HCA Gut Cell Atlas v1 Myeloid Lineage

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Cell Metadata

Granulocytes Mast Cells

Ontology Term: mast cellCL:0000097
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: mucosal mast cell
Category Class of which the cell type is a subclass.: granulocyteCL:0000094
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CPA3, TPSB2, TPSAB1, CTSG, HPGDS, KIT
Canonical Marker Genes: KIT, TPSAB1, CPA3
Rationale: presence of KIT, FCER1A, FCER1G could point to matured Mast cells with chymase, something to look out for here. In general, CPA3 and tryptase (TPSAB*) genes are highly expressed and unique to mast cell populations, making them easy to annotate in gut data
Rationale DOI: 10.1182/bloodadvances.2022006969

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: mast cellCL:0000097
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: mucosal mast cell
Category Class of which the cell type is a subclass.: granulocyteCL:0000094
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CPA3, TPSB2, TPSAB1, CTSG, HPGDS, KIT
Canonical Marker Genes: KIT, TPSAB1, CPA3
Rationale: presence of KIT, FCER1A, FCER1G could point to matured Mast cells with chymase, something to look out for here. In general, CPA3 and tryptase (TPSAB*) genes are highly expressed and unique to mast cell populations, making them easy to annotate in gut data
Rationale DOI: 10.1182/bloodadvances.2022006969

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