Ontology highlight
ABSTRACT:
PROVIDER: PRJNA448040 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6917643_1.fastq.gz | Fastqsanger.gz | |||
| SRR6917643_2.fastq.gz | Fastqsanger.gz | |||
| SRR6917644_1.fastq.gz | Fastqsanger.gz | |||
| SRR6917644_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Background: In the life history of Daphnia, the reproductive mode of parthenogenesis and sexual reproduction alternate in aquatic ecosystem, which are often affected by environmental and genetic factor. Although several functional genes on reproductive transition of Daphnia had been determined, molecular mechanism on the reproductive mode of Daphnia are still not known well, including differentially expressed genes in different developmental stages. Results: In this study, four developmental stages, juvenile female (JF), parthenogenetic female (PF), sexual female (SF) and male (M), of D. similoides sinensis were performed for transcriptome sequence, and candidate genes related to male sex determination were screened. A total of 110437 transcripts were obtained and assembled into 22996 unigenes. In the four developmental stages (JF, PF, SF and M), the number of unique unigenes is respectively 2863, 445, 437 and 586, and the number of common unigenes is 9708. The differentially expressed genes (DEGs) between male and other three female stages (M vs JF, M vs PF and M vs SF) were obtained. The GO gene enrichment analysis showed that the up-regulated genes in male were mainly enriched in hydrolase activity and peptidase activity. Thirty-six candidate genes related to male sex determination in male were significantly higher expression than those in the other three stages, including one Doublesex (Dsx) gene, one laminin gene, five trypsin genes and one serine protease genes, and one chitin synthase gene and two chitinase genes. In addition, in D. similoides sinensis male, the relative expression levels of two genes (Dsx1, antp) related to male sex determination observed in other Daphnia species were also significantly higher than those in other developmental stages. Conclusions: Our results showed that thirty-six candidate genes may involve in sex differetiation of D. similoides sinensis male, and it will provide a reference for further exploring the functional genes related to sex determination mechanism in Daphnia species. Moreover, according to previous investigations, we thought that the expression level of functional genes may be related to the development stage of organisms, and may be also affected by different Daphnia species.
2022-08-17 | GSE197943 | GEO
Project description:Toxic chemical contaminants have variety of detrimental effects on various species and the impact of pollutants on ecosystems has become an urgent issue. However, very limited species have been examined to date and those studies are mainly limited to vertebrates. In this study, we aimed to establish an ecotoxicogenomic bases for Daphnia magna. Based on a daphnia EST database, we made oligonucleotide-based DNA microarray that has high reproducibility. The DNA microarray was applied to evaluate gene expression profiles of daphnid exposed to chemicals. Characteristic gene expression patterns depending on chemicals indicate that the Daphnia microarray can be used for mechanistic understanding of chemical toxicity. Although acute toxicity test or reproductive toxicity test can provide hazardous concentrations of chemicals, they give no information about mode of action. Our study can be a breakthrough for the evaluation of chemical toxicity on environmental organisms. Keywords: Chemical response
2005-12-31 | GSE3445 | GEO
Project description:A long-lived species of zooplankton microcrustaceans, Daphnia magna, sometimes exhibits late-life rebound of reproduction, briefly reversing reproductive senescence. Such events are often interpreted as terminal investment in anticipation of imminent mortality. We demonstrate that such post-senescence reproductive events (PSREs) neither cause not anticipate increased mortality. We analyze an RNAseq experiment comparing young, old reproductively senescent, and old PSRE Daphnia females. We first show that overall age-related transcriptional changes are dominated by the increase transcription of guanidine monophosphate synthases and guanylate cyclases, as well as two groups of presumed transposon-encoded proteins and by a drop in transcription of protein synthesis-related genes. We then focus on gene families and functional groups in which full or partial reversal of age-related transcriptional changes occur. This analysis reveals reversal, in the PSRE individuals, of age-related up-regulation of apolipoproteins D, lysosomal lipases, and peptidases and of age-related down-regulation of E3 ubiquitin kinases, V-type proton ATPases, and numerous proteins related to mitochondrial and muscle functions. While it is certain which of these changes enable reproductive rejuvenation, and which are by-products of processes that lead to it, we present some evidence that post-senescence reproductive events are associated with the reversal of age-related protein and lipid aggregates removal, apoptosis, and with restoration of mitochondrial integrity.
2025-04-11 | GSE263788 | GEO
Project description:Transcriptomic profiling of Daphnia magna samples exposed to carbamazepine (CBZ), diazepan (DZP), propranolol (PR) and to an equitoxic mixture of them (M). Assessing the risks of emerging contaminants such as neuro-active pharmaceuticals in the environment requires an understanding of their joint effects at low concentrations across species. Here, we assessed reproductive and transcriptional effect of propranolol, diazepam and carbamazepine on the crustacean Daphnia magna at environmentally relevant concentrations. The three compounds enhanced reproductive parameters in adults, and induced specific transcriptome changes in pre-adolescent individuals. Comparing results from single exposures and of ternary equi-effective mixtures showed additive action for both effects. Transcriptomic analyses identified 3248 genes affected by at least one of the treatment, which were grouped into four clusters. Two clusters included 1897 gene transcripts in total, that behaved similarly (appearing either over- or underrepresented relative to control) in single and mixture treatments. The third and fourth clusters grouped genes differently transcribed upon exposure to diazepam and propranolol, respectively. Functional transcriptomics indicated that the four clusters shared major de-regulated signalling pathways implicated on energy, growth, reproduction, and neurologically- related processes, which may be responsible for the observed reproductive effects. Our study, thus, showed additive effects at the transcriptional and physiological level and is providing a novel approach to the analysis of environmental relevant mixtures of neuro-active compounds
2020-05-20 | GSE131587 | GEO
Project description:Daphnia (Daphnia pulex) is a small planktonic crustacean and a key constituent of aquatic ecosystems. It is commonly used as a model organism for studying environmental toxic challenges. In the past decade, a Daphnia genomic information and proteomic dataset has been developed. This dataset has expanded the opportunity to relate toxicological effects with “Daphnia proteomics” as it integrates proteomic knowledge in Daphnia, those approach will provide greater insights for toxicological research. In order to exploit Daphnia for ecotoxicological research, information on the post-translational modification (PTM) of proteins is necessary as this is a critical regulator of biological processes. Acetylation of lysine (Kac) is a reversible and highly regulated PTM that is associated with diverse biological functions. However, a comprehensive description of Kac in Daphnia is not yet available. Here, to understand the cellular distribution of lysine acetylation in Daphnia, we identified 98 acetylation sites in 65 proteins by immunoprecipitation using an anti-acetyllysine antibody and an liquid chromatography system supported by mass spectroscopy. We identified 28 acetylated sites connected with metabolic proteins and 6 acetylated enzymes associated with the TCA cycle in Daphnia. From GO and KEGG enrichment analyses, we showed that Kac in D. pulex is highly enriched in proteins associated with metabolic processes. Our data provide the first global analysis of lysine acetylation in D. pulex. The expanded proteomic dataset will be an important resource for the functional analysis of Kac in D. pulex and it will be nice to have a first step done using a promising future model organism.
2016-01-05 | PXD002441 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE29854: Daphnia magna exposed to narcotics and polar narcotics - aniline GSE29856: Daphnia magna exposed to narcotics and polar narcotics - 4-chloroaniline GSE29857: Daphnia magna exposed to narcotics and polar narcotics - 3,5-dichloroaniline GSE29858: Daphnia magna exposed to narcotics and polar narcotics - 2,3,4-trichloroaniline GSE29862: Daphnia magna exposed to narcotics and polar narcotics - ethanol GSE29864: Daphnia magna exposed to narcotics and polar narcotics - isopropanol GSE29867: Daphnia magna exposed to narcotics and polar narcotics - methanol Refer to individual Series
2012-02-01 | E-GEOD-29993 | biostudies-arrayexpress
Project description:Age- and reproductive rejuvanation-related single-nuclei transcriptomics of Daphnia magna
| PRJNA1222346 | ENA
Project description:Background/Objectives: The waterflea Daphnia is an interesting candidate for biore- generative life support systems (BLSS). These animals are particularly promising be- cause of their central role in the limnic food web and its mode of reproduction. How- ever, the response of Daphnia to altered gravity conditions has to be investigated, especially on the molecular level, to evaluate the suitability of Daphnia for BLSS in space. Methods: In this study, we applied a proteomic approach to identify key proteins and pathways involved in the response of Daphnia to simulated microgravity gener- ated by a 2D-clinostat. We analysed 5 biological replicates using 2D-DIGE proteomic analysis. Results: We identified 109 protein spots differing in intensity (p < 0.05). Substan- tial fractions of these proteins are involved in actin microfilament organisation, in- dicating the disruption of cytoskeletal structures during clinorotation. Furthermore, proteins involved in protein folding were identified, suggesting altered gravity in- duced break-down of protein structures in general. In addition, simulated micro- gravity increased the abundance of energy metabolism related proteins, indicating an enhanced energy demand of Daphnia. Conclusion: The affected biological processes were also described in other studies using different organisms and systems either aiming to simulate microgravity con- ditions or providing real microgravity conditions. Moreover, most of the Daphnia protein sequences are well conserved throughout taxa, indicating that the response to altered gravity conditions in Daphnia follows a general concept.
2015-09-08 | PXD002096 | Pride
Project description:Determine gene expression in daphnia exposed to biotic and abiotic stressors. Identify in Daphnia pulex unique gene regulatory patterns involved in the regulation of limited phosphorous. One-condition experiment: Exposed Daphnia pulex for 5 days to phosphorous-limited algae. Biological replicates: 4 exposures, 4 nonexposed controls, grown and harvested in groups of 20 daphnia. One replicate per array.
2012-03-13 | E-GEOD-27959 | biostudies-arrayexpress