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Single-cell RNA-Seq of porcine peripheral blood monocytes

ABSTRACT: We performed 10× Genomics single-cell RNA sequencing on a mixed population of CD3+ PBMCs isolated from three healthy Large White pigs. Considering that cell resolution of scRNA-seq analysis can be improved based on large datasets, we also downloaded 7 pbulic PBMC scRNA-seq datasets using the same technique (10× Genomics). After rigorous quality control and the removal of batch effects, a total of 14,595 transcriptomes were obtained from 34,220 cells in 8 PBMC samples for subsequent analyses. Using the graph-based uniform manifold approximation and projection (UMAP) clustering algorithm in Seurat package, we identified 14 major cell types (32 clusters) from peripheral blood circulating cells of pigs, and observed remarkable heterogeneity among CD8 T cell types. Upon re-clustering of CD8+ T cells, we defined 4 CD8 T cell subtypes and revealed their potential differentiation trajectories and transcriptomic differences among them. Through single-cell regulatory network inference, we identified key regulatory factors during CD8 T cell differentiation. Moreover, cell-cell communication analysis underscored extensive intercellular interactions among different cell types. Lastly, our cross-species analysis highlighted both similarities and potential differences between species.

ORGANISM(S): Sus scrofa domesticus

PROVIDER: GSE247126 | GEO | 2024/03/07

REPOSITORIES: GEO

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