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ABSTRACT: Global study of mRNA in rice young panicle

PROVIDER: PRJNA836359 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19140391_1.fastq.gz	Fastqsanger.gz
	SRR19140391_2.fastq.gz	Fastqsanger.gz
	SRR19140392_1.fastq.gz	Fastqsanger.gz
	SRR19140392_2.fastq.gz	Fastqsanger.gz
	SRR19140393_1.fastq.gz	Fastqsanger.gz

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Project description:Global study of rice young panicle small RNA

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Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice

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:rice young panicle

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The drought-responsive gene expression in rice panicle

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

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine in rice

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

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Project description:RNA-Seq of rice young panicle

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Project description:rice young panicle Raw sequence reads

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Identification of downstream genes regulated by OsMADS2

Project description:To gain mechanistic insights on OsMADS2 functions in rice spikelet development, we have employed global expression profilling to identify the genes regulated by OsMADS2. Transgenic rice panicle RNAs were compared with the wild type panicle RNA of similar developmental stage. Genes downregulated in transgenic lines will be those which expression requires functional OsMADS2 whereas upregulated genes will need OsMADS2 for their repression. Keywords: Comparative expression profile analysis

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