HCA Gut Cell Atlas v1 Stromal Lineage

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Cell Metadata

Fibroblasts Myofibroblasts

Ontology Term: myofibroblast cellCL:0000186
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.: ACTA2, TAGLN, DCN
Canonical Marker Genes: ACTA2, TAGLN, MYH11
Rationale: Myofibroblasts and SMCs could be mixed up in some places. I had used HHIF to annotated SMCs but in absense of GREM1/GREM2 it's possible these SMCs are really myofibroblasts.

Set of Labels Description: Cell annotations (Prelim annotation) are based on the finest possible label that could be used to describe each of the ~500 clusters found during integration and subclustering
Annotation Method: both
Algorithm Name: scVI
Algorithm Version: 1.3.2
Algorithm URL: https://github.com/scverse/scvi-tools

Ontology Term: myofibroblast cellCL:0000186
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.: ACTA2, TAGLN, DCN
Canonical Marker Genes: ACTA2, TAGLN, MYH11
Rationale: Myofibroblasts and SMCs could be mixed up in some places. I had used HHIF to annotated SMCs but in absense of GREM1/GREM2 it's possible these SMCs are really myofibroblasts.

Set of Labels Description: Cell annotations (Prelim annotation) are based on the finest possible label that could be used to describe each of the ~500 clusters found during integration and subclustering
Annotation Method: both
Algorithm Name: scVI
Algorithm Version: 1.3.2
Algorithm URL: https://github.com/scverse/scvi-tools