Similar Datasets
Project description:Effect of zinc on zerafish brain
| PRJNA798905 | ENA
Project description:This SuperSeries is composed of the following subset Series: GSE21894: Dynamic transcriptomic profiles of zebrafish gills in response to zinc depletion GSE21907: Dynamic transcriptomic profiles of zebrafish gills in response to zinc supplementation. Refer to individual Series
2010-05-19 | E-GEOD-21914 | biostudies-arrayexpress
Project description:To identify the molecular pathways that are perturbed due to transient zinc chelation Zinc is known to regulate the functions of about 10% of the human proteome and a large number of physiological processes that are zinc dependent have been identified and characterized under conditions of zinc deficiency and supplementation. As zinc homeostasis is closely linked to the normal functioning of both prokaryotic and eukaryotic cells, many pathogens are directly or indirectly affected by perturbations in zinc homeostasis. Dengue virus (DENV), a mosquito-borne, positive-strand RNA virus from the family Flaviviridae, has emerged as one of the major public health concerns in India and recent estimates suggest that over 60 million people globally get infected with DENV every year. The crystal structures of NS5 protein of DENV and West Nile virus have identified zinc binding site in RdRp domain and propose an important structural role for zinc ions in polymerase activity. Therefore, we investigated whether perturbation in intracellular zinc pools influence dengue infection. We utilized N,N,N’,N’-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine (TPEN), a zinc-specific chelator, to mimic zinc-deficiency in cell culture models of infection and investigated the effect of zinc depletion on DENV life-cycle.
2019-10-29 | GSE135873 | GEO
Project description:Effect of zinc chelation in Caco-2 cells
| PRJNA560386 | ENA
Project description:Zinc deficiency is detrimental to organisms highlighting its role as an essential micronutrient contributing to numerous biological processes. To investigate the underlying molecular events invoked by zinc depletion we performed a temporal analysis of transcriptome changes observed within zebrafish gill. This tissue represents a model system for studying ion absorption across polarised cells as it provides a major pathway for fish to acquire zinc directly from water whilst sharing a conserved zinc transporting system with mammals. Zebrafish were treated with either zinc-depleted (water = 2.61 μg L-1; diet = 26 mg kg-1) or zinc-adequate (water = 16.3 μg L-1; diet = 233 mg kg-1) conditions for two weeks. Gill samples were collected at five time points and transcriptome changes analysed in quintuplicate using a 16K oligonucleotide array. Global transcript levels were measured in zebrafish gills using a oligonucleotide array either zinc-depleted or zinc-adequate diet. Gill samples were collected at five time points and transcriptome changes analysed in quintuplicate using a 16K oligonucleotide array
2010-05-20 | E-GEOD-21894 | biostudies-arrayexpress
Project description:We evaluated the intestinal responses of pigs under zinc restriction and under different zinc sources through RNA-seq of ileal samples. We identified changes in genes related to zinc transport, immune response, cell proliferation, DNA damage and stress resposne. Our findings demonstrate that swine intestine is responsive to zinc restriction and can be a model sentinel tissue for human zinc deficiency. Further research is needed to define the intestinal responses to organic and inorganic zinc sources.
2021-08-05 | GSE181343 | GEO
Project description:To gain a better understanding of the zinc effect on prostate cells, gene expression profiling analyses were conducted using HPR-1 and PC-3 cells treated with or without zinc (1,500 ng/ml) after 24 hrs serum-depletion. Zinc effect on gene expression was evaluated at 1, 3, and 6 hrs of zinc treatment compared to the control, using human genome survey microarray chips. A total of 6,110 identified genes exhibited three expression patterns in response to zinc a threshold of ±2.5 folds: suppressed (3,534 in PC-3; 1,953 in HPR-1), increased (571 in PC-3; 872 in HPR-1), and otherwise altered (16 in PC-3; 13 in HPR-1). Keywords: Zinc effect, time course, cell type comparison
2006-09-24 | GSE5590 | GEO
Project description:Zinc Finger Nucleases (ZFNs) facilitate precise editing of DNA enabling targeted genomic modifications in vivo. ZFNs have been employed to obtain genetically modified plants and animals, and cell-based therapies utilizing ZFNs are undergoing clinical trials. However, many ZFNs display dose-dependent toxicity presumably due to the generation of undesired double stranded breaks at off-target sites within the genome. To evaluate the parameters influencing the functional specificity of ZFNs, we compared the in vivo activity of ZFN variants targeting the zebrafish kdrl locus, which display both high on-target activity and dose-dependent toxicity. We evaluated their functional specificity by assessing lesion frequency at 141 potential off-target sites within the zebrafish genome using Illumina sequencing. Only a minority of these off-target sites displayed significant lesion frequency with kdrl ZFNs. Furthermore, we find that active off-target sites appear to be defined by the thermodynamics of zinc finger-DNA recognition. Surprisingly, we observed that the zinc finger protein specificity and the choice of the engineered dimerization domain of the FokI nuclease could independently influence the fidelity of these ZFNs. The results of this study have implications for the assessment of likely off-target sites within a genome and point to both ZFP-dependent and –independent mechanisms of potential improvement for engineering ZFNs with higher levels of precision. Examined lesions at 141 off-target sites for various treatments of ZFNs and compare to the untreated sample stage 1: raw read but missing quality values stage 2: fastq files available from SRA
2010-08-25 | E-GEOD-23762 | biostudies-arrayexpress
Project description:Dietary zinc is routinely supplemented to promote growth, boost the immune system, protect against diabetes or aid recovery from diarrhoea. We exploited the zebrafish (Danio rerio) gill as a unique vertebrate ion transporting epithelium model to study the time-dependent regulatory networks of gene-expression leading to homeostatic control during zinc supplementation. This organ forms a conduit for zinc uptake whilst exhibiting conservation of zinc trafficking components. Fish were maintained with zinc supplemented water (4.0 uM) and diet (2023 mg zinc kg-1) or in un-amended water and diet, containing Zn2+ at 0.25 µM and 233 mg zinc kg-1 respectively. Gill tissues were harvested at five time points (8 hours to 14 days) and transcriptome changes analysed in quintuplicate using a 16K microarray. Global transcript levels were measured in zebrafish gills using a oligonucleotide array either zinc-adequate or zinc-supplemented diet. Gill samples were collected at five time points and transcriptome changes analysed in quintuplicate using a 16K oligonucleotide array
2010-05-20 | E-GEOD-21907 | biostudies-arrayexpress