Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA404067 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6025580_1.fastq.gz | Fastqsanger.gz | |||
| SRR6025580_2.fastq.gz | Fastqsanger.gz | |||
| SRR6025590_1.fastq.gz | Fastqsanger.gz | |||
| SRR6025590_2.fastq.gz | Fastqsanger.gz | |||
| SRR6025600_1.fastq.gz | Fastqsanger.gz |
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Project description:We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified, suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting.
2018-02-19 | GSE103692 | GEO
Project description:Dr. Schwarting's research is focused on the analysis of developmentally regulated cell surface molecules and their role in axon guidance and neuronal migration, using the olfactory system as a model. The interaction of cell surface glycans with endogenous lectins in the extracellular matrix provides one mechanism by which axons can utilize specific pathways as they grow towards their targets.
2011-03-02 | GSE27590 | GEO
Project description:Dr. Schwarting's research is focused on the analysis of developmentally regulated cell surface molecules and their role in axon guidance and neuronal migration, using the olfactory system as a model. The interaction of cell surface glycans with endogenous lectins in the extracellular matrix provides one mechanism by which axons can utilize specific pathways as they grow towards their targets. We have a mutant mouse (b3GNT2 KO) that up-regulates the expression of lactosamine containing glycans in a subset of olfactory neurons. Gene expression profiling was performed using control and mutant mice that up-regulate the expression of lactosamine containing glycans in a subset of olfactory neurons. Glycosyltransferase expression that differed between control and mutant mice were identified.
2011-03-02 | E-GEOD-27590 | biostudies-arrayexpress
Project description:Using the highly sensitive miRNA array, we screened 40 microRNAs abundant in the olfactory bulb and we explored the functions of these miRNAs in the olfactory bulb by Gene Ontology and Kyoto Encyclopedia of Genes annotation. The enrichment results indicated that these miRNAs mainly participated in the axon guidance process. Furthermore, the quantitative real-time polymerase chain reaction, immunohistochemistry, and dual luciferase reporter assay results showed that miR-30c is a specific regulator of semaphorin-3A, which will give new insights in disclosing the mechanism of functional maintenance and sexual-specific differentiation of the olfactory bulb. In this study, three samples from steady-state mice were used to acquire the miRNA expression profiling and the function of the abudant miRNAs in the olfactory bulb were analyzed by bioinformatic methods.Finally, miR-30c was experimentally validated to be a regulator of semaphorin-3A, an important axon guidance cue in the nervous system.
2014-08-27 | E-GEOD-55463 | biostudies-arrayexpress
Project description:Dr. Schwarting's research is focused on the analysis of developmentally regulated cell surface molecules and their role in axon guidance and neuronal migration, using the olfactory system as a model. The interaction of cell surface glycans with endogenous lectins in the extracellular matrix provides one mechanism by which axons can utilize specific pathways as they grow towards their targets. Beta3GnT1 mutant mice lose lactosamine expression and have an olfactory axon guidance phenotype (Henion et al, 2005). Olfactory neurons are capable of regeneration and we know that when these neurons regenerate in beta3GnT1 mutant they synthesize lactosamine by a secondary mechanism. By comparing RNA from the olfactory epithelium from wild type and mutant mice, we would expect to see the upregulation of glycosyltransferases that could produce lactosamine in the absence of beta3GnT1. In a preliminary experiment carried out by the CFG staff, we saw that radical fringe, a beta 3GnT, was upregulated in the olfactory epithelium, although it is probably not responsible for the new lactosamine expression. beta3GnT1 Knock out. Strain info: The b3GnT1 mice were generated on a mixed 129Ola-C57BL/6 background and backcrossed to C57BL/6 for four generations. They were then crossed to I7-Internal ribosomal entry site (IRES)-tau greeen fluorescent protein (GFP) mice generated by Dr. Peter Mombaerts.
2011-04-29 | GSE28926 | GEO
Project description:Increasing frequency and geographical distribution of harmful algal blooms (HABs) presents a growing threat to the public health. Saxitoxin (STX) is a potent neurotoxin naturally produced by dinoflagellates and cyanobacteria during HAB events. Consumption of seafood contaminated with STX is responsible for paralytic shellfish poisoning (PSP). STX inhibits voltage-gated sodium channels, affecting the propagation of action potentials. Humans are among the species most sensitive to PSP, and neurological symptoms of exposure range from tingling of the extremities to severe paralysis. To protect humans against PSP, there is a ban on harvesting of seafood when the STX levels reach 80 μg/100 g of shellfish tissue. However, shellfish with toxin levels below this regulatory limit often are harvested for consumption. Our objective is to understand the potential health effects of exposure to low levels of STX during sensitive windows of development. Zebrafish embryos were exposed to STX (24 or 48 pg) or vehicle (0.3 mM HCl) at 6 hours post fertilization (hpf) via microinjection. There was no overt toxicity, but starting at 36 hpf there was a temporary lack of pigmentation in STX-injected embryos, which resolved by 72 hpf. Using HPLC, we found that STX was retained in embryos up to 72 hpf in a dose dependent manner. We examined transcriptional profiles in embryos at 24, 36 and 48 hpf. There were no differentially expressed genes (DEGs) in STX-injected embryos at 24 hpf, but at 36 and 48 hpf there were_x000B_3547 and 3356 DEGs, respectively, in response to STX. KEGG pathway analysis revealed significant enrichment of genes related to focal adhesion, adherens junction and regulation of actin cytoskeleton, suggesting that cell-cell and cell-extracellular matrix interactions were affected by STX. The genes affected are critical for axonal growth and the development of functional neural networks. We also observed differential expression of axon guidance factors (netrins, semaphorins, and ephrins), which can control axon outgrowth. We are currently using immunohistochemistry to confirm these findings. Overall, these results suggest that STX exposure might affect axon outgrowth by modulating cell adhesion molecules. [NIH P01ES021923 and NSF OCE-1314642].
2022-07-31 | GSE204989 | GEO
Project description:During the development of the Drosophila central nervous system the process of midline crossing is orchestrated by a number of guidance receptors and ligands. Many key axon guidance molecules have been identified in both invertebrates and vertebrates, but the transcriptional regulation of growth cone guidance remains largely unknown. One open question is whether transcriptional regulation plays a role in midline crossing, or if local translation can account for the necessary fine tuning of protein levels. To investigate this issue, we conducted a genome wide analysis of transcription in Drosophila embryos using wild type and a number of well-characterized Drosophila guidance mutants and transgenics. We also analyzed a publicly available microarray time course of Drosophila embryonic development with an axon guidance focus. Using hopach, a novel clustering method which is well suited to microarray data analysis, we identified groups of genes with similar expression patterns across guidance mutants and transgenics. We then systematically characterized the resulting clusters with respect to their relevance to axon guidance using two complementary controlled vocabularies: the Gene Ontology (GO) and anatomical annotations of the Atlas of Pattern of Gene Expression (APoGE) in situ hybridization database. The analysis indicates that regulation of gene expression does play a role in the process of axon guidance in Drosophila. We also find a strong link between axon guidance and hemocyte migration, a result that agrees with mounting evidence that axon guidance molecules are co-opted in vertebrate vascularization. Cell cyclin activity in the context of axon guidance is also suggested from our array data. RNA and protein patterns of cell cyclin in axon guidance mutants and transgenics support this possible link. This study provides important insights into the regulation of axon guidance in vivo and suggests that transcription does play a role in control of axon guidance. Experiment Overall Design: Several mutants and transgenics were analyzed, totalizing 17 distinct conditions. Individual descriptions are included in each microarray. For each condition there are 3 or 4 replicates. The file's name indicates the replicates, e.g., comm.a reflects the replicate a of mutant commissureless. The experiment design covers a range of mutants and transgenics of key axon guidance mutans, in different dosages. The protocol was the standard Affymetrix protocol.
2008-06-15 | E-GEOD-6515 | biostudies-arrayexpress
Project description:In the developing brain, heightened plasticity during the critical period enables the proper formation of neural circuits. Here we identify the “navigator” neurons, a group of perinatally born olfactory sensory neurons, as playing an essential role in establishing the olfactory map during the critical period. The navigator axons project circuitously in the olfactory bulb and traverse multiple glomeruli before terminating in perspective glomeruli. These neurons undergo a phase of exuberant axon growth and exhibit a shortened lifespan. Single cell transcriptome analyses reveal distinct molecular signatures for the navigators. Extending their lifespan prolongs the period of exuberant growth and perturbs axon convergence. Conversely, genetic ablation experiment indicates that, despite postnatal neurogenesis, only the navigators are endowed with the ability to establish a convergent map. The presence and the proper removal of the navigator neurons are both required to establish tight axon convergence into the glomeruli.
2018-10-03 | GSE120199 | GEO
Project description:During the development of the Drosophila central nervous system the process of midline crossing is orchestrated by a number of guidance receptors and ligands. Many key axon guidance molecules have been identified in both invertebrates and vertebrates, but the transcriptional regulation of growth cone guidance remains largely unknown. One open question is whether transcriptional regulation plays a role in midline crossing, or if local translation can account for the necessary fine tuning of protein levels. To investigate this issue, we conducted a genome wide analysis of transcription in Drosophila embryos using wild type and a number of well-characterized Drosophila guidance mutants and transgenics. We also analyzed a publicly available microarray time course of Drosophila embryonic development with an axon guidance focus. Using hopach, a novel clustering method which is well suited to microarray data analysis, we identified groups of genes with similar expression patterns across guidance mutants and transgenics. We then systematically characterized the resulting clusters with respect to their relevance to axon guidance using two complementary controlled vocabularies: the Gene Ontology (GO) and anatomical annotations of the Atlas of Pattern of Gene Expression (APoGE) in situ hybridization database. The analysis indicates that regulation of gene expression does play a role in the process of axon guidance in Drosophila. We also find a strong link between axon guidance and hemocyte migration, a result that agrees with mounting evidence that axon guidance molecules are co-opted in vertebrate vascularization. Cell cyclin activity in the context of axon guidance is also suggested from our array data. RNA and protein patterns of cell cyclin in axon guidance mutants and transgenics support this possible link. This study provides important insights into the regulation of axon guidance in vivo and suggests that transcription does play a role in control of axon guidance. Keywords: Mutant Analysis
2006-12-14 | GSE6515 | GEO
Project description:Cortico-ponto-cerebellar topographic circuit formation requires patterned expression of chemotropically active molecules as well as differential expression of axon guidance molecules within the pontine nuclei. We carried out RNA-sequencing experiments on different sets of genetically identified or manipulated pontine nuclei neurons followed by comparative transcriptome analysis to identify genes which are potentially involved in controlling PN circuit formation and are regulated by Hoxa5.
2017-09-02 | GSE72710 | GEO