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

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Cell Metadata

Mono/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.: monocyteCL:0000576
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: HLA-DRA, HLA-DPA1, CST3, AIF1, CD74, CD1C, LYZ
Canonical Marker Genes: CD1C, LYZ
Rationale: This cluster is high for CD1C and antigen presentation markers but also high in other monocyte markers like LYZ, pointing to some intermediate stage between monocyte precursors/mature monocytes and 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.: monocyteCL:0000576
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: HLA-DRA, HLA-DPA1, CST3, AIF1, CD74, CD1C, LYZ
Canonical Marker Genes: CD1C, LYZ
Rationale: This cluster is high for CD1C and antigen presentation markers but also high in other monocyte markers like LYZ, pointing to some intermediate stage between monocyte precursors/mature monocytes and 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/