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| Status |
Public on Feb 04, 2020 |
| Title |
HHD_2341 |
| Sample type |
SRA |
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| Source name |
Epicardial Adipose tissue
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| Organism |
Sus scrofa |
| Characteristics |
tissue: Epicardial Adipose tissue
diet: Heart Healthy
rna id: 26146
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| Extracted molecule |
total RNA |
| Extraction protocol |
EAT was homogenized and RNA was isolated using RNeasy Universal Midi kit (Qiagen, Valencia, CA). Isolated RNA was treated with Turbo DNase (Ambion, Waltham, MA) to minimize genomic DNA contamination. RNA quality was assessed using the Experion RNA analysis electrophoresis kit (Bio-Rad, Hercules, CA). Only samples with an RNA Quality Indicator (RQI) greater than 7 were sequenced.
Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (mRNA purification and fragmentation, cDNA synthesis, end repair, 3’ adenylation, adaptor ligation, and DNA enrichment) per the manufacturer’s instructions. DNA fragment size was determined using Experion DNA 1K chips (Bio-Rad, Hercules, CA) and library quantification was performed using the KAPA Library Quantification kit (KAPA Biosystems, Wilmington, MA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Base-calling was performed using bcl2fastq v2.17.1.14
Alignment 1 (*_NR112918.csv files): RNA-seq reads were trimmed for adapter sequence and quality then aligned to reference (see genome build) using CLC Bio's Genomics Workbench v10.1.2 with parameters: quality limit = 0.01, min length = 100, Length fraction = 0.95, Similarity fraction = 0.95.
Alignment 2 (*_Sscrofa10.2.csv files): RNA-seq reads were trimmed for adapter sequence and quality then aligned to the Sus scrofa 10.2 genome assembly using CLC Bio's Genomics Workbench v9.0.1 with parameters: quality limit = 0.01, min length = 100, Length fraction = 0.95, Similarity fraction = 0.95
Reads that mapped uniquely to exons were used as counts (Unique Exon Reads) for differential expression analysis using the Bioconductor package: edge R. Genes were filtered based on a minimum of at least one count per million across six samples in all groups and normalized using the TMM method. Differentially expressed genes were identified using the Cox-Reid profile-adjusted likelihood method and likelihood ratio test. A Benjamini-Hochberg false discovery rate (FDR) method was used to adjust p-values for multiple comparisons
Genes were considered differentially expressed based on an FDR adjusted p <0.1 and absolute fold change ≥1.5. Fold change for genes identified by the edge R two-factor model were interpreted as diet effect: fold change of WD relative to HHD and statin effect: fold change of atorvastatin relative to no atorvastatin. Differentially expressed genes were only attributed to main effects (diet and statin) if there was no significant diet x statin interaction. A significant diet x stain interaction is indicated by a FDR adjusted p <0.1.
Ingenuity Pathway Analysis (IPA; v 9.0, Mountain View, CA, USA) was used to determine relevant biological pathways and functional annotation of differentially expressed genes. Pathways with an absolute Z score ≥ 2 and an FDR adjusted p-value ≤ 0.05 were considered statistically significant.
Genome_build: Alignment 1: "Assembly 11/29/18" from Porcine Translational Research Database (Dawson, Harry D., et al. "The porcine translational research database: a manually curated, genomics and proteomics-based research resource." BMC genomics 18.1 (2017): 643.)
Genome_build: Alignment 2: Sscrofa10.2
Supplementary_files_format_and_content: comma-separated value files with Unique Exon Read values for each sample
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| Submission date |
Apr 03, 2019 |
| Last update date |
Feb 04, 2020 |
| Contact name |
Alice H Lichtenstein |
| E-mail(s) |
[email protected]
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| Organization name |
Tufts University
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| Department |
Jean Mayer USDA Human Nutrition Research Center on Aging
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| Lab |
Cardiovascular Nutrition Laboratory
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| Street address |
711 Washington St
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02111 |
| Country |
USA |
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| Platform ID |
GPL20983 |
| Series (1) |
| GSE129301 |
A Western Dietary Pattern and Atorvastatin Induce Epicardial Adipose Tissue Interferon Signaling in the Ossabaw Pig |
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| Relations |
| BioSample |
SAMN11334436 |
| SRA |
SRX5632035 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3704235_26146-Heart-1-C2R-DRNA-A-2341-CCGTCC_S16_NR112918.csv.gz |
107.5 Kb |
(ftp)(http) |
CSV |
| GSM3704235_26146-Heart-1-C2R-DRNA-A-2341-CCGTCC_S16_Sscrofa10.2.csv.gz |
197.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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