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Series GSE5075 Query DataSets for GSE5075
Status Public on Sep 01, 2006
Title Aerobic transcriptional responses of Escherichia coli to NO under defined chemostat conditions.
Platform organism Escherichia coli K-12
Sample organism Escherichia coli
Experiment type Expression profiling by array
Summary Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under
continuous culture (chemostat) conditions. Cells were grown in defined media containing 8 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. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen

tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a

Broadley James D140 OxyProbe® electrode and automated adjustment of stirring rate. Cells were grown as above to steady-state, At steady-state, NOC-5 and NOC-7 was added to the chemostat culture and to the nutrient feed at a final concentration of 10 uM of each unless stated otherwise. Samples were taken immediately prior to the addition of NOCs and after a period of 5 min exposure to NOCs 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 control and NOC-supplemented 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.
Keywords: Stress Reponse, Continuous culture, Chemostat, NO, Nitric oxide
Overall design Two biological repeats (ie. two chemostat runs) were grown. Control and exposed samples were taken as described in summary. For each chemostat run 2 hybridisations were performed. One in which the control was Cy3 labelled whilst the exposed was Cy5 labelled, and a dye swap.
Contributor(s) Pullan ST, Barrett J, Green JR, Poole RK
Citation(s) 17189370
Submission date Jun 14, 2006
Last update date Mar 17, 2012
Contact name Robert Poole
Phone 01142224447
Organization name University of Sheffield
Department Molecular Biology & Biotechnology
Lab F13
Street address Firth Court, Western Bank
City Sheffield
State/province South Yorkshire
ZIP/Postal code S10 2TN
Country United Kingdom
Platforms (1)
GPL534 MWG E. coli K12 Array
Samples (4)
GSM114368 Aerobic NO Chemostat Run 1
GSM114370 Aerobic NO Chemostat Run 1, dye-swap
GSM114371 Aerobic NO Chemostat Run 2
This SubSeries is part of SuperSeries:
GSE5098 Aerobic and anaerobic transcriptional responses of wild type, hmp and norR to strains to NO in a chemostat
BioProject PRJNA104505

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