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Skeletal muscle transcriptomics identifies common pathways in nerve crush injury and ageing

ABSTRACT: Skeletal muscle transcriptomics identifies common pathways in nerve crush injury and ageing

PROVIDER: PRJEB45782 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR6088020_1.fastq.gz	Fastqsanger.gz
	ERR6088020_2.fastq.gz	Fastqsanger.gz
	ERR6088030_1.fastq.gz	Fastqsanger.gz
	ERR6088030_2.fastq.gz	Fastqsanger.gz
	ERR6088040_1.fastq.gz	Fastqsanger.gz

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Skeletal muscle transcriptomics identifies common pathways in nerve crush injury and ageing

2022-01-10 | E-MTAB-10601 | biostudies-arrayexpress

Skeletal muscle transcriptomics identifies common pathways in nerve crush injury and ageing.

Project description:Motor unit remodelling involving repeated denervation and re-innervation occurs throughout life. The efficiency of this process declines with age contributing to neuromuscular deficits. This study investigated differentially expressed genes (DEG) in muscle following peroneal nerve crush to model motor unit remodelling in C57BL/6 J mice. Muscle RNA was isolated at 3 days post-crush, RNA libraries were generated using poly-A selection, sequenced and analysed using gene ontology and pathway tools. Three hundred thirty-four DEG were found in quiescent muscle from (26mnth) old compared with (4-6mnth) adult mice and these same DEG were present in muscle from adult mice following nerve crush. Peroneal crush induced 7133 DEG in muscles of adult and 699 DEG in muscles from old mice, although only one DEG (ZCCHC17) was found when directly comparing nerve-crushed muscles from old and adult mice. This analysis revealed key differences in muscle responses which may underlie the diminished ability of old mice to repair following nerve injury.

| S-EPMC8800362 | biostudies-literature

Expression data from mouse optic nerve head after optic nerve crush

Project description:Reactive gliosis is a complex process that involves profound changes in gene expression. We used microarray to indentify differentially expressed genes and to investigate the molecular mechanisms of reactive gliosis in optic nerve head in response to optic nerve crush injury. C57Bl/6 female mice were 6-8 weeks old at the time of optic nerve crush surgery. The optic nerve in the left eye was crush 1 mm behind the globe for 10 seconds and the right eye served as contralateral control. The animals were allowed to recover for 1 day, 3 day, 1 week, 3 weeks and 3 months before the optic nerve heads were collected. The naive control mice did not receive any surgery in either eye. Due to the small tissue size of the mouse optic nerve head, two optic nerve heads were pooled together for each microarray chip. The left eyes and the right eyes of two mice were combined respectively to form one pair of experiment and control samples. There were five biological replicates (10 mice) for each condition.

2013-07-15 | E-GEOD-40857 | biostudies-arrayexpress

Quantitative Proteomic Analysis of C57BL/6J mice after optic nerve crush Using iTRAQ Labeling

Project description:We used two groups of C57BL/6J mice, one with optic nerve crush on one eye, and another with no crush as control. Three mice were subjected to optic nerve crush, with sample names 121, 113, 114 and two were used as control with sample names 118 and 119. For the optic nerve crush, a surgical peritomy was made behind and above the eyeball and the eye muscles were gently retracted to expose the optic nerve. Dumont #5 forceps (FST) were used to crush the optic nerve approximately 0.5-1 mm behind the globe without damaging retinal vessels or affecting the blood supply.

2020-05-26 | PXD016197 | Pride

Gene expression timecourse in zebrafish whole eye in response to optic nerve crush

Project description:It is well-established that neurons in the adult mammalian central nervous system are terminally differentiated and, if injured, will be unable to regenerate their connections. In contrast to mammals, zebrafish and other teleosts display a robust neuroregenerative response. Following optic nerve crush (ONX), retinal ganglion cells (RGC) regrow their axons to synapse with topographically correct targets in the optic tectum, such that vision is restored in ~21 days. What accounts for these differences between teleostean and mammalian responses to neural injury is not fully understood. A time course analysis of global gene expression patterns in the zebrafish eye after optic nerve crush can help to elucidate cellular and molecular mechanisms that contribute to a successful neuroregeneration. We used microarrays to detail the global gene expression patterns underlying a successful regeneration or the optic nerve following injury. Experiment Overall Design: Microarray analysis was performed on total RNA extracted from whole eye following optic nerve crush (ONX) or sham surgery at defined intervals (4, 12, & 21 days).

2010-02-21 | E-GEOD-19298 | biostudies-arrayexpress

Expression data from mouse optic nerve head after optic nerve crush

2013-07-15 | GSE40857 | GEO

Differential response of C57BL/6J mouse and DBA/2J mouse to optic nerve crush

Project description:Retinal ganglion cell (RGC) death is the final consequence of many blinding diseases, where there is considerable variation in the time course and severity of RGC loss. Indeed, this process appears to be influenced by a wide variety of genetic and environmental factors. In this study we explored the genetic basis for differences in ganglion cell death in two inbred strains of mice. We found that RGCs are more susceptible to death following optic nerve crush in C57BL/6J mice (54% survival) than in DBA2/J mice (62% survival). Using the Illumina Mouse-6 microarray, we identified 1,580 genes with significant change in expression following optic nerve crush in these two strains of mice. Our analysis of the changes occurring after optic nerve crush demonstrated that the greatest amount of change (44% of the variance) was due to the injury itself. This included changes associated with ganglion cell death, reactive gliosis, and abortive regeneration. The second pattern of gene changes (23% of the variance) was primarily related to differences in gene expressions observed between the C57BL/6J and DBA/2J mouse strains. The remaining changes in gene expression represent interactions between the effects of optic nerve crush and the genetic background of the mouse. We extracted one genetic network from this dataset that appears to be related to tissue remodeling. One of the most intriguing sets of changes included members of the crystallin family of genes, which may represent a signature of pathways modulating the susceptibility of cells to death. Differential responses to optic nerve crush between two widely used strains of mice were used to define molecular networks associated with ganglion cell death and reactive gliosis. These results form the basis for our continuing interest in the modifiers of retinal injury. 18 Samples: 9 per strain (C57BL/6J & DBA/2J); 3 conditions per strain

2010-08-19 | E-GEOD-17117 | biostudies-arrayexpress

Sciatic nerve crush regulation of RNA alternative poly-adenylation

Project description:Poly-adenylation regulates post-transcriptional processing and localization of mRNA. To study the effect of nerve injury on poly-adenylation across the transcriptome, 3'-end RNAseq was carried on DRG neurons following sciatic nerve injury. Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

2025-05-16 | GSE230721 | GEO

RNA seq of the retina and optic nerve from goats 1 day after pre-chiasmatic optic nerve crush injury

Project description:Transcriptomic changes in the pre-chiasmatic optic nerve, retrobulbar optic nerve and retina of goats 1 day after optic nerve crush injury

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mRNA seq after hypothermia treatment of crush injury of the pre-chiasmatic optic nerve

Project description:Transcriptomic changes in the pre-chiasmatic optic nerve, retrobulbar optic nerve of goats 1 day after hypothermia treatment of optic nerve crush injury

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