Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression data from differentiating primary culture of equine satellite cells (ESC) incubated with gamma-oryzanol (GO)

ABSTRACT: Transcriptional profiling of gamma-oryzanol-treated (24h) differentiating equine satellite cells (3rd day of differentiation) compared to control GO-untreated cells. Goal was to determine the effects of gamma-oryzanol influence on gene expression in equine satellite cells during in vitro myogenesis Two-condition experiment, GO-treated (24h) differentiating equine satellite cells (3rd day of differentiation) vs. differentiating equine satellite cells without GO treatment (control). Biological replicates: 4 reps of examined condition (Cy5), 4 control replicates (Cy3)

ORGANISM(S): Equus caballus

SUBMITTER: Tomasz Sadkowski

PROVIDER: E-GEOD-73730 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Background: Follistatin (FS) is an activin-binding glycoprotein, known for its antagonistic action on the TGF-M-NM-2 super-family of cytokines. It has ability to prevent muscle atrophy and to stimulate muscle growth through binding of myostatin (GDF8). FS does not cause these changes only by inhibition of GDF8 but this mechanism is still not well elucidated. In order to identify GDF8-dependent and GDF8-independent action of FS, we performed comprehensive transcriptomic analysis of differentiating C2C12 mouse myoblasts. Results: To evaluate influence of FS-288 (200ng/ml) on differentiating C2C12 myoblasts was used immunofluorescence analysis of MyHC protein expression in the culture and counting of the number and type of myotubes. Differentiating myoblasts treated with FS showed increase in number and size of myotubes. Microarray studies performed by us identified 30 genes oppositely regulated by FS and GDF8. Analyses of the transcriptomic profiles showed that FS has highly significant influence, associated with GDF8 binding, on the regulation of cell cycle, transport processes, cell communication, cell adhesion, cell motion, developmental processes and binding functions. The signalling pathways that may play a primary role in the myogenesis stimulation by FS are associated with TGF-M-NM-2, Delta-Notch and Wnt signalling pathways, integrin and actin cytoskeleton signalling and adipogenesis regulation. Changes in expression of Hgf, Sort1, Trdn, Stmn2, Hdac1 genes, significantly involved in the process of myoblasts differentiation were validated with Real-Time PCR method. Conclusions: Our results implicate which aspects of transcriptional regulation of myogenesis process by FS could have significant and protective influence. We have shown that FS activity is associated not only with GDF8 binding but also with inhibited expression of genes involved in TGF-M-NM-2 signalling and by regulating of genes associated with vesicle transport apoptosis signalling pathway, inflammatory pathways and adipogenesis expression. Our analysis showed that follistatin GDF8-independent on differentiating myotubes involves regulation of localization processes, cell-matrix adhesion, mRNA processing, apoptosis, fatty acid metabolic processes, SNAP receptor activity functions and partial regulation of transcription processes. These results give a new and complete image of the follistatin role in the muscle cell differentiation and indicate target genes for FS which in the future may be a good therapeutic approach. After scanning of hybridized microarrays, quantitation of slide images were performed using Feature Extraction Software 10.7.3.1 (Agilent) using default parameters. Normalized raw data was exported to GeneSpring GX 11.0.5 (Agilent, Santa Clara, CA). For identification of genes significantly altered in cells treated with FSl compared with untreated cells. T total detected entities were filtered by flags (present, marginal) and error (coefficient of variation: CV < 50.0 percent) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, separated for experiment with myoblasts treated with FS(FS vs. CTRL 1-4) was used t-test unpaired (p < 0.05) with multiple testing correction: Benjamini-Hochberg <0.05, all significant changes over fold change 1.6 were selected. Analysis of GO, GSEA and signaling pathway was carried out using GeneSpring GX 12 (Agilent) and the DAVID, KEEG and PANTHER Classification System (p<0.01). In the analysis of signaling pathways using GeneSpring GX 12 (Agilent) and Ariadne Pathway Studio.

Project description:GDF8 (myostatin) is a unique cytokine strongly affecting the skeletal muscle phenotype in human and animals. The aim of the present study was to elucidate the molecular mechanism of myostatin influence on the differentiation of mouse C2C12 myoblasts, using the global-transcriptome analysis with the DNA microarray technique. Treatment with exogenous GDF8 strongly affected the growth and development of C2C12 mouse myoblasts. This was manifested by the inhibition of proliferation and differentiation as well as the impairment of cell fusion. DNA microarray analysis revealed 778 genes regulated by GDF8 in differentiating myoblasts (543 down-regulated and 235 up-regulated). Ontological analysis revealed their involvement in 17 types of biological processes, 10 types of molecular functions and 68 different signaling pathways. The effect of GDF8 was mainly mediated by the disruption of the cell cycle, calcium and insulin signaling pathways and expression of cytoskeletal and muscle specific proteins. The identified key-genes that could play a role as GDF8 targets in differentiating myoblasts are: Mef2, Hgf, Ilb1, Itgb1, Edn1, Ppargc1a. After scanning of hybridized microarrays, quantitation of slide images was performed using Feature Extraction Software (Agilent) using default parameters. The raw data were normalized by Loess normalization method, and then the normalized raw data was exported to GeneSpring GX 11.0.5 (Agilent, Santa Clara, CA). For identification of genes significantly altered in cell compared with the control normal gene set, total detected entities were filtered by flags (present, marginal) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, separated for experiment with myoblasts treated with GDF8 ([C2C12]-[GDF8]1-4) was used t-test unpaired (p < 0.05) and fold change over 1.6. Analysis of GO and signaling pathway was carried out using GeneSpring GX 12 (Agilent), KEGG and PANTHER Classification System (http://www.pantherdb.org/). In the analysis of signaling pathways using Panther, a total of 68 cellular pathways were identified.

Dataset Information

Expression data from differentiating primary culture of equine satellite cells (ESC) incubated with gamma-oryzanol (GO)

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure