Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome sequencing of human Duchenne muscular dystrophy and CRISPR-corrected myogenic cultures during secondary myogenic differentiation.

ABSTRACT: Transcriptome sequencing of human Duchenne muscular dystrophy and CRISPR-corrected myogenic cultures during secondary myogenic differentiation.

PROVIDER: PRJNA668173 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12798464_1.fastq.gz	Fastqsanger.gz
	SRR12798464_2.fastq.gz	Fastqsanger.gz
	SRR12798465_1.fastq.gz	Fastqsanger.gz
	SRR12798465_2.fastq.gz	Fastqsanger.gz
	SRR12798466_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Genetic Modifiers of Duchenne Muscular Dystrophy

Project description:Genetic Modifiers of Duchenne Muscular Dystrophy

| PRJNA1124393 | ENA

A scalable, clinically severe pig model for Duchenne muscular dystrophy

Project description:Large animal models for Duchenne muscular dystrophy (DMD) are indispensible for preclinical evaluation of novel diagnostic procedures and treatment strategies. To evaluate functional consequences of Duchenne muscular dystrophy (DMD) in skeletal muscle and myocardium, we used a new genetically engineered dystrophin KO pig model displaying hallmarks of human DMD. Heart and skeletal muscle tissue samples of DMD pigs and wild-type (WT) controls at three different ages were analyzed by label-free proteomics.

2021-12-01 | PXD027772 | Pride

Gpr18 agonist dampens inflammation, enhances myogenesis, and restores muscle function in models of Duchenne muscular dystrophy

Project description:Muscle wasting in Duchenne Muscular Dystrophy is caused by myofiber fragility and poor regeneration that leads to chronic inflammation and muscle replacement by fibrofatty tissue. Our recent findings demonstrated that Resolvins, a class bioactive lipids derived from omega-3 fatty acids, have the capacity to dampen inflammation and stimulate muscle regeneration to alleviate disease progression. This therapeutic avenue has many advantages compared to glucocorticoids, the current gold-standard treatment for Duchenne Muscular Dystrophy. However, the use of bioactive lipids as therapeutic drugs also faces many technical challenges such as their short-half life. Here, we explored the potential of synthetic agonist of bioactive lipid receptor, namely the Gpr18 agonist PSB-KD107, as a therapeutic alternative for Duchenne Muscular Dystrophy. We showed that PSB-KD107 can stimulate the myogenic capacity of human iPSC-derived myoblasts in vitro. RNAseq analysis revealed an enrichment in biological processes related to lipid metabolism, small molecule biosynthesis, and steroid-related processes in PSB-KD107-treated cells, as well as pathways related to fatty acid signaling such as Peroxisome proliferator-activated receptors, AMP-activated protein kinase, and sphingolipid signaling pathways. In vivo, the treatment of dystrophic mdx mice with PSB-KD107 resulted in reduced inflammation, enhanced myogenesis, and improved muscle function compared to vehicle-treated mice. Overall, our findings identified a novel therapeutic target for the treatment of Duchenne Muscular Dystrophy.

2023-08-04 | GSE222773 | GEO

Effect of Oxandrolone on Muscle in Duchenne Muscular Dystrophy

Project description:Three subjects with Duchenne muscular dystrophy (8.3, 10.4, and 16.7 years old) were studied. Baseline studies included stable isotope infusion followed by gastrocnemius muscle biopsy to determine myosin heavy chain synthesis rates. RNA was isolated from the muscle biopsy as well. The subjects were then treated for 3 months with oxandrolone (a synthetic anabolic steroid, 0.1 mg/kg/day) and the studies repeated. Keywords = muscle Keywords = Duschenne muscular dystrophy Keywords = oxandrolone Keywords = androgen Keywords: parallel sample

2004-10-15 | GSE1764 | GEO

Atrogin-1 regulates BiP levels - novel therapeutic targets for Duchenne Muscular Dystrophy

Project description:Skeletal muscle wasting results from numerous pathological conditions impacting both the musculoskeletal and nervous systems. A unifying feature of these pathologies is the upregulation of members of the E3 ubiquitin ligase family, resulting in increased proteolytic degradation of target proteins. Despite the critical role E3 ubiquitin ligases in regulating muscle mass, the specific proteins they target for degradation and the mechanisms by which they regulate skeletal muscle homeostasis remain ill-defined. Here, using zebrafish loss of function models combined with in vivo cell biology and proteomic approaches, we identified the endoplasmic reticulum chaperone, BiP, as a novel target of the E3 ubiquitin ligase atrogin-1. A loss in atrogin-1 results in an accumulation of BiP, leading to impaired mitochondrial dynamics and a subsequent loss in muscle fibre integrity. We further implicate a disruption in atrogin-1 mediated BiP regulation in the pathogenesis of Duchenne Muscular Dystrophy. We reveal that BiP is not only upregulated in Duchenne Muscular Dystrophy, but its inhibition using pharmacological strategies, or by upregulating atrogin-1, significantly ameliorates pathology in a zebrafish model of Duchenne Muscular Dystrophy. Collectively, our data implicates a novel disease axis in the pathogenesis of Duchenne Muscular Dystrophy, and highlights atrogin-1’s essential role in maintaining muscle homeostasis.

2024-03-07 | PXD038406 | Pride

Epigenetic control of myogenic identity of human muscle stem cells in Duchenne Muscular Dystrophy

Project description:In Duchenne Muscular Dystrophy (DMD), the absence of the subsarcolemmal dystrophin protein leads to repeated myofiber damages inducing cycles of muscle regeneration that is driven by muscle stem cells (MuSCs). With time, MuSC regenerative capacities are overwhelmed, leading to fibrosis and muscle atrophy. Whether MuSCs from DMD muscle have intrinsic alterations or are primed by their degenerative/regenerative environment is still debated. We investigated cell behavior and gene expression in human using MuSCs derived from DMD or healthy muscles. We found that proliferation, differentiation and fusion were not altered in DMD-MuSCs, but with time, they lost the expression of the myogenic marker CD56 twice as fast as healthy MuSCs. The rapid drift towards a fibroblast-like cell identity was observed at the clonal level, and resulted from the altered expression of epigenetic enzymes required to maintain the myogenic cell fate. Indeed, the reexpression of CBX3, SMC3, H2AFV and H3F3B prevented the MuSC identity drift. Amongst the epigenetic changes, a closing of chromatin at the gene encoding the transcription factor MEF2B caused a down-regulation of its expression and a loss of the myogenic fate. Thus, MEF2B is a key mediator of the myogenic identity in human MuSCs, that is altered in DMD pathology.

2024-06-30 | GSE232667 | GEO

Elevated numbers of infiltrating eosinophils accelerate the progression of Duchenne Muscular Dystrophy pathology in mdx mice.

Project description:Eosinophils are implicated in the development of many chronic diseases. However, their function in muscular dystrophy is understudied. Here we demonstrate that muscle hyper-eosinophilia could be a marker of poor outcomes in Duchenne Muscular Dystrophy.

2022-03-14 | GSE189846 | GEO

Epigenetic control of myogenic identity of human muscle stem cells in Duchenne Muscular Dystrophy

Project description:Epigenetic control of myogenic identity of human muscle stem cells in Duchenne Muscular Dystrophy

| PRJNA973125 | ENA

Transcriptome analysis of human DMD-K2957fs and CRISPR-corrected (CORR-K2957fs ) myogenic cultures during secondary myogenic differentiation.

Project description:To investigate transcriptomes of skeletal muscle cells in health and Duchene muscular dystrophy (DMD), we performed RNA sequencing of DMD-K2957fs and CRISPR-corrected (CORR-K2957fs ) myogenic cultures during secondary differentiation at 5 time points.

2022-11-16 | GSE189053 | GEO

Targeting Duchenne Muscular Dystrophy by Skipping DMD Exon 45 with Base Editors

Project description:Duchenne muscular dystrophy is an X-linked monogenic disease caused by mutations in the dystrophin gene (DMD) and characterized by progressive muscle weakness leading to loss of ambulation and significantly decreased life expectancy. Since the current standard of care for Duchenne muscular dystrophy is to merely treat symptoms, there is a dire need for novel treatment modalities that can correct the underlying genetic mutations. While several gene replacement therapies are being explored in clinical trials, one emerging approach that can directly correct mutations in genomic DNA is base editing. We have recently developed CRISPR-SKIP, a base editing strategy to induce permanent exon skipping by introducing C>T or A>G mutations at splice acceptors in genomic DNA, which can be utilized therapeutically to recover dystrophin expression when a genomic deletion leads to an out-of-frame DMD transcript. We now demonstrate that CRISPR-SKIP can be adapted to correct some forms of Duchenne muscular dystrophy by disrupting the splice acceptor in human DMD exon 45 with high efficiency, which enables open reading frame recovery and restoration of dystrophin expression. We also demonstrate that AAV-delivered split-intein base editors edit the splice acceptor of DMD exon 45 in cultured human cells and in vivo, highlighting the therapeutic potential of this strategy.

2023-07-20 | GSE235673 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data