Achilles tendon atlas - muscle cells

Main

Cell Metadata

NEGR1hi VCANhi fibroblasts

Full Name: NEGR1hi VCANhi fibroblasts
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.: No CL term for "fibroblast of peritenon". These have specific transcriptomic signatures and spatial location in the peritenon adjacent to blood vessels. Extensively characterised in 10.1152/ajpcell.00838.2025
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: COL1A2, COL3A1, DCN, NEGR1, DCLK1, VCAN
Canonical Marker Genes: COL1A2, COL3A1, DCN, NEGR1
Rationale: This cell was annotated manually using canonical markers in the field (COL1A2, COL3A1, DCN). We noticed NEGR1, DCLK1, VCAN running differential expression. Spatial transcriptomics shows specialised location in peritenon surrounding blood vessels.
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

Main

Cell Metadata

Full Name: NEGR1hi VCANhi fibroblasts
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.: No CL term for "fibroblast of peritenon". These have specific transcriptomic signatures and spatial location in the peritenon adjacent to blood vessels. Extensively characterised in 10.1152/ajpcell.00838.2025
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: COL1A2, COL3A1, DCN, NEGR1, DCLK1, VCAN
Canonical Marker Genes: COL1A2, COL3A1, DCN, NEGR1
Rationale: This cell was annotated manually using canonical markers in the field (COL1A2, COL3A1, DCN). We noticed NEGR1, DCLK1, VCAN running differential expression. Spatial transcriptomics shows specialised location in peritenon surrounding blood vessels.
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