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Sample GSM7061076 Query DataSets for GSM7061076
Status Public on Jun 26, 2023
Title 2 h LPS, scRNA-seq
Sample type SRA
 
Source name Whole blood
Organism Bos taurus
Characteristics tissue: Whole blood
breed: Holstein
age: 2 years
Sex: female
cell type: peripheral blood mononuclear cells
treatment: 2 h LPS
Extracted molecule total RNA
Extraction 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.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing Cell Ranger Single-Cell Software Suite (release 3.1.0) was used to process the raw data, demultiplex raw base-call files into FASTQ files by “mkfastq”, perform alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting by “count”, and align raw reads to cattle reference genome (ARS-UCD1.2/bosTau9) by “pipeline.
Assembly: ARS-UCD1.2/bosTau9
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date Feb 23, 2023
Last update date Jun 26, 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
 
Platform ID GPL26012
Series (1)
GSE225962 The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese Holstein cattle
Relations
BioSample SAMN33426230
SRA SRX19487478

Supplementary file Size Download File type/resource
GSM7061076_T1.scRNAexpression.txt.gz 17.8 Mb (ftp)(http) TXT
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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