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

pDC

Ontology Term

plasmacytoid dendritic cellCL:0000784

SynonymsTerms 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

CategoryClass of which the cell type is a subclass.

dendritic cellCL:0000451

Marker Gene EvidenceGene 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.

Inherited from celltype

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/