Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28477808_1.fastq.gz | Fastqsanger.gz | |||
| SRR28477808_2.fastq.gz | Fastqsanger.gz | |||
| SRR28477809_1.fastq.gz | Fastqsanger.gz | |||
| SRR28477809_2.fastq.gz | Fastqsanger.gz | |||
| SRR28477810_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
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Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.
2024-09-02 | MODEL2408160001 | BioModels
Project description:<p>Metabolic and inflammatory diseases often coexist, and become important challenges facing global health, and obesity has shown to be a susceptibility factor for osteoarthritis (OA). As a metabolic regulatory drug for lowering blood sugar and body weight, semaglutide has shown additional therapeutic effects in OA, but the underlying mechanism requires further investigation. Here we employed cross-tissue single-cell RNA sequencing (scRNA-seq) analysis, and found that semaglutide significantly improved metabolic disorders in muscle tissue under high-fat diet (HFD) and OA conditions in mice. The results of scRNA-seq and mitochondrial proteomics indicated that semaglutide targeted muscle mitochondria to regulate glutamate metabolism during OA. Intriguingly, intramuscular injection of semaglutide pre-stimulated mitochondria from muscle stem cell could significantly alleviate OA inflammation and pain symptoms. These findings reveal the mitochondrial regulatory mechanism in the muscle-OA axis, and provide a new perspective for the application of semaglutide in OA treatment.</p>
2026-05-06 | MTBLS14059 | MetaboLights
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>
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Project description:Genotype?Tissue Expression atlas of cattle using 7,180 publicly available RNA-sequencing (RNA-seq) samples
2023-02-10 | PRJEB59574 | EVA
Project description:<p>Metabolic and inflammatory diseases often coexist, and become important challenges facing global health, and obesity has shown to be a susceptibility factor for osteoarthritis (OA). As a metabolic regulatory drug for lowering blood sugar and body weight, semaglutide has shown additional therapeutic effects in OA, but the underlying mechanism requires further investigation. Here we employed cross-tissue single-cell RNA sequencing (scRNA-seq) analysis, and found that semaglutide significantly improved mitochondrial metabolic disorders in muscle tissue under high-fat diet (HFD) and OA conditions in mice. The results of metabolome and mitochondrial proteomics indicated that semaglutide targeted muscle mitochondria to regulate glutamine metabolism during OA. Intramuscular injection of semaglutide pre-stimulated mitochondria from myoblasts could significantly alleviate OA inflammation and pain symptoms, which was achieved by inhibiting muscle glutaminase activity, upregulating circulating glutamine concentration, and thereby alleviating cartilage inflammation. In vitro experiments further confirmed the alleviating effect of glutamine produced by myoblasts stimulated by semaglutide on chondrocyte inflammation. These findings reveal the mitochondrial regulatory mechanism in the muscle-OA axis, and provide a new perspective for the application of semaglutide in OA treatment.</p>
2026-05-06 | MTBLS14295 | MetaboLights
Project description:Collection of RNA-Seq data from early muscle tissue after skeletal muscle injury
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Project description:<p>Skeletal muscles, accounting for 40% of mammalian body mass, exhibit pronounced heterogeneity due to distinct anatomical locations. Animal husbandry excessively focuses on longissimus dorsi (LDM) development, while neglecting other muscles. In this study, we integrated Bulk RNA Sequencing (bulk RNA-seq) and Liquid Chromatography-Mass Spectrometery (LC-MS) analyses of Soleus (SOL), Gastrocnemius (GAS), and Psoas major (PMM) across three key stages in Duroc pigs. As a result, we identified 9 critical genes (S100A1, MBOAT2, CA3, GYG2, ACTN3, ENO3, SLC3A2, SLC16A10, and GAPDH) and 8 metabolites potentially involved in regulating both skeletal muscle development and fiber-type transformation. The heterogeneity between SOL and GAS was low at birth but increased gradually during development. In contrast, PMM exhibited high heterogeneity compared to SOL and GAS from birth. Notably, expression levels of MYH7, MYH1, and MYH4 displayed stage-specific and muscle type-dependent variations. Moreover, we observed a developmental shift from the MAPK signaling pathway (1-21 d) to the regulation of actin cytoskeleton (21-120 d). Pairwise comparisons between SOL, GAS, and PMM revealed signaling pathways enriched in muscle fiber-type switching. Collectively, through the integration of bulk RNA-seq and LC-MS data, this study provides novel molecular breeding strategies for genetic improvement in meat-producing animals.</p>
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