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

Fibro

Ontology Term: fibroblastCL:0000057
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: mesenchymal cells, stromal cells
Category Class of which the cell type is a subclass.: stromal cellCL:0000499
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: PDGFRA, PDGFRB, VIM, ADAMDEC1, LUM
Canonical Marker Genes: VIM, FN1, COL1A1, P4HA1, FAP
Negative Marker Genes Genes expected to be absent, or expressed at a notably low level, in these cells, and whose absence supports the assignment of this cell annotation.: —
Rationale: VIM - mesenchymal origin ADAMDEC1 - often seen in gut fibroblasts PDGFRA/B - fibroblast migration markers

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/