|
| Status |
Public on Nov 05, 2023 |
| Title |
PWAT, Sedentary; Bulk_P38 |
| Sample type |
SRA |
| |
|
| Source name |
PWAT, Sedentary
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: Pericardial White Adipose Tissue
treatment: Sedentary
|
| Treatment protocol |
Animals were divided into two exercise (sedentary vs exercised) and two coronary artery (non-occluded and occluded) treatment groups. Surgeries were performed to place an ameroid constrictor (2.5-3.5 mm) around the proximal left circumflex artery.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol® (Thermofisher Scientific, Waltham, MA) for Bulk RNA-seq and
cDNA libraries for Bulk RNA-seq were prepared, and sequencing was performed at the Molecular Genomics Core, Texas A&M University. Single nuclei 3` sequencing libraries were generated following the 10x Genomics dual index manual preparation v3.1 reagent kit with a target nuclei recovery of approximately 5,000 – 10,000 nuclei for each reaction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Bulk_P38
|
| Data processing |
Bulk RNA-seq: QC Reports completed with: FastQC v0.11.9. Mapping performed using Bowtie2 version 2.3.5.1 64-bit with default settings. Counting performed using htseq-count version 2.0.2. Data was normalized using upperquartile method. DE analysis preformed in R using edgeR version 3.34.1 and limma 3.48.3.
scRNA-seq: Sample demultiplexing, STAR alignment to the Landrace_pig_v1 transcriptome, filtering, and UMI counting were achieved using Cell Ranger 3.0.1 (10X Genomics)44.
Assembly: Sscrofa11.1
Supplementary files format and content: HDF5 files include filtered counts for scRNA-seq samples
Supplementary files format and content: comma-delimited text files include raw counts for Bulk RNA-seq samples
|
| |
|
| Submission date |
Oct 31, 2023 |
| Last update date |
Nov 05, 2023 |
| Contact name |
Annie Newell-Fugate |
| Organization name |
Texas A&M University
|
| Department |
Department of Veterinary Physiology & Pharmacology
|
| Street address |
4466 TAMU
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843-4466 |
| Country |
USA |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE246709 |
Single-nucleus transcriptomics of epicardial adipose tissue from female pigs reveals effects of exercise training on resident innate and adaptive immune cells |
|
| Relations |
| BioSample |
SAMN38049535 |
| SRA |
SRX22297309 |
