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

ABSTRACT: 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.

ORGANISM(S): Sus scrofa

PROVIDER: GSE214732 | GEO | 2023/08/30

REPOSITORIES: GEO

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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.

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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

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.

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RNA-seq of Staphylococcus aureus and Staphylococcus aureus challenged with squalene compared to control growth

Project description:Squalene makes up 12 % of human skin surface lipids, however little is known about its affects on the host skin microbiome. Here we tested the effect of squalene on genetic regulation of staphylococci, showing that it profoundly affects expression virulence or colonisation determinants, and of iron uptake systems.

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

Project description:Purpose: The goal of this study was to determine erythrodiol effect on hepatic transcriptome by comparing high-throughput data for tested group vs. control group. Method: Hepatic mRNA profile of two Apoe deficient male mice groups fed over 12 weeks with either western diet or same diet enriched with 10 mg/kg erythrodiol was analysed by Transcriptome sequencing using BGISEQ-500 platform. Sequence reads that passed quality filters were mapped onto reference genome, followed by novel gene prediction, SNP & INDEL calling and gene-splicing detection. Results: When using optimized Bioinformatics Workflow, mapping ratio for both tested groups was about 74%. There was no significant difference in SNPs between both groups. Splicing patterns _including Skipped Exon (SE), Alternative 5' Splicing Site (A5SS), Alternative 3' Splicing Site (A3SS), Mutually exclusive exons (MXE) and Retained Intron (RI) _allowed the production of a variety of DSGs with a total of 14,920 novel transcripts, 13,439 coding and 1,481 non coding transcripts. Coding genes showed 11,605 previously unknown splicing events for known genes and 1,834 coding transcripts previously unknown. DEGs were 554 in control group vs. 488 in erythrodiol group. Applying a 2-fold change and P value <0.001 led to 68 up regulated genes and 124 down-regulated genes. Gene Ontology Analysis of DEG With the GO annotation and functional enrichment classified DEGs to 3 main classification with liver-dependent properties. Altered expression of 21 genes was confirmed with RT-qPCR, demonstrating the high degree of sensitivity and accuracy of RNA-seq technique Conclusions: This study represents the first analysis of hepatic transcriptome in respond to erythrodiol. Result data confirm that RNA-Sequencing is a sensitive and accurate tool that provides a framework for comparative investigations of known and novel DEGs.

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Project description:We performed bulk RNA-seq on squalene/M-CSF-treated macrophages to compute the fold change of genes in the squalene/M-CSF compared to M-CSF alone treated macrophages. We then looked at the distribution of the log fold changes in the skin-derived TREM2 (607 genes) and M2-like (709 genes) macrophage scRNA-seq signatures. We found that the TREM2 gene signature was more highly induced by squalene/M-CSF than the M2-like macrophage signature. In these squalene-induced macrophages, we found upregulation of several of the lipid metabolism and pro-inflammatory genes present in the skin-derived TREM2 macrophage gene signature.

2021-11-09 | GSE188363 | GEO

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

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

| PRJNA886962 | ENA

Universal alternative splicing of noncoding exons

Project description:Universal alternative splicing of noncoding exons

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Mouse Alt-Splice Tissue Panel (Brain vs Non-Brain)

Project description:22 Normal adult mouse tissues on custom alternative transcript sensitive Affymetrix microarray used to address differeneces in tissue specific alternative splicing. Abstract: Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe expression of RNA containing at least two alternative splice junctions for about a third of the 3200 alternative events we could detect. Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues, and another 28 exons whose splicing is different in muscle. A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of protein-coding exons. By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation. Of note is a motif strikingly similar to the branchpoint consensus, but which is located downstream of the 5' splice site of exons included in muscle. Analysis of three paralogous membrane-associated guanylate kinase (MAGUK) genes reveals that each contains a paralogous tissue regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families. Keywords: Alternative splicing isoform specific, adult mouse tissues

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