Human Gut Cell Atlas (HGCA) v1 - All Cells

CD4 Tfh

Ontology Term: T follicular helper cellCL:0002038
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: Tfh, follicular helper CD4 T cell
Category Class of which the cell type is a subclass.: CD4-positive, alpha-beta T cellCL:0000624
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: BCL6, CXCR5, CD40LG, CXCL13, FOXP3
Canonical Marker Genes: BCL6, CXCR5, PDCD1, FOXP3
Rationale: CD40LG and ICOS are used to annotate Tfh in this data. These are also found in larger clusters of CD4 naive cells

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