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Oryza sativa Japonica Group

ABSTRACT: Genome sequencing analysis of a japonica rice (Oryza sativa) variety, 'Kitaake'

PROVIDER: PRJDB12738 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	DRR333428_subreads.fastq.gz	Fastqsanger.gz
	DRR333429_subreads.fastq.gz	Fastqsanger.gz

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Oryza sativa Japonica cultivar:Kitaake Transcriptome or Gene expression

Project description:RNA-seq of Oryza sativa Japonica cultivar Kitaake

2015-02-11 | E-MTAB-4326 | biostudies-arrayexpress

RNA-Seq analysis of Oryza sativa, ssp. japonica, cv. Kitaake leaves from plants lacking carbonic anhydrase in the chloroplast

Project description:The aim of this experiment was to assess the impact on the transcriptome of relocalisaiton of carbonic anhydrase activity from the chloroplast to the cytosol in Oryza sativa, ssp. japonica, cv. Kitaake. Four genome edited lines and one wil-type control line were analysed.

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Oryza sativa japonica Transcriptome or Gene expression

Project description:In this study, we examined the transcriptome dynamics within the matured fully expanded rice leaf and used strand-specific RNA sequencing to generate a comprehensive transcriptome dataset for the mature rice leaf. The rice Nipponbare (Oryza sativa l. japonica) seedlings were grown in the greenhouse. About 20 days after planting, the fully opened 4th leaves was cut it into seven 3-cm segments, from bottom to tip and labeled as sections 1 to 7, respectively. The tissues were immediately frozen in liquid nitrogen for total RNA extraction. Two biological replicates were collected for each section. Note: All samples in SRA were assigned the same sample accession (SRS685294). This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

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Expression data from Oryza sativa and Arabidopsis thaliana

Project description:In this study, we used a cross-species network approach to uncover nitrogen (N)-regulated network modules conserved across a model and a crop species. By translating gene network knowledge from the data-rich model Arabidopsis (Arabidopsis thaliana, ecotype Columbia-0) to a crop, rice (Oryza sativa spp. japonica (Nipponbare)), we identified evolutionarily conserved N-regulatory modules as targets for translational studies to improve N use efficiency in transgenic plants.

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Gene expression ATLAS of Oryza sativa sp japonica (cv. Nipponbare) during photomorphogenesis (transition from dark to light)

Project description:Oryza sativa Japonica (rice) is the staple food for all over world population. At the time of germination, the exposure to light may play an important role in the early development of the rice seedling. In order to survey the genes, their functions and role in biological processes, an RNA-Seq based study of 6 libraries prepared from poly-A rich mRNA fraction was carried out to explore transcriptional programs operating in dark and light conditions. For each treatment type, three individual plants were used as biological replicates.

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Transcriptome profiling in reciprocal hybrids and tetraploids constructed from subspecies japonica and indica of Asian rice (Oryza sativa L.)

Project description:Hybrids and allopolyploids typically exhibit radically altered gene expression patterns relative to their parents, a phenomenon termed âtranscriptomic shock.â To distinguish the effects of hybridization from polyploidization on coregulation of divergent alleles, we analyzed expression of parental copies (homoeologs) of 11,608 genes using RNA-seq-based transcriptome profiling in reciprocal hybrids and tetraploids constructed from subspecies japonica and indica of Asian rice (Oryza sativa L.)

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Characterize novel lncRNAs responding to stresses in Oryza sativa at transcriptional and post-transcriptional levels

Project description:We performed poly(A)+, poly(A)-, nuclear, small RNA-seq analysis on Oryza sativa japonica WT plants.

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Response to salt stress treatment over time in Oryza sativa L. Japonica Nipponbare, microarray dataset

Project description:Oryza sativa L. Japonica nipponbare seedlings were treated with 300mM NaCl or water, and then samples were taken after one hour, five hours and 24 hours, to assess which genes are differentially expressed over time during salt stress treatment. The results from this dataset are also compared with those from the same samples assayed using RNA-seq.

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Response to salt stress treatment over time in Oryza sativa L. Japonica Nipponbare, RNA-seq dataset

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Oryza sativa Japonica Group

Project description:Rice plants (Oryza sativa var. japonica): WT vs. MIT knockdown plant

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