Oryza sativa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA858547 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20255800_1.fastq.gz | Fastqsanger.gz | |||
| SRR20255800_2.fastq.gz | Fastqsanger.gz | |||
| SRR20255900_1.fastq.gz | Fastqsanger.gz | |||
| SRR20255900_2.fastq.gz | Fastqsanger.gz | |||
| SRR20256000_1.fastq.gz | Fastqsanger.gz |
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Project description:In this study, we examined the transcriptome dynamics within the matured fully expanded rice leaf and used strand-specific RNA sequencing to generate a comprehensive transcriptome dataset for the mature rice leaf. The rice Nipponbare (Oryza sativa l. japonica) seedlings were grown in the greenhouse. About 20 days after planting, the fully opened 4th leaves was cut it into seven 3-cm segments, from bottom to tip and labeled as sections 1 to 7, respectively. The tissues were immediately frozen in liquid nitrogen for total RNA extraction. Two biological replicates were collected for each section. Note: All samples in SRA were assigned the same sample accession (SRS685294). This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
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Project description:To understand the dynamics and global gene reprogramming in the early response to mechanical wounding in rice, the transcriptional response to mechanical injury was analyzed. A time-course experiment revealed the highly dynamic nature of the wound response in rice. Mechanical wounding triggered extensive gene expression reprogramming in the locally wounded leaf, affecting various physiological processes, including defense mechanisms and potentially tissue repair and regeneration. The rice response to mechanical wounding displayed both differences and similarities compared to the response to jasmonate treatment. These results highlight the importance of early JA signaling in response to mechanical stress in rice. This analysis provides an overview of the global transcriptional response to mechanical stress in rice, offering valuable insights for future studies on rice's response to injury, insect attack, and abiotic stresses.
2024-10-21 | GSE279814 | GEO
Project description:Arsenic (As) is a carcinogenic metalloid that is a contaminant widely polluting rice paddy soils around the world. In order to gain better insight into molecular mechanism of rice exposed to As(III) stress, we used next-generation sequencing technology to acquire global transcriptome alteration and miRNA regulation in rice upon As(III) treatments. Our results suggest time course and As(III)-dosing treatments were devised. Cluster analyses show that root and shoot samples were differentially grouped. For roots, sub-clusters were more distinct in the dosage course whereas for shoots they were most recognizable for the time course treatments. Other than the significantly regulated gene expression in the heavy metal-responsive sulfur and glutathione metabolism pathways, the expression of genes related to heavy metal transportation, jasmonate biosynthesis and signaling pathways, lipid metabolism and gene transcription were sharply regulated, indicating that rice allocates energy and resources from growth to stress response under As(III) stress. In addition to the detection of previously identified stress-related miRNAs, we further discovered 36 new As(III)-responsive miRNAs. These results expand our understanding of As(III) stress mechanism to the As(III)-responsive mRNA and miRNA transcriptomes, which provide a foundation for subsequent functional research.
2013-01-09 | GSE36696 | GEO
Project description:Arsenic (As) is a carcinogenic metalloid that is a contaminant widely polluting rice paddy soils around the world. In order to gain better insight into molecular mechanism of rice exposed to As(III) stress, we used next-generation sequencing technology to acquire global transcriptome alteration and miRNA regulation in rice upon As(III) treatments. Our results suggest time course and As(III)-dosing treatments were devised. Cluster analyses show that root and shoot samples were differentially grouped. For roots, sub-clusters were more distinct in the dosage course whereas for shoots they were most recognizable for the time course treatments. Other than the significantly regulated gene expression in the heavy metal-responsive sulfur and glutathione metabolism pathways, the expression of genes related to heavy metal transportation, jasmonate biosynthesis and signaling pathways, lipid metabolism and gene transcription were sharply regulated, indicating that rice allocates energy and resources from growth to stress response under As(III) stress. In addition to the detection of previously identified stress-related miRNAs, we further discovered 36 new As(III)-responsive miRNAs. These results expand our understanding of As(III) stress mechanism to the As(III)-responsive mRNA and miRNA transcriptomes, which provide a foundation for subsequent functional research. 10 mRNA samples examined 10 miRNA samples examined
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Project description:We used RNA-Seq to systematically investigate the global transcriptomes of rice which was inoculated with viruliferous SBPH, or inoculated with insect-derived RSV or plant-derived RSV by mechanical inoculation, and generated a useful resource for the immune reaction of rice in face of different kinds of RSV. The changes in the expression of candidate transcripts may provide valuable information for future studies on molecular mechanisms of rice stripe disease.
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Project description:A biological phenomenon in which hybrids exhibit superior phenotypes from its parental inbred lines known as heterosis, has been widely exploited in plant breeding and extensively used in crop improvement. Hybrid rice has immense potential to increase yield over other rice varieties and hence is crucial in meeting increasing demand of rice globally. Moreover, the molecular basis of heterosis is still not fully understood and hence it becomes imperative to unravel its genetic and molecular basis. In this context, RNA sequencing technology (RNA-Seq) was employed to sequence transcriptomes of two rice hybrids, Ajay and Rajalaxmi, their parental lines, CRMS31A (sterile line, based on WA-CMS) and CRMS32A (sterile line based on Kalinga-CMS) respectively along with the common restorer line of both hybrids, IR-42266-29-3R at two critical rice developmental stages viz., panicle initiation (PI) and grain filling (GF). Identification of differentially expressed genes (DEGs) at PI and GF stages will further pave the way for understanding heterosis. In addition, such kind of study would help in better understanding of heterosis mechanism and genes up-regulated and down-regulated during the critical stages of rice development for higher yield.
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Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5’ rapid amplification of cDNA ends (RLM 5’-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice.
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