HCA Gut Cell Atlas v1 Myeloid Lineage

Main

Cell Metadata

Granulocytes

Ontology Term: granulocyteCL:0000094
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: polymorphonuclear leukocytes, PMN, PML, PMNL
Category Class of which the cell type is a subclass.: myeloid cellCL:0000763
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CLC, IL4, CPA3, FCGR2B
Canonical Marker Genes: CLC, FCGR3B, S100A12
Rationale: Expresses granulocytic effectors including CLC, IL4 inducible modules, CPA3, and Fcγ receptor associated genes, hint at polymorphonuclear granulocytes distinct from mast cells. Obviously a big ? given difficulty in picking these up with typical droplet-based protocols
Rationale DOI: 10.1038/s41586-021-03852-1

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

Ontology Term: granulocyteCL:0000094
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: polymorphonuclear leukocytes, PMN, PML, PMNL
Category Class of which the cell type is a subclass.: myeloid cellCL:0000763
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CLC, IL4, CPA3, FCGR2B
Canonical Marker Genes: CLC, FCGR3B, S100A12
Rationale: Expresses granulocytic effectors including CLC, IL4 inducible modules, CPA3, and Fcγ receptor associated genes, hint at polymorphonuclear granulocytes distinct from mast cells. Obviously a big ? given difficulty in picking these up with typical droplet-based protocols
Rationale DOI: 10.1038/s41586-021-03852-1

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