4.8 Article

Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins

Journal

NATURE BIOTECHNOLOGY
Volume -, Issue -, Pages -

Publisher

NATURE PORTFOLIO
DOI: 10.1038/s41587-023-01734-7

Keywords

-

Ask authors/readers for more resources

Dandelion is a computational pipeline for single-cell V(D)J sequence analysis, which improves V(D)J sequence annotation and identifies nonproductive and partially spliced sequences. It enhances the accuracy of predicting human thymic development trajectories and provides insights into the origins of human B1 cells and ILC/NK cell development.
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.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.8
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available