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RNA-seq of the developing human eye (Day 41-44 of embryonic development) comparing gene expression in ventral optic fissure margins with dorsal optic cup

ABSTRACT: RNA-seq of the developing human eye (Day 41-44 of embryonic development) comparing gene expression in ventral optic fissure margins with dorsal optic cup

PROVIDER: PRJEB39797 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4436660_1.fastq.gz	Fastqsanger.gz
	ERR4436660_2.fastq.gz	Fastqsanger.gz
	ERR4436670_1.fastq.gz	Fastqsanger.gz
	ERR4436670_2.fastq.gz	Fastqsanger.gz
	ERR4436661_1.fastq.gz	Fastqsanger.gz

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RNA-seq of the developing human eye (Day 41-44 of embryonic development) comparing gene expression in ventral optic fissure margins with dorsal optic cup

Project description:We sought to identify gene expression signatures confined to the small group of cells at the fissure margins that are involved in OFC. Serial cryosections perpendicular to the optic fissure were prepared from human embryonic eyes (n=3, CS17-18, Day41-44(CS 17-18). The fissure margins and a corresponding control region of dorsal optic cup were isolated using laser capture microdissection. This study design aimed to identify the signature of gene expression in the OFC margins and to identify those genes that were more highly expressed along the ventral (inferior) fissure compared to the opposing dorsal (superior region). As CS17-18 (Day41-44) stages have active points of closure they were considered suitable for transcriptomic analyses of the process of human fissure closure.

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RNA-Seq of developing mouse eye (E11.5 and E12.5) comparing optic fissure margins with dorsal optic cup

Project description:RNA-Seq of developing mouse eye (E11.5 and E12.5) comparing optic fissure margins with dorsal optic cup

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Transcriptome profiling of zebrafish optic fissure fusion

Project description:Incomplete fusion of the optic fissure leads to ocular coloboma, a congenital eye defect that affects up to 7.5 per 10,000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before (32 hours post fertilisation, hpf), during (48 hpf) and after (56 hpf) optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT-PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a (ntn1a) as highly differentially expressed across optic fissure fusion, with a resultant ocular coloboma phenotype following morpholino antisense translation-blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies, we have generated an online open-access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma.

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