Human PBMC atlas - TCD4 naive cells

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Cell Metadata

T CD4 CM quiesc

Full Name: quiescent central memory CD4-positive, alpha-beta T cell
Closest Ontology Term: central memory CD4-positive, alpha-beta T cellCL:0000904
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.: central memory CD4-positive, alpha-beta T cellCL:0000904
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Cluster with canonical markers of central memory cells and ribosomal genes suggesting quiescence
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: unknown
Canonical Marker Genes: CD4, CCL5
Rationale: Cluster with canonical markers of central memory cells and ribosomal genes suggesting quiescence

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: quiescent central memory CD4-positive, alpha-beta T cell
Closest Ontology Term: central memory CD4-positive, alpha-beta T cellCL:0000904
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.: central memory CD4-positive, alpha-beta T cellCL:0000904
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Cluster with canonical markers of central memory cells and ribosomal genes suggesting quiescence
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: unknown
Canonical Marker Genes: CD4, CCL5
Rationale: Cluster with canonical markers of central memory cells and ribosomal genes suggesting quiescence

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