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

ABSTRACT: The CrdR-ChIP profiling is comparing H. pylori gDNA without crdR interaction as control and CrdR interact with H. pylori gDNA (WT vs crdR). The goal was determine the crdR binding site on H. pylori genome, it provide possible crdR-regulated genes.

ORGANISM(S): Helicobacter pylori 26695

PROVIDER: GSE69847 | GEO | 2015/06/13

SECONDARY ACCESSION(S): PRJNA286938

REPOSITORIES: GEO

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

Project description:The CrdR-ChIP profiling is comparing H. pylori gDNA without crdR interaction as control and CrdR interact with H. pylori gDNA (WT vs crdR). The goal was determine the crdR binding site on H. pylori genome, it provide possible crdR-regulated genes. 2 samples: H. pylori 26695 is control, and CrdR is experiment.

2015-06-13 | E-GEOD-69847 | biostudies-arrayexpress

CNA analysis of ionizing radiation related basal cell carcinoma

Project description:gDNA from patient samples with multiple basal cell carcinomas and possible exposure to ionizing radiation was hybridized Vs. GM12878 gDNA to assess CNAs. We aimed to find a possible common aberration pattern related to ionizing radiation or a rare metastasis.

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ISL1-binding site

Project description:ISL1-binding site

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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. Keywords: Logical Set

2006-01-07 | GSE3988 | GEO

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

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).

2005-11-03 | E-SMDB-1734 | biostudies-arrayexpress

Indel array-based genotyping of pupariation site preference among Drosophila sechellia backcross progeny

Project description:We identified 6,975 insertion/deletion events of between 10 and 100 bp in length from the Drosophila simulans and Drosophila sechellia Mercator/MAVID genomic sequence alignment. Replicate pure samples of Drosophila simulans and Drosophila sechellia gDNA were competitively hybridized to measure the expected relative hybridization intensity of alleles from each species. We used these measured intensities to assess the likelihood that the hybridization signal at each probe in an experimental animal reflected homozygosity or heterozygosity at that locus.

2013-02-26 | GSE44443 | GEO

H. pylori 26695: wild-type vs nitro-oxide (NO) treated; knockout-crdS in H. pylori 26695 vs knockout-crdS with NO treatment

Project description:There are two transcription profiles. The first profiling is comparing control untreated H. pylori with H. pylori with NO treatment. And the second profiling is comparing knockout-crdS in H. pylori untreated with knockout-crdS with NO treatment. The goal was determine the effects of NO-responsive gene and crdS-regulated genes on H. pylori gene expression.

2015-06-13 | GSE69846 | GEO

Homo sapiens

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Drosophila Divergence 20091001

Project description:D. yakuba, D. simulans, and D. sechellia gDNA competitively hybridized against D. melanogaster to evaluate aCGH as a means to identify diverged orthologs. 2 D. sechellia vs D. melanogaster hybs - with dye swap, 2 D. simulans vs D. melanogaster hybs with dye swap, and 8 D. yakuba vs D. melanogaster hybs with balanced dye swaps. D. yakuba vs. D. melanogaster were then analyzed in all 2,4,6,8 possible combinations that incorporated dye-swap to asses sources of variation.

2010-06-21 | E-GEOD-18416 | biostudies-arrayexpress

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