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Chronic Helicobacter pylori Infection with Sydney Strain 1 and Mouse-Adapted Sydney Strain 2000

ABSTRACT: 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

ORGANISM(S): Helicobacter pylori

PROVIDER: GSE3988 | GEO | 2006/01/07

SECONDARY ACCESSION(S): PRJNA94259

REPOSITORIES: GEO

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Chronic Helicobacter pylori Infection with Sydney Strain 1 and Mouse-Adapted Sydney Strain 2000

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

Comparative genomic hybridization of pre- and post-mouse H. pylori strains SS1 and SS2000

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. This data was used for the manuscript: L. J. Thompson, S. J. Danon, J.E. Wilson, J. L. O'Rourke, N. R. Salama, S. Falkow, H. Mitchell, and A. Lee. (2004) Chronic Helicobacter pylori infection in C57BL/6 and BALB/c mice using SS1 and a newly identified mouse-adapted strain (SS2000). Infect. Immun. (in press).

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Mouse adapted strain CGH

Project description:Microarray based comparative genomic hybridization of mouse adapted strains: 10700 pre-mouse SS1, SS1(A.L.)Sydney strain obtained directly from Adrian Lee, NSH79 Salama lab strain labeled as SS1-now know distinct, G27 obtained from Antonello Covacci. Genomic DNA from est strain (Cy5), genomic DNA from reference strains used for array fabrication (equimolar mix of 26695 and J99 genomic DNA) An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs

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Array CGH of Mexican Patient Isolates and BCS100 Strain

Project description:Array CGH of human H. pylori isolates from natrually infected Mexican patients and BCS-100 strain used for experimental infection of humans which is labeled as OVX-34 in this sample set(Graham et al., 2004, Gut, 53:1235-1243). Each Mexican isolate has a three digit number indicating the patient, a letter indicating biopsy site location and number indicating single colony clone number. Patient 249,259 and 251 are adults and patient 291,293,612 and 653 are children. Multiple single clonies were isolated from 2-4 gastric biopsy sites (a- antrum, c-corpus, f- fundus, i-incisura angularis). Genomic DNA prepared from each experimental strain (500 ng) was labeled with Cy5 (red channel) and co-hybridized with an equimolar mixture of genomic DNA from the reference strains 26659 and J99 (500 ng). Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

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Array CGH of Mexican Patient Isolates and BCS100 Strain

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Project description:Helicobacter pylori enhances the risk for ulcer disease and gastric cancer, yet only a minority of H. pylori-colonized individuals develop disease. We examined the ability of two H. pylori isolates to induce differential host responses in vivo or in vitro, and then used an H. pylori whole genome microarray to identify bacterial determinants related to pathogenesis. Gastric ulcer strain B128 induced more severe gastritis, proliferation, and apoptosis in gerbil mucosa than did duodenal ulcer strain G1.1, and gastric ulceration and atrophy occurred only in B128+ gerbils. In vitro, gerbil-passaged B128 derivatives significantly increased IL-8 secretion and apoptosis compared with G1.1 strains. DNA hybridization to the microarray identified several strain-specific differences in gene composition including a large deletion of the cag pathogenicity island in strain G1.1. Partial and complete disruption of the cag island in strain B128 attenuated induction of IL-8 in vitro and significantly decreased gastric inflammation in vivo. These results indicate that the ability of H. pylori to regulate epithelial cell responses related to inflammation depends on the presence of an intact cag pathogenicity island. Use of an H pylori whole genome microarray is an effective method to identify differences in gene content between H. pylori strains that induce distinct pathological outcomes in a rodent model of H. pylori infection. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

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Transcription profiling of gastric tissues from mice infected with H. pylori strain SS1 for 6 or 12 months

Project description:12 C57BL/6 mice were infected orogastrically with the H. pylori strain SS1. After 6 and 12 months, 3 non-infected and 3 infected mice were sacrificed and stomachs isolated. Gastric tissues were disaggregated and total RNA were isolated by TRIzol extraction and then purified on RNeasy minicolumns. After synthesis of the first cDNA strand (In vitrogen), the double-stranded cDNA was obtained and used to produce biotin-labeled cRNA (Enzo Diagnostic). FRagmented cRNA was hybridized to GeneChip Mouse expression array 430A (Affymetrix).

2009-02-25 | E-MEXP-1135 | biostudies-arrayexpress

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Chromatin-immunoprecipitant (ChIP) for CrdR binding site analysis in whole-genome tilling array

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