HCA Gut Cell Atlas v1 Myeloid Lineage

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Cell Metadata

Macrophages Cycling

Ontology Term: cycling macrophageCL:4033076
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: proliferating macrophages
Category Class of which the cell type is a subclass.: macrophageCL:0000235
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: NRG1, KLF4, GPR183, C1QB, CCL3L3, MS4A6A, MS4A7, CXCL2, MKI67, STMN, H2*
Canonical Marker Genes: MKI67, STMN1, H2AFZ
Rationale: Coexpression of MKI67, STMN1, and often histones with macrophage core genes (C1QB, MS4A7) identify proliferating macrophages engaged in local self renewal or inflammatory expansion
Rationale DOI: 10.1016/j.cell.2019.06.029

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: cycling macrophageCL:4033076
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: proliferating macrophages
Category Class of which the cell type is a subclass.: macrophageCL:0000235
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: NRG1, KLF4, GPR183, C1QB, CCL3L3, MS4A6A, MS4A7, CXCL2, MKI67, STMN, H2*
Canonical Marker Genes: MKI67, STMN1, H2AFZ
Rationale: Coexpression of MKI67, STMN1, and often histones with macrophage core genes (C1QB, MS4A7) identify proliferating macrophages engaged in local self renewal or inflammatory expansion
Rationale DOI: 10.1016/j.cell.2019.06.029

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