Single cell transcriptome of the Mouse Neural Retina in Response to Sodium Iodate
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE312010 | GEO | 2026/06/03
REPOSITORIES: GEO
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Project description:Single cell transcriptome of the Mouse Neural Retina in Response to Sodium Iodate
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Project description:Single-cell RNA-seq of mouse WT retinas and two Nr2e3 mutant retinas, ∆27 and ∆E8 (containing a 27 nucleotide in-frame deletion or a complete exon 8 deletion, respectively). The ∆27 retinas were used as a model for enhanced S-cone syndrome phenotype in humans, while the ∆E8 retinas show a progressive retinal degeneration similar to human retinitis pigmentosa patients. This data was used to explore the role of Nr2e3 in cone and rod photoreceptor differentiation.
2024-05-18 | E-MTAB-12183 | biostudies-arrayexpress
Project description:The retina constitutes a segment of the central nervous system (CNS). Both retinal and CNS neurons lack the inherent capacity to spontaneously regenerate axons following injury. Retinal ganglion cells (RGCs) serve as the neurons connecting the eyes to the brain. Diseases such as glaucoma initiate damage to RGC axons at the optic nerve, ultimately leading to cell death and irreversible vision loss. While enhancing the survival of RGCs is a crucial initial step, especially for those with pre-existing axonal injuries in the optic nerve due to prolonged insults, effective therapies should also promote axon regeneration. Neuro-regeneration and reintegration into the brain remain to be enormous challenges in neurology and ophthalmology. Despite decades of effort and resources invested in the research of neuro-regeneration, scientists are still rather far from comprehensively identifying all intrinsic axonal growth regulators and their collaborative roles. Data-independent acquisition mass spectrometry (DIA-MS) is a next-generation proteomic methodology that generates permanent digital proteome maps offering highly reproducible retrospective analysis of cellular and tissue specimens. Compared to conventional mass-spectrometry, DIA-MS provides better reproducibility and sensitivity. In this study, we employed DIA-MS to conduct a comprehensive protein expression mapping in retinas from mouse models of degeneration and regeneration, and to gain insights into the complex molecular mechanisms associated with degeneration and regeneration processes in the retina.
2024-07-29 | PXD049992 | Pride
Project description:The goal of this study focues on comparing the molecular signatures of immune cells, primarily microglia, in ectopically distinct mouse models of outer retinal degeneration. These models include the sodium iodate induced RPE injury model, rhodopsin-P23H knockin mice, an advanced aging model of 2-year-old mice and young (2-month old) wild-type control mice.
2024-01-07 | GSE195891 | GEO
Project description:Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers, and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas.
| EGAS00001004561 | EGA
Project description:Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish, an important animal model for vision science. Methods: Zebrafish rods, and non-rod retinal cells of the XOPS:eGFP transgenic line, were separated by cell dissociation and fluorescence-activated cell sorting (FACS), followed by RNA-seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas, and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01, 597 transcripts were upregulated in rods vs. non-rod retinal cells, and 1032 were downregulated. 13,324 total transcripts were detected in rods, including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas, and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA-seq dataset describing the rod transcriptome of the zebrafish, which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics.
2018-02-08 | GSE100062 | GEO
Project description:The early retinal progenitor-expressed gene Sox11 regulates the timing of the differentiation of retinal cells. Sry-related HMG box (Sox) proteins play diverse and critical roles in a variety of morphogenetic processes during embryonic development. Sox11 and Sox4 are members of the SoxC subtype, and we found that Sox11 was strongly expressed in early retinal progenitor cells, and that when expression of Sox11 subsided around birth, Sox4 expression began. To analyze the role of Sox11 and Sox4 in retinal development, we perturbed their expression pattern by expressing them ectopically in retinal explant culture. Overexpression of Sox11 or Sox4 in retinal progenitors resulted in similar phenotypes, that is, increased cone cells and decreased Muller glia. Sox11-knockout retinas showed delayed onset and progress of differentiation of early-born retinal cells during the embryonic period. After birth, retinal differentiation took place relatively normally, probably because of the redundant activity of Sox4, which starts to differentiate around birth. Neither overexpression nor loss-of-function analysis gave any evidence that Sox11 and Sox4 directly regulate transcription of genes critical to early-born retinal cells. However, histone H3 acetylation status of the early neurogenic genes was lowered in knockout retinas, suggesting that Sox11 regulates the timing of differentiation in early-born retinas by creating an epigenetic state that helps to establish the competency to differentiate. We also found that the unique expression patterns of Sox11 and Sox4 may be achieved by the Notch signaling pathway and by epigenetic regulation. Taking our findings together, we propose that the precise regulation of Sox11 and Sox4 expression during retinogenesis by multiple mechanisms leads to the fine adjustment of retinal differentiation. To delineate the molecular mechanisms underlying the retinal action of Sox11, we performed microarray analysis of E18 retinas from wild-type and Sox11 knockout mice. Total RNA was obtained from each one retina of Sox11 knockout and wild-type littermate embryos at E18.
2012-12-28 | E-GEOD-43089 | biostudies-arrayexpress
Project description:Following acute retinal damage, zebrafish possess the ability to regenerate all neuronal subtypes. This regeneration requires Müller glia (MG) to reprogram and divide asymmetrically to produce a multipotent Müller glia-derived neuronal progenitor cell (MGPC). This raises three key questions. First, does loss of different retinal cell subtypes induce unique MG regeneration responses? Second, do MG reprogram to a developmental retinal progenitor cell state? And finally, to what extent does regeneration recapitulate retinal development? We examined these questions by performing single-nuclear and single-cell RNA-Seq and ATAC-Seq in both developing and regenerating retinas. While MG reprogram to a state similar to late-stage retinal progenitors in developing retinas, there are transcriptional differences between reprogrammed MG/MGPCs and late progenitors, as well as reprogrammed MG in outer and inner retinal damage models. Validation of candidate genes confirmed that loss of different subtypes induces differences in transcription factor gene expression and regeneration outcomes. This work identifies major differences between gene regulatory networks activated following the selective loss of different subtypes of retina neurons, as well as between retinal regeneration and development.
2023-08-31 | GSE239410 | GEO
Project description:Mice lacking the beta 2 subunit (Chrnb2) of the neuronal nicotinic acetylcholine receptor display altered retinal waves and disorganized projections of the retinal ganglion cells to the lateral geniculate nucleus (LGN). mRNA populations from retinas and LGN from Chrnb2-/-and wild type (C57BL/6J) mice were compared at 4 days postnatal, when RGC segregation to the LGN begins in WT mice. Retinal mRNAs were also compared at adulthood. Using microarray hybridization, we identified transcripts which are differentially expressed between Chrnb2-/- and wild type animals in these two tissues at these two ages. mRNA was isolated from retina and LGN of three male littermates each of WT and Chrnb2-/- mice at P4. mRNA from retinas of two adult male littermates of each type was also examined.
2011-01-01 | E-GEOD-22824 | biostudies-arrayexpress