Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Carolina_Gastritis_DU_GC_series

ABSTRACT: Array CGH of Mexican patient strains from Javier Torres laboratory analyzed by Carolina Romo. Patients have a range of pathologies form gastritis to ulcer to cancer. Multiple strains were isolated from each patient and all those giving distinct RAPD patterns were profiled against a reference sample of 26695/J99 genomic DNA. For each array 0.25-1 micrograms of genomic DNA of a test strains was labeled with Cy5 and 0.5 micrograms of an equimolar mix of 26695 and J99 genomic DNA was labeled with Cy3. A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. Individual: Patient from whom the strain was isolated (#) Disease State: Disease of patient from whom the strain was isolated Replicate: strain isolate (within patient) (#) Keywords: clinical_history_design

ORGANISM(S): Helicobacter pylori J99 Helicobacter pylori Helicobacter pylori 26695

PROVIDER: GSE12932 | GEO | 2009/09/25

SECONDARY ACCESSION(S): PRJNA110855

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Carolina_Gastritis_DU_GC_series

Project description:Array CGH of Mexican patient strains from Javier Torres laboratory analyzed by Carolina Romo. Patients have a range of pathologies form gastritis to ulcer to cancer. Multiple strains were isolated from each patient and all those giving distinct RAPD patterns were profiled against a reference sample of 26695/J99 genomic DNA. For each array 0.25-1 micrograms of genomic DNA of a test strains was labeled with Cy5 and 0.5 micrograms of an equimolar mix of 26695 and J99 genomic DNA was labeled with Cy3. A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. Individual: Patient from whom the strain was isolated (#) Disease State: Disease of patient from whom the strain was isolated Replicate: strain isolate (within patient) (#) Keywords: clinical_history_design Computed

2010-06-25 | E-GEOD-12932 | biostudies-arrayexpress

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

2006-12-15 | GSE6530 | GEO

Emory_Pediatric_Strains_1

Project description:Array CGH analysis of Helicobacter pylori strains isolated from a North American cohort of symptomatic pediatric patients. Keywords: genotyping_design A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Patients enrolled under Benjamin Gold's Emory IRB protocol. Initial strain isolation from antral biopsies performed at Emory and culture sweeps sent to FHCRC (Seattle) for analysis. Single colony isolates (4) from each patient antral biopsy were isolated and profiled using RAPD. A single clone of each RAPD type detected in each patient (1-2) were analyzed on duplicate arrays. For analysis 500 ng of genomic DNA of each test strain was labeled with Cy5 and 500 ng of genomic DNA of a reference sample (equimolar mix of 26695 and J99) was labeled with Cy3. Strains identified as Em-patient#-clone#.

2009-11-04 | E-GEOD-13317 | biostudies-arrayexpress

Comparative genomic hybridization of mouse adapted strains of Helicobacter pylori

2006-12-15 | E-SMDB-3902 | biostudies-arrayexpress

USU101 gene content determined by array CGH

Project description:The monkey infecting Helicobacter pylori strain USU101 used in a long term infection of macaques with and without the dietary carcinogen ENNG was analyzed for gene content compared to the sequenced strains 26695 and J99

2014-08-18 | GSE60404 | GEO

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

2007-08-09 | GSE7618 | GEO

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

Comparative genomic hybridization of human H. pylori isolates from naturally infected Mexican patients and BCS-100 strain

2007-05-11 | E-SMDB-3981 | biostudies-arrayexpress

Array CGH of Mexican Patient Isolates and BCS100 Strain

2007-08-08 | E-GEOD-7618 | 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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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