HCA Gut Cell Atlas v1 Myeloid Lineage

Main

Cell Metadata

DC 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
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: 10.1084/jem.20222129

Set of Labels Description: Cell annotations (Prelim annotation) are based on the finest possible label that could be used to describe each of the ~500 clusters found during integration and subclustering
Annotation Method: both
Algorithm Name: scVI
Algorithm Version: 1.3.2
Algorithm URL: https://github.com/scverse/scvi-tools

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
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: 10.1084/jem.20222129

Set of Labels Description: Cell annotations (Prelim annotation) are based on the finest possible label that could be used to describe each of the ~500 clusters found during integration and subclustering
Annotation Method: both
Algorithm Name: scVI
Algorithm Version: 1.3.2
Algorithm URL: https://github.com/scverse/scvi-tools