GEO DataSets

(Submitter supplied) In this study we compare logarithmically grown Burkholderia thailadensis wildtype to a transposon mutant that is disrupted in gshA1, or gshA2, which are involved in glutathione biosynthesis or egtB, involved in ergothioneine biosynthesis using RNASeq to identify novel pathways where glutathione or ergothioneine may be involved.

Organism:

Burkholderia thailandensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33677

8 Samples

Download data: CSV, XLSX

(Submitter supplied) Plant pathogens require lethal virulence factors, susceptible hosts, and optimal environmental conditions for disease establishment. High soil salinity, exacerbated by climate change, significantly impacts agro-biological ecosystems. However, the overall interactions between plant pathogens and salt stress are not fully characterized or understood. This study examines the effects of salt stress on representative plant pathogens: Burkholderia gladioli, Pectobacterium carotovorum subsp. more...

Organism:

Ralstonia solanacearum; Pectobacterium carotovorum subsp. carotovorum; Burkholderia gladioli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29295 GPL34740 GPL34741

18 Samples

Download data: TXT

(Submitter supplied) We identified BP1026b_II1561 to be an important transcriptional regulator controling late stages of intracellular infection. RNA-seq analysis was performed to further investigate the regulatory network of II1561 regulation. ChIP-seq was also performed under the same conditions.

Organism:

Burkholderia pseudomallei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32930

2 Samples

Download data: XLSX

(Submitter supplied) We identified BP1026b_II1561 to be an important transcriptional regulator controling late stages of intracellular infection. RNA-seq analysis was performed to further investigate the regulatory network of II1561 regulation. ChIP-seq was also performed under the same conditions.

Organism:

Burkholderia pseudomallei

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32930

2 Samples

Download data: XLSX

(Submitter supplied) We identified BP1026b_II1046 (SapR) to be an important transcriptional regulator controling surface attachment factor 1 (sap1). RNA-seq analysis was performed to further investigate the regulatory network of SapR regulation.

Organism:

Burkholderia pseudomallei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32930

6 Samples

Download data: XLSX

(Submitter supplied) To verify genes that are directly regulated by BysR, we used DNA affinity purification sequencing analysis (DAP-seq) for genome-wide recognition of BysR binding sites in vitro. The HALO-fusion BysR protein was successfully expressed and purified. After affinity purification and sequencing, at least 22 million double-end reads per sample were generated and with > 99 % of reads uniquely mapped to the JP2-270 genome. more...

Organism:

Burkholderia sp. JP2-270

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL31243

3 Samples

Download data: FA, TXT, WIG

(Submitter supplied) B. pseudomallei strain K96243 is sensitive to the drug ceftazidime (CAZ), but has been shown to exhibit transient CAZ tolerance when in a biofilm form. To investigate an observed shift in gene expression profile during ceftazidime (CAZ) tolerance and to better understand the mechanistic aspects of this transient tolerance, RNA-sequencing was performed on B. pseudomallei K96243 from the following three growth states: planktonic-free, biofilm, and planktonic shedding cells. more...

Organism:

Burkholderia pseudomallei K96243

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29815

9 Samples

Download data: FPKM_TRACKING, GTF, XLSX

(Submitter supplied) While nucleotide sequences determine an organism’s proteins, methylation of the nucleotides themselves can confer additional properties. In bacteria, differences in methylation can be used to identify incoming DNA, for example from bacteriophages. Restriction enzymes detect the methylation status at specific sequence motifs, and cleave improperly methylated, foreign DNA. Furthermore, methylation of key genetic regions can influence gene expression and hence phenotype. more...

Organism:

Burkholderia cenocepacia H111

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23128

4 Samples

Download data: TXT

(Submitter supplied) Interactions between plants and each neighboring microbial species are fundamental building blocks that collectively determine the structure and function of the plant microbiota, but the molecular basis of such interactions is poorly characterized. Here, we monocolonized Arabidopsis leaves with nine plant-associated bacteria from all major phyla of the plant microbiota and profiled co-transcriptomes of plants and bacteria. more...

Organism:

Exiguobacterium sp. Leaf187; Acinetobacter sp. Leaf130; Arthrobacter sp. Soil763; Flavobacterium sp. Root935; Arabidopsis thaliana; Pedobacter sp. Leaf176; Burkholderia sp. Leaf177; Chryseobacterium sp. Leaf404; Plantibacter sp. Leaf1; Rhizobium sp. Leaf155

Type:

Expression profiling by high throughput sequencing

10 related Platforms

125 Samples

Download data: FNA, TXT

(Submitter supplied) Purpose - To establish the response of B. cenocepacia K56-2 to growth in copper, and to characterise the BCAM0442/3 copper-sensing TCS. Methods - RNA-seq of the response WT and Δbcam0442/3 B. cenocepacia K56-2 to mid-log phase growth in LB with or without 1 mM CuCl2 was performed. Results - Characterisation of the overall response of B. cenocepacia K56-2 to copper, as well as establishing that BCAM0442/3 regulates the CopABCDE system in B. more...

Organism:

Burkholderia cenocepacia

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29736

12 Samples

Download data: CSV

(Submitter supplied) Introduction. Burkholderia thailandensis is a clinically rare opportunistic pathogen in the genus Burkholderia, and the genomic features and virulence characteristics of B. thailandensis strains that cause human infection remain unclear.Gap Statement. B. thailandensis strains with different virulence induce different host innate immune responses in vitro.Aim. This work aimed to understand the sequence diversity, phylogenetic relationship, and virulence of B. more...

Organism:

Burkholderia thailandensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23641

6 Samples

Download data: TXT

(Submitter supplied) The goal of this study was to identify reciprocal commnication between fungi and bacteria during a mutualistic and antagonistin interaction at two time points.

Organism:

Rhizopus microsporus ATCC 52813; Burkholderia sp. b13

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23355 GPL23356 GPL23357

24 Samples

Download data: TXT

(Submitter supplied) Persister cells are genetically identical variants in a bacterial population that have phenotypically modified their physiology to survive environmental stress. . To better define general persistence mechanisms that can be targeted to develop anti-persistence therapeutics, we performed transcriptomics analyses of Burkholderia thailandensis enriched for persisters using three methods: flow sorting by low proton motive force, meropenem treatment, and culture aging. more...

Organism:

Burkholderia thailandensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21997

18 Samples

Download data: CSV, TSV

(Submitter supplied) Members of the diazeniumdiolate class of natural compounds show great potential for drug development. Yet, their biosynthesis has remained elusive to date. Here, we identify a gene cluster directing the biosynthesis of the diazeniumdiolate compound fragin in Burkholderia cenocepacia H111. We provide evidence that fragin is a metallophore and that metal chelation is the molecular basis of its antifungal activity. more...

Organism:

Burkholderia cenocepacia H111

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23128

9 Samples

Download data: TXT

(Submitter supplied) Comparison of transcriptomes of wild-type cells and cells deleted for MftR as well as both strain grown in absence and presence of 5 mM urate

Organism:

Burkholderia thailandensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23641

12 Samples

Download data: XLSX

(Submitter supplied) In this study, we have analysed the transcriptional profile of B. cenocepacia H111 upon artificially altering the global cellular c-di-GMP levels. A total of 111 genes was found to be differentially expressed, of which 96 genes were down-regulated when c-di-GMP concentrations were increased. The BDSF, AHL and c-di-GMP regulons overlap for the regulation of 24 genes. Intriguingly, at a high intracellular c-di-GMP level expression of the AHL synthase cepI was found to be more than 10-fold down-regulated. more...

Organism:

Burkholderia cenocepacia H111

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16128

8 Samples

Download data: TXT

(Submitter supplied) We report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type. The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters.

Organism:

Burkholderia pseudomallei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24097

8 Samples

Download data: TXT

(Submitter supplied) In Burkholdeira gladioli BSR3, quorum sensing (QS) signal plays a pivotal role in many bacterial behaviors, including motility, toxin production and oxalogenesis. To understand transcriptional profiling of QS-dependent genes, we carried out RNA-Seq analysis of the wild type B. gladioli BSR3, and a QS-defective mutant under different culture states (10h and 24h after incubation), representing exponential phase and stationary phase.

Organism:

Burkholderia gladioli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19093

4 Samples

Download data: TXT

(Submitter supplied) Burkholderia cenocepacia is a versatile opportunistic pathogen that survives in a wide variety of environments, which can be limited in nutrients such as nitrogen. We previously showed that B. cenocepacia sigma factor s54 played a major role in control of nitrogen assimilation and virulence. In this work, we investigated the role of the s54 enhancer binding protein NtrC in controlling the response to nitrogen limitation and virulence. more...

Organism:

Burkholderia cenocepacia H111

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23128

6 Samples

Download data: TXT

(Submitter supplied) Comparision of transcriptome between Burkholderia glumae wild type BGR1 and isocitrate lyase mutant BICL39

Organism:

Burkholderia glumae BGR1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20666

3 Samples

Download data: TXT