HCA Gut Cell Atlas v1 Stromal Lineage

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Cell Metadata

Glia Mucosal/Type III

Ontology Term: type 3 mucosal gliaCL:4047045
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.: glial cellCL:0000125
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: RELN, MBP, PLLP
Canonical Marker Genes: RELN, MBP, PLLP
Rationale: Mucosal type III glia are defined by RELN, MBP and PLLP expression together with canonical glial markers, and are the predominant glial population in mucosa/submucosa-enriched samples. Several clusters annotated as Glia Mucosal/Type III recur across many datasets, suggesting a conserved mucosal glial state. We therefore treat this as a robust mucosal glial subtype with moderate-confidence mapping to the CL type 3 mucosal glia term. 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 3 mucosal gliaCL:4047045
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.: glial cellCL:0000125
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: RELN, MBP, PLLP
Canonical Marker Genes: RELN, MBP, PLLP
Rationale: Mucosal type III glia are defined by RELN, MBP and PLLP expression together with canonical glial markers, and are the predominant glial population in mucosa/submucosa-enriched samples. Several clusters annotated as Glia Mucosal/Type III recur across many datasets, suggesting a conserved mucosal glial state. We therefore treat this as a robust mucosal glial subtype with moderate-confidence mapping to the CL type 3 mucosal glia term. 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