Human intercostal skeletal muscle aging atlas (scRNA-seq and snRNA-seq, young vs aged)

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Cell Metadata

MF-Isc(fg)

Full Name: Type I myofiber fragment (single-cell / scRNA-seq)
Closest Ontology Term: slow muscle cellCL:0000189
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: MF-I fragment (sc), type I sarcoplasm fragment
Category Class of which the cell type is a subclass.: extrafusal muscle fiberCL:0008046
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Not a distinct cell type — technical artefact: type I (slow-twitch) myofiber sarcoplasmic fragments captured in scRNA-seq libraries. Should NOT receive its own CL term; reusing CL:0000189 (slow muscle cell) is appropriate. Enriched slow-type markers (TNNT1, MYH7) as well as abundant cytoplasmic myofiber transcripts (CKM, MB and COX6C).
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: MYH7, TNNT1, CKM, MB, COX6C
Canonical Marker Genes: MYH7, TNNT1, MYL2
Rationale: This cell was annotated using slow-twitch myofiber markers (MYH7, TNNT1) with abundant cytoplasmic transcripts (CKM, MB and COX6C) showing increased expression compared to fast-twitch nuclei as well as ratio of spliced transcripts (~97%) which indicates this cell likely respresents a myofiber fragment captured in scRNA-seq libraries due to incomplete dissociation.

Set of Labels Description: Displayed cell annotations represent 43 coarse cell type clusters derived using combined manual and automatic annotation using CellTypist.
Annotation Method: both
Algorithm Name: CellTypist
Algorithm Version: v1.7
Algorithm URL: https://github.com/Teichlab/celltypist

Full Name: Type I myofiber fragment (single-cell / scRNA-seq)
Closest Ontology Term: slow muscle cellCL:0000189
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: MF-I fragment (sc), type I sarcoplasm fragment
Category Class of which the cell type is a subclass.: extrafusal muscle fiberCL:0008046
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Not a distinct cell type — technical artefact: type I (slow-twitch) myofiber sarcoplasmic fragments captured in scRNA-seq libraries. Should NOT receive its own CL term; reusing CL:0000189 (slow muscle cell) is appropriate. Enriched slow-type markers (TNNT1, MYH7) as well as abundant cytoplasmic myofiber transcripts (CKM, MB and COX6C).
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: MYH7, TNNT1, CKM, MB, COX6C
Canonical Marker Genes: MYH7, TNNT1, MYL2
Rationale: This cell was annotated using slow-twitch myofiber markers (MYH7, TNNT1) with abundant cytoplasmic transcripts (CKM, MB and COX6C) showing increased expression compared to fast-twitch nuclei as well as ratio of spliced transcripts (~97%) which indicates this cell likely respresents a myofiber fragment captured in scRNA-seq libraries due to incomplete dissociation.

Set of Labels Description: Displayed cell annotations represent 43 coarse cell type clusters derived using combined manual and automatic annotation using CellTypist.
Annotation Method: both
Algorithm Name: CellTypist
Algorithm Version: v1.7
Algorithm URL: https://github.com/Teichlab/celltypist