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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide analysis of Sox2-ablated optic cups compared with wild-type control optic cups at E16.5

ABSTRACT: To test the hypothesis that ablation of the SOX2 in the developing optic cup leads to expansion of peripheral optic cup signaling pathways, we screened whole-genome changes in gene expression in Sox2-mutant eyes compared with controls. Results confirm that ciliary epithelial (peripheral) identity is gained at the expense of neural retinal identity in Sox2-ablated optic cups. Total RNA was isolated from whole eyes enucleated from six wild-type controls and six Sox2-mutant embryos for a total of twelve eyes per genotype. Each embryo (pair of eyes) was analyzed as a single sample.

ORGANISM(S): Mus musculus

SUBMITTER: Whitney Heavner

PROVIDER: E-GEOD-46796 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide analysis of Sox2-ablated optic cups compared with wild-type control optic cups at E16.5

Project description:To test the hypothesis that ablation of the SOX2 in the developing optic cup leads to expansion of peripheral optic cup signaling pathways, we screened whole-genome changes in gene expression in Sox2-mutant eyes compared with controls. Results confirm that ciliary epithelial (peripheral) identity is gained at the expense of neural retinal identity in Sox2-ablated optic cups.

2013-05-10 | GSE46796 | GEO

RNA-Seq of developing mouse eye (E11.5 and E12.5) comparing 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 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

Expression data of different regions of E11.5 mouse optic cups

Project description:Optic fissue is a transient opening on the ventral side of developing optic cup. Failure in optic fissue closure will cause coloboma formation. The aim of this study was to compare optic fissue transcriptome with center optic cup to find optic fissue specific genes.

2018-05-01 | GSE109501 | GEO

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.

2020-12-17 | E-MTAB-9426 | biostudies-arrayexpress

Expression data from mouse optic nerve head after optic nerve crush

Project description:Reactive gliosis is a complex process that involves profound changes in gene expression. We used microarray to indentify differentially expressed genes and to investigate the molecular mechanisms of reactive gliosis in optic nerve head in response to optic nerve crush injury. C57Bl/6 female mice were 6-8 weeks old at the time of optic nerve crush surgery. The optic nerve in the left eye was crush 1 mm behind the globe for 10 seconds and the right eye served as contralateral control. The animals were allowed to recover for 1 day, 3 day, 1 week, 3 weeks and 3 months before the optic nerve heads were collected. The naive control mice did not receive any surgery in either eye. Due to the small tissue size of the mouse optic nerve head, two optic nerve heads were pooled together for each microarray chip. The left eyes and the right eyes of two mice were combined respectively to form one pair of experiment and control samples. There were five biological replicates (10 mice) for each condition.

2013-07-15 | E-GEOD-40857 | biostudies-arrayexpress

Single-cell transcriptional analysis reveals developmental stage-dependent changes in retinal progenitors in the murine early optic vesicle

Project description:The optic vesicle in the developing embryonic eye contains a multitude of neuroepithelial progenitors that subsequently differentiate into functionally distinct domains of the optic cup, such as the neural retina, pigment epithelium, and optic stalk. To investigate cell-type diversity across early optic vesicles before regionalization of the optic cup, we performed single-cell RNA-sequencing (scRNA-seq) using 7,989 cells from the presumptive eye area in mouse embryos at the 12–26-somite stages at five developmental time points. We demonstrated the presence of seven optic vesicle populations, including three unique cell types located in the ventricular surface or dorsoventral areas of the optic vesicle structure. Moreover, the remaining four populations of retinal progenitor cells could be classified according to their stage-dependent time point, and these cells exhibited altered expression of several structural and metabolic key genes, such as Col9a1 and Ckb, just before regionalization of the optic cup. From these data, we provide the first report on stage-dependent transcriptional profiles during initial retinal specification at single-cell resolution and highlight the unexpected developmental heterogeneity of the murine optic vesicle structure.

2021-02-08 | GSE148063 | GEO

Wnt ligands from the embryonic surface ectoderm regulate bimetallic strip optic cup morphogenesis in the mouse

Project description:Wnt signaling in early eye development, specifically the lens placode shows expression of 12 out of 19 Wnt ligands. We these Wnt activities were suppressed using conditional deletion of Wntless, dramatic phenotypic changes in morphogensis occurred. Microarray analysis of the genes that were changed in response to deletion of Wnt ligands in the developing eye region show direct or indirect responses from the surface ectoderm to the developing RPE and optic cup curvature, creating an overal shape change phenotype in the bilayerd epithelium of the optic cup.

2015-01-22 | GSE65154 | GEO

Comparative transcriptomic analysis of self-organized, in vitro generated optic tissues

2015-05-18 | GSE62432 | GEO

Comparative transcriptomic analysis of self-organized, in vitro generated optic tissues

Project description:Embryonic stem (ES) cells have a remarkable capacity to self-organize complex, multi-layered optic cups in vitro via a culture technique called SFEBq. During both SFEBq and in vivo optic cup development, Rax (Rx) expressing neural retina epithelial (NRE) tissues utilize Fgf and Wnt/β-catenin signalling pathways to differentiate into neural retina (NR) and retinal-pigmented epithelial (RPE) tissues, respectively. How these signaling pathways affect gene expression during optic tissue formation has remained largely unknown, especially at the transcriptome scale. We generated Day 10 Rx+ optic tissue using SFEBq, exposed these tissues to either Fgf or Wnt/β-catenin stimulation, and assayed their gene expression at Days 12 and 15 using RNA-Seq. We measured gene expression in these 5 sample groups in biological triplicate using RNA-seq (Illumina HiSeq) .

2015-05-18 | E-GEOD-62432 | biostudies-arrayexpress

Transcription profiling of mouse optic nerves as a model for axonal injury

Project description:We used optic nerve injury as a model to study early signaling events in the neuronal soma following axonal injury. Optic nerve injury results in the selective death of retinal ganglion cells (RGCs). The time course of cell death takes place over a period of days with the earliest detection of RGC death at about 48 hr post injury. We hypothesized that in the period immediately following axonal injury, there are changes in the soma that signal surrounding glia and neurons and that start programmed cell death. In the current study, we investigated early changes in cellular signaling and gene expression that occur within the first 6 hrs post optic nerve injury. We detected differences in phosphoproteins and gene expression within this time period that we used to interpret temporal events. Our studies revealed that the entire retina has been signaled by the RGC soma within 30 min after optic nerve injury and that pathways that modulate cell death are likely to be active in RGCs within 6 hrs following axonal injury Experiment Overall Design: In the treated animals, axons of the optic nerve were crushed with fine forceps for 10 sec, 1 mm posterior to the globe, under direct visualization, within an intact meningeal sheath. Controls were contralateral eyes from the same animals in each group that had not been injured. After 6 hr eyes were enucleated and processed for tissue sectionin

2008-10-25 | E-GEOD-11862 | biostudies-arrayexpress

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