JUN ChIP-seq in injured nerve
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA788755 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17259211.fastq.gz | Fastqsanger.gz | |||
| SRR17259212.fastq.gz | Fastqsanger.gz | |||
| SRR17259213.fastq.gz | Fastqsanger.gz | |||
| SRR17259214.fastq.gz | Fastqsanger.gz |
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Project description:ChIP-seq of c-JUN in injured rat peripheral nerve
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Project description:ChIP-seq of H2AK119ub1 in sham and injured rat peripheral nerve.
2020-12-24 | GSE159265 | GEO
Project description:The striking PNS regenerative response to injury rests on the plasticity of adult Schwann cells and their ability to transit between differentiation states, a highly unusual feature in mammals. Using mice with inactivation of Schwann cell c-Jun, we show that the injury response involves c-Jun dependent natural reprograming of differentiated cells to generate a distinct Schwann cell state specialized to promote regeneration. Transected distal stumps of c-Jun mutants show 172 disregulated genes, resulting in abnormal expression of growth factors, adhesion molecules and cytoskeletal changes that lead to neuronal death, inhibition of axon growth and striking failures of functional repair after injury. These observations provide a molecular basis for understanding Schwann cell plasticity and nerve regeneration. They offer conclusive support for the notion that Schwann cells control repair in the PNS, using dedicated transcriptional controls to generate a distinct repair cell, a transition that shows similarities to transdifferentiation seen in other systems. Total RNA was purified from a 10mm segment of the distal stump and uninjured contralateral nerve from c-Jun mutants and control mice 7 days after nerve cut. For each condition (injured/uninjured) and genotype (control/ knock-out) 2 independent samples (replicates) were generated from pooled nerves of 4/6 mice resulting in a total of 8 samples: CTRL.cut.R1, CTRL.cut.R2, CTRL.uncut.R1, CTRL.uncut.R2, KO.cut.R1, KO.cut.R2, KO.uncut.R1,KO.uncut.R2.
2012-06-13 | E-GEOD-38693 | biostudies-arrayexpress
Project description:ChIP-seq of H3K4me3 in rat peripheral nerve was used to identify transcription start sites associated with Schwann cell-expressed genes. The analysis was performed in injured and control nerve to identify injury-responsive changes in Schwann cells. H3K4me3 ChIP samples were prepared from rat sciatic nerve at 1 day post-transection using both the distal stump of the injured nerve and the contralateral (sham) nerve.
2016-08-01 | E-GEOD-84272 | biostudies-arrayexpress
Project description:Proteomic analysis of injured human peripheral nerves, particularly focusing on events occurring in the proximal and distal nerve ends, remains relatively underexplored. This study aimed to investigate the molecular patterns underlying a digital nerve injury, concentrating on differences in protein expression between the proximal and distal nerve ends. A total of 26 human injured digital nerve samples (24 men; 2 women; median age 47 [30-66] years), harvested during primary nerve repair within 48 hours post-injury from proximal and distal nerve ends, were analyzed using mass spectrometry. A total of 3914 proteins were identified, with 127 proteins showing significant differences in abundance between the proximal and the distal nerve ends. The downregulation of proteins in the distal nerve end was associated with synaptic transmission, autophagy, neurotransmitter regulation, cell adhesion and migration. Conversely, proteins upregulated in the distal nerve end were implicated in cellular stress response, neuromuscular junction stability and muscle contraction, neuronal excitability and neurotransmitter release, synaptic vesicle recycling and axon guidance and angiogenesis. Investigation of proteins, with functional annotations analysis, in proximal and the distal ends of human injured digital nerves, revealed dynamic cellular responses aimed at promoting tissue degeneration and restoration, while suppressing non-essential processes.
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Project description:Sciatic nerve crush (SNC) triggers sterile inflammation within the distal nerve and de-afferented dorsal root ganglia (DRGs). In the nerve, neutrophils and pro-inflammatory Ly6Chigh monocytes appear first and rapidly give way to Ly6Clow resolving macrophages. Transcriptional profiling of injured nerve tissue identifies six macrophage subpopulations, repair Schwann cells and mesenchymal cells as the main cell types. Macrophages at the nerve crush site are distinct from macrophages associated with degenerating nerve fibers. Monocytes and macrophages in the injured nerve “eat” apoptotic cell corpses of leukocytes and thereby contribute to an anti-inflammatory milieu. Studies with chimeric mice show that following SNC few blood-derived immune cells enter DRGs. Myeloid cells in the injured nerve, but not DRGs, express the receptor for the chemokine GM-CSF. In the absence of GM-CSF, conditioning-lesion induced regeneration of DRG neuron central projections is abrogated. Thus, a carefully orchestrated immune response in the nerve is required for conditioning-lesion induced neurorepair.
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Project description:ChIP-seq of H3K27acetylation in sham and injured nerve 2 independent ChIP samples each for Sham and Injury conditions, with respective inputs
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Project description:The goal of the experiment was to determine the role of the polycomb repressive complex 2 in the nerve injury response in peripheral nerve. A Schwann cell specific knockout of the Eed subunit of PRC2 was generated to compare with wild type mice in sham and injured mice at 1d and 14d timepoints after nerve injury.
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Project description:ChIP-seq of H3K27me3 in rat peripheral nerve was used to identify sites of polycomb repression associated with genes in Schwann cells, which constitute the majority of cells in peripheral nerve. H3K27me3 ChIP samples were prepared from rat sciatic nerve and then sequenced. Inputs for these ChIP samples have previously been submitted as samples GSM1541282 and GSM1541283 in Series GSE63103
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Project description:The lingual nerves are incidentally injured in many oral and maxillofacial surgical procedures, traumatic neuroma was observed at the proximal stump of the injured lingual nerve in patients with severe lingual nerve disturbance. Various genes including genes related to nerve regeneration are expressed in the rat and mouse traumatic neuroma, as regeneration mechanism works after lingual nerve injury. Few reported have showed the expressed genes in the traumatic neuroma of the human lingual nerve. In this study, we compared the gene expression between pooled RNA sample from three traumatic neuromas removed in microneurosurgery in the lingual nerve and an RNA sample from the normal lingual nerve on the unaffected side of the removed tongue with cancer. The 2,357 genes increased more than twofold in the traumatic neuroma compared with the normal lingual nerve. Then, we analyzed the upregulated genes in DAVID and DAVID indicated that the 20 upregulated genes were associated with protein secretion to the extracellular space in the pathways. This study identified the 20 candidate genes at the nerve regeneration stage in the traumatic neuroma in the human lingual nerve.
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