TY - JOUR
T1 - The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese holstein cattle
AU - Wang, Xiao
AU - Gao, Yahui
AU - Li, Cong jun
AU - Fang, Lingzhao
AU - Liu, George E.
AU - Zhao, Xiuxin
AU - Zhang, Yuanpei
AU - Cai, Gaozhan
AU - Xue, Guanghui
AU - Liu, Yan
AU - Wang, Lingling
AU - Zhang, Fan
AU - Wang, Kun
AU - Zhang, Miao
AU - Li, Rongling
AU - Gao, Yundong
AU - Li, Jianbin
N1 - Publisher Copyright:
© 2023, BioMed Central Ltd., part of Springer Nature.
PY - 2023/12
Y1 - 2023/12
N2 - 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 ~ 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.
AB - 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 ~ 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.
KW - Chinese Holstein cattle
KW - Chromatin
KW - Lipopolysaccharide
KW - Peripheral blood mononuclear cell
KW - Single-cell accessibility dataset
KW - Transcriptome
UR - http://www.scopus.com/inward/record.url?scp=85166784314&partnerID=8YFLogxK
U2 - 10.1186/s12863-023-01139-0
DO - 10.1186/s12863-023-01139-0
M3 - Journal article
C2 - 37550629
AN - SCOPUS:85166784314
SN - 2730-6844
VL - 24
JO - BMC Genomic Data
JF - BMC Genomic Data
IS - 1
M1 - 39
ER -