Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1145997 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30184300_1.fastq.gz | Fastqsanger.gz | |||
| SRR30184300_2.fastq.gz | Fastqsanger.gz | |||
| SRR30184301_1.fastq.gz | Fastqsanger.gz | |||
| SRR30184301_2.fastq.gz | Fastqsanger.gz | |||
| SRR30184302_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:To gain a better understanding of the factors necessary for successful CNS regeneration, a temporal analysis of the changes in gene expression in the eye caused by optic nerve injury was conducted. Dual color oligonucleotide microarrays were used to compare total RNA harvested from the eyes of sham-operated and optic nerve-injured fish at 3, 24, and 168 hours following surgery. Optic nerve injured fish are compared to sham-operated fish in order to eliminate gene expression due to non-neuronal damage and inflammatory response. Statistical analyses identified 131 genes with a 2.0-fold or greater difference in expression. Wild type zebrafish were obtained from a local pet store. Optic nerve injury was conducted using a severing model accomplished as follows. Zebrafish were anesthetized in 0.2% MS-222 dissolved in tank water. The muscles surrounding the eye were cut and the eye angled rostrally to expose the nerve. The optic nerve was then severed using microsissors without damaging the ophthalmic artery. In sham operated fish the muscles surrounding the eye were severed but the nerve was not damaged. RNA was extracted from the eye at three time points following surgery 3 hours, 24 hours, and 168 hours. RNA was pooled from multiple fish to achieve 10 ug total RNA. Samples were collected in triplicate per time point. Gene expression was analyzed on a dual color oligonucleotide array where the optic nerve injured fish were compared to sham-operated fish. Four samples of RNA were also collected from control fish and compared to each other on the microarray to confirm that processing did not create expression differences.
2010-05-16 | E-GEOD-17854 | biostudies-arrayexpress
Project description:To gain a better understanding of the factors necessary for successful CNS regeneration, a temporal analysis of the changes in gene expression in the eye caused by optic nerve injury was conducted. Dual color oligonucleotide microarrays were used to compare total RNA harvested from the eyes of sham-operated and optic nerve-injured fish at 3, 24, and 168 hours following surgery. Optic nerve injured fish are compared to sham-operated fish in order to eliminate gene expression due to non-neuronal damage and inflammatory response. Statistical analyses identified 131 genes with a 2.0-fold or greater difference in expression.
2009-12-25 | GSE17854 | GEO
Project description:Differential gene expression in Danio rerio during optic nerve regeneration
| PRJNA120093 | ENA
Project description:Zebrafish (Danio Rerio) have the capacity for successful adult optic nerve regeneration, unlike mammals. Optic nerve regeneration is frequently studied using optic nerve crush (ONC). For ONC, animals were deeply anesthetized in 0.033% tricaine methane-sulfonate (MS-222). The right optic nerve was exposed by gently removing the connective tissue on the dorsal half of the eye and rotating the eye ventrally out of the orbit with a pair of number 5 forceps. A nerve crush was then performed using number 5 forceps to crush the nerve ~0.5 to 1 mm from the optic nerve head for 5 seconds. Success of crush was assessed by identifying the generation of a translucent stripe in the nerve that completely separated two areas of white myelination with no bleeding. Fish were then revived in fresh aquatic system water in individual tanks. After 1 hour the tanks were returned to the fish system and animals were maintained normally with daily feeding until 3 days post injury.
Female and male (6 month to 1 year old) Zebrafish optic nerves (right side/OD) were crushed and collected three days after. The associated retinas and tecta were also collected under the same conditions. Contralateral, uninjured optic nerves, retinas and tecta were collected as controls. For tissue collection, animals were euthanized by overdose of MS-222 (>400mg/L) followed by dissection. The tissue was collected from the optic nerve head to the optic chiasm. The tissues were immediately frozen on dry ice. Optic nerve samples were pooled for each category (female crush, female control, male crush, male control) and pooled at n = 31 to obtain sufficient protein concentrations for analysis (pooled optic nerves served as one sample). Retina and tectum samples were pooled using the same categories (female crush, female control, male crush, male control) at n = 10-12 (pooled tissue served as one sample).
Protein extraction was carried out by homogenizing the optic nerve tissue in TEAB, NaCl and SDS. Three synthetic peptide standards (Regen III) were added to the samples during the extraction to measure extraction efficiency. Each standard was spiked into samples for a total concentration of 48uM per standard. After extraction was carried out, protein amounts were estimated using dot blot densitometry and ImageJ and normalized to 50ug/ul. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin. All samples were labelled using 2 sets of 14 tags from a 18plex TMT (Tandem Mass Tag) kit (A52045: Thermo Fisher Scientific, Waltham, MA) for quantification. After combination and drying of all peptide samples, the samples were fractionated into 9 fractions using Pierce High pH Reversed-Phase Peptide Fractionation Kit (84868: Thermo Fisher Scientific, Waltham, MA). After fractionation and drying of all peptide samples, each fractionated TMT sample was spiked with two additional peptide standards (Regen II) containing isobaric labels. The final concentration of the post extraction spiked peptides was 54uM per plex. These standards (Regen II) were spiked directly before mass spectrometry analysis to be used as an ionization control. Additionally, all five standards serve as a normalization method that may be used to compare protein abundance data across multiple datasets. Untargeted liquid chromatography-mass spectrometry was performed on an Easy-nLC 1000 liquid chromatograph coupled to a QExactive mass spectrometer (LC-MS/MS). Raw mass spectrometry data files were analyzed using Proteome Discoverer 3.0. The Danio rerio proteome was downloaded from UniProt and used as the target database for protein identification. Max missed cleavage site was set to 2 and minimum peptide length to 6 . Precursor Mass Tolerance was set to 10ppm and Fragment Mass Tolerance to 0.02 Da. Post-translational modifications for experimental proteins included oxidation, acetylation, carbamidomethylation and TMTpro. The Normalization was set to total peptide amount and confidence to low. Two additional local databases were created for the pre- and post- extraction peptides and ran separately from experimental protein identification.
2024-06-25 | MSV000095140 | MassIVE
Project description:Integrated analyses of zebrafish miRNA and mRNA expression profiles identify miR-29b and miR-223 as potential regulators of optic nerve regeneration
| PRJNA288093 | ENA
Project description:Gene expression timecourse in zebrafish whole eye in response to optic nerve crush
| PRJNA120883 | ENA
Project description:Epigenetical regulation in zebrafish heart regeneration
| PRJNA386461 | ENA
Project description:We used microarrays to analyse expression profiles of zebrafish retina after optic nerve crush to identify potential regulatory mechanisms that underpin central nerve regeneration Total RNA extracted from 4 samples (pooling 4 animals) of Zebrafish retinae after performing optic nerve crush (at day 3 post crush) vs 4 samples (pooling 4 animals) of control (unoperated) Zebrafish retinae
2015-06-26 | E-GEOD-70261 | biostudies-arrayexpress
Project description:Expressing HDAC5 mutant whose serine 259 and 488 have been replaced by alanine (HDAC5AA) promotes optic nerve regeneration in retinal ganglion cells. However, expressing GFP, HDAC5WT and HDAC5DAD, whose serine 259 and 498 have been replaced by aspartic acid and serine 280 by alanine, do not promote optic nerve regeneration. The goal of this experiment was to determine the underlying mechanisms leading to the phenotypical differences in optic nerve regeneration between control GFP, HDAC5DAD, and HDAC5AA by analyzing the retinal transcriptome of the different treatments.
2019-06-10 | GSE120257 | GEO
Project description:To identify a novel clinically-relevant therapy, fluvastatin and matrix bound nanovesicles (MBV) were focused in this study. We found that fluvastatin and MBV synergistically enhance optic nerve regeneration and RGC protection after optic nerve injury in mouse. To identify the molecular mechanisms underlying enhancement of RGC protection and axon regeneration after optic nerve injury, bulk RNA sequencing analysis of the whole retina treated with MBV, fluvastatin and the combination of MBV and fluvastatin or PBS as a control two days after optic nerve crush, was performed. Bulk RNA-seq analysis revealed that genes and cellular pathways related to inflammation, were robustly altered.
2024-06-05 | GSE226780 | GEO