Project description:This SuperSeries is composed of the following subset Series: GSE5075: Aerobic transcriptional responses of Escherichia coli to NO under defined chemostat conditions. GSE5076: Anaerobic transcriptional responses of Escherichia coli to NO under defined chemostat conditions. GSE5084: Anaerobic NO-exposed Chemostat Comparison of Wt & norR mutant Responses GSE5137: Aerobic NO-exposed Chemostat Comparison of Wt & norR mutant Responses GSE5139: Aerobic NO-exposed Chemostat Comparison of Wt & hmp mutant Responses Keywords: SuperSeries Refer to individual Series
Project description:Escherichia coli strain MG1655 response to NO released from NOC compounds. Under contiuous steady state chemostat conditions, in chemically defined media.
Project description:The transcriptional response of Escherichia coli MG1655 to NO released from NOC-5 and NOC-7 under anerobic conditions in contiuous chemostat culture on chemically defined minimal media
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ?fnr mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the FNR protein. WT strains were grown under aerobic and anaerobic growth conditions. A six chip study using total RNA recovered from two separate cultures of Escherichia coli MG1655 K-12 WT (aerobic and anaerobic) and two separate cultures of the ?fnr mutant strain (anaerobic). Each chip measures the expression level of 4,661 genes from Escherichia coli MG1655 K-12 with eight 60-mer probes per gene, with each probe represented twice on the array.
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ?fnr mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the FNR protein. WT strains were grown under aerobic and anaerobic growth conditions.
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 M-bM-^HM-^Fhns/M-bM-^HM-^FstpA strain from exponental growth under aerobic and anaerobic growth conditions. The results are further described in the article Genome-scale Analysis of E.coli FNR Reveals the Complex Features of Transcrtipion Factor Binding. A four chip study using total RNA recovered from two separate cultures of Escherichia coli MG1655 K-12 M-bM-^HM-^Fhns/M-bM-^HM-^FstpA mutant strain under aerobic and anaerobic growth conditions. Each chip measures the expression level of 4,661 genes from Escherichia coli MG1655 K-12 using a high-density tiling array consisting of ~385,000 60mer probes spaced every 12 bp.
Project description: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 0.1 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 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, 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, unless otherwise stated. Samples were taken immediately prior to the addition of NOCs and 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 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
