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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #402805
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese Holstein cattle

Author
item WANG, XIAO - Shandong Academy Of Agricultural Sciences
item GAO, YAHUI - University Of Maryland
item Li, Congjun - Cj
item FANG, LINGZHAO - University Of Edinburgh
item Liu, Ge - George
item ZHAO, XIUXIN - Collaborator
item ZHANG, YUANPEI - Collaborator
item CAI, GAOZHAN - Collaborator
item XUE, GUANGHUI - Collaborator
item LIU, YAN - Collaborator
item WANG, LINGLING - Collaborator
item ZHANG, FAN - Shandong Academy Of Agricultural Sciences
item WANG, KUN - Shandong Academy Of Agricultural Sciences
item ZHANG, MIAO - Shandong Academy Of Agricultural Sciences
item LI, RONGLING - Shandong Academy Of Agricultural Sciences
item GAO, YUNDONG - Shandong Academy Of Agricultural Sciences
item LI, JIAN-BIN - Shandong Academy Of Agricultural Sciences

Submitted to: BMC Genomic Data
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/30/2023
Publication Date: 8/7/2023
Citation: Wang, X., Gao, Y., Li, C., Fang, L., Liu, G., Zhao, X., Zhang, Y., Cai, G., Xue, G., Liu, Y., Wang, L., Zhang, F., Wang, K., Zhang, M., Li, R., Gao, Y., Li, J. 2023. The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese Holstein cattle. BMC Genomic Data. 24:39. https://doi.org/10.1186/s12863-023-01139-0.
DOI: https://doi.org/10.1186/s12863-023-01139-0

Interpretive Summary: Comprehensive analyses of tissues at single-cell level will benefit our understanding of genetic bases for complex traits. We reported the first cell type profiles for cattle peripheral blood mononuclear cells and examined their responses to lipopolysaccharide. These results fill our knowledge gaps and provide the foundation for incorporating new transcriptome insights into the future animal breeding program. Farmers, scientists, and policy planners who need to improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: This study was performed in the frame of a more extensive study dedicated to the integrated analysis of the single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells (PBMCs) with a large-scale GWAS of 45 complex traits in Chinese Holstein cattle. Lipopolysaccharide (LPS) is a crucial mediator of chronic inflammation to modulate immune responses. PBMCs include primary T and B cells, natural killer (NK) cells, monocytes (Mono), and dendritic cells (DC). How LPS stimulates PBMCs at the single-cell level in dairy cattle remains largely unknown. We sequenced 30,756 single cells with approximately 62,254 reads per cell for four whole-blood treatments (no, 2 h, 4 h, and 8 h LPS) by single-cell RNA sequencing (scRNA-seq) and single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq). Finally, 7,107 (no), 9,174 (2 h), 6,741 (4 h), and 3,119 (8 h) cells were generated with'~'15,000 total genes in the whole population. Therefore, the single-cell transcriptome and chromatin accessibility datasets in this study enable a further understanding of the cell types and functions of PBMCs and their responses to LPS stimulation in vitro.