Human PBMC atlas - DC_DC2 cells

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Cell Metadata

pDC3_IRF4_CXCR4

Full Name: IRF4/CXCR4+ plasmacytoid dendritic cell 3
Closest Ontology Term: plasmacytoid dendritic cellCL:0000784
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.: plasmacytoid dendritic cellCL:0000784
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Cluster with canonical pDC3 markers and +IRF4/CXCR4
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: IRF4, CXCR4, SEMA7A, GPR183, SOX4, RGS1, DSTN, ZFP36
Canonical Marker Genes: IL3RA, TCF4, IRF7, IRF8, JCHAIN, LILRA4
Rationale: Cluster with canonical pDC3 markers and +IRF4/CXCR4
Rationale DOI: https://doi.org/10.1038/s41598-025-87344-6

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: IRF4/CXCR4+ plasmacytoid dendritic cell 3
Closest Ontology Term: plasmacytoid dendritic cellCL:0000784
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.: plasmacytoid dendritic cellCL:0000784
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Cluster with canonical pDC3 markers and +IRF4/CXCR4
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: IRF4, CXCR4, SEMA7A, GPR183, SOX4, RGS1, DSTN, ZFP36
Canonical Marker Genes: IL3RA, TCF4, IRF7, IRF8, JCHAIN, LILRA4
Rationale: Cluster with canonical pDC3 markers and +IRF4/CXCR4
Rationale DOI: https://doi.org/10.1038/s41598-025-87344-6

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