Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenetic characterization of carbon dots functions in rice

ABSTRACT: Epigenetic characterization of carbon dots functions in rice

PROVIDER: PRJNA782997 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17019568_1.fastq.gz	Fastqsanger.gz
	SRR17019568_2.fastq.gz	Fastqsanger.gz
	SRR17019569_1.fastq.gz	Fastqsanger.gz
	SRR17019569_2.fastq.gz	Fastqsanger.gz
	SRR17019570_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Epigenetic characterization of carbon dots functions in rice

Project description:Nanoparticles (NPs) can serve as efficient carriers for delivery of genetic materials in plants. They can regulate normal growth and development, and responses to stresses in plants. However, epigenetic mechanisms underlying NPs or carbon dots (CDs) affecting plant growth and development are still largely unknown. Here we showed that CDs reprogrammed gene transcription associated with some biological processes such as stress responses and photosynthesis. Moreover, CDs resulted in subtle but significant DNA hypermethylation, especially for CHG and CHH hypermethylation, which is possibly caused by CDs induced up-regulation of OsCMTs. Interestingly, we found that CDs stabilized i-motif in the promoter regions of OsCMTs1/2, therefore resulting in CHG and CHH hypermethylation. Thus, our study for the first time reveals possible mechanisms underlying impacts of CDs on cytosine context-dependent DNA methylation on a genome-wide scale, which may regulate genes responsible for CDs-induced phenotypic changes in plants. It will be helpful for considering future application of CDs in improving crop agronomic traits.

2024-11-23 | GSE189428 | GEO

Transcriptomic analyses reveal carbon dot-based seed priming in regulation of root growth in rice

Project description:Carbon dots (CDs) can affect plant growth and disease resistance and assist siRNA/DNA delivery. Salvia miltiorrhiza-Derived Carbon Dots were recently found to facilitate plants to adapt to environmental stresses through amplifying Ca2+ signaling and scavenging reactive oxygen species (ROS). More importantly, CDs can be degraded into CO2 and H2O within plant cells, thereby having fewer biosafety issues as compared to those undegradable ones and receiving more attentions in the plant community. However, the molecular mechanisms underlying effects of CD priming on plant growth and development have not been well characterized. In this study, we conducted transcriptomic assays and aim to reveal how CD priming affect root development through transcriptional reprogramming in rice.

2025-05-10 | GSE202652 | GEO

Transcriptome Profile of Quantum Dots on Saccharomyces cerevisiae

Project description:Transcriptome Profile of CdSe/ZnS and InP/ZnS Quantum Dots on Saccharomyces cerevisiae

2021-01-30 | GSE165805 | GEO

Microarray analysis of rice plants irradiated with carbon ion beams (HIMAC)

2008-03-29 | GSE9765 | GEO

Effect of Carbon Nanoparticle Treatment in Rice Adult plants

Project description:Carbon Nanoparticle (CNP, Graphite nano powder,Type 1, APS : 400 nm, Sisco Research Laboratories Pvt. Ltd. India ) was applied to roots of rice (Oryza sativa) plants (SWARNA (MTU7029) seeds were dehulled, surface genotype) in potted condition. The treatment was given in vegetative stage and the effect was noted in reproductive stage by taking several agronomic parameters. Experiment was repeated in 3 different seasons to take a conclusion.

2024-07-31 | GSE200357 | GEO

Transcription profiling of rice plants irradiated with carbon ion beams (HIMAC)

Project description:In this study, carbon-ion beams generated via the heavy-ion medical accelerator in Chiba (HIMAC) were targeted to growing rice seedlings (7-days-old) to examine their effect on this genome model. Both physiological parameters, such as growth, and molecular events, specially the gene expression profiles were examined immediately after irradiation (at 270 Gy dose) by rice oligo (22K) DNA microarrays. Genome-wide transcriptional profiling of radiation-response genes in rice provides us with first report on how our radioactive environment affects a plant species. Experiment Overall Design: An in vivo 7-days-old rice seedling model system was used, where whole seedlings were used for exposure to the emitted radiation from HIMAC (carbon ion beams). Dye-swap or reverse labeling with Cy3 and Cy5 dyes procedure was applied followed by hybridization and wash processes, and the hybridized microarrays (G4138A) were scanned using a GenePix microarray scanner followed by the Gene Pix 4000 analysis application program for image analysis and data extraction processes. The GeneSpring Ver. 4 software was used for normalization.

2008-06-16 | E-GEOD-9765 | biostudies-arrayexpress

Quantitative Analysis of erythroblast cells Transcriptomes treated with Carbon Dots(CDs) derived from Codonopsis pilosula or not

Project description:Quantitative Analysis of erythroblast cells Transcriptomes treated with Carbon Dots(CDs) derived from Codonopsis pilosula or not

| PRJNA1030350 | ENA

Effect of Carbon Nanoparticle Treatment in Rice Adult plants

Project description:Effect of Carbon Nanoparticle Treatment in Rice Adult plants

| PRJNA824303 | ENA

Integrated proteomics and metabolomics analysis of rice leaves in response to rice straw return

Project description:Straw return is crucial for the sustainable development of rice planting. To investigate the response of rice leaves to rice straw return, we analyzed the physiological index of rice leaves and measured differentially expressed protein (DEPs) and differentially expressed metabolites (DEMs) levels in rice leaves by the use of proteomics and metabolomics approaches. The results showed that, compared with no rice straw return, rice straw return significantly decreased the dry weight of rice plants and nonstructural carbohydrate contents and destroyed the chloroplast ultrastructure. In rice leaves under rice straw return, 329 DEPs were upregulated, 303 DEPs were downregulated, 44 DEMs were upregulated, and 71 DEMs were downregulated. These DEPs and DEMs were mainly involved in various molecular processes, including photosynthesis, carbon fixation in photosynthetic organisms, glycolysis, and the citric acid cycle. Rice straw return promoted the accumulation of osmotic adjustment substances, such as organic acids, amino acids, and other substances, and reduced the material supply and energy production of carbon metabolism, thus inhibiting the growth of rice.

2022-09-12 | PXD035835 | Pride

Characterization of G-quadruplexes in the rice genome

Project description:DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure functioning in various biological processes in mammals. G4 ChIP-seq assay, In this study, we developed a robust BG4-DNA ChIP-seq for global identification of DNA G4 in rice..We found that G4s harbored some functional motifs for binding of certain trans-factors, were co-localized with R-loops and DHSs in the rice genome. Importantly, G4s exhibited differential effects on DNA methylation between TE and non-TE genes in rice. Especially, G4 intensity-dependent enrichment occurred between DNA 5mC and 6mA.These DNA-related features suggest potential regulatory roles of G4 in rice. Thus, our study will pave the way for prompting intensive characterization towards identifying novel functions of G4 in plants, especially for agronomic important crops.

2021-07-01 | GSE132775 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data