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

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Cell Metadata

Mac/DC

Ontology Term: dendritic cellCL:0000451
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: interdigitating cell, veiled cell, macrophage/dendritic cell intermediate
CategoryClass of which the cell type is a subclass.: myeloid cellCL:0000763
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: FTL, LYZ, HLA-DRA, HLA-DRB1, C1QA, C1QB
Canonical Marker Genes: C1QA, C1QB, HLA-DRA
Rationale: Another cluster of high antigen-presentation structure expression that also displays other myeloid markers, in this case C1Q which points to some intermediate or doublet of macrophages and dendritic cells

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: dendritic cellCL:0000451
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: interdigitating cell, veiled cell, macrophage/dendritic cell intermediate
CategoryClass of which the cell type is a subclass.: myeloid cellCL:0000763
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: FTL, LYZ, HLA-DRA, HLA-DRB1, C1QA, C1QB
Canonical Marker Genes: C1QA, C1QB, HLA-DRA
Rationale: Another cluster of high antigen-presentation structure expression that also displays other myeloid markers, in this case C1Q which points to some intermediate or doublet of macrophages and dendritic cells

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/