Ontology highlight
ABSTRACT:
PROVIDER: PRJNA836709 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19152336_1.fastq.gz | Fastqsanger.gz | |||
| SRR19152336_2.fastq.gz | Fastqsanger.gz | |||
| SRR19152337_1.fastq.gz | Fastqsanger.gz | |||
| SRR19152337_2.fastq.gz | Fastqsanger.gz | |||
| SRR19152338_1.fastq.gz | Fastqsanger.gz |
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Project description:Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements. In this study, the gene expression patterns across six tissues including leaves and roots at tillering stage and panicle elongation stage, leaves and young panicle at booting stage ( TL: leaves at tillering stage; TR: roots at tillering stage; PL: leaves at panicle elongation stage; PR: roots at panicle elongation stage; BP: young panicle at booting stage; BL: leaves at booting stage) were characterized by using the Affymetrix rice microarray platform based on a drought tolerant rice line derived from IR64.
2010-12-23 | E-GEOD-26280 | biostudies-arrayexpress
Project description:We generated a genome-wide map of 5hmC in rice panicle using a sensitive chemical labeling method to capture DNA fragments with 5hmC modification, followed by NGS sequencing. We showed that the 5hmC peaks distribution is non-random, about 52% 5hmC was located in gene bodies, 25% in intergenic regions, 11% in promoters, and 12% in immediate downstream. It was significantly enriched in heterochromatic regions of chromosomes 4 and 10, and especially located around TE genes. Combined with RNA-seq transcriptome data, we found that the gene-specific alterations of 5hmC can result in gene activation or repression, suggesting a potential role for 5hmC in gene regulation. From the compared distribution analysis among super-hybrid rice cultivars LYP9, and its parental lines 93-11 and PA64s, we investigated the cultivar-specificity of both the global levels and locus-specific distribution of 5hmC. Our data provided an overview of the genomic distribution of 5hmC in rice panicle. This will set the stage for further functional characterization of this novel DNA modification and its biosynthesis in rice. Examination of 5hmC modifications in rice panicle This submission represents ChIP-Seq component of study.
2014-04-15 | E-GEOD-37242 | biostudies-arrayexpress
Project description:To examine the rice genome methylation landscape and assess its functional significance, we generated the first single-base resolution genome methylation maps for Oryza sativa ssp. japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara. The methylation level of rice genomes is four times higher than that of Arabidopsis. Methylation in the promoter and gene body regions have similar patterns and effects on gene expression as those in Arabidopsis but different from a previous study on rice chromosomes 4 and 10. Most interestingly, we discovered for the first time that methylation in gene transcriptional termination regions can significantly repress gene expression, and the effect is even stronger than promoter methylation, which opens a new direction in the study of epigenetic regulation of gene expressions. Through integrated analysis of genetic, methylome and expression variation between cultivated and wild rice, we found that the genetic factor reflected by DNA variations may be the major determinant for methylation patterns at the whole-genome level and that methylation variation can only account for limited expression variation of genes between cultivated and wild rice. A single young panicle from each of the cultivated rice subspecies and the two wild rice species was ground in liquid nitrogen to fine powder using mortar and pestle. Total RNAs were isolated using the RNeasy Plant Mini Kit (Qiagen). DGE-tag libraries were constructed using the DGE-Tag Profiling NlaIII Sample Prep Kit (Illumina) according to the manufacturer's instructions. This submission represents the gene expression component of the study.
2011-11-04 | E-GEOD-20871 | biostudies-arrayexpress
Project description:The young panicles 2 cm length were used for expression analysis in well watered control and drought stressed treatment. The panicle samples from biological replicates of six rice varieties were obtained in three independent experiments. The expression profiles were generated using Affymetrix rice genome arrays.
2017-06-14 | GSE83378 | GEO
Project description:Transcriptional profiling of young leaves of rice (Oryza sativa) comparing control wild-type plants with transgenic plants transformed with a pBI-nptII-OsDDM1 gene. The latter makes the methylation level of the genomic DNA decreased. Goal was to determine the effects of decreased level of genomic DNA on global rice gene expression.
2012-10-02 | GSE31775 | GEO
Project description:rice young panicle Raw sequence reads
| PRJNA427770 | ENA