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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome of soleus muscle of 129/SV mice

ABSTRACT: 1 year-old male 129/SV mice. Animals were acclimatized to housing in single cages for one week. Soleus muscle was harvested, total RNA isolated and subjected to transcript profiling with custom microarrays with custom-designed ATLASTM cDNA nylon filter as described (Dapp, C., Schmutz, S., Hoppeler, H. & Fluck, M. (2004) Physiol Genomics 20, 97-107). Keywords: Transcriptome Seven replicas

ORGANISM(S): Mus musculus

SUBMITTER: Martin FlÃ¼ck

PROVIDER: E-GEOD-8552 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Mechano-regulated tenascin-C orchestrates muscle repair.

Flück Martin M Mund Sonja I SI Schittny Johannes C JC Klossner Stephan S Durieux Anne-Cécile AC Giraud Marie-Noëlle MN

Proceedings of the National Academy of Sciences of the United States of America 20080829 36

Tenascin-C (TNC) is a mechano-regulated, morphogenic, extracellular matrix protein that is associated with tissue remodeling. The physiological role of TNC remains unclear because transgenic mice engineered for a TNC deficiency, via a defect in TNC secretion, show no major pathologies. We hypothesized that TNC-deficient mice would demonstrate defects in the repair of damaged leg muscles, which would be of functional significance because this tissue is subjected to frequent cycles of mechanical d ...[more]

PMID: 18757758

Similar Datasets

Transcriptome of soleus muscle of Tenascin-C deficient 129/SV mice

Project description:1 year-old male Tenascin-C deficient 129/SV mice with the targeted insertion of a beta-lactamase cassette in the NcoI site of exon 2 of the TNC gene (Forsberg, E., Hirsch, E., Frohlich, L., Meyer, M., Ekblom, P., Aszodi, A., Werner, S. & Fassler, R. (1996) Proc. Natl. Acad. Sci U. S. A 93, 6594-6599) were used for the study. Animals were derived from the original strain and back-crossed with wildtype 129/SV mice (Institut fÃ¼r Labortierkunde, University of Zurich). Animals were acclimatized to housing in single cages for one week. Soleus muscle was harvested, total RNA isolated and subjected to transcript profiling with custom microarrays with custom-designed ATLASTM cDNA nylon filter as described (Dapp, C., Schmutz, S., Hoppeler, H. & Fluck, M. (2004) Physiol Genomics 20, 97-107). Keywords: Transcriptome Seven biological replicas

2010-06-25 | E-GEOD-8550 | biostudies-arrayexpress

Transcriptome analysis of mouse muscle

Project description:This SuperSeries is composed of the following subset Series: GSE8549: Transcriptome of reloaded soleus muscle of 129/SV mice GSE8550: Transcriptome of soleus muscle of Tenascin-C deficient 129/SV mice GSE8551: Transcriptome of reloaded soleus muscle of Tenascin-C deficient 129/SV mice GSE8552: Transcriptome of soleus muscle of 129/SV mice Keywords: SuperSeries Refer to individual Series

2010-06-25 | E-GEOD-10050 | biostudies-arrayexpress

Transcriptome of reloaded soleus muscle of Tenascin-C deficient 129/SV mice

Project description:1 year-old male Tenascin-C deficient 129/SV mice with the targeted insertion of a beta-lactamase cassette in the NcoI site of exon 2 of the TNC gene (Forsberg, E., Hirsch, E., Frohlich, L., Meyer, M., Ekblom, P., Aszodi, A., Werner, S. & Fassler, R. (1996) Proc. Natl. Acad. Sci U. S. A 93, 6594-6599) were used for the study. Animals were derived from the original strain and back-crossed with wildtype 129/SV mice (Institut fÃ¼r Labortierkunde, University of Zurich). Animals were acclimatized to housing in single cages for one week followed by 7 days of hindlimb suspension and one day of reloading. Soleus muscle was harvested, total RNA isolated and subjected to transcript profiling with custom microarrays with custom-designed ATLASTM cDNA nylon filter as described (Dapp, C., Schmutz, S., Hoppeler, H. & Fluck, M. (2004) Physiol Genomics 20, 97-107). Keywords: Transcriptome Six biological replicas

2010-06-25 | E-GEOD-8551 | biostudies-arrayexpress

Transcriptome of reloaded soleus muscle of 129/SV mice

Project description:1 year-old male 129/SV mice. Animals were acclimatized to housing in single cages for one week followed by 7 days of hindlimb suspension and one day of reloading. Soleus muscle was harvested, total RNA isolated and subjected to transcript profiling with custom microarrays with custom-designed ATLASTM cDNA nylon filter as described (Dapp, C., Schmutz, S., Hoppeler, H. & Fluck, M. (2004) Physiol Genomics 20, 97-107). Keywords: transcriptome Six biological replicas

2010-06-25 | E-GEOD-8549 | biostudies-arrayexpress

A Dach2-Hdac9-Myog-Gdf5 signaling system regulates regeneration of neuromuscular synapses

Project description:Muscle denervation due to injury, disease or aging results in impaired motor function. Restoring neuromuscular communication requires axonal regrowth and regeneration of neuromuscular synapses. Muscle activity inhibits neuromuscular synapse regeneration. The mechanism by which muscle activity regulates regeneration of synapses is poorly understood. Dach2 and Hdac9 are activity-regulated transcriptional co-repressors that are highly expressed in innervated muscle and suppressed following muscle denervation. Here, we report that Dach2 and Hdac9 inhibit regeneration of neuromuscular synapses. Importantly, we identified Myog and Gdf5 as muscle-specific Dach2/Hdac9-regulated genes that stimulate neuromuscular regeneration in denervated muscle. Interestingly, Gdf5 also stimulates presynaptic differentiation and inhibits branching of regenerating neurons. Finally, we found that Dach2 and Hdac9 suppress miR206 expression, a microRNA involved in enhancing neuromuscular regeneration. RNAseq on innervated and 3 day denervated adult soleus muscle from wildtype mice is compared with that from 3 day denervated soleus muscle from Dach2/Hdac9 deleted mice to identify Dach2/Hdac9-regulated genes.

2015-10-29 | E-GEOD-58669 | biostudies-arrayexpress

Transcription profiling of normal adult rat extraocular muscle, cardiac muscle, leg (gastrocnemius-soleus) muscle and smooth muscle (stomach wall)

Project description:Comparison of normal adult rat extraocular muscle, cardiac muscle, leg (gastrocnemius-soleus) muscle and smooth muscle (stomach wall). Affymetrix microarray chip RG-U34A was used. MAS version 5 was used to analyze the muscle group differences. Data form part of publication: FASEB Journal 17: 1370-1372, 2003 (full length article available at http://www.fasebj.org/cgi/doi/10.1096/fj.02-1108fje).

2007-10-27 | E-GEOD-142 | biostudies-arrayexpress

Homozygous expression of the myofibrillar myopathy-associated p.W2710X filamin C variant reveals major pathomechanisms of sarcomeric lesion formation

Project description:Filamin C is mainly expressed in striated muscle cells where it localizes to Z-discs, myotendinous junctions and intercalated discs. Recent studies have revealed numerous mutations in the FLNC gene causing familiar and sporadic myopathies and cardiomyopathies with marked clinical variability. The most frequent myopathic mutation, p.W2710X, which is associated with myofibrillar myopathy, deletes the carboxy-terminal 16 amino acids from filamin C and abolishes the dimerization property of Ig-like domain 24. We previously characterized "knock-in" mice heterozygous for this mutation (p.W2711X), and have now investigated homozygous mice using protein and mRNA expression analyses, mass spectrometry, and extensive immunolocalization and ultrastructural studies. Although the latter mice display a relatively mild myopathy under normal conditions, our analyses identified major mechanisms causing the pathophysiology of this disease: (i) the expression level of filamin C protein is drastically reduced; (ii) mutant filamin C is relocalized from Z-discs to particularly mechanically strained parts of muscle cells, i.e. myotendinous junctions and myofibrillar lesions; (iii) the number of lesions is greatly increased and these lesions lack BAG3; (iv) the expression of HSPB7 is almost completely abolished. These findings indicate grave disturbances of BAG3-dependent and -independent autophagy pathways that are required for efficient lesion repair. In addition, our studies reveal general mechanisms of lesion formation and demonstrate that defective filamin C dimerization via its carboxy-terminal domain does not disturb assembly and basic function of myofibrils. An alternative dimerization site might compensate for that loss. Since filamins function as stress sensors, our data further substantiate that filamin C is important for mechanosensing in the context of Z‑disc stabilization and maintenance.

2020-09-09 | PXD020097 | Pride

MicroRNA expression in rat soleus muscle during atrophy induced by hindlimb suspension

Project description:The objective of the study was to identify microRNAs expressed in the rat soleus muscle and determine if their expression was changed in response to hindlimb suspension. The microRNA expression profile (Sanger miRBase 9.0) of the rat soleus muscle was determined in the following three groups: control (C), hindlimb suspended for 2 days (HS-2) or 7 days (HS-7). Three replicates were performed for each group.

2009-08-25 | E-GEOD-17776 | biostudies-arrayexpress

Targeted genetical genomic to identify genetic mechanisms affecting complex traits: example of meat pH in the chicken

Project description:Abstract:Genetical genomics has been suggested and proven to be a powerful approach to study the genotype-phenotype gap. However, the relatively low power of these experiments (usually related to the high cost) has hindered fulfilment of its promise, especially for loci (QTL) of moderate effects. One strategy to overcome the issue is to use a targeted approach: to focus the experiment on one QTL of particular interest. It has two clear advantages: (i) It reduces the problem to a simple comparison between different genotypic groups at the QTL and (ii) it is a good starting point to investigate downstream effects of the QTL. In the present study, from 698 F2 birds used for QTL mapping, gene expression profiles of 24 (12 from each homozygote genotypes at the QTL) were investigated. The targeted QTL was located on chromosome 1 and affected initial pH of meat. The biological mechanisms controlling this trait can be similar to those affecting malignant hyperthermia or muscle fatigue in human. The gene expression study identified ten strong local signals (potentially cis-eQTL) which were markedly more significant compared to the rest of the genome. The differentially expressed genes all mapped to a region < 1 Mb, suggesting a remarkable reduction of the QTL interval compared to the linkage study. These results combined with analysis of downstream effect of the QTL (using gene network analysis) suggest that the QTL is controlling pH by governing oxidative stress. The eQTL results were reproducible with using as few as 4 arrays on pooled samples (with lower significance level). The results demonstrate that this cost effective approach is promising not only for characterization of a QTL also for studying its downstream effects. there are 24 samples from to different genotypes. Each group of genotype has 12 samples. The two groups are compared using a dye balanced design.

2014-05-02 | E-GEOD-47800 | biostudies-arrayexpress

Advanced fiber type-specific protein profiles derived from adult murine skeletal muscle

Project description:Skeletal muscle is a heterogeneous tissue consisting of blood vessels, connective tissue, and muscle fibers. The last are highly adaptive and can change their molecular composition depending on external and internal factors, such as exercise, age, and disease. Thus, examination of the skeletal muscles at the fiber type level is essential to detect potential alterations. Therefore, we established a protocol in which myosin heavy chain isoform immunolabeled muscle fibers were laser microdissected and separately investigated by mass spectrometry to develop advanced proteomic profiles of all murine skeletal muscle fiber types. Our in-depth mass spectrometric analysis revealed unique fiber type protein profiles, confirming fiber type-specific metabolic properties and revealing a more versatile function of type IIx fibers. Furthermore, we found that multiple myopathy-associated proteins were enriched in type I and IIa fibers. To further optimize the assignment of fiber types based on the protein profile, we developed a hypothesis-free machine-learning approach (available at: https://github.com/mpc-bioinformatics/FiPSPi), identified a discriminative peptide panel, and confirmed our panel using a public data set.

2021-06-07 | PXD025359 | Pride

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