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

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Cell Metadata

Mstcl

Ontology Term: mast cellCL:0000097
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: tissue basophil, histaminocyte, mastocyte, labrocyte
CategoryClass of which the cell type is a subclass.: granulocyteCL:0000094
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: TPSAB1, TPSB2, ANXA1, CD63, HDC, KIT
Canonical Marker Genes: KIT, FCER1A, CMA1, TPSAB1, TPSD2, HDC
Rationale: Mast cells are typically easy to identify in gut scRNAseq data as they cluster seperately and have high expression of tryptase (TPSA), chymase (CMA1), IgE receptors, and Histamine (HDC)

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: mast cellCL:0000097
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: tissue basophil, histaminocyte, mastocyte, labrocyte
CategoryClass of which the cell type is a subclass.: granulocyteCL:0000094
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: TPSAB1, TPSB2, ANXA1, CD63, HDC, KIT
Canonical Marker Genes: KIT, FCER1A, CMA1, TPSAB1, TPSD2, HDC
Rationale: Mast cells are typically easy to identify in gut scRNAseq data as they cluster seperately and have high expression of tryptase (TPSA), chymase (CMA1), IgE receptors, and Histamine (HDC)

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/