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RNA sequencing for KSHV circular RNAs

ABSTRACT: RNA sequencing for KSHV circular RNAs

PROVIDER: PRJNA498320 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR8107700_1.fastq.gz	Fastqsanger.gz
	SRR8107700_2.fastq.gz	Fastqsanger.gz
	SRR8107701_1.fastq.gz	Fastqsanger.gz
	SRR8107701_2.fastq.gz	Fastqsanger.gz
	SRR8107702_1.fastq.gz	Fastqsanger.gz

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Circular DNA tumor viruses make circular RNAs

Project description:Epstein-Barr virus (EBV) and Kaposi’s sarcoma herpesvirus (KSHV) cause ~2% of all human cancers. RNase R-resistant RNA sequencing revealed that both gammaherpesviruses encode multiple, uniquely stable, circular RNAs (circRNA). EBV abundantly expressed both exon-only and exon-intron circRNAs from the BART locus (circBARTs) formed from a spliced BART transcript and excluding the EBV miRNA region. CircBARTs were expressed in all verified EBV latency types, including EBV- positive post-transplant lymphoproliferative disease (PTLD), Burkitt lymphoma, nasopharyngeal carcinoma, and AIDS-associated lymphoma tissues and cell lines. Only cells infected with the B95-8 EBV strain, with a 12-kb BART locus deletion, were negative for EBV circBARTs. Less abundant levels of EBV circRNAs originating from LMP2 and BHLF1-encoding genes were also identified. CircRNA sequencing of KSHV- infected PEL cells revealed a KSHV-encoded circRNA from the vIRF4 locus (circvIRF4) that was constitutively expressed. In addition, KSHV polyadenylated nuclear (PAN) RNA locus generated a swarm (>100) of multiply backspliced, low-abundance RNase R- resistant circRNAs originating in both sense and antisense directions consistent with a novel hyper-backsplicing mechanism. In EBV and KSHV co-infected cells, exon-only EBV circBARTS were located more in the cytoplasm, whereas the intron-retaining circBARTs were found in the nuclear fraction. KSHV circvIRF4 and circPANs were detected in both nuclear and cytoplasmic fractions. Among viral circRNAs tested, none were found in polysome fractions from KSHV-EBV co-infected BC1 cells although low abundance protein translation from viral circRNAs could not be excluded. CircRNAs are a new class of viral transcripts expressed in gammaherpesvirus-related tumors that might contribute to viral oncogenesis.

2018-07-28 | GSE117798 | GEO

Back-splice junctions of KSHV circular RNAs

Project description:Total RNA of KSHV-infected cells were extracted and RT-PCR was performed using viral circRNA specific divergent primers. Amplicons were sequenced with MiSeq.

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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

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