Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1238082 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32767052_1.fastq.gz | Fastqsanger.gz | |||
| SRR32767052_2.fastq.gz | Fastqsanger.gz | |||
| SRR32767053_1.fastq.gz | Fastqsanger.gz | |||
| SRR32767053_2.fastq.gz | Fastqsanger.gz | |||
| SRR32767054_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goals of this study are to compare differentially expressed transcripts in roots and leaves of spinach cultivars with distinct oxalate contents using transcriptome profiling (RNA-seq)
2021-05-18 | GSE146711 | GEO
Project description:Purpose: To examine the gene expression within the spinach root tissues as a response to exposure to nanoparticles. Methods: Sequenced reads were processed using CLC Genomics Workbench 7.0. The reads were trimmed based on quality, length and ambiguity. Resulting reads were assembled into transcript assemblies. Sequence reads were mapped back to the constructed transcriptome. TAs were BLAST searched against a local blast database of coding sequences of Arabidopsis thaliana. Statistical analysis was performed using Baggerley’s test. Transcript assemblies were tested for gene enrichment using GO annotations and the functional categories were determined. MapMan was used to visualize gene expression data of TAs and study the biological pathways. Results: De novo assembly of the trimmed reads yielded 147,733 Transcript Assemblies (TA) with an average length of 645 bp. Largest TA was 16,379 bp. Approximately 89% of the quality trimmed reads from the different samples mapped successfully to the assembly reference. Gene expression data for spinach TAs homologous to Arabidopsis genes show upregulation of protein degradation pathways in the nano-ZnO treatment compared to the non-nanoZnO, this upregulation is coupled with a down regulation of the genes in the protein synthesis pathways crucial role in the spinach plant responses to ZnO nanoparticle exposure. Genes associated (REDOX, signaling and transcription factors) with responses to stresses (both abiotic and biotic) were upregulated upon exposure to ZnO nanoparticles. Additionally genes in biosynthesis pathways of jasmonate and gibberellins genes were up-regulated upon exposure to ZnO nanoparticles in spinach. Conclusions: A de novo transcriptome was developed for spinach. When spinach plants were exposed to ZnO nanoparticles, they seem to sense the nanoparticles similarly to external chemicals or pathogens and induced production of reactive oxygen species. Hormone signaling pathways were activated leading to the induced expression of hormones with different roles in defense.
2018-09-10 | GSE72912 | GEO
Project description:The 20-hydroxyecdysone (20E) hierarchy of gene activation serves as an attractive model system for studying the mode of steroid hormone regulated gene expression and development. Primary genes are activated by the direct action of the hormone and often code for proteins with regulatory function, some of which are responsible for the perpetuation of the response through the activation of secondary genes. Here we identify 35 primary 20E-response genes that are induced by 20E in the absence of protein synthesis in the embryonic cell line Kc167, and of those with known functions, most encode proteins with catalytic activity. Comparison of the genome-wide transcriptional response to 20E and to its plant derived structural analog ponasterone A (PoA) revealed a large difference in the transcriptional targets of these molecules. Despite the structural similarity of these two compounds, many more genes related to various aspects of development appear to be significantly induced by 20E than by PoA. Furthermore, we compared the 20E response in Kc cells to that of a natural 20E target tissue where the function of 20E has been well described, the salivary glands of wandering 3rd instar larvae, and found little overlap in 20E-responsive genes. Analysis of 20E-induced transcription of EcR, a known 20E-inducible gene and regulator of early and late 20E-responsive genes, reveals differences in the fold induction of EcR isoforms EcR-RA, ER-RC, and EcR-RD/E between Kc cells and salivary glands suggesting a possible cause for the observed differences in 20E-regulated gene transcription.
2011-12-01 | GSE23928 | GEO
Project description:Transcriptome analysis of Sonicated Spinach
| PRJDB10558 | ENA
Project description:The current work describes molecular mechanism used by the Negative elongation complex (NELF) to control the Pol II pause at genes whose transcription is induced by 20-hydroxyecdysone (20E). According to our data NELF complex is recruited to the promoters and enhancers of 20E-dependent genes. Its presence at the regulatory sites of 20E-dependent genes correlates with the described interaction of its NELF-A subunit with EcR receptor. The NELF complex, consisting of at least three subunits, is formed at the 20E-dependent promoters and participates in their active transcription and maintenance of their repressed state. NELF depletion causes a significant decrease in transcription induced by 20E. We associate this effect with the disruption of Pol II elongation complexes formation. A considerable reduction in the promoter-bound level of Spt5 subunit of DSIF was observed at the 20E-dependent genes upon NELF depletion. We presume that participation in stabilization of the Pol II-DSIF complex can be an important function of NELF with a big impact on transcription of its target genes. Part of our study was to directly link NELF to regulation of 20E-dependent genes in development. We showed presence of NELF at the promoters of 20E-dependent genes during their active transcription both in embryogenesis and metamorphosis. We also demonstrate that 20E-dependent promoters remain in a Pol II paused state at the larva stage, where they are temporarily repressed.
2021-01-10 | GSE156847 | GEO
Project description:To perform mRNA expression analysis through deep sequencing, RNA was isolated from prostate mice treated with normolipidic diets based on linseed oil, soybean oil or lard (varying saturated and unsaturated FA contents and ω-3/ω-6 ratios (ω ratio) for 12 or 32 weeks after weaning
2020-04-14 | GSE131143 | GEO
Project description:Transcriptional activation by 20-hydroxyecdysone (20E) in Drosophila provides an excellent model for studying tissue-specific response to steroids. An increase in 20E titer controls degradation of larval and proliferation of adult tissues during metamorphosis. To study 20E-dependent transcription, we used the natural system for controlling the 20E titer – E23 membrane transporter, which exports 20E from the cell. We artificially expressed the E23 in tissues to suppress the first wave of 20E-inducible transcription at metamorphosis. Expression of E23 revealed a plethora of 20H dependent genes in salivary glands, but mildly affected the transcription in brain/eye-antennal discs. We described the mechanisms controlling the transcriptional activation by 20E in Drosophila salivary glands. 20E depletion caused a decreased binding of Pol II and TFIID subunit, TBP, to target promoters, demonstrating 20E role in the stimulation of transcription initiation. At the target loci 20E depletion resulted in a malfunctioning of sites co-bound with EcR and CBP/Nejire and enriched with H3K27Ac histone mark inherent to active enhancers. At these sites, 20E titer was found to control chromatin accessibility and acetylation. We presume that the activity of these ‘active’ ecdysone-sensitive elements – (ESEs) is responsible for an active status of 20E targets in the salivary glands of wandering larvae.
2025-03-31 | GSE260939 | GEO
Project description:RNA-Sequencing of spinach tissues with contrasting oxalate contents
| PRJNA611735 | ENA
Project description:Insects, unlike vertebrates, are generally believed to lack steroid hormones with functions predominantly associated with adult male biology. In the malaria mosquito Anopheles gambiae, the ecdysteroid 20-hydroxyecdysone (20E) appears to both control egg development in females and induce mating refractoriness and oviposition when sexually transferred by males. Here we show that these sex-specific functions are instead carried out by distinct steroids. We identify a male-specific oxidized form of 20E (3D20E) that upon sexual transfer switches off female mating receptivity, ensuring male paternity. Endogenous female 20E does not induce mating refractoriness, while it triggers oviposition in mated females when expression of a 20E-inhibiting kinase is repressed. 3D20E and 20E have different downstream targets, with 3D20E inducing expression of a tolerance factor that preserves female fitness during Plasmodium infection. The evolution of this male steroid has therefore not only shaped the mating biology of An. gambiae, but also impacted malaria transmission.
2022-04-21 | PXD032157 | Pride