Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MATT mapping of transposon insertions sites of H. pylori strain G27 GPS-cat library

ABSTRACT: Genomic DNA from pools of H. pylori strain G27 Clones as indicated (pools of 300 (300p) or insertions in specific mapped genes) were amplifed using the MATT method to label DNA adjacent to the site of transposon insertion with the primer pairs indicated. The left side of the transposon was labeled in the Cy3 channel (Primer S) and the right side of the transposon was labeled in the Cy5 channel (Primer N). The results of these experiments are published in Salama et al. 2004. J Bact. 186(23):7926-7935.

ORGANISM(S): Helicobacter pylori

SUBMITTER: Nina Salama

PROVIDER: E-SMDB-3048 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Global transposon mutagenesis and essential gene analysis of Helicobacter pylori.

Salama Nina R NR Shepherd Benjamin B Falkow Stanley S

Journal of bacteriology 20041201 23

We have constructed a genome-saturating mutant library of the human gastric pathogen Helicobacter pylori. Microarray tracking of transposon mutants (MATT) allowed us to map the position of 5,363 transposon mutants in our library. While we generally found insertions well distributed throughout the genome, 344 genes had no detectable transposon insertions, and this list is predicted to be highly enriched for essential genes. Comparison to the essential gene set of other bacteria revealed a surpris ...[more]

PMID: 15547264

Similar Datasets

MATT mapping of Transposon insertions sites of strain G27 GPS-cat library

Project description:Genomic DNA from pools of H. pylori strain G27 Clones as indicated (pools of 300 (300p) or insertions in specific mapped genes) were amplifed using the MATT method to label DNA adjacent to the site of transposon insertion with the primer pairs indicated. The left side of the transposon was labeled in the Cy3 channel (Primer S) and the right side of the transposon was labeled in the Cy5 channel (Primer N). Keywords: reference_design

2005-08-26 | GSE3197 | GEO

MATT mapping of Transposon insertions sites of strain G27 GPS-cat library

2005-08-26 | E-GEOD-3197 | biostudies-arrayexpress

Bacillus cereus g27

Project description:Bacillus cereus g27 Genome sequencing

| PRJNA235152 | ENA

Helicobacter pylori G27

Project description:Helicobacter pylori G27 Genome sequencing

| PRJNA249072 | ENA

Transcription profiling of H. pylori wild type G27 and Fur mutant derivative exposed to pH 5.0

Project description:Wildtype G27 and it's Fur mutant derivative were exposed to pH 5.0 for the indicated length of time. Bacterial cells in the exponential phase of growth (denoted log) and stationary phase of growth were used. fur1 denotes a single fur mutant while fur2 denotes an additional fur mutant.

2006-06-06 | E-SMDB-3498 | biostudies-arrayexpress

Helicobacter pylori G27

Project description:Helicobacter pylori G27 Transcriptome or Gene expression

| PRJNA545152 | ENA

H. pylori G27 HP0518 mutant showed greater motility

Project description:Helicobacter pylori is a human gastric pathogen associated with gastric and duodenal ulcers as well as specific gastric cancers. It is well-evidenced that motility is essential for this pathogen to colonize human gastric tissues. We found that the H. pylori G27 HP0518 mutant showed greater motility than the parental strain, leading to increased cell adhesion and subsequent CagA translocation and NF-κB activation in AGS cells. This mutant expressed a higher molecular mass flagellin A (FlaA) than the parental wild-type strain and the complemented HP0518 mutant, which correlated with differences in motility. Deglycosylation assays indicated that the increased molecular mass of the FlaA protein expressed by the mutant was due to O-linked glycoside modifications. Electron micrographs demonstrated that expression of bundle-formed flagellin filaments in the HP0518 mutant was enhanced in comparison to the wild-type strain. Different degrees of FlaA glycosylation between H. pylori strains suggested that glycosylation could affect both virulence and persistence in vivo. In conclusion, HP0518 inactivation resulted in FlaA hyper-glycosylation leading to increased virulence and motility.

2010-12-22 | GSE14752 | GEO

H. pylori G27 HP0518 mutant showed greater motility

2010-12-22 | E-GEOD-14752 | biostudies-arrayexpress

Transcription profiling of human gastric epithelial (AGS) cells infected with wild type H. pylori (G27) and isogenic mutants in cagA and vacA for 0, 0.5, 3, 6, and 12 hours

Project description:TC1: gastric epithelial (AGS) cells infected with wild type H. pylori (G27) and isogenic mutants in cagA and vacA for 0, 0.5, 3, 6, and 12 hours. Total RNA was used to make single stranded Cy5 labelled probe and compared to Cy3 labelled probe from uninfected AGS cells. Hybridizations of G27 (trial 4) and cagA- (trial 3) timecourses were done in parallel. A technical replicate of the G27 time course (trial 5) and hybridization of vacA- (trial 3) time course were done in parallel. The cagA 6 and 12 hour time points were technically replicated (trial 4) (the cagA 6 hour sample of trial 3 was lost). TC2: Biological replication and expansion of TC1, using more isogenic mutants and timepoints. AGS cells were mock infected, infected with G27, and isogenic mutants in cagN, cagA, cagE, and a deletion of the cag PAI for 0. 1, 3, 6, 12, and 24 hours. Probe synthesis and hybridization was done as in TC1. Note: there may have been a sample mix-up with PAI 12, swapping it with G27 or cagN 12.

2005-09-30 | E-SMDB-1661 | biostudies-arrayexpress

Transcription profiling of Helicobacter pylori strain NSH57 transposon mutants in a mouse colonization screen

Project description:Microarray Tracking of transposon mutants for a H. pylori mouse colonization screen described in Baldwin DN et al. 2007, I&I, 75(2):??, doi:10.1128/IAI.01176-06. Screen in NSH57 H. pylori strain background. Original 50,000 clone transposon library was plated and patched to make 25 pools of 48 clones. Clones were infected into 4-8 C57Bl/6 mice and stomach bacteria from at least two mice were harvested at 1 week or one month. Semi-random PCR was used to amplify and label the DNA next to the transposon insertion from the input (Cy3) and output pool (Cy5) genomic DNA for each array. Two arrays were done per mouse. One array labeled from the left side of transposon (primers S, 2C) and one array labeled from the right side of the transposon (primers N3, 2C). Transposon insertions were defined by spots with signal four standard deviations above background in both arrays. We also counted insertions where two adjacent gene spots (after arranging the data in genome order) gave signal from the two different sides of the transposon (but not both).

2006-12-15 | E-SMDB-3900 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data