Oryza sativa
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ABSTRACT:
PROVIDER: PRJNA138141 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In order to identify new miRNAs, NAT-siRNAs and possibly abiotic-stress regulated small RNAs in rice, three small RNA libraries were constructed from control rice seedlings and seedlings exposed to drought or salt stress, and then subjected to pyrosequencing.
2008-12-08 | GSE12317 | GEO
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: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.
2010-01-01 | GSE19050 | GEO
Project description:Purpose: The goal of our study is to compare two different ecotypes of Oryza sativa L., PHS-susceptible rice trait and PHS-resistant rice trait under three different maturation stages in rice seed embryo with profile of miRNA-seq. Methods: Oryza sativa. L miRNA profiles of two different ecotypes with 3 different maturation stages of rice seed embryo were generated by NGS, in duplicate, following Illumina NGS workflow. Results: We found the differentially expressed microRNAs between PHS-susceptible rice trait and PHS-resistant rice trait according to the three different seed maturation stages. Target transcripts of differentially expressed microRNAs have been predicted via psRNATarget web server, and a part of those target genes are likely to be regulated by microRNAs, affecting overall responses to heat stress and the regulation of seed dormancy during maturation. Conclusions: Our study represents the analysis of rice seed small RNAs, specifically microRNAs, under two different ecotypes, three different seed maturation stages in rice seed embryo. Our results show that microRNAs are involved in response to heat stress and the regulation of seed dormancy. This study will provide a foundation for understanding dynamics of seed dormancy during the seed development and overcoming pre-harvest sprouting.
2021-07-04 | GSE175561 | GEO
Project description:Genome-wide analysis for rice small RNAs by MPSS
| PRJNA107871 | ENA
Project description:In order to identify new miRNAs, NAT-siRNAs and possibly abiotic-stress regulated small RNAs in rice, three small RNA libraries were constructed from control rice seedlings and seedlings exposed to drought or salt stress, and then subjected to pyrosequencing. Totally three sets of small RNAs, which were obtained under normal condition as well as salt and drought stress conditions
2008-12-08 | E-GEOD-12317 | biostudies-arrayexpress
Project description:Genome-wide profiling of small RNAs in rice under abiotic stresses
| PRJNA136743 | 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: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 5M-bM-^@M-^Y rapid amplification of cDNA ends (RLM 5M-bM-^@M-^Y-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. The degradome sequence of Young inflorescences from Oryza sativa L. ssp. indica (93-11) was sequenced
2010-01-01 | E-GEOD-19050 | biostudies-arrayexpress