NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7875121 Query DataSets for GSM7875121
Status Public on Nov 05, 2023
Title PWAT, Exercise; Bulk_P42
Sample type SRA
 
Source name PWAT, Exercise
Organism Sus scrofa
Characteristics tissue: Pericardial White Adipose Tissue
treatment: Exercise
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_P42
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 SAMN38049537
SRA SRX22297311

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap