RNA-seq for transcriptome analysis in myoblasts, myotubes and osteoblasts trans-differentiated from C2C12 myoblasts
ABSTRACT: We performed total transcriptome analysis by RNA-seq to find novel long non-coding RNAs which are differentiatlly expressed in myogenesis or osteogenesis. Overall design: Total RNA extracted from C2C12 myoblasts, 3-days differentiated myotubes, and 3-days trans-differentiated osteoblasts using BMP2 was used for transcriptome analysis.
Project description:Sin3A and Sin3B bind to distinct and overlapping target sites. Sin3 proteins bind to distinct sites in cycling myoblasts whereas there is a converge of Sin3A and Sin3B proteins to sites in differentiated myotubes. We identified a subset of Sin3 target genes involved in muscle differentiation and physiology and showed that conditional ablation of Sin3 proteins in vivo in mouse results in sarcomere defects Examination of Sin3A and Sin3B binding during myogenesis
Project description:Sin3A and Sin3B bind to distinct and overlapping target sites. Sin3 proteins bind to distinct sites in cycling myoblasts whereas there is a converge of Sin3A and Sin3B proteins to sites in differentiated myotubes. We identified a subset of Sin3 target genes involved in muscle differentiation and physiology and showed that conditional ablation of Sin3 proteins in vivo in mouse results in sarcomere defects Overall design: Examination of Sin3A and Sin3B binding during myogenesis
Project description:The novel lncRNA ChRO1 (Chromatin ReOrganization associated lncRNA 1) which we discovered seems to be involved in myogenesis by association with heterochromatin reorganization during muscle differentiation. We wanted to identify which genes are influenced by ChRO1 depletion in muscle differentiation. Analysis of the function of ChRO1 during myogenesis in gene expression level. The hypothesis in present study was that ChRO1 promotes myogenesis. Results provide important information that ChRO1 is involved in expression of various myogenic genes. Overall design: mRNA obtained from wild-type myoblasts and myotubes (Scr_MB,Scr_MT), and ChRO1 depleted myoblasts and myotubes (sh#1_MB,sh#1_MT)
Project description:Chick is an ideal model system for myogenesis study. Lots of genes would change their expression during myogenesis, however, is there any difference about gene expression between chick and mice? Our study represents the first detailed analysis of the transcriptomes of chicken primary myoblasts and myotubes, with biologic replicates, generated by RNA-seq technology. The data reported here may provide an important understanding of the genes involved in the regulation of chicken myogenesis. Overall design: Examination of differentially expressed genes in chicken myoblasts versus myotubes
Project description:Maps of genomic regions in proximity to the nuclear lamina were determined in undifferentiated C2C12 myoblasts (MBs) and 6 day differentiated C2C12 myotubes (MTs) using DamID with a Dam-Lamin B1-encoding lentivirus. Overall design: Examination of Lamin B1-chromatin contacts in one cell line in undifferentiated myoblast and differentiated myotube conditions.
Project description:During the last decade, skeletal muscle-secreted proteins have been identified with important roles in intercellular communications. To investigate whether muscle-derived exosomes participate in this molecular dialog, we determined and compared the protein contents of the exosome-like vesicles (ELVs) released from C2C12 murine myoblasts during proliferation (ELV-MB), and after differentiation into myotubes (ELV-MT). Using a proteomic approach combined with electron microscopy, western-blot and bioinformatic analyses, we compared the protein repertoires within ELV-MB and ELV-MT. RAW files were processed using MaxQuant  version 126.96.36.199. Spectra were searched against the Uniprot database (August 2012 version, Mus musculus taxonomy 10090, 86644 sequences, Bos taurus taxonomy 9913, 34280 sequences and Equus caballus taxonomy 9796, 24299 sequences) and the frequently observed contaminants database (notably containing protein sequences from serum proteins) embedded in MaxQuant. Trypsin was chosen as the enzyme and 2 missed cleavages were allowed. Precursor mass error tolerances were set respectively at 20 ppm and 6 ppm for first and main searches. Fragment mass error tolerance was set to 0.5 Da. Peptide modifications allowed during the search were: trioxidation (C, fixed), acetyl (N-ter, variable), dioxidation (M, variable), oxidation (M, variable) and deamidation (NQ, variable). Minimum peptide length was set to 7 amino acids. Minimum number of peptides, razor+unique peptides and unique peptides were set respectively to 2, 2 and1. Maximum false discovery rates - calculated by employing a reverse database strategy - were set to 0.01 at peptide and protein levels.
Project description:This analysis compares various timepoints from Day -1, 50% confluency myoblasts to Day 5 post differentiation myotubes. Consecutive timepoints and myoblasts vs. myotubes are compared. Keywords: time course http://www.biodatamining.org/content/1/1/4 Overall design: 8 time points from Day -1 to Day 5, three replicates for each time point.
Project description:By applying ChIP-seq, we generated genome-wide maps of c-Myc in skeletal myoblasts and myotubes. We found that c-Myc binds to 19354 confident target with a large portion residing in the intergenic regions. In addition, c-Myc was found to regulate many loci. Further detailed study revealed that c-Myc can regulate some genes, miRNAs, and lincRNAs which are fucntional in skeletal myogenesis. In this study, we identified a c-Myc induced regulatory pathway in myogensis. Overall design: Examination of c-MYC targets in myoblasts versus myotubes
Project description:Prion infection in animals results in neurodegeneration and eventually death. To examine the cellular impact of Prion disease, we profiled non-proliferative fully differentiated C2C12 cells, which can replicate prions to high levels. Results suggest that accumulation of high levels of PrPSc in C2C12 myotubes does not cause any overt cellular dysfunction or molecular pathology. C2C12 cells were differentiated into confluent myotubes. Cells were infected or not with 100ul of 10% brain homogenate obtained from a C57BL/6 mouse clinically affected with RML prions. 16 days after infection, cells were collected by scraping and RML was purified.
Project description:This analysis compares various timepoints from Day -1, 50% confluency myoblasts to Day 5 post differentiation myotubes. Consecutive timepoints and myoblasts vs. myotubes are compared. Experiment Overall Design: 8 time points from Day -1 to Day 5, three replicates for each time point.