HCA Gut Cell Atlas v1 Stromal Lineage

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Cell Metadata

Fibroblasts Subserosal

Ontology Term: intestinal subserosal fibroblastCL:4052005
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.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: DPT, C7, POSTN
Canonical Marker Genes: POSTN, DPT, COL1A1
Rationale: Fibroblasts annotated as Subserosal are enriched for DPT, C7 and POSTN and tend to form deeper fibroblast clusters with lower dataset diversity (for example Stroma_8_0 and 8_1). We note that some clusters labeled as Subserosal in the original annotations appear in many biopsy-derived datasets, so we question whether they are truly subserosal versus generally deeper S3 fibroblasts. Do we need a deeper S3 fibroblast annotation? We therefore sometimes use the Intestinal Subserosal Fibroblasts and sometimes S3 term for DPT+/C7+/POSTN+ deeper fibroblasts while acknowledging that the exact boundary between subserosal and submucosal S3 fibroblasts is still being refined.

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: intestinal subserosal fibroblastCL:4052005
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.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: DPT, C7, POSTN
Canonical Marker Genes: POSTN, DPT, COL1A1
Rationale: Fibroblasts annotated as Subserosal are enriched for DPT, C7 and POSTN and tend to form deeper fibroblast clusters with lower dataset diversity (for example Stroma_8_0 and 8_1). We note that some clusters labeled as Subserosal in the original annotations appear in many biopsy-derived datasets, so we question whether they are truly subserosal versus generally deeper S3 fibroblasts. Do we need a deeper S3 fibroblast annotation? We therefore sometimes use the Intestinal Subserosal Fibroblasts and sometimes S3 term for DPT+/C7+/POSTN+ deeper fibroblasts while acknowledging that the exact boundary between subserosal and submucosal S3 fibroblasts is still being refined.

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