GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Series GSE2129

Query DataSets for GSE2129

Status

Public on Apr 06, 2005

Title

Transcriptional responses of Anaerobically grown 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. 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 to anaerobic medium 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, 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

Jan 06, 2005

Last update date

Mar 16, 2012

Contact name

Jason Barrett

E-mail(s)

J.A.Barrett@sheffield.ac.uk