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

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Cell Metadata

Endth

Ontology Term: endothelial cellCL:0000115
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: endotheliocyte
Category Class of which the cell type is a subclass.: epithelial cellCL:0000066
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: VWF, CLDN5, PECAM1
Canonical Marker Genes: VWF, PECAM1, CLDN5
Rationale: Based on PECAM1, PLVAP, and CLDN5 expression, these are endothelial cells, but compared to other endothelial clusters, these are high for mitochondrial and housekeeping genes - they seem to be a lower quality cluster of cells which is why we give them a lower resolution annotation

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: endothelial cellCL:0000115
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: endotheliocyte
Category Class of which the cell type is a subclass.: epithelial cellCL:0000066
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: VWF, CLDN5, PECAM1
Canonical Marker Genes: VWF, PECAM1, CLDN5
Rationale: Based on PECAM1, PLVAP, and CLDN5 expression, these are endothelial cells, but compared to other endothelial clusters, these are high for mitochondrial and housekeeping genes - they seem to be a lower quality cluster of cells which is why we give them a lower resolution annotation

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/