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Next Generation Sequencing Quantitative Analysis of Wild Type and Shoc2 -/- sox10-positive cells in zebrafish

ABSTRACT: Next Generation Sequencing Quantitative Analysis of Wild Type and Shoc2 -/- sox10-positive cells in zebrafish

PROVIDER: PRJNA814245 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18278438.fastq.gz	Fastqsanger.gz
	SRR18278439.fastq.gz	Fastqsanger.gz
	SRR18278440.fastq.gz	Fastqsanger.gz
	SRR18278441.fastq.gz	Fastqsanger.gz
	SRR18278442.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Quantitative Analysis of Wild Type and Shoc2 -/- sox10-positive cells in zebrafish

Project description:To determine how Shoc2-mediated signals affect expression of genes controlling specification of neural crest cells in zebrafish development, we applied RNA-sequencing. shoc2 CRISPR/Cas9 mutants that are transgenic for sox10:dsRed – marking neural crest progenitors were utilized in these experiments. mRNAs was isolated from the FACS-purified sox10:dsRed positive cells of shoc2 CRISPR/Cas9 mutant and wild type larvae. This approach allows for a robust and targeted quantitative assessment of how Shoc2-ERK1/2 signaling affects emergence of several neural crest lineages. The differences in the transcriptome of cells purified from shoc2 crispants and control embryos were determined.

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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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