HCA Gut Cell Atlas v1 Myeloid Lineage

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Cell Metadata

Fibroblasts Follicular Dendritic Cells (fDC)

Ontology Term: follicular dendritic cellCL:0000442
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: fDCs
Category Class of which the cell type is a subclass.: fibroblastCL:0000057
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CR1, CR2, CXCL13, TNFSF13B
Canonical Marker Genes: CR1, CR2, CXCL13
Rationale: Displays CR1, CR2, CXCL13, TNFSF13B, and complement receptor driven antigen retention machinery. These also express stroma lineage markers, making them easy to annotate within the myeloid lineage.
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: follicular dendritic cellCL:0000442
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: fDCs
Category Class of which the cell type is a subclass.: fibroblastCL:0000057
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CR1, CR2, CXCL13, TNFSF13B
Canonical Marker Genes: CR1, CR2, CXCL13
Rationale: Displays CR1, CR2, CXCL13, TNFSF13B, and complement receptor driven antigen retention machinery. These also express stroma lineage markers, making them easy to annotate within the myeloid lineage.
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