Human Gut Cell Atlas (HGCA) v1 - Epithelial Lineage

Lower Crypt Colonocytes

Ontology Term: early colonocyteCL:4047018
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: colonocytes early, lower crypt colonocyte
Category Class of which the cell type is a subclass.: colonocyteCL:1000347
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: LEFTY1, ADH1C
Canonical Marker Genes: LEFTY1, ADH1C
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: Colonocytes down in the lower crypt. Absorptive markers like LGALS4, CA2, FABP1 and SLC26A2 are up with LEFTY1 and ADH1C, but AQP8 is still missing, which points to an early crypt-base colonocyte that hasn't differentiated yet.

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