Ontology highlight
ABSTRACT:
PROVIDER: PRJNA593938 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10598200_1.fastq.gz | Fastqsanger.gz | |||
| SRR10598200_2.fastq.gz | Fastqsanger.gz | |||
| SRR10598201_1.fastq.gz | Fastqsanger.gz | |||
| SRR10598201_2.fastq.gz | Fastqsanger.gz | |||
| SRR10598202_1.fastq.gz | Fastqsanger.gz |
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Project description:To contrastively analyze the expression pattern of circRNAs in cervical squamous carcinoma, adenocarcinoma and adenosquamous carcinoma variants. CircRNAs expression in cervical squamous carcinoma, adenocarcinoma and adenosquamous carcinoma tissues together with the adjacent normal tissues were profiled by high-throughput RNA sequencing.
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Project description:To explore the potential involvement of circular RNAs (circRNAs) in pancreatic ductal adenocarcinoma (PDAC) oncogenesis, we conducted circRNA profiling in six pairs of human PDAC and adjacent normal tissue by microarray. Our results showed that clusters of circRNAs were aberrantly expressed in PDAC compared with normal samples, and provided potential targets for future treatment of PDAC and novel insights into PDAC biology. Analyze circular RNA expression in pancreatic ductal adenocarcinoma (PDAC) by microarray platform.
2015-11-20 | E-GEOD-69362 | biostudies-arrayexpress
Project description:To determine the circRNA expression profile in early stage lung adenocarcinoma and matched non-tumor tissues, we used circRNA microArray analysis form Arraystar to examine the expression of circRNAs Lung adenocarcinoma, a form of NSCLC with high lethality at advanced stage, is becoming more popular in women, non- or never-smokers, and even young adult. However, there are no effective early diagnosis methods at present for patients to cure timely. Circular RNAs (circRNAs) as a special novel, stable, and conserved non-coding RNA in mammalian cells have been reported to be widely involved in the processes of cancer disease. Yet, it is still a puzzle which specific circRNAs are involved in the development of early stage lung adenocarcinoma. Here, tumour samples and paired adjacent normal tissues from 4 patients with early stage lung adenocarcinoma were selected for investigating the expression profile of circRNAs by using the high-throughput circRNA microarray. Bioinformatic analyses were conducted to screen those differentially expressed circRNAs. This work illustrates that clusters of circRNAs are aberrantly expressed in early stage lung adenocarcinoma, which might be able to provide potential targets for the early diagnosis of this disease and new genetic insights into lung cancer.
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Project description:Spinal cord injury (SCI) is a common pathologic disorder that often presents with sensory and motor deficits, severely affecting patients' daily lives. Circular RNAs (circRNAs), a class of non-coding RNAs, have been reported to be involved in regulating the development of SCI. We used RNA sequencing technology and bioinformatics analysis to find the expression and regulation patterns of circRNAs and mRNAs in a mouse model of SCI, from which we screened the potential RNA-mmu_circ_0000296 that affects the progression of SCI in the acute phase. Based on STRING, ENCORI, miRTarBase database and Cytoscape software to construct the relational network of endogenous competing RNAs (ceRNAs) and protein-protein interaction (PPI) network. Finally, in order to validate the above bioinformatics results, the differential expression of circ_0000296 was verified in mouse SCI model and LPS-induced cell model, respectively. Not only that, in in vitro experiments, we found that circ_0000296 overexpression could inhibit microglia polarization toward M1 type, reduce inflammation level, and then inhibit neuronal apoptosis. These findings will help to elucidate and refine the effects of circRNAs on the pathophysiological progression of spinal cord injury and suggest that mmu_circ_0000296 may be one of the targets for spinal cord injury therapy.
2023-10-31 | GSE245437 | GEO
Project description:Cervical artery dissection (CeAD), a special cerebrovascular disease and the main cause of stroke in young people, can present with ischemic stroke, headache, subarachnoid hemorrhage, and other symptoms, increasing the possibility of misdiagnosis. As a special class of non-coding RNAs, circRNAs are commonly found in organisms and can play regulatory roles in transcription and post-transcription processes, affecting gene expression.CircRNAs have reported to be associated with neurological diseases; however, their role in CeAD has not been discerned. In this study, we aimed to elucidate the pathophysiological changes in patients with CeAD and identify biomarkers. Peripheral blood mononuclear cells from patients with CeAD and healthy controls were sequenced using high-throughput sequencing. We detected 460 differently \ expressed circRNAs in patients with CeAD (p < 0.5, fold difference ≥ 2), of which 240 were upregulated and 220 were downregulated. Four circRNAs showed significant differences in expression, which were validated using qRT-PCR. These results suggested that three circRNAs were consistent with high-throughput sequencing results. Bioinformatics analysis demonstrated that these differentially expressed circRNAs were involved in protein metabolism, regulation, synapses, and other pathophysiological processes during CeAD-induced stroke. Additionally, various pathways related to inflammation were closely associated with circRNAs. Based on our results, we suggest that the aberrant expression of circRNAs in CeAD may serve as a biomarker for its diagnosis and as a potential therapeutic target.
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Project description:Objective: As one kind of novel non-coding RNA with high stability and conservatism, circular RNAs (circRNAs) are involved in different biological processes. Although growing evidence has supported the important role of circRNAs in renal diseases, the specific mechanism still remains unknown in neonatal acute kidney injury (AKI). Methods: High throughput sequencing analysis was applied to investigate the expression patterns of circRNAs in the comparison between hypoxia induced AKI neonates and controls. Then, bioinformatics analysis was conducted to predict the function of differentially expressed circRNAs and construct the network of circRNA-miRNA interaction. Results: (1) We identified 296 differentially expressed circRNAs (circRNAs with Fold change > 2 and P value < 0.05). Of them, 184 circRNAs were markedly up-regulated and 112 were significantly down-regulated in the AKI group. (2) Bioinformatics analysis indicated that the parental genes of the differentially expressed circRNAs were predominantly implicated in the cell and cell part, cellular process and cancer pathways. Conclusion: This study could contribute to future research of circRNAs in the pathogenesis of neonatal AKI and facilitate the identification of novel therapeutic targets of circRNAs.
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Project description:Inflammatory transcription networks have been linked with the development of pancreatic ductal adenocarcinoma (PDAC). Here, we demonstrate that NFATc1 is both necessary and sufficient to drive progression of KrasG12D-initiated PDAC, particularly in the context of inflammation. Significantly, nuclear NFATc1 accelerates PDAC development in KrasG12D mice, whereas conditional NFATc1 deletion or pharmacological inhibition attenuates inflammation-mediated carcinogenesis. Mechanistically, NFATc1 induces STAT3 expression, complex formation and signal integration in PDAC. Genome-wide ChIP-sequencing and expression analysis in cells derived from c.n.NFATc1;KrasG12D mice identified combinatorial NFATc1/STAT3 binding at chromatin enhancer sites and subsequent regulation of key molecules involved in oncogenic signaling, growth and inflammation. Together, this study supports the relevance of inflammatory transcription factor networks in pancreatic carcinogenesis and provides a theoretical platform for therapeutic targeting of NFATc1 nucleoprotein complexes in PDAC. NFATc1 ChIP followed by high throughput sequencing in primary murine pancreatic cancer cells (referred to as NKC cells) derived from transgenic mice with pancreas-specific constitutive activation of NFATc1 and KrasG12D mutation in the presence or absence of STAT3 shRNA; 2 ChIP samples (scramble DNA and shSTAT3 DNA) and 1 unenriched input control from the same chromatin pool.
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Project description:Purpose:It has been shown that circular RNA (circRNA) is a key regulatory factor in development and progression of human tumors. However, the working mechanism and clinical significance of most circRNAs remain unknown in human cancer, including multiple myeloma (MM), a hematologic malignancy. Patients and methods:In the present study, high-throughput circRNA microarray was combined with bioinformatics to identify differentially expressed circRNAs in MM. The hsa_circ_0007841 expressions were shown in MM tissues of 86 patients and drug-resistant cell lines and pathological features were detected. Further, the relationship between hsa_circ_0007841 expressions in the MM tissues and pathological features of MM patients were discussed. The role of hsa_circ_0007841 as a potential biomarker and therapeutic target was analyzed. Results:Our results indicated that in MM tissues collected from patients, MM cell lines and drug-resistant cell lines, the hsa_circ_0007841 expression was significantly upregulated. A close connection with prognosis was observed. That is, hsa_circ_0007841 upregulation was correlated with chromosomal aberrations, such as gain 1q21, t(4:14) and mutations in ATR and IRF4 genes. This finding was further verified in large samples. Finally, bioinformatics analysis indicated interaction that 8 differentially expressed miRNAs and 10 candidate mRNAs interacted with hsa_circ_0007841. These results sheds new light on the basic functional research in the future. Conclusion:It was reported for the first time that hsa_circ_0007841 was significantly upregulated in MM. Our study indicated that hsa_circ_0007841 may be a novel biomarker for MM and involved in the progression of MM.
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