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Next Generation Sequencing of circRNAs in bladder cancer derived ITGA6+EVs

ABSTRACT: Next Generation Sequencing of circRNAs in bladder cancer derived ITGA6+EVs

PROVIDER: PRJNA1034078 | ENA |

REPOSITORIES: ENA

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			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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Next Generation Sequencing of circRNAs in bladder cancer derived ITGA6+EVs

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

Next Generation Sequencing Quantitative Analysis of altered expression of genes in bladder cancer derived EVs educated draining LNs

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.

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Next Generation Sequencing Quantitative Analysis of altered expression of genes in bladder cancer derived EVs educated draining LNs

Project description:Next Generation Sequencing Quantitative Analysis of altered expression of genes in bladder cancer derived EVs educated draining LNs

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Next Generation Sequencing of total RNA from 9 bladder cancer cell lines and 3 fractionated bladder cancer cell lines

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

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Project description:The crosstalk between tumor cells and LECs triggers the LN metastasis in bladder cancer (BCa), but the underlying mechanisms are not completely understood. Previously, we identified that BCa-secreted extracellular vesicles (EVs)-packaged lncRNAs mediated the communication with LECs and promoted LN metastasis. To evaluate whether EV-packaged lncRNAs triggered the LN metastasis of BCa, next-generation sequencing (NGS) to the global expression profiles of lncRNAs was utilized in the urinary EVs (urinary-EV) of five MIBC patients and five healthy volunteers.

2020-11-16 | GSE156308 | GEO

Next Generation Sequencing Analysis of CircRNAs/linear RNA in Isolated Renal Proximal Tubule tissues from Acute kidney injury mice

Project description:The goal of this study was to find the differentially expressed circRNAs/linear RNA in AKI mice model compared to normal mice. We established cisplatin-induced AKI mice models and then extracted RNAs from isolated renal tubular tissues for Next Generation Sequencing(NGS) at different time points during early stage of AKI. CircRNA library was constructed by NEB Next®Ultra™ small RNA Sample Library Prep Kit for Illumina®. NGS was performed by using Illumina HiSeq 2500 Genome Sequencers.The original image data file was transformed into Raw Data by Base Calling. Clean Data was obtained by removing reads that containing joints and more than 5% N (undetermined base information). Mapped Reads were obtained by sequence alignment between Clean Reads and reference genome sequenced using BWA software package. CIRI software was used to predict circRNAs. Finally, we identified 2162 circRNAs and our study represents the first detailed analysis of AKI mice circRNA transcriptomes, which provide a framework for investigations of circRNAs expression profiles in AKI

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Project description:Bladder cancer (BCa) is one of the most common genitourinary malignancies worldwide, with approximately 429,800 new cases and 165,100 deaths annually in the world. Recently, circular RNA (circRNA), a class of non-coding RNA generated from pre-mRNA back splicing, has emerged as crucial mediator in various tumor initiation and progression. To identify molecular mechanism of circNCOR1 in the progression of BCa, Next generation sequencing (NSG) was performed to explore the target genes of circNCOR1 in BCa.

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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.

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Next generation sequence analysis

Project description:Next generation sequence analysis

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