Human Gut Cell Atlas (HGCA) v1 - Lymphoid Lineage

CD8 TRM

Ontology Term: Tc17 cellCL:0002128
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: TRM, tissue resident memory CD8 T cell
Category Class of which the cell type is a subclass.: CD8-positive, alpha-beta T cellCL:0000625
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD8A, CD8B, ITGAE, CD69, ITGA1, RORA
Canonical Marker Genes: ITGAE, CD69, ITGA1
Rationale: ITGAE and RORA point to granzyme positive t resident memory populations, and clusters of these tend to be more unique to certain sections of the gut, driving down the number of datasets they are found in (dataset diversity metric)
Rationale DOI: https://doi.org/10.1038/s41591-020-1003-4

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