Effects on mRNA levels of a Numb and Numb-like conditional knockout in skeletal muscle fibers
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA704557 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13776300_1.fastq.gz | Fastqsanger.gz | |||
| SRR13776300_2.fastq.gz | Fastqsanger.gz | |||
| SRR13776301_1.fastq.gz | Fastqsanger.gz | |||
| SRR13776301_2.fastq.gz | Fastqsanger.gz | |||
| SRR13776302_1.fastq.gz | Fastqsanger.gz |
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Project description:We investigated the gene expression changes resulting from loss of Numb from skeletal muscle fibers using a conditional, inducible knockout of Numb and its close homolog Numb-like (NumbL) bulk RNA-sequencing.
2022-02-16 | GSE167390 | GEO
Project description:Here, we investigated mechanisms by which aging-related reductions of the levels of Numb in skeletal muscle fibers contribute to loss of muscle strength and power, two critical features of sarcopenia. Numb is an adaptor protein best known for its critical roles in development including asymmetric cell division, cell-type specification and termination of intracellular signaling. Numb expression is reduced in old humans and mice. We previously showed that, in mouse skeletal muscle fibers, Numb is localized to sarcomeres where it is concentrated near triads; conditional inactivation of Numb and a closely related protein Numb-like (NumbL) in mouse myofibers caused weakness, disorganization of sarcomeres and smaller mitochondria with impaired function. Here, we found that a single knockout of Numb in myofibers causes reduction in tetanic force comparable to a double Numb, NumbL knockout. We found by proteomics analysis of protein complexes isolated from C2C12 myotubes by immunoprecipitation using antibodies against Numb, that Septin 7 is a potential Numb binding partner. Septin 7 is a member of the family of GTP-binding proteins that organize into filaments, sheets and rings, and is considered part of the cytoskeleton. Immunofluorescence evaluation revealed a partial overlap of staining for Numb and Septin 7 in myofibers. Conditional, inducible knockouts of Numb led to disorganization of Septin 7 staining in myofibers. These findings indicate that Septin 7 is a Numb binding partner and suggest that interactions between Numb and Septin 7 are critical for structural organization of the sarcomere and muscle contractile function.
2022-04-28 | MSV000089327 | MassIVE
Project description:Numb has 4 known variants and we are reporting two novel Numb variants, Numb5 and Numb6 in this study. The metastaticability variations between the numb variants were evaulated through the transcriptome.
2011-05-09 | GSE29137 | GEO
Project description:In contrast to the well-established role of oxidative muscle fibers in regulating fatty acid oxidation and whole body metabolism, little is known that about the function of fast/glycolytic muscle fibers in these processes. Here, we generated a skeletal muscle-specific, conditional transgenic mouse expressing a constitutively-active form of Akt1. Transgene activation led to muscle hypertrophy due to the growth of type IIb muscle fibers, which was accompanied by an increase in strength. These mice were then used to assess the consequence of building fast/glycolytic muscle fibers on adiposity and metabolism. Akt1 transgene induction in obese mice resulted in reductions in body weight and fat mass, a resolution of hepatic steatosis and improved metabolic parameters. These effects were achieved independent of changes in physical activity and levels of food consumption. Akt1-mediated skeletal muscle growth opposed the effects of high fat/sucrose diet on transcript expression patterns in the liver, and increased hepatic fatty acid oxidation and ketone body production. Our findings indicate that an increase in fast/glycolytic muscle mass can result in the regression of obesity and obesity-related metabolic disorders in part through its ability to alter fatty acid metabolism in remote tissues. Experiment Overall Design: 11 samples are included in this series. 3 wild-type mice fed on a normal diet, 4 wild-type mice fed on a HF diet, and 4 Akt1 double transgenic mice fed on a HF diet. All samples are on the mixed background.
2008-06-16 | E-GEOD-9484 | biostudies-arrayexpress
Project description:Purpose: Reduced Representation Bisulfite Sequencing (RRBS) DNA input requirements become a challenge when working with small pools of tissue-specific cell types. We describe an application of the RRBS method to assess DNA methylation on low-DNA input from human slow-twitch (MHC I) and fast-twitch (MHC IIa) skeletal muscle fibers. Methods : Fiber-type specific (MHC I and MHC IIa muscle fibers) total DNA was extracted from vastus lateralis muscle biopsies of 8 young physically active men (~25 yrs). A total of 16 DNA samples were generated : 8 DNA samples from pure MHC I and 8 DNA samples from pure MHC IIa muscle fibers. An equal quantity of DNA (4 ng) from each sample was combined to generate a "pooled" DNA sample representing all 8 subjects for each fiber type. Two fiber-type specific "pooled" samples of 32 ng of DNA were generated for library construction and sequencing, creating a Type 1 (MHC I muscle fibers) and Type 2a (MHC IIa muscle fibers) sample. Sequencing was performed using the HiSeq 2500 (Illumina) with 50 bp paired-end read parameters. Minimum sequencing read coverage of 5 (5x) was used as the cutoff for CpG-sites inclusion in the DNA methylation analysis. Fisher’s exact test was performed on CpG-sites that overlapped (i.e. identified in both samples) Type 1 and Type 2a samples to obtain p-values that indicate the likelihood of the site being a differentially methylated CpG-site (DMS). DMS with p<0.05 were classified as hypermethylated or hypomethylated if they were more or less methylated than the Type 1 sample, which was used as the reference sample. Results: The 32 ng of DNA from fiber-type specific muscle samples (Type 1 and 2a) used in this study ensured similar sequencing quality as compared to other studies using greater DNA input (>50 ng). Mapping ratios of ~47% and bisulfite conversion rates of ~97-98% were obtained.The unique and best alignment was successfully assessed for each of 17,376,728 CpG-sites in the Type 1 sample and 17,006,993 in the Type 2a sample, which represents ~30% of the total CpG number in the human genome. We identified 143,160 differentially methylated CpG-sites (DMS) across 14,046 genes among MHC I and MHC IIa muscle fibers. The analysis revealed that some genes predominantly expressed in MHC I were hypermethylated in MHC IIa muscle fibers. Conclusion: This study validates a low-DNA input RRBS method for human skeletal muscle samples to investigate the methylation patterns at a fiber-type specific level. These are the first fiber-type specific methylation data reported from human skeletal muscle. Considering the metabolic and structural differences between MHC I and MHC IIa muscle fibers, this technique could provide novel insights into the skeletal muscle methylation profile in relation to health, performance, disease or disuse.
2017-01-10 | GSE83741 | GEO
Project description:Satellite cells (SCs), or muscle stem cells, are the resident somatic stem cells responsible for skeletal muscle regeneration. Most SCs remain quiescent in resting adult muscles but can activate rapidly upon receiving a stimulus. While alternative splicing has been reported to play important role in stem cells , its role in the activation process of SCs remains elusive. We identified Numb as one of the genes that display rapid splicing change during SC activation. To investigate the role of Numb splicing during satellite cell activation, we use morpholino to inhibit the inculstion of Numb exon 6 on early activated SCs and performed RNA-seq to profile the transcriptome changes upon Numb splicing change.
2025-12-30 | GSE290586 | GEO
Project description:Skeletal muscles are composed of a heterogeneous collection of fiber types with different physiological adaption in response to a stimulus and disease-related conditions. Each fiber has a specific molecular expression of myosin heavy chain molecules (MyHC). So far MyHCs are currently the best marker proteins for characterization of individual fiber types and several proteome profiling studies have helped to dissect the molecular signature of whole muscles and individual fibers. Herein, we describe a mass spectrometric workflow to measure skeletal muscle fiber type-specific proteomes. To bypass the limited quantities of protein in single fibers, we developed a Proteomics high-throughput Fiber Typing (ProFiT) approach enabling profiling of MyHC in single fibers. Aliquots of protein extracts from separated muscle fibers were subjected to capillary LC-MS gradients to profile MyHC isoforms in a 96-well format. Muscle fibers with the same MyHC protein expression were pooled and subjected to proteomic, pulsed-SILAC and phosphoproteomic analysis. Our fiber type-specific quantitative proteome analysis confirmed the distribution of fiber types in the soleus muscle, substantiates metabolic adaptions in oxidative and glycolytic fibers, and highlighted significant differences between the proteomes of type IIb fibers from different muscle groups, including a differential expression of desmin and actinin-3. A detailed map of the Lys-6 incorporation rates in muscle fibers showed an increased turnover of slow fibers compared to fast fibers. In addition, labeling of mitochondrial respiratory chain complexes revealed a broad range of Lys-6 incorporation rates, depending on the localization of the subunits within distinct complexes.
2021-02-02 | PXD017755 | Pride
Project description:Numb has 4 known variants and we are reporting two novel Numb variants, Numb5 and Numb6 in this study. The metastaticability variations between the numb variants were evaluated through the transcriptome. breast cancer cells were transfected with GFP-Numb4, GFP-Numb5, GFP-Numb6 or GFP-only vectors and their transcriptome were assessed on Affymetrix platform
2011-05-09 | E-GEOD-29137 | biostudies-arrayexpress
Project description:Skeletal muscle satellite cells, endothelial cells and single muscle fibers
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Project description:Numb is an endocytic adaptor protein that functions in the endocytosis and intracellular trafficking of membrane receptors and adhesion molecules. Numb localization and function have been shown to be regulated by phosphorylation through atypcial protein kinase C at several key sites. Here, we use Liquid Chromatogrpahy, Tandem Mass Spectrometry to identify additional Numb phosphorylation sites not yet characterized.
2014-12-16 | PXD000997 | Pride