Gene expression profile in mouse skeletal muscle after 4F induction
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE148911 | GEO | 2021/03/22
REPOSITORIES: GEO
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Project description:Skeletal muscle is heterogeneous in nature and distinguished as red muscle and white muscle because of their myofiber composition. Soleus (SOL) is a typical red muscle and extensor digitorum longus (EDL) is a typical white muscle. In this study, we compared the transcriptome difference of soleus and extensor digitorum longus from three 10-week-old Yorkshire boars with porcine Affymetrix microarray.
2014-12-31 | E-MTAB-2419 | biostudies-arrayexpress
Project description:To determine the gene expression profile of extensor digitorum longus (EDL) and soleus (SO) muscles of wild-type and Ts1Cje mouse model of Down Syndrome (DS). Two types of skeletal muscles (EDL and SO) were harvested from both Ts1Cje and its disomic littermate.
2018-09-06 | GSE96572 | GEO
Project description:Amyotrophic lateral sclerosis (ALS) is a lethal motor neuron disease that progressively debilitates neuronal cells that control voluntary muscle activity. In a mouse model of ALS that expresses mutated human superoxide dismutase 1 (SOD1-G93A) skeletal muscle is one of the tissues affected early by mutant SOD1 toxicity. Fast-twitch and slow-twitch muscles are differentially affected in ALS patients and in the SOD1-G93A model, fast-twitch muscles being more vulnerable. We used miRNA microarrays to investigate miRNA alterations in fast-twitch (EDL) and slow-twitch (soleus) skeletal muscles of symptomatic SOD1-G93A animals and their age-matched wild type littermates. At age of 90 days RNA was extracted from extensor digitorum longus (EDL) and soleus (SOL) muscles of male SOD1-G93A animals and their age-matched wild type male littermates. RNA was hybridized on Affymetrix Multispecies miRNA-2_0 Array.
2014-03-04 | E-GEOD-55507 | biostudies-arrayexpress
Project description:The mdx mouse (C57BL/10ScSn-DMDmdx/J), like Duchenne muscular dystrophy (DMD) patients, lacks the protein dystrophin. However, the mdx mouse has a normal lifespan and mild pathology while DMD remains a severe, fatal disease. New mouse models have been developed that are more severely affected but they have not replaced the mdx mouse in DMD research. A few years ago RNA-sequencing (RNA-seq) results of biopsies from DMD and normal human muscle were published but we could not find equivalent data for the mouse. We now report RNA-sequencing of three wild-type and mdx mouse muscles: the flexor digitorum brevis (FDB), the extensor digitorum longus (EDL), and the soleus (SOL). The FDB, a plantar foot muscle is often used for in vivo and ex vivo experiments but may be less affected by the lack of dystrophy than the hindlimb muscles. We compared muscles from 2- and 5-month old mice to investigate the time-course of the mdx pathology. The results show a muscle- and age-dependent parallel between mdx and DMD muscles. Although the FDB is less affected than EDL and SOL at 2 months, the three muscles show, at both ages, activation of close to 100 genes from 7 pathways that are affected in presymptomatic DMD patients and have been called "DMD disease signature".
2021-06-22 | GSE162455 | GEO
Project description:Skeletal muscle is a heterogeneous tissue. To study the myo-specific epigenetic landscape in the slow soleus and fast extensor digitorum longus (EDL) muscle, myonuclei were purified with PCM1 -an endogenous mark specific for mature myonuclei. Chromatin immunoprecipitation sequencing (ChIP-Seq) was performed using antibodies against the histone marks H3K4me3 and H3K27ac. Comparison of the differently enriched areas between the two muscles shows that the epigenetic landscape reflects the functional properties of the muscles, each with a distinct regulatory program involving distal regulatory enhancers.
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2008-10-01 | GSE11465 | GEO
Project description:This a model from the article:
Common phenotype of resting mouse extensor digitorum longus and soleus muscles:
equal ATPase and glycolytic flux during transient anoxia.
Vinnakota KC, Rusk J, Palmer L, Shankland E, Kushmerick MJ. J Physiol
2010 Jun 1;588(Pt 11):1961-83 20308252
,
Abstract:
Rates of ATPase and glycolysis are several times faster in actively contracting
mouse extensor digitorum longus muscle (EDL) than soleus (SOL), but we find
these rates are not distinguishable at rest. We used a transient anoxic
perturbation of steady state energy balance to decrease phosphocreatine (PCr)
reversibly and to measure the rates of ATPase and of lactate production without
muscle activation or contraction. The rate of glycolytic ATP synthesis is less
than the ATPase rate, accounting for the continual PCr decrease during anoxia in
both muscles. We fitted a mathematical model validated with properties of
enzymes and solutes measured in vitro and appropriate for the transient
perturbation of these muscles to experimental data to test whether the model
accounts for the results. Simulations showed equal rates of ATPase and lactate
production in both muscles. ATPase controls glycolytic flux by feedback from its
products. Adenylate kinase function is critical because a rise in [AMP] is
necessary to activate glycogen phosphorylase. ATPase is the primary source of H+
production. The sum of contributions of the 13 reactions of the glycogenolytic
and glycolytic network to total proton load is negligible. The stoichiometry of
lactate and H+ production is near unity. These results identify a default state
of energy metabolism for resting muscle in which there is no difference in the
metabolic phenotype of EDL and SOL. Therefore, additional control mechanisms,
involving higher ATPase flux and [Ca2+], must exist to explain the well-known
difference in glycolytic rates in fast-twitch and slow-twitch muscles in
actively contracting muscle.
This model was taken from the CellML repository
and automatically converted to SBML.
The original model was:
Vinnakota KC, Rusk J, Palmer L, Shankland E, Kushmerick MJ. (2010) - version=1.0
The original CellML model was created by:
Geoffrey Nunns
gnunns1@jhu.edu
The University of Auckland
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2005-01-01 | MODEL1006230100 | BioModels
Project description:This a model from the article:
Common phenotype of resting mouse extensor digitorum longus and soleus muscles:
equal ATPase and glycolytic flux during transient anoxia.
Vinnakota KC, Rusk J, Palmer L, Shankland E, Kushmerick MJ. J Physiol
2010 Jun 1;588(Pt 11):1961-83 20308252
,
Abstract:
Rates of ATPase and glycolysis are several times faster in actively contracting
mouse extensor digitorum longus muscle (EDL) than soleus (SOL), but we find
these rates are not distinguishable at rest. We used a transient anoxic
perturbation of steady state energy balance to decrease phosphocreatine (PCr)
reversibly and to measure the rates of ATPase and of lactate production without
muscle activation or contraction. The rate of glycolytic ATP synthesis is less
than the ATPase rate, accounting for the continual PCr decrease during anoxia in
both muscles. We fitted a mathematical model validated with properties of
enzymes and solutes measured in vitro and appropriate for the transient
perturbation of these muscles to experimental data to test whether the model
accounts for the results. Simulations showed equal rates of ATPase and lactate
production in both muscles. ATPase controls glycolytic flux by feedback from its
products. Adenylate kinase function is critical because a rise in [AMP] is
necessary to activate glycogen phosphorylase. ATPase is the primary source of H+
production. The sum of contributions of the 13 reactions of the glycogenolytic
and glycolytic network to total proton load is negligible. The stoichiometry of
lactate and H+ production is near unity. These results identify a default state
of energy metabolism for resting muscle in which there is no difference in the
metabolic phenotype of EDL and SOL. Therefore, additional control mechanisms,
involving higher ATPase flux and [Ca2+], must exist to explain the well-known
difference in glycolytic rates in fast-twitch and slow-twitch muscles in
actively contracting muscle.
This model was taken from the CellML repository
and automatically converted to SBML.
The original model was:
Vinnakota KC, Rusk J, Palmer L, Shankland E, Kushmerick MJ. (2010) - version=1.0
The original CellML model was created by:
Geoffrey Nunns
gnunns1@jhu.edu
The University of Auckland
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2005-01-01 | MODEL1006230112 | BioModels
Project description:The right legs of 8 Brown-Norway male rats were denervated by a high sciatic nerve section in the hip region of the hind limb.Two months after denervation (6 months of age), extensor digitorum longus (EDL) muscles were removed from the operated legs. The EDL muscles from 8 age-matched non-operated rats served as innervated controls. Total RNA was isolated, labeled cDNA was prepared and hybridized to the Rat Atlas 1.2 Array II membranes (Clontech Laboratories, Palo Alto, CA).
2004-09-10 | E-GEOD-1741 | biostudies-arrayexpress
Project description:In order to study the subcellular localization of lncRNAs in myofibers of skeletal muscle, single myofibers were isolated from Soleus, Extensor Digitorum Longus (EDL) and Tibialis Anterior (TA) of 9 mice. RNA was extracted from nuclei and cytoplasmic fractions of 5-10 isolated myofibers and than separately hybridized on microarrays. Preferential expression in nuclear or cytoplasmic compartment of each lncRNA was determined.
2019-01-07 | GSE112768 | GEO