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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression after deletion of Bmp4 in the mouse optic vesicle

ABSTRACT: Bmp4 was conditionally deleted from the mouse optic vesicle with Rx-Cre. The heads of wild type and knockout E10.5 mouse embryos were laser micodissected to isolate the lens ectoderm and prospective retina from three embryos of each genotype. Total RNA was purified and reverse transcribed and amplified using a NuGEN Ovation Pico WTA system V2 kit. cDNA was biotinylated and hybridized to Illumina Mouse6 V2 bead arrays. Three wild type and three knockout embryos were used. RNA obtained from the lens ectoderm or prospective retina (distal optic vesicle) was pooled, amplified and used for microarray analysis. Statistical analysis was performed using the values from the 25-50 beads on each array.

ORGANISM(S): Mus musculus

SUBMITTER: David Beebe

PROVIDER: E-GEOD-62536 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression after deletion of Bmp4 in the mouse optic vesicle

Project description:Bmp4 was conditionally deleted from the mouse optic vesicle with Rx-Cre. The heads of wild type and knockout E10.5 mouse embryos were laser micodissected to isolate the lens ectoderm and prospective retina from three embryos of each genotype. Total RNA was purified and reverse transcribed and amplified using a NuGEN Ovation Pico WTA system V2 kit. cDNA was biotinylated and hybridized to Illumina Mouse6 V2 bead arrays.

2015-02-20 | GSE62536 | GEO

Gene regulation by Pax6 in the lens placode - E9.5 (1)

Project description:Wild type or Pax6 fx/fx; Le-Cre-positive (Pax6-/-) surface ectoderm from E9.5 mouse embryos was laser micodissected from three embryos of each genotype. Total RNA was purified and reverse transcribed and amplified using a NuGEN kit. cDNA was biotinylated and hybridized to Illumina Mouse6 bead arrays. Three wild type and three knockout embryos were used. Each array used the cDNA obtained from the two prospective lens tissues (left and right eyes) from each embryo.

2013-09-01 | E-GEOD-49227 | biostudies-arrayexpress

Expression data from pooled RNA of various ocular tissues

Project description:The normal gene expression profiles of the tissues in the eye are a valuable resource for considering genes likely to be involved with disease processes. This is based on the assumption that transcript abundances in healthy tissue are correlated to the continued health of that tissue. Expression values were compared with publically available EST and RNA-sequencing resources. The estimated gene and exon level abundances are available online on the Ocular Tissue Database. Ten different tissues were obtained from 6 different individuals and RNA was pooled. The tissues included: retina, optic nerve head (ONH), optic nerve (ON), ciliary body (CB), trabecular meshwork (TM), sclera, lens, cornea, choroid/RPE and iris.

2013-04-17 | E-GEOD-41102 | biostudies-arrayexpress

Gene regulation by Pax6 in the lens placode - E10.25

Project description:Wild type or Pax6 fx/fx; Le-Cre-positive surface ectoderm from E10.25 mouse embryos was laser micodissected from three embryos of each genotype. Total RNA was purified and reverse transcribed and amplified using a NuGEN kit. cDNA was biotinylated and hybridized to Illumina Mouse6 bead arrays. Three wild type and three knockout embryos were used. Each array used the cDNA obtained from the two prospective lens tissues from one embryo.

2013-09-23 | E-GEOD-49216 | biostudies-arrayexpress

Rat retina and optic nerve LC-MS/MS

Project description:Various retinal disorder such as glaucomatous, retinal ischemia reperfusion, and traumatic optic neuropathy, are involved in the pathogenesis of neurodegeneration via glutamate exicitotoxicity. However, the proteomic characteristics and modulation of the neural-microenvironment with NMDA-induced neurodegeneration in retina and optic nerve remain partly understood. We established a protein sketch of NMDA-induced injury by comparing the proteomes of the PBS-operated, NMDA-operated and control groups. We carried out mass spectrometry-based label-free quantitative proteomics to investigate the exicitotoxic neurodegeneration mechanisms and identify key proteins that regulated neural cell death related signaling pathway in retina and optic nerve spatially. Using LC-MS/MS proteomics analysis, in total, we identified 3532 proteins in retina, 2593 proteins in optic nerve. According to Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), the protein changes and energy metabolism in retina and optic nerve tissue were comprehensively evaluated.

2021-12-30 | PXD022466 | Pride

Rat retina and optic nerve LC-MS/MS

2021-12-30 | PXD022729 | Pride

Yap and Taz regulate retinal pigment epithelial cell fate

Project description:The optic vesicle comprises a pool of bi-potential progenitor cells from which the retinal pigment epithelium (RPE) and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation, but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz-Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises, and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap (yap1) mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz (wwtr1) mutant alleles such that, when Yap and Taz are both absent, optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co-factor. In contrast to loss of Yap and Taz, overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall, this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.

2015-08-06 | E-GEOD-71681 | biostudies-arrayexpress

Regulation of Mouse Lens Development and Gene Expression by KrÃ¼ppel-Like Factor 4

Project description:Conditional disruption of Klf4 in the ectoderm-derived tissues of the eye results in defective cornea, conjunctiva and the lens. Expression of Klf4 is first detected in the embryonic day-12 (E12) mouse lens, peaks at E16, and declines thereafter. Lenses from Mice which were conditional null for Klf4 (Klf4CN) were characterized by morphology and transcriptome. Wild type and Klf4-conditional null mouse lens gene expression at embryonic day 16.5 (E16.5) and postnatal day 56 (PN56) was surveyed using Affymetrix mouse whole genome 430 2 arrays.

2013-07-01 | E-GEOD-47694 | biostudies-arrayexpress

Proteomics analysis of guinea pig retina at the early stage of myopia

Project description:This is a combined SWATH database of early myopic guinea pig retina. The retinal tissues were divided into lens induced myopia 4 days group (4-day LIM) and control group; 5 individual animals (10 retinas) were included. The potential biomarkers and underlying biochemical pathways during early myopia could be investigated using SWATH based proteomics approach.

2021-05-13 | PXD025003 | Pride

Single-cell transcriptional analysis of lens placode development in Mab21l1 knockout mice

Project description:In mouse early organogenic stages, a Mab21l1-null mutation causes severe defects in invagination of the lens placode toward optic cup due to its severe defects in both cell proliferation and survival, which subsequently results in severe microphthalmia after birth. In human, loss of function variants in MAB21L1 have recently been described in Cerebello-Oculo-Facio-Genital syndrome (COFG syndrome). The close similarity between mouse and human phenotypes including microphthalmia indicates the importance of Mab21l1 function in human lens placode. To approach the molecular function of MAB21L1 in eye morphogenesis, we examined single cell transcriptomes in lens placode and its surrounding surface ectoderm at 26 somite stage (E9.25), just prior to the onset of lens defects in Mab21l1-null embryos. Here we demonstrate the identification of several key genes immediately downstream of Mab21l1 function, together with the early lens placode-/surface ectoderm-specific single cell transcriptomes during murine lens placode specification.

2021-11-30 | GSE167126 | GEO

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