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Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Squalene in Swine model

ABSTRACT: Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Squalene in Swine model

PROVIDER: PRJNA886962 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21799023.fastq.gz	Fastqsanger.gz
	SRR21799024.fastq.gz	Fastqsanger.gz
	SRR21799025.fastq.gz	Fastqsanger.gz
	SRR21799026.fastq.gz	Fastqsanger.gz
	SRR21799027.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Squalene in Swine model

Project description:Purpose: The goal of this study was to determine squalene effect on hepatic transcriptome by comparing high-throughput data for tested group vs. control group in male Large White x Landrace Large swine animals Method: Study the Hepatic mRNA profile of swine animals in response to a steatotic diet supplied with 0.5% squalene over a month by Transcriptome sequencing using DNBseq platform. Sequence reads that passed quality filters were mapped onto reference genome, followed by SNP & INDEL variants calling and Gene expression detection. Results: Squalene intake did not significantly influence single nucleotide polymorphisms. When alternative splicing events were tested, squalene administration had significant influence on splicing events including alternative 5' splicing, alternative 3' splicing , retained intron, skipped exons and mutually exclusive exons. Splicing patterns led to variety of differentially splicing genes and a variety of different isoforms from one gene. Differentially expressed genes were 18,659 in the squalene group and 18,602 in control group.

2023-08-30 | GSE214732 | GEO

Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Squalene

Project description:Purpose: The goal of this study was to determine squalene effect on hepatic transcriptome by comparing high-throughput data for tested group vs. control group in Wildtype New Zealand white rabbits. Method: Hepatic mRNA profile of two Wildtype New Zealand white rabbits groups fed over 4 weeks with 1% of sunflower oil and the second fed with purified 1% of sunflower oil and 0.5% of squalene was analysed by Transcriptome sequencing using DNBseq platform. Sequence reads that passed quality filters were mapped onto reference genome, followed by SNP & INDEL calling and Gene expression detection. Results: Squalene intake did not significantly influence single nucleotide polymorphisms. When alternative splicing events were tested, squalene administration had significant influence on splicing events, alternative 5' splicing, alternative 3' splicing Site and retained intron while no effect was found on skipped exons or mutually exclusive exons. Splicing patterns led to variety of differentially splicing genes and a variety of different isoforms from one gene. Differentially expressed genes were 18,485 in the squalene group and 18,286 in the control group. Conclusions: This study represents the first analysis of hepatic transcriptome in respond to squalene. Result data confirm that RNA-Sequencing is a sensitive and accurate tool that provides a framework for comparative investigations of known and novel DEGs.

2024-12-19 | GSE191236 | GEO

Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Squalene

Project description:Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Squalene

| PRJNA790658 | ENA

Hepatic transcriptomics of squalene in male Apoe-deficient mice on Western diet

Project description:Background and Purpose: Squalene is the main hydrocarbon present in extra virgin olive oil and it has been reported to have anti-steatotic properties in different animal models. The aims of this study were to investigate its effects on liver transcriptomics in Male C57BL/6J Apoe-deficient mice. Experimental Approaches: Male C57BL/6J Apoe-deficient mice were fed a purified Western diet with or without squalene during 11 weeks and hepatic squalene content was assessed. Hepatic transcriptomic changes were studied and confirmed by RT-qPCR. Key Results: Squalene supplementation increased its hepatic content. The Cyp2b10 and Cyp2c55 gene expressions were significantly up-regulated by the squalene intake in all animal models, with independence of sex, sexual hormones, dietary fat content, genetic background and dose, and were strongly associated with antioxidant defense capacity and with lipid content and composition. Conclusions and Implications: hepatic squalene exerts its activity through overexpression of these cytochromes and their changes in virgin olive oil diets may be due to squalene.

2021-04-30 | GSE145343 | GEO

Effect of squalene on liver transcriptome of mice lacking apolipoprotein E

2016-03-30 | GSE36932 | GEO

Effect of squalene on liver transcriptome of mice lacking apolipoprotein E

Project description:The hypothesis that the squalene of olive oil might influence hepatic gene expression in an apoE and sex-dependent ways was tested in mice. Gene expression was analyzed using DNA microarrays in male apoE-deficient mice that received 1 g/kg/day of squalene for 10 weeks. As initial screening of potential candidate genes involved in a differential response, only genes with remarkably modified expression (signal log2 ratio > 1.5 or < -1.5) were further considered

2016-03-30 | E-GEOD-36932 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Zfyve19-/- hepatic Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived hepatic transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

2021-03-27 | GSE169737 | GEO

Hepatic transcriptomics of squalene in male Apoe-deficient mice on Western diet

Project description:Hepatic transcriptomics of squalene in male Apoe-deficient mice on Western diet

| PRJNA606788 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of miRNAs in hepatic fibrosis and normal tissues.

Project description:Aim: Hepatic fibrosis is a major worldwide medical problem and can develop into liver cirrhosis and hepatocellular carcinoma(HCC). Until now, there are no effective drugs for liver ?brosis because the molecular mechanism of progression of liver fibrosis is not fully understood. MicroRNAs (miRNAs) are an important class of small non-coding functional RNAs that play a key role in many biological processes. The purpose of this study was to clarify how the aberrant expression of miRNAs participates in development of the liver fibrosis in rat liver fibrosis model. Methods: Fibrotic and paired normal liver tissues were collected and assesssed by deep sequencing technology. MiRNA pro?ling results were validated by quantitative real-time polymerase chain reaction (qRT-PCR) and bioinformatics was used to predict miRNA targets. Results: Nine deregulated miRNAs were induced in porcine serum (PS)-induced hepatic fibrosis versus normal liver. Further analysis revealed several signaling pathways (e.g., gap junction and neuroactive ligand-receptor interaction) may be associated with hepatic fibrogenesis. Conclusion: Several miRNAs are dysregulated in PS-induced hepatic fibrosis and seem to be closely associated with hepatic fibrogenesis. These results provide an experimental basis for understanding the mechanism of hepatic fibrosis. We sequenced two samples, including case and control. Each sample has two replicates.

2015-06-04 | E-GEOD-54028 | biostudies-arrayexpress

Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Txndc5

Project description:Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Txndc5

| PRJNA769409 | ENA