Next Generation Sequencing of circRNAs in bladder cancer derived ITGA6+EVs
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1034078 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26618885_1.fastq.gz | Fastqsanger.gz | |||
| SRR26618885_2.fastq.gz | Fastqsanger.gz | |||
| SRR26618886_1.fastq.gz | Fastqsanger.gz | |||
| SRR26618886_2.fastq.gz | Fastqsanger.gz | |||
| SRR26618887_1.fastq.gz | Fastqsanger.gz |
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Project description:EVs served as crucial mediators preferably achieve their biological effect in recipient cells to create a supportive pre-metastatic niche via delivering distinct biomolecules, among which circular RNAs (circRNAs) with high stability and abundance in tumor derived EVs were under extensive exploration. Moreover, it is well-established that circRNAs play a significant role in BCa lymphatic metastasis. To explore the crucial circRNAs in BCa derived ITGA6+EVs, the ITGA6+EVs from total UM-UC-3-EVs were isolated by affinity capture using anti-ITGA6 magnetic beads and the circRNA expression profile was investigated using next-generation sequencing (NGS).
2024-10-10 | GSE246659 | GEO
Project description:Metastasis of tumors to LNs predicts disease progression and poor outcomes of patients. Recent studies revealed that tumor cells deliver EVs to particular targeted recipient cells in draining LNs and subsequently alter their gene expression patterns to create a supportive pre-metastatic niche to promote LN metastasis. Yet, the biological role and underlying mechanism of bladder cancer derived EVs (BCa derived EVs) in mediating lymphatic pre-metastatic niche formation remain unclear. The present study aim to explore the differential genes of BCa derived EVs educated draining LNs and underlying mechanism in the lymphatic pre-metastatic niche formation.
2024-10-10 | GSE246070 | GEO
Project description:We profile the cell line expression of 279 circRNAs, that are highly expressed across 457 bladder cancer patient samples. Additionally, we investigate their cellular location in fractionated cell lines
2017-11-01 | GSE100971 | GEO
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
Project description:In order to find out circular RNAs profiles in human bladder cancer tissues and normal bladder tissues, we characterized circuclar RNA transcripts by performing RNA-Seq on ribosomal RNA-depleted total RNA from three pairs of human bladder cancer tissues and paired normal bladder tissues.A computational pipeline based on the anchor alignment of unmapped reads was used to identify circular RNAs. Collectively, we identified16,535 distict circular RNAs, most of them origined from exons (88.96%), others from introns, linc RNA, intergenic region, 3’UTR and 5’UTR. Among all these circRNAs, 571 circRNAs were differentially expressed between bladder cancer tissues and normal bladder tissues, and 524 circRNAs were downregulated in bladder cancer tissues (91.2%), others were upreguluated. These significantly differential expressed circular RNA might have regulatory function in bladder cancer, and worth to be further explored.
2017-08-04 | GSE97239 | GEO
Project description:Next Generation Sequencing Quantitative Analysis of altered expression of genes in bladder cancer derived EVs educated draining LNs
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Project description:Extracellular vesicles (EVs) are small particles that are released by cells and mediate cell-cell communication by transferring bioactive molecules such as RNA. RNA cargo of EVs, including coding and non-coding RNAs, can change the behavior of recipient cells, affecting processes including gene expression, proliferation, and apoptosis. CircRNAs are stable and resistant to degradation and have been shown to be enriched in EVs. They play key roles in gene regulation and are also emerging as promising biomarkers for disease diagnosis due to their stability and disease-specific expression. While microRNAs (miRNAs) are the most well studied RNA cargo of EVs, very little is known about the mechanisms of enrichment of circular RNAs (circRNAs) as well as long linear RNAs. Here, we take a comprehensive genome-wide approach to investigate the role of structuredness and shape along with GC%, size, exon count, and coding potential, in the sorting and enrichment of circular and long linear RNAs into EVs. We developed a model using these parameters to predict the likelihood of EV packaging of RNA and it was validated by using single molecule RNA imaging of EV bound RNAs. Furthermore, we found that structuredness could explain the relative enrichment of circRNAs over their linear counterparts. These results were validated on existing public databases of circular and linear RNAs in EVs. By identifying and analyzing these factors, we aim to better understand the complex mechanisms behind EV-mediated RNA transfer and its impact on cell communication in both health and disease. This mechanistic understanding of RNA enrichment in EVs is crucial for engineering EVs with selective RNA cargo.
2025-07-07 | GSE279376 | GEO
Project description:Bladder cancer is one of the most common cancers. Since prognosis ameliorates with early detection, it is a challenge to develop techniques that could replace or complement the current diagnosis protocols. The study of extracellular vesicles (EVs) that are present in urine samples has become an attractive alternative. The present study describes the mRNA content of vesicles isolated from voided urine samples within bladder cancer context. To discover a genetic signature of cancer, RNA associated to EVs was analyzed by microarray technique. Total RNA isolated from Extracellular Vesicles obtained from urine of bladder cancer patients was compared with RNA isolated from urinary vesicles of non-cancer patients.
2014-01-29 | E-GEOD-51843 | biostudies-arrayexpress
Project description:To explore circular RNA (circRNA) expression profiling and their biological functions in bladder cancer, we surveyed the circRNA expression signature of 4 pairs of matched bladder cancer and para-cancer tissues from clinical patients using microarray. Hundreds of significantly changed circRNAs were identified. Our findings provide a novel perspective on transcriptional group and lay the foundation for future research of potential roles of circRNAs in bladder carcinoma.
2016-12-22 | GSE92675 | GEO
Project description:To explore the overall circRNAs involved in growth and development of Arabidopsis thaliana across the lifespan, we deeply sequenced samples of whole plants from different developmental stages (cotyledons emergence, rosette leavesï¹¥1 mm, rosette growth complete, first flower open, flourishing florescence, first silique shattered, senescence). The total RNA was purified by rRNA-depletion and linear RNA removal with RNAseR, and sequenced by the Illumina HiSeq2500 platform. We obtained 31 Gb raw data and identified 1217 circRNAs with expression quantity. We annotated these circRNAs and predicted their targeted microRNA. The circRNAs involved in growth and development of Arabidopsis thaliana across lifespan were identified and analyzed using the Illumina HiSeq2500 platform.
2016-09-01 | E-GEOD-77672 | biostudies-arrayexpress