GEO DataSets

(Submitter supplied) Helicobacter pylori colonizes the gastric epithelium and is the leading cause of gastric adenocarcinoma. There is increasing evidence that DNA methylation regulates gene expression in addition to its role in genome protection. In this study, we characterize the impact of acidity, the Two-Component System (TCS) ArsRS, Autoinducer-2, and the Type I m6A DNA methyltransferase HsdM1 (HP0463) on the Helicobacter pylori methylome. more...

Organism:

Helicobacter pylori

Type:

Other

Platform:

GPL33724

6 Samples

Download data: CSV, GFF

(Submitter supplied) Helicobacter pylori (H. pylori) is a highly successful pathogen that constitutes a serious threat to human health. However, the dynamic interaction between H. pylori and human gastric epithelium has not been fully documented. Here, by leveraging the advantage of dual RNA sequencing technology, we characterized a cytotoxin-associated genes A (CagA)-modulated bacterial adoption strategy by reinforcing the expression of ATP-binding cassette (ABC) transporter-related genes, metQ and HP_0888 upon co-culturing with human gastric epithelial cells (GES-1), thus, to benefit intracellular H. more...

Organism:

Helicobacter pylori; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28668 GPL24676 GPL33770

21 Samples

Download data: XLSX

(Submitter supplied) To investigate the impact of the cagPAI on transcript regulation of H. pylori, RNA-seq was performed on bacterial samples with presence or absence of the cagPAI.

Organism:

Helicobacter pylori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19488

4 Samples

Download data: XLSX

(Submitter supplied) Purpose: Next-generation sequencing (NGS) was used to analyze gene expression in H. pylori strains expressing either WT Fur or a Fur variant (i.e. Fur-R88H). The goals of this study are to examine the role that WT Fur and Fur-R88H play in affecting salt-responsive gene expression in the 2 different strains. The H. pylori strains were grown in the presence of routine salt (0.5% added NaCl) or high salt (1.0% added NaCl).

Organism:

Helicobacter pylori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28668

15 Samples

Download data: XLSX

(Submitter supplied) Next-generation sequencing (NGS) was used to analyze gene expression in H. pylori CrdRS two-component system deletion strains. The goal of this study was to examine the role that the CrdRS two-component system plays in H. pylori gene expression through identification of regulon differences

Organism:

Helicobacter pylori 26695

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32960

6 Samples

Download data: TXT, XLSX

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

Organism:

Oxytricha trifallax; mixed culture metagenome; Helicobacter pylori; Escherichia coli

Type:

Methylation profiling by high throughput sequencing; Other

4 related Platforms

22 Samples

Download data: CSV, TXT

(Submitter supplied) DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. more...

Organism:

Helicobacter pylori; Escherichia coli; mixed culture metagenome

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL21222 GPL30645 GPL30644

14 Samples

Download data: CSV

(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:

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; Neisseria meningitidis; Staphylococcus epidermidis; Streptococcus pyogenes; Listeria monocytogenes; Salmonella enterica; Achromobacter xylosoxidans; Helicobacter pylori; Enterococcus faecalis; Borreliella burgdorferi; Pseudomonas aeruginosa; Legionella pneumophila; Klebsiella pneumoniae; Yersinia pseudotuberculosis; Vibrio cholerae; Streptococcus suis; Streptococcus agalactiae; Streptococcus pneumoniae; Mycobacterium tuberculosis; Burkholderia pseudomallei

Type:

Expression profiling by high throughput sequencing

30 related Platforms

1122 Samples

Download data: TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) was used to analyze pH-responsive gene expression in H. pylori. The goals of this study are to compare H. pylori pH-responsive gene expression in H. pylori strain 26695 and 26695 dervatives containing mutations to the ArsS, CrdS and FlgS sensor kinases.

Organism:

Helicobacter pylori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28668

24 Samples

Download data: TSV, XLSX

(Submitter supplied) Purpose: Next-generation sequencing (NGS) was used to analyze pH-responsive gene expression in H. pylori. The goals of this study are to compare H. pylori pH-responsive gene expression in H. pylori strain 26695 and 26695 dervatives containing mutations to the ArsRS two component system.

Organism:

Helicobacter pylori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28668

24 Samples

Download data: TSV, XLSX

(Submitter supplied) To further examine the roles of DppA, we performed RNA-seq analysis and investigated the genes expressed differentially between H. pylori 26695 and a ΔdppA strain.We found that 253 genes were differentially expressed with a |Log2 (fold change)| > 1, including 116 genes that were upregulated and 137 genes that were downregulated in ∆dppA (P < 0.05). We also performed functional classification of the genes upregulated and downregulated in ∆dppA. more...

Organism:

Helicobacter pylori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28668

4 Samples

Download data: XLS

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

Organism:

Helicobacter pylori

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19488 GPL19489

10 Samples

Download data: WIG

(Submitter supplied) In this study several putative targets of the RRM protein RbpH (HP0827/HPG27_786) were identified. RNA binding targets of RbpH in two strains of H. pylori (G27 and 26695) were identified using RIP-seq.

Organism:

Helicobacter pylori

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19489 GPL19488

6 Samples

Download data: WIG

(Submitter supplied) In this study several putative targets of the RRM protein RbpH (HPG27_786) were identified. Potential targets of RbpH in H. pylori (G27) were identified using total RNA-seq.

Organism:

Helicobacter pylori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19488

4 Samples

Download data: WIG

(Submitter supplied) As the number of bacterial genomes and transcriptomes increases, so does the number of newly identified toxin–antitoxin (TA) systems. However, their functional characterization remains challenging, often requiring the use of overexpression vectors that can lead to misinterpretations. To fill this gap, we developed a systematic approach called FASTBAC-Seq (Functional AnalysiS of Toxin–Antitoxin Systems in BACteria by Deep Sequencing). more...

Organism:

Helicobacter pylori

Type:

Other

Platform:

GPL25687

6 Samples

Download data: XLS

(Submitter supplied) We investigated an improved method that combines competitive PCR and microarray techniques. This approach allowed us to quantify specific bacterial groups mounted on DNA chips with accuracy close to that of real-time PCR, despite a measurement at the end point of PCR, and also to estimate the bacterial DNA content in sample DNA.

Organism:

Bacteria; Acinetobacter baumannii; Escherichia coli; Staphylococcus aureus; Staphylococcus epidermidis; Bacillus cereus; Schaalia odontolytica; Fusobacterium nucleatum subsp. nucleatum; Neisseria meningitidis; Porphyromonas gingivalis; Fusobacterium nucleatum; Clostridium beijerinckii; Lactobacillus gasseri; Tannerella forsythia; Campylobacter rectus; Helicobacter pylori; Pseudomonas aeruginosa; Aggregatibacter actinomycetemcomitans; Phocaeicola vulgatus; Capnocytophaga gingivalis; Deinococcus radiodurans; Streptococcus mutans; Streptococcus intermedius; Cutibacterium acnes; Treponema denticola; Cereibacter sphaeroides; Streptococcus gordonii; Streptococcus agalactiae; Enterococcus faecalis; Bifidobacterium adolescentis; Homo sapiens; Prevotella intermedia; Prevotella nigrescens

Type:

Other

Platform:

GPL25612

178 Samples

Download data: CSV

(Submitter supplied) Background Gastric Helicobacter pylori colonization leads to iron deficiency anemia (IDA), especially in children and adolescents. However the pathogenesis is poorly understood. Objective We sought to identify specific H. pylori genes involved in IDA development, by comparing bacterial genome-wide expression profiling in patients affected or not. Methods H. pylori were isolated from four children with IDA and four from matched controls without IDA. more...

Organism:

Helicobacter pylori 26695; Helicobacter pylori

Type:

Expression profiling by array

Platform:

GPL23824

12 Samples

Download data: PAIR, TXT

(Submitter supplied) Purpose: The goals of this study are to clarify the CsrA-regulatory system in H. pylori by NGS-derived transcriptome profiling (RNA-seq). Method: CsrA regulatory system was determined by comparative transcriptomic analysis carried out with RNA-seq on strain J99 and csrA mutant. Results: Using an optimized data analysis workflow, fifty-three genes in the csrA mutant were found to be differentially expressed compared with the wild-type. more...

Organism:

Helicobacter pylori J99

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23077

6 Samples

Download data: XLS

(Submitter supplied) Next-generation sequencing (NGS) can reveal putative target which can be regulated by m4C modification. Comparison of wild-type strain with the strain harboring deleted M2.hpyAII mtase gene was done to identify the differentially expressed gene.

Organism:

Helicobacter pylori 26695

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19992

4 Samples

Download data: XLS

(Submitter supplied) In this study targets of the RNA pyrophosphohydrolase RppH in H. pylori 26695 (HP1228) were identified.

Organism:

Helicobacter pylori 26695

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19991

9 Samples

Download data: WIG