Achilles tendon atlas - muscle cells

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Cell Metadata

MERTKhi LYVE1hi macrophages

Full Name: MERTKhi LYVE1hi macrophages
Closest Ontology Term: macrophageCL:0000235
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.: mononuclear phagocyteCL:0000113
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: No CL term for MERTKhi LYVE1hi macrophage or homeostatic tissue resident macrophage in synovium/tendon
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: MERTK, LYVE1, CD163, F13A1, MAMDC2
Canonical Marker Genes: MERTK, CD163, HMOX1, CTSB
Rationale: This cell was annotated manually using canonical markers in the field (MERTK, LYVE1, CD163). We noticed F13A1, MAMDC2 running differential expression. Similar to LYVE1pos homeostatic tissue resident macrophages in synovial tissue and tendon
Rationale DOI: https://doi.org/10.1038/s41584-022-00790-8 https://doi.org/10.1113/JP287812 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: MERTKhi LYVE1hi macrophages
Closest Ontology Term: macrophageCL:0000235
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.: mononuclear phagocyteCL:0000113
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: No CL term for MERTKhi LYVE1hi macrophage or homeostatic tissue resident macrophage in synovium/tendon
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: MERTK, LYVE1, CD163, F13A1, MAMDC2
Canonical Marker Genes: MERTK, CD163, HMOX1, CTSB
Rationale: This cell was annotated manually using canonical markers in the field (MERTK, LYVE1, CD163). We noticed F13A1, MAMDC2 running differential expression. Similar to LYVE1pos homeostatic tissue resident macrophages in synovial tissue and tendon
Rationale DOI: https://doi.org/10.1038/s41584-022-00790-8 https://doi.org/10.1113/JP287812 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