Gene Expression Profiles in Skeletal Muscle and Liver of Type 2 Diabetes Rats
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE41832 | GEO | 2012/10/27
SECONDARY ACCESSION(S): PRJNA178306
REPOSITORIES: GEO
Similar Datasets
Project description:Analyzing changes in gene expression in liver and skeletal muscle from streptozotocin-diabetic rats. From the 9,929 expressed genes across the genome, 1,305 and 997 differentially expressed genes (DEGs, P < 0.01) were identified in comparisons of skeletal muscle and liver, respectively. Interestingly, large numbers of DEGs (200) were common to both comparisons, which was clearly more than the predicted number (131 genes, P < 10−4). Further interpretation of gene ontology used three over-representation analysis software (WebGestalt, Expander and GATHER). All the tools detected one KEGG pathway (MAPK signaling) and two GO biological processes (response to stress and cell death), with enrichment of DEGs in both tissues. In addition, PPI (protein-protein interaction) networks constructed using human homologs not only revealed the tendency of DEGs to form a highly connected module, but also suggested a “hub” role of MAPK related genes (such as MAPK14) in the pathogenesis of T2D. Total RNA obtained from liver and skeletal muscle of streptozotocin-diabetic rats and controls, respectivly.
2012-10-27 | E-GEOD-41832 | biostudies-arrayexpress
Project description:Mitogen activated protein kinase (MAPK) signaling regulates differentiation of many cell types. During myogenesis in particular, p38a MAPK (MAPK14) phosphorylates multiple transcriptional regulators to modulate muscle-specific gene expression. Among the p38a MAPK modulated genes is the muscle-specific transcriptional regulator Myogenin (Myog) that is also essential to complete the muscle differentiation program, and while it is known that both p38a MAPK and Myog are critically required for myogenesis, the individual contribution of each of these proteins is poorly defined. Here we show that Myog expression (in the absence of p38a MAPK signaling) is sufficient to establish expression of many late markers of muscle differentiation and to mediate cell migration. However, Myog expression alone did not led to the formation of multinucleated muscle cells, highlighting a critical role for p38a MAPK in myoblast fusion. Using comparative microarray analysis we identified p38a MAPK-dependent genes that are not regulated by Myog We generated a stable C2C12-derived cell line (C2i-Myog) that expresses a Doxycycline (Dox)-inducible cDNA encoding Flag-tagged Myog. In this system, the chemical induction of exogenous Myog (Dox) combined with the pharmacological inhibition of p38a/b MAPK signaling by SB203580 (SB) would allow us to assess the functional contribution of these two pathways during myogenesis
2012-08-01 | E-GEOD-25763 | biostudies-arrayexpress
Project description:Mitogen activated protein kinase (MAPK) signaling regulates differentiation of many cell types. During myogenesis in particular, p38a MAPK (MAPK14) phosphorylates multiple transcriptional regulators to modulate muscle-specific gene expression. Among the p38a MAPK modulated genes is the muscle-specific transcriptional regulator Myogenin (Myog) that is also essential to complete the muscle differentiation program, and while it is known that both p38a MAPK and Myog are critically required for myogenesis, the individual contribution of each of these proteins is poorly defined. Here we show that Myog expression (in the absence of p38a MAPK signaling) is sufficient to establish expression of many late markers of muscle differentiation and to mediate cell migration. However, Myog expression alone did not led to the formation of multinucleated muscle cells, highlighting a critical role for p38a MAPK in myoblast fusion. Using comparative microarray analysis we identified p38a MAPK-dependent genes that are not regulated by Myog
2012-08-02 | GSE25763 | GEO
Project description:The pig could be a useful model to characterize molecular aspects determining several delicate phenotypes because they have been bred for those characteristics. The Korean native pig (KNP) is a regional breed in Korea that was characterized by relatively high intramuscular fat content and reddish meat color compared to other western breeds such as Yorkshire (YS). YS grew faster and contained more lean muscle than KNP. We compared the KNP to Yorksire to find molecular clues determining muscle characteristics. The comparison of skeletal gene expression profiles between these two breeds showed molecular differences in muscle. We found 82 differentially expressed genes (DEGs) defined by fold change (more than 1.5 fold difference) and statistical significance (within 5% of false discovery rate). Functional analyses of these DEGs indicated up-regulation of most genes involved in cell cycle arrest, down-regulation of most genes involved in cellular differentiation and its inhibition, down-regulation of most genes encoding component of muscular-structural system, and up-regulation of most genes involved in diverse metabolism in KNP. Especially, DEGs in above-mentioned categories included a large number of genes encoding proteins directly or indirectly involved in p53 pathway. Our results indicated a possible role of p53 to determine muscle characteristics between these two breeds. Experiment Overall Design: Comparing gene expression profiles to discover differentially expressed genes from skeletal muscles of two different pig breeds.
2009-10-31 | E-GEOD-18653 | biostudies-arrayexpress
Project description:Cannabidiol (CBD), a cannabinoid from the cannabis plant, is widely used in sports for recovery, pain management, and sleep improvement, yet its effects on muscle are not well understood. This study aimed to determine the transcriptional response of murine skeletal muscle myotubes to broad-spectrum CBD and synthetic CBD (sCBD), hypothesizing significant changes in metabolism, myogenesis, and inflammation, with unique gene expression profiles for broad-spectrum CBD due to its additional compounds. Differentiated C2C12 myotubes were treated with 10 µM CBD, sCBD, or vehicle control (DMSO) for 24 hours before RNA extraction. Poly-A tail enriched mRNA libraries were constructed and sequenced using 2x50 bp paired-end sequencing. CBD and sCBD treatment induced 4489 and 1979 differentially expressed genes (DEGs; p <0.001, FDR step-up <0.05), respectively, with common upregulation of 857 genes and common downregulation of 648 genes. Common upregulated DEGs were associated with “response to unfolded protein”, “cell redox homeostasis”, “endoplasmic reticulum stress”, “oxidative stress” and “cellular response to hypoxia”. Common downregulated DEGs were linked to “sarcomere organization”, “skeletal muscle tissue development”, “regulation of muscle contraction”, “skeletal muscle contraction” and “muscle contraction”. CBD treatment induced 1342 unique upregulated DEGs and 1137 unique downregulated DEGs, compared to 154 and 152 unique up- and downregulated DEGs in sCBD. The transcriptional data indicate that CBD may induce mild cellular stress, activating pathways associated with altered redox balance, unfolded protein response, and endoplasmic reticulum stress. We hypothesize that CBD interacts with muscle and may elicit a ‘mitohormetic’ effect that warrants further investigation.
2024-09-25 | GSE272113 | GEO
Project description:The growth and development of duck skeletal muscle is an important economic trait that is genetically regulated. The internal mechanism underlying the regulation of skeletal muscle growth and development in ducks remains unclear. The purpose of this study was to identify candidate genes related to growth of duck skeletal muscle. RNA-sequencing technology was used to com-pare the transcriptome of duck breast muscles in an F2 population with the high breast muscle rate (HB) and the low breast muscle rate (LB). A total of 14,522 genes were confirmed to be ex-pressed in the breast muscle, and 173 differentially expressed genes (DEGs) were identified be-tween the HB and LB groups. Functional analysis showed that these DEGs were mainly involved in biological processes and pathways of fat metabolism and muscle growth, especially the FABP3 and MYL4 involved in the PPAR signaling pathway and cardiac muscle contraction pathway. These findings deepened our understanding of the molecular mechanisms involved in muscle growth in ducks, and provided a theoretical basis for improving duck production and breeding of ducks.
2021-10-24 | GSE185612 | GEO
Project description:The goal was to identify beef marbling related genes. Comparisons of skeletal muscle of well-marbled beef (HER, H-F) vs. lean beef (LIM). H-F vs. LIM -Dye-swap experiment
2014-02-28 | E-GEOD-46411 | biostudies-arrayexpress
Project description:The PDZ-LIM superfamily member is present in the nucleus of many cells and consists of one PDZ domain at the N-terminus and one or more LIM domains at the C-terminus. The family includes 10 genes, of which PDLIM3, PDLIM5 and LMO7 genes have been shown to promote mouse myoblast differentiation and participate in the regulation of skeletal muscle growth and development. To explore whether chicken PDLIM3, PDLIM5 and LMO7 genes have the same function, this study explored the expression of these genes in the before and after birth of chicken, and after the chicken skeletal muscle satellite cells cultured in vitro interfered with the expression of these genes. The proliferation and differentiation of satellite cells were finally analyzed by transcriptome sequencing. The molecular pathways involved in the regulation of cell proliferation and differentiation were analyzed. The main results are as follows: Transcriptome sequencing revealed that the differentially expressed genes of chicken skeletal muscle satellite cells interfering with PDLIM3 gene expression were mainly enriched in cGMP-PKG, Oxytocin, MAPK, Tight junction and other signaling pathways, and involved in cytoskeletal protein binding, actin binding, muscle tissue regeneration and development, adhesion and other functions. Transcriptome sequencing revealed that compared with the control group, the differentially expressed genes of chicken skeletal muscle satellite cells that interfered with PDLIM5 gene expression were mainly enriched in signaling pathways such as Tight junction, Oxytocin, p53, MAPK, and involved in myocyte production and muscle contraction. Muscle cell differentiation, and participate in cytoskeletal protein binding, actin cytoskeleton formation, actin and actin binding.
2020-05-30 | GSE151450 | GEO
Project description:Skeletal muscle aging results in a gradual loss of skeletal muscle mass, skeletal muscle function and decreased regenerative capacity, which can lead to sarcopenia and increased mortality. While the mechanisms underlying sarcopenia remain unclear, the skeletal muscle stem cell, or satellite cell, is required for muscle regeneration. Therefore, identification of signaling pathways affecting satellite cell function during aging may provide insights into therapeutic targets for combating sarcopenia. Here, we show that a cell-autonomous loss in self-renewal occurs via novel alterations in FGF and p38αβ MAPK signaling in old satellite cells. We further demonstrate that pharmacological manipulation of these pathways can ameliorate age-associated self-renewal defects. Thus, our data highlight an age-associated deregulation of a satellite cell homeostatic network and reveals potential therapeutic opportunities for the treatment of progressive muscle wasting. Satellite cells were isolated from young (3-6mo) and aged (20-25mo) adult mice; individual date files represent 2 independent pools of RNA from 4-8 mice at each timepoint.
2013-09-01 | E-GEOD-47104 | biostudies-arrayexpress
Project description:Training at sustainable swimming speeds can produce changes in fish skeletal muscle that are important for aquaculture due to their growth-potentiating effects. Such changes may be even more relevant when fish are fed diets containing an increasing proportion of carbohydrates as an energy source. We evaluated the effects of moderate-intensity sustained swimming on the transcriptomic response of red and white muscle in rainbow trout fed a carbohydrate-rich diet using microarray and qPCR. Analysis of the red and white muscle transcriptome revealed significant changes in the expression of a large number of genes (395 and 597, respectively), with a total of 218 differentially expressed genes (DEGs) common for both muscles. A large number of the genes involved in glucose use and energy generation, contraction, development, synthesis and catabolism of proteins were up-regulated in red and white muscle. Additionally, DEGs in both muscles were involved in processes of defense response and apoptosis. Skeletal muscle contraction activates a transcriptional program required for the successful adaptation of both muscles to the changing demands imposed by swimming conditions. Future studies should further clarify the mechanisms involved in the adaptation of both tissues to exercise and assess possible benefits of such conditions for cultured fish. Total RNA from pooled red and white skeletal muscle samples of individual rainbow trout from each group (resting fish, n=8; swimming fish, n=8) was labeled with Cy3-dUTP and Cy5-dUTP (GE Healthcare, Barcelona, Spain). We used a dye swap experimental design and each cDNA from a pooled RNA sample was hybridized to two microarrays. For the first slide, cDNAs from resting and swimming fish were labeled with Cy5 and Cy3, respectively, and for the second array dye assignment was reversed. Therefore, samples from individual fish within each group were pooled and expression values shown represent the means of 6 M-CM-^W 2 = 12 technical replicates. A total of four slides were used in this study
2014-05-01 | E-GEOD-47141 | biostudies-arrayexpress