HCA Gut Cell Atlas v1 Stromal Lineage

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Cell Metadata

Fibroblasts Crypt Top (S2B)

Ontology Term: crypt-top fibroblastCL:4052009
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.: subepithelial intestinal fibroblastCL:4052007
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: NRG1, NPY
Canonical Marker Genes: PDGFRA, VEGFD, NRG1
Rationale: S2B fibroblasts are positioned toward the crypt top or villus tip and are characterized by NRG1 and NPY, we also highlight VEGFD and TRPA1 as convincing markers of villus-tip subepithelial fibroblasts. Clusters annotated as Fibroblasts Crypt Top (S2B) (for example Stroma_1_1 and 12_1–12_4) show these markers along with the broader S2 program and are present in multiple datasets, albeit with varying mitochondrial content and dataset diversity. We therefore treat S2B as a robust positional subtype of S2, capturing villus-tip fibroblasts with strong NRG1/VEGFD/TRPA1 signatures.

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: crypt-top fibroblastCL:4052009
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.: subepithelial intestinal fibroblastCL:4052007
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: NRG1, NPY
Canonical Marker Genes: PDGFRA, VEGFD, NRG1
Rationale: S2B fibroblasts are positioned toward the crypt top or villus tip and are characterized by NRG1 and NPY, we also highlight VEGFD and TRPA1 as convincing markers of villus-tip subepithelial fibroblasts. Clusters annotated as Fibroblasts Crypt Top (S2B) (for example Stroma_1_1 and 12_1–12_4) show these markers along with the broader S2 program and are present in multiple datasets, albeit with varying mitochondrial content and dataset diversity. We therefore treat S2B as a robust positional subtype of S2, capturing villus-tip fibroblasts with strong NRG1/VEGFD/TRPA1 signatures.

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