HCA Gut Cell Atlas v1 Stromal Lineage

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Cell Metadata

Glia Muscularis propria/Type IV

Ontology Term: type 4 muscularis propria gliaCL:4047048
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.: SLC5A7, APOD, KCNS3
Canonical Marker Genes: SLC5A7, APOD, KCNS3
Rationale: This label captures glia associated with the muscularis propria that show markers such as SLC5A7, APOD and KCNS3 in addition to a core glial program. These clusters are enriched in full-thickness specimens with abundant muscle, and rare or absent in superficial biopsies, consistent with a muscularis propria 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 4 muscularis propria gliaCL:4047048
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.: SLC5A7, APOD, KCNS3
Canonical Marker Genes: SLC5A7, APOD, KCNS3
Rationale: This label captures glia associated with the muscularis propria that show markers such as SLC5A7, APOD and KCNS3 in addition to a core glial program. These clusters are enriched in full-thickness specimens with abundant muscle, and rare or absent in superficial biopsies, consistent with a muscularis propria 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