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Next Generation Sequencing facilitates quantitative analysis of spinal cord tissue to explore the mechanisms of hyperbaric oxygen treatment alleviating the spinal cord inury

ABSTRACT: Next Generation Sequencing facilitates quantitative analysis of spinal cord tissue to explore the mechanisms of hyperbaric oxygen treatment alleviating the spinal cord inury

PROVIDER: PRJNA768474 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16201000_1.fastq.gz	Fastqsanger.gz
	SRR16201000_2.fastq.gz	Fastqsanger.gz
	SRR16201001_1.fastq.gz	Fastqsanger.gz
	SRR16201001_2.fastq.gz	Fastqsanger.gz
	SRR16201002_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing facilitates quantitative analysis of spinal cord tissue to explore the mechanisms of hyperbaric oxygen treatment alleviating the spinal cord inury

Project description:Aims: To better understand the potential mechanisms of hyperbaric oxygen (HBO) treatment alleviating spinal cord injury (SCI). Materials and methods: The SCI model was firstly built in mice, which were randomly divided into three groups: Sham (SH), SCI and HBO groups, followed by hind limb motor function evaluation. Then the spinal cord tissue samples were harvested for histological evaluation and genome-wide transcriptional analysis at 1 week after injury. Finally, some oxidative stress and cell death related differently expressed genes were selected to be analyzed followed by the functional analysis. Results: HBO treatment significantly improved the recovery of hind limb motor function and decreased the histology score compared to the SCI group. In the genome-wide transcriptional analysis, a total of 76 common differently expressed gene among the three groups were obtained at 1 week after injury, which were enriched in functional pathway such as ferroptosis, calcium signaling pathway, serotonergic synapse, etc. Trends in expression of the six genes were consistent with transcriptional analysis. Conclusions: Identified differentially expressed genes and related signaling pathways may be associated with HBO treatment alleviating second spinal cord injury. These results contribute to elucidate the mechanism of HBO in the treatment of SCI.

2021-10-08 | GSE185301 | GEO

Analysis of long noncoding RNAs expression profiles explores mechanisms of hyperbaric oxygen treatment promoting spinal cord injury recovery

Project description:Aims: To better understand the potential mechanisms of hyperbaric oxygen (HBO) treatment alleviating spinal cord injury (SCI). Materials and methods: The SCI model was firstly built in mice, which were randomly divided into three groups: Sham (SH), SCI and HBO groups, followed by hind limb motor function evaluation. Then the spinal cord tissue samples were harvested for genome-wide transcriptional analysis at 1 week after injury. Finally, some highly expressed lnc-rna were selected for functional analysis. Results: the present study uncovered the lncRNAs expression profile of spinal cord following HBO treatment, and identified 577 DE lncRNAs in spinal cord sample among the SH, SCI and HBO groups. The key biological process and pathways were also identified and may be important mechanisms by which HBO treatment alleviating SCI Conclusions: Moreover, this study indicated that lncRNAs NONMMUT 092674.1 and NONMMUT042986.2 may be involved in the process of HBO treatment promoting the recovery of neurological function after SCI.

2022-03-24 | GSE199043 | GEO

Hyperbaric oxygen therapy after mid-cervical spinal contusion injury

Project description:Hyperbaric oxygen (HBO) therapy is frequently used to treat peripheral wounds or decompression sickness. Evidence suggests that HBO therapy can provide neuroprotection and has an anti-inflammatory impact after neurologic injury including spinal cord injury (SCI). Our primary purpose was to conduct an unbiased, genome-wide screening of mRNA expression changes in the injured spinal cord after HBO therapy. A mRNA gene array was used to evaluate samples taken from the contused region of the spinal cord following a lateralized mid-cervical contusion injury in adult female rats. HBO therapy consisted of daily, 1-hour sessions (3.0 ATA, 100% O2) initiated on the day of SCI. Gene set enrichment analyses indicated that HBO upregulated genes in pathways associated with electron transport, mitochondrial function, and oxidative phosphorylation, and downregulation genes in pathways associated with inflammation (including cytokines and NF-B) and apoptotic signaling. In a separate cohort, spinal cord histology was performed to verify whether the HBO treatment impacted neuronal cell counts or inflammatory markers. Compared to untreated rats, there was increased NeuN positive cells in the spinal cord of HBO treated rats (p=0.007). Further, staining for anti-ionized calcium binding adaptor protein (Iba-1, a microglial marker) was reduced after HBO (p=0.028). We conclude that HBO therapy, initiated shortly after SCI and continued for 10-days, can alter the molecular signature of the lesioned spinal cord in a manner consistent with an anti-inflammatory and neuroprotective impact.

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Danio spinal cord injury

Project description:Adult zebrafish have the ability to recover from spinal cord injury and exhibit re-growth of descending axons from the brainstem to the spinal cord. We performed gene expression analysis using microarray to find damage-induced genes after spinal cord injury, which shows that Sox11b mRNA is up-regulated at 11 days after injury. However, the functional relevance of Sox11b for regeneration is not known. Here, we report that the up-regulation of Sox11b mRNA after spinal cord injury is mainly localized in ependymal cells lining the central canal and in newly differentiating neuronal precursors or immature neurons. Using an in vivo morpholino-based gene knockout approach, we demonstrate that Sox11b is essential for locomotor recovery after spinal cord injury. In the injured spinal cord, expression of the neural stem cell associated gene, Nestin, and the proneural gene Ascl1a (Mash1a), which are involved in the self-renewal and cell fate specification of endogenous neural stem cells, respectively, is regulated by Sox11b. Our data indicate that Sox11b promotes neuronal determination of endogenous stem cells and regenerative neurogenesis after spinal cord injury in the adult zebrafish. Enhancing Sox11b expression to promote proliferation and neurogenic determination of endogenous neural stem cells after injury may be a promising strategy in restorative therapy after spinal cord injury in mammals. Spinal cord injury or control sham injury was performed on adult zebrafish. After 4, 12, or 264 hrs, a 5 mm segment of spinal cord was dissected and processed (as a pool from 5 animals) in three replicate groups for each time point and treatment.

2010-10-19 | E-GEOD-20460 | biostudies-arrayexpress

Gene expression of spinal cord in neuropathic pain rats treated by paeoniflorin- liquiritin combination

Project description:To investigate the alleviating effect of paeoniflorin-liquiritin combination on neuropathic pain, we performed gene expression profiling analysis using data obtained from RNA-seq of spinal cord in spared nerve injury rats

2022-09-28 | GSE205906 | GEO

Engineered thoracic spinal cord organoids for transplantation after spinal cord injury

Project description:Human iPSC-derived thoracic spinal cord organoids were transplanted into spinal cord injury mice, and spinal cord tissue was collected after 7 weeks. The transplantation resulted in functional recovery and neural circuit remodeling in the injured mice.

2025-08-21 | GSE305911 | GEO

Transcriptome analysis of spinal cord microglia and total spinal cord

Project description:Transcriptome analysis of spinal cord microglia and total spinal cord from Lewis rats intratracheally treated with PBS, neomycin or vancomycin.

2021-12-21 | GSE192411 | GEO

Transcriptome analysis of spinal cord microglia and total spinal cord

Project description:Transcriptome analysis of spinal cord microglia and total spinal cord

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Spinal cord RNA-seq

Project description:Spinal cord RNA-seq

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