Transcriptome profiling of zebrafish optic fissure fusion
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA670550 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12874633_1.fastq.gz | Fastqsanger.gz | |||
| SRR12874633_2.fastq.gz | Fastqsanger.gz | |||
| SRR12874634_1.fastq.gz | Fastqsanger.gz | |||
| SRR12874634_2.fastq.gz | Fastqsanger.gz | |||
| SRR12874635_1.fastq.gz | Fastqsanger.gz |
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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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Project description:The different stages of the optic fissure can be clearly visualized by making sagittal sections through the mouse eye during early development which represent the optic fissure at open (E10.5), closing (E11.5) and fused (E12.5) states. Laser capture microdissection (LCM) was employed to dissect tissue from the margins of the optic fissure consisting of the outer (presumptive RPE) and inner (presumptive neurosensory retina) layers of the retina. An approximately square-shaped block of optic fissure (50 x 50 mm) was dissected from each side of the fissure. Two rounds of linear amplification were performed on RNA isolated from each of the samples prior to microarray hybridization. Expression data were gathered in biological triplicate at E10.5, E11.5 and duplicate at E12.5, each array representing pooled optic fissure tissue from three embryos from a single litter. Expression signals were ascertained from 45,101 probe sets and normalized across arrays. Experiment Overall Design: Differential gene expression over the course of three days in laser capture microdissected tissue from wild type mouse embryos.
2008-10-26 | E-GEOD-13103 | biostudies-arrayexpress
Project description:The different stages of the optic fissure can be clearly visualized by making sagittal sections through the mouse eye during early development which represent the optic fissure at open (E10.5), closing (E11.5) and fused (E12.5) states. Laser capture microdissection (LCM) was employed to dissect tissue from the margins of the optic fissure consisting of the outer (presumptive RPE) and inner (presumptive neurosensory retina) layers of the retina. An approximately square-shaped block of optic fissure (50 x 50 mm) was dissected from each side of the fissure. Two rounds of linear amplification were performed on RNA isolated from each of the samples prior to microarray hybridization. Expression data were gathered in biological triplicate at E10.5, E11.5 and duplicate at E12.5, each array representing pooled optic fissure tissue from three embryos from a single litter. Expression signals were ascertained from 45,101 probe sets and normalized across arrays. Keywords: Time course
2008-10-08 | GSE13103 | GEO
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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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 mouse embryonic eyes (n=3 at E11.5 and n=3 at E12.5). 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). Fissure closure is active at E11.5 and complete by E12.5
2020-12-17 | E-MTAB-9427 | biostudies-arrayexpress
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.
2020-12-17 | E-MTAB-9426 | biostudies-arrayexpress
Project description:Heterozygous adults of the zebrafish transgenic line Tg(flk1:RFP)is18 develop tumors in the retina, optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 month old sibling wild type and Tg(flk1:RFP)is18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT (wild type); 3 grossly normal retina from Tg(flk1:RFP)is18/+ were pooled to create Sample PT (pre tumor) and 2 large tumors from Tg(flk1:RFP)is18/+ were pooled to create Sample T (tumor). Each sample was run in an individual lane on the HiSeq system.
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Project description:To identify genes regulated by Rx3 during optic vesicle morphogenesis, adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hours post fertilization (hpf), the earliest time point at which optic vesicle evagination phenotypes could be reliably detected, offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild-type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants (rx3-/-) or phenotypically wild-type siblings (rx3+/+ or rx3+/-), and one replicate of 13 hpf wild-type zebrafish larva were collected for whole transcriptome sequencing. Whole transcriptome sequencing (RNA-seq) was performed on zebrafish rx3-/- mutants, wild-type siblings and wild-type AB strains at 13 hpf
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Project description:Mice that are mutant for both Fgfr1 and Fgfr2 specifically in the developing retina develop coloboma. To analyze the transcripts that are affected by defective FGF signaling, we micro-dissected the optic fissure region from the control and FGFR condtional mutant mice and did microarray analysis. E11.5 control and Six3Cre+; Fgfr1fx/fx;Fgfr2 fx/fx optic fissures are dissected using laser-assisted micro-dissection microscope, RNAs are extracted and labelled and hybridyzed to chips
2012-10-02 | E-GEOD-41260 | biostudies-arrayexpress
Project description:Mice that are mutant for both Fgfr1 and Fgfr2 specifically in the developing retina develop coloboma. To analyze the transcripts that are affected by defective FGF signaling, we micro-dissected the optic fissure region from the control and FGFR condtional mutant mice and did microarray analysis.
2012-10-02 | GSE41260 | GEO