Oryza sativa
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ABSTRACT:
PROVIDER: PRJNA257965 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this study, we aim to generate genome-scale DNA methylation profiles at single-base resolution in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. Using high-throughput whole genome bisulfite Sequencing, we generated DNA methylation maps covering the vast majority of cytosines in the rice genome. More than 152 million high quality reads were obtained for each tissue sample using Illumina platform. We discovered extensive DNA methylation in rice cultivars, identified the context and level of methylation at each site.Numerous differentially methylated regions (DMRs) among different cultivars under control and stress conditions were identified and many of them were associated with differential gene expression. The high resolution methylome maps of different rice genotypes and differentially methylated regions will serve as reference for understanding the epigenetic regulation of stress responses in plants. Whole genome bisulfite sequencing of seven control/stressed samples from three rice cultivars (IR64, N22 and Pokkali)
2015-12-31 | E-GEOD-60288 | biostudies-arrayexpress
Project description:In this study, we aim to generate genome-scale DNA methylation profiles at single-base resolution in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. Using high-throughput whole genome bisulfite Sequencing, we generated DNA methylation maps covering the vast majority of cytosines in the rice genome. More than 152 million high quality reads were obtained for each tissue sample using Illumina platform. We discovered extensive DNA methylation in rice cultivars, identified the context and level of methylation at each site.Numerous differentially methylated regions (DMRs) among different cultivars under control and stress conditions were identified and many of them were associated with differential gene expression. The high resolution methylome maps of different rice genotypes and differentially methylated regions will serve as reference for understanding the epigenetic regulation of stress responses in plants.
2015-12-31 | GSE60288 | GEO
Project description:Floral organs are extremely sensitive to stress during anthesis and lead to severe yield loss. Rice anthers and pollinated pistils of two cultivars with contrasting tolerance to heat and drought stress under variable conditions, including control, heat, combined heat and drought stress, were used to explore gene expression pattern in male and female reproductive organs during anthesis under control and stress conditions. More gene regulation was induced by combined drought and heat stress than heat in anthers of both cultivars. N22 showed less regulation under combined stress than Moroberekan. The overlap of regulated genes between two cultivars was rather low, indicated the distinct molecular stress responses. We used whole genome microarrays to explore gene expression pattern and molecular mechanisms in male and female reproductive organs during anthesis under control and stress conditions in two rice cultivars, sought to identify the key transcripts that play roles in inducing heat and drought tolerance during reproduction in rice.
2015-05-31 | GSE57154 | GEO
Project description:In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample.
2015-12-31 | GSE60287 | GEO
Project description:Transcript and metabolite profiling were performed in leaf segments (sheath, base, middle, tip) of six rice cultivars with different sensitivity to high night temperatures (HNT). On the phenotypic level, leaves of HNT-sensitive rice cultivars showed clear stress symptoms by chlorosis and necrosis while almost no leaf phenotype different from the control was observed for the tolerant varieties. The aim of this study was to identify molecular key-player for HNT-sensitivity causing leaf senescence.
2021-09-27 | GSE179662 | GEO
Project description:A heat and drought tolerant rice cultivar (N22) was grown in the field under control and drought conditions during the dry season in 2013. Drought was applied during early grain filling and resulted in simultaneous heat stress, leading to reduced grain yield and quality. Total RNA was extracted from developing seeds under stress and control (fully flooded) conditions and RNA-seq analysis was performed. These samples are a part of a bigger experiment analysing the responses of three contrasting rice cultivars (N22, Dular, Anjali) to combined heat and drought stress including different organs (developing seeds, flag leaves, flowering spikelets) and developmental stages (early grain filling, flowering) at the transcriptomic level.
2020-11-04 | GSE153030 | GEO
Project description:To improve our understanding of the relationships between methylation and expression we profiled mRNA expression and single-base resolution methylation levels for two breast cancer cell lines, MCF7 and T47D. Expression was profiled using RNA-seq. Methylation was assayed using Methyl-MAPS, which uses methylation-sensitive and -dependent restriction enzyme digests followed by high-throughput sequencing to identify methylation levels at individual CpGs (Edwards et al. 2010, Genome Research). RNA-Seq was used to generate mRNA expression profiles of MCF7 and T47D cells under standard growth conditions.
2013-06-15 | E-GEOD-45335 | biostudies-arrayexpress
Project description:In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample. We collected seedlings of three rice cultivars subjected to control (kept in water), desiccation (transferred on folds of tissue paper) and salinity (transferred to beaker containing 200 mM NaCl solution) treatments. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequence data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to Japonica reference genome using Tophat software. Cufflinks was used for reference-based assembly and differential gene expression was studied using cuffdiff software. The differentially expressed genes during various abiotic stress conditions were identified.
2015-12-31 | E-GEOD-60287 | biostudies-arrayexpress
Project description:Rice is susceptible to both heat and drought stress, in particular during flowering and grain filling, when both grain yield and quality may be severely compromised. However, under field conditions, these two stresses rarely occur separately. Under well-watered conditions, plants avoid heat stress by transpirational cooling, while this is not possible under drought conditions. Although investigating combined heat and drought stress is clearly more agronomically relevant than analyzing the effects of the single stresses, only a few studies of this stress combination, in particular under field conditions, have been published. Furthermore, little is known about how plants respond during recovery from drought stress, which also determines plant survival. To address these knowledge gaps, three rice cultivars differing in heat and drought tolerance were grown in the field under control and drought conditions in three consecutive years. Drought was applied either during flowering or during early grain filling, resulting in simultaneous heat stress, leading to reduced grain yield and quality. Analysis by gas chromatography-mass spectrometry (GC-MS) showed distinct metabolic profiles for the three investigated organs (flag leaves, flowering spikelets, developing seeds). The metabolic responses of the plants also strongly differed between cultivars and organs, and between stress and rewatering conditions. Correlation analysis identified potential metabolic markers for grain yield and quality under combined heat and drought stress from stress- and rewatering-regulated metabolites and from metabolites with constitutive differences between the cultivars. These results show that GC-MS can resolve metabolic responses to combined heat and drought stress and subsequent rewatering in different organs of field-grown rice. The metabolite profiles can be used to identify potential marker metabolites for yield stability and grain quality that are expected to improve breeding efforts towards climate change resilient rice.
2019-04-25 | MTBLS801 | MetaboLights
Project description:Here, we reported transcriptome-wide m6A modification maps within single-base resolution using m6A-SAC-seq in rice and Arabidopsis. Our analysis uncovered a total of 205,691 m6A sites distributed across 22,574 genes in rice, and 188,282 m6A sites across 19,984 genes in Arabidopsis.
2024-04-19 | GSE243722 | GEO