Human Gut Cell Atlas (HGCA) v1 - Myeloid Lineage

migDC

Full Name: migratory dendritic cell
Closest Ontology Term: dendritic cellCL:0000451
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: migratory DCs, migratory dendritic cells
Category Class of which the cell type is a subclass.: dendritic cellCL:0000451
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: migratory DCs are a well described rare celltype relevant to mucosal biology that are increasingly being annotated in single cell atlases - they should have a cell ontology label!
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: LAMP3, IDO1, CCR7, CD40, CCL5
Canonical Marker Genes: LAMP3, CCR7, IDO1
Negative Marker Genes Genes expected to be absent, or expressed at a notably low level, in these cells, and whose absence supports the assignment of this cell annotation.: —
Rationale: LAMP3, CCR7, IDO1, CD40, CCL5, capture the antigen experienced, lymph node directed migratory DC state which has been repeatedly observed in barrier tissues
Rationale DOI: https://doi.org/10.1084/jem.20222129

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