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Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1-/- Zebrafish Embryo Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1-/- Zebrafish Embryo Transcriptomes

PROVIDER: PRJNA637219 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1-/- Zebrafish Embryo Transcriptomes

Project description:Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level, we performed full genome RNA-Seq between aldh3a1+/+ and aldh3a1-/- larvae at 48 hpf.An overview of RNA-Seq, including quality control, principal component analysis (PCA), volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis (normalized enrichment score, -1.72; p=0.0006). Interestingly, endocrine pancreas but not exocrine pancreas development pathway was significantly down-regulated in aldh3a1 mutants . Taken together, these results further suggest Aldh3a1 as an important regulator in the development, morphology and insulin secretion function of primary pancreas. Furthermore, we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2020-10-06 | GSE151770 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype, akr1a1a-/- and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype, akr1a1a-/- and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of Endometrium Transcriptomes During Porcine Embryo Implantation.

Project description:In this study, deep sequencing of endometrial RNA samples during early pregnancy were performed using RNA sequencing (RNA-Seq). The changes of genes expressed among three stages (day 12, 18 and 25) of pregnancy were investigated by the multiple comparisons. Analysis of reads, between 1557 and 8951 differentially expressed genes (DEGs) were revealed among different periods of implantation. Expression of selected genes was validated by the use of quantitative real-time RT-PCR. Bioinformatics analysis of differentially expressed genes in the endometrium revealed a number of biological processes and pathways potentially involved in embryo implantation in the pig, most noticeably cell proliferation, regulation of immune response, interaction of cytokine-cytokine receptor, and cell adhesion. This revealed specific gene expression patterns reflecting the different functions of the endometrium on three stages (maternal recognition, conceptus attachment and embryo implantation). This study identified comprehensive transcriptomic profile in the porcine endometrium, it could be a foundation for targeted studies of genes and pathways potentially involved in abnormal endometrial receptivity and embryo loss in early pregnancy.

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RNAseq facilitates quantitative analysis of wildtype, pdia6 -/- and focad -/- zebrafish livers transcriptome

Project description:RNAseq facilitates quantitative analysis of wildtype, pdia6 -/- and focad -/- zebrafish livers transcriptome

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Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype, akr1a1a-/- and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes

Project description:Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors (insra/insrb) expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level, we performed full genome RNA-Seq between akr1a1a+/+, akr1a1a-/- and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA-Seq, including quality control, principal component analysis (PCA), and volcano plots of regulated genes showed comparable properties between akr1a1a mutants, wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down-regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis (normalized enrichment score, -1.888, p=0.028; -1.93, p=0.019). Intriguingly, downstream signaling pathways including MAPK, signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down-regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together, these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore, we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA-seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions.

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Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum bud and flower Transcriptomes

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Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.

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Next Generation Sequencing Facilitates Quantitative Analysis of Zebrafish Osteoporosis Model Transcriptomes

Project description:The development of predictive markers to determine the tipping point prior to the onset of osteoporosis is essential to mitigate further irrevocable deterioration. In order to determine the early warning signs before osteoporosis, we used the dynamic network biomarker (DNB) approach to analyze the time series gene expression data in the zebrafish osteoporosis model and revealed that cyclin-dependent kinase inhibitor 1A (cdkn1a) is one core member of DNB. We demonstrated that cdkn1a negatively regulates osteogenesis, evidenced by the loss-of-function and gain-of-function studies. On one hand, CRISPR/Cas9-mediated cdkn1a knockout in the zebrafish significantly altered skeletal development and increased bone mineralization. On the other hand, inducible cdkn1a expression significantly contributed to the osteoclast differentiation. We also provide mechanistic clues that cdkn1a participates in osteoclast differentiation by regulating its upstream signaling cascades. Our data provided new insights into the dynamic nature of osteoporosis, and identified cdkn1a as the early-warning signals of osteoporosis onset.

2023-01-01 | GSE194301 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Pou4f3(Δ/+) Cochlear Transcriptomes

Project description:We report application of RNA-seq for transcriptomic analyses of cochlear tissues from wildtype and DFNA15 deafness mouse model Pou4f3(Δ/+) to reveal gene expressions altered by Pou4f3 mutation

2019-10-22 | GSE139145 | GEO