Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative Gene Expression Profiling between Xenopus Optic Nerve and Spinal Cord Injury to Identify Genes Involved in Successful Regeneration of Vertebrate CNS Axons

ABSTRACT: Comparative Gene Expression Profiling between Xenopus Optic Nerve and Spinal Cord Injury to Identify Genes Involved in Successful Regeneration of Vertebrate CNS Axons

PROVIDER: PRJNA573657 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10163200.fastq.gz	Fastqsanger.gz
	SRR10163201.fastq.gz	Fastqsanger.gz
	SRR10163202.fastq.gz	Fastqsanger.gz
	SRR10163203.fastq.gz	Fastqsanger.gz
	SRR10163204.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 51

Similar Datasets

Comparative Gene Expression Profiling between Xenopus Optic Nerve and Spinal Cord Injury to Identify Genes Involved in Successful Regeneration of Vertebrate CNS Axons

Project description:Xenopus is uniquely suited for addressing the question of whether a core gene expression program for successful CNS axon regeneration exists, because parts of its CNS (e.g., eye), regenerate axons throughout life, whereas others (e.g., hindbrain) do so only as tadpoles. We performed RNA-Seq after optic nerve and spinal cord injury to identify trauma-induced genes shared between two regenerative CNS regions, but not shared with a non-regenerative one. We provide these data as a resource for new avenues of investigation into the molecular basis of tissue regeneration.

2020-08-07 | GSE137844 | GEO

Gene expression timecourse in zebrafish whole eye in response to optic nerve crush

Project description:It is well-established that neurons in the adult mammalian central nervous system are terminally differentiated and, if injured, will be unable to regenerate their connections. In contrast to mammals, zebrafish and other teleosts display a robust neuroregenerative response. Following optic nerve crush (ONX), retinal ganglion cells (RGC) regrow their axons to synapse with topographically correct targets in the optic tectum, such that vision is restored in ~21 days. What accounts for these differences between teleostean and mammalian responses to neural injury is not fully understood. A time course analysis of global gene expression patterns in the zebrafish eye after optic nerve crush can help to elucidate cellular and molecular mechanisms that contribute to a successful neuroregeneration. We used microarrays to detail the global gene expression patterns underlying a successful regeneration or the optic nerve following injury. Experiment Overall Design: Microarray analysis was performed on total RNA extracted from whole eye following optic nerve crush (ONX) or sham surgery at defined intervals (4, 12, & 21 days).

2010-02-21 | E-GEOD-19298 | biostudies-arrayexpress

Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate (Xenopus laevis) Central Nervous System Characterized by Whole Genome Bisulfite Sequencing (WGBS)

Project description:Xenopus is uniquely suited for identifying core features of successful CNS axon regeneration, because parts of its CNS (e.g., eye), regenerate axons throughout life, whereas others (e.g., hindbrain) do so only as tadpoles. We performed bisulfite whole genome bisulfite methylation sequencing (WGBS) on juvenile frog eye after optic nerve injury, and on hindbrain samples from tadpole and juvenile frog after spinal cord injury during the peak phase of axon regeneration, to compare tissue-related and injury-induced differences in DNA methylation among them.

2022-01-05 | GSE183355 | GEO

Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate (Xenopus laevis) Central Nervous System assayed by 5hmC MeDIP and by ChIP-seq for Histone Markers

Project description:Xenopus is uniquely suited for identifying core features of successful CNS axon regeneration, because parts of its CNS (e.g., eye), regenerate axons throughout life, whereas others (e.g., hindbrain) do so only as tadpoles. To aid in the interpretation of bisulfite whole genome methylation sequencing (WGBS) on juvenile frog eye after optic nerve injury, and on hindbrain samples from tadpole and juvenile frog after spinal cord injury during the peak phase of axon regeneration, we performed ChIP-seq for histone modifications associated with active gene expression (H3K4me3 & H3K27ac) and repressed gene expression (H3K27me3 & H3K9me3) on these same tissues, as well as DNA-immunoprecipitation sequencing (DIP seq) for 5-hydroxymethyl cytosine (5hmC) on eye samples during optic nerve regeneration.

2022-01-05 | GSE183350 | GEO

Gene expression timecourse in zebrafish whole eye in response to optic nerve crush

2010-02-01 | GSE19298 | GEO

The regulatory landscape of optic fissure closure in the vertebrate eye

Project description:The regulatory landscape of optic fissure closure in the vertebrate eye

| PRJNA1419705 | ENA

The regulatory landscape of optic fissure closure in the vertebrate eye

Project description:The process of optic fissure closure (OFC) is a critical tissue fusion event in eye development. Failure of OFC results in coloboma, a persistent gap in the eye that can significantly affect vision. Most coloboma cases do not have a genetic diagnosis, reflecting poor understanding of the genes required for OFC and how these are regulated and their impact on cell behaviours. The chicken is a good model for interrogating developmental gene expression and regulatory networks, and the embryonic chicken eye develops similarly to humans. Results: Here we performed integrated profiling of accessible chromatin and gene expression during OFC in the chicken embryonic eye. This revealed domains of accessible chromatin during active fusion and in the broader ventral retina that were distinct from the dorsal retina, implicating these as active during fusion of the optic fissure and important for gene regulation in this distinct region of the developing vertebrate eye. Open chromatin elements could be linked by proximity and TAD boundaries to adjacent genes that have distinct spatial and temporal expression profiles during optic fissure closure. Using a combination of de novo motif enrichment and transcription factor (TF) foot-printing occupancy analyses in silico, we found evidence for TEAD/ZIC/SOX activity during OFC, and retinoic-acid related TF activity in the developing dorsal eye. We were able to map a sub-set of chicken OFC specific peaks to cis-regulatory elements in the human genome and identified loci proximity to known human coloboma genes or in coloboma candidate genes identified by our analyses in chicken. Conclusions: This study leverages eye development in the chicken embryo to deliver the first evidence for dynamic cis-regulatory activity of gene expression during OFC and identifies candidate loci for future mutational and activity analyses, providing the first genetic clues to identify non-coding loci as candidates for coloboma.

2026-02-10 | GSE318644 | GEO

Subcellular expression profiling of the growth cones of retinal ganglion cells (RGC)

Project description:Cue-directed axon guidance depends partly on local translation in growth cones. Many mRNA transcripts are known to reside in developing axons yet little is known about their subcellular distribution or, specifically, which transcripts are in growth cones. Laser capture microdissection (LCM) was used to isolate the growth cones of retinal ganglion cell (RGC) axons of two vertebrate species, mouse and Xenopus, coupled with unbiased genome-wide microarray profiling. Localized mRNA from the isolated growth cones of Xenopus laevis and Mus musculus retinal ganglion cells were subjected to microarray analysis

2010-11-23 | E-GEOD-25166 | biostudies-arrayexpress

Novel in vivo models of autosomal optic atrophy show conserved pathological changes in mitochondrial structure and function ZEBRAFISH DATASET

Project description:Autosomal optic atrophy (AOA) is a form of hereditary optic neuropathy characterized by the irreversible and progressive degermation of the retinal ganglion cells. Most cases of AOA are associated with a single dominant mutation in OPA1, which encodes a protein required for fusion of the inner mitochondrial membrane. It is unclear how loss of OPA1 leads to neuronal death, and despite ubiquitous expression appears to disproportionately affect the RGCs. This study introduces two novel in vivo models of OPA1-mediated AOA, including the first developmentally viable vertebrate Opa1 knockout (KO). These models allow for the study of Opa1 loss in neurons, specifically RGCs. Though survival is significantly reduced in Opa1 deficient zebrafish and Drosophila, both models permit the study of viable larvae. Moreover, zebrafish Opa1 KO larvae show impaired visual function but unchanged locomotor function, indicating that retinal neurons are particularly sensitive to Opa1 loss. Proteomic profiling of both models reveals marked disruption in protein expression associated with mitochondrial function, consistent with an observed decrease in mitochondrial respiratory function. Similarly, mitochondrial fragmentation and disordered cristae organization were observed in neuronal axons in both models highlighting Opa1’s highly conserved role in regulating mitochondrial morphology and function in neuronal axons. Importantly, in Opa1 deficient zebrafish, mitochondrial disruption and visual impairment precede degeneration of RGCs. These novel models mimic key features of AOA and provide valuable tools for therapeutic screening. Our findings suggest that therapies enhancing mitochondrial function may offer a potential treatment strategy for AOA.

2025-05-07 | PXD059584 | Pride

Novel in vivo models of autosomal optic atrophy show conserved pathological changes in mitochondrial structure and function Dataset 2 Drosophila

2025-05-07 | PXD059645 | Pride