Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA234770 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1111980.fastq.gz | Fastqsanger.gz | |||
| SRR1111981.fastq.gz | Fastqsanger.gz | |||
| SRR1111982.fastq.gz | Fastqsanger.gz | |||
| SRR1111983.fastq.gz | Fastqsanger.gz | |||
| SRR1111984.fastq.gz | Fastqsanger.gz |
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Project description:Otx2 has been shown to be non cell autonomously required for photoreceptor cell survival in the adult mouse RPE. This study aims to identify Otx2 DNA binding profile in both RPE and neural retina to i) identify direct targets of Otx2 in the RPE ii) compare Otx2 binding profile in neural retina and RPE to unveil hidden functions in the neural retina. WT and GFP antibodies were used to perform two independent ChIP-seq experiments using Illumina GAIIx.
2014-01-15 | E-GEOD-54084 | biostudies-arrayexpress
Project description:Otx2 has been shown to be non cell autonomously required for photoreceptor cell survival in the adult mouse RPE. This study aims to identify Otx2 DNA binding profile in both RPE and neural retina to i) identify direct targets of Otx2 in the RPE ii) compare Otx2 binding profile in neural retina and RPE to unveil hidden functions in the neural retina.
2014-01-15 | GSE54084 | GEO
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
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Project description:The retinal pigment epithelium (RPE) exhibits a diverse range of plasticity across vertebrates and is a potential source of cells for the regeneration of retinal neurons. Embryonic amniotes possess a transitory ability to regenerate neural retina through the reprogramming of RPE cells in an FGF-dependent manner. Chicken RPE can regenerate neural retina at embryonic day 4 (E4) of development, but RPE neural competence is lost by embryonic day 5 (E5). To identify mechanisms that underlie loss of regenerative competence, we performed RNA and ATAC sequencing using E4 and E5 chicken RPE, as well as at both stages following retinectomy and FGF2 treatment. We find that genes associated with neural retina fate remain FGF2-inducible in the non-regenerative E5 RPE. Coinciding with fate restriction, RPE cells stably exit the cell cycle and dampen the expression of cell cycle progression genes normally expressed during regeneration, including E2F1. E5 RPE exhibits progressive activation of gene pathways associated with mature function independently of retinectomy or FGF2 treatment, including retinal metabolism, pigmentation synthesis, and ion transport. Moreover, the E5 RPE fails to efficiently repress OTX2 expression in response to FGF2. Predicted OTX2 binding motifs undergo robust accessibility increases in E5 RPE, many of which coincide with putative regulatory elements for genes known to facilitate RPE differentiation and maturation. Together, these results uncover widespread alterations in gene regulation that culminate in the loss of RPE neural competence and implicate OTX2 as a key determinant in solidifying the RPE fate. These results yield valuable insight to the basis of RPE lineage restriction during early development and will be of importance in understanding the varying capacities for RPE-derived retinal regeneration observed among vertebrates.
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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.
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