GEO DataSets

(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) 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) 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) 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) 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) We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with  Xanthomonas oryzae pv. oryzae strain PXO99A heterologously expressing the Tal2a effector, the designer TAL effector dT280 which targets a sequence overlapping the predicted Tal2a binding sequence in UCH, or the Tal11b effector. Results provide insight into the genes differentially regulated in a Tal2a- and dT280-specific manner.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13834

6 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) affy_xoo_rice - affy_xoo_rice - The Bacterial Leaf Blight disease of rice is due to Xanthomonas oryzae pv. oryzae. As for many pathogenic bacteria, it relies on a type 3 secretion system that is devoted to the injection of type 3 effectors into the eukaryotic host cell. These proteins are meant to suppress host basal defense responses and/or mimic some host regulatory function promoting bacterial survey in the plant. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

9 Samples

Download data: CEL

(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:

GPL18525 GPL27908

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) 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) Determining how a bacterial pathogen responds to its host and other bacterial species by altering gene expression is key to understand its pathogenesis and environmental adaption. Here, we used RNA-Seq to comprehensively and quantitatively assess the transcriptional response of the rice bacterial pathogen Acidovorax avenae subsp. avenae strain RS-1 cultivated in vitro, in vivo and in co-culture with rice rhizobacterium Burkholderia seminalis R456. more...

Organism:

Paracidovorax avenae RS-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17669

6 Samples

Download data: TXT

(Submitter supplied) Xanthomonas oryzae pv. oryzae (Xoo) causes the bacterial leaf blight of rice, which leads to as much as 50% yield losses. To understand the landscape of virulence mechanisms, we constructed in planta transcriptional profiling of Xoo KACC10331 using RNA-seq. Three in planta transcriptome of Xoo KACC10331 derived from infected rice leafs were compared to three in vitro data from rich media. To obtain differentially expressed genes, we used the DEGseq package with MA-plot-based method in the R statistical environment and identified 2,094 transcripts that were significantly altered.

Organism:

Xanthomonas oryzae pv. oryzae KACC 10331

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22653

6 Samples

Download data: TXT