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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Comparison of age-related changes in gene expression of 2 rat skeletal muscles

ABSTRACT: In this study we compared Gastrocnemius and Triceps gene expression with age. Our results show that gene expression is massively modulated with age in Gastroc but on the contrary very stable in Triceps, suggesting that Triceps is resistant to age-related defects. 3 groups of age (8 months, 18 months and 24 months) were analyzed, with 9-10 replicates per group. Gastrocnemius and Triceps were collected for each animal.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Jerome Feige

PROVIDER: E-GEOD-78702 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A robust neuromuscular system protects rat and human skeletal muscle from sarcopenia.

Pannérec Alice A Springer Margherita M Migliavacca Eugenia E Ireland Alex A Piasecki Mathew M Karaz Sonia S Jacot Guillaume G Métairon Sylviane S Danenberg Esther E Raymond Frédéric F Descombes Patrick P McPhee Jamie S JS Feige Jerome N JN

Aging 20160401 4

Declining muscle mass and function is one of the main drivers of loss of independence in the elderly. Sarcopenia is associated with numerous cellular and endocrine perturbations, and it remains challenging to identify those changes that play a causal role and could serve as targets for therapeutic intervention. In this study, we uncovered a remarkable differential susceptibility of certain muscles to age-related decline. Aging rats specifically lose muscle mass and function in the hindlimbs, but ...[more]

PMID: 27019136

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Comparison of age-related changes in gene expression of 2 rat skeletal muscles (20 months, 22 months)

Project description:In this study we compared Gastrocnemius and Triceps gene expression with age. Our results show that gene expression is massively modulated with age in Gastroc but on the contrary very stable in Triceps, suggesting that Triceps is resistant to age-related defects.

2020-03-14 | GSE146976 | GEO

Comparison of age-related changes in gene expression of 2 rat skeletal muscles (8 months, 18 months and 24 months)

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Molecular signatures of heterogeneous stem cell populations are resolved by linking single cell functional assays to single cell gene expression

Project description:The discovery of significant heterogeneity in the self-renewal durability of adult haematopoietic stem cells (HSCs) has challenged our understanding of the molecules involved in population maintenance throughout life. Gene expression studies in bulk populations are difficult to interpret since multiple HSC subtypes are present and HSC purity is typically less than 50% of the input cell population. Numerous groups have therefore turned to studying gene expression profiles of single HSCs, but again these studies are limited by the purity of the input fraction and an inability to directly ascribe a molecular program to a durable self-renewing HSC. Here we combine single cell functional assays with flow cytometric index sorting and single cell gene expression assays to gain the first insight into the gene expression program of HSCs that possess durable self-renewal. This approach can be used in other stem cell systems and sets the stage for linking key molecules with defined cellular functions. single-cell RNA-Seq of haematopoietic stem cells

2015-05-26 | E-GEOD-61533 | biostudies-arrayexpress

Decoding the Transcriptional Program for Blood Development from Single Cell Gene Expression Measurements

Project description:Blood and cardiovascular development represent paradigms of embryonic organ formation, with increasingly specialised cells generated from early mesoderm. Here, we map the progression of mesoderm towards blood by single cell expression analysis of 3,934 cells, aiming to capture an entire embryo equivalent of cells with blood-forming potential at four sequential developmental stages. Using novel computational approaches, we reconstruct the developmental journey at single cell resolution, which reveals asynchrony of maturation and sequential waves of expression for major regulators. Considering transitions between individual cellular states, we synthesise executable transcriptional regulatory network models that recapitulate blood development. Using mouse embryos and embryonic stem cells, we validate model predictions by showing that Sox7 inhibits primitive erythropoiesis, and that Sox and Hox factors control early expression of Erg. We therefore demonstrate that single cell analysis of a developing organ coupled with novel computational approaches can reveal the transcriptional programs that control organogenesis. Transcriptome analysis in populations of 50 cells from each of 5 mouse embryos at primitive streak, neural plate and head fold stages of development

2015-02-09 | E-GEOD-61470 | biostudies-arrayexpress

Tracking transcript abundance changes of D. vulgaris co-cultures with M. maripaludis in fluctuating resource environment

Project description:Managing tradeoffs through gene regulation is believed to maintain resilience of a microbial community in a fluctuating resource environment. To investigate this hypothesis we imposed a fluctuating environment that required the sulfate-reducing generalistÂ Desulfovibrio vulgaris to manage tradeoffs associated with repeated ecologically-relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen consuming Methanococcus maripaludis. Strikingly, the microbial community became progressively less proficient at restoring the environmentally-relevant physiological state after each perturbation. Most cultures collapsed within 3-7 shifts with only a few collapsing later. We demonstrate that the collapse was caused by conditional gene regulation, which drove precipitous decline in intracellular abundance of essential transcripts and proteins, imposing greater energetic burden of regulation to restore function in a fluctuating environment. The microbial community collapse was rescued by a single regulatory mutation that could then potentially serve as a stepping stone for further adaptive evolution in a variable resource environment. Co-culture strains of M. maripaludis wild type and either wild type or DVU0744::Tn5 mutant of D. vulgaris strains were grown anaerobically in replicates. Samples were transitioned between syntrophic and sulfate respiratory growth conditions at early log phases.

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Gene expression in gastrocnemius muscle in response to calorie restriction in wildtype and Sirt3 knockout mice

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2021-11-25 | GSE64229 | GEO

Gene expression profiling of muscles from transgenic humanSODG93A mice at symptomatic stage

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2010-03-04 | E-GEOD-16361 | biostudies-arrayexpress

Effect of wheel running exercise on gene expression in skeletal muscles of mice

Project description:This analysis was done to determine which muscle group has the most skeletal muscle transcriptional reponses to wheel running activity. Seven male mice with C57BL/6 genetic background were placed individually in cages with running wheels and allowed free access to the wheels 24 hr per day. Access to running wheels began when the mice were 6 months old, and continued for 12 weeks. The morning after the night of running, the mice were euthanized and several muscle groups were snap froze in liquid nitrogen to preserve RNA. The same muscle groups were collected from three age-matched "sedentary" mice that were housed in ordinary cages that did not permit sustained running. For each muscle group, separate pools of polyadenylated RNA from the sedentary and wheel-running mice were prepared for deep sequencing of cDNA with the SOLiD 3 platform. Four muscle groups were examined (quadriceps femoris; gastrocnemius/plantaris; tibialis anterior; triceps brachii). For each muscle, RNA was pooled from 3 sedentary or 7 wheel-running mice (8 pools total).

2011-09-03 | E-GEOD-31843 | biostudies-arrayexpress

Gene expression profiling of muscles from transgenic humanSODG93A mice at presymptomatic stage

Project description:The transgenic mice expressing the human mutated form (G93A) of the SOD1 gene represent a valuable model of Amyotrophic Lateral Sclerosis (ALS). SOD1 is one of the main causative genes of familial ALS which accounts for 10% of cases. These transgenic animals develop a motorneuronal pathology that recapitulates well the neuropathological features occuring in ALS patients, and the progression of the disease can be monitored by a series of motor tests. Gastrocnemius is the first and most affected muscle in the disease, while triceps is relatively spared. Gene expression data of degenerating motor neurons at different disease stages are already available, while gene expression data on the muscle tissue are missing. Our aim is to define the role of muscle in motor neuron degeneration in ALS. Keywords: Single stage analysis (presymptomatic stage, 7 week-old mice) We considered two sets of muscle at presymptomatic stage (7 weeks): gastrocnemius and triceps from 4 transgenic SOD1G93A and 4 non-transgenic mice (NTg).

2010-03-04 | E-GEOD-16360 | biostudies-arrayexpress

Transcriptome changes in Slc7a5-null mouse embryos

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