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Kohanski,2007Experimentsantibiotic exposure (norfloxacin, ampicillin, kanamycin, spectinomycin)E. coli K-12 MG1655Affymetrix Antisense2Publication focuses on differential gene expression between bactericidal and bacteriostatic drug exposure to MG1655(WT) cells. Authors used p-values to determine significance; this was a time course study in which the authors merged all time points (instead of doing replicates at one time point, citing Dwyer et al. 2007) to get overall expression changes between bactericidal (norfloxacin + ampicillin + kanamycin) and bacteriostatic (spectinomycin) drug exposure; EcoArray presents all time points as individual experiments. Data is included in M3D database, J. Collins
Li,2007ExperimentsQuorum sensing E. coli K-12 W3110 Affymetrix E. coli Antisense Genome 2.0 array A transcriptome analysis was completed to survey the physiological response of lsrR and lsrK genomic deletion. William E. Bentley
Alper,2007Experimentstranscription engineering E. coli K-12 DH5 Affymetrix E. coli 2.0 arrays Global transcriptional machinery engineering in E. coli in the presence and absence of ethanol.Gregory Stephanopoulos
Reigstad,2007ExperimentsIntracellular Bacterial Communities E. coli K-12 MG1655; E. coli UTI89 Affymetrix E. coli Antisense Array The study compares gene expression in the pathogenic UT189 and non-pathogenic MG1655 strains. Profiling of RNA prepared from the cecal contents of individual mice identified a total of 162 transcripts that were differentially expressed by UTI89 compared with MG1655.Jeffrey I. Gordon
Harr,2006ExperimentsF plasmid presence E. coli K-12 MG1655 vs. E. coli DH5? Affymetrix E. coli Antisense ArrayA large-scale survey for genes that are affected by the conjugative F-plasmid was completed on two E. coli strains. The expression pattern of 107 genes was affected by the presence of the F-plasmid, and the presence of the F-plasmid resulted in host-specific gene expression. Cultures were grown at 37 degrees C and cells were harvested at 0D(600)=0.4 (early log).Bettina Harr
Soupene,2003ExperimentsGene Expression Cross-regulationE. coli K-12 MG1655 Affymetrix E. coli Antisense GeneChipThe authors confirmed that the use of strains designated MG1655 that differ from the E. coli Genetic Stock Center (ECGS) can be used with MG1655-based DNA microarrays. Thirty genes in MG1655 were up-regulated when the strain was grown on lactose or galactose as the carbon source instead of glucose. Sydney Kustu
Giel,2006ExperimentsO2-regulated genesE. coli K-12 MG1655Affymetrix E. coli Antisense GeneChipsGlobal transcriptional profiling of Escherichia coli IscR+ and IscR– strains grown under aerobic and anaerobic conditions show that IscR contributes to the O2 regulation of several promoters controlling the expression of anaerobic Fe-S proteins.Patricia Kiley
Wang,2005ExperimentsluxS-Dependent Regulation E. coli K-12 W3110 Affymetrix E. coli antisense genome array Microarray analysis was used to compare the genomic transcript levels of the wild type and ?luxS mutant of E. coli W3110 under two different growth conditions. William E. Bentley
Ito,2009Experimentsantibiotic resistance; Mature Biofilms E. coli K-12 MG1655 (pOX38Km) Affymetrix E. coli Antisense Genome Array A global gene expression analysis was performed to investigate physiological differences between the outside and the inside of biofilms.Satoshi Okabe
Singh,2010ExperimentsIncreased mutation frequency; redox-impaired Escherichia E. coli K-12 BW25113 Affymetrix E. coli Antisense Genome Array Whole-genome transcriptional profiles were compared between wild-type cells and a double deletion mutant to isolates genes involved in DNA repair. Ryan T. Gil