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

文献类型： 外文期刊

作者： Wang, Xiao 1 ; Gao, Yahui 2 ; Li, Cong-jun 2 ; Fang, Lingzhao 3 ; Liu, George E. 2 ; Zhao, Xiuxin 4 ; Zhang, Yuanpei 4 ; Cai, Gaozhan 4 ; Xue, Guanghui 4 ; Liu, Yan 4 ; Wang, Lingling 4 ; Zhang, Fan 1 ; Wang, Kun 1 ; Zhang, Miao 1 ; Li, Rongling 1 ; Gao, Yundong 1 ; Li, Jianbin 1 ;

作者机构： 1.Shandong Acad Agr Sci, Inst Anim Sci & Vet Med, Jinan 250100, Peoples R China

2.Agr Res Serv, Henry A Wallace Beltsville Agr Res Ctr, Anim Genom & Improvement Lab, USDA, Beltsville, MD 20705 USA

3.Aarhus Univ, Ctr Quantitat Genet & Genom, DK-8000 Aarhus, Denmark

4.Shandong OX Livestock Breeding Co Ltd, Jinan 250100, Peoples R China

关键词： Chinese Holstein cattle; Peripheral blood mononuclear cell; Lipopolysaccharide; Single-cell accessibility dataset; Transcriptome; Chromatin

期刊名称：BMC GENOMIC DATA （ 影响因子：1.9； 五年影响因子：1.9 ）

ISSN：

年卷期： 2023 年 24 卷 1 期

页码：

收录情况： SCI

摘要： Objectives 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. Data description We sequenced 30,756 estimated single cells and mapped 26,141 of them (96.05%) with approximately 60,075 mapped reads per cell after quality control 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 similar to 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.

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