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ABSTRACT:
PROVIDER: PRJNA872349 | 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:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone H3 trimethylation in rice endosperm. By obtaining about four hundred million bases of sequence from rice chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of rice endosperm. We find that the presence of H3K27me3 in either upstream or downstream of a gene is predominately associated with repression of the gene, while its absence is mainly associated with high gene expression. Examination of Histone H3 lysine 27 trimethylation in rice endosperm.
2011-12-06 | E-GEOD-27048 | biostudies-arrayexpress
Project description:In this study, we provide a global overview of genome-wide OsHOX24 binding sites in rice under control and desiccation stress conditions in wild-type and OsHOx24 overexpressing rice plants (H49 line) via chromatin immunoprecipitation sequencing (ChIP-sequencing) approach. We identified numerous downstream targets of OsHOX24 under desiccation stress and control by analyzing the comprehensive binding site map of OsHOX24 at whole genome level in rice.
2021-04-04 | GSE144419 | GEO
Project description:There are multiple types of small RNAs that may affect rice pollen’s development. To investigate the small RNA populations’ change during rice pollen development, 13-40 nt RNA were extracted from uninucleate microspores (UNM) and bicellular pollen (BCP) for high throughput sequencing. Together with our laboratory’s previous published rice tricellular pollen (TCP) small RNA sequencing data (GSM722128), sharp increase of tRNA fragments (tRFs) in BCP stage and a slightly decreased tRFs in TCP were found. Among which, new lengths of tRFs were also discovered. Our work accomplished the knowledge about tRFs in rice pollen development.
2017-09-01 | GSE101998 | GEO
Project description:We report the application of methylacytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq) for high-throughput profiling of DNA methylation in rice embryo 3, 6, 9 DAP and endosperm 2, 3, 6, 9 DAP. A total number of 12-14 million of 2×49 bp paired-end reads was generated for each sample, and BOWTIE2 was used for read mapping. We generated genome-wide DNA methylation profiles of rice embryo and endosperm. This study provides a framework to systemically characterize the effect of DNA methylation in developing seeds and will help to illustrate the epigenetic regulation of rice seed development. Rice embryo and endosperm were selected for DNA extraction and methylacytosine immunoprecipetation combined with Illumina sequencing. We sought to obtain the genome-wide DNA methylation profilings of embryo at 3,6,9 days after pollination(DAP) and endosperm at 2,3,6,9 DAP. To that end, we hand-selected embryo at 3,6,9 DAP and endosperm at 2,3,6,9 DAP according to morphological criteria.
2015-09-01 | E-GEOD-57706 | biostudies-arrayexpress
Project description:The expanding scale and nature of rice fraud in the global food system has caused major economic and human health concerns. Herein, an untargeted metabolomics approach based on the UHPLC-Q-Orbitrap-HRMS system was utilized for the discrimination between authentic and commercial Sengcu rice, a local specialty cultivated by terraced farming in northern Vietnam. A total of 8398 positive and 5250 negative mode compounds were introduced to multivariate statistical analyses for the construction of classification models. The first two principal components explaining 52% of the total variance in both datasets exhibited distinguished clusters of authentic against commercial Sengcu rice. Partial least squares-discriminant analysis models were optimized to obtain the optimal number of retained components, the optimal number of variables retained in each component and the best prediction distance type for model evaluation. One component containing five positive (DMG, RSA, RCA, PAL and BOSe) and six negative mode variables (PXP, RXP, TDHP, ISS, MXP and RGB) was sufficient to discriminate between authentic and commercial Sengcu rice. The classification error rate was less than 1.1310-4, as determined from repeated k-fold cross validation. These putative signature metabolites clearly separated authentic and commercial Sengcu rice in the hierarchical clustering models. In addition, the isolated metabolites also reflected the cultivation practices of terraced farming of authentic Sengcu rice. Overall, we have proposed an effective method for the identification of key metabolites from fingerprinting metabolomics, and it could serve as a fundamental approach for other in-depth food authentication studies.
2022-05-08 | ST002169 | MetabolomicsWorkbench
Project description:IDS1 is a rice AP2-type transcription factor with transcritpional repression activity. To understand how IDS1 regulate rice salt tolerance, the ChIP-seq experiments were performed to identify IDS1 binding site in globle genomic level. The two-weeks-old rice seedlings were lysated and sonificated and IDS1-DNA complexes were immune precipated with myc-antibody and protein A beads. The purified DNA samples were used to construct sequencing libraries and sequenced with Illumina. The data were then analyzed with bio-informatic tools.
2018-04-30 | E-MTAB-6504 | biostudies-arrayexpress
Project description:Rice NF-YC11 is a transcription factor that plays a key regulatory role in storage substance accumulation during rice grain filling. To reveal the transcription regulatory network of NF-YC11 in rice, we performed genome-wide identification of NF-YC11 targets by immunoprecipitation sequencing (ChIP-seq) analyses in the NF-YC11-overexpression plants.
2019-08-21 | GSE119575 | GEO
Project description:Purpose: To understand the miRNAome changes during coleoptile senescence, small RNA libraries were constructed from control and senescence tissues and subjected to Illumina sequencing. Methods: Rice seeds were surface sterilized and submerged for seven days in sterile water. The seeds with coleoptile was transferred to aerobic condition. Senescence progression was monitored and tissues of un-senesced and senesced coleoptiles were harvested. Total RNA was isolated from the harvested tissues. Total four small RNA libraries of coleoptile senescence were constructed and high-throughput sequencing was performed using Illumina GA IIx system . . Results: Small RNA sequencing identified forty-one known and twenty-one novel miRNAs that were differentially expressed during coleoptile senescence. Integration of expression data of transcriptome and miRNAome identified 148 miRNA-mRNA modules, mainly comprised of miRNAs regulating TFs, signaling-associated factors and transporters, thereby demonstrating multi-tiered regulation of coleoptile senescence. Conclusions: The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.
2022-07-21 | GSE199238 | GEO