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Showing 71-80 of 309 paper
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García-Contreras,2008Experimentsprotein translation; cell death E. coli K-12 BW25113 Affymetrix; E. coli Genechip Genome 2.0 array A whole transcriptome analysis of E. coli BW25113 in biofilms following deletion of the hha gene was performed under various conditions. All experiments were conducted at 37 degrees Celsius.Thomas K. Wood
Bross,2008Experimentschaperonin function E. coli K-12 B178 Affymetrix antisense E. coli arrays A microarray analysis was performed on cells expressing Hsp60-(p.V98I), a mutant Hsp60 chaperonin protein. Peter Bross
Traxler,2008ExperimentsStringent ResponseE. coli K-12 MG1655Chip, Affymetrix custom GeneChipsIsoleucine starvation was used to induce ppGpp production to evaluate the response of ppGpp on transcriptome. The Affymetrix chips used in this study contained probes for E. coli K-12 MG1655, E. coli O157:H7 Sakai, E. coli EDL933, Bacteriodes thetaiotaomicron VPI-5482, Enterococcus faecalis V583, Salmonella typhimurium LT2, and Bacillus anthracis. Biolog assays were conducted and compared to transcript alterations.Tyrrell Conway
Zhang,2008Experimentscolanic acid and biofilm formation E. coli K12 MG1655; E. coli K12 BW25113 Affymetrix E. coli Genechip 2.0 Array The transcriptome analysis showed that deletion of the yncC gene up-regulated 30 genes and down-regulated 10 genes.Thomas K. Wood
Dürrschmid,2008Experimentsrecombinant protein expression E. coli HMS 174 (DE3) E. coli K12 V2 arrays (MWG Biotech) Karl Bayer
Cardinale,2008ExperimentsRho inactivation by bicyclomycinE. coli K-12 MG1655Chip, Affymetrix, E. coli Genome 2.0 ArraySupplemental information can be accessed at Bicyclomycin inhibition was used because rho is an essential gene therefore use of a TS mutant may have secondary effects on transcriptome. Therefore chemical inhibition of rho allows exact transcriptome profiles between test and control until the time of inhibition. The chip used includes oligos for four genomes: E. coli K-12 MG1655, E. coli O157:H7 EDL933 and Saki, and E. coli CFT073. Alternatively data can be found on NCBI GEO website Nudler
Yang,2008ExperimentsR1 plasmid; biofilm formation E. coli K-12 BW25113; E. coli K-12 MG1655; E. coli K-12 ATCC 25404 Affymetrix antisense E. coli arrays Gene expression profiles of the biofilm cells of E. coli K-12 strains BW25113,MG1655, and ATCC 25404 were determined to understand the basis of enhanced biofilm formation upon the addition of conjugative plasmid R1drd19.Thomas K. Wood
Gunasekera,2008Experimentsosmotic stress; heat stress E. coli K-12 NCM3722Affymetrix E. coli Genechip 2.0 Array The cross-regulation of osmotic and heat stress responses were probed on the E.coli K-12 transcriptome by characterizing the effects of external osmolarity and temperature.Oleg Paliy
Ito,2008ExperimentsrpoS(Sigma S); biofilms; growth phaseE. coli K-12 MG1655Affymetrix AntisenseUsed Blattner (1997) E. coli Genome Project as functional list for cluster analysis. Additionally data can be found on NCBI GEO ( accession #GSE7885.Satoshi Okabe
Dong,2008ExperimentsrpoSE. coli K-12 MG1655Affymetrix AntisensePublication uses 2-fold change and p-value p<0.05 for significance criteria. This data is also available in GEO accession number GSE9814. Publication notes that 29 genes were identified to be regulated by RpoS in exponential phase when tested by lacZ fusions (Vijayakumar et al. 2004. J Bacteriol. 186:8499-8507); the 17 genes identified in this study correspond to those findings.H.E. Schellhorn