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Comparative transcriptional analysis of Acinetobacter baumannii strain ATCC 17978 and strain 17978hm

ABSTRACT: In this study the transcriptomes of Acinetobacter baumannii strains ATCC 17978 and 17978hm were compared. Strain 17978hm is a hns knockout derivative of strain ATCC 17978. Strain 17978hm displays a hyper-motile phenotype on semi-solid Mueller-Hinton (MH) media (0.25% agar). ATCC 17978 and 17978hm from an 37C overnight culture were transferred to the centre of the semi-solid MH plate and incubated at 37C for 8 hours. Only 17978hm cells displayed a motile phenotype and covered the complete surface of the plate. These motile 17978hm cells and the non-motile wild-type ATCC 17978 cells were harvested and RNA was isolated. The comparative transcriptome analysis was performed using the FairPlay labeling kit and a custom made Agilent MicroArray with probes designed to coding regions of the ATCC 17978 genome. The data was analyzed using Agilent GeneSpring GX9 and the significance analysis of microarray MS Excel add-on.

ORGANISM(S): Acinetobacter baumannii

PROVIDER: GSE40681 | GEO | 2013/08/05

SECONDARY ACCESSION(S): PRJNA174607

REPOSITORIES: GEO

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Comparative transcriptional analysis of Acinetobacter baumannii strain ATCC 17978 and strain 17978hm

Project description:In this study the transcriptomes of Acinetobacter baumannii strains ATCC 17978 and 17978hm were compared. Strain 17978hm is a hns knockout derivative of strain ATCC 17978. Strain 17978hm displays a hyper-motile phenotype on semi-solid Mueller-Hinton (MH) media (0.25% agar). ATCC 17978 and 17978hm from an 37C overnight culture were transferred to the centre of the semi-solid MH plate and incubated at 37C for 8 hours. Only 17978hm cells displayed a motile phenotype and covered the complete surface of the plate. These motile 17978hm cells and the non-motile wild-type ATCC 17978 cells were harvested and RNA was isolated. The comparative transcriptome analysis was performed using the FairPlay labeling kit and a custom made Agilent MicroArray with probes designed to coding regions of the ATCC 17978 genome. The data was analyzed using Agilent GeneSpring GX9 and the significance analysis of microarray MS Excel add-on. The motile 17978hm cells and the non-motile wild-type ATCC 17978 cells were harvested and RNA was isolated. The comparative transcriptome analysis was performedThe probes on the microarray cover all predicted open reading frames (at least 4 per ORF) and additional replicates of housekeeping genes of the A. baumannii ATCC 17978 genome .

2013-08-05 | E-GEOD-40681 | biostudies-arrayexpress

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Transcriptional responses of Acinetobacter baumannii ATCC 17978 to limiting iron availability

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Expression Data from Acinetobacter baumannii strain ATCC 17978 and isogenic lpsB mutant cells

Project description:lpsB encodes a glycosyltransferase involved in lipopolysaccharide (LPS) synthesis. LPS is a major component of the Gram-negative bacterial outer membranes. We used custom-made Affymetrix A. baumannii strain ATCC 17978 derived GeneChips to compare the gene expression properties of wild type and isogenic lpsB mutant cells. Two mutants were evaluated; A. baumannii strain 5A7 is a ATCC 17978 derivative harboring a transposon (Tn5) within lpsB (A1S_0430 locus); A. baumannii strain containing a deletion of lpsB (A1S_0430). A. baumannii strain ATCC 17978, 5A7 (lpsB:Tn5) or IH1∆lpsB (∆lpsB) were grown to mid-exponential phase growth, total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis. We sought to determine the transcription profile of lpsB mutated cells.

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Characterization of two Acinetobacter baumannii rifampin-spontaneous mutants lacking twitching motility

Project description:Transcriptional profiling of A. baumannii ATCC 17978 comparing two spontaneous rpoB mutants (Rif5 and Rif 8) with the wild-type parental strain

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Transcriptional response to carbapenem treatment in Acinetobacter baumannii

Project description:We report transcriptome sequencing analysis on A. baumannii strain ATCC 17978 cultures treated with or without meropnem at 0.5, 3 and 9 h, in triplicate.

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Transcriptomic analysis of chlorhexidine shock in Acinetobacter baumannii

Project description:In this study the transcriptomic changes occurring in A. baumannii ATCC 17978 in response to shock treament using the biocide chlorhexdine were determined. A. baumannii ATCC 17978 cells were grown at 37°C with shaking (200rpm) in 35mL cultures in MH broth to OD600=0.75, at which time they were split into 15mL cultures. One 15mL sample was treated with 4µg/mL chlorhexidine (0.5x MIC), whereas the other was not treated and used as a reference. Cultures were allowed to grow for a further 30 mins (to an average final OD600= ~1.35 for untreated cells and 1.25 for chlorhexidine treated samples), when cells were harvested by centrifugation and immediately suspended in Trizol reagent (Invitrogen). Total RNA was extracted using the PureLinkTM Micro-to-Midi Total RNA Purification kit (Invitrogen), incorporating an on-column DNAseI (Invitrogen) digestion.

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Transcriptomic analysis of chlorhexidine shock in Acinetobacter baumannii

Project description:In this study the transcriptomic changes occurring in A. baumannii ATCC 17978 in response to shock treament using the biocide chlorhexdine were determined. A. baumannii ATCC 17978 cells were grown at 37Â°C with shaking (200rpm) in 35mL cultures in MH broth to OD600=0.75, at which time they were split into 15mL cultures. One 15mL sample was treated with 4Âµg/mL chlorhexidine (0.5x MIC), whereas the other was not treated and used as a reference. Cultures were allowed to grow for a further 30 mins (to an average final OD600= ~1.35 for untreated cells and 1.25 for chlorhexidine treated samples), when cells were harvested by centrifugation and immediately suspended in Trizol reagent (Invitrogen). Total RNA was extracted using the PureLinkTM Micro-to-Midi Total RNA Purification kit (Invitrogen), incorporating an on-column DNAseI (Invitrogen) digestion. The experiment included using four grids of a custom Agilent 8 x 15000 spot microarray. Three biological replicates and one flip dye experiment.

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