HCA Gut Cell Atlas v1 Stromal Lineage

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Cell Metadata

Fibroblasts mLTo Cells (mesenchymal lymphoid tissue organizer cells)

Full Name: mesenchymal lymphoid tissue organizer fibroblast
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.: RANKL, CXCL14, TNFSF11
Canonical Marker Genes: TNFSF11, CXCL14, PDPN
Rationale: Clusters annotated as Fibroblasts mLTo Cells show expression of RANKL (TNFSF11), CXCL14 and other lymphoid-organizing genes in addition to a fibroblast matrix program, and Stroma_19_0 especially "could be mLTo because RANKL, CXCL14, TNFSF11". These cells likely represent a specialized organizer subset related to fibroblastic reticular cells but with stronger RANKL-driven lymphoid organizing functions. The population is relatively small and has moderate dataset diversity, consistent with tissue-restricted lymphoid niches, so we annotate it as a candidate mesenchymal lymphoid tissue organizer fibroblast class.

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: mesenchymal lymphoid tissue organizer fibroblast
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.: RANKL, CXCL14, TNFSF11
Canonical Marker Genes: TNFSF11, CXCL14, PDPN
Rationale: Clusters annotated as Fibroblasts mLTo Cells show expression of RANKL (TNFSF11), CXCL14 and other lymphoid-organizing genes in addition to a fibroblast matrix program, and Stroma_19_0 especially "could be mLTo because RANKL, CXCL14, TNFSF11". These cells likely represent a specialized organizer subset related to fibroblastic reticular cells but with stronger RANKL-driven lymphoid organizing functions. The population is relatively small and has moderate dataset diversity, consistent with tissue-restricted lymphoid niches, so we annotate it as a candidate mesenchymal lymphoid tissue organizer fibroblast class.

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