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E. coli O157:H7 phage type 21/28 & 32 CGH analysis

ABSTRACT: Six isolates of PT21/28 and six of PT32 were analysed by CGH using UBECarray3 microarrays (containing probes for E. coli K-12 str. MG1655 and O157:H7 str. EDL933 and Sakai) to define genotypic differences between phage types. gDNA from E.coli O157 str. Sakai was hybridised to all arrays to provide a universal control channel on all arrays.

ORGANISM(S): Escherichia coli Escherichia coli O157:H7 str. Sakai Escherichia coli O157:H7

PROVIDER: GSE28838 | GEO | 2012/04/21

SECONDARY ACCESSION(S): PRJNA140613

REPOSITORIES: GEO

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E. coli O157:H7 phage type 21/28 & 32 CGH analysis

Project description:Six isolates of PT21/28 and six of PT32 were analysed by CGH using UBECarray3 microarrays (containing probes for E. coli K-12 str. MG1655 and O157:H7 str. EDL933 and Sakai) to define genotypic differences between phage types. gDNA from E.coli O157 str. Sakai was hybridised to all arrays to provide a universal control channel on all arrays. gDNA from 12 PT 21/28 & 32 isolates were labelled with Cy5 and control gDNA from str. Sakai was labelled with Cy3. Test and control gDNA was hybridised to UBECarray3 microarrays. The LOWESS normalised relative signal to the Sakai control channel was used to compare between samples.

2012-04-20 | E-GEOD-28838 | biostudies-arrayexpress

Escherichia coli O157:H7 str. Sakai

Project description:Escherichia coli O157:H7 str. Sakai Genome sequencing

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PhoB Activates Escherichia coli O157:H7 Virulence Factors in Response to Inorganic Phosphate Limitation

Project description:In E. coli the phosphate homeostasis is regulated by the Pst system and the two-component system PhoB/R. Pathogens like E. coli O157:H7 are responsible for many outbreaks and can be found and survive in poor inorganic phosphate (Pi) environments. To understand global EHEC O157:H7 EDL933 strain responses to Pi-starvation, we compared the transcriptomes of EDL933 the WT strain grown in MOPS Pi rich medium and that grown in MOPS Pi poor medium, using the Affymetrix GeneChip® E. coli Genome 2.0 Array. Also we investigated the EDL933 global response to the absence of PhoB by comparing the transcriptomes of the WT strain the ΔphoB mutant both grown in Low Pi

2014-03-15 | GSE50529 | GEO

Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock using microarrays

Project description:The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of heat shock on E. coli O157:H7, global transcript levels of strain EDL933 cells shifted from 37°C to 50°C for 15 min were compared to cells left at 37°C using microarrays. Keywords: Stress Response Twelve independent RNA samples from heat shocked cultures were paired with twelve independent RNA samples from control cultures for hybridization to twelve two-color microarrays. For six arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other six arrays to overcome dye bias.

2009-04-01 | E-GEOD-11463 | biostudies-arrayexpress

Escherichia coli O157:H7 str. EDL933

Project description:Escherichia coli O157:H7 str. EDL933 Genome sequencing

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Transcriptome analysis of Escherichia coli O157:H7 EDL933 during anaerobic growth using microarrays

Project description:The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of an anaerobic environment on E. coli O157:H7, global transcript levels of strain EDL933 cells grown aerobically were compared to cells grown anaerobically using microarrays. Eight independent RNA samples from aerobic cultures were paired with eight independent RNA samples from anaerobic cultures for hybridization to eight two-color microarrays. For four arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other six arrays to overcome dye bias.

2010-12-01 | E-GEOD-13301 | biostudies-arrayexpress

Transcriptome analysis of Escherichia coli O157:H7 EDL933 during anaerobic growth using microarrays

2010-12-01 | GSE13301 | GEO

Escherichia coli O157:H7 str. EDL933

Project description:Escherichia coli O157:H7 str. EDL933 Targeted Locus (Loci)

| PRJNA207831 | ENA

Escherichia coli O157:H7

Project description:EHEC O157 EDL933 & sdhA mutant comparison

| PRJNA342468 | ENA

EHEC O157:H7 Sakai vs. TW14359: Secreted and Cytosolic iTRAQ; sepD secretome analysis of TW14359

Project description:Comparative analysis of EHEC O157:H7 Sakai vs. TW14359 secreted and cytosolic protein using iTRAQ and mass spectrometry on an LTQ Orbitrap. Samples were fractionated through strong cation exchange and HPLC before analsyis. For TW14359 sepD secretome analysis, strains were similarly prepared and analyzed. All samples were searched against a TW14359 specific protein database (Uniprot) coupled with randomized protein sequences.

2013-09-05 | PXD000023 | Pride

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