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Series GSE2095 Query DataSets for GSE2095
Status Public on Apr 06, 2005
Title Transcriptional responses of Escherichia coli to GSNO 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 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.2 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, GSNO was added to the chemostat culture and to the nutrient feed at a final concentration of 200 uM unless otherwise stated. Samples were taken immediately prior to the addition of GSNO and after a period of 5 min exposure to GSNO 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 GSNO-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: dose response
 
 
Contributor(s) Flately J, Barrett J, Pullan ST, Hughes MN, Green J, Poole RK
Citation(s) 15647275
Submission date Dec 21, 2004
Last update date Mar 16, 2012
Contact name Jason Barrett
E-mail(s) J.A.Barrett@sheffield.ac.uk
Phone (+44) 114 2222834
Organization name University of Sheffield
Department Department of Molecular Biology and Biotechnology
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)
GSM37885 Aerobic GSNO Chemostat Run 1
GSM37886 Aerobic GSNO Chemostat Run 2
GSM37887 Aerobic GSNO Chemostat 2 Run 1
Relations
BioProject PRJNA91787

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