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The Regulatory Network and Role of the circRNA-miRNA-mRNA ceRNA Network in the Progression and the Immune Response of Wilms Tumor based on RNA-seq

ABSTRACT: The Regulatory Network and Role of the circRNA-miRNA-mRNA ceRNA Network in the Progression and the Immune Response of Wilms Tumor based on RNA-seq

PROVIDER: PRJNA808605 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18076719_1.fastq.gz	Fastqsanger.gz
	SRR18076719_2.fastq.gz	Fastqsanger.gz
	SRR18076720_1.fastq.gz	Fastqsanger.gz
	SRR18076720_2.fastq.gz	Fastqsanger.gz
	SRR18076721_1.fastq.gz	Fastqsanger.gz

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The Regulatory Network and Role of the circRNA-miRNA-mRNA ceRNA Network in the Progression and the Immune Response of Wilms Tumor based on RNA-seq

Project description:Circular RNA (circRNA), which is a newly discovered non-coding RNA, has been documented to play important roles in miRNA sponges, and the dysregulation of which is involved in cancer development. However, circRNA expression profiles and their role in initiation and progression of Wilms tumor (WT) remain largely unclear at present. Here, we used paired WT samples and high-throughput RNA sequencing to identify differentially expressed circRNAs.

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Comprehensive Analysis of ceRNA Network Composed of circRNA, miRNA, and mRNA in septic acute kidney injury patients based on RNA-seq

Project description:Sepsis is a complex, life-threatening clinical syndrome that can cause other related diseases, such as acute kidney injury (AKI). Circular RNA (circRNA) is a type of non-coding RNA with a diverse range of functions, and it plays essential roles in miRNA sponge. CircRNA plays a huge part in the development of various diseases. CircRNA and the competing endogenous RNA (ceRNA) regulatory network are unknown factors in the onset and progression of septic AKI (SAKI). This study aimed to clarify the complex circRNA-associated regulatory mechanism of circRNAs in SAKI.

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Environmental cadmium-induced circRNA-miRNA-mRNA network regulatory mechanism in human normal liver cell model [circRNA]

Project description:Cadmium is a naturally existing heavy metal and a typical environmental pollutant which is a significant threat to human health and can lead to acute and chronic damage to various organs. At present, hundreds of lncRNAs and miRNAs have been confirmed to be related to the toxicity of Cd. However, the role of circRNA in the toxicity of Cd and the involved regulatory mechanism has not been clarified. In this work, human normal liver cell (L-02) was selected as model to identify the changes in the expression level of circRNA after exposure to Cd. Total RNA of each sample was extracted by Trizol method, the original data of circRNA, miRNA and mRNA expression levels of each sample were obtained by microarray hybridization and scanning were standardized and differentially expressed. Differential circRNAs, miRNAs, and mRNAs associated with the toxic effects of Cd were identified. Construct a ceRNA network by screening the predicted circRNA, miRNA and mRNA and predict the main biological functions and metabolic pathways of the network. A total of 266 different circRNAs, 223 different miRNAs and 519 different mRNAs were identified by differential expression analysis. After screening, seven circRNAs, 10 miRNAs and 97 mRNAs were constructed into ceRNA network. After GO enrichment and KEGG pathway analysis of 97 mRNAs in circRNA-miRNA-mRNA network, indicated that circRNA in the ceRNA network may regulate cell proliferation, apoptosis, oxidative stress and inflammatory response under the toxic effect of Cd to damage L-02, and it has obvious dose-response effect and time effect.

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Environmental cadmium-induced circRNA-miRNA-mRNA network regulatory mechanism in human normal liver cell model [miRNA]

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Comprehensive circRNA expression profile and construction of circRNAs-related ceRNA network in a mouse model of autism

Project description:Purpose: We aimed to detected the circRNA expression profile and constructed a circRNA-based competing endogenous RNA (ceRNA) network in autism. Methods:Valproate acid was used to establish an in vivo model of autism in mice. circRNAs in autism group was identified by RNA sequencing. The expression of circRNAs were detected by real-time PCR. Module analysis was conducted followed by GO and KEGG pathway enrichment analysis. Results: A total of 1059 differentially expressed circRNAs (477 upregulated and 582 downregulated) in autism group. The expression of novel_circ_015779 and novel_circ_035247 were detected by real-time PCR. A ceRNA network based on altered circRNAs was established, with 9715 nodes and 150408 edges. The top three modules were all correlated with autism-related pathways involving ‘TGF-beta signaling pathway’, ‘Notch signaling pathway’, ‘MAPK signaling pathway’, ‘long term depression’, ‘thyroid hormone signaling pathway’, etc. Conclusions: The present study reveals a novel circRNA involved mechanisms in the pathogenesis of autism.

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Environmental cadmium-induced circRNA-miRNA-mRNA network regulatory mechanism in human normal liver cell model [mRNA]

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Project description:The transition from vegetative growth to reproductive growth involves many pathways. Vernalization is crucial to the formation of floral organs, the regulation of flowering time and plant breeding. The purpose of this study was to identify the mRNA, microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) related to vernalization of Chinese cabbage, and to construct a competitive endogenous RNA (ceRNA) network, so as to provide valuable information for exploring the molecular mechanism of vernalization of Chinese cabbage. Results: The results of whole-transcriptome sequencing showed that 2702 mRNAs, 151 lncRNAs, 16 circRNA, and 233 miRNAs were differentially expressed in vernalized (‘Ver’) and non-vernalized (‘Nor’) seeds of Chinese cabbage. Some transcription factors and regulatory proteins that play important roles in vernalization pathway have been identified, such as the transcription factors of WRKY, MYB, NAC, bHLH, and MADS-box, zinc finger protein CONSTANS like gene and B3 domain protein. We constructed vernalization-related ceRNA-miRNA-target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA-DEmRNA, 67 DEmiRNA-DElncRNA, and 12 DEmiRNA-DEcircRNA interactions in Chinese cabbage. Meanwhile, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs were identified, which were involved in the regulation of flowering time, floral organ formation, bolting and flowering. Conclusions: The candidate differentially expressed mRNA, miRNA, lncRNA and circRNA for vernalization of Chinese cabbage were identified by the whole-transcriptome sequencing, and the ceRNA network was constructed. This study laid a foundation for further study on the molecular mechanism of vernalization in Chinese cabbage.

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