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SRX19487477: GSM7061075: no LPS, scRNA-seq; Bos taurus; RNA-Seq
4 ILLUMINA (Illumina NovaSeq 6000) runs: 398M spots, 119.4G bases, 42.7Gb downloads

External Id: GSM7061075_r1
Submitted by: Konge Larsen Aps
Study: The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese Holstein cattle
show Abstracthide Abstract
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.
Sample: no LPS, scRNA-seq
SAMN33426231 • SRS16878454 • All experiments • All runs
Organism: Bos taurus
Name: GSM7061075
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Selection: cDNA
Layout: PAIRED
Construction protocol: On Hanks' Balanced Salt Solution (Solarbio; Beijing, China), PBMCs were finally isolated from the whole-blood treated replicates by centrifugation at 500 g for 20 min at room temperature. Following the user guide of Chromium Single Cell 3' Reagent Kits v3 (CG000183), reverse transcriptase was mixed with the barcoded isolated cells into the Gel Beads-In-Emulsions (GEMs), where read 1 primer sequence (R1) was put into during its incubation. Via end repair, tailing, adaptor ligation, and PCR procedures, the sample index, P5, P7, and read 2 primer sequence (R2) were included in library construction to generate single-cell RNA sequencing (scRNA-seq) library. Following the user guide of Chromium Single Cell ATAC Reagent Kits v1.1 (CG000209), nuclei suspensions were incubated with transposase to preferentially fragment the DNA in open regions of the chromatin and adapter sequences were added to the ends of the DNA fragments instantaneously. The single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) library was constructed via PCR when nuclei were barcoded into the GEMs, where the sample index, P7, and R2 were added.
Runs: 4 runs, 398M spots, 119.4G bases, 42.7Gb
Run# of Spots# of BasesSizePublished


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