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

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Cell Metadata

Endth/Mural

Ontology Term: mural cellCL:0008034
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.: perivascular cellCL:4033054
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: PLVAP, CLDN5, NOTCH3, PECAM1
Canonical Marker Genes: NOTCH3
Rationale: This cluster expresses PLVAP, PECAM1, and CLDN5, but when compared to other endothelial cells is quite distinct with high DE NOTCH3 - which points to mural/perivascular cells. Could be a doublet of mural / endothelial cells.

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: mural cellCL:0008034
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.: perivascular cellCL:4033054
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: PLVAP, CLDN5, NOTCH3, PECAM1
Canonical Marker Genes: NOTCH3
Rationale: This cluster expresses PLVAP, PECAM1, and CLDN5, but when compared to other endothelial cells is quite distinct with high DE NOTCH3 - which points to mural/perivascular cells. Could be a doublet of mural / endothelial cells.

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/