Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1025908 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26321223_1.fastq.gz | Fastqsanger.gz | |||
| SRR26321223_2.fastq.gz | Fastqsanger.gz | |||
| SRR26321224_1.fastq.gz | Fastqsanger.gz | |||
| SRR26321224_2.fastq.gz | Fastqsanger.gz | |||
| SRR26321225_1.fastq.gz | Fastqsanger.gz |
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Project description:We studied the transcriptome changes of Vibrio parahaemolyticus under normal culture condition and copper stress by RNA sequencing. The data showed that genes in copA and cusFABC operon were significantly upregulated by copper.
2024-08-01 | GSE268489 | GEO
Project description:We used high-throughput sequencing to identify conserved and nonconserved miRNAs and other short RNAs in Paeonia ostii under control and copper stressed condition. 102 previously known plant miRNAs were identified and classified into 89 families according to their gene sequence identity. Some miRNAs were highly conserved in the plant kingdom suggesting that these miRNA play important and conserved roles. Combined our transcriptome sequencing data of Paeonia ostii under same conditions, 34 novel potential miRNAs were identified. The potential targets of the identified known and novel miRNAs were also predicted based on sequence homology search. Comparing the two libraries, it was observed that 12 conserved miRNAs and 18 novel miRNAs showed significantly changes in response to copper stress. Some of the new identified potential miRNAs might be involved in Paeonia ostii-specific regulating mechanisms under copper stress. These results provide a framework for further analysis of miRNAs and their role in regulating Paeonia ostii response to copper stress.
2016-04-23 | GSE62661 | GEO
Project description:Copper-related cell death, cuproptosis, involves accumulation of intracellular copper that triggers mitochondrial lipoylated protein aggregation and destabilization of iron–sulfur cluster proteins. Here, glioblastoma (GBM) stem cells (GSCs) displayed resistance to cuproptosis with circadian variation of intracellular copper levels, unlike differentiated GBM cells (DGCs) or neural stem cells (NSCs). CRISPR screening of copper regulators under concurrent treatment with copper ionophore or clock disruption revealed dependency on ATPase Copper Transporting Alpha (ATP7A). Circadian control of copper homeostasis was mediated by core clock transcription factor, Basic helix-loop-helix ARNT-like protein 1 (BMAL1). In turn, ATP7A promoted tumor cell growth through regulation of fatty acid desaturation. Copper levels negatively fed back onto the circadian clock through SQSTM1 (sequestosome 1/p62)-mediated lysosomal degradation of BMAL1. Targeting cuproptosis and circadian clock or fatty acid desaturation generated synergistic anti-tumor effects. Thus, crosstalk between the circadian rhythm and copper sustains GSCs, reshaping fatty acid metabolism and promoting drug resistance.
2025-10-14 | GSE278671 | GEO
Project description:We report the application of RNA-sequencing of VUMC-DIPG10 and HSJD-DIPG007 human diffuse intrinsic pontine glioma cells treated with copper chelator Tetraethylenepentamine (TEPA) for 24 hours. We show transcriptome changes following copper chelation vs. control untreated cells.vs. control samples
2026-01-11 | GSE215220 | GEO
Project description:We report the application of RNA-sequencing of MDA-MB-231 human triple-negative breast cancer cells treated with copper chelator Tetraethylenepentamine (TEPA) for 8 and 24 hours. We show transcriptome changes following copper chelation vs. control untreated cells.vs. control samples
2024-04-24 | GSE185760 | GEO
Project description:Higher plants have developed sophisticated mechanisms to efficiently acquire and use micronutrients such as copper and iron. In the present work, we studied effects produced by the presence of a wide copper range in growth media and altered copper transport on iron homeostasis in Oryza sativa plants. The global analysis of gene expression in the rice seedlings grown under copper deficiency versus excess in the medium showed an increased expression of the genes involved in iron homeostasis. Different iron-related genes are expressed under either copper deficiency and excess, such as those that encode ferredoxin and transcriptional regulator IRON-RELATED TRANSCRIPTION FACTOR 2 (OsIRO2), respectively. As expected, the expression of OsCOPT1, which encodes a high affinity copper transport protein, was up-regulated under copper deficiency, and the expression of OsIRO2 targets were increased under copper excess. Arabidopsis COPT1 overexpression (C1OE) in rice causes root shortening under copper excess, modifies the expression of the putative Fe-sensing factor HEMERYTHRIN MOTIF-CONTAINING REALLY INTERESTING NEW GENE- AND ZINC-FINGER (OsHRZ1) and enhances the expression of OsIRO2 and its targets, which suggests a role of copper in iron signaling. Our studies conducted under simultaneous copper and iron deficiencies indicate that C1OE plants are more sensitive than the wild-type controls to root growth inhibition. The C1OE rice plants grown on soil contained higher endogenous iron concentration in grains than the wild-type plants (both brown and white grains). The results obtained herein showed the interaction between homeostatic networks of iron and copper, and suggest that strategies to obtain crops with optimized nutrient concentrations in edible parts should take into account this interaction.
2017-06-20 | GSE89109 | GEO
Project description:This study investigates the combined effects of copper availability and carbon source (methane versus methanol) on the physiology and transcriptome of Methylosinus trichosporium OB3b, a model Type II methanotroph. Methanotrophs oxidize methane to carbon dioxide through intermediates such as methanol, formaldehyde, and formate, using two forms of methane monooxygenase (MMO): the copper-dependent particulate MMO (pMMO) and the soluble MMO (sMMO). Although Msn. trichosporium OB3b can utilize both methane and methanol as sole carbon sources, growth on methanol is significantly affected by copper. In the presence of copper, methanol-grown cells exhibited impaired growth, formate accumulation, and decreased pH, while buffering with MOPS restored growth. NADH/NAD ratios increased nearly tenfold in methanol-grown cultures with copper, indicating redox imbalance. Transmission electron microscopy revealed disrupted intracytoplasmic membranes under these conditions. Transcriptomic analysis showed that genes involved in methanol oxidation were differentially expressed in response to copper and carbon source, and two siderophore biosynthetic gene clusters were repressed during methanol growth with copper. Overall, the findings suggest that Msn. trichosporium OB3b modulates metallophore expression and carbon metabolism to manage oxidative and redox stress under methanol growth conditions. Understanding these regulatory mechanisms is critical for optimizing methanotroph-based biotechnological applications, including methanol-driven biosynthesis of valuable compounds such as methanobactin.
2026-01-03 | GSE310588 | GEO
Project description:To identify genes which are differentially expressed in Corynebacterium glutamicum in the absence of copper, we performed DNA microarray analyses of cells cultivated under copper starvation conditions compared to copper sufficiency.
2018-08-28 | GSE117530 | GEO
Project description:Thermomacidophilic archaea, such as Metallosphaera sedula, are lithoautotrophs that occupy metal-rich environments. In previous studies, a M. sedula mutant lacking the primary copper efflux transporter, CopA, became copper sensitive. In contrast, the basis for supra-normal copper resistance remained unclear in the spontaneous M. sedula mutant, CuR1. Here, transcriptomic analysis of copper-shocked cultures indicated that CuR1 had a unique regulatory response to metal challenge corresponding to up-regulation of 55 genes. Genome re-sequencing identified 17 confirmed mutations unique to CuR1 that were likely to change gene function. Of these, 12 mapped to genes with annotated function associated with transcription, metabolism or transport. These mutations included 7 non-synonymous substitutions, 4 insertions and 1 deletion. One of the insertion mutations mapped to pseudogene, Msed_1517, and extended its reading frame an additional 209 amino acids. The extended mutant allele was identified as a homolog of Pho4, a family of phosphate symporters that include the bacterial PitA proteins. Orthologs of this allele were apparent in related extremely thermoacidophilic species, suggesting M. sedula was naturally lacking this gene. Phosphate transport studies combined with physiologic analysis demonstrated M. sedula PitA was a low affinity high velocity secondary transporter implicated in copper resistance and arsenate sensitivity. Genetic analysis demonstrated spontaneous arsenate resistant mutants derived from CuR1 all underwent mutation in pitA and non-selectively became copper resistant. Taken together, these results point to archaeal PitA as a key requirement for the increased metal resistance of strain CuR1 and its accelerated capacity for copper bioleaching. The study comprises 5 samples, described in detail below. WT_CuR1: Differential transcriptional response of Metallosphaera sedula DSM 5348, WT, to the supra-normal copper resistant spontaneous Metallosphaera sedula mutant, CuR1 under normal growth conditions. This experiment was done to analyze the differential transcription of WT cells compared with CuR1 cells at mid log phase. WT-15_CuR1-15: Differential transcription of Metallosphaera cells under sub-inhibitory copper challenge (2.0 mM). This experiment was done to analyze the differential transcription of Metallosphaera sedula WT and CuR1 15 minutes post copper challenge. The copper cultures were harvested 15 minutes after the shock. WT-60_CuR1-60: Differential transcription of Metallosphaera cells under sub-inhibitory copper challenge (2.0 mM). This experiment was done to analyze the differential transcription of Metallosphaera sedula WT and CuR1 60 minutes post copper challenge. The copper cultures were harvested 60 minutes after the shock. WT-15_WT-60: Differential transcription of Metallosphaera cells under sub-inhibitory copper challenge (2.0 mM). This experiment was done to analyze the differential transcription of Metallosphaera sedula WT 15 and 60 minutes post copper challenge. The copper cultures were harvested 15 and 60 minutes after the shock, respectively. CuR1-15_CuR1-60: Differential transcription of Metallosphaera cells under sub-inhibitory copper challenge (2.0 mM). This experiment was done to analyze the differential transcription of Metallosphaera sedula CuR1 15 and 60 minutes post copper challenge. The copper cultures were harvested 15 and 60 minutes after the shock, respectively.
2014-07-10 | E-GEOD-59253 | biostudies-arrayexpress
Project description:In an approach to generate Saccharomyces cerevisiae strains with increased intracellular copper amounts for technical applications we over-expressed the copper transporter CTR1 and a variant of CTR1 with a truncation in the C-terminus after the 300 amino acids (CTR1 delta-300). We determined the copper sensitivity of the generated strains and used inductively coupled plasma spectrometry (ICP-OES and ICP-MS) analysis to investigate the effects of over-expression of both constructs under excess copper on the cellular content of different elements in S. cerevisiae. In addition, we ran DNA microarray analysis to obtain the gene expression profile under the changed element contents. Over-expression of CTR1 increased the copper content in the cells up to 160% and 78 genes were differentially regulated. Over-expression of the truncated CTR1 delta-300 resulted in an increased copper, iron and zinc content of more than 200% and 980 genes showed differential expression. We found that transition metal ion homeostasis was disrupted in CTR1 delta-300 over-expressing strains under excess copper and that this was combined with a transcriptional remodelling of cellular processes
2014-01-28 | GSE44043 | GEO