GEO DataSets

(Submitter supplied) Host-pathogen interactions, in particular during the early stages of infection, are important for the fate of both the invading pathogen and host. In pathogens, these interactions activate diverse pathogenic signals to cause disease in the host and evade the inevitably activated immune responses of the infected host. In this study, we used in vitro assay system and RNA-seq to analyze the time-resolved genome-wide gene expressions of Xanthomonas oryzae pv. more...

Organism:

Xanthomonas oryzae pv. oryzae KACC 10331

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19216

14 Samples

Download data: TXT

(Submitter supplied) Host-pathogen interactions, in particular during the early stage of infection, are important for the fate of boththe invading pathogen and host. In pathogens, these interactions activate diverse pahogenic signals to cause disease in the host and evade the inevitably activated immune responses of the infected host. In this study, we used in vitro assay system and RNA-seq to analyze the time-resolved genome-wide gene expressions of Xoo evoked by the interactions with rice leaf extracts. more...

Organism:

Xanthomonas oryzae pv. oryzae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28880

6 Samples

Download data: CSV

(Submitter supplied) African Xanthomonas oryzae pv. oryzae strains seem most closely related to and share several genetic features with pathovar oryzicola despite causing symptoms of bacterial leaf blight. The ability of most Xanthomonas plant pathogenic bacteria to infect their host relies on the action of a specific family of type III effectors called the TAL effectors. These microbial transcription factors are injected into the plant and manipulate the host transcriptome upon binding to the promoters of plant genes. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13834

6 Samples

Download data: TXT

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

Organism:

Xanthomonas oryzae pv. oryzae KACC 10331; Xanthomonas oryzae pv. oryzicola BLS256

Type:

Expression profiling by array

Platform:

GPL6123

48 Samples

Download data: TXT

(Submitter supplied) To dissect the molecular mechanisms of resistance mediated by Xa39,the transcriptome profiling of a rice line carrying Xa39 and its parents at the early stage of Xoo infection were investigated. A rice introgression line H471 carrying Xa39 exhibited a typical local hypersensitive response phenotype, accompanied by programmed cell death after inoculation with the Xoo Philippines’ race 9b.Our results indicated there might be cross-talk between the Xa39-mediated signal transduction cascades and the GA/BR signaling pathway, and the defense mechanism was related to diverse kinases, transcription factors, post-translational regulation, and R genes.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

18 Samples

Download data: XLSX

(Submitter supplied) An attempt has been made to investigate gene expression patterns of three Xoo strains in XOM2, PXO99 (P6) and PXO86 (P2) from Phillipines, and GD1358 (C5) from China, which exhibited different virulence in 30 rice varieties, with putative virulence factors using deep sequencing. In total, 4759 transcripts were identified in this study, and 1151 and 3076 genes were differentially expressed when P6 compared with P2 and P6 compared with C5, respectively. more...

Organism:

Xanthomonas oryzae pv. oryzae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16609

3 Samples

Download data: XLS

(Submitter supplied) We sequenced mRNA from two-week old rice seedlings of jmj704 and wild-type (ZH11) plants to obtain the differntially expressed genes in jmj704 mutant.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

2 Samples

Download data: TXT

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

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL27908 GPL18525

20 Samples

Download data: TXT

(Submitter supplied) we emphatically monitored the responsive changes of rice miRNAs at 0, 8, 24 hours across Xoo strain PXO86 infection in its compatible rice variety IR24 and incompatible variety IRBB5 by small RNA sequencing, and the genes targeted by miRNAs were also detected via degradome technology. These findings provide new insights into the complex roles of characteristic miRNAs and their targets in rice-Xoo interactions.

Organism:

Oryza sativa Japonica Group

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL27908

18 Samples

Download data: TXT

(Submitter supplied) we emphatically monitored the responsive changes of genes targeted by rice miRNAs miRNAs at 0, 8, 24 hours across Xoo strain PXO86 infection in its compatible rice variety IR24 and incompatible variety IRBB5 by degradome technology.These findings provide new insights into the complex roles of characteristic miRNAs in rice-Xoo interactions.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

2 Samples

Download data: TXT

(Submitter supplied) In this study, using a novel dual RNA-seq approach we monitored the global transcriptional changes in real time of Xanthomonas oryzae pv. oryzicola and rice during infection. Our transcriptome maps of Xoc strains infecting rice provide mechanistic insights into the bacterias adaptive responses to the host niche, with modulation of central metabolism being an important signature. The study also uncovers that infected rice responds by substantial alteration of the cell wall, stress and structural proteins.

Organism:

Xanthomonas oryzae pv. oryzicola; Oryza sativa

Type:

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

Platforms:

GPL26222 GPL13160

5 Samples

Download data: TXT

(Submitter supplied) Endogenous small RNAs are newly identified players in plant immune responses, yet their roles in rice (Oryza sativa) responding to pathogens are still less understood, especially for pathogens that can cause severe yield losses. Here, we examined the small RNA expression profiles of rice leaves at 2, 6, 12, and 24 hours post infection of Xanthomonas oryzae pv. oryzae (Xoo) virulent strain PXO99, the causal agent of rice bacterial blight disease. more...

Organism:

Oryza sativa Japonica Group

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15370

8 Samples

Download data: TXT

(Submitter supplied) RESEARCH SUMMARY Bacterial blight and bacterial leaf streak, two of the most serious diseases of rice, are caused by Xanthomonas oryzae pathovar (pv.) oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) respectively. Xoo is a vascular pathogen that invades the xylem, whereas Xoc is non-vascular and colonizes the mesophyll apoplast. These distinctive types of infection represent the two most common ways plant pathogenic bacteria produce disease. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

60 Samples

Download data: CEL

(Submitter supplied) An indica rice cultivar IET8585 (Ajaya), resists diverse races of the Xanthomonas oryzae pv oryzae (Xoo) pathogen attack, and is often cultivated as bacterial leaf blight (blb) resistant check in India. Earlier we reported a recessive blb resistance gene mapped to the long arm of chromosome 5 in IET8585. To further understand the mechanism of recessive and durable resistance response, two indica rice genotypes namely, i) IET8585 (Ajaya), a disease resistant indica veriety from India and ii) IR24, a bacterial leaf blight disease susceptible genotype were selected for this study. more...

Organism:

Oryza sativa Indica Group; Oryza sativa Japonica Group

Type:

Expression profiling by array

Platform:

GPL892

6 Samples

Download data: TXT

(Submitter supplied) The plant volatilebeta-cyclocitral plays important roles in the regulation of defense responses in rice. To clarify the response to beta-cyclocitral in rice at gene expression level, we performed a microarray analysis using the Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA). As a result, treatment of linalool caused high upregulation of many defense-related genes including pathogenesis-related (PR) genes in rice.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

8 Samples

Download data: TXT

(Submitter supplied) We examined the transcriptional data in rice leaves of TOP6A3 overexpressed line (TOP6A3-OE1) with WT (K3) plants under normal growth.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

4 Samples

Download data: XLSX

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to investigate NGS-derived rice leaf transcriptome profiling (RNA-seq) exposed to green rice leafhopper (GRH) and validated RNA-Seq results using quantitative reverse transcription polymerase chain reaction (qRT–PCR). Methods: Rice leaf mRNA profiles of 21-day-old wild-type (WT) and Near Isogenic Line (NIL) rice were generated by deep sequencing, in triplicate, using Illumina’s HiSeq™ 4000 Sequencing System. more...

Organism:

Oryza sativa; Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23013 GPL21812

4 Samples

Download data: GTF, TAB, TXT, XLS

(Submitter supplied) Transcriptional profiling of Oryza sativa japonica Nipponbare roots after 14 days post inoculation with Azoarcus olearius BH72, the goal is to understand the transcriptomic response of rice roots to colonization by bacterial endophyte

Organism:

Oryza sativa; Oryza sativa Japonica Group

Type:

Expression profiling by array

Platform:

GPL27404

4 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of Oryza sativa japonica Nipponbare roots after 14 days post infection with Xanthomonas oryzae pv. oryzae strain PXO99 , the goal is to understand the transcriptomic response of rice roots to colonization by bacterial pathogen

Organism:

Oryza sativa; Oryza sativa Japonica Group

Type:

Expression profiling by array

Platform:

GPL27404

4 Samples

Download data: TXT

(Submitter supplied) We report about the effects of temperature increase on rice response to Xanthomonas oryzae pv. oryzae using high throughput sequencing (RNA-Seq). The time course transcriptomic analysis revealed that temperature enhanced IRBB67 resistance to combined heat and Xoo. Our findings highlight altered cellular compartment by Xoo and heat stress in both susceptible (IR24) and the resistant (IRBB67). Interestingly, up-regulation of trehalose-6-phosphatase gene and low affinity cation transporter in IRBB67 suggest that IRBB67 maintained a certain homeostasis under high temperature to have its resistance enhanced. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

48 Samples

Download data: CSV