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

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Cell Metadata

T/NK

Ontology Term: natural killer cellCL:0000623
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: cytotoxic lymphocyte
CategoryClass of which the cell type is a subclass.: lymphocyteCL:0000542
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: CCL4, NKG7, CCL5, GZMA, CCL4L2, KLRD1, TRDC, GZMK, CD69
Canonical Marker Genes: NKG2D, CD8A, CD8B, KLRG1, KRLD1
Rationale: These are a cluster. of cytotoxic lymphocytes that are hard to categorize as either T or NK cells (or NKT for that matter). They display markers for both lineages, including T cell receptor subunit C TRDC as well as many NK markers such as KLRD1, and they display generally activated cytotoxic markers in high relative abundance - CCL4, CD69, GZMA/K, and NKG7

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: natural killer cellCL:0000623
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: cytotoxic lymphocyte
CategoryClass of which the cell type is a subclass.: lymphocyteCL:0000542
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: CCL4, NKG7, CCL5, GZMA, CCL4L2, KLRD1, TRDC, GZMK, CD69
Canonical Marker Genes: NKG2D, CD8A, CD8B, KLRG1, KRLD1
Rationale: These are a cluster. of cytotoxic lymphocytes that are hard to categorize as either T or NK cells (or NKT for that matter). They display markers for both lineages, including T cell receptor subunit C TRDC as well as many NK markers such as KLRD1, and they display generally activated cytotoxic markers in high relative abundance - CCL4, CD69, GZMA/K, and NKG7

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/