Human Gut Cell Atlas (HGCA) v1 - All Cells

Secretory Progenitors

Full Name: secretory progenitor cell
Closest Ontology Term: secretory epithelial cellCL:1100001
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: secretory TA, secretory progenitor
Category Class of which the cell type is a subclass.: epithelial cellCL:0000066
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: GCA supports an intermediate between TA/ISCs and mature, subtype differentiated secretory lineage cells like EEC progenitors or early goblet cells.
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: ATOH1, TFF3, CLCA1, HEPACAM2, ANXA13, PHLDA2, KLK1
Canonical Marker Genes: ATOH1, TFF3, CLCA1
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: Epithelial secretory lineage progenitors clearly separate from early absorptive lineages in the gut cell atlas. These appear to be on their way to goblet, paneth, or EEC fates, with treffoils (TFF3), KLK1, CLCA1, and clear proliferative markers. Overlaps with TA and goblet cells so could be clearer.

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