Influence of Liver Fibrosis on Pien Tze Huang by RNA-Seq Analysis of Circular RNAs
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PROVIDER: PRJNA633910 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: We investigate the regulation circRNAs in the damaged fibrotic liver treated with Pien Tze Huang (PZH) by RNA-seq. Methods: Liver tissue circRNAs expression profiles from 8-week carbon tetrachloride (CCl4)-induced, and PZH-treated and CCl4-induced liver fibrosis control mice were investigated by RNA-seq and dysregulated circRNAs in PZH-treated were identified. Various bioinformatics analyses established competing endogenous RNA (ceNRA) in circRNAs-miRNAs-mRNAs axis. Moreover, GO annotation and Kegg pathway were analyzed to identify the relational biological processes and pathway. qRT–PCR validation was performed using LX-2 cell sample pairs and SYBR Green assays. Results: We identified 91 differentially expressed circRNAs in the PZH-treated compared with control mice, of which 58 up-regulated circRNAs and 43 down-regulated circRNAs. The ceRNA network were constructed suggesting the potential role of circRNAs is the regulation of target gene expression as a miRNAs sponge. Moreover, GO and Kegg pathway analysis showed that these predicted mRNAs were related to liver fibrosis-related pathways such as TNF, PI3K-Akt, and MAPK signaling pathway. Meanwhile, the results of validation qRT-PCR of target genes in LX-2 cells were in accordance with RNA-seq with high confidence. Conclusions: We identified the dysregulated circRNAs and established functional network of circRNA-miRNA-mRNA to further reveal the potential interactions and biological processes in PZH-treated liver fibrosis mice. These findings indicate that mmu_circ_Slc25a25 may modulate the transcription of certain genes, such as Slc7a11 and Slc39a14, which may provide a more precise and comprehensive perspective for clarifying the role of PZH therapy as a potential agent for treatment of liver fibrosis.
2021-03-01 | GSE150883 | GEO
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2017-02-13 | GSE85771 | GEO
Project description:Heart failure is one of the leading causes of death and it often accompanies activation of quiescent cardiac myofibroblasts, which results in cardiac fibrosis and resulting cardiac remodeling. Circular RNA, one form of non-coding RNA discovered recently, is formed by backsplicing of 3’ end to 5’ end of exons and is known to be closely related to the variety of pathophysiological function as well as normal homeostasis. However, its roles in the cardiovascular diseases, especially in cardiac fibrosis, are not fully studied. Circular RNAs (circRNAs) are formed by backsplicing events of 3′ end to 5′ end. To identify circRNA candidates, RNA sequencing (RNA-seq) datasets were obtained from transverse aortic constriction (TAC)-induced hearts. Especially, we were interested in cardiac fibroblast-specific circRNAs that affect its differentiation and cardiac fibrosis. Thus, in the present study, by utilizing RNA sequencing analysis followed by diverse bioinformatic or biochemical studies, we identified and characterized circRNA that may affect the pathologic remodeling of heart.
2023-12-14 | GSE240332 | GEO
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
Project description:Pien Tze Huang (PZH) is herbal traditional Chinese medicine which was widely utilized in Asia for hepatic diseases. We constructed two groups hepatic fibrosis mice model using CCl4, one group using PZH treatment and another group replacing PZH with double distilled water. All 12 mice were fed for 8 weeks and then killed to have their liver tissue taken out. Small RNA-seq were used to identify miRNAs of PZH medicine effect for hepatic fibrosis. We found the expression of these miRNAs (mmu-miR-205-5p, mmu-miR-3064-5p, mmu-miR-205-5p, mmu-miR-370-3p, mmu-miR-665-3p) were changed in PZH medicine treatment for hepatic fibrosis study. Furthermore, Hmga2 and Fgf9, miRNAs corresponding target genes (Sp4, Slc2a6, Tln2, Hmga2, Ank3, Pax9, Fgf9), have been reported association with hepatic fibrosis.
2021-06-28 | GSE137100 | GEO
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2018-11-20 | GSE121756 | GEO