|
| Status |
Public on Jul 28, 2006 |
| Title |
E. coli Transcriptome Dynamics during the Transition from Anaerobic to Aerobic Conditions - 5 min exposure to air |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Steady-state continuous cultured control samples in absence of oxygen
|
| Organism |
Escherichia coli |
| Characteristics |
MG1655
|
| Extracted molecule |
total RNA |
| Label |
Cy3/5 dye swap
|
| |
|
| Channel 2 |
| Source name |
Steady-state continuous cultured experimental samples after 5 min exposure to oxygen
|
| Organism |
Escherichia coli |
| Characteristics |
MG1655
|
| Extracted molecule |
total RNA |
| Label |
Cy3/5 dye swap
|
| |
|
| |
| Description |
Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow 1000 fermentation vessels (1.8 l capacity) with culture agitation speed constant at 400 rpm and the temperature maintained at 37 °C. Oxygen levels were monitored using galvanic oxygen electrodes while the pH was maintained at 7.2 ±0.2 by automatic titration with sterile KOH. Evans defined medium was used as the growth medium with glucose (30 mM) as the carbon source with the dilution rate being 0.2 h-1. Anaerobic cultures were maintained by sparging the chemostat with oxygen-free nitrogen (95 %) and carbon dioxide (5 %) (0.2 l min-1). The switch to aerobic conditions was achieved by sparging the culture with air (2.0 l min-1) in place of the above gas mix. After a period of 5 min exposure to air cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA before total RNA purification using Qiagen’s Rneasy Midi kit as recommended by manufacturer’s instructions. Data from control samples were used in indirect comparisons with 5 min, 10 min, 15 min and 60 min exposures. Dye swaps and biological repeats were carried out giving two biological repeats and two technical repeats (see supplementary files).
|
| Data processing |
Control (anaerobic) and 5 min oxygen exposure samples from two biological replicates and two dye swap experiments were compared, LOG2 LOWESS normalized data is shown.
|
| |
|
| Submission date |
Apr 28, 2006 |
| Last update date |
Jul 28, 2006 |
| Contact name |
Jonathan Partridge |
| Organization name |
The University of Sheffield
|
| Department |
Molecular Biology and Biotechnology
|
| Lab |
F10
|
| Street address |
Firth Court, Western Bank
|
| City |
Sheffield |
| ZIP/Postal code |
S10 2TN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL534 |
| Series (1) |
| GSE4735 |
E. coli Transcriptome Dynamics during the Transition from Anaerobic to Aerobic Conditions |
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