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

Plsma/IgM

Ontology Term

IgM plasma cellCL:0000986

SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.

unknown

CategoryClass of which the cell type is a subclass.

plasma cellCL:0000786

Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.

IGHM, JCHAIN, MZB1, SSR4

Canonical Marker Genes

IGHM, JCHAIN, CD138, HLA

Rationale

These are clear plasma cells of B provenance based on SSR4/JCHAIN/MZB1 expression and their most differentially expressed genes is IGHM

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/