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Expression profile analysis of circular RNAs during embryonic lung development of C57BL/6 mice

ABSTRACT: Expression profile analysis of circular RNAs during embryonic lung development of C57BL/6 mice

PROVIDER: PRJNA545100 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9134403_1.fastq.gz	Fastqsanger.gz
	SRR9134403_2.fastq.gz	Fastqsanger.gz
	SRR9134404_1.fastq.gz	Fastqsanger.gz
	SRR9134404_2.fastq.gz	Fastqsanger.gz
	SRR9134405_1.fastq.gz	Fastqsanger.gz

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Expression profile analysis of circular RNAs during embryonic lung development of C57BL/6 mice

Project description:Objectives: The contribution of circular RNAs (circRNAs) in the regulation of embryonic lung development is not yet clear. This study aims to uncover the differentially expressed circRNAs in mouse embryonic lung tissue. Methods: High-throughput sequencing (HTS) was used to determine the cirRNA expression profiles at four time points of mouse embryonic lung tissue [embryonic (E) Day 14.5 (E14.5/S1), (E16.5/S2), (E18.5/S3), and newborn (N) Day 7.5 (N7.5/S4)]. CircRNAs that were significantly differential were subjected to bioinformatic analysis and functional prediction for their host genes. Finally, quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) was conducted to examine their levels. Results: Dynamically expressed circRNAs in the mouse embryonic lung tissue were identified. After that, a total of 231 circRNAs differentially expressed between the three groups (S1 vs. S2, S1 vs. S3 and S1 vs. S4) in embryonic lung tissue (fold change ≥ 2.0; p < 0.05). These circRNAs were subjected to bioinformatic analysis to predict their potential biological functions. Finally, six circRNAs (circRNA3_Ttn, circRNA56_Galnt18, circRNA38_Alg12, circRNA42_Filip1l, circRNA43_Ptprm, and circRNA57_Ncoa3) that were further validated using qRT-PCR. Conclusions: These findings illustrate the vital functions of circRNAs in mouse embryonic lung development. Combined with our results and previous researches, circRNAs may serve as potential miRNA sponges in the embryonic lung development. Our research is conducive to further explore the development of embryonic lungs, and the dynamic expressed circRNAs may be novel molecules that regulate mouse lung development.

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Circular DNA tumor viruses make circular RNAs

Project description:Circular DNA tumor viruses make circular RNAs

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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

Circular RNAs are abundant and dynamically expressed during the embryonic lung development of C57BL/6 mice.

Project description:Circular RNAs (circRNAs), a novel type of endogenous RNAs, can function as microRNA (miRNA) sponges capable of regulating gene transcription, binding to RNA-associated proteins, and even encoding proteins. CircRNAs are involved in various cell behaviors, such as proliferation and apoptosis. The mouse model has also been demonstrated to be similar to that of humans in many studies. To explore the profile of circRNAs during embryonic lung development and their potential functions in lung development-related diseases, mouse embryos at the pseudoglandular phase, canalicular phase, saccular phase, and alveolar phase were collected. High-throughput sequencing was then used to identify a total of 1,735 circRNAs (junction reads ≥5 and p < 0.05). It is well known that the functions of circRNAs are related to host genes. In our study, bioinformatics analysis indicated that the screened host genes were closely associated with lung development and included the Hippo signaling pathway, PI3K-Akt signaling pathways, and TGF-β signaling pathways. Moreover, miRNA sponges are another mechanism involved in lung development. Therefore, we predicted many miRNAs binding to circRNAs, such as miR-17 and miR-20, using the TargetScan and miRanda databases. Previously, miRNAs were proven to be necessary for lung development. The peak expression of circRNAs is distributed at different time points, suggesting their involvement in different stages of embryonic mouse lung development.

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Circular RNAs affect mRNA stability

Project description:Circular RNAs affect mRNA stability

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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

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Project description:Noncoding RNAs play important roles in various biological processes and diseases, including cancer. Expression profile of circular RNAs (circRNA) is largely unknown in lung adenocarcinoma. This study is designed to explore mRNA, long noncoding RNA (lncRNA), and circRNA in lung adenocarcinoma.

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