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Profiling circular RNAs in HeLa cell

ABSTRACT: Profiling circular RNAs in HeLa cell

PROVIDER: PRJNA490742 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7826903.fastq.gz	Fastqsanger.gz
	SRR7826904.fastq.gz	Fastqsanger.gz
	SRR7826905.fastq.gz	Fastqsanger.gz
	SRR7826906.fastq.gz	Fastqsanger.gz

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Profiling circular RNAs in HeLa cell

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An improved method for identifying biological circular RNAs

Project description:Purpose: We are using the illumina sequencing to compare the false positive and true positive circular RNA findings to confine the method to detect the true circular RNAs Methods: The testis whole transcriptome profiling was generated from 4-week mouse testis using illumina Nextseq, duplicated. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: our data suggest that circular RNAs identified based on junction sequences in the RNA-seq reads, especially those from Illumina Hiseq sequencing, mostly result from template-switching events during reverse transcription by MMLV-derived reverse transcriptases. It is critical to employ reverse transcriptases lacking terminal transferase activity (e.g., MonsterScript) to construct sequencing library or perform RT-PCR for identification and quantification of true circular RNAs. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. The wild type mouse testis RNAs were constructed NGS library by two different enzyme, then parallel sequenced in illumina Nextseq

2016-07-05 | E-GEOD-83992 | biostudies-arrayexpress

Expression profiling of circular RNAs in human islet samples

Project description:There is already strong evidence indicating that different types of non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs, are key players in the regulation of β-cell functions and in the development of diabetes. However, the role of the newly discovered class of circular RNAs remains to be elucidated. We therefore analysed circular RNA expression in human islet samples.

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Expression profiling of circular RNAs in human islet samples

Project description:Expression profiling of circular RNAs in human islet samples

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Circular RNAs affect mRNA stability

Project description:Circular RNAs affect mRNA stability

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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

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