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

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Cell Metadata

pDC

Ontology Term: plasmacytoid dendritic cellCL:0000784
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: IPC, lymphoid dendritic cell, interferon-producing cell, plasmacytoid T cell, pDC, type 2 DC, DC2, plasmacytoid monocyte, T-associated plasma cell
Category Class of which the cell type is a subclass.: dendritic cellCL:0000451
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD74, HLA-DRA, HLA-DRB, IL3RA
Canonical Marker Genes: IL3RA, HLA-DR, CD74
Rationale: This is a small cluster that shows antigen presentation machinery as well as distinct expression of IL3RA, a canonical pDC marker.

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: plasmacytoid dendritic cellCL:0000784
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: IPC, lymphoid dendritic cell, interferon-producing cell, plasmacytoid T cell, pDC, type 2 DC, DC2, plasmacytoid monocyte, T-associated plasma cell
Category Class of which the cell type is a subclass.: dendritic cellCL:0000451
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD74, HLA-DRA, HLA-DRB, IL3RA
Canonical Marker Genes: IL3RA, HLA-DR, CD74
Rationale: This is a small cluster that shows antigen presentation machinery as well as distinct expression of IL3RA, a canonical pDC marker.

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/