Comparative analysis of gene expression in retinal layers
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE19304 | GEO | 2010/01/01
SECONDARY ACCESSION(S): PRJNA120895
REPOSITORIES: GEO
Similar Datasets
Project description:Purpose: The aim of this study was to give a comprehensive overview on spatial distribution of gene expression in the adult mouse retina and integrate this information into existing retinal gene expression databases. Methods: Total RNA was collected by laser capture microdissection from the ganglion cell layer, inner nuclear layer, photoreceptors and the retinal pigmented epithelium of adult mice and was analyzed by oligonucleotide microarrays. The results were validated by quantitative real time PCR and in situ hybridization. Results: The applied method resulted in good separation of cells of different retinal layers. The spatial distribution of gene expression was determined on a global scale in the retina and the RPE. Our results show good correlation with previously reported retinal gene expression and describe genes not yet characterized in the context of the retina. Conclusions: The complexity of the vertebrate retina makes it necessary to determine not only temporal but spatial distributions of gene expression .Our work expands the already significant but still incomplete knowledge of retinal gene expression and hopefully facilitates functional characterization of key factors of retinal development and maintenance. Laser capture microdissected regions of the adult mouse neuronal retina and retinal pigmented epithelium were subjected to microarray analysis. 5 conditions were investigated: ganglion cell layer (GCL, 3 biological replicates), innner nuclear layer (INL, 3 biological replicates), photoreceptor layer from Blk6 (PR-WT, 3 biological replicates) and NrlKO animals (PR-Nrl, 2 biological replicates) and retinal pigmented epithelium (RPE, 1 biological replicate). All samples are co-hybridized with a reference sample (retina). 2 or 3 technical replicates were used for each biological sample. technical replicate - labeled-extract: GC1-1, GC1-2, GC1-3 technical replicate - labeled-extract: GC2-1, GC2-2, GC2-3 technical replicate - labeled-extract: GCpool-1, GCpool-2, GCpool-3 technical replicate - labeled-extract: INL1-1, INL1-2, INL1-3 technical replicate - labeled-extract: INL2-1, INL2-2, INL2-3 technical replicate - labeled-extract: INLpool-1, INLpool-2, INLpool-3 technical replicate - labeled-extract: PR-Nrl1-1, PR-Nrl1-2 technical replicate - labeled-extract: PR-Nrl2-1, PR-Nrl2-2, PR-Nrl2-3 technical replicate - labeled-extract: PR-WT1-1, PR-WT1-2, PR-WT1-3 technical replicate - labeled-extract: PR-WT2-1, PR-WT2-2, PR-WT2-3 technical replicate - labeled-extract: PR-WTpool-1, PR-WTpool-2, PR-WTpool-3 technical replicate - labeled-extract: RPE-1, RPE-2, RPE-3
2009-12-31 | E-GEOD-19304 | biostudies-arrayexpress
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:Ocular growth is regulated locally by signals produced in the retina that ultimately act on the growth of the scleral tissue. Consequently, a number of studies have investigated changes in retinal gene expression during manipulation of ocular growth in an attempt to elucidate the biochemical pathways underlying eye growth. However, due to the highly heterogenous nature of the retina, important changes in gene expression can be masked. Therefore, this study has investigated changes in gene expression specifically within the retinal amacrine cell layer, the most likely generator of growth signals, during manipulations of ocular growth. Chicks were monocularly treated with either -7D (n=3, growth stimulant) or +7D (n=3, growth suppressant) lenses for 24hrs, with untreated age-matched chicks serving as a control (n=3). Total RNA from the amacrine cell layer was isolated from laser-capture microdissected (Zeiss, Bernried, Germany) 10µm thick sections. Labeled cRNA was prepared from three separate samples per condition and hybridized to Affymetrix GeneChip Chicken Genome arrays.
2010-07-08 | E-GEOD-17758 | biostudies-arrayexpress
Project description:Ocular growth is regulated locally by signals produced in the retina that ultimately act on the growth of the scleral tissue. Consequently, a number of studies have investigated changes in retinal gene expression during manipulation of ocular growth in an attempt to elucidate the biochemical pathways underlying eye growth. However, due to the highly heterogenous nature of the retina, important changes in gene expression can be masked. Therefore, this study has investigated changes in gene expression specifically within the retinal amacrine cell layer, the most likely generator of growth signals, during manipulations of ocular growth.
2010-06-17 | GSE17758 | GEO
Project description:The retina is a light-sensitive highly-organized tissue, which is vulnerable to aging and age-related retinal diseases. However, the effects of aging on retinal cell types including those present in neural retina and retinal pigment epithelium (RPE), as well as cell types in choroid layer remain largely unknown. Here, we established the single-cell transcriptomic atlas of the retina and adjacent choroid in young and aged non-human primates (NHPs), identifying 15 cell types with distinct gene expression signatures and finding several novel markers. Our analysis reveals that oxidative stress is a major aging feature of the cells in the neural retinal layer, whereas an enhanced inflammatory response is that of RPE and choroidal cells. We also found that the RPE cell is the cell type most susceptible to aging in retina, as evidenced by the decreased cell density as well as the highest numbers of differentially expressed genes overlapping with genes underlying aging and aging-related retinal diseases, along with aberrant cell-cell interactions with its two adjacent layers. Altogether, our study provides the roadmap for understanding retinal aging in a NHP model at single-cell resolution, enabling the identification of new diagnostic biomarkers and potential therapeutic targets for age-related human retinal disorders.
2020-10-20 | GSE113917 | GEO
Project description:Differentiation of distinct neurons in the developing retina is controlled by combinatorial action of a small subset of transcription factors and signalling molecules. Protein inhibitor of activated STAT3 (PIAS3) has been implicated in guiding the specification of both rod and cone photoreceptors through posttranslational modification of key retinal transcription factors. To investigate its role during retinal development, we deleted exon 2-5 of the mouse Pias3 gene, which resulted in complete loss of the PIAS3 protein. Pias3-/- mice did not exhibit any overt phenotype, and retinal lamination appeared normal by histology even at 18 months. We detected reduced photopic b-wave amplitude by electroretinography (ERG) analysis following green light stimulation of Pias3-/- retina at postnatal day (P) 21, suggesting a compromised visual response of medium wavelength (M) cones. No change was evident in response of short wavelength (S) cones or rod photoreceptors until 7 months. Immunohistochemistry demonstrated altered distribution of cone photoreceptors as revealed by increased S-opsin expression in the M-cone dominant dorsal retina. Transcriptome profiling of P21 and 18-month old Pias3-/- retina revealed aberrant expression of genes associated with photoreceptor function. Our studies suggest redundancy in SUMOylation-associated transcriptional control mechanisms and identify a specific though limited role of PIAS3 in modulating spatial patterning and optimal function of cone photoreceptor subtypes in the mouse retina.
2017-05-29 | GSE94011 | GEO
Project description:Recently we reported that the rat inner retina undergoes significant functional changes during maturation. Aiming to gain knowledge on additional aspects of retinal development and maturation, we used the microarray system to monitor gene expression patterns in the rat retina at ages 5, 11, and 20 weeks. The analysis revealed the expression of many well-documented retinal genes as well as a high number of nonâ??annotated genes. Quantitative realtime PCR analysis verified the microarray results in the majority of studied genes. A statistical analysis of the 4 microarray slides revealed 603 differentially expressed genes which were grouped into 6 expression clusters. A bioinformatic analysis of these clusters revealed sets of genes encoding proteins with functions that are likely to be relevant to inner retinal function (e.g. potassium, sodium, calcium, and chloride channels, synaptic vesicle transport, and axonogenesis). In addition, we performed a histological analysis of the maturing retina and studied different aspects of retinal structure. The analysis revealed a significant reduction of outer nuclear layer thickness between 11 and 19 weeks of age and a significant reduction of retinal ganglion cell number at 11 and 19 weeks comparing to 5 weeks. We identified in this study genes with differential expression pattern during retinal maturation. Some of the genes encode proteins that may be involved in the functional maturation of inner retinal cells. These data, taken together with our histological and electrophysiological data, contribute to our understanding of the developmental processes occurring in the retina of this widely-used animal model. Experiment Overall Design: Rat retinal samples at ages 5, 11, and 20 weeks were studied using 4 microarray slides in a dye-swap design: 5-11, 11-5, 5-20, and 20-5.
2008-06-16 | E-GEOD-8423 | biostudies-arrayexpress
Project description:Eye development and photoreceptor maintenance requires the retinal pigment epithelium (RPE), a thin layer of cells that underlies the neural retina. Despite its importance, RPE development has not been studied by a genomic approach. A microarray expression profiling methodology was established in this study for studying RPE development. The intact retina with RPE attached was dissected from developing embryos, and differentially expressed genes in RPE were inferred by comparing the dissected tissues with retinas without RPE using microarray and statistical analyses. We found 8810 probesets to be significantly expressed in RPE at 52 hours post-fertilization (hpf), of which 1443 might have biologically meaningful expression levels. Further, 78 and 988 probesets were found to be significantly over- or under-expressed in RPE respectively compared to retina. Also, 79.2% (38/48) of the known over-expressed probesets have been independently validated as RPE-related transcripts. The results strongly suggest that this methodology can obtain in vivo RPE specific gene expression from the zebrafish embryos and identify novel RPE markers. Experiment Overall Design: The gene expression levels of three independent replicates of retina with RPE attached consisting of ten samples each at 52hpf (WRR52) were compared with three independent pure retinal samples consisting of ten retinas each at 52hpf (WR52). The yield-adjusted WR52 expression values were assumed to be equivalent to the retinal contribution in WRR52 samples and deducted from WRR52 expression values to obtain estimations of RPE gene expression at 52hpf (RPE52). Differential gene expressions between RPE and retina were inferred by comparing the RPE52 estimates and WR52 expression values.
2008-06-13 | E-GEOD-5048 | biostudies-arrayexpress
Project description:Recently we reported that the rat inner retina undergoes significant functional changes during maturation. Aiming to gain knowledge on additional aspects of retinal development and maturation, we used the microarray system to monitor gene expression patterns in the rat retina at ages 5, 11, and 20 weeks. The analysis revealed the expression of many well-documented retinal genes as well as a high number of non–annotated genes. Quantitative realtime PCR analysis verified the microarray results in the majority of studied genes. A statistical analysis of the 4 microarray slides revealed 603 differentially expressed genes which were grouped into 6 expression clusters. A bioinformatic analysis of these clusters revealed sets of genes encoding proteins with functions that are likely to be relevant to inner retinal function (e.g. potassium, sodium, calcium, and chloride channels, synaptic vesicle transport, and axonogenesis). In addition, we performed a histological analysis of the maturing retina and studied different aspects of retinal structure. The analysis revealed a significant reduction of outer nuclear layer thickness between 11 and 19 weeks of age and a significant reduction of retinal ganglion cell number at 11 and 19 weeks comparing to 5 weeks. We identified in this study genes with differential expression pattern during retinal maturation. Some of the genes encode proteins that may be involved in the functional maturation of inner retinal cells. These data, taken together with our histological and electrophysiological data, contribute to our understanding of the developmental processes occurring in the retina of this widely-used animal model. Keywords: Dye-swap, Ganglion cells, Gene, Gene expression, Histology, Inner retina, Maturation, Microarray, Rat, Retina, Vision.
2007-10-01 | GSE8423 | GEO
Project description:Cone photoreceptors are the primary initiator of visual transduction in the human retina. Dysfunction or death of rod photoreceptors precedes cone loss in many retinal and macular degenerative diseases, suggesting a rod-dependent trophic support for cone survival. Rod differentiation and homeostasis are dependent on the basic motif leucine zipper transcription factor NRL. The loss of Nrl in mice (Nrl-/-) results in a retina with predominantly S-opsin containing cones that exhibit molecular and functional characteristics of WT cones. Here we report that Nrl-/- retina undergoes a rapid but transient period of degeneration in early adulthood, with cone apoptosis, retinal detachment, alterations in retinal vessel structure, and activation and translocation of retinal microglia. However, cone degeneration stabilizes by four months of age, resulting in a thinned but intact outer nuclear layer with residual cones expressing S- and M-opsins and a preserved photopic ERG. At this stage, microglia translocate back to the inner retina and reacquire a quiescent morphology. Gene profiling analysis during the period of transient degeneration reveals misregulation of stress response and inflammation genes, implying their involvement in cone death. The Nrl-/- retina illustrates the long-term viability of cones in the absence of rods and may serve as a model for elucidating mechanisms of cone homeostasis and degeneration that would be relevant to understanding diseases of the cone-dominant human macula. Targets were generated from a pair of retinas (one Nrl-/- mouse) per biological replicate. Four biological replicates were generated for each of the five aging timepoints (1, 2, 4, 6, and 10 months post natal).
2011-11-15 | E-GEOD-33674 | biostudies-arrayexpress