Human Gut Cell Atlas (HGCA) v1 - Lymphoid

CD4 Th17

Ontology Term: T-helper 17 cellCL:0000899
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: Th17 CD4 T cell, Th17
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.: RORC, IL17A, IL22, IL21, CSF2, IL23R
Canonical Marker Genes: RORC, IL17A, CCR6
Negative Marker Genes Genes expected to be absent, or expressed at a notably low level, in these cells, and whose absence supports the assignment of this cell annotation.: —
Rationale: Since both ILC3s and Th17 express RORC and IL7R, these can be difficult to separate. Th17 were annotated when larger clusters of naive T cells showed a clear IL7R and RORC expressing subcluster

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