Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1004885 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25641943_1.fastq.gz | Fastqsanger.gz | |||
| SRR25641943_2.fastq.gz | Fastqsanger.gz | |||
| SRR25641944_1.fastq.gz | Fastqsanger.gz | |||
| SRR25641944_2.fastq.gz | Fastqsanger.gz | |||
| SRR25641945_1.fastq.gz | Fastqsanger.gz |
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Project description:Although cyanobacteria produce a wide range of natural toxins that impact aquatic organisms, food webs and water quality, the mechanisms of toxicity are still insufficiently understood. Here, we implemented a whole-genome expression microarray to identify pathways, gene networks and paralogous gene families responsive to Microcystis stress in Daphnia pulex. Therefore, neonates of a sensitive isolate were given a diet contaminated with Microcystis to contrast with those given a control diet for sixteen days. The microarray revealed 2247 differentially expressed (DE) genes (7.6% of the array) in response to Microcystis, of which 17% are lineage specific and 49% are gene duplicates (paralogs). We identified four pathways/gene networks and eight paralogous gene families affected by Microcystis. Differential regulation of the ribosome including 3 paralogous gene families encoding 40S, 60S and mitochondrial ribosomal proteins, suggests an impact of Microcystis on protein synthesis of Daphnia. In addition, differential regulation of the oxidative phosphorylation pathway, including the NADH ubquinone oxidoreductase gene family, and trypsin paralogous gene family, major component of the digestive system in Daphnia, could explain why fitness is reduced based on energy budget considerations. For others (.e.g Neurexin IV), a link with fitness remains to be established.
2012-07-27 | GSE36635 | GEO
Project description:Comparison of the immune response of human whole blood to lipoteichoic acid (LTA) derived from the Staphylococcus aureus SA113 delta-lgt mutant (lacks lipoproteins), LTA from S. aureus SA113 wt. and PAM2Cys, a lipoprotein analogue. Background: Our goal was to expand our report that LTA from SA 113 wildtype (wt LTA) and delta-lgt (lgt LTA) induce equal amounts of TNF release by human whole blood (von Aulock et al., J Immunol, 2007). Therefore we traced the translational activation by both LTA in comparison to the synthetic diacylated lipoprotein Pam2Cys-SK4 in human whole blood on an immunology microarray comprising 1076 genes related to apoptosis and signal transduction, cell cycle, chemokines, cytokines and their receptors, extracellular matrix proteins, inflammation and complement system. Results and Discussion: The results show extensive overlaps of the clustered heat-maps of SA113 wt and lgt LTA, which are clearly different from those of Pam2Cys-SK4 stimulation. Only four of the 1076 genes were significantly differently regulated after stimulation with the LTAs, whereas stimulation with Pam2Cys-SK4 led to a significantly different regulation of 43 genes compared to SA 113 wt LTA and 39 compared to SA 113 lgt LTA. Mainly chemokines were upregulated by both LTA, which is consistent with our previous findings (von Aulock et al., Immunobiol, 2003) and different from stimulations with Pam2Cys-SK4. The gene array results support our protein data obtained from LTA-stimulated human whole blood and point to a significant concordance between the immunostimulatory activity of lgt and wt LTA preparations. In contrast, a distinct difference is observed between both LTA and the synthetic lipoprotein Pam2Cys-SK4. This supports the conclusion that the immunostimulatory activity of wt LTA in human whole blood is not determined by possible lipoprotein contaminations.
2015-04-05 | GSE21188 | GEO
Project description:Although cyanobacteria produce a wide range of natural toxins that impact aquatic organisms, food webs and water quality, the mechanisms of toxicity are still insufficiently understood. Here, we implemented a whole-genome expression microarray to identify pathways, gene networks and paralogous gene families responsive to Microcystis stress in Daphnia pulex. Therefore, neonates of a sensitive isolate were given a diet contaminated with Microcystis to contrast with those given a control diet for sixteen days. The microarray revealed 2247 differentially expressed (DE) genes (7.6% of the array) in response to Microcystis, of which 17% are lineage specific and 49% are gene duplicates (paralogs). We identified four pathways/gene networks and eight paralogous gene families affected by Microcystis. Differential regulation of the ribosome including 3 paralogous gene families encoding 40S, 60S and mitochondrial ribosomal proteins, suggests an impact of Microcystis on protein synthesis of Daphnia. In addition, differential regulation of the oxidative phosphorylation pathway, including the NADH ubquinone oxidoreductase gene family, and trypsin paralogous gene family, major component of the digestive system in Daphnia, could explain why fitness is reduced based on energy budget considerations. For others (.e.g Neurexin IV), a link with fitness remains to be established. RNA was isolated from three independent and concurrently replicated exposures of Daphnia to control and Microcystis conditions. RNA was hybridized to 4 microarrays using a standard, control vs. treated design that included dye swaps.
2012-07-26 | E-GEOD-36635 | biostudies-arrayexpress
Project description:Comparison for gene expression of Microcystis aeruginosa PCC7806 after hydrogen peroxide treatment
2021-01-07 | GSE164328 | GEO
Project description:This project detected the protein composition of extracellular vesicles (EV) produced by S. aureus WT JE2 strain and its lgt mutant (lipoprotein deficient mutant). Our recent study found that mutation of lgt in S. aureus USA300 JE2 strain significantly increased EV production in S. aureus and decreased the pore-forming toxin content of vesicles, indicatiung that lipoproteins modulate the EV biogenesis of S. aureus. To gain a better understanding of this process, we detected the protein compositions associated with EVs purified from both WT and lgt mutant EVs by LC-MS/MS. Compared to WT EVs, more cytosoli proteins and less extracellular proteins were identified in lgt mutant EVs. A total of 180 and 198 proteins were identified from WT and lgt mutant EVs, respectively.In addition 27.2% and 33.8% of identified proteins were unique to WT or lgt mutant EVs respectively.
2021-09-08 | PXD014888 | Pride
Project description:Genome editing was conducted on a t(3;8) K562 model to investigate the effects of deleting different modules or CTCF binding sites within the MYC super-enhancer. To check mutations after targeting with CRISPR-Cas9 we performed amplicon sequencing using the Illumina PCR-based custom amplicon sequencing method using the TruSeq Custom Amplicon index kit (Illumina). The first PCR was performed using Q5 polymerase (NEB), the second nested PCR with KAPA HiFi HotStart Ready mix (Roche). Samples were sequenced paired-end (2x 250bp) on a MiSeq (Illumina).
2021-07-26 | E-MTAB-9937 | biostudies-arrayexpress
Project description:This project investigated the role of lipoproteins in immune signaling by the model probiotic Lactobacillus plantarum, by mutagenesis of the prolipoprotein diacylglyceryltransferase encoding lgt gene involved in lipoprotein acylation.
2020-07-13 | PXD019218 | Pride
Project description:Microcystis is a genus of unicellular cyanobacteria capable of growing massively in freshwater ecosystems around the world and producing various toxins such as microcystins. We studied using an RNA-Seq approach the transcriptomes of three axenic strains of Microcystis, comprising the modele strain PCC 7806, selected because of their genetic potential for natural products. We assessed the expression of biosynthetic gene clusters during a 24-hour day/night cycle.
2025-02-01 | GSE255450 | GEO
Project description:Little is known about the influence that environmental stressors may have on genome-wide methylation patterns, and to what extent epigenetics may be involved in environmental stress response. Yet, studies of methylation patterns under stress could provide crucial insights on stress response and toxicity pathways. Here, we focus on genome-wide methylation patterns in the micro-crustacean Daphnia magna, a model organism in ecotoxicology and risk assessment, exposed to the toxic cyanobacterium Microcystis aeruginosa. Bisulfite sequencing of exposed and control animals highlighted differential methylation patterns in Daphnia upon exposure to Microcystis primarily in exonic regions. These patterns are enriched for serine/threonine amino acid codons and genes related to protein synthesis, transport and degradation. Furthermore, we observed that genes with differential methylation corresponded well with genes susceptible to alternative splicing in response to Microcystis stress. Overall, our results suggest a complex mechanistic response in Daphnia characterized by interactions between DNA methylation and gene regulation mechanisms. These results underscore that DNA methylation is modulated by environmental stress and can also be an integral part of the toxicity response in our study species.
2016-12-16 | GSE83407 | GEO