HCA Gut Cell Atlas v1 Stromal Lineage

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Cell Metadata

Fibroblasts Crypt Bottom (S2A)

Ontology Term: crypt-bottom fibroblastCL:4052008
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.: VSTM2A
Canonical Marker Genes: PDGFRA, VSTM2A, POSTN
Rationale: S2A fibroblasts sit near the crypt base and are enriched for VSTM2A together with PDGFRA, BMP4, WNT5A, POSTN and other S2 markers. Several clusters annotated as Fibroblasts Crypt Bottom (S2A) show very low dataset diversity but reproducible expression of POSTN, F3 and BMPs, and differences between individual S2A annotation clusters are subtle (see annotation_cluster) and may largely reflect activation and quality flags (for example high mitochondrial content) rather than true subtypes. We therefore annotate a single S2A cell type corresponding to crypt-bottom fibroblasts with high-confidence positional identity and variable activation 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-bottom fibroblastCL:4052008
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.: VSTM2A
Canonical Marker Genes: PDGFRA, VSTM2A, POSTN
Rationale: S2A fibroblasts sit near the crypt base and are enriched for VSTM2A together with PDGFRA, BMP4, WNT5A, POSTN and other S2 markers. Several clusters annotated as Fibroblasts Crypt Bottom (S2A) show very low dataset diversity but reproducible expression of POSTN, F3 and BMPs, and differences between individual S2A annotation clusters are subtle (see annotation_cluster) and may largely reflect activation and quality flags (for example high mitochondrial content) rather than true subtypes. We therefore annotate a single S2A cell type corresponding to crypt-bottom fibroblasts with high-confidence positional identity and variable activation 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