|
Status |
Public on Nov 05, 2023 |
Title |
EAT, Sedentary, Non-occluded; N2_Landrace |
Sample type |
SRA |
|
|
Source name |
EAT, Sedentary, Non-occluded
|
Organism |
Sus scrofa |
Characteristics |
tissue: Epicardial Adipose Tissue treatment: Sedentary, Non-occluded
|
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 single cell |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
N2_Landrace
|
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
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|
|
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 |
SAMN38049532 |
SRA |
SRX22297305 |