generated through iterative hierarchical clustering. Broad lineages were first identified and then recursively subdivided into finer sublineages and sub-sublineages (e.g., T → CD4 T → Effector CD4 T). Clusters were iteratively re-clustered at multiple resolutions, split or merged based on biological evidence, and refined through repeated quality-control steps. Final annotations were determined by consensus of an international group using canonical marker genes, one-vs-all and all-vs-all differential expression analyses, and cluster relationships within the hierarchical framework. Low-quality cells, doublets, and contaminating populations were identified and removed throughout the annotation process; following each round of removal, datasets were reprocessed and re-clustered to improve cluster resolution and biological consistency before subsequent annotation refinement.
Annotation Method: manual

Full Name: naive, central memory regulatory T cell
Closest Ontology Term: regulatory T cellCL:0000815
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: unknown
Category Class of which the cell type is a subclass.: regulatory T cellCL:0000815
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Regulatory T cells have been reported previously, but we differentiate subtypes, here defined by canonical naive and central memory genes
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CCR7, LEF1
Canonical Marker Genes: CD4, FOXP3
Rationale: Regulatory T cells have been reported previously, but we differentiate subtypes, here defined by canonical naive and central memory genes

Set of Labels Description: Cell annotations were generated through iterative hierarchical clustering. Broad lineages were first identified and then recursively subdivided into finer sublineages and sub-sublineages (e.g., T → CD4 T → Effector CD4 T). Clusters were iteratively re-clustered at multiple resolutions, split or merged based on biological evidence, and refined through repeated quality-control steps. Final annotations were determined by consensus of an international group using canonical marker genes, one-vs-all and all-vs-all differential expression analyses, and cluster relationships within the hierarchical framework. Low-quality cells, doublets, and contaminating populations were identified and removed throughout the annotation process; following each round of removal, datasets were reprocessed and re-clustered to improve cluster resolution and biological consistency before subsequent annotation refinement.
Annotation Method: manual