Gallus gallus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA351792 | 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:One-day old white Leghorn chicks were housed in brooders with a 12 hr light:dark cycle, using General Electric chroma 50 fluorescent lighting with irradiance of approximately 50μW/cm2 at chick eye level. They received Purina Chick Chow food and water ad libitum. At one week of age and at the onset of the light phase, the chicks were anesthetized with inhalation ether, and a unilateral translucent white plastic goggle was glued to the periorbital feathers to induce ipsilateral form-deprivation myopia, alternating between the left or right eye. After either 6 hrs (n=8) or 3 days (n=8) of goggle wear, the chicks were killed by decapitation. The enucleated eyes were opened at the equator, and the retina/RPE was dissected together from both the goggled and control eyes. The tissues were individually frozen and stored in liquid nitrogen until processed Experiment Overall Design: Six biological replicates used for each: 3 day control retina, 3 day experimental, 6 hour control retina, and 6 hour experimental.
2008-11-08 | E-GEOD-6543 | biostudies-arrayexpress
Project description:We investigated diurnal changes in gene expression in the retina and choroid at the onset of experimental myopia. We induced visual form deprivation myopia in young chicks, and isolated retinal and choroidal tissues separately in form- deprived and contralateral control eyes every 4 hours over a single 24-hour period.
2023-12-20 | GSE227724 | GEO
Project description:We sequenced mRNA from 16 retina/RPE/choroid samples taken from the right eyes of male chicks across control, form-deprivation occlusion, and recovery from form deprivation conditions.
2020-12-31 | GSE80327 | GEO
Project description:Microarray analysis was performed on retina/RPE/choroid samples taken from the right eyes of male chicks across control and recovery from form deprivation conditions.
2018-06-05 | GSE89325 | GEO
Project description:Purpose: The complement system is closely linked to the pathogenesis of age-related macular degeneration (AMD). Several complement genes are expressed in retinal pigment epithelium (RPE), and complement proteins accumulate in drusen. Further, a common variant of complement factor H (CFH) confers increased risk of developing AMD. Because the mechanisms by which changes in the function of CFH influence development of AMD are unclear, we examined ocular complement expression as a consequence of age in control and CFH null mutant mice. Methods: Gene expression in neuroretinas and RPE/choroid from young and aged WT and Cfh-/- C57BL/6J mice was analysed by microarrays. Expression of a wide range of complement genes was compared to expression in splenocytes and in liver tissue by qRT-PCR. Results: An age-associated increased expression of complement, particularly C1q, C3 and Factor B, in the RPE/choroid coincided with increased expression of the negative regulators Cfh and Cd59a in the neuroretina. Young mice deficient in CFH expressed Cd59a similar to WT, but failed to upregulate Cd59a expression with age. Both hepatic and splenic expression of Cd59a increased with age regardless of Cfh genotype. Conclusions: While the connection between CFH deficiency and failure to up-regulate CD59a remains unknown, these results suggest that expression of CD59 is tissue-specific and that neuroretinal regulation depends on CFH. This could contribute to the visual functional deficits and morphological changes in the Cfh-/- mouse retina that occur with age, and further suggests that deficient neuroretinal regulation of complement could represent an early event in AMD. Gene expression in neuroretinas and RPE/choroid from young and aged WT and Cfh-/- mice, 4 biological replicates in each group.
2012-10-02 | E-GEOD-38671 | biostudies-arrayexpress
Project description:One-day old white Leghorn chicks were housed in brooders with a 12 hr light:dark cycle, using General Electric chroma 50 fluorescent lighting with irradiance of approximately 50μW/cm2 at chick eye level. They received Purina Chick Chow food and water ad libitum. At one week of age and at the onset of the light phase, the chicks were anesthetized with inhalation ether, and a unilateral translucent white plastic goggle was glued to the periorbital feathers to induce ipsilateral form-deprivation myopia, alternating between the left or right eye. After either 6 hrs (n=8) or 3 days (n=8) of goggle wear, the chicks were killed by decapitation. The enucleated eyes were opened at the equator, and the retina/RPE was dissected together from both the goggled and control eyes. The tissues were individually frozen and stored in liquid nitrogen until processed Keywords: Gene expression
2007-07-26 | GSE6543 | GEO
Project description:<p>Proper spatial differentiation of retinal cell types is necessary for normal human vision. Many retinal diseases, such as Best disease and male germ cell associated kinase (MAK)-associated retinitis pigmentosa, preferentially affect distinct topographic regions of the retina. While much is known about the distribution of cell types in the retina, the distribution of molecular components across the posterior pole of the eye has not been well-studied. To investigate regional difference in molecular composition of ocular tissues, we assessed differential gene expression across the temporal, macular, and nasal retina and retinal pigment epithelium (RPE)/choroid of human eyes using RNA-Seq. RNA from temporal, macular, and nasal retina and RPE/choroid from four human donor eyes was extracted, poly-A selected, fragmented, and sequenced as 100 bp read pairs. Digital read files were mapped to the human genome and analyzed for differential expression using the Tuxedo software suite. Retina and RPE/choroid samples were clearly distinguishable at the transcriptome level. Numerous transcription factors were differentially expressed between regions of the retina and RPE/choroid. Photoreceptor-specific genes were enriched in the peripheral samples, while ganglion cell and amacrine cell genes were enriched in the macula. Within the RPE/choroid, RPE-specific genes were upregulated at the periphery while endothelium associated genes were upregulated in the macula. Consistent with previous studies, BEST1 expression was lower in macular than extramacular regions. The MAK gene was expressed at lower levels in macula than in extramacular regions, but did not exhibit a significant difference between nasal and temporal retina. The regional molecular distinction is greatest between macula and periphery and decreases between different peripheral regions within a tissue. Datasets such as these can be used to prioritize candidate genes for possible involvement in retinal diseases with regional phenotypes. </p> <p>Reprinted from <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=25446321">Whitmore, S.S., Wagner, A.H., DeLuca, A.P., Drack, A.V., Stone, E.M., Tucker, B.A., Zeng, S., Braun, T.A., Mullins, R.F., Scheetz, T.E., 2014. Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq. Experimental Eye Research</a>. Used under <a href="http://creativecommons.org/licenses/by-nc-sa/3.0/">Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported </a>license.</p> <p>Additional RNA sequencing was performed on temporal, macular, nasal, inferior, and superior retina from a fifth subject and is included in this dataset. See original publication for details.</p>
| phs001151 | dbGaP
Project description:Development of myopia is associated with large-scale changes in ocular tissue gene expression. Although differential expression of coding genes underlying development of myopia has been a subject of intense investigation, the role of non-coding genes such as microRNAs in the development of myopia is largely unknown. In this study, we explored myopia-associated miRNA expression profiles in the retina and sclera of C57Bl/6J mice with experimentally induced myopia using microarray technology. We found a total of 53 differentially expressed miRNAs in the retina and no differences in miRNA expression in the sclera of C57BL/6J mice after 10 days of visual form deprivation, which induced -6.93 ± 2.44 D (p < 0.000001, n = 12) of myopia. We also identified their putative mRNA targets among mRNAs found to be differentially expressed in myopic retina and potential signaling pathways involved in the development of form-deprivation myopia using miRNA-mRNA interaction network analysis. Analysis of myopia-associated signaling pathways revealed that myopic response to visual form deprivation in the retina is regulated by a small number of highly integrated signaling pathways. Our findings highlight substantial involvement of miRNAs in the regulation of refractive eye development, and in the development of myopia through the retinal gene regulation.
2017-02-09 | GSE84220 | GEO