Human Gut Cell Atlas (HGCA) v1 - Myeloid Lineage

Classical Monocytes

Ontology Term: classical monocyteCL:0000860
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: CD14+ monocyte, inflammatory monocyte, monocyte
Category Class of which the cell type is a subclass.: monocyteCL:0000576
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: VCAN, FCN1, S100A8, S100A9
Canonical Marker Genes: VCAN, FCN1, S100A8
Rationale: FCN1, VCAN, S100A8, S100A9 and LYZ. classical monocytes performing inflammatory role, these can mix with M1 macrophages, which we did not annotate

Set of Labels Description: Cell annotations based on two rounds of subclustering with scVI integration, sample_id as batch key. Cell annotations were refined by expert feedback based on "prelim annotation" on CAP. Prelim annotation is renamed "hgca_celltype_v0" here and the feedback on the "prelim annotation" is available by selecting a previous version of the Integrated Human Gut Atlas on CAP.
Annotation Method: both
Algorithm Name: scIB
Algorithm Version: 1.2.1
Algorithm URL: https://github.com/theislab/scib