Achilles tendon atlas - muscle cells

Main

Cell Metadata

NEGR1hi COL15A1hi fibroblasts

Full Name: NEGR1hi COL15A1hi fibroblasts
Closest Ontology Term: skeletal muscle fibroblastCL:0011027
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.: No CL term for "universal fibroblast". These have specific transcriptomic signatures and spatial location in the muscle, but are transcriptionally similar to other universal fibroblasts. Extensively characterised in 10.1152/ajpcell.00838.2025
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: NEGR1, FBN1, COL15A1, GREB1L
Canonical Marker Genes: COL1A2, COL3A1, DCN
Rationale: This cell was annotated manually using canonical markers in the field (COL1A2, COL3A1, DCN). We noticed NEGR1, FBN1, COL15A1, GREB1L running differential expression. Spatial transcriptomics showed distribution in muscle, similar phenotype to "universal" fibroblast.
Rationale DOI: https://doi.org/10.1113/JP287812 https://doi.org/10.1096/fj.202300601RRR https://doi.org/10.1038/s41586-021-03549-5 https://doi.org/10.1038/s43587-024-00613-3

Set of Labels Description: Lineage annotations were determined by Louvain clustering at resolution 0.1. Each lineage (fibroblast, muscle, immune, stromal) was then subsetted and reclustered. Final annotation resolution was chosen according to expression of biological markers; smaller clusters were combined were appropriate
Annotation Method: manual

Full Name: NEGR1hi COL15A1hi fibroblasts
Closest Ontology Term: skeletal muscle fibroblastCL:0011027
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.: No CL term for "universal fibroblast". These have specific transcriptomic signatures and spatial location in the muscle, but are transcriptionally similar to other universal fibroblasts. Extensively characterised in 10.1152/ajpcell.00838.2025
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: NEGR1, FBN1, COL15A1, GREB1L
Canonical Marker Genes: COL1A2, COL3A1, DCN
Rationale: This cell was annotated manually using canonical markers in the field (COL1A2, COL3A1, DCN). We noticed NEGR1, FBN1, COL15A1, GREB1L running differential expression. Spatial transcriptomics showed distribution in muscle, similar phenotype to "universal" fibroblast.
Rationale DOI: https://doi.org/10.1113/JP287812 https://doi.org/10.1096/fj.202300601RRR https://doi.org/10.1038/s41586-021-03549-5 https://doi.org/10.1038/s43587-024-00613-3

Set of Labels Description: Lineage annotations were determined by Louvain clustering at resolution 0.1. Each lineage (fibroblast, muscle, immune, stromal) was then subsetted and reclustered. Final annotation resolution was chosen according to expression of biological markers; smaller clusters were combined were appropriate
Annotation Method: manual