Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins.
Nat Biotechnol
; 42(1): 40-51, 2024 Jan.
Article
em En
| MEDLINE
| ID: mdl-37055623
ABSTRACT
Assessment of single-cell gene expression (single-cell RNA sequencing) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here we introduce Dandelion, a computational pipeline for scVDJ-seq analysis. It enables the application of standard V(D)J analysis workflows to single-cell datasets, delivering improved V(D)J contig annotation and the identification of nonproductive and partially spliced contigs. We devised a strategy to create an AIR feature space that can be used for both differential V(D)J usage analysis and pseudotime trajectory inference. The application of Dandelion improved the alignment of human thymic development trajectories of double-positive T cells to mature single-positive CD4/CD8 T cells, generating predictions of factors regulating lineage commitment. Dandelion analysis of other cell compartments provided insights into the origins of human B1 cells and ILC/NK cell development, illustrating the power of our approach. Dandelion is available at https//www.github.com/zktuong/dandelion .
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1
Base de dados:
MEDLINE
Assunto principal:
Taraxacum
Idioma:
En
Ano de publicação:
2024
Tipo de documento:
Article
País de afiliação:
Reino Unido