Single-nucleus transcriptomic profiling of human skeletal muscle from healthy adults

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Cell Metadata

Fibroblast

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.: stromal cellCL:0000499
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: DCN, COL6A3, COL1A1, COL3A1, LAMA2, LAMC1, NID1, APOD
Canonical Marker Genes: PDGFRA, ABCA8, CFD, COL6A3, DCN, FBN1, GALNT15, GPX3, LAMC1, NEGR1, NOVA1, TGFBR2, TGFBR3
Rationale: Fibroblasts were identified by a strong ECM/stromal program, with high DCN, COL6A3, LAMA2, LAMC1, NID1, and APOD, and clear differential upregulation of matrix components such as DCN and COL6A3.

Set of Labels Description: Cell annotations were generated with scType using marker genes curated from related publications, and then manually reviewed and adjusted based on the top highly variable genes in each Leiden cluster.
Annotation Method: both
Algorithm Name: scType
Algorithm Version: v1
Algorithm URL: https://github.com/IanevskiAleksandr/sc-type

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.: stromal cellCL:0000499
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: DCN, COL6A3, COL1A1, COL3A1, LAMA2, LAMC1, NID1, APOD
Canonical Marker Genes: PDGFRA, ABCA8, CFD, COL6A3, DCN, FBN1, GALNT15, GPX3, LAMC1, NEGR1, NOVA1, TGFBR2, TGFBR3
Rationale: Fibroblasts were identified by a strong ECM/stromal program, with high DCN, COL6A3, LAMA2, LAMC1, NID1, and APOD, and clear differential upregulation of matrix components such as DCN and COL6A3.

Set of Labels Description: Cell annotations were generated with scType using marker genes curated from related publications, and then manually reviewed and adjusted based on the top highly variable genes in each Leiden cluster.
Annotation Method: both
Algorithm Name: scType
Algorithm Version: v1
Algorithm URL: https://github.com/IanevskiAleksandr/sc-type