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

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Cell Metadata

EC

Ontology Term: epithelial cellCL:0000066
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: epitheliocyte
CategoryClass of which the cell type is a subclass.: epithelial cellCL:0000066
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: KRT20, KRT19, EPCAM, ELF3, S100G
Canonical Marker Genes: KRT19, EPCAM
Rationale: Epithelial cells of the ileum are marked by keratins and S100G, a marker of the villus. In this dataset, we only mark epithelial stem cells, proliferating epithelial cells, and the rest of the epithelial cells as individual groups.

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 cellCL:0000066
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: epitheliocyte
CategoryClass of which the cell type is a subclass.: epithelial cellCL:0000066
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: KRT20, KRT19, EPCAM, ELF3, S100G
Canonical Marker Genes: KRT19, EPCAM
Rationale: Epithelial cells of the ileum are marked by keratins and S100G, a marker of the villus. In this dataset, we only mark epithelial stem cells, proliferating epithelial cells, and the rest of the epithelial cells as individual groups.

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/