Human Gut Cell Atlas (HGCA) v1 - Myeloid Lineage

Tolerogenic cDC2

Full Name: RORgt+ tolerogenic type 2 conventional dendritic cells
Closest Ontology Term: CD11b-positive dendritic cellCL:0002465
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: RORgt+ cDC2s
Category Class of which the cell type is a subclass.: CD11b-positive dendritic cellCL:0002465
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: See DOIs for evidence in support of this cDC2 subset
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: PRDM16
Canonical Marker Genes: PRDM16, RORC
Rationale: There is a subcluster of cDC2s that display PRDM16 and RORC, evidence that they could be antigen presenting cells responsible for induction of gut tolerance to food/gut antigens
Rationale DOI: https://doi.org/10.1038/s41586-025-08982-4 https://doi.org/10.1016/j.cell.2025.03.020

Set of Labels Description: Cell annotations based on two rounds of subclustering with scVI integration, sample_id as batch key. Cell annotations were refined by expert feedback based on "prelim annotation" on CAP. Prelim annotation is renamed "hgca_celltype_v0" here and the feedback on the "prelim annotation" is available by selecting a previous version of the Integrated Human Gut Atlas on CAP.
Annotation Method: both
Algorithm Name: scIB
Algorithm Version: 1.2.1
Algorithm URL: https://github.com/theislab/scib