Helicobacter pylori Shi470
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA29045 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This experiment set contains the raw data for 8 arrays that were used in the genomic typing of the pre- and post-mouse H. pylori strains SS1 and SS2000. 10700 is the pre-mouse clinical isolate of SS1 and PMSS2000 is the pre-mouse clinical isolate of SS2000. gDNA from these strains were labeled and hybridized to H. pylori microarrays as described in Salama et al. {Salama et al. 2000 PNAS 97:14668-73}. In each case the test gDNA sample was labeled with Cy5 (red) and this was hybridized with Cy3 (green) labeled reference DNA of equal amount. The reference DNA consisted of equal amounts of gDNA from the two H. pylori strains used to make the H. pylori microarray, 26695 and J99. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2006-01-07 | GSE3988 | GEO
Project description:Helicobacter pylori colonizes the stomach of half of the world's population, causing a wide spectrum of disease ranging from asymptomatic gastritis to ulcers to gastric cancer. Although the basis for these diverse clinical outcomes is not understood, more severe disease is associated with strains harboring a pathogenicity island. To characterize the genetic diversity of more and less virulent strains, we examined the genomic content of 15 H. pylori clinical isolates by using a whole genome H. pylori DNA microarray. We found that a full 22% of H. pylori genes are dispensable in one or more strains, thus defining a minimal functional core of 1281 H. pylori genes. While the core genes encode most metabolic and cellular processes, the strain-specific genes include genes unique to H. pylori, restriction modification genes, transposases, and genes encoding cell surface proteins, which may aid the bacteria under specific circumstances during their long-term infection of genetically diverse hosts. We observed distinct patterns of the strain-specific gene distribution along the chromosome, which may result from different mechanisms of gene acquisition and loss. Among the strain-specific genes, we have found a class of candidate virulence genes identified by their coinheritance with the pathogenicity island. Keywords: other
2001-07-25 | GSE6 | GEO
Project description:This experiment set contains the raw data for 8 arrays that were used in the genomic typing of the pre- and post-mouse H. pylori strains SS1 and SS2000. 10700 is the pre-mouse clinical isolate of SS1 and PMSS2000 is the pre-mouse clinical isolate of SS2000. gDNA from these strains were labeled and hybridized to H. pylori microarrays as described in Salama et al. {Salama et al. 2000 PNAS 97:14668-73}. In each case the test gDNA sample was labeled with Cy5 (red) and this was hybridized with Cy3 (green) labeled reference DNA of equal amount. The reference DNA consisted of equal amounts of gDNA from the two H. pylori strains used to make the H. pylori microarray, 26695 and J99. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
2006-01-06 | E-GEOD-3988 | biostudies-arrayexpress
Project description:To distinguish between Helicobacter pylori isolates that may cause greater disease in patients, we used whole genome expression profiling as a platform to study host-pathogen interactions and identify gene signatures associated with isolates from patients with higher cancer risk. Expression profiles were studied for 3 clinical isolates from a region of high gastric cancer incidence (PZ5056, PZ5080, PZ5086) in Colombia and 3 isolates from a region with low gastric cancer incidence in Colombia (PZ5004, PZ5024, PZ5026). Each experiment was done in triplicate by infecting monolayers of gastric epithelial cells for 1 hour with the isolates.
2013-08-05 | E-GEOD-41497 | biostudies-arrayexpress
Project description:Helicobacter pylori from clinical gastric infection
| PRJNA395900 | ENA
Project description:Sexual reproduction and recombination are essential for the survival of most eukaryotic populations. Until recently, the impact of these processes on the structure of bacterial populations has been largely overlooked. The advent of large-scale whole-genome sequencing and the concomitant development of molecular tools, such as microarray technology, facilitate the sensitive detection of recombination events in bacteria. These techniques are revealing that bacterial populations are comprised of isolates that show a surprisingly wide spectrum of genetic diversity at the DNA level. Our new awareness of this genetic diversity is increasing our understanding of population structures and of how these affect host?pathogen relationships. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-10-20 | GSE3479 | GEO
Project description:Helicobacter pylori is a common bacterial infection. It can lead to severe stomach problems, including stomach cancer. Researchers want to look at samples of the bacteria. These H. pylori strains will be taken from chronically infected people. They want to identify the genetic and epigenetic differences in H. pylori strains. This could help predict which people who get infected with the bacteria will get stomach cancer. This could lead to the cancer being detected earlier. It could also mean less people get stomach cancer.
Objectives:
To study genetic variations of H. pylori strains based on samples from chronically infected people. To identify the features of strains that might lead to severe stomach problems or stomach cancer.
Eligibility:
People ages 30-70 years who need an upper endoscopy or who were recently diagnosed with stomach cancer
Design:
Participants will be screened by the doctor who does their procedure and a study nurse.
Participants who have endoscopy will have ~6 biopsies removed. These are tissue samples. They are about the size of a grain of rice. Participants will allow the study team to access reports from their stomach exam.
Participants with stomach cancer will donate some of the tissue that will be removed during their clinical care. They will allow the study team to access reports of their surgery. They will also allow them to access the microscope slides of their stomach.
| 2216372 | ecrin-mdr-crc