Ontology highlight
ABSTRACT:
PROVIDER: PRJNA485433 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7666344_1.fastq.gz | Fastqsanger.gz | |||
| SRR7666344_2.fastq.gz | Fastqsanger.gz | |||
| SRR7666345_1.fastq.gz | Fastqsanger.gz | |||
| SRR7666345_2.fastq.gz | Fastqsanger.gz |
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Project description:To gain a better understanding of the diurnal variation in gene expression, we analyzed the changes in gene expression in the eye of zebrafish. Dual color oligonucleotide microarrays were used to compare total RNA harvested from eyes of adult zebrafish at midday and midnight. Statistical analyses identified 44 genes which showed significant, 2-fold or more change; 26 genes showed decreased expression at midnight (D/L ≤ 0.5) and 18 genes showed increased expression at midnight (D/L ≥ 2). Seven genes were further analyzed using qPCR. The results of qPCR identified AANAT, Mel1a1, Mel1a3, Mel1b1, Mel1b2 and Melc as genes that showed significant change in expression at dawn, dusk, midday and midnight. These results suggest that expression of melatonin receptors is subject to diurnal regulation.
2012-05-10 | GSE29696 | GEO
Project description:Mammalian and fish pineals play a key role in adapting behaviour to the ambient light conditions through the release of melatonin. In mice, light inhibits nocturnal locomotor activity via the nonvisual photoreceptor Melanopsin. In contrast to the extensively studied function of Melanopsin in the indirect regulation of the rodent pineal, its role in the intrinsically photosensitive zebrafish pineal has not been elucidated. Therefore, it is not evident if the light signalling mechanism is conserved between distant vertebrates, and how Melanopsin could affect diurnal behaviour. A double knockout of melanopsins (opn4.1-opn4xb) was generated in the diurnal zebrafish, which manifests attenuated locomotor activity during the wake state. Transcriptome sequencing gave insight into pathways downstream of Melanopsin, implying that sustained repression of the melatonin pathway is required to elevate locomotor activity during the diurnal wake state. Moreover, we show that light induces locomotor activity during the diurnal wake state in an intensity-dependent manner. These observations suggest a common Melanopsin-driven mechanism between zebrafish and mammals, while the diurnal and nocturnal chronotypes are inversely regulated downstream of melatonin.
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Project description:Zebrafish organ proteomics was carried out for proteogenomic analysis. High resolution mass spectrometry-based proteomic profiling of 11 adult organs (eye, brain, liver, spleen, intestine-pancreas, ovary, testes, muscle, heart and head) and two developmental stages (embryos 48 and 120 hours post-fertilization) of zebrafish (SAT line) was carried out. Protein extracts were reduced and alkylated (iodoacetamide). Off-loine fractionation was carried out by SDS-PAGE and basic RPLC. MS analysis was cariied on Agilent 6540 Q-TOF. Spleen and Testis samples were also analyzed on Thermo Orbitrap LTQ Velos.
2014-02-26 | PXD000479 | Pride
Project description:To gain a better understanding of the diurnal variation in gene expression, we analyzed the changes in gene expression in the eye of zebrafish. Dual color oligonucleotide microarrays were used to compare total RNA harvested from eyes of adult zebrafish at midday and midnight. Statistical analyses identified 44 genes which showed significant, 2-fold or more change; 26 genes showed decreased expression at midnight (D/L ≤ 0.5) and 18 genes showed increased expression at midnight (D/L ≥ 2). Seven genes were further analyzed using qPCR. The results of qPCR identified AANAT, Mel1a1, Mel1a3, Mel1b1, Mel1b2 and Melc as genes that showed significant change in expression at dawn, dusk, midday and midnight. These results suggest that expression of melatonin receptors is subject to diurnal regulation. Wild-type ZDR zebrafish (Danio rerio) were obtained from Animal Wonders, San Marcos, TX, and Aquatica Tropicals, Plant City, FL. Fish were conditioned on a 12 hour light/dark cycle for a minimum of 14 days before use. The design of this analysis compared the experimental to the control: midnight samples were used as experimental and midday as control. Samples were collected in triplicate per time point with each replicate representing total RNA pooled from 9 fish. Dual-color microarray was used to compare the midnight and midday samples. A statistically significant (p-value ≤ 0.05) and 2-fold or more change in an experimental sample as compared to a control indicated an up- or down-regulation in gene expression. Supplementary files: In Complete processed data file, "x" marked spots show intensities of less than 1000. In Intensity trimmed data file, all genes with signal intensities of less than 1000 in all triplicate time points were removed from the analysis.
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Project description:The present study aims to apply a high-resolution and label-free proteomics approach to identify and quantify proteins in the eye of zebrafish. First, the results of the present study will provide a comprehensive list of proteins in the eye of zebrafish, and second, establish a platform based on sex-biased proteins that may offer clues to answer crucial questions such as sex-based differences in visual perception and impairments. Our results may improve the outcome of behavioural, developmental, toxicological, and medical experiments considering the zebrafish eye.
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Project description:We compare dissected ocular tissues from wild-type and lrp2-/- mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2, a transmembrane receptor, cause ocular enlargement and high-myopia. LRP2 is expressed by the RPE and eye ciliary epithelia, binding many extracellular ligands, including Bmp4 and Shh. Signaling mediated by LRP2 is very context-dependent, and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled, sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia (proper refraction). Using human iPSC-derived RPE, and zebrafish, we demonstrate that BACE sheddase-dependent LRP2 cleavage produces a soluble domain that binds BMP4, inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand-binding receptor forms available: a soluble BMP trap, and a membrane-bound RPE signaling facilitator. By modulating LRP2 cleavage, cells can fine-tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth.
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Project description:Purpose: We performed an NGS study on the circadian changes in zebrafish eye and pineal gland transcriptome in order to elucidate novel and conserved elements in the circadian clock. Methods: Poly-A selected RNA from zebrafish eyes and pineaal glands of animals eutanized at 2 timepoints (Mid-Day, Midnight) was deep sequenced, using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of genes that show circadian activivty in both eye and pineal gland of Zebrafish. Conclusions: Our study represents part of a comparative analysis of retinal(eye) and pineal gland transcriptome of several species, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
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