Transcriptomic changes of optic nerves under crush during hibernation stage
Ontology highlight
ABSTRACT:
ORGANISM(S): Ictidomys tridecemlineatus
PROVIDER: GSE148651 | GEO | 2023/04/14
REPOSITORIES: GEO
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Project description:EAE mice were injected with LPC 18:1 and Isobaric C13-His at the optic nerve when they exhibited a clinical score of 2. Visual function was assessed via pattern electroretinogram and optic nerves were harvested 12 days post optic nerve injection. Optic nerves were processed for mass spectrometry to identify the integration of C13-His in newly synthesized proteins.
2022-02-17 | PXD025176 | Pride
Project description:Optic nerves are an accessible part of the CNS, providing a source of glia without the presence of neuronal cell bodies. Therefore, an analysis was carried out of gene expression in optic nerves at P4, before myelination begins and at P10, when myelination is very actively proceeding. The goal was to obtain a profile of the changing gene expression that accompanies this transition from unmyelinated CNS nerve to myelinated nerve. Two microarray experiments were combined here. In the first, RNA was prepared from the optic nerves of 75 P4 C57BL/6J mice and 70 P10 C57BL/6J mice. In the second experiment, RNA was prepared from the optic nerves of 55 P4 C57BL/6J mice and two groups of 50 P10 C57Bl/6J mice. In total, there are 2 P4 RNA samples and 3 P10 RNA samples being hybridized to Affymetrix GeneChip 430A for Mouse Expression.
2011-05-16 | E-GEOD-24513 | biostudies-arrayexpress
Project description:Optic nerves are an accessible part of the CNS, providing a source of glia without the presence of neuronal cell bodies. Therefore, an analysis was carried out of gene expression in optic nerves at P4, before myelination begins and at P10, when myelination is very actively proceeding. The goal was to obtain a profile of the changing gene expression that accompanies this transition from unmyelinated CNS nerve to myelinated nerve.
2011-05-16 | GSE24513 | GEO
Project description:To investigate the potential function of lncRNAs in Schwann cell (SCs) response to sciatic nerve damage and repair, we extracted the total RNA of crushed sciatic nerves and intact contralateral nerves for RNA-sequencing (RNA-seq). A total of 98 differentially expressed lncRNAs (including 46 up-regulated and 52 down-regulated lncRNAs) and 77 differentially expressed mRNAs (including 55 up-regulated and 22 down-regulated mRNAs) were identified between crushed sciatic nerves and normal control (log 2 FC > 1 and p < 0.001).
2022-07-06 | GSE149657 | GEO
Project description:Differential gene expression in a wide range of tissues including brown adipose tissue (BAT), liver, heart, hypothalamus, and skeletal muscle in hibernating arctic ground squirrels during multiple stages in torpor-arousal cycles compared to non-hibernating (post-reproductive) animals with illumina beadarray technology. Keywords: Multiple stage comparison
2006-08-03 | GSE5414 | GEO
Project description:We used optic nerve injury as a model to study early signaling events in the neuronal soma following axonal injury. Optic nerve injury results in the selective death of retinal ganglion cells (RGCs). The time course of cell death takes place over a period of days with the earliest detection of RGC death at about 48 hr post injury. We hypothesized that in the period immediately following axonal injury, there are changes in the soma that signal surrounding glia and neurons and that start programmed cell death. In the current study, we investigated early changes in cellular signaling and gene expression that occur within the first 6 hrs post optic nerve injury. We detected differences in phosphoproteins and gene expression within this time period that we used to interpret temporal events. Our studies revealed that the entire retina has been signaled by the RGC soma within 30 min after optic nerve injury and that pathways that modulate cell death are likely to be active in RGCs within 6 hrs following axonal injury Experiment Overall Design: In the treated animals, axons of the optic nerve were crushed with fine forceps for 10 sec, 1 mm posterior to the globe, under direct visualization, within an intact meningeal sheath. Controls were contralateral eyes from the same animals in each group that had not been injured. After 6 hr eyes were enucleated and processed for tissue sectionin
2008-10-25 | E-GEOD-11862 | biostudies-arrayexpress
Project description:Reactive gliosis is a complex process that involves profound changes in gene expression. We used microarray to indentify differentially expressed genes and to investigate the molecular mechanisms of reactive gliosis in optic nerve head in response to optic nerve crush injury. C57Bl/6 female mice were 6-8 weeks old at the time of optic nerve crush surgery. The optic nerve in the left eye was crush 1 mm behind the globe for 10 seconds and the right eye served as contralateral control. The animals were allowed to recover for 1 day, 3 day, 1 week, 3 weeks and 3 months before the optic nerve heads were collected. The naive control mice did not receive any surgery in either eye. Due to the small tissue size of the mouse optic nerve head, two optic nerve heads were pooled together for each microarray chip. The left eyes and the right eyes of two mice were combined respectively to form one pair of experiment and control samples. There were five biological replicates (10 mice) for each condition.
2013-07-15 | E-GEOD-40857 | biostudies-arrayexpress
Project description:Differential gene expression in a wide range of tissues including brown adipose tissue (BAT), liver, heart, hypothalamus, and skeletal muscle in hibernating arctic ground squirrels during multiple stages in torpor-arousal cycles compared to non-hibernating (post-reproductive) animals with illumina beadarray technology. Arctic Ground Squirrels were sampled at four stages of hibernation: early arousal denoted as EA (1-2 hrs after Tb cross 30¡C, n=4), late arousal denoted as LA (7-8 hrs after Tb cross 30¡C, n=4), early torpor denoted as ET (10-20% of torpid episode, n=4) and late torpor denoted as LT (80-90% of torpid episode, n=5), where Tb is the body temperature and the length of torpid episode is estimated from the previous torpor bout. Post-reproductive animals denoted as PR (n=7) were used as non-hibernating control. Five tissue types: brown adipose tissue (BAT), liver, heart, hypothalamus, and skeletal muscle were hybridized on two customized 700-gene beadarray platforms: 1A and 2A on 96-sample Illumina ArrayMatrix. The data of a pilot study involving brown adipose tissue (BAT), liver, and skeletal muscle on 16-sample Illumina BeadChip denoted as 16chip are also included in this series.
2010-07-01 | E-GEOD-5414 | biostudies-arrayexpress
Project description:Zebrafish (Danio Rerio) have the capacity for successful adult optic nerve regeneration. In contrast, mammals lack this intrinsic ability and undergo irreversible neurodegeneration seen in glaucoma and other optic neuropathies. Optic nerve regeneration is often studied using optic nerve crush, a mechanical neurodegenerative model. Untargeted metabolomic studies within successful regenerative models are deficient. Evaluation of tissue metabolomic changes in active zebrafish optic nerve regeneration can elucidate prioritized metabolite pathways that can be targeted in mammalian systems for therapeutic development. Female and male (6 month to 1 year old) right Zebrafish (Tg(gap43:GFP)) optic nerves were crushed and collected three days after. Contralateral, uninjured optic nerves were collected as controls. The tissue was dissected from euthanized fish and frozen on dry ice. Samples were pooled for each category (female crush, female control, male crush, male control) and pooled at n = 31 to obtain sufficient metabolite concentrations for analysis. Optic nerve regeneration was verified by microscope visualization of GFP fluorescence. Metabolites were extracted using a Precellys Homogenizer and a serial extraction method: (1) 1:1 Methanol/Water and (2) 8:1:1 Acetonitrile/Methanol/Acetone. Metabolites were analyzed by untargeted liquid chromatography-mass spectrometry (LC MS-MS) profiling using a Q-Exactive Orbitrap instrument coupled with Vanquish Horizon Binary UHPLC LC-MS system. Metabolites were identified and quantified using Compound Discoverer 3.3 and isotopic internal metabolites standards.
2022-12-19 | ST002444 | MetabolomicsWorkbench
Project description:Reactive gliosis is a complex process that involves profound changes in gene expression. We used microarray to indentify differentially expressed genes and to investigate the molecular mechanisms of reactive gliosis in optic nerve head in response to optic nerve crush injury.
2013-07-15 | GSE40857 | GEO