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

Main

Cell Metadata

Mono/Mac

Ontology Term: monocyteCL:0000576
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: myeloid
Category Class of which the cell type is a subclass.: myeloid cellCL:0000763
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: FTL, LYZ, FTH1, C1QA, C1QB
Canonical Marker Genes: CD14, CD68, CCR2, CD16
Rationale: This is another cluster of some difficult to determine group of monocyte or macrophages. It expresses markers for both, e.g. C1Q and LYZ (macrophage) but has highest expression of FTH1 and FTL, players in the ferritin blood cell iron scavenging pathway used generally by monocytes and macrophages to recycle RBCs. These may be closer to macrophage given predominance of catabolic pathways

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: monocyteCL:0000576
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: myeloid
Category Class of which the cell type is a subclass.: myeloid cellCL:0000763
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: FTL, LYZ, FTH1, C1QA, C1QB
Canonical Marker Genes: CD14, CD68, CCR2, CD16
Rationale: This is another cluster of some difficult to determine group of monocyte or macrophages. It expresses markers for both, e.g. C1Q and LYZ (macrophage) but has highest expression of FTH1 and FTL, players in the ferritin blood cell iron scavenging pathway used generally by monocytes and macrophages to recycle RBCs. These may be closer to macrophage given predominance of catabolic pathways

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/