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.

Inherited from hgca_celltype_v1

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