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

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Cell Metadata

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Ontology Term: macrophageCL:0000235
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: histiocyte
CategoryClass of which the cell type is a subclass.: myeloid cellCL:0000763
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: CD68, C1QA, C1QB, AIF1, LYZ
Canonical Marker Genes: CD68, CD14, ITGAM, CSF1R
Rationale: This cluster expresses CD68, the canonical macrophage marker, as well as several less specific myeloid/granulocyte markers such as LYZ and C1q. It also expresses CD74 and AIF1, which may point to activated macrophages

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: macrophageCL:0000235
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: histiocyte
CategoryClass of which the cell type is a subclass.: myeloid cellCL:0000763
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: CD68, C1QA, C1QB, AIF1, LYZ
Canonical Marker Genes: CD68, CD14, ITGAM, CSF1R
Rationale: This cluster expresses CD68, the canonical macrophage marker, as well as several less specific myeloid/granulocyte markers such as LYZ and C1q. It also expresses CD74 and AIF1, which may point to activated macrophages

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/