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| Status |
Public on Jun 26, 2023 |
| Title |
8 h LPS, scRNA-seq |
| Sample type |
SRA |
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| Source name |
Whole blood
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| Organism |
Bos taurus |
| Characteristics |
tissue: Whole blood
breed: Holstein
age: 2 years
Sex: female
cell type: peripheral blood mononuclear cells
treatment: 8 h LPS
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| 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
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| Submission date |
Feb 23, 2023 |
| Last update date |
Jun 26, 2023 |
| Contact name |
Xiao Wang |
| E-mail(s) |
xiao@kongelarsen.dk
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| Organization name |
Konge Larsen Aps
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| Street address |
Bagsværdvej 103, ST
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| City |
Kongens Lyngby |
| ZIP/Postal code |
2800 |
| Country |
Denmark |
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| Platform ID |
GPL26012 |
| Series (1) |
| GSE225962 |
The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese Holstein cattle |
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| Relations |
| BioSample |
SAMN33426228 |
| SRA |
SRX19487480 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7061078_T3.scRNAexpression.txt.gz |
8.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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