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Genome-wide studies of circular RNAs in Marek's tumorigenesis in Chicken (circRNA-Seq)

ABSTRACT: Genome-wide studies of circular RNAs in Marek's tumorigenesis in Chicken (circRNA-Seq)

PROVIDER: PRJNA576486 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10247278_1.fastq.gz	Fastqsanger.gz
	SRR10247278_2.fastq.gz	Fastqsanger.gz
	SRR10247279_1.fastq.gz	Fastqsanger.gz
	SRR10247279_2.fastq.gz	Fastqsanger.gz
	SRR10247280_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Genome-wide studies of circular RNAs in Marek's tumorigenesis in Chicken (circRNA-Seq)

Project description:Marek's disease (MD), induced by Marek's disease virus (MDV), is a lymphotropic neoplastic disease and causes huge economic losses to the poultry industry. Non-coding RNAs play important regulatory roles in disease pathogenesis. To investigate host circRNA and miRNA expression profile, RNA sequencing was performed in tumorous spleens (TS), spleens from the survivors (SS) without any lesion after MDV infection, and noninfected chicken spleens (NS).

2020-01-21 | GSE138600 | GEO

Genome-wide studies of microRNAs in Marek's tumorigenesis in Chicken (miRNA-Seq)

Project description:Marek's disease (MD), induced by Marek's disease virus (MDV), is a lymphotropic neoplastic disease and causes huge economic losses to the poultry industry. Non-coding RNAs play important regulatory roles in disease pathogenesis. To investigate host miRNA expression profile, RNA sequencing was performed in tumorous spleens (TS), spleens from the survivors (SS) without any lesion after MDV infection, and noninfected chicken spleens (NS).

2020-01-21 | GSE138601 | GEO

Genome-wide studies of microRNAs in Marek's tumorigenesis in Chicken (miRNA-Seq)

Project description:Genome-wide studies of microRNAs in Marek's tumorigenesis in Chicken (miRNA-Seq)

| PRJNA576489 | ENA

The expression profiling of circular RNAs (circRNA) in human intervertebral disc degeneration (IDD)

Project description:Circular RNA expression profiling of human nucleus pulposus derived from patients with IDD in comparison with those derived from cadaveric disc as normal control. We have identified the expression profiles of miRNAs (GSE63492), lncRNAs, mRNAs (GSE56081) in IDD using 5 normal discs as control and 5 IDD discs. Accumulating evidence indicates that circRNAs are key regulators of gene expression by interacting with miRNAs. circRNA is a novel type of RNA that, unlike linear RNA, forms a covalently closed continuous loop, and is highly represented in the eukaryotic transcriptome. Two-condition experiment: control nucleus pulposus vs. degenerative nucleus pulposus. Biological replicates: 5 control, 5 degenerated, independently harvested (the same samples as GSE56081 and GSE63492). Four replicates per array.

2016-08-04 | E-GEOD-67566 | biostudies-arrayexpress

Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity

Project description:Circular RNAs (circRNAs), formed by the atypical head-to-tail splicing of exons, have re-emerged as a potentially interesting RNA species given recent reports of a surprising diversity and abundance of circRNA in organisms ranging from worm to human. Here, using deep RNA sequencing, we profiled different RNA species in mouse and observed that circRNAs are significantly enriched in neural tissue, relative to other tissues. Using PacBio sequencing, we determined, for the first time, the circular structure of this population of circRNAs as well as their full-length sequences. We discovered that a disproportionate fraction of the brain circRNA population is derived from host genes that code for synaptic proteins. Moreover, based on the separate profiling of the RNAs localized in neuronal cell bodies and neuropil (enriched in axons and dendrites), we found that, on average, circular RNAs are more enriched in the neuropil than their host gene mRNA isoforms. Using high resolution in situ hybridization we, for the first time, directly visualized circRNA punctae in the dendrites of neurons. The host gene origin and location of the circRNA in neurons suggest the possibility that circRNAs might participate in the regulation of synaptic function and plasticity. Consistent with this idea, we observed via profiling at different developmental stages, that the abundance of many circular RNAs changes abruptly at a time corresponding to synaptogenesis. In addition, following a homeostatic downscaling of neuronal activity many circRNAs exhibit significant up or down-regulation. These data indicate that brain circRNAs are positioned to respond to and regulate synaptic function. Circular RNA profiling in 13 different samples in mice and four samples in rat, using Illumina sequencing

2015-02-25 | E-GEOD-61991 | biostudies-arrayexpress

Engineered extrachromosomal circular DNAs promote tumorigenesis (WGS)

Project description:Engineered extrachromosomal circular DNAs promote tumorigenesis (WGS)

| PRJNA1100545 | ENA

Circular RNA (circRNA) expression profiles in hypopharyngeal carcinoma tissues vs. adjacent normal mucosae detected by microarray

Project description:Circular RNA (circRNA) expression profiles in hypopharyngeal carcinoma tissues vs. adjacent normal mucosae detected by microarray

2017-04-06 | GSE97418 | GEO

Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals

Project description:Circular RNAs (circRNAs) are a large class of animal RNAs. To investigate possible circRNA functions, it is important to understand circRNA biogenesis. Besides human Alu repeats, sequence features that promote exon circularization are largely unknown. We experimentally identified new circRNAs in C. elegans. Reverse complementary sequences between introns bracketing circRNAs were significantly enriched compared to linear controls. By scoring the presence of reverse complementary sequences in human introns we predicted and experimentally validated novel circRNAs. We show that introns bracketing circRNAs are highly enriched in RNA editing or hyper-editing events. Knockdown of the double-strand RNA editing ADAR1 enzyme significantly and specifically up-regulated circRNA expression. Together, our data support a model of animal circRNA biogenesis in which competing RNA:RNA interactions of introns form larger structures which promote circularization of embedded exons, while ADAR1 antagonizes circRNA expression by melting stems within these interactions. Thus, we assign a new function to ADAR1. Examination of 12 samples in different stages of C.elegans development.

2015-01-06 | E-GEOD-63823 | biostudies-arrayexpress

Microarray expression profile analysis of circular RNAs in human pancreatic ductal adenocarcinoma

Project description:To explore the potential involvement of circular RNAs (circRNAs) in pancreatic ductal adenocarcinoma (PDAC) oncogenesis, we conducted circRNA profiling in six pairs of human PDAC and adjacent normal tissue by microarray. Our results showed that clusters of circRNAs were aberrantly expressed in PDAC compared with normal samples, and provided potential targets for future treatment of PDAC and novel insights into PDAC biology. Analyze circular RNA expression in pancreatic ductal adenocarcinoma (PDAC) by microarray platform.

2015-11-20 | E-GEOD-69362 | biostudies-arrayexpress

Profiling of protein interactions of the circRNA cZNF292 in endothelial cells

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

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