Gene expression induced by TSA in undifferentiated human primary myoblasts versus terminally differentiated human myotubes
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE27073 | GEO | 2011/03/01
SECONDARY ACCESSION(S): PRJNA137561
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression analysis in human skeletal myoblasts (undifferentiated mononucleated cells, cultured in growth medium - 15% FBS) and human skeletal myotubes (pre-formed myotubes, cultured in differentiation medium – 2% horse serum) exposed to the HDACi TSA (50nM) for 24 hours TSA treated undifferentiated human primary myoblasts and terminally differentiated human myotubes
2011-03-01 | E-GEOD-27073 | biostudies-arrayexpress
Project description:This study aimed to interrogate the interrelationship between 3D genome organization and global gene expression during muscle development using a mouse C2C12 cell line as an in vitro model. The C2C12 cell line is a well-established and extensively studied in vitro model derived from serial passage of myoblasts cultured from the thigh muscle of C3H mice after a crush injury. C2C12 cells divide when mitogens are present in the culture medium and spontaneously differentiate into muscle-like multinucleated (myotubes) cells if the medium is depleted of mitogens (i.e. serum; (Bischoff 1986)). C2C12 cells were either harvested as: 1) proliferating myoblasts (Myoblasts); 2) myotubes that were not treated with AraC (as such these myotubes contained myoblasts) - Myotubes(Day3); or 3) myotubes which were treated with AraC (myoblasts were largely depleted from these myotube cultures; Myotubes(Day7+AraC).
2017-04-07 | GSE84158 | GEO
Project description:Analysis of C2C12 myotubes treated with dexamethasone (Dex) for 6 or 24 hours. Dex is a synthetic glucorticoid receptor agonist. Results provide insight to the effect of glucocorticoids on myotubes. C2C12 myotubes were cultured in DMEM supplemented with 2% horse serum, and treated with 1 u? Dex or an equal volume (0.01% v/v of media) of vehicle control ethanol for 6 or 24 hours. Total cellular RNA was isolated utilizing the NucleoSpin RNA II kit (Macherey-Nagel). RNA isolates were first quantified by standard spectrophotometry, and then qualitatively evaluated by capillary electrophoresis employing the Bio-Rad Experion system per manufacturer’s instruction. The final labeled cRNA samples were hybridized overnight to Illumina mouseWG-6 BeadChip arrays, which was performed at UCSF Genomic Core. All treatments were done in triplicates and the same batch of microarrays were used for all treatments. The Illumina expression arrays were pre-processed using lumi package. The differential expression analysis was performed using the Limma package.
2011-04-25 | E-GEOD-28840 | biostudies-arrayexpress
Project description:Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells. Time course: 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days. Experiment Overall Design: this experiment include 10 samples and 90 replicates
2008-04-05 | E-GEOD-10424 | biostudies-arrayexpress
Project description:Aging of skeletal muscle tissue is characterized by loss of metabolic and contractile competence. It is thought that this phenomenon is driven via extrinsic and intrinsic factors. In order to identify age-dependent changes intrinsic to the muscle cell, microarray transcriptional profiles and measurements of glucose metabolism were performed in primary cultured human myotubes at different time points over seven weeks. Aging in culture tended to reduce myotube glucose metabolism, oxidative and storage capacities, despite elevation of glucose transport. The mitochondrial membrane potential slightly increased, whereas peroxidation of cell membrane lipids declined and membrane integrity was preserved. Transcriptional analysis revealed a fall in genes involved in glucose metabolism and oxidative phosphorylation, while stress defense genes were elevated. Expression of numerous genes coding for muscle contractile proteins and calcium-regulating proteins, was gradually decreased during aging of cultured myotubes. Transcripts of genes involved in cell growth, matrix and motility markedly rose while those involved in cell adhesion dropped. In conclusion, aging myotubes in culture exhibit a loss of glucose metabolic capacity. They are characterized by a shift from a contractile to a growth-survival, matrix-remodeling phenotype. This pattern of changes, linked to intrinsic factors, displays significant similarities with aging of muscle from primates and human subjects. Keywords = aging Keywords = muscle cell biopsy Keywords = myotubes Keywords = glucose Keywords: time-course
2004-05-31 | GSE1144 | GEO
Project description:ATF4 is a bZIP transcription factor that that promotes skeletal muscle atrophy. The goal of these studies was to determine the effects of ATF4 overexpression on mRNA levels in differentiated C2C12 myotubes. For additional details see Ebert et al, Stress-Induced Skeletal Muscle Gadd45a Expression Reprograms Myonuclei and Causes Muscle Atrophy. JBC epub. June 12,2012 C2C12 myotubes were infected with adenovirus co-expressing eGFP and ATF4-FLAG. Control myotubes were infected with adenovirus co-expressing eGFP and a transcriptionally inactive ATF4 construct (ATF4∆bZIP).
2012-09-15 | E-GEOD-39194 | biostudies-arrayexpress
Project description:Traditional differentiation of myoblasts is usually induced by serum starvation method, in which 2%HS is used to induce myoblasts to differentiate into myotubes. But, traditional serum starvation method is difficult to differentiate large yellow croaker muscle satellite cells efficiently. Although myotubes were induced within 2-3 days with medium containing 2% horse serum (HS), they detached shortly and died soon after. To improve differentiation efficiency and survival rate, different combinations of basal medium, serum ratios and myogenic factors were evaluated. Finally, the F12 medium containing 8% HS, 10 ng/ml IGF-1, 50 nM necrosulfonamide and 200 μM ascorbic acid was identified as an effective recipe for myogenic differentiation. On day 3 of culture in this differentiation medium, elongated myotubes began to appear, and on day 6, striations similar to skeletal muscle were observed in some of myotubes. But it is still inefficient, the fusion index (the proportion of nuclei in multinucleated myotubes) was 6.39% on day 3 and 1.30% on day 6 (1.30%) .Therefore, we need to find a more efficient method to induce myogenic differentiation. We then performed gene expression profiling analysis using data obtained from RNA-seq of Large yellow croaker muscle satellite cells during differentiation at three time points(day0,day3,day6).
2023-08-08 | GSE212904 | GEO
Project description:Metabolically healthy skeletal muscle is characterized by the ability to switch easily between glucose and fat oxidation, whereas loss of this ability seems to be related to insulin resistance. The aim of this study was to investigate whether different fatty acids (FAs) and the LXR ligand T0901317 affected metabolic switching in human skeletal muscle cells (myotubes). Pretreatment of myotubes with eicosapentaenoic acid (EPA) increased suppressibility, the ability of glucose to suppress FA oxidation, and metabolic flexibility, the ability to increase FA oxidation when changing from “fed” to “fasted” state. Adaptability, the capacity to increase FA oxidation with increasing FA availability, was increased after pretreatment with EPA, linoleic acid (LA) and palmitic acid (PA). T0901317 counteracted the effect of EPA on suppressibility and adaptability, but did not affect these parameters alone. EPA itself accumulated less, however, EPA, LA, OA and T0901317 increased the number of lipid droplets (LDs) in myotubes, whereas LD size and mitochondria amount were independent of pretreatment. Microarray analysis showed that EPA regulated more genes than the other FAs. Some pathways involved in carbohydrate metabolism were induced only by EPA. The present study suggests a possible favorable effect of EPA on skeletal muscle metabolic switching and glucose utilization. Keywords: Analysis of target gene regulation by using microarrays. Primary human myotubes, derived from 3 healthy, female donors, were preincubated with different fatty acids (oleic acid [OA], palmitic acid [PA], eicosapentaenoic acid [EPA] or linoleic acid [LA], each at 100 µM) or bovine serum albumin [BSA] (40 µM) for 24 h.
2010-06-23 | E-GEOD-18589 | biostudies-arrayexpress
Project description:Aging of skeletal muscle tissue is characterized by loss of metabolic and contractile competence. It is thought that this phenomenon is driven via extrinsic and intrinsic factors. In order to identify age-dependent changes intrinsic to the muscle cell, microarray transcriptional profiles and measurements of glucose metabolism were performed in primary cultured human myotubes at different time points over seven weeks. Aging in culture tended to reduce myotube glucose metabolism, oxidative and storage capacities, despite elevation of glucose transport. The mitochondrial membrane potential slightly increased, whereas peroxidation of cell membrane lipids declined and membrane integrity was preserved. Transcriptional analysis revealed a fall in genes involved in glucose metabolism and oxidative phosphorylation, while stress defense genes were elevated. Expression of numerous genes coding for muscle contractile proteins and calcium-regulating proteins, was gradually decreased during aging of cultured myotubes. Transcripts of genes involved in cell growth, matrix and motility markedly rose while those involved in cell adhesion dropped. In conclusion, aging myotubes in culture exhibit a loss of glucose metabolic capacity. They are characterized by a shift from a contractile to a growth-survival, matrix-remodeling phenotype. This pattern of changes, linked to intrinsic factors, displays significant similarities with aging of muscle from primates and human subjects.
2007-07-19 | E-GEOD-1144 | biostudies-arrayexpress
Project description:In muscle, reactive oxygen species (ROS) generation increases with strenuous activity, chronic unloading, and inflammatory stimuli; skeletal muscle function is very sensitive to ROS; and there are redox-sensitive signaling pathways. Using myogenic cell cultures, we asked whether hydrogen peroxide (H2O2) induces adaptive changes in skeletal muscle gene expression. H2O2 downregulated or failed to induce antioxidant or apoptotic genes in the myotubes. Instead, H2O2 changed the expression of genes for cytosolic and mitochondrial enzymes, and upregulated inflammatory mediators. Finally, H2O2 had a mostly inhibitory effect on the expression of many transcription factors. The results indicate that mild oxidative stress may induce an adaptive response in skeletal muscle without antioxidant upregulation or apoptosis. Experiment Overall Design: Cell Culture: Experiment Overall Design: C2C12 myoblasts (ATCC, Rockville, MD) were cultured in DMEM supplemented with 10% fetal calf serum at 37°C in 5% CO2. Myoblast differentiation was initiated by switching to differentiation medium (DMEM supplemented with 2% heat-inactivated horse serum) and allowed to continue for 96 hrs. Differentiated myotubes were treated for 2 hours with H2O2 (Sigma-Aldrich, St. Louis, MO) 0, 1, 10, 100, or 1000 uM in DMEM supplemented with 0.5% heat-inactivated horse serum. Experiment Overall Design: cDNA microarrays: Experiment Overall Design: Total RNA was obtained from treated C2C12 myotubes with TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer's recommended protocol.Oligonucleotide microarray studies with Affymetrix Mouse Genome 430A gene chips (n=20 chips) were conducted as described earlier. Microarrays were washed and stained with a streptavidin-bound marker and scanned. Data were analyzed with Affymetrix Microarray Suite 5.0 software. Only genes with consistent absent/present calls in all four independent replicates per group were considered for further analysis. Treatment comparisons were crossed so that each H2O2 sample was compared to each control. The software uses the one-sided Wilcoxon's signed rank test to estimate increase/no change/ decrease difference calls for each pair-wise comparison. Only difference calls consistent in all pair-wise comparisons and with average changes > 1.75 were considered significant, resulting in a conservative list of genes with changed expression levels. Functional classification of genes was based on an extensive literature review.
2007-09-07 | E-GEOD-3078 | biostudies-arrayexpress