Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA380770 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We sequenced mRNA from 34 retina/RPE/choroid samples taken from the right eyes of male chicks across a time-course of normal development or refractive error induction (defocus-induced myopia and hyperopia).
2016-09-17 | GSE78042 | GEO
Project description:We compare dissected ocular tissues from wild-type and lrp2-/- mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2, a transmembrane receptor, cause ocular enlargement and high-myopia. LRP2 is expressed by the RPE and eye ciliary epithelia, binding many extracellular ligands, including Bmp4 and Shh. Signaling mediated by LRP2 is very context-dependent, and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled, sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia (proper refraction). Using human iPSC-derived RPE, and zebrafish, we demonstrate that BACE sheddase-dependent LRP2 cleavage produces a soluble domain that binds BMP4, inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand-binding receptor forms available: a soluble BMP trap, and a membrane-bound RPE signaling facilitator. By modulating LRP2 cleavage, cells can fine-tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth.
2018-06-01 | GSE97125 | GEO
Project description:To gain a better understanding of the factors necessary for successful CNS regeneration, a temporal analysis of the changes in gene expression in the eye caused by optic nerve injury was conducted. Dual color oligonucleotide microarrays were used to compare total RNA harvested from the eyes of sham-operated and optic nerve-injured fish at 3, 24, and 168 hours following surgery. Optic nerve injured fish are compared to sham-operated fish in order to eliminate gene expression due to non-neuronal damage and inflammatory response. Statistical analyses identified 131 genes with a 2.0-fold or greater difference in expression. Wild type zebrafish were obtained from a local pet store. Optic nerve injury was conducted using a severing model accomplished as follows. Zebrafish were anesthetized in 0.2% MS-222 dissolved in tank water. The muscles surrounding the eye were cut and the eye angled rostrally to expose the nerve. The optic nerve was then severed using microsissors without damaging the ophthalmic artery. In sham operated fish the muscles surrounding the eye were severed but the nerve was not damaged. RNA was extracted from the eye at three time points following surgery 3 hours, 24 hours, and 168 hours. RNA was pooled from multiple fish to achieve 10 ug total RNA. Samples were collected in triplicate per time point. Gene expression was analyzed on a dual color oligonucleotide array where the optic nerve injured fish were compared to sham-operated fish. Four samples of RNA were also collected from control fish and compared to each other on the microarray to confirm that processing did not create expression differences.
2010-05-16 | E-GEOD-17854 | biostudies-arrayexpress
Project description:The retinal pigment epithelium (RPE) is a monolayer of polarized epithelial cells lying between the retina and the choroid/sclera, with a major function in supporting photoreceptor homeostasis, but the role of RPE in eye size regulation is yet to be further explored. it was recently reported that selective deletion of Low density lipoprotein receptor-related protein 2 (Lrp2) in the mouse RPE resulted in large eyes, similar to the phenotypes of Lrp2 whole eye knockout mice, suggesting that the RPE is the tissue in which LRP2 functions. Here, to investigate which downstream pathways of Srebp2 and Lrp2 are responsible for regulating eye growth, we performed RNA-seq analysis with the mouse RPE tissues. Postnatal day 0 (P0) mice were injected with AAV8-Best1-GFP/nSrebp2/ctrl sh/Lrp2 sh1/Lrp2 sh2 viruses to overexpress the constitutively active form of Srebp2 or to knockdown Lrp2 in the RPE specifically. At P14, RPE cells were carefully dissociated for RNA extraction. Via RNA-seq analysis and functional validation, we identified that Bmp2 is the target and the effector of the Srebp2-Lrp2 pathway. Overall, the present study unveils an essential role of RPE in regulating eye size via the Srebp2-Lrp2-Bmp2 signaling pathway, shedding light on the underlying mechanism of eye size control.
2022-05-31 | GSE204715 | GEO
Project description:Refractive eye development is regulated by optical defocus in a process of emmetropization. Excessive exposure to negative optical defocus often leads to the development of myopia. However, it is still largely unknown how optical defocus is detected by the retina. Here, we used genome-wide RNA-sequencing (RNA-seq) to conduct analysis of the retinal genetic networks underlying contrast perception and refractive eye development. We report that the genetic network subserving contrast perception plays an important role in optical defocus detection and emmetropization. Our results demonstrate an interaction between contrast perception, the retinal circadian clock pathway and the signaling pathway underlying optical defocus detection. We also observe that the relative majority of genes causing human myopia are involved in the processing of optical defocus. Together, our results support the hypothesis that optical defocus is perceived by the retina using contrast as a proxy and provide new insights into molecular signaling underlying refractive eye development.
2021-06-03 | GSE158732 | GEO
Project description:Transcriptional profiling performed from total eye RNA extracts of wildtype control fishes versus Prpf31 morpholino injected larvae (at ~72hpf) two-condition experiment: wildtype zebrafish versus MO-Prpf31 injected zebrafish eye RNA; 6 replicates each (extraction from 6 pools (~200 eyes each) of controls and 6 pools MO-Prpf31 (~200 eyes each))
2010-05-06 | E-GEOD-20424 | biostudies-arrayexpress
Project description:Transcriptional profiling performed from total eye RNA extracts of wildtype control fishes versus Prpf31 morpholino injected larvae (at ~72hpf)
2010-03-01 | GSE20424 | GEO
Project description:NEI Refractive Error Collaboration (KORA)
| PRJNA75817 | ENA