GEO DataSets

(Submitter supplied) RNA-seq based transcriptome analysis was employed to understand the genome-wide expression patterns of B. glumae BGR1 under infected rice panicle tissue.

Organism:

Burkholderia glumae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27527

3 Samples

Download data: TXT

(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:

Pectobacterium carotovorum subsp. carotovorum; Ralstonia solanacearum; 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) Purpose: In order to identify the differentially expressed genes between wild type and ΔbysR, we performed RNA-seq analysis.Methods：All the isolates were cultured in CM medium for 24 h at 28℃. Three repetitions were performed for each treatment. The samples were sequenced on an Illumina Hiseq 2000 platform.Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. more...

Organism:

Burkholderia sp. JP2-270

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31232

6 Samples

Download data: TXT

(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) Burkholderia pseudomallei, the etiological agent of melioidosis in humans and animals, often occupies environmental niches and infection sites characterized by limited concentrations of oxygen. Versatile genomic features enable this pathogen to maintain its physiology and virulence under hypoxia, but the crucial regulatory networks employed to switch from oxygen dependent respiration to alternative terminal electron acceptors (TEA) like nitrate, remains poorly understood. more...

Organism:

Burkholderia pseudomallei K96243; Burkholderia pseudomallei

Type:

Expression profiling by genome tiling array

Platform:

GPL16432

44 Samples

Download data: PAIR, TXT

(Submitter supplied) Burkholderia cepacia complex bacteria comprise opportunistic pathogens causing chronic respiratory infections in cystic fibrosis (CF) patients. These microorganisms produce exopolysaccharides which are considered virulence determinants. Here, we report the isolation of an evolved nonmucoid variant (17616nmv) after the ancestor, Burkholderia multivorans ATCC 17616, was subjected to prolonged stationary phase. more...

Organism:

Burkholderia multivorans; Burkholderia cenocepacia J2315; Burkholderia multivorans ATCC 17616

Type:

Expression profiling by array

Platform:

GPL13356

6 Samples

Download data: CEL

(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:

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

Type:

Expression profiling by high throughput sequencing

10 related Platforms

125 Samples

Download data: FNA, TXT

(Submitter supplied) Pathogenic bacteria encounter a variety of stressful host environments during infection. Their responses to meet these challenges protect them from deadly damages and aid in adaption to harmful environments. Bacterial products critical for this protection are therefore interesting as suitable targets for new antimicrobials. To shed light on the complex array of molecular pathways involved in bacterial stress responses we challenged 32 diverse human pathogenic bacteria to 11 infection related stress conditions and catalogued their transcriptomes. more...

Organism:

Helicobacter pylori; Enterococcus faecalis; Campylobacter jejuni; Francisella tularensis; Acinetobacter baumannii; Neisseria gonorrhoeae; Escherichia coli; Shigella flexneri; Aggregatibacter actinomycetemcomitans; Haemophilus influenzae; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus MSSA476; Borreliella burgdorferi; Pseudomonas aeruginosa; Legionella pneumophila; Klebsiella pneumoniae; Yersinia pseudotuberculosis; Vibrio cholerae; Streptococcus suis; Streptococcus agalactiae; Streptococcus pneumoniae; Mycobacterium tuberculosis; Burkholderia pseudomallei; Neisseria meningitidis; Staphylococcus epidermidis; Streptococcus pyogenes; Listeria monocytogenes; Salmonella enterica; Achromobacter xylosoxidans

Type:

Expression profiling by high throughput sequencing

30 related Platforms

1122 Samples

Download data: TXT

(Submitter supplied) In this work, high-throughput RNA sequencing was used to assess transcriptomic alteration in Burkholderia cenocepacia K56-2 in the early stages of interaction with host-cell surface. Giant plasma membrane vesicles (GPMVs) from 16HBE14o- bronchial epithelial cell line were produced and used as a cell-like alternative. RNAseq was performed and the expression of the adherent (GPMV-attached) and non-adherent (planktonic control) bacteria were compared. more...

Organism:

Burkholderia cenocepacia

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28995

6 Samples

Download data: 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) Prokaryotic cell transcriptomics have been limited to mixed or sub-population dynamics and individuality of cells within heterogeneous populations. This significantly hampers further knowledge into spatiotemporal and stage-specific processes of prokaryotic cells within complex environments. Herein, we developed a ‘TRANSITomic’ approach to profile transcriptomes of single Burkholderia pseudomallei (Bp) cells as they transit through host cell infection at defined stages, yielding pathophysiological insights. more...

Organism:

Burkholderia mallei; Burkholderia pseudomallei

Type:

Expression profiling by array

Platform:

GPL29071

9 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) We report the methylome sequencing and annotation of Burkholderia pseudomallei D286 based on high-throughput profiling using PacBio SMRT technology

Organism:

Burkholderia pseudomallei

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18301

5 Samples

Download data: TXT