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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data for C2C12 differentiation disrupted by Lrrfip1 knockdown

ABSTRACT: C2C12 myoblasts differentiation is a precise controlled process. Splicing of many genes changes during the differentiation process. Some muscle-specific splicing isoforms play important role in myogenesis. We used microarrays to detail the global programme of gene expression underlying defect of lrrfip1a, a muscle specific splicing isoform of Lrrfip1. Differentiated C2C12 myoblasts shLUCI or shLrrfip1a were collected and extracted RNA, then hybridizated on Affymetrix. We sought to obtain the different expressed genes between shLUCI and shLrrfip1a samples.

ORGANISM(S): Mus musculus

SUBMITTER: Ning Wei

PROVIDER: E-GEOD-66924 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data for C2C12 differentiation disrupted by Lrrfip1 knockdown

Project description:C2C12 myoblasts differentiation is a precise controlled process. Splicing of many genes changes during the differentiation process. Some muscle-specific splicing isoforms play important role in myogenesis. We used microarrays to detail the global programme of gene expression underlying defect of lrrfip1a, a muscle specific splicing isoform of Lrrfip1.

2015-04-01 | GSE66924 | GEO

Comprehensive analysis of the proteome, phosphoproteome and N-linked sialylated glycoproteome of C2C12 myoblasts

Project description:C2C12 myoblast is a model that has been used extensively to study the process of skeletal muscle differentiation. Proteomics has advanced our understanding of skeletal muscle biology and the process of myogenesis. However, there is still no deep coverage of C2C12 myoblast proteome, which is important for the understanding of key drivers for the differentiation of skeletal muscle cells. Here, we conducted a multi-dimensional proteome profiling with TiSH strategy to get a comprehensive analysis of proteome, phosphoproteome and N-linked sialylated glycoproteome of C2C12 myoblasts. A total of 8313 protein groups were identified in C2C12 myoblasts, including 7827 protein groups from non-modified peptides, 3803 phosphoproteins and 977 formerly N-linked sialylated glycoproteins.

2020-11-27 | PXD011334 | Pride

Transcriptome-wide Regulation of Splicing and mRNA Localization by Muscleblind Proteins

Project description:The Muscleblind-like (Mbnl) family of RNA-binding proteins plays important roles in muscle and eye development and in Myotonic Dystrophy (DM), where expanded CUG or CCUG repeats functionally deplete Mbnl proteins. We identified transcriptome-wide functional and biophysical targets of Mbnl proteins in brain, heart, muscle, and myoblasts using RNA sequencing and crosslinking/immunoprecipitation-sequencing approaches. This analysis identified several hundred splicing events whose regulation depended on Mbnl function, in a pattern indicative of functional interchangeability between Mbnl1 and Mbnl2. A nucleotide resolution RNA map associated repression or activation of exon splicing with Mbnl binding near either 3' splice site or near the downstream 5' splice site, respectively. Transcriptomic analysis of sub-cellular compartments uncovered a global role for Mbnls in regulating localization of mRNAs encoding membrane, synaptic and other proteins in both mouse and Drosophila cells, and Mbnls also contribute to protein secretion. These findings hold several new implications for DM pathogenesis. To assess global functions of Muscleblind proteins, RNA-Seq was performed using WT and Mbnl1 KO brain, heart, and muscle (5 mice each). Additionally, C2C12 mouse myoblasts were depleted of Mbnl1, Mbnl2, or both. Subcellular fractionation experiments were performed to analyze mRNA localization following depletion of Mbnl1 and Mbnl2 in C2C12 mouse myoblasts, and following depletion of Mbnl in Drosophila S-2R+ cells. CLIP-Seq was also performed against Mbnl1 in mouse brain, heart, muscle, and C2C12 myoblasts. Finally, ribosome footprinting was performed with C2C12 mouse myoblasts that were depleted of Mbnl1, Mbnl2, or both.

2012-08-17 | E-GEOD-39911 | biostudies-arrayexpress

Quaking is a global regulator of muscle-specific alternative splicing in vertebrates [siRNA data]

Project description:This work provides the first evidence that Qk is a global regulator of splicing in vertebrates, defines a new splicing regulatory network in muscle, and suggests that overlapping splicing networks contribute to the complexity of changes in alternative splicing during differentiation. Alternative splicing contributes to muscle development and differentiation, but the complete set of muscle splicing factors and their combinatorial interactions are not known. Previously work identifies ACUAA (STAR motif) as an enriched sequence near muscle-specific alternative exons such as Capzb exon 9. We did mass spectrometry of proteins selected by wild type and mutant Capzb intron 9 RNA affinity chromatography, and identified Quaking (Qk), a protein known to regulate mRNA function through ACUAA motifs in 3' UTRs. We show that in myoblasts, Qk promotes inclusion of Capzb exon 9 in opposition to repression by PTB. Qk knockdown in myoblasts has little effect on transcript levels, but alters inclusion of 824 cassette exons whose adjacent intron sequences are enriched in ACUAA motifs. During differentiation to myotubes, Qk levels increase 2-3 fold, suggesting a mechanism for Qk-responsive exon regulation. We captured the PTB splicing regulatory network and intersected it with the Qk network, identifying overlap between the functions of Qk and PTB. Approximately 60% of exons whose inclusion is altered during myogenesis appear to be under control of one or both of these splicing factors in myoblasts. This series is the C2C12 Qk and PTB siRNA data. It is 12 arrays: 3 PTB siRNA arrays , 3 Qk siRNA arrays, and 6 mock siRNA arrays.

2013-06-05 | E-GEOD-40961 | biostudies-arrayexpress

Quaking is a global regulator of muscle-specific alternative splicing in vertebrates [differentiation data]

Project description:This work provides the first evidence that Qk is a global regulator of splicing in vertebrates, defines a new splicing regulatory network in muscle, and suggests that overlapping splicing networks contribute to the complexity of changes in alternative splicing during differentiation. Alternative splicing contributes to muscle development and differentiation, but the complete set of muscle splicing factors and their combinatorial interactions are not known. Previously work identifies ACUAA (STAR motif) as an enriched sequence near muscle-specific alternative exons such as Capzb exon 9. We did mass spectrometry of proteins selected by wild type and mutant Capzb intron 9 RNA affinity chromatography, and identified Quaking (Qk), a protein known to regulate mRNA function through ACUAA motifs in 3' UTRs. We show that in myoblasts, Qk promotes inclusion of Capzb exon 9 in opposition to repression by PTB. Qk knockdown in myoblasts has little effect on transcript levels, but alters inclusion of 824 cassette exons whose adjacent intron sequences are enriched in ACUAA motifs. During differentiation to myotubes, Qk levels increase 2-3 fold, suggesting a mechanism for Qk-responsive exon regulation. We captured the PTB splicing regulatory network and intersected it with the Qk network, identifying overlap between the functions of Qk and PTB. Approximately 60% of exons whose inclusion is altered during myogenesis appear to be under control of one or both of these splicing factors in myoblasts. This series is the C2C12 differentiation data. It is 9 arrays, 3 timepoints, with 3 replicates. The time points are 0 hrs, 24 hrs, and 72hrs.

2013-06-05 | E-GEOD-40956 | biostudies-arrayexpress

Transcriptome changes during the differentiation of myoblasts into myotubes

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

The transcriptome and m6A-epitranscriptome during skeletal muscle differentiation

Project description:Mouse C2C12 myoblasts were used to mimic skeletal muscle differentiation in vitro.Using RNA-seq and MeRIP-seq, we generated the tascriptome and epitranscriptome data of undifferentited C2C12 myoblasts in growth medium (GM) and differentiated myotubes in differentitation medium for 4 days (D4).

2021-07-22 | GSE180431 | GEO

Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation

Project description:We report that differentiation of the C2C12 myoblast line on patterened hydrogels results in the increased expression of muscle sarcomere genes and more closely models expression changes that happen in in vivo muscle differentiation than do C2C12 myoblasts cultured on unpatterened substrates.

2020-04-15 | GSE148667 | GEO

Characteristics of the transcriptome of a nurse cell harboring muscle larva of Trichinella spiralis

Project description:Muscle larva of a parasitic nematode Trichinella spp. lives a portion of muscle fiber transformed to a nurse cell (NC). The NC is formed from miss-differentiated muscle satellite cells which have fused with a parasite-invaded degenerating myofiber. Though originating from muscle cells, the NC is of non-muscular type.The NC is multinuclear and hypertrophic. Molecular mechanism of the NC development remains largely unknown. The microarray project was aimed at characterization of the NC transcriptome. The NCs were isolated by enzymatic digestion from infected mouse striated muscles. Murine C2C12 myogenic cell line (ATCC) was cultured in vitro. Differentiation of myoblasts into myotubes was carried out for 6 days in a high-glucose DMEM supplemented with 2% heat-inactivated horse serum, on the plates covered with laminin and collagen IV.The NC transcriptome was referred to the transcriptomes of C2C12 myoblasts and C2C12 myotubes in two sets of camparative expression microarray hybridization experiments, NC vs myoblasts and NC vs myotubes, respectively.

2022-07-26 | E-MTAB-12042 | biostudies-arrayexpress

Expression data from C2C12 myotubes infected with adenovirus expressing Gli1

Project description:We sought to determine the effects of over-expression of Gli1 on gene expression in C2C12 myotube cultures. C2C12 myoblasts were induced to differentiate for 4 days. At that time, when >80% of nuclei were incorporated into multi-nucleated syncitial myotubes, we infected the cultures with recombinant adenovirus expressing GFP alone or GFP and a full length human Gli1. Media was changed 12 hours later. Cultures were lysed 60 hours after the initial infection. Gli1 over-expression induces de-differentiation of myotubes and proliferation of myoblasts. Results provide insight into the molecular basis of SHH signaling on skeletal muscle cells.

2013-12-01 | E-GEOD-37702 | biostudies-arrayexpress

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