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

Main

Cell Metadata

Fibro/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.: VIM, CR2, CR1, FCER2, CXCL13
Canonical Marker Genes: CR1, CR2, FCER2, FDC-SP
Rationale: These a vimentin-expression stromal cells, (which is why we call them fibroblasts), which have clear expression of CR1, CR2, and FCER2, placing them firmly as fDCs, despite how small a cluster they are!

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.: VIM, CR2, CR1, FCER2, CXCL13
Canonical Marker Genes: CR1, CR2, FCER2, FDC-SP
Rationale: These a vimentin-expression stromal cells, (which is why we call them fibroblasts), which have clear expression of CR1, CR2, and FCER2, placing them firmly as fDCs, despite how small a cluster they are!

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/