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

Main

Cell Metadata

cDC1

Ontology Term: conventional dendritic cellCL:0000990
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: cDC, dendritic reticular cell, DC1, type 1 DC, veiled cell, interdigitating cell, cDC1
Category Class of which the cell type is a subclass.: dendritic cellCL:0000451
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: HLA-DPB1, HLA-DRA, LYZ, CST3, XCR1, CD74, CLEC9A
Canonical Marker Genes: HLA-D---, ITGAX/CD11c, XCR1
Rationale: These are clear dendritic cells based on HLA, CD74 (MHC class 2 presentation molecules) and because they display increased XCR1 when compared to all other myeloid cells, we call them cDC1, because this is the marker that differentiates from cDC2

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: conventional dendritic cellCL:0000990
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: cDC, dendritic reticular cell, DC1, type 1 DC, veiled cell, interdigitating cell, cDC1
Category Class of which the cell type is a subclass.: dendritic cellCL:0000451
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: HLA-DPB1, HLA-DRA, LYZ, CST3, XCR1, CD74, CLEC9A
Canonical Marker Genes: HLA-D---, ITGAX/CD11c, XCR1
Rationale: These are clear dendritic cells based on HLA, CD74 (MHC class 2 presentation molecules) and because they display increased XCR1 when compared to all other myeloid cells, we call them cDC1, because this is the marker that differentiates from cDC2

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/