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

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

PROVIDER: PRJNA713989 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13951234.fastq.gz	Fastqsanger.gz
	SRR13951235.fastq.gz	Fastqsanger.gz
	SRR13951236.fastq.gz	Fastqsanger.gz
	SRR13951237.fastq.gz	Fastqsanger.gz
	SRR13951238.fastq.gz	Fastqsanger.gz

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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 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.

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