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

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Cell Metadata

Mono/Mac/cDC2

Ontology Term: CD1c-positive myeloid dendritic cellCL:0002399
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: cDC2, type 2 conventional dendritic cell
CategoryClass of which the cell type is a subclass.: myeloid cellCL:0000763
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: HLA-DRA, CD74, CST3, LYZ, CLEC10A, AIF1
Canonical Marker Genes: CST3, HLA-DRA, LYZ, AIF1, CD74
Rationale: Another cluster of high antigen-presentation structure expression including CD1C and CLEC10A, definitive cDC2 markers, but is also high for other myeloid 'precursors' of cDC2s, both macrophages and monocytes, with LYZ, AIF1, CST3, and more

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
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: cDC2, type 2 conventional dendritic cell
CategoryClass of which the cell type is a subclass.: myeloid cellCL:0000763
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: HLA-DRA, CD74, CST3, LYZ, CLEC10A, AIF1
Canonical Marker Genes: CST3, HLA-DRA, LYZ, AIF1, CD74
Rationale: Another cluster of high antigen-presentation structure expression including CD1C and CLEC10A, definitive cDC2 markers, but is also high for other myeloid 'precursors' of cDC2s, both macrophages and monocytes, with LYZ, AIF1, CST3, and more

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/