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

Main

Cell Metadata

Mono/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, DC
CategoryClass of which the cell type is a subclass.: myeloid cellCL:0000763
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: LYZ, HLA-DRA, HLA-DPA1, SOD2
Canonical Marker Genes: LYZ, CD48
Rationale: This small cluster expresses antigen presentation machinery, dendritic cell markers, and SOD2 which points to macrohpages. It's possible it could be a DC, but it also shows high expression of CD48, so it could be an eosinophil. Here it is grouped generally with the other myeloid types because it is a small cluster of unknown myeloid provenance

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, DC
CategoryClass of which the cell type is a subclass.: myeloid cellCL:0000763
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: LYZ, HLA-DRA, HLA-DPA1, SOD2
Canonical Marker Genes: LYZ, CD48
Rationale: This small cluster expresses antigen presentation machinery, dendritic cell markers, and SOD2 which points to macrohpages. It's possible it could be a DC, but it also shows high expression of CD48, so it could be an eosinophil. Here it is grouped generally with the other myeloid types because it is a small cluster of unknown myeloid provenance

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/