Human Gut Cell Atlas (HGCA) v1 - Epithelial Lineage

Transiently Amplifying Cells (TA)

Ontology Term: paneth cellCL:0000510
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: unknown
Category Class of which the cell type is a subclass.: epithelial cellCL:0000066
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: DEFA5, DEFA6, LYZ, PRSS2, ITLN2, REG3A, PLA2G2A
Canonical Marker Genes: DEFA5, LYZ, PLA2G2A
Rationale: Paneth cells are found mostly in small intestine and are identified here with defensins DEFA* alongside high PLA2G2A. These are even rarer than tuft 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