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

Main

Cell Metadata

ILC

Ontology Term: innate lymphoid cellCL:0001065
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: ILC
Category Class of which the cell type is a subclass.: lymphocyteCL:0000542
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: KLRB1, IL7R
Canonical Marker Genes: TBX21 (T-bet), IL7RA, KLRB1 (CD161)
Rationale: This cluster was highest in KLRB1, which led us to name them generally ILC's, however it expressed several other strange markers that point to other general lymphocyte functions (ID2, KLRC1, TRDC) or interactions with epithelial cells (KRT86, KRT81)

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: innate lymphoid cellCL:0001065
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: ILC
Category Class of which the cell type is a subclass.: lymphocyteCL:0000542
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: KLRB1, IL7R
Canonical Marker Genes: TBX21 (T-bet), IL7RA, KLRB1 (CD161)
Rationale: This cluster was highest in KLRB1, which led us to name them generally ILC's, however it expressed several other strange markers that point to other general lymphocyte functions (ID2, KLRC1, TRDC) or interactions with epithelial cells (KRT86, KRT81)

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/