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

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Cell Metadata

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
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-DPB1, HLA-DRA, IDO1, CD74, CCR7
Canonical Marker Genes: CD11c, HLA-DRA, HLA-DPA
Rationale: These display much of the antigen presentation machinery (HLA, CD74), but without any expression of known canonical markers of DC subsets (XCR1, CD1c, CD123, CD303, CD304, CD21/CR2) we couldn't be more specific. CCR7 points to an activation state, which could be causing us to capture of markers of activation rather than lineage.

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
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-DPB1, HLA-DRA, IDO1, CD74, CCR7
Canonical Marker Genes: CD11c, HLA-DRA, HLA-DPA
Rationale: These display much of the antigen presentation machinery (HLA, CD74), but without any expression of known canonical markers of DC subsets (XCR1, CD1c, CD123, CD303, CD304, CD21/CR2) we couldn't be more specific. CCR7 points to an activation state, which could be causing us to capture of markers of activation rather than lineage.

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/