CircRNA sequence authenticity in live cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA912729 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22753278_1.fastq.gz | Fastqsanger.gz | |||
| SRR22753278_2.fastq.gz | Fastqsanger.gz | |||
| SRR22753279_1.fastq.gz | Fastqsanger.gz | |||
| SRR22753279_2.fastq.gz | Fastqsanger.gz | |||
| SRR22753280_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:Exogenous RNA, such as circRNA, could be edited by endogenous editors, such as C-to-U editor activation-induced deaminase and apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (AID/APOBEC), and A-to-I editor Adenosine deaminases acting on RNA (ADAR) (I: inosine, recognized as G). Editing of circRNA may interfere with IRES and Kozak sequence to initiate antigen translation, and may alter antigen products or mutate stop codons.
2023-12-31 | GSE221086 | GEO
Project description:Many studies have demonstrated the importance of circRNA in regulating gene expression through functioning as microRNA sponges. However, the roles of circRNA-protein interaction are not fully understood. Importantly, how circRNA-protein interaction contributes the progression of pancreatic ductal adenocarcinoma is largely unexplored. Therefore, RNA Pull down assay for investigating RNA-protein interaction was performed in PANC-1 cells.
2022-02-15 | PXD015048 | Pride
Project description:Arraystar Human circRNA Microarray is designed for the global profiling of human circRNAs. In this study, we applied a circRNA microarray to screen the potential biomarker for HCC. 20 samples extracted from plasma samples including HCC group before operation, and after operation, CH group and control group. Each group contained five samples.
2021-03-02 | E-MTAB-8799 | biostudies-arrayexpress
Project description:Purpose: To profile the circular RNAs (circRNAs), microRNAs (miRNA), and mRNAs expression in BPA exposed GC-2 cells and normally cultured cells. Methods: For circRNA sequencing, total RNA was depleted of rRNA and then linear RNAs by RNase R digestion. cDNA library was constructed according to the Illumina TruSeq library preparation protocol. The Hiseq3000 sequencing platform (Illumina, San Diego, CA, USA) was used for circRNA sequencing. The sequence depth is 10G. Sequences were mapped using STAR software against GRCm38/mm10 mouse reference genome in UCSC Known Genes databases. CIRCexplorer software was applied to analyze the back-spliced junction for circular RNA prediction. Small RNA sequencing was performed on Hiseq2500in 10M sequence depth after regular small RNA library preparation. After adaptor trimming by FASTXToolkit (0.0.14), reads were aligned to the mouse genome (GRCm38/mm10) with Bowtie software (version 1.1.0). miRBase v21 and miRDeep2 were used to annotate or forecast new miRNAs respectively.Hiseq2500 platform was used to sequence mRNA in 6G depth after strand-specific library construction with TruSeq RNA LTPrep Kit (Illumina, San Diego, CA, USA). Clean reads were aligned to reference genome (mouse GRCm38/mm10) with STAR software. And StringTie and Cuffcompare were used for transcription assembly and novel transcription prediction. Results: A total of 4706 and 6486 circRNAs were identified in normally grow GC-2 cells and BPA treated cells respectively, with most not reported in circBase. According to the screening criterion of two folds, 4821 circRNAs were up-regulated and 2855 circRNAs were down-regulated compared to control group. The amounts and kinds of circRNAs were generally enhanced under BPA stress. Similar to circRNAs, miRNA sequencing also showed that more miRNAs were up-regulated than down-regulated under BPA stress (689 up and 98 down by ≥2 folds). In mRNA sequencing, 2978 genes were up-regulated and 2381 were down-regulated by at least 2 folds after BPA treatment. Conclusions: Our study was the first to delineate the full landscape of circRNAs/miRNAs/mRNAs in BPA induced reproductive toxicity. Many functional circRNAs and miRNAs were found to be activated under BPA exposure. They hold great promise to be developed as sensitive biomarkers for BPA exposure and targets for BPA toxity blocking.
2019-01-24 | GSE120921 | GEO
Project description:Live-seq for live cell transcriptome profiling
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Project description:circRNA/miRNA/mRNA sequence data of BPA exposed GC-2 cells and normally cultured cells.
| PRJNA495021 | ENA
Project description:Circular RNAs (circRNAs), a noncoding RNA class originating from alternative splicing, are highly abundant in neural tissues and were shown to regulate gene expression e.g. by interacting with microRNAs and RNA-binding proteins. Neuroblastoma is an embryonal neoplasia, which arises from undifferentiated neural crest cells. Here, we aimed to explore, whether circRNAs influence the pathogenesis of high-risk neuroblastoma. We performed whole-transcriptome sequencing of 104 primary neuroblastoma samples of all risk-groups and identified 5,203 unique circRNAs involving 2,302 genes. Candidate circRNA expression did not correlate with host gene expression, indicating independent regulatory mechanisms. circRNAs were significantly downregulated in the MYCN-amplified high-risk tumors. These findings were independently reproduced in a tetracycline-inducible MYCN-overexpression system based on a non MYCN-amplified neuroblastoma cell line, suggesting that MYCN drives this global circRNA repression. We identified the RNA helicase DHX9 as a mediator of this global suppressive effect of MYCN on circRNAs. Comparing our RNA sequencing data with other cancers and controls revealed a circRNA subset specifically upregulated in neuroblastoma that included a circRNA derived from the ARID1A tumor suppressor gene. Specific circARID1A knockdown resulted in reduced proliferation, cell numbers and viability, prompted apoptosis and induced a differentiated phenotype. Neither knockdown, nor overexpression of circARID1A influenced ARID1A mRNA and protein levels significantly. To dissect the potential mode of function, we performed a pulldown assay with subsequent mass spectrometry. We identified the RNA-binding protein KHSRP as an interaction partner that participates in the mechanism of action of circARID1A. In summary, this study highlights an important role of circRNAs in neuroblastoma biology and may establish this RNA class as a future therapeutic target and biomarker.
2023-04-06 | PXD026053 | Pride
Project description:Circular RNAs are a class of non-coding RNAs mostly generated by back-splicing RNA transcripts of protein-coding gene loci. In difference to canoncial splicing, back-splicing ligates downstream splice donor site with an upstream splice acceptor generating a covalently closed circular RNA. CircRNAs have been reported to influence cellular functions by acting as miRNA sponges, regulation of host gene transcription or by protein interactions. The circRNA cZNF292 has been previously reported to be regulated under hypoxia and to influence endothelial cell angiogenesis and functions. The present data set aims to identfy protein interactions partners of cZNF292 in endothelial cells to further characterize the mechanism of action of cZNF292. Dataset comprises 8 replicates of proteins identified after biotin-based 2'O-Me RNA antisense affinity purification of the circRNA cZNF292 from HUVEC (human umbilical vein endothelial cell) lysates compared to a control probe dataset. Purification was performed without cross-linking under low salt and mild detergent conditions.
2022-11-29 | PXD029794 | Pride
Project description:CircRNA analysis in depolarized neuroblastoma cells
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Project description:To develop circRNA expression approach, we have used Arraystar Human Circular RNA Array as a discovery platform to identify circRNA with the potential to distinguish between glioblastoma (G cells) and neural progenitor cells (N cells). Circular RNA expression patterns separate N and G cells.
2020-06-01 | GSE146463 | GEO