HCA Gut Cell Atlas v1 Stromal Lineage

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Cell Metadata

Glia Myenteric Plexus / Type I

Ontology Term: type 1 myenteric plexus gliaCL:4047042
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.: type I enteric glial cellCL:4047047
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: TF, BCAN, CACLB
Canonical Marker Genes: BCAN, TF, GJB1
Rationale: Myenteric plexus type I glia are identified by TF, BCAN and CACLB expression on top of a pan-glial program, and occupy clusters that align with deeper muscularis propria / submucosal regions in the integrated object. These clusters are present across datasets with full-thickness or muscularis-enriched sampling, consistent with myenteric plexus localization. The glial subtypes performed poorly in reference mapping benchmarks, so a lesser resolution is likely best for the data currently. Annotation experts also point to less confidence in glial subtypes

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: type 1 myenteric plexus gliaCL:4047042
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.: type I enteric glial cellCL:4047047
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: TF, BCAN, CACLB
Canonical Marker Genes: BCAN, TF, GJB1
Rationale: Myenteric plexus type I glia are identified by TF, BCAN and CACLB expression on top of a pan-glial program, and occupy clusters that align with deeper muscularis propria / submucosal regions in the integrated object. These clusters are present across datasets with full-thickness or muscularis-enriched sampling, consistent with myenteric plexus localization. The glial subtypes performed poorly in reference mapping benchmarks, so a lesser resolution is likely best for the data currently. Annotation experts also point to less confidence in glial subtypes

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