E-GEOD-5084 - Anaerobic NO-exposed Chemostat Comparison of Wt & norR mutant Responses

Status
Released on 31 August 2006, last updated on 2 March 2012
Organism
Escherichia coli
Samples (8)
Array (1)
Protocols (3)
Description
Escherichia coli strains MG1655 and an isogenic norR::Tn5 mutant were grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. In order to establish anaerobic growth, nitrogen was sparged through the chemostat medium prior to inoculation and throughout the course of the experiment at a rate of 0.2 l/min. No dissolved oxygen was detectable using the OxyProbe. Sodium fumarate was added at a final concentration of 50 mM to act as a terminal electron acceptor. Cells were grown as above to steady-state, At steady-state, NOC-5 and NOC-7 were added to the chemostat culture and to the nutrient feed at a final concentration of 10 uM of each. Samples were taken after a period of 5 min exposure to NOC for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers. Equal quantities of RNA from Wild type and norR::Tn5 cultures were labelled using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes. The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5). The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalized values Each strain was grown twice in seperate chemostat runs, exposed to NO. Samples were hybridised as WT vs NorR::Tn5 and each hybridisation had a corresponding dye-swap performed.
Experiment type
unknown experiment type 
Contacts
Robert Poole <R.poole@shef.ac.uk>, Jeffrey R Green, Robert K Poole, Steven T Pullan
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-5084.idf.txt
Sample and data relationshipE-GEOD-5084.sdrf.txt
Processed data (1)E-GEOD-5084.processed.1.zip
Array designA-GEOD-534.adf.txt
Links