Comparative genomic hybridization of E. coli O157 strains to illustrate a method for the analysis of CGH studies
Ontology highlight
ABSTRACT:
INSTRUMENT(S): GenePix 4000B [Axon Instruments]
ORGANISM(S): Escherichia coli
SUBMITTER: Ben Carter
PROVIDER: E-MEXP-945 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Compare the diversity among E.coli strains with CGH
2007-12-31 | E-MEXP-1059 | biostudies-arrayexpress
Project description:Bdellovibrio is a Gram-negative bacterium that preys upon other Gram-negative bacteria, including many pathogens, and as such has potential as a biocontrol agent. Little is known of the molecular and genetic control of Bdellovibrioâ??s attack upon its prey and of the nature of the HI phenotype. Here, we apply microarray technology to monitor changes of gene expression during the initial stages of prey infection to determine which predatory genes are important in this stage and to gain insight into possible regulatory mechanisms controlling the predation process. Comparison to gene expression during HI growth reveals a â??predatosomeâ?? of genes specifically upregulated during predation and implicates some of those important in HI growth. 3 replicates of attack phase cells and 3 replicates of Host-Independent grown cells were analysed on individual arrays.
2010-05-18 | E-GEOD-16034 | biostudies-arrayexpress
Project description:The expression profile of an S. Typhimurium mutant strain unable to synthesise ppGpp (relAspoT deletions) was compared to the wild-type strain. The effect of ppGpp on virulence gene expression was studied under 4 different growth conditions that induce virulence gene expression. Keywords: genetic modification Study comprised 4 separate experiments (with 2 strains and 4 replicates for each strain per growth condition). The experiments were indirect comparisons using Salmonella genomic DNA as the comparator which also acted as the control for spot quality.
2010-06-11 | E-GEOD-4631 | biostudies-arrayexpress
Project description:The control of amino acid synthesis and transport in bacteria has been well-investigated at the transcriptional level. The discovery of a small Hfq-dependent regulatory RNA, GcvB, added another layer of gene expression control at the post-transcriptional level. GcvB RNA has been shown to directly regulate multiple ABC transporters for amino acids in E. coli and Salmonella using a highly conserved G/U-rich domain, R1. To identify additional GcvB targets, we have combined a sRNA pulse-expression and microarray analysis of whole transcriptome changes with biocomputational target searches for C/A- rich target sites in Salmonella. Moreover, we have included GcvB mutant RNAs in our microarray approach providing a new target search approach by inactivating conserved domains or target interaction sites. This dual approach revealed further amino acid transporters and, in addition, genes involved in amino acid metabolism as consensus R1-dependent GcvB targets. Moreover, GcvB RNA seems to bind with at least two binding sites to an R1-independent target, the glycine transporter cycA. Using GFP reporter gene fusions we have now validated 21 GcvB targets which is best to our knowledge with ~1% of all Salmonella protein coding genes, the largest bacterial sRNA-controlled regulon. Intriguingly, GcvB rewires many primary control circuits and, thus, constitutes an important metabolic knot. To predict direct GcvB targets with better confidence, we expanded the sRNA pulse-expression approach to assay effects of several versions of GcvB sRNA. We cloned GcvB wild-type and mutants RNAs deleted for the conserved regions R1 or R2 (Fig. 1A) under control of an arabinose-inducible PBAD promoter, yielding plasmid pBAD-GcvB (pKP1-1), pBAD-GcvB delta R1 (pKP2-6) and pBAD-GcvB delta R2 (pKP30-1). For confirmation of inducible expression, Salmonella wild-type carrying pBAD control vector (pKP8-35), and Salmonella ΔgcvB carrying either control vector (Ctr) or the above GcvB expression plasmids were grown to mid-exponential phase (OD600 of 1) and treated with L-arabinose for up to 15 min. We used whole-genome S. typhimurium microarrays to determine relative mRNA expression changes at 10 min of induction, comparing the mRNA profiles of the pBAD-GcvB, pBAD-GcvB delta R1 or pBAD-GcvB delta R2 strains to that of the delta gcvB deletion mutant strain carrying the control vector. Microarrays used in this study were produced by in-situ synthesis as 8x15k multipack format from Agilent Technologies. Each microarray comprises 13268 60-mer S. typhimurium strain SL1344 specific oligonucleotides supplemented with 319 60-mer S. enterica subsp. serovar Typhimurium 14028S specific oligonucleotides, 360 60-mer S. typhimurium LT2 specific oligonucleotides and 360 60-mer oligonucleotides specific for 149 Salmonella sRNAs. The experimental design involves the use of Salmonella enterica serovar Typhimurium genomic DNA as the co-hybridized control for one channel on all microarrays. Two independent biological eperiments were analyzed.
2011-07-01 | E-GEOD-26573 | biostudies-arrayexpress
Project description:Transcriptional profiling of Salmonella Typhimurium SL1344 parental starin and isogenic M-bM-^HM-^FrelA, M-bM-^HM-^FspoT ppGpp null strain grown in LB medium with RNA samples talken at AD600=1.0 (mid log, ML), 2.3 (early stationary phase, ESP), 3.0 (mid stationary phase MSP) and 3.6 (Late stationary phase (LSP) Each array used labelled cDNA against a common genomic DNA reference. Triplicate biologically independent RNA samples were arrayed for each of the 2 strains at each of the 4 growth phases
2013-07-03 | E-GEOD-48478 | biostudies-arrayexpress
Project description:The expression profile of an S. Typhimurium hfq mutant-strain was compared to the parental strain under 2 different growth conditions; early stationary phase and SPI-1 (Salmonella pathogenicity island 1) inducing condition. Keywords: Genetic modification This study comprises two separate experiments performed under different growth conditions, were the gene expression profile was compared to that of the parental strain. Three biological replicates were performed for each strain and condition. For this study, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality.
2008-08-23 | E-GEOD-8985 | biostudies-arrayexpress
Project description:It is well established that small noncoding RNAs (sRNAs) of bacteria recognize the 5â?? regions of target mRNAs, generally at the ribosome binding site. Until now, the translated coding sequence (CDS) of mRNA appeared to be refractory to sRNA interactions. We have discovered that Salmonella MicC RNA silences ompD mRNA by targeting the CDS, at codons 23-26. Analyses of MicC-ompD RNA complexes in vitro, and of chimeric sRNAs and ompD reporter fusions in vivo, show that interactions are confined to the CDS, and that a â?¤12 bp RNA duplex involving the conserved 5â?? end of MicC is essential and sufficient for target repression. MicC cannot act as a translational repressor at this downstream position being unable to inhibit 30S or 70S ribosome activity on the ompD mRNA. Instead, MicC accelerates RNase E-dependent ompD mRNA decay. The degradosome contributes to target destabilization, and facilitates the efficient degradation of processed ompD mRNA. Our data show that bacterial gene silencing by sRNAs can take place downstream of the translational initiation site by triggering irreversible mRNA decay. This ability of sRNAs allows targets in the CDS to be silenced without interference from the strong RNA helicase activity of elongating ribosomes. To determine the targets of the small regulatory RNA MicC in S. Typhimurium, we looked at the effect of a short pulse of MicC over-expression on the Salmonella transcriptome. To achieve over-expression, the micC gene was cloned in the pBAD plasmid and induced with 0.2% L-arabinose for 10 min. We then extracted the total RNA for transcriptional profiling. A strain carrying the pBAD plasmid w/o insert was used as negative control. 3 biological replicates were performed. This sRNA target identification strategy has been described in Papenfort et al; Molecular Microbiology (2006) 62(6), 1674â??1688.
2010-05-16 | E-GEOD-16540 | biostudies-arrayexpress
Project description:Transcriptional profiling of early stationary phase S. Typhimurium, comparing wild type SL1344 with an isogenic ∆relA,∆spoT strain (JH3370). Each array used labelled cDNA against a common genomic DNA reference. The wild type strain was arrayed in triplicate and the ∆relA,∆spoT strain in quadruplicate using RNA isolated from biologically independent cultures.
2011-12-09 | E-GEOD-34269 | biostudies-arrayexpress
Project description:double transgenic mice (tTA/IkappaBalpha-AA) were treated with doxycycline (DOX), which represses expression of the transgenic IkappaBalpha. Double transgenic mice without Dox-treatment overexpress the transdominant IkappaBalpha, which represses NFkappaB activation.
2006-05-10 | E-MEXP-358 | biostudies-arrayexpress
Project description:StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. The regulatory role of StpA varied at different growth phases; StpA only controlled sigma38 levels at mid-exponential phase when it prevented inappropriate activation of sigma38 during rapid bacterial growth. In contrast, StpA only activated the CRP-cAMP regulon during late exponential phase. To test the hypothesis that stpA prevents Sigma38-dependent transcription during mid-exponential growth in S. Typhimurium, we analysed the effect of the stpA deletion on transcription in the presence and absence of rpoS. Three biological replicates were performed for each strain. For this study, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality.
2010-06-20 | E-GEOD-18428 | biostudies-arrayexpress