Oryza sativa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA357146 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5110430.fastq.gz | Fastqsanger.gz | |||
| SRR5110440.fastq.gz | Fastqsanger.gz | |||
| SRR5110450.fastq.gz | Fastqsanger.gz | |||
| SRR5110460.fastq.gz | Fastqsanger.gz | |||
| SRR5110431.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 32 |
Similar Datasets
Project description:Temporal analysis of mRNA from panicle tissue from field grown rice
2023-06-15 | E-GEOD-92302 | ExpressionAtlas
Project description:Temporal analysis of mRNA from leaf tissue in field grown rice
| PRJNA667622 | ENA
Project description:Transcriptome analysis of field grown rice
| PRJDB12927 | ENA
Project description:Changes in patterns of gene expression are believed to be responsible for the phenotypic differences within and between species. Although the evolutionary significance of functional mutations has been emphasized in rice domestication, little is known about the differences in gene regulation underlying the phenotypic diversification among rice varieties. MicroRNAs (miRNAs) are small regulatory RNAs that play crucial roles in regulating post-transcriptional gene expression. Here, we studied the variation in the expression of both miRNAs and mRNA transcripts in three indica and three japonica rice varieties using RNA sequencing (RNA-seq) to examine the miRNA regulatory effect on target gene expression in rice. In total, 71.0%, 9.2%, and 1.5% of the expressed mature miRNAs showed tissue, subspecies, and tissue-subspecies interaction-biased expression. Most of these differentially expressed miRNAs are evolutionarily weakly conserved. To examine the miRNA regulatory effect on global gene expression under endogenous conditions, we performed pair-wise correlation coefficient analyses on the expression levels of 240 mature miRNAs and 1178 messenger RNAs (mRNAs) both globally and for each specific miRNA-mRNA pair. We found that the deeply conserved miRNAs can significantly decrease the target mRNA abundance. In addition, a total of 109 miRNA-mRNA pairs were identified as significantly correlated pairs (Adjusted p<0.01). Of those, 41 pairs showed positive correlations, while 68 pairs showed negative correlations. Functional analysis elucidated that these mRNAs belonged to different biological pathways that could regulate the stress response, metabolic processes, and rice development. In conclusion, the joint interrogation of miRNA and mRNA expression profiles in this study proved useful for the study of the role of miRNA expression and regulation in the plant transcriptome.
2017-02-09 | GSE71925 | GEO
Project description:RNAseq analysis on mature leaf tissue of 60 individual B104 maize inbred plants grown in the field
2020-12-09 | E-MTAB-8944 | ExpressionAtlas
Project description:The small RNAs presented here were produced as a preliminary exploration of small RNAs in rice, and as such, various tissues and stress conditions were sampled. Small RNAs present in these samples were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682. The datasets contain Oryza sativa var Nipponbar endogenous small RNA sequences in the size range 18 to 34 nt. Plants were grown in a Conviron Environmental Chamber at high light intensity using both high pressure sodium and metal halide lamps for 10.5 hr at 28 degrees C and for 13.5 hr at 26 degrees C in the dark. RNA was extracted from rice tissues at various stages of development and under different abiotic and biotic stresses. The small RNAs presented here were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682.
2009-06-08 | GSE16248 | GEO
Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.
2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress
Project description:Rice anthers at the anthesis stage were collected from the wild type (Dongjin cultivar) and far1-1 mutant grown in the paddy field located in the KyungHee University. The collected samples were immediately frozen with liquid nitrogen. RNA from these samples was extracted with RNeasy plant mini kit according to the manufacture's documentation.
2022-12-31 | E-MTAB-10106 | biostudies-arrayexpress
Project description:Rice blast is one of the most serious diseases and is caused by Magnaporthe grisea. SHZ-2, an indica cultivar with broad spectrum resistance to multiple races of the blast pathogen, was crossed to TXZ-13, a blast susceptible but high-quality variety, to produce one BC3 line, BC10 line, which showed strong to moderate blast resistance over eight cropping seasons in the field. In this study, we compared the transcription between blast-resistant and -susceptive lines by custom microarray. Keywords: time course, blast infection, disease response Comparison between blast- and mock-infected rice. Biological replicates: 3 control (mock) and 3 blast-infected at each time point, independently grown and harvested at 24 and 48 hours after inoculation. Each sample was prepared with whole plant 5 cm above ground and was pooled from 5 plants grown under the same conditions.
2011-05-31 | E-GEOD-16470 | biostudies-arrayexpress
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