HCA Gut Cell Atlas v1 Epithelial Lineage

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Cell Metadata

Secretory TA

Full Name: Transiently amplifying cells with predominant secretory signature
Closest Ontology Term: transit amplifying cellCL:0009010
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: unknown
Category Class of which the cell type is a subclass.: transit amplifying cellCL:0009010
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Since absorptive epithelial cells lay on a continuum, it's not clear if or how we should have subdivisions of epithelial subtypes. We argue it could be useful for high-res compositional analysis to have some type of subdivision.
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: ATOH1, TFF3, CLCA1, HEPACAM2, ANXA13, PHLDA2, KLK1
Canonical Marker Genes: ATOH1, HEPACAM2, ANXA13
Rationale: TA biased towards secretory fate, we also define these with distinct differentiation markers HEPACAM2 and ANXA13

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: algorithmic

Full Name: Transiently amplifying cells with predominant secretory signature
Closest Ontology Term: transit amplifying cellCL:0009010
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: unknown
Category Class of which the cell type is a subclass.: transit amplifying cellCL:0009010
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Since absorptive epithelial cells lay on a continuum, it's not clear if or how we should have subdivisions of epithelial subtypes. We argue it could be useful for high-res compositional analysis to have some type of subdivision.
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: ATOH1, TFF3, CLCA1, HEPACAM2, ANXA13, PHLDA2, KLK1
Canonical Marker Genes: ATOH1, HEPACAM2, ANXA13
Rationale: TA biased towards secretory fate, we also define these with distinct differentiation markers HEPACAM2 and ANXA13

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: algorithmic