GEO DataSets

(Submitter supplied) Exploiting the symbiotic interaction between crops and nitrogen-fixing bacteria is a simple and ecological solution to promote plants growth in prospective extraterrestrial human outposts. In this study, we investigated the adaptation of the legume symbiont Paraburkholderia phymatum to simulated microgravity (s0-g) at the transcriptome level by performing an RNA-Seq analysis. The results revealed a drastic effect on gene expression, with roughly 23 % of P. more...

Organism:

Paraburkholderia phymatum STM815

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22728

6 Samples

Download data: TXT

(Submitter supplied) The goals of this study were to determine differential gene expression between Achromobacter xylosoxidans clinical isolate Ax 7 in a synthetic artificial sputum media compared to a rich media control (LB).

Organism:

Achromobacter xylosoxidans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33525

6 Samples

Download data: CSV, TXT

(Submitter supplied) Bacterial pathogens exhibit a remarkable ability to persist and thrive in diverse ecological niches. Understanding the mechanisms enabling their transition between environments is crucial to control dissemination and potential disease outbreaks. Here, we use Ralstonia solanacearum, the causing agent of the bacterial wilt disease, as a model to investigate the bacterial transcriptomic adaptation to two environments, water and soil, and compare it with the well-studied in planta gene expression. more...

Organism:

Ralstonia solanacearum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33632

6 Samples

Download data: CSV, XLSX

(Submitter supplied) Volatilization of lower-chlorinated polychlorinated biphenyls (LC-PCBs) from sediment poses health threats to nearby communities and ecosystems. Biodegradation combined with black carbon (BC) materials is an emerging approach to remove PCBs from sediment, but development of aerobic biofilms on BC for long-term, sustained LC-PCBs remediation is poorly understood. This work aimed to characterize cell enrichment and activity of biphenyl- and benzoate-grown Paraburkholderia xenovorans strain LB400 on various BCs. more...

Organism:

Paraburkholderia xenovorans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33884

12 Samples

Download data: XLSX

(Submitter supplied) To investigate the molecular mechanisms of how Cupriavidus basilensis SRS may aid bioextraction of metals from ores, we exposed C. basilensis SRS to different metals, as well as natural ores

Organism:

Cupriavidus basilensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32789

10 Samples

Download data: TXT

(Submitter supplied) To comprehend the underlying mechanisms of NSC proliferation and differentiation, microRNA expression was investigated. Total RNA was extracted from NSCs, ESCs, and MEFs, and microRNA expression was examined using RT-PCR. This was accomplished utilizing the System Biosciences' Mouse miRNome Sanger miRVase microRNA Profiler Set.

Organism:

Mus musculus; Bordetella pertussis

Type:

Expression profiling by RT-PCR

Platform:

GPL29570

3 Samples

Download data: XLSX

(Submitter supplied) In this study, we describe the development and use of an ad hoc protein microarray to study the immune response induced by the OMV component of 4CMenB vaccine in infant sera before and after vaccination

Organism:

Neisseria meningitidis; Homo sapiens

Type:

Protein profiling by protein array

Platform:

GPL33085

6 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus; Neisseria meningitidis

Type:

Protein profiling by protein array

Platforms:

GPL33085 GPL33086

10 Samples

Download data: TXT

(Submitter supplied) In this study, we describe the development and use of an ad hoc protein microarray to study the immune response induced by the OMV component of 4CMenB vaccine in mouse sera before and after immunization.

Organism:

Neisseria meningitidis; Mus musculus

Type:

Protein profiling by protein array

Platform:

GPL33086

4 Samples

Download data: TXT

(Submitter supplied) A longitudinal multi-omics analysis was carried out over a 26-hour small-scale fermentation of B. pertussis. Fermentations were performed in batch mode and under culture conditions intended to mimic industrial processes.

Organism:

Bordetella pertussis Tohama I

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32624

21 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) Investigation of replication dynamics (detection of origin of replication, bidirectionality, …)

Organism:

Neisseria elongata subsp. glycolytica ATCC 29315

Type:

Other

Platform:

GPL31260

3 Samples

Download data: TXT

(Submitter supplied) Carbon catabolite repression (CCR) is a gene regulation process that allows bacteria to use carbon-energy sources in a hierarchical manner. Thus, the presence of a preferred sugar, usually D-glucose, results in downregulation of genes participating in the transport and catabolic pathways of secondary carbon sources. Further, CCR controls the expression of global regulators that control expression of many genes involved in multiple aspects of bacterial physiology such as stress response proteins and virulence factors. more...

Organism:

Neisseria gonorrhoeae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22011

8 Samples

Download data: XLSX

(Submitter supplied) Deep sequencing of cDNA of Neisseria gonorrhoeae bacteria that were grown in suspension or adherent to acid-washed glass coverslips, in media where zinc was sequestered or available in excess.

Organism:

Neisseria gonorrhoeae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28673

18 Samples

Download data: RESULTS

(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) Widely reported discrepancies between metabolic flux and transcripts or enzyme levels in bacterial metabolism imply complex regulation mechanisms need to be considered, especially in new bacterial platforms for bioremediation and bioproduction. Comamonas testosteroni strains, which metabolize various natural and xenobiotic aromatic compounds, represent such platforms whose metabolic regulations are still unknown. more...

Organism:

Comamonas testosteroni

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31156

12 Samples

Download data: TSV

(Submitter supplied) Poly(ethylene terephthalate) (PET)-degrading bacterium Ideonella sakaiensis produces hydrolytic enzymes that convert PET, via mono(2-hydroxyethyl) terephthalate (MHET), into the monomeric compounds, terephthalic acid (TPA) and ethylene glycol (EG). Understanding PET metabolism is critical if this bacterium is to be engineered for bioremediation and biorecycling. TPA uptake and catabolism in I. sakaiensis have previously been studied, but EG metabolism remains largely unexplored despite its importance. more...

Organism:

Piscinibacter sakaiensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32339

3 Samples

Download data: TXT

(Submitter supplied) To investigate the regulon of the novel transcriptional regulator TssR discovered in our study We then performed gene expression profiling analysis using data obtained from RNA-seq of wild type Azoarcus olearius sp. BH72 and tssR deleted mutant cultured under microaerobic conditions with additional ammonium

Organism:

Azoarcus olearius

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32567

6 Samples

Download data: CSV

(Submitter supplied) Chemical signaling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via a novel auxin degradation locus was essential for maintaining stereotypic root development in an ecologically-relevant bacterial synthetic community. more...

Organism:

Variovorax paradoxus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32559

31 Samples

Download data: TSV