Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of Vibro cholerae from rabbit ileal loop fluid 12 h post infection to identify differentially expressed genes

ABSTRACT: Transcriptional analysis of wild-type V. cholerae isolated from the rabbit ileal loop was performed by quickly pelleting bacteria from the fluid accumulated in the ileal loops after 12 h of infection. The bacteria were then resuspended in Trizol reagent and frozen on dry ice. The wild-type bacteria from two independent experiments in two different rabbits were analyzed. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Labeling of cDNA and microarray hybridizations were performed as described [Yiliz et al. 2001, Mol. Micro. 53: 497-515]. Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software.

ORGANISM(S): Vibrio cholerae

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-3832 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

RpoS controls the Vibrio cholerae mucosal escape response.

Nielsen Alex Toftgaard AT Dolganov Nadia A NA Otto Glen G Miller Michael C MC Wu Cheng Yen CY Schoolnik Gary K GK

PLoS pathogens 20061001 10

Vibrio cholerae causes a severe diarrhoeal disease by secreting a toxin during colonization of the epithelium in the small intestine. Whereas the initial steps of the infectious process have been intensively studied, the last phases have received little attention. Confocal microscopy of V. cholerae O1-infected rabbit ileal loops captured a distinctive stage in the infectious process: 12 h post-inoculation, bacteria detach from the epithelial surface and move into the fluid-filled lumen. Designat ...[more]

PMID: 17054394

Similar Datasets

Microarray analysis of V. cholerae genes differentially expressed in 12 h rabbit ileal loop fluid

Project description:Transcriptional analysis of wild-type V. cholerae isolated from the rabbit ileal loop was performed by quickly pelleting bacteria from the fluid accumulated in the ileal loops after 12 h of infection. The bacteria were then resuspended in Trizol reagent and frozen on dry ice. The wild-type bacteria from two independent experiments in two different rabbits were analyzed. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Labeling of cDNA and microarray hybridizations were performed as described [Yiliz et al. 2001, Mol. Micro. 53: 497-515]. Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2006-11-03 | GSE6217 | GEO

Microarray analysis of V. cholerae genes differentially expressed in 8h rabbit ileal loop fluid.

2010-09-29 | GSE24407 | GEO

Microarray analysis of V. cholerae genes differentially expressed in 8h rabbit ileal loop fluid.

Project description:Transcriptional analysis of wild-type V. cholerae isolated from the rabbit ileal loop was performed by quickly pelleting bacteria from the fluid accumulated in the ileal loops after 8 h of infection. The bacteria were then resuspended in Trizol reagent and frozen on dry ice. The wild-type bacteria from three independent experiments in three different rabbits were analyzed. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.

2010-09-28 | E-GEOD-24407 | biostudies-arrayexpress

Transcription profiling of Vibrio cholerae wild type, hapR and rpoS deletions in mid-exponential or stationary phase concluding that rpoS controls the Vibrio cholerae mucosal escape response

Project description:For expression analysis of wild-type V. cholerae, hapR, and rpoS deletion mutants in mid-exponential or stationary phase, the strains were grown to either OD600 of 0.3 or for 11 h in LB media at 37 0C, and bacteria from 2-ml culture were quickly pelleted, resuspended in Trizol reagent (GIBCO/BRL, San Diego, California, United States), and frozen on dry ice. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Labeling of cDNA and microarray hybridizations were performed as described [Yiliz et al. 2001, Mol. Micro. 53: 497-515]. Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software. At least four microarray experiments were performed for each of two biological replicates for the tested strains. Gene expression of V. cholerae, rpoS, and hapR deletion mutants in stationary phase LB cultures was analyzed and compared to the wild-type parent under identical conditions. Gene expression of the wild-type parent during stationary phase after 11 h growth in LB was analyzed using RNA from an exponentially growing culture as a reference.

2006-11-06 | E-SMDB-3833 | biostudies-arrayexpress

Microarray analysis of gene expression in wt, rpoS and hapR mutants in stationary phase

2006-11-03 | GSE6218 | GEO

Microarray analysis of V. cholerae genes differentially expressed in 12 h rabbit ileal loop mucus

Project description:The mucus and cell-associated bacteria were isolated as a single fraction from ileal loops twelve hours post inoculation by scraping the epithelial surface of the intestine with a disposable plastic cell scraper after the loops had been cut open and gently rinsed in PBS buffer to wash away remaining luminal fluid. The mucus gel/cell associated fraction was suspended in Trizol and frozen on dry ice. Total RNA, which includes RNA from the infecting bacteria and from the host (see below), was isolated from the thawed Trizol suspension, treated with DNaseI (Applied Biosystems, Austin, TX) and cleaned by using the RNeasy kit (Qiagen, Valencia, CA).

2010-09-29 | GSE24406 | GEO

Microarray analysis of V. cholerae genes differentially expressed in 8 h rabbit ileal loop mucus

Project description:The mucus and cell-associated bacteria were isolated as a single fraction from ileal loops eight hours post inoculation by scraping the epithelial surface of the intestine with a disposable plastic cell scraper after the loops had been cut open and gently rinsed in PBS buffer to wash away remaining luminal fluid. The mucus gel/cell associated fraction was suspended in Trizol and frozen on dry ice. Total RNA, which includes RNA from the infecting bacteria and from the host (see below), was isolated from the thawed Trizol suspension, treated with DNaseI (Applied Biosystems, Austin, TX) and cleaned by using the RNeasy kit (Qiagen, Valencia, CA).

2010-09-29 | GSE24405 | GEO

Microarray analysis of V. cholerae genes differentially expressed in 12 h rabbit ileal loop mucus

2010-09-28 | E-GEOD-24406 | biostudies-arrayexpress

Microarray analysis of V. cholerae genes differentially expressed in 8 h rabbit ileal loop mucus

2010-09-28 | E-GEOD-24405 | biostudies-arrayexpress

Differential early pathogenic changes in human ileal gene expression in Crohn's disease and ulcerative colitis

Project description:The aim of this study is to identify early pathogenic changes in ileal gene expression that precede the development of macroscopic disease in inflammatory bowel diseases (IBDs). We focused on two IBD phenotypes that were unlikely to overlap: 1) ileal Crohn‚Äôs disease (CD) patients undergoing initial ileocolic resection of diseased ileum; and 2) ulcerative colitis (UC) patients undergoing total colectomy. The Control patients were those patients without IBD undergoing initial right hemicolectomy or total colectomy. In order to identify early pathogenic changes in the human ileum in inflammatory bowel diseases, we analyzed 99 two-color whole human genome expression profiles (Agilent 4410A) of a test human ileal cRNA probe vs. a common reference human ileal RNA from a Control patient (N17). A minimum of four biopsies were taken from the macroscopically disease-unaffected proximal ileal margin of freshly resected specimens from 47 ileal Crohn's disease patients undergoing initial ileocolic resection, 27 ulcerative colitis patients undergoing total colectomy and 25 Control patients undergoing either right hemicolectomy or total colectomy. The test and common reference probes were synthesized using the Agilent Low Input Linear Amplification Kit. Hybridization was carried out in DNA hybridization chambers, washed and scanned on an Axon GenePix 4000B scanner. The preprocessing, filtering and normalization of the array data was carried out using the R package LIMMA.

2010-09-26 | E-GEOD-24287 | 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