Human Gut Cell Atlas (HGCA) v1 - Epithelial Lineage

Crypt Top Colonocytes

Full Name: crypt top colonocyte
Closest Ontology Term: colonocyteCL:1000347
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: colonocytes late, surface colonocyte
Category Class of which the cell type is a subclass.: colonocyteCL:1000347
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: No specific CL term for late/crypt top colonocytes - we separate these from other colonocytes to provide more resolution on epithelial subtypes
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CEACAM5, FABP1, AQP8, TFF1, SLC26A3, CEACAM7, GUCA2A
Canonical Marker Genes: CEACAM5, FABP1, AQP8
Rationale: Mature surface colonocytes at the crypt top, AQP8 high with SLC26A3, CEACAM5, CEACAM7, GUCA2A and TFF1.

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