Human Gut Cell Atlas (HGCA) v1 - Epithelial Lineage

Intestinal Stem Cells (ISC)

Ontology Term: intestinal crypt stem cellCL:0002250
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: ISC, crypt base columnar cell
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.: LGR5, ASCL2, SMOC2, RGMB, CLDN3, TSPAN8, OLFM4
Canonical Marker Genes: LGR5, ASCL2, SMOC2
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: Crypt base stem cells of small and large intestines both display LGR5 and general stemness genes like OLFM4. These are defined in GCA in the area where early epithelial cells of the small and large intestines begin to overlap.

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