Human PBMC atlas - TCD4 effector and nonnaive cells

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Cell Metadata

T CD4 CTL ADGRG1hi HLA

Full Name: HLA, ADGRG1high CD4-positive, alpha-beta cytotoxic T cell
Closest Ontology Term: CD4-positive, alpha-beta cytotoxic T cellCL:0000934
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.: CD4-positive, alpha-beta cytotoxic T cellCL:0000934
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: We differentiate canonical cytotoxic cells by ADGRG1 expressions, here ADGRG1 high expression in addition to HLA genes
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: ADGRG1, HLA-DRB1
Canonical Marker Genes: CD4, GZMH, PRF1, GNLY
Rationale: We differentiate canonical cytotoxic cells by ADGRG1 expressions, here ADGRG1 high expression in addition to HLA genes
Rationale DOI: https://doi.org/10.3389/fimmu.2025.1653970 https://doi.org/10.1038/s41467-022-31519-6

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: HLA, ADGRG1high CD4-positive, alpha-beta cytotoxic T cell
Closest Ontology Term: CD4-positive, alpha-beta cytotoxic T cellCL:0000934
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.: CD4-positive, alpha-beta cytotoxic T cellCL:0000934
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: We differentiate canonical cytotoxic cells by ADGRG1 expressions, here ADGRG1 high expression in addition to HLA genes
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: ADGRG1, HLA-DRB1
Canonical Marker Genes: CD4, GZMH, PRF1, GNLY
Rationale: We differentiate canonical cytotoxic cells by ADGRG1 expressions, here ADGRG1 high expression in addition to HLA genes
Rationale DOI: https://doi.org/10.3389/fimmu.2025.1653970 https://doi.org/10.1038/s41467-022-31519-6

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