Human Gut Cell Atlas (HGCA) v1 - Stromal Lineage

Glia

Ontology Term: glial cellCL:0000125
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: unknown
Category Class of which the cell type is a subclass.: stromal cellCL:0000499
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: NRXN1, S100B, SOX10, CDH19, CRYAB, PLP1, SPP1, FXYD1
Canonical Marker Genes: NRXN1, S100B, SOX10
Rationale: Enteric glia with S100B, PLP1, SOX10, NRXN1 and CRYAB. We collapsed higher resolution enteric glial subtypes (plexus versus enervating) as differential expression and markers were not clear enough, and mapping benchmark showed low generalization across datasets. There could still be hidden heterogeneity here.

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