Crypt Top Fibroblasts (S2B)
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
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.
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
