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ABSTRACT: circRNA identification and differential expression

PROVIDER: PRJNA762602 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15860182_1.fastq.gz	Fastqsanger.gz
	SRR15860182_2.fastq.gz	Fastqsanger.gz
	SRR15860183_1.fastq.gz	Fastqsanger.gz
	SRR15860183_2.fastq.gz	Fastqsanger.gz
	SRR15860184_1.fastq.gz	Fastqsanger.gz

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circRNA expression in idiopathic pulmonary fibrosis (IPF) and matched non-fibrotic plasma samples

Project description:We used circRNA microArray analysis from Arraystar to identify differential expression of circRNA in IPF patients compared to healthy controls.

2017-08-16 | GSE102660 | GEO

Circular RNA expression profile in human bladder cancer cell line and human urothelial immortalized cell line

Project description:To further explore the differential expression profile of circRNA in human bladder cancer, we have employed circRNA microarray expression profiling as a discovery platform to identify potential differential expression profile of circRNA between human bladder cancer cell (UM-UC-3 cell) and urothelial immortalized cell (SV-HUC-1 cell). Results showed a large number of differentially expressed circRNAs. In this study, we screened the eight circRNAs that were most significantly downregulated in the circRNA differential expression profile of bladder cancer cells, designed primers across the splice site, and detected them using qPCR. We found that hsa_circ_0047253 (circLAMA3) was most significantly decreased in the bladder cancer cells, then its biological function and action mechanism have been further explored in this study.

2022-02-08 | GSE159239 | GEO

rat bladder LC-MS/MS proteomics

Project description:Objective: Bladder outlet obstruction (BOO) is a common urologic disease associated with poorly understood molecular mechanisms. This study aimed to investigate the possible involvements of circRNAs (circular RNAs) and circRNA-encoded proteins in BOO development. Methods: The rat BOO model was established by the partial bladder outlet obstruction surgery. Differential expression of circRNA and protein profiles were characterized by deep RNA sequencing and iTRAQ quantitative proteomics respectively. Novel proteins encoded by circRNAs were predicted through ORF (open reading frame) selection using the GETORF software and verified by the mass spectrometry in proteomics, combined with the validation of their expressional alterations by quantitative RT-PCR. Results: Totally 3051 circRNAs were differentially expressed in bladder tissues of rat BOO model with widespread genomic distributions, including 1414 up-regulated and 1637 down-regulated circRNAs. Our following quantitative proteomics revealed significant changes of 85 proteins in rat BOO model, which were enriched in multiple biological processes and signaling pathways such as the PPAR and Wnt pathways. Among them, 21 differentially expressed proteins were predicted to be encoded by circRNAs and showed consistent circRNA and protein levels in rat BOO model. The expression of five protein-encoding circRNA were further validated by quantitative RT-PCR and mass spectrometry. Conclusion: The circRNA and protein profiles were substantially altered in rat BOO model, with great expressional changes of circRNA-encoded novel proteins.

2022-02-22 | PXD029337 | Pride

CircRNA expression profile analysis of myocardial reperfusion injury in rats

Project description:To explore the differences in the expression of circRNA in myocardial ischemia-reperfusion injury and the potential effects of these differences in circRNA. Methods 6 SPF male SD rats were randomly divided into two groups, including 3 in Myocardial ischemia reperfusion group and 3 threading without ligation in control group by ligating the left anteriors branch for 40 minutes and reperfusing for 2 hours to establish a model of myocardial ischemia reperfusion injury. The myocardial specimens from the infarct area were taken for high-throughput sequencing analysis to obtain differently expressed circRNA. After that, GO and KEGG analysis were performed to speculate on the biological functions and possible biological pathways involved. RT-qPCR was used to verify the sequencing results of differential circRNA, and bioinformatics analysis predicted that circRNA could combine with miRNA to construct a visual network diagram and their interaction. Results Analyzing of 13576 circRNAs detected in 6 rats from MIRI group and control group, A total of 132 circRNAs showed significant differential expression, of which 82 were up-regulated and 50 were down-regulated. The results of GO and KEGG analysis suggest that differential circRNA is closely related to myocardial ischemia reperfusion injury, and KEGG analysis suggests that differential circRNA is involved in calcium, AMPK, mTOR and adrenaline signal pathways. 4 circRNAs were extracted from the up-regulated circRNA for RT-qPCR verification, and the results of 2 were consistent with the high-throughput sequencing results. circRNA-miRNA interaction analysis shows that circRNA interacts with a variety of miRNAs. Conclusions The expression of circRNA in myocardial reperfusion injury rats is significantly different, which may be involved in the occurrence and development of myocardial ischemia-reperfusion injury through miRNA sponge action of circRNA.

2022-06-30 | GSE207093 | GEO

Micropterus salmoides

Project description:LMB circRNA identification

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Project description:In order to study the biological function and regulatory mechanism of circRNA in the occurrence and development of HCC, we collected cancer and adjacent tissues of 5 HCC patients, extracted total RNA and mixed samples of equal quality. RNA-seq was used to obtain the expression profiles of differential circRNA in HCC tissues, and the expression profiles were annotated and analyzed for differential expression.

2023-08-10 | GSE216115 | GEO

Analysis of differential circRNA expression in mouse retina isolated from mice that harbor the Y2334N mutation in both alleles of the pre-mRNA splicing factor PRPF8

Project description:The autosomal-dominant Y2334N mutation in PRPF8 is associated with retinitis pigmentosa, a progressive retinal disorder. Here, we investigated how the Y2334N mutation affects circRNA differential expression in the retinas of homozygous Y2334N mutant mice.

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Circular RNA landscapes in primary and metastatic breast cancer cells across native, differentiated, and stem-like states

Project description:Microarray analysis was used to identify differential circRNA expression profiles between breast cancer cell lines derived from primary tumors and metastatic lesions. Furthermore, the influence of differentiation- and stemness-inducing culture conditions on the circRNA landscape was assessed.

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Project description:Differential circRNA expression in stored red blood cells

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