Transcriptomics

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Using RNA Seq to define the regulon of the Pseudomonas aeruginosa transcription factor Anr in low-oxygen colony biofilms.


ABSTRACT: Purpose : The goal of this study was to use RNA Seq to define the regulon of the transciption factor Anr by comparing global transcriptional profiles of Pseudomonas aeruginosa strain PAO1 and a clinical isolate with their isogenic ∆anr mutants, grown in colony biofilms at 1% oxygen. Methods : mRNA profiles were generated for laboratory strain PAO1 and for a clinical isolate J215, as well as for ∆anr derivatives of each strain, in duplicate, by deep sequencing. Strains were grown for 12 hours in colony biofilms at 1% O2, 5% CO2 prior to RNA harvest. Ribosomal and transfer RNAs were removed using the MICROBExpress kit (Life Technologies). mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using the ClC Genomics Workbench platform and defaut parameters.

ORGANISM(S): Pseudomonas aeruginosa PAO1 Pseudomonas aeruginosa

PROVIDER: GSE68534 | GEO | 2015/06/29

SECONDARY ACCESSION(S): PRJNA283002

REPOSITORIES: GEO

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