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Series GSE225962 Query DataSets for GSE225962
Status Public on Jun 26, 2023
Title The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese Holstein cattle
Organism Bos taurus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
 
Overall design Four whole blood samples were collected from four 2-year old Holstein female lactating cattle through the tail vein. Afterwards, they were mixed in one pool and evenly divided into four replicates. Four whole-blood treatments for each replicate included one control (no LPS) treatment and three case treatments (2 h, 4 h, and 8 h LPS), where 2 µg/ml LPS (Product Number: L2880, Sigma-Aldrich, Saint Louis, MO, USA) was used at 37 °C.
Web link https://bmcgenomdata.biomedcentral.com/articles/10.1186/s12863-023-01139-0
 
Contributor(s) Wang X, Li J
Citation(s) 37550629
Submission date Feb 23, 2023
Last update date Sep 25, 2023
Contact name Xiao Wang
E-mail(s) xiao@kongelarsen.dk
Organization name Konge Larsen Aps
Street address Bagsværdvej 103, ST
City Kongens Lyngby
ZIP/Postal code 2800
Country Denmark
 
Platforms (1)
GPL26012 Illumina NovaSeq 6000 (Bos taurus)
Samples (8)
GSM7061075 no LPS, scRNA-seq
GSM7061076 2 h LPS, scRNA-seq
GSM7061077 4 h LPS, scRNA-seq
Relations
BioProject PRJNA938112

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE225962_RAW.tar 82.1 Mb (http)(custom) TAR (of TXT)
GSE225962_summary.xlsx 3.6 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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