txid4530[Organism] - GEO DataSets

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Select item 2002785011.

Land plant-specific H3K27 methyltransferases ATXR5 and ATXR6 control plant development and stress responses [Rice RNA-seq]

(Submitter supplied) The colonization of land by plants relies on numerous evolutionary innovations crucial for terrestrial adaptation. These include advances in sexual reproduction and the ability to properly respond to various environmental stresses, which involve precise control of their regulatory genes. A notable genetic innovation in land plants is the emergence of histone lysine methyltransferases ATXR5/6, which specifically catalyse the repressive histone H3 lysine 27 monomethylation (H3K27me1). more...

Organism:: Oryza sativa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27660
9 Samples

Download data: TXT

Series

Accession:: GSE278501

ID:: 200278501

Select item 2001130672.

The involvement of long non-coding RNAs in the formation of high temperature-induced grain chalkiness in rice

(Submitter supplied) A period of exposure to high ambient temperatures can damage the process of grain filling in rice, potentially inducing the endosperm to become chalky. Given the established involvement of long non-coding RNAs (lncRNAs) in regulating plant development and its stress response, the purpose here was to reveal the extent to which lncRNA activity contributes to the endosperm chalkiness syndrome. Among 578 lncRNAs identified in spikelets harvested ten days post anthesis from plants exposed to high temperature stress, 14 were found to be more abundant than in control plants, while 45 were less abundant. more...

Organism:: Oryza sativa Japonica Group

Type:: Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:: GPL21812
6 Samples

Download data: TXT, XLSX

Series

Accession:: GSE113067

ID:: 200113067

SRA Run Selector

Select item 2002798143.

Transcriptional response to mechanical wounding stress in Oryza sativa

(Submitter supplied) To understand the dynamics and global gene reprogramming in the early response to mechanical wounding in rice, the transcriptional response to mechanical injury was analyzed. A time-course experiment revealed the highly dynamic nature of the wound response in rice. Mechanical wounding triggered extensive gene expression reprogramming in the locally wounded leaf, affecting various physiological processes, including defense mechanisms and potentially tissue repair and regeneration. more...

Organism:: Oryza sativa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL19290
30 Samples

Download data: TXT

Series

Accession:: GSE279814

ID:: 200279814

Select item 2001863724.

Transcritome provides insights into predicting the heterosis level

(Submitter supplied) we compared the change of transcritome between the parents and their F1 hybrids showing different heterosis level and obtained the potential index for predicting the heterosis level between rice parental lines.

Organism:: Oryza sativa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL23013
81 Samples

Download data: TXT

Series

Accession:: GSE186372

ID:: 200186372

SRA Run Selector

Select item 2002782945.

Co-cultivating rice plants with Azolla filiculoides modifies root architecture and timing of developmental stages

(Submitter supplied) Innovative strategies for increasing the yield of rice, the staple food for more than half of the global population, are needed to keep pace with the expected worldwide population increase, and sustainably forefront the challenges posed by climate change. Traditionally, in Southern-East Asian countries, rice farming benefits from the use of Azolla spp., either as green manure or as co-cultivated plants, for the supply of nitrogen. more...

Organism:: Oryza sativa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27660
6 Samples

Download data: XLSX

Series

Accession:: GSE278294

ID:: 200278294

Select item 2002782026.

Identification and analysis of microRNAs responsible for brown planthopper resistance in BPH14/BPH15 pyramiding rice

(Submitter supplied) Background Rice farming faces a serious challenge from the brown planthopper (BPH), with the pyramiding of BPH14 and BPH15 genes delivering effective protection in elite rice strains. However, the molecular basis behind this resistance is still unclear. Results The study investigated miRNA levels in BPH14/BPH15 pyramiding line (B1415) and their recurrent parent (RP) under BPH infestation employing high-throughput sequencing and revealed 136 differentially expressed miRNAs (DEMs) among 550 known miRNAs. more...

Organism:: Oryza sativa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27660
18 Samples

Download data: TXT

Series

Accession:: GSE278202

ID:: 200278202

Select item 2002424607.

H3K9ac-marked three-dimensional genome dynamics in rice under drought stress

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Oryza sativa

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

Platform:: GPL24468
29 Samples

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Series

Accession:: GSE242460

ID:: 200242460

PubMed Full text in PMC Similar studies

Select item 2002424598.

H3K9ac-marked three-dimensional genome dynamics in rice under drought stress [RNA-Seq]

(Submitter supplied) Drought stress response involves vigorous reprogramming of transcriptome while the mechanism modulating this process remains elusive. The role of 3D-genome in the regulation of rice development has recently been unveiled in rice, which exhibited characteristics distinct from that in mammals and other plants. However, the relationship between spatial chromosome organization and drought responsive gene reprogramming is still poorly understood. more...

Organism:: Oryza sativa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24468
8 Samples

Download data: TXT

Series

Accession:: GSE242459

ID:: 200242459

PubMed Full text in PMC Similar studies

Select item 2002424559.

H3K9ac-marked three-dimensional genome dynamics in rice under drought stress [ChIA-PET]

Organism:: Oryza sativa

Type:: Other

Platform:: GPL24468
8 Samples

Download data: BW

Series

Accession:: GSE242455

ID:: 200242455

PubMed Full text in PMC Similar studies

Select item 20024245310.

H3K9ac-marked three-dimensional genome dynamics in rice under drought stress [ChIP-Seq]

Organism:: Oryza sativa

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL24468
13 Samples

Download data: BW

Series

Accession:: GSE242453

ID:: 200242453

PubMed Full text in PMC Similar studies

Select item 20027689411.

Simultaneous Profiling of Chromatin-Associated RNA at Targeted DNA Loci and RNA-RNA Interactions through TaDRIM-Seq II

(Submitter supplied) The enormous variety of different RNAs are transcribed from eukaryotic genome. Some RNAs, particular long non-coding RNAs (lncRNAs), enrich on chromatin via transcribed RNAs to retain at their transcription site (Cis-acting RNAs) and recruited to different genomic regions (Trans-acting RNAs), which play significant roles in regulating gene transcription, epigenomic modifications and mediating chromatin states. more...

Organism:: Arabidopsis thaliana; Homo sapiens; Oryza sativa Indica Group

Type:: Other

Platforms:: GPL23157 GPL26667 GPL20795
12 Samples

Download data: TXT

Series

Accession:: GSE276894

ID:: 200276894

Select item 20026237112.

Transcriptomic and metabolomic reveal OsCOI2 as the jasmonate-receptor master switch in rice root

(Submitter supplied) Jasmonate is an essential phytohormone involved in plant development and stress responses. Jasmonate perception occurs through the COI nuclear receptor allowing to target the JAZs repressors for degradation by the 26S proteasome. Consequently, repressed transcription factors are released and expression of JA-responsive genes is induced. In rice, three OsCOI genes have been identified, OsCOI1a and the closely related OsCOI1b homolog, and OsCOI2. more...

Organism:: Oryza sativa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27660
18 Samples

Download data: TXT

Series

Accession:: GSE262371

ID:: 200262371

Select item 20023185613.

Rice amino acid transporter OsMP1 is involved in amino acid homeostasis and mediates broad-spectrum resistance to blast fungus and bacterial blight through upregulating JA signaling pathway

(Submitter supplied) To investigate the molecular mechanisms about how OsMP1 regulates rice blast resistance, we established the CR4 line in which target gene has been knocked down by CRISPR-Cas9 gene editing. We then performed gene expression profiling analysis using data obtained from RNA-seq of CR4 and wild-type Hei.

Organism:: Oryza sativa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27660
6 Samples

Download data: TXT

Series

Accession:: GSE231856

ID:: 200231856

Select item 20024400914.

An improved terminal ribose-modified small RNA sequencing (TRM-sRNA-seq) reveals novel features of miRNA modification and identifies HEN1-independent 2’-O-modified sRNAs derived from tRNAs

(Submitter supplied) Concomitant cloning of RNA degradation products is a major issue in standard small RNA-sequencing practices. It not only adds complexity in bona fide sRNA characterization, but also affects experimental replicability and sometimes results in library construction failure. Given that all kinds of canonical plant small RNAs bearing the 3’ end 2’-O-methylation modification, we here developed an sRNA-seq method (named terminal ribose-modified sRNA sequencing, TRM-sRNA-seq).

Organism:: Oryza sativa; Arabidopsis thaliana; Solanum lycopersicum; Zea mays

Type:: Non-coding RNA profiling by high throughput sequencing

4 related Platforms
54 Samples

Download data: TXT

Series

Accession:: GSE244009

ID:: 200244009

PubMed Full text in PMC Similar studies

Select item 20025204015.

A cis-regulatory atlas of rice single cells

(Submitter supplied) Cis-regulatory elements (CREs) are essential in precisely regulating gene expression, contributing significantly to the evolution of species. Identifying cell-type-specific CREs is essential for understanding plant evolution, domestication, and improving crops through genome editing. Here, we built a cis-regulatory atlas in Oryza sativa, encompassing 106,143 nuclei representing 138 discrete cell states from nine distinct organs. more...

Organism:: Oryza sativa

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL27660
18 Samples

Download data: TXT

Series

Accession:: GSE252040

ID:: 200252040

Select item 20018180916.

Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [anti-H2A.Z & H3 ChIP-seq]

(Submitter supplied) INO80, one member of ATP-ase remodeler factor, play a role on chromatin dynamic modulation. OsINO80 (LOC_Os03g22900) is identified as a homologue of INO80 in rice. To study the function of OsINO80 on H2A.Z, we analyzed the distribution of OsINO80 and H2A.Z in 14-week-old seedling of Oryza stative Japanese rice plant through ChIP assay following by high through sequencing (ChIP-seq).Integrated analysis showed that OsINO80 regulate the H2A.Z level.

Organism:: Oryza sativa

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL27660
12 Samples

Download data: BIGWIG

Series

Accession:: GSE181809

ID:: 200181809

SRA Run Selector

Select item 20018180817.

Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [OsINO80 ChIP-seq]

Organism:: Oryza sativa

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL19290
8 Samples

Download data: BIGWIG

Series

Accession:: GSE181808

ID:: 200181808

SRA Run Selector

Select item 20018966518.

Spermidine augments salt stress resilience in rice roots potentially by enhancing OsbZIP73’s RNA binding capacity

(Submitter supplied) Background: Rice is a staple crop for over half of the global population, but soil salinization poses a significant threat to its production. As a type of polyamine, spermidine (Spd) has been shown to reduce stress-induced damage in plants, but its specific role and mechanism in protecting rice roots under salt stress require further investigation. Results: This study suggested spermidine (Spd) mitigates salt stress on rice root growth by enhancing antioxidant enzyme activity and reducing peroxide levels. more...

Organism:: Oryza sativa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27660
12 Samples

Download data: CSV

Series

Accession:: GSE189665

ID:: 200189665

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20017164619.

Nitrogen fertilizer reduces salicylic acid-mediated immunity by activating gibberellin signaling in rice

(Submitter supplied) The environment plays important role in the interaction between plant hosts and pathogens. The application of chemical fertilizer is a crucial breeding technology to enhance crop yield since last century. As the most abundant fertilizer, nitrogen often increases disease susceptibility for crop plants. The underlying mechanism for nitrogen induced disease susceptibility is elusive. Here we found that nitrogen application activate gibberellin signaling by degradation of SLR1, the repressor protein in gibberellin signaling, which result in simultaneously promoting plant growth and disease susceptibility. more...

Organism:: Oryza sativa Japonica Group

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27860
12 Samples

Download data: TDF

Series

Accession:: GSE171646

ID:: 200171646

SRA Run Selector

Select item 20020035720.

Effect of Carbon Nanoparticle Treatment in Rice Adult plants

(Submitter supplied) Carbon Nanoparticle (CNP, Graphite nano powder,Type 1, APS : 400 nm, Sisco Research Laboratories Pvt. Ltd. India ) was applied to roots of rice (Oryza sativa) plants (SWARNA (MTU7029) seeds were dehulled, surface genotype) in potted condition. The treatment was given in vegetative stage and the effect was noted in reproductive stage by taking several agronomic parameters. Experiment was repeated in 3 different seasons to take a conclusion.

Organism:: Oryza sativa

Type:: Expression profiling by array

Platform:: GPL20752
4 Samples

Download data: TXT

Series

Accession:: GSE200357

ID:: 200200357

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