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Global gene expression analysis of Bacillus cereus to proanthocyanidin exposure

ABSTRACT: B. cereus RNA isolation were taken at OD 0.5 just before addition of 0.02 mg/mL EEC, and at 30 min of exposure. Water was added instead of EEC for control. Total RNA was isolated and we performed DNA microarray for genome-wide transcriptional analysis of B. cereus ATCC 14579 in the presence or absence of EEC. The microarray used in this study was custom-made B. cereus ATCC 14579 developed by Agilent Technologies (https://earray.chem.agilent.com/earray/). The B. cereus microarray design was based on the predicted chromosomal open reading frames (NCBI Accession No. AE016877). It targets the 5234 annotated CDS, three non-overlapping probes were designed, low-quality probes were eliminated, and finally 15242 could be spotted. Microarray data was normalized to 75th percentile and the difference was found to be significant by unpaired T-test (P = 0.05). Next, ratio changes of 2-fold (for up-regulated genes in the EEC stress condition) and 0.5-fold (for down-regulated genes in the EEC stress condition) were regarded as biologically significant. 596 were up-regulated and 495 were down-regulated.

ORGANISM(S): Bacillus cereus

PROVIDER: GSE68767 | GEO | 2015/05/12

SECONDARY ACCESSION(S): PRJNA283794

REPOSITORIES: GEO

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Global gene expression analysis of Bacillus cereus to proanthocyanidin exposure

Project description:B. cereus RNA isolation were taken at OD 0.5 just before addition of 0.02 mg/mL EEC, and at 30 min of exposure. Water was added instead of EEC for control. Total RNA was isolated and we performed DNA microarray for genome-wide transcriptional analysis of B. cereus ATCC 14579 in the presence or absence of EEC. The microarray used in this study was custom-made B. cereus ATCC 14579 developed by Agilent Technologies (https://earray.chem.agilent.com/earray/). The B. cereus microarray design was based on the predicted chromosomal open reading frames (NCBI Accession No. AE016877). It targets the 5234 annotated CDS, three non-overlapping probes were designed, low-quality probes were eliminated, and finally 15242 could be spotted. Microarray data was normalized to 75th percentile and the difference was found to be significant by unpaired T-test (P = 0.05). Next, ratio changes of 2-fold (for up-regulated genes in the EEC stress condition) and 0.5-fold (for down-regulated genes in the EEC stress condition) were regarded as biologically significant. 596 were up-regulated and 495 were down-regulated. Bacillus cereus was selected at 0, 30 min exposure for RNA extraction and hybridization on Agilent microarrays.

2015-05-12 | E-GEOD-68767 | biostudies-arrayexpress

Insight into the response of Bacillus cereus towards the polysaccharide chitosan

Project description:Comparison of chitosan-treated B. cereus ATCC 14579 cells with non-treated B. cereus ATCC 14579 cells. 2 chitosans with similar molecular weight (Mw) but different degrees of acetylation (Fa) were used: chitosan B (Mw: 28.4 kDa, Fa: 0.16) (samples 1-3) and chitosan A (Mw: 36.0 kDa, Fa: 0.01) (samples 4-6).

2011-10-19 | GSE29024 | GEO

Bacillus cereus proteomics - Deciphering the interactions between the Bacillus cereus linear plasmid, pBClin15, and its host by high-throughput comparative proteomics

Project description:This project contributes to the proteomic comparison of Bacillus cereus ATCC 14579 wild-type strain and the derivative strain cured of the linear plasmid, B. cereus ATCC 14579 -pBClin15, grown in aerobiosis condition and harvested at three growth stages.

2016-07-19 | PXD002789 | Pride

Bacillus cereus proteomics - Deciphering the interactions between the Bacillus cereus linear plasmid, pBClin15, and its host by high-throughput comparative proteomics

2016-07-19 | PXD002788 | Pride

Insight into the response of Bacillus cereus towards the polysaccharide chitosan

2011-10-18 | E-GEOD-29024 | biostudies-arrayexpress

Multiple roles for CodY in the type strain Bacillus cereus ATCC 14579

Project description:Comparison of the B cereus codY deletion mutant with wild type strain (ATCC 14579)

2012-07-05 | GSE31017 | GEO

Comparative transcriptome analysis of biofilm and planktonic cells of Bacillus cereus ATCC 10987

Project description:Planktonic and biofilm cells of Bacillus cereus ATCC 14579 and ATCC 10987 were studied using microscopy and transcriptome analysis. By microscopy, clear differences could be observed between biofilm and planktonic cells as well as between the two strains. By using hierarchical clustering of the transcriptome data, little difference was observed between the biofilm cells of B. cereus ATCC 14579 and ATCC 10987. Different responses between biofilm and planktonic cells could be identified using transcriptome analysis. Biofilm formation seemed to cause a shift in metabolism with up- or down-regulation of genes involved in different metabolic pathways. Genes involved in motility were down-regulated. No clear up-regulation related to capsular or extracellular polysaccharides was observed. Sporulation was observed in biofilm cells using microscopy, which was corroborated with up-regulation of genes involved in sporulation in biofilm cells. The results obtained in this study provide insight in general and strain specific behavior of B. cereus cells in multicellular communities.

2015-10-10 | GSE24620 | GEO

Comparative transcriptome analysis of biofilm and planktonic cells of Bacillus cereus ATCC 14579

2015-10-10 | GSE24619 | GEO

Multiple roles for CodY in the type strain Bacillus cereus ATCC 14579

Project description:Comparison of the B cereus codY deletion mutant with wild type strain (ATCC 14579) One condition design comparision of mutant vs wild type including a dye swap, 4 biological replicate

2012-07-04 | E-GEOD-31017 | biostudies-arrayexpress

Gene transcription from the linear plasmid pBClin15 leads to cell lysis and extracellular DNA dependent aggregation of B. cereus ATCC 14579 in response to quinolone induced stress

Project description:Several members of the Bacillus cereus group of bacteria carry lysogenic phages of the family Tectiviridae. The Bacilus cereus reference strain (ATCC 14579) harbor a linear plasmid (pBClin15) that is highly similar to the genomes of the Tectiviruses. Production of active phages has however never been reported for pBClin15 and the role of pBClin15 in B. cereus physiology has been enigmatic. We have for the first time demonstrated an effect of pBClin15 on the physiology of B. cereus ATCC 14579 whereby the wild type is more sensitive to DNA damaging antibiotics compared to a pBClin15 cured strain. The microarray experiments in this study were designed to highlight transcriptional differences between the B. cereus ATCC 14579 wild type and a plasmid cured variant that potentially could explain the impact of pBClin15 on the B. cereus physiology. Microarray experiments were carried out under non-stressful conditions (growth in logarithmic phase in LB medium) under which there were no phenotypic difference between the wild type and pBClin15 cured strain as well as under stressful conditions under which there were phenotypic differences between the two strain (growth in LB medium supplemented with 0.5M-5g norfloxacin per ml).

2013-09-10 | E-MEXP-3894 | biostudies-arrayexpress

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