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

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

PROVIDER: PRJNA938112 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23602500_1.fastq.gz	Fastqsanger.gz
	SRR23602500_2.fastq.gz	Fastqsanger.gz
	SRR23602501_1.fastq.gz	Fastqsanger.gz
	SRR23602501_2.fastq.gz	Fastqsanger.gz
	SRR23602502_1.fastq.gz	Fastqsanger.gz

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

Project description:This study is performed in the frame of a bigger 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. In dairy 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). It still remains unknown how LPS stimulated PBMCs at the single-cell level in dairy cattle. Therefore, the single-cell transcriptome and chromatin accessibility datasets in this study enable the further understanding and application of the cell types and functions of PBMCs and their responses to LPS stimulation in vitro in other studies.

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Project description:ObjectivesThis 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 descriptionWe 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 ~ 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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