Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

57 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

T44625-cgh

ABSTRACT: comparative genomic hybridization (CGH) analysis was perfromed in order to identify coding regions present in strain T44625 that are either absent or contain a high degree of sequence divergence compared to the RB50 reference strain.

ORGANISM(S): Bordetella bronchiseptica

SUBMITTER: Tracy Nicholson

PROVIDER: E-MEXP-3968 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of Bordetella bronchiseptica strains RM50 and 1289

Project description:B. bronchiseptica strains RB50 and 1289 were grown in SS broth, subcultured at a starting OD600 of 0.02 into 50mL of SS broth, grown at 37C for 24 hours while shaking and harvested in log phase (OD600 1.0). Total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA), treated with RNase-free DNase I (Invitrogen, Carlsbad, CA) and purified using RNeasy columns (Qiagen, Valencia, CA) according to the manufacturers instructions. RNA was isolated from two independent biological replicates of strains RB50 and 1289. A 2-color hybridization format was used and dye-swap experiments were performed. For each reaction, 5ug of cDNA was fluorescently labeled. The two differentially labeled reactions to be compared were combined and hybridized to a B. bronchiseptica strain RB50 specific long-oligonucleotide microarray.

2009-01-01 | E-MEXP-1736 | biostudies-arrayexpress

Comparative genomic hybridization of Bordetella bronchiseptica strains RB50 and 1289

Project description:B. bronchiseptica strains RB50 and 1289 strains were grown in SS broth at 37°C with shaking overnight and genomic DNA was isolated from bacterial cultures using a DNA extraction kit (Qiagen, Valencia, CA) and digested with DpnII. For each labeling reaction, 2 ug of digested genomic DNA was randomly primed using Cy-5 and Cy-3 dye-labeled nucleotides, with BioPrime DNA labeling kits (Invitrogen, Carlsbad, CA) and the two differentially labeled reactions to be compared were combined and hybridized to a B. bronchiseptica RB50 specific long-oligonucleotide microarray.

2008-12-31 | E-MEXP-1737 | biostudies-arrayexpress

T44625

Project description:Whole genome transcriptome analysis was performed to determine which genes were differentially expressed between strains T44625 and RB50

2013-12-01 | E-MEXP-3967 | biostudies-arrayexpress

Transcription profiling by array of Bordetella bronchiseptica strains RB50 and 761 grown in normal or high carbon dioxide conditions

Project description:Comparison of B. bronchiseptica strains RB50 and 761 grown in either atmospheric concentrations of oxygen and carbon dioxide (normal conditions) or in atmospheric levels of oxygen with the addition of 5% carbon dioxide into a sealed incubator (5% CO2 conditions).

2010-10-01 | E-MEXP-2875 | biostudies-arrayexpress

Transcription profiling of Bordetella bronchiseptica virulent swine isolate KM22, wild type and fhaB and prn deletion mutants

Project description:B. bronchiseptica strain KM22, a virulent swine isolate, and strains TN27 and TN28, fhaB and prn deletion mutants of KM22, respectively, were cultured in Stainer-Scholte broth and grown at 37C with shaking at 275 rpm until an OD600 of 0.8 was reached. RNA extracted from KM22 was then compared to RNA extracted from TN27 and TN28.

2008-09-20 | E-MEXP-1558 | biostudies-arrayexpress

Transcription profiling of Bordetella bronchiseptica strains 253 and RB50 to investigate adenylate cyclase toxin (ACT) expression

Project description:Bordetella bronchiseptica is a gram-negative respiratory pathogen that causes a diverse spectrum of respiratory disease in a wide-range of hosts. We sought to determine if strains of B. bronchiseptica differed in virulence using the mouse model of infection. Mean lethal doses (LD50) of different B. bronchiseptica strains varied widely in the murine model. B. bronchiseptica strain 253 had a LD50 that was 10-fold lower than the prototypical and fully sequenced B. bronchiseptica strain RB50. Using whole genomic transcriptome analysis covering 100% of B. bronchisetpctica strain RB50ÃÂÃÂs predicted open reading frames (ORFs), 253 was identified as lacking expression of adenylate cyclase toxin (ACT).

2007-10-01 | E-MEXP-1203 | biostudies-arrayexpress

Transcription profiling of Bordetella bronchiseptica RB50 and its Bvg- phase-locked derivative, RB54 to test and validate a long oligonucleotide B. bronchiseptica microarray

Project description:Based on the genomic sequence and using the freely available software ArrayOligoSelector, a long oligonucleotide B. bronchiseptica microarray was designed and assembled. This long-oligonucleotide microarray was subsequently tested and validated by comparing changes in the global expression profiles between B. bronchiseptica RB50 and its Bvg- phase-locked derivative, RB54.

2007-01-31 | E-MEXP-961 | biostudies-arrayexpress

Comparative genomic hybridization of Bordetella bronchiseptica strains 253 and RB50 to investigate the cya adenylate cyclase toxin (ACT) operon

Project description:Bordetella bronchiseptica is a gram-negative respiratory pathogen that causes a diverse spectrum of respiratory disease in a wide-range of hosts. We sought to determine if strains of B. bronchiseptica differed in virulence using the mouse model of infection. Mean lethal doses (LD50) of different B. bronchiseptica strains varied widely in the murine model. B. bronchiseptica strain 253 had a LD50 that was 10-fold lower than the prototypical and fully sequenced B. bronchiseptica strain RB50. Using whole genomic transcriptome analysis covering 100% of B. bronchisetpctica strain RB50ÃÂs predicted open reading frames (ORFs), 253 was identified as lacking expression of adenylate cyclase toxin (ACT). Using whole genomic comparative genomic hybridization analysis and whole genome sequencing, we determined that the cya operon, which is required for ACT production, was absent from the 253 genome.

2007-10-01 | E-MEXP-1205 | biostudies-arrayexpress

Transcription profiling of three Bordetella bronchiseptica strains at three distinct phases of growth: mid-log phase, late-log phase, and late-stationary phase

Project description:Microarray analysis was performed to determine if the growth-dependent gene expression changes occurred on a global scale for B. bronchiseptica strains RB50, RB53, and RB54. For this analysis cDNA representing three distinct phases of growth: mid-log phase (15H), late-log phase (24H), and late-stationary phase (48H) were directly compared.

2009-07-01 | E-MEXP-2015 | biostudies-arrayexpress

Bordetella pertussis Tohama I iron limitation 1

Project description:B. pertussis Tohama I was grown in iron-depleted or iron-replete media and sampled at several time points to assess global gene expression

2011-09-08 | E-MEXP-3263 | 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