Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Oryza sativa cultivar:Nippobare

ABSTRACT: Oryza sativa cultivar:Nippobare Transcriptome or Gene expression

PROVIDER: PRJNA264125 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1614250.fastq.gz	Fastqsanger.gz
	SRR1614260.fastq.gz	Fastqsanger.gz
	SRR1614251.fastq.gz	Fastqsanger.gz
	SRR1614261.fastq.gz	Fastqsanger.gz
	SRR1614252.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

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

Dynamic Profiles of transcriptome in Oryza sativa leaf

Project description:To evaluate the roles of gene regulation in Oryza sativa leaf, dynamic profiles of transcriptome were investigated in Oryza sativa L. spp. indica with different treatments, the aerial tissues of one-month-old plants from four different areas (groups 1–4) were treated with 0, 40 mL of 25% azoxystrobin, 0.01 g of VdAL, or 40 mL of 25% azoxystrobin plus 0.01 g VdAL, respectively.

2018-12-18 | GSE108204 | GEO

Screening Salinity Tolerance and Transcriptome Analysis in Rice (Oryza sativa L.)

Project description:Comparative transcriptome sequencing in leaf and root tissues of Control and Salt-treated Oryza sativa generated 52.2 and 17.29 million high-quality reads.

2019-06-05 | GSE132153 | GEO

Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5’ rapid amplification of cDNA ends (RLM 5’-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice.

2010-01-01 | GSE19050 | GEO

Expression data from Oryza sativa 3037 (wild-type) and sd37 (mutant) seedlings

Project description:We characterized a rice (Oryza sativa L ssp. indica cultivar 3037) semi-dwarf mutant sd37, in which CYP96B4 gene (Cytochrome P450 96B subfamily) was identified as the target gene by map-based cloning and complementation test. A point mutation in CYP96B4 leads to a substitution of Thr to Lys in the SRS2 region. The sd37 leaves, panicles and seeds are all smaller compared with those of wild-type, and histological analysis showed that the decreased cell number was the main reason for the dwarf phenotype. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up- and down- regulated genes during this process.

2013-07-09 | GSE48593 | GEO

Oryza sativa cultivar:Oryza sativa japonica

Project description:Oryza sativa cultivar:Oryza sativa japonica Transcriptome or Gene expression

| PRJNA343834 | ENA

Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5M-bM-^@M-^Y rapid amplification of cDNA ends (RLM 5M-bM-^@M-^Y-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice. The degradome sequence of Young inflorescences from Oryza sativa L. ssp. indica (93-11) was sequenced

2010-01-01 | E-GEOD-19050 | biostudies-arrayexpress

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.

2015-06-10 | GSE38102 | GEO

RNA-seq of Oryza sativa L. Dongjin and Iksan 526 seeds at 20 days after heading

Project description:The resveratrol-producing rice (Oryza sativa L.) inbred line, Iksan 526 (I.526), developed by the expression of the groundnut (Arachis hypogaea) resveratrol synthase 3 (AhRS3) gene in the japonica rice cultivar Dongjin, accumulated both resveratrol and its glucoside, piceid, in leaves and seeds. Especially, ultra-performance liquid chromatography (UPLC) analysis revealed that the biosynthesis of piceid reached peak levels at 20 days after heading (DAH) seeds. To investigate endogenous piceid biosynthesis genes (UGTs), total RNA samples of 20 DAH seeds was used for RNA-seq.

2020-12-20 | E-MTAB-9695 | biostudies-arrayexpress

Rice (Oryza sativa) lysine-acetylation LC-MS/MS

Project description:Lysine acetylation is a dynamic and reversible post-translational modification that plays an imporant role in the gene transcription regulation. Here, we report high quality proteome-scale data for lysine-acetylation sites and proteins in rice (Oryza sativa). A total of 1337 Kac sites in 716 Kac proteins with diverse biological functions and subcellular localizations were identified in rice seedlings.

2016-02-24 | PXD002291 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data