HCA Gut Cell Atlas v1 Stromal Lineage

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Cell Metadata

Fibroblastic reticular cells

Ontology Term: fibroblastic reticular cellCL:0009101
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.: CCL19, CCL21, TNFSF13B, CXCL13,
Canonical Marker Genes: PDPN, CXCL13, CCL19
Rationale: Fibroblastic reticular cells are defined by expression of CCL19, CCL21, TNFSF13B and CXCL13 and cluster within lymphoid-enriched regions, consistent with FRCs organizing lymphoid tissue. Multiple clusters labeled as Fibroblastic reticular cells show similar marker profiles across datasets and samples, while a related cluster (Stroma_19_0) expresses RANKL and CXCL14 and may correspond to mesenchymal lymphoid tissue organizer cells. We note that FRC and mLTo-like states have some overlap. we annotate them with the intestinal fibroblastic reticular cell term and note the close relationship to mLTo.

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: fibroblastic reticular cellCL:0009101
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.: CCL19, CCL21, TNFSF13B, CXCL13,
Canonical Marker Genes: PDPN, CXCL13, CCL19
Rationale: Fibroblastic reticular cells are defined by expression of CCL19, CCL21, TNFSF13B and CXCL13 and cluster within lymphoid-enriched regions, consistent with FRCs organizing lymphoid tissue. Multiple clusters labeled as Fibroblastic reticular cells show similar marker profiles across datasets and samples, while a related cluster (Stroma_19_0) expresses RANKL and CXCL14 and may correspond to mesenchymal lymphoid tissue organizer cells. We note that FRC and mLTo-like states have some overlap. we annotate them with the intestinal fibroblastic reticular cell term and note the close relationship to mLTo.

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