HCA Gut Cell Atlas v1 Stromal Lineage

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Cell Metadata

Fibroblasts Muscularis Propria

Full Name: muscularis propria fibroblast
Closest Ontology Term: fibroblastCL:0000057
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.: fibroblastCL:0000057
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Do we need a "deep S3 fibroblast" sublabel?
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: DPT, C7, KCNN3, CA8, PLCB4
Canonical Marker Genes: DPT, KCNN3, PDGFRA
Rationale: These fibroblasts are defined by DPT, C7, KCNN3, CA8 and PLCB4 expression and were initially annotated as Muscularis Propria fibroblasts in the hierarchy, but our experts repeatedly note that some clusters with this label are present in many biopsy-derived datasets, which is difficult to reconcile with a strictly muscularis-only population. Marker profiles suggest a deeper S3-like or muscle-adjacent fibroblast population, but current spatial evidence is insufficient to cleanly separate muscularis propria fibroblasts from subserosal or submucosal fibroblasts in the integrated data. We therefore keep this label as a provisional deeper muscle-layer fibroblast class with moderate confidence and flag the spatial assignment as uncertain. Do we need a "deep S3" sub-label?

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

Full Name: muscularis propria fibroblast
Closest Ontology Term: fibroblastCL:0000057
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.: fibroblastCL:0000057
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Do we need a "deep S3 fibroblast" sublabel?
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: DPT, C7, KCNN3, CA8, PLCB4
Canonical Marker Genes: DPT, KCNN3, PDGFRA
Rationale: These fibroblasts are defined by DPT, C7, KCNN3, CA8 and PLCB4 expression and were initially annotated as Muscularis Propria fibroblasts in the hierarchy, but our experts repeatedly note that some clusters with this label are present in many biopsy-derived datasets, which is difficult to reconcile with a strictly muscularis-only population. Marker profiles suggest a deeper S3-like or muscle-adjacent fibroblast population, but current spatial evidence is insufficient to cleanly separate muscularis propria fibroblasts from subserosal or submucosal fibroblasts in the integrated data. We therefore keep this label as a provisional deeper muscle-layer fibroblast class with moderate confidence and flag the spatial assignment as uncertain. Do we need a "deep S3" sub-label?

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