RNAseq of Rhesus macaque adipose tissue and skeletal muscle in response to FGF21 treatment
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ABSTRACT:
ORGANISM(S): Macaca mulatta
PROVIDER: GSE134213 | GEO | 2019/07/13
REPOSITORIES: GEO
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Project description:<p>The Finland-United States Investigation of NIDDM Genetics (FUSION) study is a long-term effort to identify genetic variants that predispose to type 2 diabetes (T2D) or that impact the variability of T2D-related quantitative traits (QTs). Skeletal muscle and adipose are major insulin target tissues and play key roles in insulin resistance. We hypothesize that a subset of T2D and related QT variants alter gene expression in skeletal muscle and adipose tissue. For this FUSION Tissue Biopsy Study, we have obtained and are analyzing RNA-Seq, microRNA (miRNA)-Seq, and DNA methylation (methyl)-Seq data on biopsy samples from 331 individuals from across the range of glucose tolerance: 124 normal glucose tolerance (NGT), 77 impaired glucose tolerance (IGT), 44 impaired fasting glucose (IFG), and 86 newly-diagnosed T2Ds. Participants completed two study visits, two weeks apart. First visits comprised most of the clinical phenotyping, including four-point OGTT (fasting, and 30, 60, and 120 minute post-load); BMI, WHR; lipids; blood pressure; and many other variables. Participants also completed FUSION health history, medication, and lifestyle questionnaires. At second visit, we obtained ~250mg <i>vastus lateralis</i> skeletal muscle, ~750mg abdominal subcutaneous adipose, and a ~5x15mm section of abdominal skin. Visits were completed in March 2013. RNA isolation is ongoing in the Collins laboratory at the NIH, RNA and miRNA sequencing at the NIH Intramural Sequencing Center (NISC), and genotyping at the Center for Inherited Disease Research (CIDR). Individual-level data is available here for the 306 individuals who consented to data deposit.</p> <p>To focus on evaluation of gene expression and its regulation in skeletal muscle, we analyzed mRNA extracted from <i>vastus lateralis</i> skeletal muscle obtained from 271 of the 331 individual subjects from Finland, along with genome-wide genotypes. Individual-level data is available here for the 250 subjects who reconsented to the use of their data. Release phs001048.v2.p1 adds muscle data for an additional 42 subjects and data from adipose tissue for 276 subjects. Total RNA was isolated using Trizol extraction in the Collins laboratory at the NIH. The mRNA was poly-A selected, 24-plex libraries were generated using the Illumina TruSeq directional mRNA-seq library protocol and RNA sequencing was performed on HiSeq2000 sequencers using 101bp paired-end reads at NISC. miRNA libraries were prepared from total RNA from 296 muscle and 270 adipose samples, pooled and sequenced 50bp single-end reads on Illumina HiSeq2500. Data for 272 muscle and 251 adipose samples are available here for individuals with consent for data deposit. DNA was extracted from blood in the Collins laboratory, and genotyping on the Illumina Omni2.5M array was performed at CIDR. Genotypes were imputed using the HRC 2016 reference panel. In order to assess regions of open chromatin in skeletal muscle, we obtained muscle tissue from a commercial provider to perform ATAC-seq; these samples were sequenced at the University of Michigan DNA Sequencing Core.</p> <p>Greater than 90% of the approximately 80 loci associated with T2D and the 100s of loci associated with T2D-related traits (glucose and insulin, anthropometrics, lipids) through genome-wide association studies occur in non-coding regions, suggesting a strong regulatory component to disease susceptibility. Regulatory element activity is often tissue-specific, which further complicates discovery of the causal/functional variation. Therefore, there is a critical need to understand the full spectrum of genetic variation and regulatory element usage in T2D-relevant tissues. To that end, this study contains whole genome sequence and whole genome bisulfite sequence, and/or Illumina MethylationEPIC Array data, of two tissues relevant to T2D: skeletal muscle and adipose tissue from individuals with glucose tolerance categories ranging from normal to T2D, providing a comprehensive survey of both individual genetic variation as well as DNA methylation across different tissues from multiple individuals.</p>
| phs001048 | dbGaP
Project description:RNAseq of Rhesus macaque adipose tissue and skeletal muscle in response to FGF21 treatment
| PRJNA554327 | ENA
Project description:Context: Glucocorticoids are frequently prescribed drugs with important side-effects such as glucose intolerance and tissue remodelling. Objective: The goal was to explore the molecular basis of the crosstalk between adipose tissue and skeletal muscle during short term glucocorticoid treatment. Design and Intervention: Healthy male subjects were assigned to a 4-d treatment with dexamethasone at 4mg/d. Main Outcome Measures: Primary outcome measures were gene expression profiling of adipose tissue and skeletal muscle. Urinary cortisol and metabolic biochemistry were also assessed. Dexamethasone was provided in 0.5 mg tablets as 4mg per day during 4 days to male healthy volunteers. Skeletal muscle and adipose tissue biopsies were obtained at the beginning and at the end of the protocol. The transcriptome analysis compared before vs. after the 4 days dexamethasone treatment using a dye swap design and whole genome 4x44k oligonucleotide arrays (Agilent Technologies).
2011-11-28 | E-GEOD-17992 | biostudies-arrayexpress
Project description:Context: Glucocorticoids are frequently prescribed drugs with important side-effects such as glucose intolerance and tissue remodelling. Objective: The goal was to explore the molecular basis of the crosstalk between adipose tissue and skeletal muscle during short term glucocorticoid treatment. Design and Intervention: Healthy male subjects were assigned to a 4-d treatment with dexamethasone at 4mg/d. Main Outcome Measures: Primary outcome measures were gene expression profiling of adipose tissue and skeletal muscle. Urinary cortisol and metabolic biochemistry were also assessed.
2011-11-28 | GSE17992 | GEO
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2008-02-03 | E-MARS-8 | biostudies-arrayexpress
Project description:The main objective of this project is to compare the miRNA expression profile of paired visceral adipose tissue and skeletal muscle from obese patients undergoing bariatric surgery. More than 300 miRNAs were identified by Next Generation Sequencing technique in both the visceral adipose tissue and the skeletal muscle of six obese women undergoing bariatric surgery.
2024-05-10 | E-MTAB-13008 | biostudies-arrayexpress
Project description:Polycystic ovary syndrome (PCOS) is an endocrine and metabolic disorder affecting women of reproductive age. The main features of PCOS are hyperandrogenism and irregular menstrual cycles together with metabolic dysfunctions including abdominal obesity, dyslipidemia and an increased risk of developing type 2 diabetes. Despite the high prevalence of >15%, the pathophysiology of the syndrome is unclear. Gene expression array data from skeletal muscle and adipose tissue have provided some information about dysregulated metabolic pathways in women with PCOS, but the transcriptomic data need to be verified by proteomics to advance our understanding of PCOS. Skeletal muscle and adipose tissue biopsies from 10 women with PCOS and 10 controls were subjected to global proteomic analysis. Protein expression differences between cases and controls were based on Student’s t-test and corrected for multiple testing. In total, we identified 5000 proteins in adipose tissue and 3480 proteins in skeletal muscle. After correction for multiple testing, 74 proteins with q < 0.05 corresponding to 72 unique proteins were found to be differentially expressed in adipose tissue from women with PCOS versus controls. And, 123 proteins with q < 0.05 corresponding to 120 unique proteins were found to be differentially expressed in skeletal muscle from women with PCOS versus control. We then applied pathway analysis to the total protein and phosphopeptide data using PRISM and Enrichr.
2024-01-09 | PXD025358 | Pride
Project description:Compare miRNA expression profiles in epididymal white adipose tissue (WAT), interscapular brown adipose tissue (BAT) and skeletal muscle from wild-type C57BL/6J mice
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