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

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Cell Metadata

Macrophage

Ontology Term: macrophageCL:0000235
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: tissue macrophage, histiocyte, M2 macrophage (LYVE1+ subset)
Category Class of which the cell type is a subclass.: group 3 innate lymphoid cell, humanCL:0001078
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD163, C1QA, F13A1, LYVE1, APOE, APOC1, FABP5, SPP1, TREM2
Canonical Marker Genes: CD68, CD163, MRC1
Rationale: This cell was annotated with CellTypist using the Immune_All_Low model trained on the cross-tissue immune cell atlas (DOI: 10.1126/science.abl5197) pan-macrophage markers: CD163, C1QC and subtype markers for LYVE1 (LYVE1, F13A1), HLAIIhi (APOE, APOC1, FABP5) and Lipid-associated macrophages (SPP1, TREM2).
Rationale DOI: 10.1126/science.abl5197 0.1126/science.aau0964 10.1016/j.cell.2019.05.054

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

Ontology Term: macrophageCL:0000235
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: tissue macrophage, histiocyte, M2 macrophage (LYVE1+ subset)
Category Class of which the cell type is a subclass.: group 3 innate lymphoid cell, humanCL:0001078
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD163, C1QA, F13A1, LYVE1, APOE, APOC1, FABP5, SPP1, TREM2
Canonical Marker Genes: CD68, CD163, MRC1
Rationale: This cell was annotated with CellTypist using the Immune_All_Low model trained on the cross-tissue immune cell atlas (DOI: 10.1126/science.abl5197) pan-macrophage markers: CD163, C1QC and subtype markers for LYVE1 (LYVE1, F13A1), HLAIIhi (APOE, APOC1, FABP5) and Lipid-associated macrophages (SPP1, TREM2).
Rationale DOI: 10.1126/science.abl5197 0.1126/science.aau0964 10.1016/j.cell.2019.05.054

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