Skin fibroblast scRNA-seq atlas in health

Main

Summary

Feedback

Cell Metadata

cell_type

F2/3: Perivascular

Full Name: Perivascular (universal)
Closest Ontology Term: skin fibroblastCL:0002620
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.: CXCL12, APOE, EFEMP1, APOC1, C7, PLA2G2A, PPARG, MYOC, GDF10
Canonical Marker Genes: unknown
Rationale: LOCATION: Enriched in superficial and deep perivascular regions (F3 was only in superficial perivascular regions). GENE EXPRESSION: Highest expression of CXCL12, but CXCL12 expression is non-specific. Zhu et al. describe CXCL12+ fibroblasts as distinct to Universal fibroblasts. A subset expressed PPARG. This population also expressed F2: Universal markers. We speculate that it may represent a universal fibroblast population, especially as 1) it expressed F2 markers, 2) in neurofibroma, we observed F2/3: Perivascular fibroblasts, and trajectory inference suggested this population gave rise to F5: Schwann-like fibroblasts. SKIN-SPECIFIC NAME: Reticular pre-adipocyte. CROSS-TISSUE INSIGHTS: Similar gene expression was seen across tissues. In lung, this population was called Lipofibroblast. In gut, this population most resembled mLN stroma, which was reported to be an adipocyte stroma like population. In both cases, and consistent with skin data, there is a pre-adipocyte enrichment reported.
Rationale DOI: 10.1016/j.jid.2023.09.288 10.1038/s41586-021-03852-1 10.1038/s41591-023-02327-2

Inherited from cell_type

Set of Labels Description: Aim to harmonise skin fibroblast labels across studies in both health and disease. This specific dataset includes only healthy/non-lesional cells.
Annotation Method: manual

F2/3: Perivascular

Full Name: Perivascular (universal)
Closest Ontology Term: skin fibroblastCL:0002620
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.: CXCL12, APOE, EFEMP1, APOC1, C7, PLA2G2A, PPARG, MYOC, GDF10
Canonical Marker Genes: unknown
Rationale: LOCATION: Enriched in superficial and deep perivascular regions (F3 was only in superficial perivascular regions). GENE EXPRESSION: Highest expression of CXCL12, but CXCL12 expression is non-specific. Zhu et al. describe CXCL12+ fibroblasts as distinct to Universal fibroblasts. A subset expressed PPARG. This population also expressed F2: Universal markers. We speculate that it may represent a universal fibroblast population, especially as 1) it expressed F2 markers, 2) in neurofibroma, we observed F2/3: Perivascular fibroblasts, and trajectory inference suggested this population gave rise to F5: Schwann-like fibroblasts. SKIN-SPECIFIC NAME: Reticular pre-adipocyte. CROSS-TISSUE INSIGHTS: Similar gene expression was seen across tissues. In lung, this population was called Lipofibroblast. In gut, this population most resembled mLN stroma, which was reported to be an adipocyte stroma like population. In both cases, and consistent with skin data, there is a pre-adipocyte enrichment reported.
Rationale DOI: 10.1016/j.jid.2023.09.288 10.1038/s41586-021-03852-1 10.1038/s41591-023-02327-2

Inherited from cell_type

Set of Labels Description: Aim to harmonise skin fibroblast labels across studies in both health and disease. This specific dataset includes only healthy/non-lesional cells.
Annotation Method: manual