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| Status |
Public on Nov 05, 2023 |
| Title |
EAT, Exercise, Occluded; O1_Landrace |
| Sample type |
SRA |
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| Source name |
EAT, Exercise, Occluded
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| Organism |
Sus scrofa |
| Characteristics |
tissue: Epicardial Adipose Tissue
treatment: Exercise, Occluded
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| 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.
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| 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.
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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 |
O1_Landrace
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| 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
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| Department |
Department of Veterinary Physiology & Pharmacology
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| Street address |
4466 TAMU
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| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843-4466 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN38049533 |
| SRA |
SRX22297307 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7875117_O1_filtered_feature_bc_matrix.h5 |
16.0 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
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