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Comprehensive analysis of circRNA expression profiles in rat cerebral cortex after moderate traumatic brain injury

ABSTRACT: Comprehensive analysis of circRNA expression profiles in rat cerebral cortex after moderate traumatic brain injury

PROVIDER: PRJNA796539 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17577006_1.fastq.gz	Fastqsanger.gz
	SRR17577006_2.fastq.gz	Fastqsanger.gz
	SRR17577007_1.fastq.gz	Fastqsanger.gz
	SRR17577007_2.fastq.gz	Fastqsanger.gz
	SRR17577008_1.fastq.gz	Fastqsanger.gz

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Comprehensive analysis of circRNA expression profiles in rat cerebral cortex after moderate traumatic brain injury

Project description:Background: Traumatic brain injury is a medical event of global concern, and a growing body of research suggests that circular RNA can play very important roles in traumatic brain injury. To explore the functions of more novel and valuable circular RNA in traumatic brain injury response, a moderate traumatic brain injury in rat was established and a comprehensive analysis of circular RNA expression profiles in rat cerebral cortex was done. Results: As a result, 301 up-regulated and 284 down-regulated circular RNAs were obtained in moderate traumatic brain injury rats, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed based on the circular RNA’s host genes, and a circRNA-miRNA interaction network based on differentially expressed circular RNAs was constructed. Also, four circular RNAs were validated by RT-qPCR and sanger sequencing. Conclusion: This study showed that differentially expressed circular RNAs existed between rat cerebral cortex after moderate traumatic brain injury and control. And this will provide valuable information for circular RNA research in the field of traumatic brain injury.

2022-01-15 | GSE193521 | GEO

Comprehensive analysis of circRNA expression profiles in rat cerebral cortex after moderate traumatic brain injury.

Project description:Traumatic brain injury is a medical event of global concern, and a growing body of research suggests that circular RNAs can play very important roles in traumatic brain injury. To explore the functions of more novel and valuable circular RNA in traumatic brain injury response, a moderate traumatic brain injury in rats was established and comprehensive analysis of circular RNA expression profiles in rat cerebral cortex was done. As a result, 301 up-regulated and 284 down-regulated circular RNAs were obtained in moderate traumatic brain injury rats, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed based on the circular RNA's host genes, and a circRNA-miRNA interaction network based on differentially expressed circular RNAs was constructed. Also, four circular RNAs were validated by RT-qPCR and Sanger sequencing. This study showed that differentially expressed circular RNAs existed between rat cerebral cortex after moderate traumatic brain injury and control. And this will provide valuable information for circular RNA research in the field of traumatic brain injury.

| S-EPMC9108397 | biostudies-literature

Cerebral hypoperfusion exacerbates traumatic brain injury in male mice

Project description:Traumatic brain injury (TBI) has been postulated to initiate a disease process that interacts with vascular dysfunction. However, the combined effects of preexisting cerebral hypoperfusion and TBI remain poorly explored. This study aimed to investigate the combined effects of bilateral carotid artery stenosis (BCAS) and mild-moderate TBI on cerebral blood flow (CBF), cognitive function, histology, and transcriptomics in Swiss-Webster mice. Male and female mice underwent BCAS using steel microcoils around the carotid arteries, followed by TBI 30 days post coil implantation. CBF, spatial learning and memory, axonal damage, and gene expression profiles were assessed. BCAS led to a ~10% reduction in CBF, while TBI caused a similar decrease. However, mice exposed to both BCAS and TBI exhibited more pronounced reductions in CBF, associated with marked spatial learning and memory deficits, particularly in males. Axonal damage in male mice was also exacerbated by the combination of BCAS and TBI. Notably, females demonstrated differential vascular and cognitive responses to BCAS and TBI, suggesting sex-specific protective mechanisms. Single nuclei RNA sequencing revealed unique, cell type-specific gene expression alterations due to BCAS, TBI, or the combination. Moreover, BCAS and TBI induced significant gene expression changes in various cell types, hinting at complex cellular interactions following vascular challenges and trauma. The cellular and molecular interplay between hypoperfusion and TBI points to intricate vascular-neuronal interactions and potential avenues for targeted interventions.

2024-08-14 | GSE241690 | GEO

Differential expression profiles of circRNA in mice with traumatic heterotopic ossification

Project description:To investigate whether circRNAs could participate in the pathological osteogenesis of traumatic heterotopic ossification (HO). RNA sequencing was performed to analyze the circRNA expression profile in mice HO tissues and to investigate the relevant mechanisms. We found that 491 circRNAs were significantly differentially expressed in mouse HO tissues by a fold-change ≥2 and p-value ≤0.05. Among these, 168 circRNAs were upregulated, while 323 were downregulated.

2022-11-05 | GSE217301 | GEO

Effects of Buyang Huanwu Decoction on circRNA-miRNA-mRNA transcriptional network of rats with cerebral ischemia

Project description:To reveal the effects of Buyang Huanwu Decoction on circRNA-miRNA-mRNA transcriptional network of rats with cerebral ischemia, explore its molecular mechanism for the treatment of cerebral ischemia.

2022-01-04 | GSE178439 | GEO

Cerebral hypoperfusion exacerbates traumatic brain injury in male mice

Project description:Cerebral hypoperfusion exacerbates traumatic brain injury in male mice

| PRJNA1009119 | ENA

Differential expression profiles of circRNA in mice with traumatic heterotopic ossification

Project description:Differential expression profiles of circRNA in mice with traumatic heterotopic ossification

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A comprehensive view of the transcriptome during development of the mouse cerebral cortex

Project description:The complexity of the mature adult brain is a result of both developmental processes and experience-dependent circuit formation. One way to look at the process of brain development is to examine gene expression changes, and previous studies have used microarrays to address this in a global manner. However, the transcriptome is more complex than gene expression levels alone, as both alternative splicing and RNA editing occur to generate a more diverse set of mature transcripts. The aim of the current study was to develop a high-resolution transcriptome dataset of mouse cortical development using RNA sequencing (RNA-Seq), thus assaying exon usage and RNA editing as well as overcoming some of the inherent limitations of microarrays. We found a large number of differentially expressed genes, but also altered splicing and RNA editing between embryonic and adult cerebral cortex. Each dataset was validated both technically and biologically, and in each case tested we found our RNA-Seq observations to have high predictive validity. We propose this dataset, and the accompanying analysis, to be a helpful resource in the understanding of changes in gene expression during development. Three young adult cerebral cortices four embryonic cerebral cortices

2013-02-10 | E-GEOD-39866 | biostudies-arrayexpress

Gene expression profiles after traumatic brain injury

Project description:Time dependent-profiles in the gene expression level following lateral moderate fluid percussion injury in the rat brain We used microarray to elucidate relationship between the alteration of gene expression levels and the progression of brain damages following traumatic brain injury. To examine the levels of gene expression in the early phase of traumatic brain injury, we analyzed the gene expression at 3, 6, 12, and 48 h after trauma using the lateral moderate fluid percussion TBI model. The ratios of the gene expression level were compared between chips corresponding to the 3, 6 and 12 h fluid percussion groups and the sham group chips. On the other hand, the rations of gene expression level after 48 h FPI were compared with 48 h sham chip, because the gene expression levels of 48 h sham chip were distinct from sham group chips (3, 6 and 12 h) in the cluster and principal components analyses.

2010-12-07 | E-GEOD-24047 | biostudies-arrayexpress

Gene expression file at single cell level of nerve cells in damaged areas of the cerebral cortex in mice with traumatic brain injury

Project description:Endothelial cells-derived extracellular vesicles can promote nerve function in mice with traumatic brain injury. We used snRNAseq to analyze the effects of extracellular vesicles derived from endothelial cells on nerve cells in mice with traumatic brain injury.

2024-09-04 | GSE276065 | GEO

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