Oryza sativa Indica Group
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ABSTRACT:
PROVIDER: PRJNA300502 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Abiotic environmental stresses cause serious economic losses in agriculture. These stresses include temperature extremes, high salinity and drought. To isolate drought-responsive novel coding and noncoding genes, we used the next generation sequencing method from three rice cultivars (wild type nipponbare, nipponbare AP2 transgenic plants, wild type vandana). 36 NGS data of mRNA-seq, small RNA-seq, riboZero-seq were analyzed. For the analyses of these data we constructed a TF-TG (Transcription Factor-Target Gene) network and an ap2 rooted cascading tree. Using these networks and tress we isolated lincRNAs, differentially expressed miRNAs and their targets. We identified several drought stress-related novel/function unknown coding transcripts (transcription factors and functional genes) and non-coding transcripts (small noncoding transcripts such as microRNA and long noncoding transcripts) from these database analyses and have constructed databases of drought stress-related coding and noncoding transcripts Identification of drought-responsive Regulatory Coding and Non-coding Transcripts from rice by deep RNA sequencing
2016-09-06 | E-GEOD-74465 | biostudies-arrayexpress
Project description:Abiotic environmental stresses cause serious economic losses in agriculture. These stresses include temperature extremes, high salinity and drought. To isolate drought-responsive novel coding and noncoding genes, we used the next generation sequencing method from three rice cultivars (wild type nipponbare, nipponbare AP2 transgenic plants, wild type vandana). 36 NGS data of mRNA-seq, small RNA-seq, riboZero-seq were analyzed. For the analyses of these data we constructed a TF-TG (Transcription Factor-Target Gene) network and an ap2 rooted cascading tree. Using these networks and tress we isolated lincRNAs, differentially expressed miRNAs and their targets. We identified several drought stress-related novel/function unknown coding transcripts (transcription factors and functional genes) and non-coding transcripts (small noncoding transcripts such as microRNA and long noncoding transcripts) from these database analyses and have constructed databases of drought stress-related coding and noncoding transcripts
2016-09-06 | GSE74465 | GEO
Project description:Drought responsive transcriptome profiling in roots of contrasting rice genotypes IR20 and Nootripathu
| PRJNA359110 | ENA
Project description:Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species (Oryza sativa cv. Nipponbare and Oryza glaberrima cv. CG14) and an endemic, perennial Australian wild species (Oryza australiensis) were grown in soil at 40% field capacity for 7-d (drought). The hypothesis was that the natural tolerance of O. australiensis to erratic water supply would be reflected in a unique proteomic profile. Leaves from droughted plants and well-watered controls were harvested for label-free quantitative shotgun proteomics. Physiological and gene ontology analysis confirmed that O. australiensis is responded uniquely to drought, with superior leaf water status and enhanced levels of photosynthetic proteins. Moreover, distinctive patterns of expression of proteins in drought were observed across the entire O. australiensis proteome. An intermediate impact of drought on photosynthetic and stress-response proteins is reported in O. glaberrima relative to O. sativa but the drought response was most striking in O. australiensis. For example, photosynthetic proteins decreased when O. sativa after drought, while a narrower range of stress-responsive proteins was up-regulated. Distinctive proteomic profiles and the expression levels of individual proteins with specific functions in response to drought in O. australiensis indicate the importance of this species as a source of stress tolerance genes.
2021-09-09 | PXD019885 | Pride
Project description:Oryza sativa Indica group IR29 (salt sensitive) seedlings were subjected to salt stress or control conditions and sampled at five time points over the course of 24 hours. RNA samples extracted were assayed using the Illumina HiSeq 2000 platform.
2017-10-02 | E-MTAB-1913 | biostudies-arrayexpress
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
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:Oryza sativa Indica group Pokkali (salt sensitive) seedlings were subjected to salt stress or control conditions and sampled at five time points over the course of 4 hours. RNA samples extracted were assayed using the Illumina HiSeq 2000 platform.
2020-01-01 | E-MTAB-1914 | biostudies-arrayexpress
Project description:Global gene expression analysis of AtDREB1A transgenic rice line (TL4) at reproductive stage under drought stress was conducted using microarray to explore the drought stress-responsive transcription pathways. Drought stress was imposed at late vegetative stage till booting of the plants. Flag leaf was collected on 14th day of the drought stress. Drought stress was imposed on T3 plants of two homozygous transgenic rice events of PS2 and NT plants by withholding irrigation for 14 days in the National Phytotron Facility, IARI.
2018-04-29 | E-MTAB-5700 | biostudies-arrayexpress
Project description:Recently, we demonstrated that RDRs had a general function to synthesize antisense RNAs from sense transcripts of protein-coding genes. In this study, we analyzed whether RDR-mediated antisense RNAs were processed into small RNAs by deep sequencing using SOLiD. Deep sequencing identified 1,645 RDR1/2/6-mediated smRNA loci in drought stress and control conditions.
2017-07-13 | GSE39024 | GEO