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

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Cell Metadata

Glial/fDC

Ontology Term: follicular dendritic cellCL:0000442
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: fDC
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.: CLU, CR2, CSTA, VIM
Canonical Marker Genes: CR2, CR1, FCER2
Rationale: These are definitely stromal cells based on CLU, VIM, CSTA, and probably glial cells based on very high expression of CLU, but they also have a definitive fDC marker in abundance: CR2

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: follicular dendritic cellCL:0000442
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: fDC
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.: CLU, CR2, CSTA, VIM
Canonical Marker Genes: CR2, CR1, FCER2
Rationale: These are definitely stromal cells based on CLU, VIM, CSTA, and probably glial cells based on very high expression of CLU, but they also have a definitive fDC marker in abundance: CR2

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/