HCA Gut Cell Atlas v1 Stromal Lineage

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Cell Metadata

Fibroblasts Submucosal (aka Crypt Support/Trophocytes/S3)

Full Name: submucosal fibroblast (S3)
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.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: GREM1, C7, OLFM4, PTGS2, THY1, SEMA3A, GLI1
Canonical Marker Genes: RSPO3, GREM1, PDGFRA
Rationale: Submucosal S3 fibroblasts occupy deeper layers and crypt base regions and are enriched for GREM1, C7, OLFM4, PTGS2, THY1, SEMA3A and GLI1, consistent with crypt-support or trophocyte roles. Cluster-level annotations describe RSPO3, GREM1, DCN and C3 as strong markers of submucosal fibroblasts (for example Stroma_2_0) and we note that S3 populations have lower dataset diversity and appear deeper than lamina propria fibroblasts, especially in resection-derived data. Multiple clusters labeled as Fibroblasts Submucosal (aka Crypt Support/Trophocytes/S3) recur with similar signatures, supporting a distinct S3 fibroblast class even though a dedicated CL term is still needed.

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: submucosal fibroblast (S3)
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.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: GREM1, C7, OLFM4, PTGS2, THY1, SEMA3A, GLI1
Canonical Marker Genes: RSPO3, GREM1, PDGFRA
Rationale: Submucosal S3 fibroblasts occupy deeper layers and crypt base regions and are enriched for GREM1, C7, OLFM4, PTGS2, THY1, SEMA3A and GLI1, consistent with crypt-support or trophocyte roles. Cluster-level annotations describe RSPO3, GREM1, DCN and C3 as strong markers of submucosal fibroblasts (for example Stroma_2_0) and we note that S3 populations have lower dataset diversity and appear deeper than lamina propria fibroblasts, especially in resection-derived data. Multiple clusters labeled as Fibroblasts Submucosal (aka Crypt Support/Trophocytes/S3) recur with similar signatures, supporting a distinct S3 fibroblast class even though a dedicated CL term is still needed.

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