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Sample GSM7875115 Query DataSets for GSM7875115
Status Public on Nov 05, 2023
Title EAT, Exercise, Non-occluded; N1_Landrace
Sample type SRA
Source name EAT, Exercise, Non-occluded
Organism Sus scrofa
Characteristics tissue: Epicardial Adipose Tissue
treatment: Exercise, 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 N1_Landrace
Data processing Bulk RNA-seq: QC Reports completed with: FastQC v0.11.9. Mapping performed using Bowtie2 version 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
BioSample SAMN38049531
SRA SRX22297304

Supplementary file Size Download File type/resource
GSM7875115_N1_filtered_feature_bc_matrix.h5 16.1 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA

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