Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

E-MTAB-5759

ABSTRACT: RNA-seq of Japonica rice with overexpression or knockdown of OsMPH1 gene, which is involved in regulation of plant height --- a major trait affecting yield potential

PROVIDER: E-MTAB-5759 | ExpressionAtlas | 2019-01-10

REPOSITORIES: ExpressionAtlas

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	E-MTAB-5759-analysis-methods.tsv	Tabular
	E-MTAB-5759-analytics.tsv	Tabular
	E-MTAB-5759-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-5759-configuration.xml	Xml
	E-MTAB-5759-g3_g1-mvaPlot.png	Other

Items per page:

1 - 5 of 33

Similar Datasets

Functional investigation of OsMPH1 by RNA-seq in rice

Project description:Plant height is a major trait affecting yield potential in rice. Using a large-scale hybrid transcription factor approach, we identified the novel MYB-like transcription factor OsMPH1 (MYB-like gene of Plant Height 1), which is involved in the regulation of plant height in rice.Overexpression of OsMPH1 leads to increases of plant height and grain yield in rice, while knockdown of OsMPH1 leads to the opposite phenotypes. RNA-seq is used for exploring differences between OsMPH1 transgenic rice and wild-type plants.

2017-07-01 | E-MTAB-5759 | biostudies-arrayexpress

The identification and characterization of a plant height and grain length related gene hfr131 in rice

Project description:Plant height and grain size are important agronomic traits affecting rice yield. Various plant hormones participate in the regulation of plant height and grain size in rice. However, how these hormones cooperate to regulate plant height and grain size is poorly understood. In this study, we identified a brassinosteroid-related gene, hfr131, from an introgression line constructed using Oryza longistaminata, that caused brassinosteroid insensitivity and reduced plant height and grain length in rice. Further study showed that hfr131 is a new allele of OsBRI1 with a single-nucleotide polymorphism (G to A) in the coding region, leading to a T988I conversion at a conserved site of the kinase domain. An auxin response factor, OsARF17, could bind to the promoter region of HFR131 and positively regulated HFR131 expression, thereby regulating the plant height and grain length, and influencing brassinosteroid sensitivity. Haplotype analysis showed that the consociation of OsAFR17Hap1/HFR131Hap6 conferred an increase in grain length. Overall, this study identified hfr131 as a new allele of OsBRI1 that regulates plant height and grain length in rice, revealed that brassinosteroid and auxin might coordinate through OsARF17–HFR131 interaction, and provided a potential breeding target for improvement of rice yield.

2023-03-17 | GSE224118 | GEO

E-MTAB-6991

Project description:RNA-seq analysis of PROX1 overexpression and knockdown in glioblastoma cell lines

2025-01-23 | E-MTAB-6991 | ExpressionAtlas

Comparative gene expression profiling analysis of RNA-seq data for WT (Nipponbare) and OsEXPA7 overexpression.

Project description:Yield and quality are the two most important traits in crop breeding. Exploring the regulatory mechanisms that affect both yield and quality traits is of great significance for understanding the molecular genetic networks controlling these key crop attributes. Expansins are cell wall loosening proteins that play important roles in regulating rice grain size. We investigated the effect of OsEXPA7, encoding an expansin, on rice grain size and quality. OsEXPA7 overexpression resulted in increased plant height, panicle length, grain length, and thousand-grain weight in rice. OsEXPA7 overexpression also affected gel consistency and amylose content in rice grains, thus affecting rice quality. Subcellular localization and tissue expression analyses showed that OsEXPA7 is localized on the cell wall and is highly expressed in the panicle. Hormone treatment experiments revealed that OsEXPA7 expression mainly responds to methyl jasmonate, brassinolide, and gibberellin. Transcriptome analysis and RT-qPCR experiments showed that overexpression of OsEXPA7 affects the expression of OsJAZs in the jasmonic acid pathway and BZR1 and GE in the brassinosteroid pathway. In addition, OsEXPA7 regulates the expression of key quantitative trait loci related to yield traits, as well as regulates the expression levels of BIP1 and bZIP50 involved in the seed storage protein biosynthesis pathway. These results reveal that OsEXPA7 positively regulates rice yield traits and negatively regulates grain quality traits by involving plant hormone pathways and other trait-related pathway genes. These findings increase our understanding of the potential mechanism of expansins in regulating rice yield and quality traits and will be useful for breeding high-yielding and high-quality rice cultivars.

2024-06-30 | GSE256331 | GEO

Polyploidized Rice Improves Plant Height and Yield through Regulating Expression of Yield Related Genes.

Project description:Polyploidization is one of the effective ways to improve plant height and yield of rice (Oryza sativa L.). However, the molecular mechanism of regulation is not yet fully understood. Here, we investigated the agronomic traits of diploid (Balilla-2x) and tetraploid (Balilla-4x) of japonica rice variety Balilla. Compared with Balilla-2x, Balilla-4x exhibited significantly increased plant height, spike length and yield per plant. RNA-seq analysis of the leaves of Balilla-2x and Balilla-4x was performed and the results showed that the expression levels of yield related genes (e.g., STH1, OsYUC9, and OsDEP1) were significantly upregulated in Balilla-4x rice plants, these genes are related to plant height and panicle development. These results indicated that polyploidization changed the expression of genes related to agronomic traits such as plant height and spike length, thereby increasing rice yield. This study provides a further basis for understanding the yield of rice after polyploidization, and can serve as a new theoretical reference for breeding high-yielding rice varieties achieved.

2024-01-30 | GSE254291 | GEO

E-MTAB-8215

Project description:mRNA-seq of SW837 USP22 knockdown cells

2025-01-16 | E-MTAB-8215 | ExpressionAtlas

E-MTAB-8247

Project description:mRNA-seq of MCF10A USP22 knockdown cells

2025-01-16 | E-MTAB-8247 | ExpressionAtlas

E-MTAB-8214

Project description:mRNA-seq of SW480 USP22 knockdown cells

2025-01-16 | E-MTAB-8214 | ExpressionAtlas

E-MTAB-7393

Project description:mRNA-seq of HCT116 USP22 knockdown cells

2025-01-23 | E-MTAB-7393 | ExpressionAtlas

E-MTAB-7791

Project description:mRNA-seq for HCT116 Parental and ARID1A knockdown cells, mRNA-seq for DLD1 Parental, ARID1A knockdown and ARID1A knockout cells, mRNA-seq for COLO320DM Parental and ARID1A knockdown and ARID1A knockout cells

2025-01-23 | E-MTAB-7791 | ExpressionAtlas

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