HCA Gut Cell Atlas v1 Lymphoid Lineage

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Cell Metadata

GC B Germinal Center

Ontology Term: germinal center B cellCL:0000844
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: germinal center B, B GC
Category Class of which the cell type is a subclass.: B cellCL:0000236
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CXCR4
Canonical Marker Genes: BCL6, CD38, CD10
Rationale: CXCR4 high b cells with no other evidence of light or dark zone markers. These had high mitochondrial content so may just be of too low quality to define

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: germinal center B cellCL:0000844
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: germinal center B, B GC
Category Class of which the cell type is a subclass.: B cellCL:0000236
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CXCR4
Canonical Marker Genes: BCL6, CD38, CD10
Rationale: CXCR4 high b cells with no other evidence of light or dark zone markers. These had high mitochondrial content so may just be of too low quality to define

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