Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade

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Cell Metadata

EpithStem

Ontology Term: epithelial fate stem cellCL:0000036
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: epithelial stem cell
CategoryClass of which the cell type is a subclass.: stem cellCL:0000034
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: OLFM4, KRT8, KRT18, EPCAM, ASCL2
Canonical Marker Genes: ASCL2, EPCAM
Rationale: These are epithelial cells based on EPCAM and OLFM4, but also are highly expressing both ASCL2, a canonical intestinal epithelial stem cell marker, and SOX4 which also points to this categorization.

Set of Labels Description: In this paper we used an automated iterative subclustering algorithm to find hundreds of cell state clusters, after which we merged unsupported clusters and annotated each resulting cluster with a better-known cell subtype. The high-res cell state clusters are annotated as subtype.gene1.gene2, so in some cases we didn't directly name some commonly named subtypes, such as pericytes. When we run DE on the resulting subtypes, we find many canonical and scRNA-suggested marker genes.
Annotation Method: both
Algorithm Name: ARBOL
Algorithm Version: v1.0
Algorithm URL: https://github.com/jo-m-lab/ARBOL/

Ontology Term: epithelial fate stem cellCL:0000036
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: epithelial stem cell
CategoryClass of which the cell type is a subclass.: stem cellCL:0000034
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: OLFM4, KRT8, KRT18, EPCAM, ASCL2
Canonical Marker Genes: ASCL2, EPCAM
Rationale: These are epithelial cells based on EPCAM and OLFM4, but also are highly expressing both ASCL2, a canonical intestinal epithelial stem cell marker, and SOX4 which also points to this categorization.

Set of Labels Description: In this paper we used an automated iterative subclustering algorithm to find hundreds of cell state clusters, after which we merged unsupported clusters and annotated each resulting cluster with a better-known cell subtype. The high-res cell state clusters are annotated as subtype.gene1.gene2, so in some cases we didn't directly name some commonly named subtypes, such as pericytes. When we run DE on the resulting subtypes, we find many canonical and scRNA-suggested marker genes.
Annotation Method: both
Algorithm Name: ARBOL
Algorithm Version: v1.0
Algorithm URL: https://github.com/jo-m-lab/ARBOL/