Submucosal Fibroblasts (S3)
Full Name
- submucosal fibroblast (S3)
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.- —
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.
Inherited from hgca_celltype_v1
- Set of Labels Description
- Cell annotations based on two rounds of subclustering with scVI integration, sample_id as batch key. Cell annotations were refined by expert feedback based on "prelim annotation" on CAP. Prelim annotation is renamed "hgca_celltype_v0" here and the feedback on the "prelim annotation" is available by selecting a previous version of the Integrated Human Gut Atlas on CAP.
- Annotation Method
- both
- Algorithm Name
- scIB
- Algorithm Version
- 1.2.1
- Algorithm URL
- https://github.com/theislab/scib
