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

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Cell Metadata

cDC2

Ontology Term: CD1c-positive myeloid dendritic cellCL:0002399
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: cDC2, type 2 conventional dendritic cell
Category Class of which the cell type is a subclass.: myeloid dendritic cellCL:0000782
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD1C, CLEC10A, HLA-DPB1, HLA-DRA
Canonical Marker Genes: CD1C, ITGAX
Rationale: This cluster shows many HLA molecules compared to all other clusters, but when compared to only other myeloid clusters, CD1C comes to the top of the list, and this is the canonical marker for cDC2's.

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: CD1c-positive myeloid dendritic cellCL:0002399
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: cDC2, type 2 conventional dendritic cell
Category Class of which the cell type is a subclass.: myeloid dendritic cellCL:0000782
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD1C, CLEC10A, HLA-DPB1, HLA-DRA
Canonical Marker Genes: CD1C, ITGAX
Rationale: This cluster shows many HLA molecules compared to all other clusters, but when compared to only other myeloid clusters, CD1C comes to the top of the list, and this is the canonical marker for cDC2's.

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/